WorldWideScience

Sample records for feasible three-dimensional structures

  1. A method for fabricating a three-dimensional carbon structure

    DEFF Research Database (Denmark)

    2017-01-01

    A method for fabricating a three-dimensional carbon structure (4) is disclosed. A mould (1) defining a three-dimensional shape is provided, and natural protein containing fibres are packed in the mould (1) at a predetermined packing density. The packed natural protein containing fibre structure (3......) undergoes pyrolysis, either while still in the mould (1) or after having been removed from the mould (1). Thereby a three-dimensional porous and electrically conducting carbon structure (4) having a three-dimensional shape defined by the three-dimensional shape of the mould (1) and a porosity defined...

  2. A Feasibility Study on the Use of a Structured Light Depth-Camera for Three-Dimensional Body Measurements of Dairy Cows in Free-Stall Barns

    Directory of Open Access Journals (Sweden)

    Andrea Pezzuolo

    2018-02-01

    Full Text Available Frequent checks on livestock’s body growth can help reducing problems related to cow infertility or other welfare implications, and recognizing health’s anomalies. In the last ten years, optical methods have been proposed to extract information on various parameters while avoiding direct contact with animals’ body, generally causes stress. This research aims to evaluate a new monitoring system, which is suitable to frequently check calves and cow’s growth through a three-dimensional analysis of their bodies’ portions. The innovative system is based on multiple acquisitions from a low cost Structured Light Depth-Camera (Microsoft Kinect™ v1. The metrological performance of the instrument is proved through an uncertainty analysis and a proper calibration procedure. The paper reports application of the depth camera for extraction of different body parameters. Expanded uncertainty ranging between 3 and 15 mm is reported in the case of ten repeated measurements. Coefficients of determination R² > 0.84 and deviations lower than 6% from manual measurements where in general detected in the case of head size, hips distance, withers to tail length, chest girth, hips, and withers height. Conversely, lower performances where recognized in the case of animal depth (R² = 0.74 and back slope (R² = 0.12.

  3. Magnetic structure of two- and three-dimensional supramolecular compounds

    Energy Technology Data Exchange (ETDEWEB)

    Decurtins, S.; Schmalle, H.W.; Pellaux, R. [Zurich Univ. (Switzerland); Fischer, P.; Fauth, F. [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Ouladdiaf, B. [Institut Max von Laue - Paul Langevin, 75 - Paris (France)

    1997-09-01

    Supramolecular chiral networks of oxalato-bridged transition metals show either two- or three-dimensional structural features. The magnetic structures of such compounds have been investigated by means of elastic neutron powder diffraction. (author) 2 figs., 2 refs.

  4. Three-dimensional structures of laccases.

    Science.gov (United States)

    Hakulinen, N; Rouvinen, J

    2015-03-01

    Laccases are phenol oxidases that belong to the family of multi-copper oxidases and the superfamily of cupredoxins. A number of potential industrial applications for laccases have led to intensive structure-function studies and an increased amount of crystal structures has been solved. The objective of this review is to summarize and analyze available crystal structures of laccases. The experimental crystallographic data are now easily available from the websites and electron density maps can be used for the interpretation of the structural models. The crystal structures can give valuable insights into the functional mechanisms and may serve as the basis for the development of laccases for industrial applications.

  5. Analysis and validation of carbohydrate three-dimensional structures

    International Nuclear Information System (INIS)

    Lütteke, Thomas

    2009-01-01

    The article summarizes the information that is gained from and the errors that are found in carbohydrate structures in the Protein Data Bank. Validation tools that can locate these errors are described. Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein–carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein–carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures

  6. Discretization model for nonlinear dynamic analysis of three dimensional structures

    International Nuclear Information System (INIS)

    Hayashi, Y.

    1982-12-01

    A discretization model for nonlinear dynamic analysis of three dimensional structures is presented. The discretization is achieved through a three dimensional spring-mass system and the dynamic response obtained by direct integration of the equations of motion using central diferences. First the viability of the model is verified through the analysis of homogeneous linear structures and then its performance in the analysis of structures subjected to impulsive or impact loads, taking into account both geometrical and physical nonlinearities is evaluated. (Author) [pt

  7. New "sandwich" structures conformed from three dimensional

    Directory of Open Access Journals (Sweden)

    Alba, Juan J.

    1996-03-01

    Full Text Available Poor interlaminar properties as well as poor-skin-to-core adhesion properties are very often the common existing problems we find when designing with "sandwich" structures. A new type of 3D-fabric "sandwich" structure is being developed in order to avoid these problems. Although the manufacturing process is very simple, a very complex "sandwich" structure is obtained as a result of the complexity of the 3D-fabric used. This 3D-fabric is a 3D woven glass fabric produced on velvet weaving machines with glass yarns. It is an integrally woven "sandwich" laminate for all kinds of composite products. The strength of the vertical fibers makes, that also after impregnation with a resin matrix, the "sandwich" structure is maintained. The result is a laminate with high strength and stiffness and low weight. On each side of this "sandwich" laminate additional reinforcement materials can be laminated and a synthetic foam can be injected in the hollow structure. This will allow to establish the mechanical properties of a finished product.

    Las pobres propiedades, tanto interlaminares como de adhesión entre piel y núcleo, constituyen uno de los grandes problemas cuando se diseñan estructuras utilizando paneles tipo "sandwich". Un nuevo tipo de panel "sandwich", configurado a partir de tejidos tridimensionales, está siendo desarrollado en la actualidad con el objetivo de eliminar esos problemas. Aunque el proceso de fabricación es muy simple, el panel "sandwich" obtenido es de estructura compleja, como resultado de la complejidad del tejido tridimensional utilizado. Este tejido tridimensional (3D es un tejido de fibra de vidrio producido en máquinas de tejer especializadas. La resistencia de las fibras verticales hace que, después de la impregnación con una resina, se mantenga la configuración tipo "sandwich". El resultado es un laminado de alta resistencia, gran rigidez y bajo peso. Sobre cada uno de los lados del panel "sandwich" se pueden

  8. Three Dimensional Cancellous Bone Structure in Hypoparathyroidism

    Science.gov (United States)

    Rubin, Mishaela R.; Dempster, David W.; Kohler, Thomas; Stauber, Martin; Zhou, Hua; Shane, Elizabeth; Nickolas, Thomas; Stein, Emily; Sliney, James; Silverberg, Shonni J.; Bilezikian, John P.; Müller, Ralph

    2009-01-01

    By conventional 2-dimensional histomorphometric analysis, we have shown that cancellous bone architecture is markedly altered in hypoparathyroidism. We have now extended these observations to a 3-dimensional analysis using microcomputed tomography. Percutaneous iliac crest bone biopsies were analyzed by high-resolution microcomputed tomography from the following 25 subjects with hypoparathyroidism: 5 postmenopausal women, 13 premenopausal women and 7 men. Thirteen living premenopausal healthy controls and 12 cadaver subjects without bone disease served as matched controls. Hypoparathyroid subjects had significantly greater bone surface density (BS/TV: 5.74 ± 4.7 vs. 3.73 ± 1.01 mm2/mm3 [mean ± SD]; p=0.04), trabecular thickness (Tb.Th: 0.25 ± 0.19 vs. 0.17 ± 0.04 mm; p=0.04), trabecular number (Tb.N: 2.99 ± 3.4 vs. 1.62 ± 0.39 mm−1; p=0.05) and connectivity density (Conn.D: 16.63 ± 18.7 vs. 8.39 ± 5.8 mm3; p=0.04) in comparison to matched controls. When an additional 8 hypoparathyorid (total n= 33) and 24 cadaver (total cadaver n= 36) subjects were added to the groups for an unmatched analysis, hypoparathyroid subjects had significantly greater cancellous bone volume (BV/TV: 26.98 ± 10 vs. 15.39 ± 4%; phypoparathyroid subjects, as assessed by microcomputed tomography, were highly correlated with those assessed by conventional histomorphometry. We conclude that cancellous bone in hypoparathyroidism is abnormal, suggesting that parathyroid hormone is required to maintain normal trabecular structure. The effect of these structural changes on bone strength remains to be determined. PMID:19782782

  9. Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data.

    Science.gov (United States)

    Xiao, Guanghua; Wang, Xinlei; Khodursky, Arkady B

    2011-03-01

    Recent genomic studies have shown that significant chromosomal spatial correlation exists in gene expression of many organisms. Interestingly, coexpression has been observed among genes separated by a fixed interval in specific regions of a chromosome chain, which is likely caused by three-dimensional (3D) chromosome folding structures. Modeling such spatial correlation explicitly may lead to essential understandings of 3D chromosome structures and their roles in transcriptional regulation. In this paper, we explore chromosomal spatial correlation induced by 3D chromosome structures, and propose a hierarchical Bayesian method based on helical structures to formally model and incorporate the correlation into the analysis of gene expression microarray data. It is the first study to quantify and infer 3D chromosome structures in vivo using expression microarrays. Simulation studies show computing feasibility of the proposed method and that, under the assumption of helical chromosome structures, it can lead to precise estimation of structural parameters and gene expression levels. Real data applications demonstrate an intriguing biological phenomenon that functionally associated genes, which are far apart along the chromosome chain, are brought into physical proximity by chromosomal folding in 3D space to facilitate their coexpression. It leads to important biological insight into relationship between chromosome structure and function.

  10. Computational study of three-dimensional wake structure

    International Nuclear Information System (INIS)

    Himeno, R.; Shirayama, S.; Kamo, K.; Kuwahara, K.

    1986-01-01

    Three-dimensional wake structure is studied by numerically solving the incompressible Navier-Stokes equations. Results are visualized by a three-dimensional color graphic system. It was found that a pair of vortex tubes separated from a body plays the most important role in the wake. Near the body vortex tubes are rather stable, however, they gradually become unsteady as they flow down

  11. Three-dimensional structure determination from a single view.

    Science.gov (United States)

    Raines, Kevin S; Salha, Sara; Sandberg, Richard L; Jiang, Huaidong; Rodríguez, Jose A; Fahimian, Benjamin P; Kapteyn, Henry C; Du, Jincheng; Miao, Jianwei

    2010-01-14

    The ability to determine the structure of matter in three dimensions has profoundly advanced our understanding of nature. Traditionally, the most widely used schemes for three-dimensional (3D) structure determination of an object are implemented by acquiring multiple measurements over various sample orientations, as in the case of crystallography and tomography, or by scanning a series of thin sections through the sample, as in confocal microscopy. Here we present a 3D imaging modality, termed ankylography (derived from the Greek words ankylos meaning 'curved' and graphein meaning 'writing'), which under certain circumstances enables complete 3D structure determination from a single exposure using a monochromatic incident beam. We demonstrate that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is in principle determined by the 2D spherical pattern. We confirm the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 A resolution, and a single poliovirus at 2-3 nm resolution, from 2D spherical diffraction patterns alone. Using diffraction data from a soft X-ray laser, we also provide a preliminary demonstration that ankylography is experimentally feasible by obtaining a 3D image of a test object from a single 2D diffraction pattern. With further development, this approach of obtaining complete 3D structure information from a single view could find broad applications in the physical and life sciences.

  12. Three-dimensional Reciprocal Structures: Morphology, Concepts, Generative Rules

    DEFF Research Database (Denmark)

    Parigi, Dario; Pugnale, Alberto

    2012-01-01

    This paper present seven different three dimensional structures based on the principle of structural reciprocity with superimposition joint and standardized un-notched elements. Such typology could be regarded as being intrinsically three-dimensional because elements sit one of the top of the oth......, causing every configuration to develop naturally out-of the plane. The structures presented here were developed and built by the students of the Master of Science in “Architectural Design” during a two week long workshop organized at Aalborg University in the fall semester 2011....

  13. Three-dimensional flow and turbulence structure in electrostatic precipitator

    DEFF Research Database (Denmark)

    Ullum, Thorvald Uhrskov; Larsen, Poul Scheel; Özcan, Oktay

    2002-01-01

    and bulk velocity U0 on secondary flows and turbulence levels and structures due to the action of the three-dimensional electrostatic field on the charged gas. At constant bulk velocity (U0 = 1 m/s) and current density (Jm = 0.4 mA/m2), secondary flows in the form of rolls of axial vorticity with swirl...

  14. Three-dimensional structure of heat shock protein 90 from ...

    Indian Academy of Sciences (India)

    Madhu Sudhan

    2007-04-02

    Apr 2, 2007 ... Using inhibitors specific to the nucleotide binding domain of Hsp90, we have shown potent growth inhibitory ... role played by PfHsp90 in parasite growth, we have modeled its three dimensional structure using recently described full length .... PfHsp90 and for the development of small-molecule targets.

  15. Three-dimensional P velocity structure in Beijing area

    Science.gov (United States)

    Yu, Xiang-Wei; Chen, Yun-Tai; Wang, Pei-De

    2003-01-01

    A detail three-dimensional P wave velocity structure of Beijing, Tianjin and Tangshan area (BTT area) was determined by inverting local earthquake data. In total 16 048 P wave first arrival times from 16048 shallow and mid-depth crustal earthquakes, which occurred in and around the BTT area from 1992 to 1999 were used. The first arrival times are recorded by Northern China United Telemetry Seismic Network and Yanqing-Huailai Digital Seismic Network. Hypocentral parameters of 1 132 earthquakes with magnitude M L=1.7 6.2 and the three-dimensional P wave velocity structure were obtained simultaneously. The inversion result reveals the complicated lateral heterogeneity of P wave velocity structure around BTT area. The tomographic images obtained are also found to explain other seismological observations well.

  16. Phonon band structures of the three dimensional latticed pentamode metamaterials

    Directory of Open Access Journals (Sweden)

    Guan Wang

    2017-02-01

    Full Text Available The artificially designed three-dimensional (3D pentamode metamaterials have such an extraordinary characteristic that the solid materials behave like liquids. Meanwhile, the ideal structure of the pentamode metamaterials arranges in the same way as that of the diamond crystals. In the present research, we regard three types of pentamode metamaterials derived from the 3D crystal lattices as research objects. The phonon band structures of the candidate pentamode structures are calculated by using the finite element method (FEM. We illustrate the relation between the ratio of the bulk modulus B and the shear modulus G of different combinations of D and d. Finally, we find out the relationship between the phonon band structure and the structure parameters. It is useful for generating the phonon band structure and controlling elastic wave propagation.

  17. The three-dimensional crystal structure of cholera toxin

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Rong-Guang; Westbrook, M.L.; Nance, S.; Spangler, B.D. [Argonne National Lab., IL (United States); Scott, D.L. [Yale Univ., New Haven, CT (United States). Dept. of Molecular Biophysics and Biochemistry; Westbrook, E.M. [Northwestern Univ., Evanston, IL (United States)

    1996-02-01

    The clinical manifestations of cholera are largely attributable to the actions of a secreted hexameric AB{sub 5} enterotoxin (choleragen). We have solved the three-dimensional structure of choleragen at 2.5 {Angstrom} resolution and compared the refined coordinates with those of choleragenoid (isolated B pentamer) and the heat-labile enterotoxin from Escherichia coli (LT). The crystalline coordinates provide a detailed view of the stereochemistry implicated in binding to GM1 gangliosides and in carrying out ADP-ribosylation. The A2 chain of choleragen, in contrast to that of LT, is a nearly continuous {alpha}-helix with an interpretable carboxyl tail.

  18. Three-dimensional periodic dielectric structures having photonic Dirac points

    Science.gov (United States)

    Bravo-Abad, Jorge; Joannopoulos, John D.; Soljacic, Marin

    2015-06-02

    The dielectric, three-dimensional photonic materials disclosed herein feature Dirac-like dispersion in quasi-two-dimensional systems. Embodiments include a face-centered cubic (fcc) structure formed by alternating layers of dielectric rods and dielectric slabs patterned with holes on respective triangular lattices. This fcc structure also includes a defect layer, which may comprise either dielectric rods or a dielectric slab with patterned with holes. This defect layer introduces Dirac cone dispersion into the fcc structure's photonic band structure. Examples of these fcc structures enable enhancement of the spontaneous emission coupling efficiency (the .beta.-factor) over large areas, contrary to the conventional wisdom that the .beta.-factor degrades as the system's size increases. These results enable large-area, low-threshold lasers; single-photon sources; quantum information processing devices; and energy harvesting systems.

  19. Three-dimensional structural characterization of nonwoven fabrics.

    Science.gov (United States)

    Venu, Lalith B Suragani; Shim, Eunkyoung; Anantharamaiah, Nagendra; Pourdeyhimi, Behnam

    2012-12-01

    Nonwoven materials are found in a gamut of critical applications. This is partly due to the fact that these structures can be produced at high speed and engineered to deliver unique functionality at low cost. The behavior of these materials is highly dependent on alignment of fibers within the structure. The ability to characterize and also to control the structure is important, but very challenging due to the complex nature of the structures. Thus, to date, focus has been placed mainly on two-dimensional analysis techniques for describing the behavior of nonwovens. This article demonstrates the utility of three-dimensional (3D) digital volumetric imaging technique for visualizing and characterizing a complex 3D class of nonwoven structures produced by hydroentanglement.

  20. Three-dimensional structure of the γ-secretase complex

    International Nuclear Information System (INIS)

    Ogura, Toshihiko; Mio, Kazuhiro; Hayashi, Ikuo; Miyashita, Hiroyuki; Fukuda, Rie; Kopan, Raphael; Kodama, Tatsuhiko; Hamakubo, Takao; Iwastubo, Takeshi; Tomita, Taisuke; Sato, Chikara

    2006-01-01

    γ-Secretase belongs to an atypical class of aspartic proteases that hydrolyzes peptide bonds within the transmembrane domain of substrates, including amyloid-β precursor protein and Notch. γ-Secretase is comprised of presenilin, nicastrin, APH-1, and PEN-2 which form a large multimeric membrane protein complex, the three-dimensional structure of which is unknown. To gain insight into the structure of this complex enzyme, we purified functional γ-secretase complex reconstituted in Sf9 cells and analyzed it using negative stain electron microscopy and 3D reconstruction techniques. Analysis of 2341 negatively stained particle images resulted in the three-dimensional representation of γ-secretase at a resolution of 48 A. The structure occupies a volume of 560 x 320 x 240 A and resembles a flat heart comprised of two oppositely faced, dimpled domains. A low density space containing multiple pores resides between the domains. Some of the dimples in the putative transmembrane region may house the catalytic site. The large dimensions are consistent with the observation that γ-secretase activity resides within a high molecular weight complex

  1. Three-dimensional protein structure prediction: Methods and computational strategies.

    Science.gov (United States)

    Dorn, Márcio; E Silva, Mariel Barbachan; Buriol, Luciana S; Lamb, Luis C

    2014-10-12

    A long standing problem in structural bioinformatics is to determine the three-dimensional (3-D) structure of a protein when only a sequence of amino acid residues is given. Many computational methodologies and algorithms have been proposed as a solution to the 3-D Protein Structure Prediction (3-D-PSP) problem. These methods can be divided in four main classes: (a) first principle methods without database information; (b) first principle methods with database information; (c) fold recognition and threading methods; and (d) comparative modeling methods and sequence alignment strategies. Deterministic computational techniques, optimization techniques, data mining and machine learning approaches are typically used in the construction of computational solutions for the PSP problem. Our main goal with this work is to review the methods and computational strategies that are currently used in 3-D protein prediction. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Three-dimensional photonic band gaps in woven structures

    CERN Document Server

    Tsai Ya Chih; Pendry, J B

    1998-01-01

    In this paper, we studied the photonic properties of dielectric fibres woven into three-dimensional (3D) structures. Such fibres can be fabricated on the micrometre scale, and hence the gaps are in the far-infrared to the infrared regime. The vector-wave transfer matrix method is applied to evaluate the photonic band structures. We have also employed the constant-frequency dispersion surface scheme to investigate the development of a full band gap. Such a 3D absolute gap is observed in a rectangular lattice, but at a fairly large dielectric constant for the fibres. Ways to improve on this have been suggested. Our study indicates that woven structures are promising materials for realizing the 3D photonic insulator in the infrared regime. (author)

  3. Feasibility of Polycaprolactone Scaffolds Fabricated by Three-Dimensional Printing for Tissue Engineering of Tunica Albuginea

    Directory of Open Access Journals (Sweden)

    Ho Song Yu

    2018-01-01

    Full Text Available Purpose: To investigate the feasibility of a polycaprolactone (PCL scaffold fabricated by three-dimensional (3D printing for tissue engineering applications for tunica albuginea. Materials and Methods: PCL scaffolds were fabricated by use of a 3D printing system. Two scaffolds were fabricated that differed in the architecture of the lay-down pattern: a 90°PCL scaffold and a 45°PCL scaffold. Mechanical properties were measured to compare tensile strength between the two scaffold types. The scaffolds were characterized by scanning electron microscope (SEM images. The scaffolds were seeded with fibroblast cells, and the ability of these scaffolds to support the cells was evaluated by immunofluorescence staining. Results: The PCL scaffolds had well-structured shapes, regular arrays, and good interconnection in SEM images. The horizontal and vertical Young’s modulus coefficients were 13 and 12 MPa for the 90°PCL scaffold and 19 and 21 MPa for the 45°PCL scaffold, respectively. Microscopy images revealed that human fibroblast cells covered the entire scaffold surface. Immunofluorescence staining of ER-TR7 confirmed that the fibroblast cells remained viable and proliferated throughout the time course of the culture. Conclusions: This preliminary study provides experimental evidence for the feasibility of 3D printing of PCL scaffolds for tissue engineering applications of tunica albuginea.

  4. Feasibility of Polycaprolactone Scaffolds Fabricated by Three-Dimensional Printing for Tissue Engineering of Tunica Albuginea.

    Science.gov (United States)

    Yu, Ho Song; Park, Jinju; Lee, Hyun Suk; Park, Su A; Lee, Dong Weon; Park, Kwangsung

    2018-01-01

    To investigate the feasibility of a polycaprolactone (PCL) scaffold fabricated by three-dimensional (3D) printing for tissue engineering applications for tunica albuginea. PCL scaffolds were fabricated by use of a 3D printing system. Two scaffolds were fabricated that differed in the architecture of the lay-down pattern: a 90°PCL scaffold and a 45°PCL scaffold. Mechanical properties were measured to compare tensile strength between the two scaffold types. The scaffolds were characterized by scanning electron microscope (SEM) images. The scaffolds were seeded with fibroblast cells, and the ability of these scaffolds to support the cells was evaluated by immunofluorescence staining. The PCL scaffolds had well-structured shapes, regular arrays, and good interconnection in SEM images. The horizontal and vertical Young's modulus coefficients were 13 and 12 MPa for the 90°PCL scaffold and 19 and 21 MPa for the 45°PCL scaffold, respectively. Microscopy images revealed that human fibroblast cells covered the entire scaffold surface. Immunofluorescence staining of ER-TR7 confirmed that the fibroblast cells remained viable and proliferated throughout the time course of the culture. This preliminary study provides experimental evidence for the feasibility of 3D printing of PCL scaffolds for tissue engineering applications of tunica albuginea. Copyright © 2017 Korean Society for Sexual Medicine and Andrology

  5. Three-dimensional structure of brain tissue at submicrometer resolution

    Energy Technology Data Exchange (ETDEWEB)

    Saiga, Rino; Mizutani, Ryuta, E-mail: ryuta@tokai-u.jp [Department of Applied Biochemistry, Tokai University, Hiratsuka, Kanagawa 259-1292 (Japan); Inomoto, Chie; Takekoshi, Susumu; Nakamura, Naoya; Tsuboi, Akio; Osawa, Motoki [Tokai University School of Medicine, Isehara, Kanagawa 259-1193 (Japan); Arai, Makoto; Oshima, Kenichi; Itokawa, Masanari [Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo 156-8506 (Japan); Uesugi, Kentaro; Takeuchi, Akihisa; Terada, Yasuko; Suzuki, Yoshio [Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), Sayo, Hyogo 679-5198 (Japan)

    2016-01-28

    Biological objects are composed of submicrometer structures such as cells and organelles that are essential for their functions. Here, we report on three-dimensional X-ray visualization of cells and organelles at resolutions up to 100 nm by imaging microtomography (micro-CT) equipped with Fresnel zone plate optics. Human cerebral tissue, fruit fly cephalic ganglia, and Escherichia coli bacteria labeled with high atomic-number elements were embedded in epoxy resin and subjected to X-ray microtomography at the BL37XU and BL47XU beamlines of the SPring-8 synchrotron radiation facility. The obtained results indicated that soft tissue structures can be visualized with the imaging microtomography.

  6. Three-dimensional solution structure of Acanthamoeba profilin-I

    Science.gov (United States)

    1993-01-01

    We have determined a medium resolution three-dimensional solution structure of Acanthamoeba profilin-I by multidimensional nuclear magnetic resonance spectroscopy. This 13-kD actin binding protein consists of a five stranded antiparallel beta sheet flanked by NH2- and COOH-terminal helices on one face and by a third helix and a two stranded beta sheet on the other face. Data from actin-profilin cross- linking experiments and the localization of conserved residues between profilins in different phyla indicate that actin binding occurs on the molecular face occupied by the terminal helices. The other face of the molecule contains the residues that differ between Acanthamoeba profilins-I and II and may be important in determining the difference in polyphosphoinositide binding between these isoforms. This suggests that lipids and actin bind to different faces of the molecule. PMID:8397216

  7. SU-E-T-429: Feasibility Study On Three-Dimensional GRID Therapy in Conventional Linacs

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Y; Meyer, J; Timmerman, R; Hrycushko, B; Chen, B; Saha, D; Jiang, S [UT Southwestern Medical Center, Dallas, TX (United States)

    2015-06-15

    Purpose: Two-dimensional GRID therapy, traditionally planned and delivered using a dedicated GRID block or MLC modulation, has shown clinical efficacy in treating bulky tumors. However, the large dose to normal tissues outside target can be limiting. We hypothesize that modulation in the third dimension will improve dose sparing of normal tissues, maximize the bystander effect within the target, and ultimately improve the therapy effectiveness. This study aims to investigate the feasibility of a three-dimensional GRID technique using conventional LINACs to achieve a 3D lattice of high dose volumes within a target. Methods: Datasets of patient’s having large tumor sizes were used to investigate the planning and delivering of 3D GRID using a Varian TrueBeam linac. Original patient contours of PTV are exported from a TPS to DICOManTX where 3D GRID targets are generated in programmable configurations. A structure of avoidance (SOA), i.e., PTV minus GRID targets, is also generated to facilitate inverse planning to achieve the desired pattern. The artificial structures were sent back to the TPS where an IMRT or VMAT plan is designed to deliver a desired high dose to GRID targets while minimizing the dose to the SOA as much as possible. Results: The programmable GRID target generator enables us to modify the target geometry to maximize the peak-to-valley ratio. Preliminary results show that plans based on spherical GRID targets achieve a higher peak-to-valley dose ratio compared with cylindrical targets. High dose spillage outside the target was eliminated. IMRT planning requires the number of beams to be larger than 16, while for VMAT the number of arcs should be at least 4 in order to achieve dosimetric goals. Conclusion: Planning and delivering 3D GRID therapy using conventional LINACs was shown to be feasible. More research and development are required before this new modality can be implemented clinically.

  8. Micromagnetic studies of three-dimensional pyramidal shell structures

    International Nuclear Information System (INIS)

    Knittel, A; Franchin, M; Fischbacher, T; Fangohr, H; Nasirpouri, F; Bending, S J

    2010-01-01

    We present a systematic numerical analysis of the magnetic properties of pyramidal-shaped core-shell structures in a size range below 400 nm. These are three-dimensional structures consisting of a ferromagnetic shell which is grown on top of a non-magnetic core. The standard micromagnetic model without the magnetocrystalline anisotropy term is used to describe the properties of the shell. We vary the thickness of the shell between the limiting cases of an ultra-thin shell and a conventional pyramid and delineate different stable magnetic configurations. We find different kinds of single-domain states, which predominantly occur at smaller system sizes. In analogy to equivalent states in thin square films we term these onion, flower, C and S states. At larger system sizes, we also observe two types of vortex states, which we refer to as symmetric and asymmetric vortex states. For a classification of the observed states, we derive a phase diagram that specifies the magnetic ground state as a function of structure size and shell thickness. The transitions between different ground states can be understood qualitatively. We address the issue of metastability by investigating the stability of all occurring configurations for different shell thicknesses. For selected geometries and directions hysteresis measurements are analysed and discussed. We observe that the magnetic behaviour changes distinctively in the limit of ultra-thin shells. The study has been motivated by the recent progress made in the growth of faceted core-shell structures.

  9. Visualization of three dimensional earth fissures in geological structure

    Directory of Open Access Journals (Sweden)

    L. Zhu

    2015-11-01

    Full Text Available This paper proposes a new method for visualizing the earth fissures of geological structure in three dimensional (3-D domains on the basis of the seismic data and features information of earth fissures. The seismic data were interpreted for obtaining the stratagraphic data with various lithological information and the depth of the earth fissures. The spatial distribution of the ground fissures including the dip, strike and width were digitalized on an ArcGIS platform. Firstly, the 3-D geological structure was rebuilt using the Generalized Tri-Prism (GTP method which is a real solid method for displaying geological structures. The GTP method can reflect the inner material of the strata and can simulate complicated geological structures such as faults and stratagraphic pinch outs. The upper and lower surfaces of each stratum consist of Triangle Irregular Networks (TIN. The inner solid between the two surfaces are a series of triangular prisms. Secondly, since the width of the ground fissure gradually decreases with depth, multiple edge lines of the earth fissures on the bottom stratum surface are deduced on the basis of the fissure characteristics. Then, the model of the earth fissures consisting of a series of triangular pyramids can be constructed using these points and the edge lines. A cutting operation was carried out on the 3-D geological structure using this ground fissures model. If the surfaces of the ground fissures model intersects with the GTPs in the geological structure model, new GTPs were generated within the local regions. During this process, the topological relations between TIN, triangular prism and lines were reconstructed so that the visualization of ground fissures in the geological structure model is realized. This method can facilitate the mechanism for studying fissures and avoid the gaps between the fissure solid and the geological structure to accurately reflect their 3-D characteristics.

  10. Dynamic Three-Dimensional Geometry of the Aortic Valve Apparatus-A Feasibility Study.

    Science.gov (United States)

    Khamooshian, Arash; Amador, Yannis; Hai, Ting; Jeganathan, Jelliffe; Saraf, Maria; Mahmood, Eitezaz; Matyal, Robina; Khabbaz, Kamal R; Mariani, Massimo; Mahmood, Feroze

    2017-08-01

    To provide (1) an overview of the aortic valve (AV) apparatus anatomy and nomenclature, and (2) data regarding the normal AV apparatus geometry and dynamism during the cardiac cycle obtained from three-dimensional transesophageal echocardiography (3D TEE). Retrospective feasibility study. A single-center university teaching hospital. The study was performed on data of 10 patients with a nonregurgitant, nonstenotic aortic valve undergoing cardiac surgery. Intraoperative 3D TEE was performed on all the participants using the Siemens ACUSON SC2000 ultrasound system and Z6Ms transducer (Siemens Medical Systems, Mountainview, CA). Dynamic offline analyses were performed with Siemens eSie valve analytical software in a semiautomated fashion. Forty-five parameters were exported of which 13 were selected and analyzed. The cardiac cycle was divided into 4 quartiles to account for frame-rate variations. The annulus, sinus of Valsalva (SoV) and sinotubular junction (STJ) areas, diameter, perimeter and height, aortic leaflet height, leaflet coaptation height, and aortic valve-mitral valve angle changed significantly during the cardiac cycle (p < 0.001). STJ expanded more than both the annulus and the SoV (p < 0.001). The maximum aortic valve leaflet height change was greater in the left and right versus noncoronary leaflet (p < 0.001). The semiautomated AV apparatus dynamic assessment using eSie valve software is a clinically feasible technique and can be performed readily in the operating room. It has the potential to significantly impact intraoperative decision-making in cases suitable for AV repair. The AV apparatus is a dynamic structure and demonstrates significant changes during the cardiac cycle. Copyright © 2017. Published by Elsevier Inc.

  11. Three-dimensional analysis of anisotropic spatially reinforced structures

    Science.gov (United States)

    Bogdanovich, Alexander E.

    1993-01-01

    The material-adaptive three-dimensional analysis of inhomogeneous structures based on the meso-volume concept and application of deficient spline functions for displacement approximations is proposed. The general methodology is demonstrated on the example of a brick-type mosaic parallelepiped arbitrarily composed of anisotropic meso-volumes. A partition of each meso-volume into sub-elements, application of deficient spline functions for a local approximation of displacements and, finally, the use of the variational principle allows one to obtain displacements, strains, and stresses at anypoint within the structural part. All of the necessary external and internal boundary conditions (including the conditions of continuity of transverse stresses at interfaces between adjacent meso-volumes) can be satisfied with requisite accuracy by increasing the density of the sub-element mesh. The application of the methodology to textile composite materials is described. Several numerical examples for woven and braided rectangular composite plates and stiffened panels under transverse bending are considered. Some typical effects of stress concentrations due to the material inhomogeneities are demonstrated.

  12. The Three Dimensional Structure and Dynamics of Magnetotail Reconnection

    Science.gov (United States)

    Walker, Raymond; Lapenta, Giovanni; Liang, Haoming; El Alaoui, Mostafa; Berchem, Jean; Goldstein, Melvyn

    2017-04-01

    Magnetic reconnection is a fundamental process by which magnetic energy is dissipated and converted into particle energy. In the next few months the Magnetosphere Multi-Scale Mission (MMS) will provide high resolution observations of reconnection and its consequences in the magnetotail. Of high priority will be observations of the electron diffusion region (EDR) where the actual process of reconnection is thought to occur. In preparation for the MMS observations we have investigated tail reconnection in a realistic magnetospheric configuration by using a new approach that combines a global magnetohydrodynamic simulation of the solar wind, magnetosphere and ionosphere system with a large scale (30X12X12RE) implicit particle-in-cell (iPic3D) simulation (see Lapenta et al., 2016 Geophys. Res. Lett. 43, 515-524, doi:10.1002/2015GL066689 for a discussion of the technique). In particular we have investigated the three dimensional structure and dynamics of tail reconnection during a substorm on February 15, 2008. We found that just earthward of the reconnection site the tail becomes highly structured in the Y direction in the GSM coordinate system. The structures result from an instability associated with strong shear flows in the Y direction within the current sheet. In particular we found that the work done by the magnetic field J•E in the electron frame alternated between positive and negative although the net J•E was positive. We used several methods for identifying the EDR (non-gyrotropy, slippage, the non-ideal terms in OHM's law as well as J•E) and found that all gave false positive results in some regions of the tail. However all of the approaches gave positive results in some of the small structures with J•E positive. These putative EDRs extended ( 2di, >1di, 1di) in the X, Y and Z directions.

  13. Three-Dimensional parton structure of light nuclei

    Science.gov (United States)

    Scopetta, Sergio; Del Dotto, Alessio; Kaptari, Leonid; Pace, Emanuele; Rinaldi, Matteo; Salmè, Giovanni

    2018-03-01

    Two promising directions beyond inclusive deep inelastic scattering experiments, aimed at unveiling the three dimensional structure of the bound nucleon, are reviewed, considering in particular the 3He nuclear target. The 3D structure in coordinate space can be accessed through deep exclusive processes, whose non-perturbative part is encoded in generalized parton distributions. In this way, the distribution of partons in the transverse plane can be obtained. As an example of a deep exclusive process, coherent deeply virtual Compton scattering off 3He nuclei, important to access the neutron generalized parton distributions (GPDs), will be discussed. In Impulse Approximation (IA), the sum of the two leading twist, quark helicity conserving GPDs of 3He, H and E, at low momentum transfer, turns out to be dominated by the neutron contribution. Besides, a technique, able to take into account the nuclear effects included in the Impulse Approximation analysis, has been developed. The spin dependent GPD \\tilde H of 3He is also found to be largely dominated, at low momentum transfer, by the neutron contribution. The knowledge of the GPDs H,E and \\tilde H of 3He is relevant for the planning of coherent DVCS off 3He measurements. Semi-inclusive deep inelastic scattering processes access the momentum space 3D structure parameterized through transverse momentum dependent parton distributions. A distorted spin-dependent spectral function has been recently introduced for 3He, in a non-relativistic framework, to take care of the final state interaction between the observed pion and the remnant in semi-inclusive deep inelastic electron scattering off transversely polarized 3He. The calculation of the Sivers and Collins single spin asymmetries for 3He, and a straightforward procedure to effectively take into account nuclear dynamics and final state interactions, will be reviewed. The Light-front dynamics generalization of the analysis is also addressed.

  14. Three dimensional Lagrangian structures in the Antarctic Polar Vortex.

    Science.gov (United States)

    Mancho, Ana M.; Garcia-Garrido, Victor J.; Curbelo, Jezabel; Niang, Coumba; Mechoso, Carlos R.; Wiggins, Stephen

    2017-04-01

    . M. Mancho, A. M. A theoretical framework for lagrangian descriptors. International Journal of Bifurcation and Chaos (2017) to appear. [5] The three-dimensional Lagrangian geometry of the Antarctic Polar Vortex circulation. Preprint.

  15. 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....

  16. Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase

    Energy Technology Data Exchange (ETDEWEB)

    Kamat, S.S.; Swaminathan, S.; Bagaria, A.; Kumaran, D.; Holmes-Hampton, G. P.; Fan, H.; Sali, A.; Sauder, J. M.; Burley, S. K.; Lindahl, P. A.; Raushel, F. M.

    2011-03-22

    Adenine deaminase (ADE) catalyzes the conversion of adenine to hypoxanthine and ammonia. The enzyme isolated from Escherichia coli using standard expression conditions was low for the deamination of adenine (k{sub cat} = 2.0 s{sup -1}; k{sub cat}/K{sub m} = 2.5 x 10{sup 3} M{sup -1} s{sup -1}). However, when iron was sequestered with a metal chelator and the growth medium was supplemented with Mn{sup 2+} prior to induction, the purified enzyme was substantially more active for the deamination of adenine with kcat and kcat/Km values of 200 s{sup -1} and 5 x 10{sup 5} M{sup -1} s{sup -1}, respectively. The apoenzyme was prepared and reconstituted with Fe{sup 2+}, Zn{sup 2+}, or Mn{sup 2+}. In each case, two enzyme equivalents of metal were necessary for reconstitution of the deaminase activity. This work provides the first example of any member of the deaminase subfamily of the amidohydrolase superfamily to utilize a binuclear metal center for the catalysis of a deamination reaction. [Fe{sup II}/Fe{sup II}]-ADE was oxidized to [Fe{sup III}/Fe{sup III}]-ADE with ferricyanide with inactivation of the deaminase activity. Reducing [Fe{sup III}/Fe{sup III}]-ADE with dithionite restored the deaminase activity, and thus, the diferrous form of the enzyme is essential for catalytic activity. No evidence of spin coupling between metal ions was evident by electron paramagnetic resonance or Moessbauer spectroscopy. The three-dimensional structure of adenine deaminase from Agrobacterium tumefaciens (Atu4426) was determined by X-ray crystallography at 2.2 {angstrom} resolution, and adenine was modeled into the active site on the basis of homology to other members of the amidohydrolase superfamily. On the basis of the model of the adenine-ADE complex and subsequent mutagenesis experiments, the roles for each of the highly conserved residues were proposed. Solvent isotope effects, pH-rate profiles, and solvent viscosity were utilized to propose a chemical reaction mechanism and the

  17. Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase

    Energy Technology Data Exchange (ETDEWEB)

    S Kamat; A Bagaria; D Kumaran; G Holmes-Hampton; H Fan; A Sali; J Sauder; S Burley; P Lindahl; et. al.

    2011-12-31

    Adenine deaminase (ADE) catalyzes the conversion of adenine to hypoxanthine and ammonia. The enzyme isolated from Escherichia coli using standard expression conditions was low for the deamination of adenine (k{sub cat} = 2.0 s{sup -1}; k{sub cat}/K{sub m} = 2.5 x 10{sup 3} M{sup -1} s{sup -1}). However, when iron was sequestered with a metal chelator and the growth medium was supplemented with Mn{sup 2+} prior to induction, the purified enzyme was substantially more active for the deamination of adenine with k{sub cat} and k{sub cat}/K{sub m} values of 200 s{sup -1} and 5 x 10{sup 5} M{sup -1} s{sup -1}, respectively. The apoenzyme was prepared and reconstituted with Fe{sup 2+}, Zn{sup 2+}, or Mn{sup 2+}. In each case, two enzyme equivalents of metal were necessary for reconstitution of the deaminase activity. This work provides the first example of any member of the deaminase subfamily of the amidohydrolase superfamily to utilize a binuclear metal center for the catalysis of a deamination reaction. [Fe{sup II}/Fe{sup II}]-ADE was oxidized to [Fe{sup III}/Fe{sup III}]-ADE with ferricyanide with inactivation of the deaminase activity. Reducing [Fe{sup III}/Fe{sup III}]-ADE with dithionite restored the deaminase activity, and thus, the diferrous form of the enzyme is essential for catalytic activity. No evidence of spin coupling between metal ions was evident by electron paramagnetic resonance or Moessbauer spectroscopy. The three-dimensional structure of adenine deaminase from Agrobacterium tumefaciens (Atu4426) was determined by X-ray crystallography at 2.2 {angstrom} resolution, and adenine was modeled into the active site on the basis of homology to other members of the amidohydrolase superfamily. On the basis of the model of the adenine-ADE complex and subsequent mutagenesis experiments, the roles for each of the highly conserved residues were proposed. Solvent isotope effects, pH-rate profiles, and solvent viscosity were utilized to propose a chemical reaction

  18. Manufacturing of Three-dimensional Micro Structure Using Proton Beam

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Suonggyu; Kwon, Wontae [Seoul University, Seoul (Korea, Republic of)

    2015-04-15

    The diameter of a proton beam emanating from the MC-50 cyclotron is about 2?3 mm with Gaussian distribution. This widely irradiated proton beam is not suitable for semiconductor etching, precise positioning, and micromachining, which require a small spot. In this study, a beam cutting method using a microhole is proposed as an economical alternative. We produced a microhole with aspect ratio, average diameter, and thickness of 428, 21 μm, and 9 mm, respectively, for cutting the proton beam. By using this high-aspect-ratio microhole, we conducted machinability tests on microstructures with sizes of tens of μm. Additionally, the results of simulation using GEANT4 and those of the actual experiment were compared and analyzed. The outcome confirmed the possibility of implementing a micro process technology for the fabrication of three-dimensional microstructures of 20 micron units using the MC-50 cyclotron with the microhole.

  19. Visualization of Three-Dimensional Nephron Structure With Microcomputed Tomography

    International Nuclear Information System (INIS)

    Bentley, M.; Jorgensen, S.; Lerman, L.; Ritman, E.; Romero, J.

    2007-01-01

    The three-dimensional architecture of nephrons in situ and their interrelationship with other nephrons are difficult to visualize by microscopic methods. The present study uses microcomputed X-ray tomography (micro-CT) to visualize intact nephrons in situ. Rat kidneys were perfusion-fixed with buffered formalin and their vasculature was subsequently perfused with radiopaque silicone. Cortical tissue was stained en bloc with osmium tetroxide, embedded in plastic, scanned, and reconstructed at voxel resolutions of 6, 2, and 1 μm. At 6 μm resolution, large blood vessels and glomeruli could be visualized but nephrons and their lumens were small and difficult to visualize. Optimal images were obtained using a synchrotron radiation source at 2 μm resolution where nephron components could be identified, correlated with histological sections, and traced. Proximal tubules had large diameters and opaque walls, whereas distal tubules, connecting tubules, and collecting ducts had smaller diameters and less opaque walls. Blood vessels could be distinguished from nephrons by the luminal presence of radiopaque silicone. Proximal tubules were three times longer than distal tubules. Proximal and distal tubules were tightly coiled in the outer cortex but were loosely coiled in the middle and inner cortex. The connecting tubules had the narrowest diameters of the tubules and converged to form arcades that paralleled the radial vessels as they extended to the outer cortex. These results illustrate a potential use of micro-CT to obtain three-dimensional information about nephron architecture and nephron interrelationships, which could be useful in evaluating experimental tubular hypertrophy, atrophy, and necrosis

  20. Energy distribution of structure-borne sound in three-dimensional structures

    DEFF Research Database (Denmark)

    Hugin, Claus Thomas

    1996-01-01

    This report deals with the prediction of energy distribution of structure-borne sound in three-dimensional structures consisting of coupled thin rectangular plates. The frequency range addressed is the medium frequency range, which is characterised by having so few modes that a traditional...

  1. 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......The design and production time for complex microfluidic systems is considerable, often up to several months. It is therefore important to be able to understand and predict the flow phenomena prior to design and fabrication of the microdevice in order to save costly fabrication resources......, 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....

  2. Three-Dimensional Cellular Structures Enhanced By Shape Memory Alloys

    Science.gov (United States)

    Nathal, Michael V.; Krause, David L.; Wilmoth, Nathan G.; Bednarcyk, Brett A.; Baker, Eric H.

    2014-01-01

    This research effort explored lightweight structural concepts married with advanced smart materials to achieve a wide variety of benefits in airframe and engine components. Lattice block structures were cast from an aerospace structural titanium alloy Ti-6Al-4V and a NiTi shape memory alloy (SMA), and preliminary properties have been measured. A finite element-based modeling approach that can rapidly and accurately capture the deformation response of lattice architectures was developed. The Ti-6-4 and SMA material behavior was calibrated via experimental tests of ligaments machined from the lattice. Benchmark testing of complete lattice structures verified the main aspects of the model as well as demonstrated the advantages of the lattice structure. Shape memory behavior of a sample machined from a lattice block was also demonstrated.

  3. The Three-Dimensional Structural Basis of Type II Hyperprolinemia

    Energy Technology Data Exchange (ETDEWEB)

    Srivastava, Dhiraj; Singh, Ranjan K.; Moxley, Michael A.; Henzl, Michael T.; Becker, Donald F.; Tanner, John J. (UNL); (UMC)

    2012-08-31

    Type II hyperprolinemia is an autosomal recessive disorder caused by a deficiency in {Delta}{sup 1}-pyrroline-5-carboxylate dehydrogenase (P5CDH; also known as ALDH4A1), the aldehyde dehydrogenase that catalyzes the oxidation of glutamate semialdehyde to glutamate. Here, we report the first structure of human P5CDH (HsP5CDH) and investigate the impact of the hyperprolinemia-associated mutation of Ser352 to Leu on the structure and catalytic properties of the enzyme. The 2. 5-{angstrom}-resolution crystal structure of HsP5CDH was determined using experimental phasing. Structures of the mutant enzymes S352A (2.4 {angstrom}) and S352L (2.85 {angstrom}) were determined to elucidate the structural consequences of altering Ser352. Structures of the 93% identical mouse P5CDH complexed with sulfate ion (1.3 {angstrom} resolution), glutamate (1.5 {angstrom}), and NAD{sup +} (1.5 {angstrom}) were determined to obtain high-resolution views of the active site. Together, the structures show that Ser352 occupies a hydrophilic pocket and is connected via water-mediated hydrogen bonds to catalytic Cys348. Mutation of Ser352 to Leu is shown to abolish catalytic activity and eliminate NAD{sup +} binding. Analysis of the S352A mutant shows that these functional defects are caused by the introduction of the nonpolar Leu352 side chain rather than the removal of the Ser352 hydroxyl. The S352L structure shows that the mutation induces a dramatic 8-{angstrom} rearrangement of the catalytic loop. Because of this conformational change, Ser349 is not positioned to interact with the aldehyde substrate, conserved Glu447 is no longer poised to bind NAD{sup +}, and Cys348 faces the wrong direction for nucleophilic attack. These structural alterations render the enzyme inactive.

  4. Three-dimensional hierarchical structures for fog harvesting.

    Science.gov (United States)

    Andrews, H G; Eccles, E A; Schofield, W C E; Badyal, J P S

    2011-04-05

    Conventional fog-harvesting mechanisms are effectively pseudo-2D surface phenomena in terms of water droplet-plant interactions. In the case of the Cotula fallax plant, a unique hierarchical 3D arrangement formed by its leaves and the fine hairs covering them has been found to underpin the collection and retention of water droplets on the foliage for extended periods of time. The mechanisms of water capture and release as a function of the surface 3D structure and chemistry have been identified. Of particular note is that water is retained throughout the entirety of the plant and held within the foliage itself (rather than in localized regions). Individual plant hairs form matlike structures capable of supporting water droplets; these hairs wrap around water droplets in a 3D fashion to secure them via a fine nanoscale groove structure that prevents them from easily falling to the ground.

  5. Evaluation of Three Dimensional Underground Structure at SAFOD Project

    International Nuclear Information System (INIS)

    Malin, Peter

    2014-01-01

    In the SAFOD project, the imaging of the fault zone was implemented using data acquired by a pilot hole array of a vertical depth of 2 km and then a main hole was drilled using these data. The trajectory of the main hole below vertical depth of 1.5 km was angled toward/through the fault zone up to a vertical depth of 3 km. An sensor array was located in the hole. As a result, the hypocenter locations of small earthquakes within the fault zone were determined with high accuracy (location error within 10 meters) and the location of the fault zone was able to be identified with high accuracy. Using this data, high resolution underground structure around the San Andreas fault zone was obtained. It was reported that this underground structure revealed the deep structure of the San Andreas Fault at the Parkfield site as well as the branch fault. (author)

  6. Guide to Three Dimensional Structure and Motion Factorization

    CERN Document Server

    Wang, Guanghui

    2011-01-01

    The problem of structure and motion recovery from image sequences is an important theme in computer vision. Considerable progress has been made in this field during the past two decades, resulting in successful applications in robot navigation, augmented reality, industrial inspection, medical image analysis, and digital entertainment, among other areas. However, many of these methods work only for rigid objects and static scenes. The study of non-rigid structure from motion is not only of academic significance, but also has important practical applications in real-world, nonrigid or dynamic s

  7. Quantized fluctuational electrodynamics for three-dimensional plasmonic structures

    DEFF Research Database (Denmark)

    Partanen, Mikko; Häyrynen, Teppo; Tulkki, Jukka

    2017-01-01

    We recently introduced a quantized fluctuational electrodynamics (QFED) formalism that provides a physically insightful definition of an effective position-dependent photon-number operator and the associated ladder operators. However, this far the formalism has been applicable only for the normal...... incidence of the electromagnetic field in planar structures. In this work, we overcome the main limitation of the one-dimensional QFED formalism by extending the model to three dimensions, allowing us to use the QFED method to study, e.g., plasmonic structures. To demonstrate the benefits of the developed...

  8. From three-dimensional GPCR structure to rational ligand discovery

    NARCIS (Netherlands)

    Kooistra, A.J.; Leurs, R.; de Esch, I.J.P.; de Graaf, C.

    2014-01-01

    This chapter will focus on G protein-coupled receptor structure-based virtual screening and ligand design. A generic virtual screening workflow and its individual elements will be introduced, covering amongst others the use of experimental data to steer the virtual screening process, ligand binding

  9. Structurally Efficient Three-dimensional Metamaterials with Controllable Thermal Expansion

    Science.gov (United States)

    Xu, Hang; Pasini, Damiano

    2016-01-01

    The coefficient of thermal expansion (CTE) of architected materials, as opposed to that of conventional solids, can be tuned to zero by intentionally altering the geometry of their structural layout. Existing material architectures, however, achieve CTE tunability only with a sacrifice in structural efficiency, i.e. a drop in both their stiffness to mass ratio and strength to mass ratio. In this work, we elucidate how to resolve the trade-off between CTE tunability and structural efficiency and present a lightweight bi-material architecture that not only is stiffer and stronger than other 3D architected materials, but also has a highly tunable CTE. Via a combination of physical experiments on 3D fabricated prototypes and numeric simulations, we demonstrate how two distinct mechanisms of thermal expansion appearing in a tetrahedron, can be exploited in an Octet lattice to generate a large range of CTE values, including negative, zero, or positive, with no loss in structural efficiency. The novelty and simplicity of the proposed design as well as the ease in fabrication, make this bi-material architecture well-suited for a wide range of applications, including satellite antennas, space optical systems, precision instruments, thermal actuators, and MEMS. PMID:27721437

  10. Three-dimensional structure of Rubella virus factories

    International Nuclear Information System (INIS)

    Fontana, Juan; Lopez-Iglesias, Carmen; Tzeng, Wen-Ping; Frey, Teryl K.; Fernandez, Jose J.; Risco, Cristina

    2010-01-01

    Viral factories are complex structures in the infected cell where viruses compartmentalize their life cycle. Rubella virus (RUBV) assembles factories by recruitment of rough endoplasmic reticulum (RER), mitochondria and Golgi around modified lysosomes known as cytopathic vacuoles or CPVs. These organelles contain active replication complexes that transfer replicated RNA to assembly sites in Golgi membranes. We have studied the structure of RUBV factory in three dimensions by electron tomography and freeze-fracture. CPVs contain stacked membranes, rigid sheets, small vesicles and large vacuoles. These membranes are interconnected and in communication with the endocytic pathway since they incorporate endocytosed BSA-gold. RER and CPVs are coupled through protein bridges and closely apposed membranes. Golgi vesicles attach to the CPVs but no tight contacts with mitochondria were detected. Immunogold labelling confirmed that the mitochondrial protein p32 is an abundant component around and inside CPVs where it could play important roles in factory activities.

  11. Computational Study of Colloidal Droplet Interactions with Three Dimensional Structures

    Science.gov (United States)

    2015-05-18

    create a novel multiphysics model that enables the prediction of colloidal droplet interactions with complex porous structures; (b) advance the...diameter and penetration depth. (2) A model for the transport and deposition of nanoparticles in the porous matrix during droplet sorption was...process. The main research goals of this proposal are to (a) create a novel multiphysics model that enables the prediction of colloidal droplet

  12. Three-Dimensional Structure and Catalytic Mechanism of Cytosine Deaminase

    Energy Technology Data Exchange (ETDEWEB)

    R Hall; A Fedorov; C Xu; E Fedorov; S Almo; F Raushel

    2011-12-31

    Cytosine deaminase (CDA) from E. coli is a member of the amidohydrolase superfamily. The structure of the zinc-activated enzyme was determined in the presence of phosphonocytosine, a mimic of the tetrahedral reaction intermediate. This compound inhibits the deamination of cytosine with a K{sub i} of 52 nM. The zinc- and iron-containing enzymes were characterized to determine the effect of the divalent cations on activation of the hydrolytic water. Fe-CDA loses activity at low pH with a kinetic pKa of 6.0, and Zn-CDA has a kinetic pKa of 7.3. Mutation of Gln-156 decreased the catalytic activity by more than 5 orders of magnitude, supporting its role in substrate binding. Mutation of Glu-217, Asp-313, and His-246 significantly decreased catalytic activity supporting the role of these three residues in activation of the hydrolytic water molecule and facilitation of proton transfer reactions. A library of potential substrates was used to probe the structural determinants responsible for catalytic activity. CDA was able to catalyze the deamination of isocytosine and the hydrolysis of 3-oxauracil. Large inverse solvent isotope effects were obtained on k{sub cat} and k{sub cat}/K{sub m}, consistent with the formation of a low-barrier hydrogen bond during the conversion of cytosine to uracil. A chemical mechanism for substrate deamination by CDA was proposed.

  13. Three-dimensional shallow velocity structure beneath Taal Volcano, Philippines

    Science.gov (United States)

    You, Shuei-Huei; Konstantinou, Konstantinos I.; Gung, Yuancheng; Lin, Cheng-Horng

    2017-11-01

    Based on its numerous historical explosive eruptions and high potential hazards to nearby population of millions, Taal Volcano is one of the most dangerous "Decade Volcanoes" in the world. To provide better investigation on local seismicity and seismic structure beneath Taal Volcano, we deployed a temporary seismic network consisting of eight stations from March 2008 to March 2010. In the preliminary data processing stage, three periods showing linear time-drifting of internal clock were clearly identified from noise-derived empirical Green's functions. The time-drifting errors were corrected prior to further data analyses. By using VELEST, 2274 local earthquakes were manually picked and located. Two major earthquake groups are noticed, with one lying beneath the western shore of Taal Lake showing a linear feature, and the other spreading around the eastern flank of Taal Volcano Island at shallower depths. We performed seismic tomography to image the 3D structure beneath Taal Volcano using the LOTOS algorithm. Some interesting features are revealed from the tomographic results, including a solidified magma conduit below the northwestern corner of Taal Volcano Island, indicated by high Vp, Vs, and low Vp/Vs ratio, and a large potential hydrothermal reservoir beneath the center of Taal Volcano Island, suggested by low Vs and high Vp/Vs ratio. Furthermore, combining earthquake distributions and tomographic images, we suggest potential existence of a hydrothermal reservoir beneath the southwestern corner of Taal Lake, and a fluid conduit extending to the northwest. These seismic features have never been proposed in previous studies, implying that new hydrothermal activity might be formed in places away from the historical craters on Taal Volcano Island.

  14. Dynamic Three-Dimensional Geometry of the Aortic Valve Apparatus-A Feasibility Study

    NARCIS (Netherlands)

    Khamooshian, Arash; Amador, Yannis; Hai, Ting; Jeganathan, Jelliffe; Saraf, Maria; Mahmood, Eitezaz; Matyal, Robina; Khabbaz, Kamal R; Mariani, Massimo; Mahmood, Feroze

    OBJECTIVE: To provide (1) an overview of the aortic valve (AV) apparatus anatomy and nomenclature, and (2) data regarding the normal AV apparatus geometry and dynamism during the cardiac cycle obtained from three-dimensional transesophageal echocardiography (3D TEE). DESIGN: Retrospective

  15. Three-dimensional structure of a pre-catalytic human spliceosomal complex B.

    Science.gov (United States)

    Boehringer, Daniel; Makarov, Evgeny M; Sander, Bjoern; Makarova, Olga V; Kastner, Berthold; Lührmann, Reinhard; Stark, Holger

    2004-05-01

    Major structural changes occur in the spliceosome during its transition from the fully assembled complex B to the catalytically activated spliceosome. To understand the rearrangement, it is necessary to know the detailed three-dimensional structures of these complexes. Here, we have immunoaffinity-purified human spliceosomes (designated B Delta U1) at a stage after U4/U6.U5 tri-snRNP integration but before activation, and have determined the three-dimensional structure of B Delta U1 by single-particle electron cryomicroscopy at a resolution of approximately 40 A. The overall size of the complex is about 370 x 270 x 170 A. The three-dimensional structure features a roughly triangular body linked to a head domain in variable orientations. The body is very similar in size and shape to the isolated U4/U6.U5 tri-snRNP. This provides initial insight into the structural organization of complex B.

  16. Three-dimensional electron diffraction as a complementary technique to powder X-ray diffraction for phase identification and structure solution of powders

    Directory of Open Access Journals (Sweden)

    Yifeng Yun

    2015-03-01

    Full Text Available Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED data collection, namely automated diffraction tomography (ADT and rotation electron diffraction (RED, have been developed. Compared with X-ray diffraction (XRD and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni–Se–O–Cl crystals, zeolites, germanates, metal–organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional

  17. Ray tracing a three-dimensional scene using a hierarchical data structure

    Science.gov (United States)

    Wald, Ingo; Boulos, Solomon; Shirley, Peter

    2012-09-04

    Ray tracing a three-dimensional scene made up of geometric primitives that are spatially partitioned into a hierarchical data structure. One example embodiment is a method for ray tracing a three-dimensional scene made up of geometric primitives that are spatially partitioned into a hierarchical data structure. In this example embodiment, the hierarchical data structure includes at least a parent node and a corresponding plurality of child nodes. The method includes a first act of determining that a first active ray in the packet hits the parent node and a second act of descending to each of the plurality of child nodes.

  18. The Effect of Three-Dimensional Simulations on the Understanding of Chemical Structures and Their Properties

    Science.gov (United States)

    Urhahne, Detlef; Nick, Sabine; Schanze, Sascha

    2009-08-01

    In a series of three experimental studies, the effectiveness of three-dimensional computer simulations to aid the understanding of chemical structures and their properties was investigated. Arguments for the usefulness of three-dimensional simulations were derived from Mayer’s generative theory of multimedia learning. Simulations might lead to a decrease in cognitive load and thus support active learning. In our studies, the learning effectiveness of three-dimensional simulations was compared to two-dimensional illustrations by use of different versions of a computer programme concerning the modifications of carbon. The first and third study with freshman students of chemistry and biochemistry show that no more knowledge was acquired when participants learnt with three-dimensional simulations than with two-dimensional figures. In the second study with 16-year old secondary school students, use of simulations facilitated the acquisition of conceptual knowledge. It was concluded that three-dimensional simulations are more effective for younger students who lack the experience of learning with different visual representation formats in chemistry. In all three studies, a significant relationship between spatial ability and conceptual knowledge about the modifications of carbon was detected.

  19. DNA Structure and Stability Tutorial: Interactive animations of the DNA three-dimensional structure

    Directory of Open Access Journals (Sweden)

    Larissa Assis Barony Valadares Fonseca

    2017-10-01

    Full Text Available The tutorial "DNA Structure and Stability" was developed articulating Ausubel's Theory of Meaningful Learning and Mayer's Multimedia principles, in order to favor the DNA structure significant learning through the guided and gradual exploration of the DNA three-dimensional structure interactive animations. In this sense, conceptual units with auxiliary medias have been established, such as texts, diagrams and tables, which assist in the explanation of animations. Several chemical and biochemical concepts are explained in order to favor understanding of DNA as a biopolymer determined by its intra/intermolecular chemical interactions that consequently establish the structure/stability relationships and structure/biological activity. In this way, was developed an interactive tutorial that can be used in several teaching and learning situations in order to favor the construction of knowledge by the learner.

  20. Controlled Ag electroless deposition in bulk structures with complex three-dimensional profiles

    DEFF Research Database (Denmark)

    Malureanu, Radu; Zalkovskij, Maksim; Andryieuski, Andrei

    2010-01-01

    In this work we show the possibility of controlled deposition of a nanometer-sized silver layer on three-dimensional 3D structures. The deposition takes place in liquid environment, allowing for an easy and fast processing with intrinsically isotropic characteristics. The obtained layers...

  1. Optimal Layout Design using the Element Connectivity Parameterization Method: Application to Three Dimensional Geometrical Nonlinear Structures

    DEFF Research Database (Denmark)

    Yoon, Gil Ho; Joung, Young Soo; Kim, Yoon Young

    2005-01-01

    The topology design optimization of “three-dimensional geometrically-nonlinear” continuum structures is still a difficult problem not only because of its problem size but also the occurrence of unstable continuum finite elements during the design optimization. To overcome this difficulty, the ele...

  2. Three-Dimensional Structure of Bovine NADH : Ubiquinone Oxidoreductase of the Mitochondrial Respiratory Chain

    NARCIS (Netherlands)

    Boekema, Egbert J.; Heel, Marin G. van; Bruggen, Ernst F.J. van

    1984-01-01

    We have studied the structure of bovine heart mitochondrial NADH:ubiquinone (Q) oxidoreductase (EC 1.6.99.3) by image analysis of electron micrographs. A three-dimensional reconstruction was calculated from a tilt-series of a two-dimensional crystal of the molecule. Our interpretation of the

  3. Selective SiO2 etching in three dimensional structures using parylene-C as mask

    NARCIS (Netherlands)

    Veltkamp, Henk-Willem; Zhao, Yiyuan; de Boer, Meint J.; Wiegerink, Remco J.; Lötters, Joost Conrad

    2017-01-01

    This abstract describes an application of an easy and straightforward method for selective SiO2 etching in three dimensional structures, which is developed by our group. The application in this abstract is the protection of the buried-oxide (BOX) layer of a silicon-on-insulator (SOI) wafer against

  4. Layout to circuit extraction for three-dimensional thermal-electrical circuit simulation of device structures

    NARCIS (Netherlands)

    Krabbenborg, B.H.; Krabbenborg, B.H.; Bosma, A.; de Graaff, H.C.; de Graaff, H.C.; Mouthaan, A.J.

    1996-01-01

    In this paper, a method is proposed for extraction of coupled networks from layout information for simulation of electrothermal device behavior. The networks represent a three-dimensional (3-D) device structure with circuit elements. The electrical and thermal characteristics of this circuit

  5. Development of Three-Dimensional Dental Scanning Apparatus Using Structured Illumination

    OpenAIRE

    Ahn, Jae Sung; Park, Anjin; Kim, Ju Wan; Lee, Byeong Ha; Eom, Joo Beom

    2017-01-01

    We demonstrated a three-dimensional (3D) dental scanning apparatus based on structured illumination. A liquid lens was used for tuning focus and a piezomotor stage was used for the shift of structured light. A simple algorithm, which detects intensity modulation, was used to perform optical sectioning with structured illumination. We reconstructed a 3D point cloud, which represents the 3D coordinates of the digitized surface of a dental gypsum cast by piling up sectioned images. We performed ...

  6. Three-dimensional window analysis for detecting positive selection at structural regions of proteins.

    Science.gov (United States)

    Suzuki, Yoshiyuki

    2004-12-01

    Detection of natural selection operating at the amino acid sequence level is important in the study of molecular evolution. Single-site analysis and one-dimensional window analysis can be used to detect selection when the biological functions of amino acid sites are unknown. Single-site analysis is useful when selection operates more or less constantly over evolutionary time, but less so when selection operates temporarily. One-dimensional window analysis is more sensitive than single-site analysis when the functions of amino acid sites in close proximity in the linear sequence are similar, although this is not always the case. Here I present a three-dimensional window analysis method for detecting selection given the three-dimensional structure of the protein of interest. In the three-dimensional structure, the window is defined as the sphere centered on the alpha-carbon of an amino acid site. The window size is the radius of the sphere. The sites whose alpha-carbons are included in the window are grouped for the neutrality test. The window is moved within the three-dimensional structure by sequentially moving the central site along the primary amino acid sequence. To detect positive selection, it may also be useful to group the surface-exposed sites in the window separately. Three-dimensional window analysis appears not only to be more sensitive than single-site analysis and one-dimensional window analysis but also to provide similar specificity for inferring positive selection in the analyses of the hemagglutinin and neuraminidase genes of human influenza A viruses. This method, however, may fail to detect selection when it operates only on a particular site, in which case single-site analysis may be preferred, although a large number of sequences is required.

  7. Three-dimensional detonation cellular structures in rectangular ducts using an improved CESE scheme

    KAUST Repository

    Shen, Yang

    2016-11-01

    The three-dimensional premixed H2-O2 detonation propagation in rectangular ducts is simulated using an in-house parallel detonation code based on the second-order space–time conservation element and solution element (CE/SE) scheme. The simulation reproduces three typical cellular structures by setting appropriate cross-sectional size and initial perturbation in square tubes. As the cross-sectional size decreases, critical cellular structures transforming the rectangular or diagonal mode into the spinning mode are obtained and discussed in the perspective of phase variation as well as decreasing of triple point lines. Furthermore, multiple cellular structures are observed through examples with typical aspect ratios. Utilizing the visualization of detailed three-dimensional structures, their formation mechanism is further analyzed.

  8. The crystal structures of three pyrazine-2,5-dicarboxamides: three-dimensional supramolecular structures

    Directory of Open Access Journals (Sweden)

    Dilovan S. Cati

    2017-05-01

    Full Text Available The complete molecules of the title compounds, N2,N5-bis(pyridin-2-ylmethylpyrazine-2,5-dicarboxamide, C18H16N6O2 (I, 3,6-dimethyl-N2,N5-bis(pyridin-2-ylmethylpyrazine-2,5-dicarboxamide, C20H20N6O2 (II, and N2,N5-bis(pyridin-4-ylmethylpyrazine-2,5-dicarboxamide, C18H16N6O2 (III, are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each molecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7° in (I, 75.83 (8° in (II and by 82.71 (6° in (III. In the crystal of (I, molecules are linked by N—H...N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. In the crystal of (II, molecules are also linked by N—H...N hydrogen bonds, forming layers lying parallel to the (10-1 plane. As in (I, the layers are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. In the crystal of (III, molecules are again linked by N—H...N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π–π interactions [intercentroid distance = 3.739 (1 Å]. The sheets are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. Compound (I crystallizes in the monoclinic space group P21/c. Another monoclinic polymorph, space group C2/c, has been reported on by Cockriel et al. [Inorg. Chem. Commun. (2008, 11, 1–4]. The molecular structures of the two polymorphs are compared.

  9. Leaving flatland: Diagnostics for Lagrangian coherent structures in three-dimensional flows

    Science.gov (United States)

    Sulman, Mohamed H. M.; Huntley, Helga S.; Lipphardt, B. L.; Kirwan, A. D.

    2013-09-01

    Finite-time Lyapunov exponents (FTLE) are often used to identify Lagrangian Coherent Structures (LCS). Most applications are confined to flows on two-dimensional (2D) surfaces where the LCS are characterized as curves. The extension to three-dimensional (3D) flows, whose LCS are 2D structures embedded in a 3D volume, is theoretically straightforward. However, in geophysical flows at regional scales, full prognostic computation of the evolving 3D velocity field is not computationally feasible. The vertical or diabatic velocity, then, is either ignored or estimated as a diagnostic quantity with questionable accuracy. Even in cases with reliable 3D velocities, it may prove advantageous to minimize the computational burden by calculating trajectories from velocities on carefully chosen surfaces only. When reliable 3D velocity information is unavailable or one velocity component is explicitly ignored, a reduced FTLE form to approximate 2D LCS surfaces in a 3D volume is necessary. The accuracy of two reduced FTLE formulations is assessed here using the ABC flow and a 3D quadrupole flow as test models. One is the standard approach of knitting together FTLE patterns obtained on adjacent surfaces. The other is a new approximation accounting for the dispersion due to vertical (u,v) shear. The results are compared with those obtained from the full 3D velocity field. We introduce two diagnostic quantities to identify situations when a fully 3D computation is required for an accurate determination of the 2D LCS. For the ABC flow, we found the full 3D calculation to be necessary unless the vertical (u,v) shear is sufficiently small. However, both methods compare favorably with the 3D calculation for the quadrupole model scaled to typical open ocean conditions.

  10. Conservation of the three-dimensional structure in non-homologous or unrelated proteins

    Directory of Open Access Journals (Sweden)

    Sousounis Konstantinos

    2012-08-01

    Full Text Available Abstract In this review, we examine examples of conservation of protein structural motifs in unrelated or non-homologous proteins. For this, we have selected three DNA-binding motifs: the histone fold, the helix-turn-helix motif, and the zinc finger, as well as the globin-like fold. We show that indeed similar structures exist in unrelated proteins, strengthening the concept that three-dimensional conservation might be more important than the primary amino acid sequence.

  11. Three-dimensional pore structure and ion conductivity of porous ceramic diaphragms

    OpenAIRE

    Wiedenmann, Daniel; Keller, Lukas; Holzer, Lorenz; Stojadinović, Jelena; Münch, Beat; Suarez, Laura; Fumey, Benjamin; Hagendorfer, Harald; Brönnimann, Rolf; Modregger, Peter; Gorbar, Michal; Vogt, Ulrich F.; Züttel, Andreas; Mantia, Fabio La; Wepf, Roger

    2013-01-01

    The ion conductivity of two series of porous ceramic diaphragms impregnated with caustic potash was investigated by electrochemical impedance spectroscopy. To understand the impact of the pore structure on ion conductivity, the three-dimensional (3-D) pore geometry of the diaphragms was characterized with synchrotron x-ray absorption tomography. Ion migration was calculated based on an extended pore structure model, which includes the electrolyte conductivity and geometric pore parameters, fo...

  12. A Three-Dimensional Enormous Surface Area Aluminum Microneedle Array with Nanoporous Structure

    OpenAIRE

    Chen, Po Chun; Hsieh, Sheng Jen; Chen, Chien Chon; Zou, Jun

    2013-01-01

    We proposed fabricating an aluminum microneedle array with a nanochannel structure on the surface by combining micromachining, electrolyte polishing, and anodization methods. The microneedle array provides a three-dimensional (3D) structure that possesses several hundred times more surface area than a traditional nanochannel template. Therefore, the microneedle array can potentially be used in many technology applications. This 3D microneedle array device can not only be used for painless inj...

  13. Manipulation of fluids in three-dimensional porous photonic structures with patterned surface properties

    Energy Technology Data Exchange (ETDEWEB)

    Aizenberg, Joanna; Burgess, Ian; Mishchenko, Lidiya; Hatton, Benjamin; Loncar, Marko

    2017-12-26

    A three-dimensional porous photonic structure, whose internal pore surfaces can be provided with desired surface properties in a spatially selective manner with arbitrary patterns, and methods for making the same are described. When exposed to a fluid (e.g., via immersion or wicking), the fluid can selectively penetrate the regions of the structure with compatible surface properties. Broad applications, for example in security, encryption and document authentication, as well as in areas such as simple microfluidics and diagnostics, are anticipated.

  14. Optical Fiber/Nanowire Hybrid Structures for Efficient Three-Dimensional Dye-Sensitized Solar Cells

    KAUST Repository

    Weintraub, Benjamin

    2009-11-09

    Wired up: The energy conversion efficiency of three-dimensional dye-sensitized solar cells (DSSCs) in a hybrid structure that integrates optical fibers and nanowire arrays is greater than that of a two-dimensional device. Internal axial illumination enhances the energy conversion efficiency of a rectangular fiber-based hybrid structure (see picture) by a factor of up to six compared to light illumination normal to the fiber axis from outside the device.

  15. Three-dimensional speckle reduction in optical coherence tomography through structural guided filtering

    Science.gov (United States)

    Gyger, Cyrill; Cattin, Roger; Hasler, Pascal W.; Maloca, Peter

    2014-07-01

    Optical coherence tomography (OCT) is a high-resolution noninvasive technology used in medical imaging for the spatial visualization of biological tissue. Due to its coherent nature, OCT suffers from speckle noise, which significantly degrades the information content of resulting scans. We introduce a new filtering method for three-dimensional OCT images, inspired by film grain removal techniques. By matching structural relatedness along all dimensions, the algorithm builds up vector paths for every voxel in the image volume representing its structural neighborhood. Then, by considering the information redundancy along these paths, our filter is able to reduce speckle noise significantly while simultaneously preserving structural information. This filter exceeds some common three-dimensional denoising algorithms used for OCT images, both in visual rendering quality and in measurable noise reduction. The noise-reduced results allow for improvement in subsequent processing steps, such as image segmentation.

  16. Three-dimensional C-arm CT-guided transjugular intrahepatic portosystemic shunt placement: Feasibility, technical success and procedural time

    Energy Technology Data Exchange (ETDEWEB)

    Ketelsen, Dominik; Groezinger, Gerd; Maurer, Michael; Grosse, Ulrich; Horger, Marius; Nikolaou, Konstantin; Syha, Roland [University of Tuebingen, Department of Diagnostic and Interventional Radiology, Tuebingen (Germany); Lauer, Ulrich M. [University of Tuebingen, Internal Medicine I, Department of Gastroenterology, Hepatology and Infectious disease, Tuebingen (Germany)

    2016-12-15

    Establishment of transjugular intrahepatic portosystemic shunts (TIPS) constitutes a standard procedure in patients suffering from portal hypertension. The most difficult step in TIPS placement is blind puncture of the portal vein. This study aimed to evaluate three-dimensional mapping of portal vein branches and targeted puncture of the portal vein. Twelve consecutive patients suffering from refractory ascites by liver cirrhosis were included in this retrospective study to evaluate feasibility, technical success and procedural time of C-arm CT-targeted puncture of the portal vein. As a control, 22 patients receiving TIPS placement with fluoroscopy-guided blind puncture were included to compare procedural time. Technical success could be obtained in 100 % of the study group (targeted puncture) and in 95.5 % of the control group (blind puncture). Appropriate, three-dimensional C-arm CT-guided mapping of the portal vein branches could be achieved in all patients. The median number of punctures in the C-arm CT-guided study group was 2 ± 1.3 punctures. Procedural time was significantly lower in the study group (14.8 ± 8.2 min) compared to the control group (32.6 ± 22.7 min) (p = 0.02). C-arm CT-guided portal vein mapping is technically feasible and a promising tool for TIPS placement resulting in a significant reduction of procedural time. (orig.)

  17. Three-dimensional vortex wake structure of flapping wings in hovering flight.

    Science.gov (United States)

    Cheng, Bo; Roll, Jesse; Liu, Yun; Troolin, Daniel R; Deng, Xinyan

    2014-02-06

    Flapping wings continuously create and send vortices into their wake, while imparting downward momentum into the surrounding fluid. However, experimental studies concerning the details of the three-dimensional vorticity distribution and evolution in the far wake are limited. In this study, the three-dimensional vortex wake structure in both the near and far field of a dynamically scaled flapping wing was investigated experimentally, using volumetric three-component velocimetry. A single wing, with shape and kinematics similar to those of a fruitfly, was examined. The overall result of the wing action is to create an integrated vortex structure consisting of a tip vortex (TV), trailing-edge shear layer (TESL) and leading-edge vortex. The TESL rolls up into a root vortex (RV) as it is shed from the wing, and together with the TV, contracts radially and stretches tangentially in the downstream wake. The downwash is distributed in an arc-shaped region enclosed by the stretched tangential vorticity of the TVs and the RVs. A closed vortex ring structure is not observed in the current study owing to the lack of well-established starting and stopping vortex structures that smoothly connect the TV and RV. An evaluation of the vorticity transport equation shows that both the TV and the RV undergo vortex stretching while convecting downwards: a three-dimensional phenomenon in rotating flows. It also confirms that convection and secondary tilting and stretching effects dominate the evolution of vorticity.

  18. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.

    Science.gov (United States)

    Cruz, José Almeida; Blanchet, Marc-Frédérick; Boniecki, Michal; Bujnicki, Janusz M; Chen, Shi-Jie; Cao, Song; Das, Rhiju; Ding, Feng; Dokholyan, Nikolay V; Flores, Samuel Coulbourn; Huang, Lili; Lavender, Christopher A; Lisi, Véronique; Major, François; Mikolajczak, Katarzyna; Patel, Dinshaw J; Philips, Anna; Puton, Tomasz; Santalucia, John; Sijenyi, Fredrick; Hermann, Thomas; Rother, Kristian; Rother, Magdalena; Serganov, Alexander; Skorupski, Marcin; Soltysinski, Tomasz; Sripakdeevong, Parin; Tuszynska, Irina; Weeks, Kevin M; Waldsich, Christina; Wildauer, Michael; Leontis, Neocles B; Westhof, Eric

    2012-04-01

    We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The results should give potential users insight into the suitability of available methods for different applications and facilitate efforts in the RNA structure prediction community in ongoing efforts to improve prediction tools. We also report the creation of an automated evaluation pipeline to facilitate the analysis of future RNA structure prediction exercises.

  19. Numerical, field and laboratory studies of three-dimensional flow structures at river channel confluences

    OpenAIRE

    Bradbrook, Kathryn Frances

    1999-01-01

    This thesis investigates controls on and the nature of three-dimensional flow structures at river channel confluences. Previous work has shown that junction angle is an important control on the flow patterns at channel junctions since it affects the degree of curvature of flow from each tributary and sets up secondary circulation cells similar to those in meander bends. Recent work has highlighted the common occurrence of, and importance of, bed discordance at river confluences due to a signi...

  20. Intraoperative application of geometric three-dimensional mitral valve assessment package: a feasibility study.

    Science.gov (United States)

    Mahmood, Feroze; Karthik, Swaminathan; Subramaniam, Balachundhar; Panzica, Peter J; Mitchell, John; Lerner, Adam B; Jervis, Karinne; Maslow, Andrew D

    2008-04-01

    To study the feasibility of using 3-dimensional (3D) echocardiography in the operating room for mitral valve repair or replacement surgery. To perform geometric analysis of the mitral valve before and after repair. Prospective observational study. Academic, tertiary care hospital. Consecutive patients scheduled for mitral valve surgery. Intraoperative reconstruction of 3D images of the mitral valve. One hundred and two patients had 3D analysis of their mitral valve. Successful image reconstruction was performed in 93 patients-8 patients had arrhythmias or a dilated mitral valve annulus resulting in significant artifacts. Time from acquisition to reconstruction and analysis was less than 5 minutes. Surgeon identification of mitral valve anatomy was 100% accurate. The study confirms the feasibility of performing intraoperative 3D reconstruction of the mitral valve. This data can be used for confirmation and communication of 2-dimensional data to the surgeons by obtaining a surgical view of the mitral valve. The incorporation of color-flow Doppler into these 3D images helps in identification of the commissural or perivalvular location of regurgitant orifice. With improvements in the processing power of the current generation of echocardiography equipment, it is possible to quickly acquire, reconstruct, and manipulate images to help with timely diagnosis and surgical planning.

  1. Three-dimensional investigation of the two-phase flow structure in a bubbly pipe flow

    International Nuclear Information System (INIS)

    Schmidl, W.; Hassan, Y.A.; Ortiz-Villafuerte, J.

    1996-01-01

    Particle image velocimetry (PIV) is a nonintrusive measurement technique that can be used to study the structure of various fluid flows. PIV is used to measure the time-varying, full-field velocity data of a particle-seeded flow field within either a two-dimensional plane or three-dimensional volume. PIV is a very efficient measurement technique since it can obtain both qualitative and quantitative spatial information about the flow field being studied. The quantitative spatial velocity information can be further processed into information of flow parameters such as vorticity and turbulence over extended areas. The objective of this study was to apply recent advances and improvements in the PIV flow measurement technique to the full-field, nonintrusive analysis of a three-dimensional, two-phase fluid flow system in such a manner that both components of the two-phase system could be experimentally quantified

  2. Three-dimensional density and compressible magnetic structure in solar wind turbulence

    Science.gov (United States)

    Roberts, Owen W.; Narita, Yasuhito; Escoubet, C.-Philippe

    2018-03-01

    The three-dimensional structure of both compressible and incompressible components of turbulence is investigated at proton characteristic scales in the solar wind. Measurements of the three-dimensional structure are typically difficult, since the majority of measurements are performed by a single spacecraft. However, the Cluster mission consisting of four spacecraft in a tetrahedral formation allows for a fully three-dimensional investigation of turbulence. Incompressible turbulence is investigated by using the three vector components of the magnetic field. Meanwhile compressible turbulence is investigated by considering the magnitude of the magnetic field as a proxy for the compressible fluctuations and electron density data deduced from spacecraft potential. Application of the multi-point signal resonator technique to intervals of fast and slow wind shows that both compressible and incompressible turbulence are anisotropic with respect to the mean magnetic field direction P⟂ ≫ P∥ and are sensitive to the value of the plasma beta (β; ratio of thermal to magnetic pressure) and the wind type. Moreover, the incompressible fluctuations of the fast and slow solar wind are revealed to be different with enhancements along the background magnetic field direction present in the fast wind intervals. The differences in the fast and slow wind and the implications for the presence of different wave modes in the plasma are discussed.

  3. Density filament and helical field line structures in three dimensional Weibel-mediated collisionless shocks

    International Nuclear Information System (INIS)

    Moritaka, Toseo; Kuramitsu, Yasuhiro; Sakawa, Youichi; Yamaura, Yuta; Ishikawa, Taishi; Takabe, Hideaki; Morita, Taichi

    2016-01-01

    Collisionless shocks mediated by Weibel instability are attracting attention for their relevance to experimental demonstrations of astrophysical shocks in high-intensity laser facilities. The three dimensional structure of Weibel-mediated shocks is investigated through a fully kinetic particle-in-cell simulation. The structures obtained are characterized by the following features: (i) helical magnetic field lines elongated in the direction upstream of the shock region, (ii) high and low density filaments inside the helical field lines. These structures originate from the interaction between counter-streaming plasma flow and magnetic vortexes caused by Weibel instability, and potentially affect the shock formation mechanism. (paper)

  4. Three-dimensional magnetization structures revealed with X-ray vector nanotomography

    Science.gov (United States)

    Donnelly, Claire; Guizar-Sicairos, Manuel; Scagnoli, Valerio; Gliga, Sebastian; Holler, Mirko; Raabe, Jörg; Heyderman, Laura J.

    2017-07-01

    In soft ferromagnetic materials, the smoothly varying magnetization leads to the formation of fundamental patterns such as domains, vortices and domain walls. These have been studied extensively in thin films of thicknesses up to around 200 nanometres, in which the magnetization is accessible with current transmission imaging methods that make use of electrons or soft X-rays. In thicker samples, however, in which the magnetization structure varies throughout the thickness and is intrinsically three dimensional, determining the complex magnetic structure directly still represents a challenge. We have developed hard-X-ray vector nanotomography with which to determine the three-dimensional magnetic configuration at the nanoscale within micrometre-sized samples. We imaged the structure of the magnetization within a soft magnetic pillar of diameter 5 micrometres with a spatial resolution of 100 nanometres and, within the bulk, observed a complex magnetic configuration that consists of vortices and antivortices that form cross-tie walls and vortex walls along intersecting planes. At the intersections of these structures, magnetic singularities—Bloch points—occur. These were predicted more than fifty years ago but have so far not been directly observed. Here we image the three-dimensional magnetic structure in the vicinity of the Bloch points, which until now has been accessible only through micromagnetic simulations, and identify two possible magnetization configurations: a circulating magnetization structure and a twisted state that appears to correspond to an ‘anti-Bloch point’. Our imaging method enables the nanoscale study of topological magnetic structures in systems with sizes of the order of tens of micrometres. Knowledge of internal nanomagnetic textures is critical for understanding macroscopic magnetic properties and for designing bulk magnets for technological applications.

  5. Resolution of the three dimensional structure of components of the glomerular filtration barrier.

    Science.gov (United States)

    Arkill, Kenton P; Qvortrup, Klaus; Starborg, Tobias; Mantell, Judith M; Knupp, Carlo; Michel, C Charles; Harper, Steve J; Salmon, Andy H J; Squire, John M; Bates, Dave O; Neal, Chris R

    2014-02-01

    The human glomerulus is the primary filtration unit of the kidney, and contains the Glomerular Filtration Barrier (GFB). The GFB had been thought to comprise 3 layers - the endothelium, the basement membrane and the podocyte foot processes. However, recent studies have suggested that at least two additional layers contribute to the function of the GFB, the endothelial glycocalyx on the vascular side, and the sub-podocyte space on the urinary side. To investigate the structure of these additional layers is difficult as it requires three-dimensional reconstruction of delicate sub-microscopic (glomerular volume). Secondly, Focused Ion Beam milling Scanning Electron Microscopy (FIB-SEM) was used to image a filtration region (48 μm3 volume). Lastly Transmission Electron Tomography (Tom-TEM) was performed on a 0.3 μm3 volume to identify the fine structure of the glycocalyx. Tom-TEM clearly showed 20 nm fibre spacing in the glycocalyx, within a limited field of view. FIB-SEM demonstrated, in a far greater field of view, how the glycocalyx structure related to fenestrations and the filtration slits, though without the resolution of TomTEM. SBF-SEM was able to determine the extent of the sub-podocyte space and glycocalyx coverage, without additional heavy metal staining. Neither SBF- nor FIB-SEM suffered the anisotropic shrinkage under the electron beam that is seen with Tom-TEM. These images demonstrate that the three dimensional structure of the GFB can be imaged, and investigated from the whole glomerulus to the fine structure of the glycocalyx using three dimensional electron microscopy techniques. This should allow the identification of structural features regulating physiology, and their disruption in pathological states, aiding the understanding of kidney disease.

  6. Comparing efficient data structures to represent geometric models for three-dimensional virtual medical training.

    Science.gov (United States)

    Bíscaro, Helton H; Nunes, Fátima L S; Dos Santos Oliveira, Jéssica; Pereira, Gustavo R

    2016-10-01

    Data structures have been explored for several domains of computer applications in order to ensure efficiency in the data store and retrieval. However, data structures can present different behavior depending on applications that they are being used. Three-dimensional interactive environments offered by techniques of Virtual Reality require operations of loading and manipulating objects in real time, where realism and response time are two important requirements. Efficient representation of geometrical models plays an important part so that the simulation may become real. In this paper, we present the implementation and the comparison of two topologically efficient data structures - Compact Half-Edge and Mate-Face - for the representation of objects for three-dimensional interactive environments. The structures have been tested at different conditions of processors and RAM memories. The results show that both these structures can be used in an efficient manner. Mate-Face structure has shown itself to be more efficient for the manipulation of neighborhood relationships and the Compact Half-Edge was more efficient for loading of the geometric models. We also evaluated the data structures embedded in applications of biopsy simulation using virtual reality, considering a deformation simulation method applied in virtual human organs. The results showed that their use allows the building of applications considering objects with high resolutions (number of vertices), without significant impact in the time spent in the simulation. Therefore, their use contributes for the construction of more realistic simulators. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Insulin as a model to teach three-dimensional structure of proteins

    Directory of Open Access Journals (Sweden)

    João Batista Teixeira da Rocha

    2018-02-01

    Proteins are the most ubiquitous macromolecules found in the living cells and have innumerous physiological functions. Therefore, it is fundamental to build a solid knowledge about the proteins three dimensional structure to better understand the living state. The hierarchical structure of proteins is usually studied in the undergraduate discipline of Biochemistry. Here we described pedagogical interventions designed to increase the preservice teacher chemistry students’ knowledge about protein structure. The activities were made using alternative and cheap materials to encourage the application of these simple methodologies by the future teachers in the secondary school. From the primary structure of insulin chains, students had to construct a three-dimensional structure of insulin. After the activities, the students highlighted an improvement of their previous knowledge about proteins structure. The construction of a tridimensional model together with other activities seems to be an efficient way to promote the learning about the structure of proteins to undergraduate students. The methodology used was inexpensiveness and simple and it can be used both in the university and in the high-school.

  8. Generation of a Three-Dimensional Kidney Structure from Pluripotent Stem Cells.

    Science.gov (United States)

    Yoshimura, Yasuhiro; Taguchi, Atsuhiro; Nishinakamura, Ryuichi

    2017-01-01

    The kidney is a vital organ that has an important role in the maintenance of homeostasis by fluid volume regulation and waste product excretion. This role cannot be performed without the three-dimensional (3D) structure of the kidney. Therefore, it is important to generate the 3D structure of the kidney when inducing functional kidney tissue or the whole organ from pluripotent stem cells. In this chapter, we describe the detailed methods to induce kidney progenitor cells from pluripotent stem cells, which are based on embryological development. We also provide a method to generate 3D kidney tissue with vascularized glomeruli upon transplantation.

  9. Three-dimensional dielectric photonic crystal structures for laser-driven acceleration

    Directory of Open Access Journals (Sweden)

    Benjamin M. Cowan

    2008-01-01

    Full Text Available We present the design and simulation of a three-dimensional photonic crystal waveguide for linear laser-driven acceleration in vacuum. The structure confines a synchronous speed-of-light accelerating mode in both transverse dimensions. We report the properties of this mode, including sustainable gradient and optical-to-beam efficiency. We present a novel method for confining a particle beam using optical fields as focusing elements. This technique, combined with careful structure design, is shown to have a large dynamic aperture and minimal emittance growth, even over millions of optical wavelengths.

  10. [Initial study of transthoracic echocardiography guided three-dimensional printing on the application of assessment of structural heart disease].

    Science.gov (United States)

    Zhu, Y B; Liu, J S; Wang, L Q; Guan, X; Luo, Y J; Geng, J; Geng, Q G; Lin, Y J; Zhang, L X; Li, X X; Lu, Y P

    2017-08-01

    Objective: To investigate the feasibility and diagnostic value of preoperative transthoracic echocardiography guided three dimensional printing model (TTE Guided 3DPM) on the assessment of structural heart disease (SHD). Methods: From February 2016 to October 2016, 44 patients underwent cardiac surgery in Tianjin Chest Hospital, forty-four patients were assessed preoperatively using TTE Guided 3DPM, including 25 males and 19 females, aged 3-75 years, with an average of (44±22) years. compared to conventional three dimensional transthoracic echocardiography (3D-TTE), and took direct intraoperative findings as "Golden Standard" simultaneously. There are twelve patients with SHD, including four cases with mitral prolapse, two cases with partial endocardial cushion defect, two cases with secondary atrial septal defect, two cases with rheumatic mitral stenosis, one case with tetralogy of Fallot, one case with ventricular septal defect (VSD), thirty-two patients without SHD were designed as negative control. Results: The sensitivity and specificity of TTE Guided 3DPM were greater than or equal to 3D-TTE, P value of McNemar test of 3D-TTE was greater than 0.05, the difference was not statistically significant, kappa =0.745, P Guided 3DPM was greater than 0.05, the difference was not statistically significant, kappa =0.955, P Guided 3DPM and gold standards were consistent. Compared with 3D-TTE and TTE Guided 3DPM, P value was greater than 0.05, the difference was not statistically significant, kappa =0.879, P Guided 3DPM were consistent. TTE Guided 3DPM displayed the three-dimensional structure of SHD cardiac lesions clearly, which were consistent with intraoperative findings. Conclusion: TTE Guided 3DPM provides essential information for the preoperative evaluation and decision of SHD.

  11. Astigmatism inducing the degenerate effect in nearly hemispherical cavities: generation of three-dimensional structured light

    Science.gov (United States)

    Tung, J. C.; Hsieh, Y. H.; Liang, H. C.; Su, K. W.; Huang, K. F.; Chen, Y. F.

    2017-04-01

    We originally perform an analytical form to explore the influence of the astigmatism on the degenerate effect in nearly hemispherical cavities. The frequency spectrum near hemispherical cavities clearly reveals that not only the difference of cavity lengths between each degeneracies but also frequency gaps have significant difference from non-hemispherical cavities. We further thoroughly demonstrate the laser experiment under the condition of nearly hemispherical cavities to confirm the theoretical exploration that the transverse topology of three-dimensional (3D) structured light in the degenerate cavities is well localized on the Lissajous curves.

  12. An efficient closed-form solution for acoustic emission source location in three-dimensional structures

    Directory of Open Access Journals (Sweden)

    Xibing Li

    2014-02-01

    Full Text Available This paper presents an efficient closed-form solution (ECS for acoustic emission(AE source location in three-dimensional structures using time difference of arrival (TDOA measurements from N receivers, N ≥ 6. The nonlinear location equations of TDOA are simplified to linear equations. The unique analytical solution of AE sources for unknown velocity system is obtained by solving the linear equations. The proposed ECS method successfully solved the problems of location errors resulting from measured deviations of velocity as well as the existence and multiplicity of solutions induced by calculations of square roots in existed close-form methods.

  13. Electronic transport on the spatial structure of the protein: Three-dimensional lattice model

    International Nuclear Information System (INIS)

    Sarmento, R.G.; Frazão, N.F.; Macedo-Filho, A.

    2017-01-01

    Highlights: • The electronic transport on the structure of the three-dimensional lattice model of the protein is studied. • The signing of the current–voltage is directly affected by permutations of the weak bonds in the structure. • Semiconductor behave of the proteins suggest a potential application in the development of novel biosensors. - Abstract: We report a numerical analysis of the electronic transport in protein chain consisting of thirty-six standard amino acids. The protein chains studied have three-dimensional structure, which can present itself in three distinct conformations and the difference consist in the presence or absence of thirteen hydrogen-bondings. Our theoretical method uses an electronic tight-binding Hamiltonian model, appropriate to describe the protein segments modeled by the amino acid chain. We note that the presence and the permutations between weak bonds in the structure of proteins are directly related to the signing of the current–voltage. Furthermore, the electronic transport depends on the effect of temperature. In addition, we have found a semiconductor behave in the models investigated and it suggest a potential application in the development of novel biosensors for molecular diagnostics.

  14. Electronic transport on the spatial structure of the protein: Three-dimensional lattice model

    Energy Technology Data Exchange (ETDEWEB)

    Sarmento, R.G. [Departamento de Ciências Biológicas, Universidade Federal do Piauí, 64800-000 Floriano, PI (Brazil); Frazão, N.F. [Centro de Educação e Saúde, Universidade Federal de Campina Grande, 581750-000 Cuité, PB (Brazil); Macedo-Filho, A., E-mail: amfilho@gmail.com [Campus Prof. Antonio Geovanne Alves de Sousa, Universidade Estadual do Piauí, 64260-000 Piripiri, PI (Brazil)

    2017-01-30

    Highlights: • The electronic transport on the structure of the three-dimensional lattice model of the protein is studied. • The signing of the current–voltage is directly affected by permutations of the weak bonds in the structure. • Semiconductor behave of the proteins suggest a potential application in the development of novel biosensors. - Abstract: We report a numerical analysis of the electronic transport in protein chain consisting of thirty-six standard amino acids. The protein chains studied have three-dimensional structure, which can present itself in three distinct conformations and the difference consist in the presence or absence of thirteen hydrogen-bondings. Our theoretical method uses an electronic tight-binding Hamiltonian model, appropriate to describe the protein segments modeled by the amino acid chain. We note that the presence and the permutations between weak bonds in the structure of proteins are directly related to the signing of the current–voltage. Furthermore, the electronic transport depends on the effect of temperature. In addition, we have found a semiconductor behave in the models investigated and it suggest a potential application in the development of novel biosensors for molecular diagnostics.

  15. Use of three-dimensional parameters in the analysis of crystal structures under compression

    DEFF Research Database (Denmark)

    Balic Zunic, Tonci

    2007-01-01

    Volume-related parameters of atomic coordinations are an important tool for the analysis of structural changes. Unlike usual tables of bond distances and angles they directly depict three-dimensional properties of coordination polyhedra, and in many instances give more profound structural...... data through use of a procrystal model. For non-regular coordination polyhedra a determination of the point with the minimum variation of distances to the vertices (the centroid of coordination) is a necessary prerequisite for a calculation of the volume-related parameters. The three parameters...... of the coordination polyhedra of cations and the voids that separate them. Analysis of individual compressional characteristics of structural components gives clues for the strong and weak parts of structures under high pressures and paths for structural transformations. The expected behaviour of distortion...

  16. Three-dimensional structure of E. Coli purine nucleoside phosphorylase at 0.99 Å resolution

    Energy Technology Data Exchange (ETDEWEB)

    Timofeev, V. I., E-mail: tostars@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Abramchik, Yu. A., E-mail: ugama@yandex.ru [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Zhukhlistova, N. E., E-mail: inna@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Muravieva, T. I.; Esipov, R. S. [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Kuranova, I. P. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2016-03-15

    Purine nucleoside phosphorylases (PNPs) catalyze the reversible phosphorolysis of nucleosides and are key enzymes involved in nucleotide metabolism. They are essential for normal cell function and can catalyze the transglycosylation. Crystals of E. coli PNP were grown in microgravity by the capillary counterdiffusion method through a gel layer. The three-dimensional structure of the enzyme was determined by the molecular-replacement method at 0.99 Å resolution. The structural features are considered, and the structure of E. coli PNP is compared with the structures of the free enzyme and its complexes with purine base derivatives established earlier. A comparison of the environment of the purine base in the complex of PNP with formycin A and of the pyrimidine base in the complex of uridine phosphorylase with thymidine revealed the main structural features of the base-binding sites. Coordinates of the atomic model determined with high accuracy were deposited in the Protein Data Bank (PDB-ID: 4RJ2).

  17. An `H'-shape three-dimensional meta-material used in honeycomb structure absorbing material

    Science.gov (United States)

    Huang, Daqing; Kang, Feiyu; Zhou, Zhuohui; Cheng, Hongfei; Ding, Heyan

    2015-03-01

    An `H'-shape three-dimensional meta-material structure which loaded on the sidewall of honeycomb structure absorbing material was designed and fabricated in this project. The simulation results demonstrated a super-wide absorption band below -10 dB between 2.3 and 18 GHz, which expanded 7 GHz compared with the absorber without meta-material. The relative impedance curve was analyzed, which showed that the meta-material has little impact on the impedance-matching characteristics of the honeycomb structure absorbing material. We further studied the distribution of both electronic field energy and magnetic field energy. The former one indicated that the low-frequency absorption peaks could easily be moved by adjusting the parameters of the parallel-plate capacitors which generate electric resonance, and the latter one illustrated that the three-dimensional meta-material could generate magnetic resonance between units which would not exist in two-dimensional meta-material. Then we verified the simulation results through experiment which display a similar absorbing curve. The differences between simulation results and experiment results were caused by the addition substrate of the meta-material, which could not be eliminated in this experiment. However, it still implied that we can obtain a meta-material absorber that has a super-wide absorbing band if we can put the meta-material on the sidewall of the honeycomb without attachments.

  18. Three-dimensionality of the bulk electronic structure in WTe2

    Science.gov (United States)

    Wu, Yun; Jo, Na Hyun; Mou, Daixiang; Huang, Lunan; Bud'ko, S. L.; Canfield, P. C.; Kaminski, Adam

    2017-05-01

    We use temperature- and field-dependent resistivity measurements (Shubnikov-de Haas quantum oscillations) and ultrahigh-resolution, tunable, vacuum ultraviolet laser-based angle-resolved photoemission spectroscopy (ARPES) to study the three-dimensionality (3D) of the bulk electronic structure in WTe 2 , a type II Weyl semimetal. The bulk Fermi surface (FS) consists of two pairs of electron pockets and two pairs of hole pockets along the X -Γ -X direction as detected by using an incident photon energy of 6.7 eV, which is consistent with the previously reported data. However, if using an incident photon energy of 6.36 eV, another pair of tiny electron pockets is detected on both sides of the Γ point, which is in agreement with the small quantum oscillation frequency peak observed in the magnetoresistance. Therefore, the bulk, 3D FS consists of three pairs of electron pockets and two pairs of hole pockets in total. With the ability of fine tuning the incident photon energy, we demonstrate the strong three-dimensionality of the bulk electronic structure in WTe 2 . The combination of resistivity and ARPES measurements reveals the complete, and consistent, picture of the bulk electronic structure of this material.

  19. Optical chracterization and lasing in three-dimensional opal-structures

    Directory of Open Access Journals (Sweden)

    Yoshiaki eNishijima

    2015-06-01

    Full Text Available The lasing properties of dye-permeated opal pyramidal structures are compared with the lasing properties of opal films. The opal-structures studied were made by sedimentation of micro-spheres and by sol-gel inversion of the direct-opals. Forced-sedimentation by centrifugation inside wet-etched pyramidal pits on silicon surfaces was used to improve the structural quality of the direct-opal structures. Single crystalline pyramids with the base length of ∼ 100 µm were formed by centrifuged sedimentation. The lasing of dyes in the well-ordered crystalline and poly-crystalline structures showed a distinct multi-modal spectrum. Gain via a distributed feedback was responsible for the lasing since the photonic band gap was negligible in a low refractive index contrast medium; the indices of silica and ethylene glycol are 1.46 and 1.42, respectively. A disordered lasing spectrum was observed from opal films with structural defects and multi-domain regions. The three dimensional structural quality of the structures was assessed by in situ optical diffraction and confocal fluorescence. A correlation between the lasing spectrum and the three-dimensional structural quality was established. Lasing threshold of a sulforhodamine dye in a silica opal was controlled via Förster mechanism by addition of a donor rhodamine 6G dye. The lasing spectrum had a well-ordered modal structure which was spectrally stable at different excitation powers. The sharp lasing threshold characterized by a spontaneous emission coupling ratio β ' 10−2 was obtained.

  20. 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.

  1. Confocal imaging reveals three-dimensional fine structure difference between ventral and dorsal nerve roots

    Science.gov (United States)

    Wu, Yuxiang; Sui, Tao; Cao, Xiaojian; Lv, Xiaohua; Zeng, Shaoqun; Sun, Peng

    2011-05-01

    Peripheral nerve injury repair is one of the most challenging problems in neurosurgery, partially due to lack of knowledge of three-dimensional (3-D) fine structure and organization of peripheral nerves. In this paper, we explored the structures of nerve fibers in ventral and dorsal nerves with a laser scanning confocal microscopy. Thick tissue staining results suggested that nerve fibers have a different 3-D structure in ventral and dorsal nerves, and reconstruction from serial sectioning images showed that in ventral nerves the nerve fibers travel in a winding form, while in dorsal nerves, the nerve fibers form in a parallel cable pattern. These structural differences could help surgeons to differentiate ventral and dorsal nerves in peripheral nerve injury repair, and also facilitate scientists to get a deeper understanding about nerve fiber organization.

  2. Computational method for calculating fluorescence intensities within three-dimensional structures in cells.

    Science.gov (United States)

    Caster, Amanda H; Kahn, Richard A

    2012-10-01

    The use of fluorescence microscopy is central to cell biology in general, and essential to many fields (e.g., membrane traffic) that rely upon it to identify cellular locations of molecules under study and the extent to which they co-localize with others. Rigorous localization or co-localization data require quantitative image analyses that can vary widely between fields and laboratories. While most published data use two-dimensional images, there is an increasing appreciation for the advantages of collecting three-dimensional data sets. These include the ability to evaluate the entire cell and avoidance of focal plane bias. This is particularly important when imaging and quantifying changes in organelles with irregular borders and which vary in appearance between cells in a population, e.g., the Golgi. We describe a method developed for quantifying changes in signal intensity of one protein within any three-dimensional structure, defined by the presence of a different marker. We use as examples of this method the quantification of adaptor recruitment to transmembrane protein cargos at the Golgi though it can be directly applied to any site in the cell. Together, these advantages facilitate rigorous statistical testing of differences between conditions, despite variations in organelle structure, and we believe that this method of quantification of fluorescence data can be productively applied to a wide array of experimental questions.

  3. Three-dimensional flow structure measurements behind a queue of studied model vehicles

    International Nuclear Information System (INIS)

    Huang, J.F.; Chan, T.L.; Zhou, Y.

    2009-01-01

    The three-dimensional flow structures of a queue of studied model vehicles (i.e., one-, two- and three-vehicle cases) were investigated comprehensively in a closed-circuit wind tunnel using particle image velocimetry (PIV) for the typical urban vehicle speeds (i.e., 10, 30 and 50 km/h). In this three-dimensional vehicle wake, a pair of longitudinal vortices is characterized by counter-rotating and moving downstream at relatively low velocity than their surrounding flow. The flow structures of multiple studied model vehicles are dominated by the wake generated from the last studied model vehicle but the preceding studied model vehicle(s) also has/have some minor effects. Cross-sectional turbulence distribution is non-uniform in the far-wake region for all studied cases. The lowest turbulence occurs at the center part of the vehicle wake while high turbulence occurs at its two sides. As such, it may lead to considerable underestimation in turbulence magnitude if the measurement is only taken along the centerline of the vehicle wake.

  4. Preservation of three-dimensional spatial structure in the gut microbiome.

    Directory of Open Access Journals (Sweden)

    Yuko Hasegawa

    Full Text Available Preservation of three-dimensional structure in the gut is necessary in order to analyze the spatial organization of the gut microbiota and gut luminal contents. In this study, we evaluated preparation methods for mouse gut with the goal of preserving micron-scale spatial structure while performing fluorescence imaging assays. Our evaluation of embedding methods showed that commonly used media such as Tissue-Tek Optimal Cutting Temperature (OCT compound, paraffin, and polyester waxes resulted in redistribution of luminal contents. By contrast, a hydrophilic methacrylate resin, Technovit H8100, preserved three-dimensional organization. Our mouse intestinal preparation protocol optimized using the Technovit H8100 embedding method was compatible with microbial fluorescence in situ hybridization (FISH and other labeling techniques, including immunostaining and staining with both wheat germ agglutinin (WGA and 4', 6-diamidino-2-phenylindole (DAPI. Mucus could be visualized whether the sample was fixed with paraformaldehyde (PFA or with Carnoy's fixative. The protocol optimized in this study enabled simultaneous visualization of micron-scale spatial patterns formed by microbial cells in the mouse intestines along with biogeographical landmarks such as host-derived mucus and food particles.

  5. A microsphere assembly method with laser microwelding for fabrication of three-dimensional periodic structures

    Science.gov (United States)

    Takagi, Kenta; Omote, Masanori; Kawasaki, Akira

    2010-03-01

    The orderly build-up of monosized microspheres with sizes of hundreds of micrometres enabled us to develop three-dimensional (3D) photonic crystal devices for terahertz electromagnetic waves. We designed and manufactured an original 3D particle assembly system capable of fabricating arbitrary periodic structures from these spherical particles. This method employs a pick-and-place assembling approach with robotic manipulation and interparticle laser microwelding in order to incorporate a contrivance for highly accurate arraying: an operation that compensates the size deviation of raw monosized particles. Pre-examination of particles of various materials revealed that interparticle laser welding must be achieved with local melting by suppressing heat diffusion from the welding area. By optimizing the assembly conditions, we succeeded in fabricating an accurate periodic structure with a diamond lattice from 400 µm polyethylene composite particles. This structure demonstrated a photonic bandgap in the terahertz frequency range.

  6. Three-dimensional P-wave velocity structure of Mt. Etna, Italy

    Science.gov (United States)

    Villasenor, A.; Benz, H.M.; Filippi, L.; De Luca, G.; Scarpa, R.; Patane, G.; Vinciguerra, S.

    1998-01-01

    The three-dimensional P-wave velocity structure of Mt. Etna is determined to depths of 15 km by tomographic inversion of first arrival times from local earthquakes recorded by a network of 29 permanent and temporary seismographs. Results show a near-vertical low-velocity zone that extends from beneath the central craters to a depth of 10 km. This low-velocity region is coincident with a band of steeply-dipping seismicity, suggesting a magmatic conduit that feeds the summit eruptions. The most prominent structure is an approximately 8-km-diameter high-velocity body located between 2 and 12 km depth below the southeast flank of the volcano. This high-velocity body is interpreted as a remnant mafic intrusion that is an important structural feature influencing both volcanism and east flank slope stability and faulting.

  7. Advances in high-resolution imaging--techniques for three-dimensional imaging of cellular structures.

    Science.gov (United States)

    Lidke, Diane S; Lidke, Keith A

    2012-06-01

    A fundamental goal in biology is to determine how cellular organization is coupled to function. To achieve this goal, a better understanding of organelle composition and structure is needed. Although visualization of cellular organelles using fluorescence or electron microscopy (EM) has become a common tool for the cell biologist, recent advances are providing a clearer picture of the cell than ever before. In particular, advanced light-microscopy techniques are achieving resolutions below the diffraction limit and EM tomography provides high-resolution three-dimensional (3D) images of cellular structures. The ability to perform both fluorescence and electron microscopy on the same sample (correlative light and electron microscopy, CLEM) makes it possible to identify where a fluorescently labeled protein is located with respect to organelle structures visualized by EM. Here, we review the current state of the art in 3D biological imaging techniques with a focus on recent advances in electron microscopy and fluorescence super-resolution techniques.

  8. Selective electroless plating of 3D-printed plastic structures for three-dimensional microwave metamaterials

    Science.gov (United States)

    Ishikawa, Atsushi; Kato, Taiki; Takeyasu, Nobuyuki; Fujimori, Kazuhiro; Tsuruta, Kenji

    2017-10-01

    A technique of selective electroless plating onto PLA-ABS (Polylactic Acid-Acrylonitrile Butadiene Styrene) composite structures fabricated by three-dimensional (3D) printing is demonstrated to construct 3D microwave metamaterials. The reducing activity of the PLA surface is selectively enhanced by the chemical modification involving Sn2+ in a simple wet process, thereby forming a highly conductive Ag-plated membrane only onto the PLA surface. The fabricated metamaterial composed of Ag-plated PLA and non-plated ABS parts is characterized experimentally and numerically to demonstrate the important bi-anisotropic microwave responses arising from the 3D nature of metallodielectric structures. Our approach based on a simple wet chemical process allows for the creation of highly complex 3D metal-insulator structures, thus paving the way toward the sophisticated microwave applications of the 3D printing technology.

  9. Three-dimensional structure of recombinant carboxypeptidase T from Thermoactinomyces vulgaris without calcium ions

    Science.gov (United States)

    Akparov, V. Kh.; Timofeev, V. I.; Kuranova, I. P.

    2011-07-01

    Crystals of recombinant carboxypeptidase T (CPT) from Thermoactinomyces vulgaris were grown in a capillary by the counterdiffusion method in the absence of calcium ions. The three-dimensional structure of CPT was solved at 1.69-Å resolution using the X-ray diffraction data collected from the crystals of the enzyme on the SPring-8 synchrotron radiation facility and was then refined to Rfact = 16.903% and Rfree = 18.165%. The coordinates of the refined model were deposited in the Protein Data Bank (PDB ID: 3QNV). A comparison of this structure with the structure of wild-type CPT containing bound calcium ions, which was determined earlier, revealed a number of conformational changes both in the calcium-binding sites and the enzyme active site. Based on the results of this comparison, the possible factors responsible for the difference in the catalytic activity of the two forms of the enzyme are considered.

  10. A microsphere assembly method with laser microwelding for fabrication of three-dimensional periodic structures

    International Nuclear Information System (INIS)

    Takagi, Kenta; Omote, Masanori; Kawasaki, Akira

    2010-01-01

    The orderly build-up of monosized microspheres with sizes of hundreds of micrometres enabled us to develop three-dimensional (3D) photonic crystal devices for terahertz electromagnetic waves. We designed and manufactured an original 3D particle assembly system capable of fabricating arbitrary periodic structures from these spherical particles. This method employs a pick-and-place assembling approach with robotic manipulation and interparticle laser microwelding in order to incorporate a contrivance for highly accurate arraying: an operation that compensates the size deviation of raw monosized particles. Pre-examination of particles of various materials revealed that interparticle laser welding must be achieved with local melting by suppressing heat diffusion from the welding area. By optimizing the assembly conditions, we succeeded in fabricating an accurate periodic structure with a diamond lattice from 400 µm polyethylene composite particles. This structure demonstrated a photonic bandgap in the terahertz frequency range.

  11. Measuring three-dimensional flow structures in the conductive airways using 3D-PTV

    Science.gov (United States)

    Janke, Thomas; Schwarze, Rüdiger; Bauer, Katrin

    2017-10-01

    Detailed information about flow patterns and mass transport in the conductive airways is of crucial interest to improve ventilation strategies as well as targeted drug delivery. Despite a vast number of flow studies in this field, there is still a dearth in experimental data of three-dimensional flow patterns, in particular for the validation of numerical results. Therefore, oscillating flow within a realistic model of the upper human conductive airways is studied here experimentally. The investigated range of Reynolds numbers is Re = 250-2000 and the Womersley number is varied between α = 1.9-5.1, whereby physiological flow at rest conditions is included. In employing the three-dimensional particle tracking velocimetry measurement technique, we can directly visualize airway specific flow structures as well as examine Lagrangian trajectory statistics, which has not been covered to date. The systematic variation of characteristic flow parameters in combination with the advanced visualization technique sheds new light on the mechanisms of evolving flow patterns. By determining Lagrangian properties such as pathline curvature and torsion, we find that both strongly depend on the Reynolds number. Moreover, the probability density function of the curvature reveals a unique shape for certain flow regions and resembles a turbulent like behavior at the small scales.

  12. EXPERIMENTAL RESEARCH OF THE THREE-DIMENSIONAL PERFORMANCE OF COMPOSITE STEEL AND CONCRETE STRUCTURES

    Directory of Open Access Journals (Sweden)

    Zamaliev Farit Sakhapovich

    2012-12-01

    steel-concrete slabs limits their use in the construction of residential housing. This article describes the composition, geometry, reinforcement, and anchors to enable the use of concrete slabs and steel beams. The article contains photographs that illustrate the load distribution model. Methods of testing of fiber strains of concrete slabs and steel profiles, deflections of beams, shear stresses in the layers of the "steel-to-concrete" contact area that may involve slab cracking are analyzed. Dynamics of fiber deformations of concrete slabs, steel beams, and layers of the "steel-to-concrete" contact areas, deflection development patterns, initial cracking and crack development to destruction are analyzed. The author also describes the fracture behavior of the floor model. Results of experimental studies of the three-dimensional overlapping of structural elements are compared to the test data of individual composite beams. Peculiarities of the stress-strain state of composite steel and concrete slabs, graphs of strains and stresses developing in sections of middle and external steel-and-concrete beams, deflection graphs depending on the loading intensity are provided. The findings of the experimental studies of the three-dimensional performance of composite steel-and-concrete slabs are provided, as well.

  13. Combined inversion for the three-dimensional Q structure and source parameters using microearthquake spectra

    Science.gov (United States)

    Scherbaum, Frank

    1990-08-01

    The estimation of Q values and/or source corner frequencies fc from single-station narrow-band recordings of microearthquake spectra is a strongly nonunique problem. This is due to the fact that the spectra can be equally well fitted with low-Q/high-fc or a high-Q/low-fc spectral models. Here, a method is proposed to constrain this ambiguity by inverting a set of microearthquake spectra for a three-dimensional Q model structure and model source parameters seismic moment (Mo ) and corner frequency (fc ) simultaneously. The inversion of whole path Q can be stated as a linear problem in the attenuation operator t* and solved using a tomographic reconstruction of the three-dimensional Q structure. This Q structure is then used as a "geometrical constraint" for a nonlinear Marquardt-Levenberg inversion of Mo and fc and a new Q value. The first step of the method consists of interactively fitting the observed microearthquake spectra by spectral models consisting of a source spectrum with an assumed high-frequency decay, a single-layer resonance filter to account for local site effects, and additional "whole path attenuation" along the ray path. From the obtained Q values, a three-dimensional Q model is calculated using a tomographic reconstruction technique (SIRT). The individual Q values along each ray path are then used as Q starting values for a nonlinear iterative Marquardt-Levenberg inversion of Mo and fc and a "new" Q value. Subsequently, the "new" Q values are used to reconstruct the next Q model which again provides starting values for the "next" nonlinear inversion of Mo, fc, and Q. This process is repeated until the "goodness of fit measure" indicates no further improvement of the results. The method has been tested on a set of approximately 2800 P wave spectra (0.9 effects close to the surface shows that site effects may cause a corruption of the resulting Q model at shallow depths. For the given data set and depths below 3-5 km, the method is believed to be

  14. Three-Dimensional Architecture and Biogenesis of Membrane Structures Associated with Plant Virus Replication

    Directory of Open Access Journals (Sweden)

    Xuejiao Jin

    2018-01-01

    Full Text Available Positive-sense (+ RNA viruses represent the most abundant group of viruses and are dependent on the host cell machinery to replicate. One remarkable feature that occurs after (+ RNA virus entry into cells is the remodeling of host endomembranes, leading to the formation of viral replication factories. Recently, rapid progress in three-dimensional (3D imaging technologies, such as electron tomography (ET and focused ion beam-scanning electron microscopy (FIB-SEM, has enabled researchers to visualize the novel membrane structures induced by viruses at high resolution. These 3D imaging technologies provide new mechanistic insights into the viral infection cycle. In this review, we summarize the latest reports on the cellular remodeling that occurs during plant virus infection; in particular, we focus on studies that provide 3D architectural information on viral replication factories. We also outline the mechanisms underlying the formation of these membranous structures and discuss possible future research directions.

  15. Three-Dimensional Architecture and Biogenesis of Membrane Structures Associated with Plant Virus Replication.

    Science.gov (United States)

    Jin, Xuejiao; Cao, Xiuling; Wang, Xueting; Jiang, Jun; Wan, Juan; Laliberté, Jean-François; Zhang, Yongliang

    2018-01-01

    Positive-sense (+) RNA viruses represent the most abundant group of viruses and are dependent on the host cell machinery to replicate. One remarkable feature that occurs after (+) RNA virus entry into cells is the remodeling of host endomembranes, leading to the formation of viral replication factories. Recently, rapid progress in three-dimensional (3D) imaging technologies, such as electron tomography (ET) and focused ion beam-scanning electron microscopy (FIB-SEM), has enabled researchers to visualize the novel membrane structures induced by viruses at high resolution. These 3D imaging technologies provide new mechanistic insights into the viral infection cycle. In this review, we summarize the latest reports on the cellular remodeling that occurs during plant virus infection; in particular, we focus on studies that provide 3D architectural information on viral replication factories. We also outline the mechanisms underlying the formation of these membranous structures and discuss possible future research directions.

  16. A Three-Dimensional Enormous Surface Area Aluminum Microneedle Array with Nanoporous Structure

    Directory of Open Access Journals (Sweden)

    Po Chun Chen

    2013-01-01

    Full Text Available We proposed fabricating an aluminum microneedle array with a nanochannel structure on the surface by combining micromachining, electrolyte polishing, and anodization methods. The microneedle array provides a three-dimensional (3D structure that possesses several hundred times more surface area than a traditional nanochannel template. Therefore, the microneedle array can potentially be used in many technology applications. This 3D microneedle array device can not only be used for painless injection or extraction, but also for storage, highly sensitive detection, drug delivery, and microelectrodes. From the calculation we made, the microneedle array not only increases surface area, but also enlarges the capacity of the device. Therefore, the microneedle array can further be used on many detecting, storing, or drug delivering applications.

  17. A Three-Dimensional Enormous Surface Area Aluminum Microneedle Array with Nanoporous Structure

    International Nuclear Information System (INIS)

    Chen, P.Ch.; Zou, J.; Hsieh, Sh.J.; Chen, Ch.Ch.

    2013-01-01

    We proposed fabricating an aluminum micro needle array with a nano channel structure on the surface by combining micromachining, electrolyte polishing, and anodization methods. The micro needle array provides a three-dimensional (3D) structure that possesses several hundred times more surface area than a traditional nano channel template. Therefore, the micro needle array can potentially be used in many technology applications. This 3D micro needle array device can not only be used for painless injection or extraction, but also for storage, highly sensitive detection, drug delivery, and microelectrodes. From the calculation we made, the micro needle array not only increases surface area, but also enlarges the capacity of the device. Therefore, the micro needle array can further be used on many detecting, storing, or drug delivering applications.

  18. Emergence of three-dimensional flow structures in shock boundary layer interactions

    Science.gov (United States)

    Gs, Sidharth; Dwivedi, Anubhav; Nichols, Joseph; Jovanovic, Mihailo; Candler, Graham

    2017-11-01

    Experiments and computations point to the emergence of three-dimensional (3D) flow structures in laminar shock boundary layer interactions in various configurations. We examine a Mach 5 flow over a double compression ramp and reveal the presence of a bifurcation from a steady 2D to a steady 3D flow state. This is done by varying the relative angle of the two ramps which increases the interaction strength. We employ global linear stability analysis and direct numerical simulation to characterize this bifurcation and demonstrate that global instability induces 3D flow structures. We use the direct and adjoint linear equations to further investigate the origin of this instability and examine the influence of uncertainty (including the effect of geometric irregularities in the ramp and free-stream disturbances in wind tunnel) on this bifurcation. This work was supported by Office of Naval Research through Grant Number N00014-15-1-2522.

  19. Prediction of the three-dimensional structure of aflatoxin of Aspergillus flavus by homology modelling.

    Science.gov (United States)

    Kasoju, Aruna; Narasu, M Lakshmi; Muvva, Charuvaka; Subbarao, Bathula Vv

    2012-01-01

    Aflatoxins are polyketide-derived secondary metabolites produced by Aspergillus spp. The toxic effects of aflatoxins have adverse consequences for human health and agricultural economics. The aflR gene, a regulatory gene for aflatoxin biosynthesis, encodes a protein containing a zinc-finger DNA-binding motif. AFLR-Protein three-dimensional model was generated using Robetta server. The modeled AFLR-Protein was further optimization and validation using Rampage. In the simulations, we monitored the backbone atoms and the C-α-helix of the modeled protein. The low RMSD and the simulation time indicate that, as expected, the 3D structural model of AFLR-protein represents a stable folding conformation. This study paves the way for generating computer molecular models for proteins whose crystal structures are not available and which would aid in detailed molecular mechanism of inhibition of aflatoxin.

  20. Impact of genetic variation on three dimensional structure and function of proteins.

    Directory of Open Access Journals (Sweden)

    Roshni Bhattacharya

    Full Text Available The Protein Data Bank (PDB; http://wwpdb.org was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings. The global PDB archive now contains more than 126,000 experimentally determined atomic level three-dimensional (3D structures of biological macromolecules (proteins, DNA, RNA, all of which are freely accessible via the Internet. Knowledge of the 3D structure of the gene product can help in understanding its function and role in disease. Of particular interest in the PDB archive are proteins for which 3D structures of genetic variant proteins have been determined, thus revealing atomic-level structural differences caused by the variation at the DNA level. Herein, we present a systematic and qualitative analysis of such cases. We observe a wide range of structural and functional changes caused by single amino acid differences, including changes in enzyme activity, aggregation propensity, structural stability, binding, and dissociation, some in the context of large assemblies. Structural comparison of wild type and mutated proteins, when both are available, provide insights into atomic-level structural differences caused by the genetic variation.

  1. Three-dimensional architecture and biogenesis of membrane structures associated with hepatitis C virus replication.

    Science.gov (United States)

    Romero-Brey, Inés; Merz, Andreas; Chiramel, Abhilash; Lee, Ji-Young; Chlanda, Petr; Haselman, Uta; Santarella-Mellwig, Rachel; Habermann, Anja; Hoppe, Simone; Kallis, Stephanie; Walther, Paul; Antony, Claude; Krijnse-Locker, Jacomine; Bartenschlager, Ralf

    2012-01-01

    All positive strand RNA viruses are known to replicate their genomes in close association with intracellular membranes. In case of the hepatitis C virus (HCV), a member of the family Flaviviridae, infected cells contain accumulations of vesicles forming a membranous web (MW) that is thought to be the site of viral RNA replication. However, little is known about the biogenesis and three-dimensional structure of the MW. In this study we used a combination of immunofluorescence- and electron microscopy (EM)-based methods to analyze the membranous structures induced by HCV in infected cells. We found that the MW is derived primarily from the endoplasmic reticulum (ER) and contains markers of rough ER as well as markers of early and late endosomes, COP vesicles, mitochondria and lipid droplets (LDs). The main constituents of the MW are single and double membrane vesicles (DMVs). The latter predominate and the kinetic of their appearance correlates with kinetics of viral RNA replication. DMVs are induced primarily by NS5A whereas NS4B induces single membrane vesicles arguing that MW formation requires the concerted action of several HCV replicase proteins. Three-dimensional reconstructions identify DMVs as protrusions from the ER membrane into the cytosol, frequently connected to the ER membrane via a neck-like structure. In addition, late in infection multi-membrane vesicles become evident, presumably as a result of a stress-induced reaction. Thus, the morphology of the membranous rearrangements induced in HCV-infected cells resemble those of the unrelated picorna-, corona- and arteriviruses, but are clearly distinct from those of the closely related flaviviruses. These results reveal unexpected similarities between HCV and distantly related positive-strand RNA viruses presumably reflecting similarities in cellular pathways exploited by these viruses to establish their membranous replication factories.

  2. Three-dimensional Crustal Structure beneath the Tibetan Plateau Revealed by Multi-scale Gravity Analysis

    Science.gov (United States)

    Xu, C.; Luo, Z.; Sun, R.; Li, Q.

    2017-12-01

    The Tibetan Plateau, the largest and highest plateau on Earth, was uplifted, shorten and thicken by the collision and continuous convergence of the Indian and Eurasian plates since 50 million years ago, the Eocene epoch. Fine three-dimensional crustal structure of the Tibetan Plateau is helpful in understanding the tectonic development. At present, the ordinary method used for revealing crustal structure is seismic method, which is inhibited by poor seismic station coverage, especially in the central and western plateau primarily due to the rugged terrain. Fortunately, with the implementation of satellite gravity missions, gravity field models have demonstrated unprecedented global-scale accuracy and spatial resolution, which can subsequently be employed to study the crustal structure of the entire Tibetan Plateau. This study inverts three-dimensional crustal density and Moho topography of the Tibetan Plateau from gravity data using multi-scale gravity analysis. The inverted results are in agreement with those provided by the previous works. Besides, they can reveal rich tectonic development of the Tibetan Plateau: (1) The low-density channel flow can be observed from the inverted crustal density; (2) The Moho depth in the west is deeper than that in the east, and the deepest Moho, which is approximately 77 km, is located beneath the western Qiangtang Block; (3) The Moho fold, the directions of which are in agreement with the results of surface movement velocities estimated from Global Positioning System, exists clearly on the Moho topography.This study is supported by the National Natural Science Foundation of China (Grant No. 41504015), the China Postdoctoral Science Foundation (Grant No. 2015M572146), and the Surveying and Mapping Basic Research Programme of the National Administration of Surveying, Mapping and Geoinformation (Grant No. 15-01-08).

  3. Implicit three-dimensional finite-element formulation for the nonlinear structural response of reactor components

    International Nuclear Information System (INIS)

    Kulak, R.F.; Belytschko, T.B.

    1975-09-01

    The formulation of a finite-element procedure for the implicit transient and static analysis of plate/shell type structures in three-dimensional space is described. The triangular plate/shell element can sustain both membrane and bending stresses. Both geometric and material nonlinearities can be treated, and an elastic-plastic material law has been incorporated. The formulation permits the element to undergo arbitrarily large rotations and translations; but, in its present form it is restricted to small strains. The discretized equations of motion are obtained by a stiffness method. An implicit integration algorithm based on trapezoidal integration formulas is used to integrate the discretized equations of motion in time. To ensure numerical stability, an iterative solution procedure with equilibrium checks is used

  4. Production of three-dimensional structures of PHB using selective laser sintering

    International Nuclear Information System (INIS)

    Pereira, Tatiana F.; Costa, Marysilvia F.; Thire, Rossana M.S.M.; Oliveira, Marcelo F.; Maia, Izaque A.; Silva, Jorge V.L.

    2011-01-01

    Selective Laser Sintering (SLS) is a technology of layer-by-layer fabrication of three-dimensional physical models directly from their computational design. The poly(3-hydroxybutyrate) (PHB) is a microbial, biodegradable and semicrystalline polyester. The objective of this work was to produce PHB parts, evaluating the reuse of material in the production of the new parts. Images of SEM of part surface showed the formation of neck that indicates sintering between PHB particles during processing. Analysis of NMR and DSC of the reused polymer showed no changes in the chemical structure and thermal properties of PHB. The parts produced from virgin and reused PHB showed no significant difference in their thermal properties. This could suggest that the reuse of raw material did not influence the process reproducibility. (author)

  5. Three-Dimensional Virtual Bone Bank System Workflow for Structural Bone Allograft Selection: A Technical Report

    Directory of Open Access Journals (Sweden)

    Lucas Eduardo Ritacco

    2013-01-01

    Full Text Available Structural bone allograft has been used in bone defect reconstruction during the last fifty years with acceptable results. However, allograft selection methods were based on 2-dimensional templates using X-rays. Thanks to preoperative planning platforms, three-dimensional (3D CT-derived bone models were used to define size and shape comparison between host and donor. The purpose of this study was to describe the workflow of this virtual technique in order to explain how to choose the best allograft using a virtual bone bank system. We measured all bones in a 3D virtual environment determining the best match. The use of a virtual bone bank system has allowed optimizing the allograft selection in a bone bank, providing more information to the surgeons before surgery. In conclusion, 3D preoperative planning in a virtual environment for allograft selection is an important and helpful tool in order to achieve a good match between host and donor.

  6. Gauge structure, anomalies and mass generation in a three dimensional thirring model

    International Nuclear Information System (INIS)

    Gomes, M.; Mendes, R.S.; Ribeiro, R.F.; Silva, A.J. da.

    1990-05-01

    We consider a three dimensional model of spinor fields with a Thirring like, quadrilinear self interaction. Using either two or four component Dirac spinors, we prove that the 1/N expansion for the model is renormalizable if a gauge structure to select physical quantities is introduced. For certain values of the coupling the leading 1/N approximation exihibits bound state poles. Dynamical breaking of parity or chiral symmetry is shown to occur as a cooperative effect of different orders of 1/N, if N is smaller than the critical value N c = 128 / x 2 D' , where D is two or four depending on wether the fermion field has two or four components. (author) [pt

  7. Spatial patterns in the effects of fire on savanna vegetation three-dimensional structure.

    Science.gov (United States)

    Levick, Shaun R; Asner, Gregory P; Smit, Izak P J

    2012-12-01

    Spatial variability in the effects of fire on savanna vegetation structure is seldom considered in ecology, despite the inherent heterogeneity of savanna landscapes. Much has been learned about the effects of fire on vegetation structure from long-term field experiments, but these are often of limited spatial extent and do not encompass different hillslope catena elements. We mapped vegetation three-dimensional (3-D) structure over 21 000 ha in nine savanna landscapes (six on granite, three on basalt), each with contrasting long-term fire histories (higher and lower fire frequency), as defined from a combination of satellite imagery and 67 years of management records. Higher fire frequency areas contained less woody canopy cover than their lower fire frequency counterparts in all landscapes, and woody cover reduction increased linearly with increasing difference in fire frequency (r2 = 0.58, P = 0.004). Vegetation height displayed a more heterogeneous response to difference in fire frequency, with taller canopies present in the higher fire frequency areas of the wetter sites. Vegetation 3-D structural differences between areas of higher and lower fire frequency differed between geological substrates and varied spatially across hillslopes. Fire had the greatest relative impact on vegetation structure on nutrient-rich basalt substrates, and it imparted different structural responses upon vegetation in upland, midslope, and lowland topographic positions. These results highlight the complexity of fire vegetation relationships in savanna systems, and they suggest that underlying landscape heterogeneity needs more explicit incorporation into fire management policies.

  8. Three-dimensional cell manipulation and patterning using dielectrophoresis via a multi-layer scaffold structure.

    Science.gov (United States)

    Chu, H K; Huan, Z; Mills, J K; Yang, J; Sun, D

    2015-02-07

    Cell manipulation is imperative to the areas of cellular biology and tissue engineering, providing them a useful tool for patterning cells into cellular patterns for different analyses and applications. This paper presents a novel approach to perform three-dimensional (3D) cell manipulation and patterning with a multi-layer engineered scaffold. This scaffold structure employed dielectrophoresis as the non-contact mechanism to manipulate cells in the 3D domain. Through establishing electric fields via this multi-layer structure, the cells in the medium became polarized and were attracted towards the interior part of the structure, forming 3D cellular patterns. Experiments were conducted to evaluate the manipulation and the patterning processes with the proposed structure. Results show that with the presence of a voltage input, this multi-layer structure was capable of manipulating different types of biological cells examined through dielectrophoresis, enabling automatic cell patterning in the time-scale of minutes. The effects of the voltage input on the resultant cellular pattern were examined and discussed. Viability test was performed after the patterning operation and the results confirmed that majority of the cells remained viable. After 7 days of culture, 3D cellular patterns were observed through SEM. The results suggest that this scaffold and its automated dielectrophoresis-based patterning mechanism can be used to construct artificial tissues for various tissue engineering applications.

  9. Three-dimensional imaging of vortex structure in a ferroelectric nanoparticle driven by an electric field.

    Science.gov (United States)

    Karpov, D; Liu, Z; Rolo, T Dos Santos; Harder, R; Balachandran, P V; Xue, D; Lookman, T; Fohtung, E

    2017-08-17

    Topological defects of spontaneous polarization are extensively studied as templates for unique physical phenomena and in the design of reconfigurable electronic devices. Experimental investigations of the complex topologies of polarization have been limited to surface phenomena, which has restricted the probing of the dynamic volumetric domain morphology in operando. Here, we utilize Bragg coherent diffractive imaging of a single BaTiO 3 nanoparticle in a composite polymer/ferroelectric capacitor to study the behavior of a three-dimensional vortex formed due to competing interactions involving ferroelectric domains. Our investigation of the structural phase transitions under the influence of an external electric field shows a mobile vortex core exhibiting a reversible hysteretic transformation path. We also study the toroidal moment of the vortex under the action of the field. Our results open avenues for the study of the structure and evolution of polar vortices and other topological structures in operando in functional materials under cross field configurations.Imaging of topological states of matter such as vortex configurations has generally been limited to 2D surface effects. Here Karpov et al. study the volumetric structure and dynamics of a vortex core mediated by electric-field induced structural phase transition in a ferroelectric BaTiO 3 nanoparticle.

  10. Effect of test structure on electromigration characteristics in three-dimensional through silicon via stacked devices

    Science.gov (United States)

    Oba, Yoshiyuki; De Messemaeker, Joke; Tyrovouzi, Anna Maria; Miyamori, Yuichi; De Vos, Joeri; Wang, Teng; Beyer, Gerald; Beyne, Eric; De Wolf, Ingrid; Croes, Kristof

    2015-05-01

    Electromigration failure locations in three-dimensional (3D) interconnect structures with high-aspect-ratio through silicon vias, (TSVs, Φ5 × 50 µm2) connected to 40-µm-pitch CuSn solder joints have been identified using test structures which were designed to avoid failures in the back-end-of-line (BEOL). The resistance of the structures with the TSV and bump connections showed a continuous increase until failure. For the structures without a bump connection, where only TSV and re-distributed line (RDL) were the electrically connected, the resistance remained constant prior to the final failure. From cross-sectional analyses after the test, the failure locations were identified at the TSV bottom or at the bump bottom. The location of void formation was changed by applied current direction. The flux divergence generated by the barrier metal and the reservoir effect plays a crucial role in the void formation, and each failure mode is considered to have a different impact on the reliability performance.

  11. KNApSAcK-3D: a three-dimensional structure database of plant metabolites.

    Science.gov (United States)

    Nakamura, Kensuke; Shimura, Naoki; Otabe, Yuuki; Hirai-Morita, Aki; Nakamura, Yukiko; Ono, Naoaki; Ul-Amin, Md Altaf; Kanaya, Shigehiko

    2013-02-01

    Studies on plant metabolites have attracted significant attention in recent years. Over the past 8 years, we have constructed a unique metabolite database, called KNApSAcK, that contains information on the relationships between metabolites and their expressing organism(s). In the present paper, we introduce KNApSAcK-3D, which contains the three-dimensional (3D) structures of all of the metabolic compounds included in the original KNApSAcK database. The 3D structure for each compound was optimized using the Merck Molecular Force Field (MMFF94), and a multiobjective genetic algorithm was used to search extensively for possible conformations and locate the global minimum. The resulting set of structures may be used for docking studies to identify new and potentially unexpected binding sites for target proteins. The 3D structures may also be utilized for more qualitative studies, such as the estimation of biological activities using 3D-QSAR. The database can be accessed via a link from the KNApSAcK Family website (http://kanaya.naist.jp/KNApSAcK_Family/) or directory at http://kanaya.naist.jp/knapsack3d/.

  12. Growth mechanism of InGaN nanodots on three-dimensional GaN structures

    Energy Technology Data Exchange (ETDEWEB)

    Park, Donghwy; Min, Daehong; Nam, Okhyun [Department of Nano-Optical Engineering, Convergence Center for Advanced Nano-Semiconductor (CANS), Korea Polytechnic University (KPU), Siheung-si, Gyeonggi-do (Korea, Republic of)

    2017-07-15

    In this study, we investigated the growth mechanism of indium gallium nitride (InGaN) nanodots (NDs) and an InGaN layer, which were simultaneously formed on a three-dimensional (3D) gallium nitride (GaN) structure, having (0001) polar, (11-22) semi-polar, and (11-20) nonpolar facets. We observed the difference in the morphological and compositional properties of the InGaN structures. From the high resolution transmission electron microscopy (HR-TEM) images, it can be seen that the InGaN NDs were formed only on the polar and nonpolar facets, whereas an InGaN layer was formed on the semi-polar facet. The indium composition variation in all the InGaN structures was observed using scanning transmission electron microscopy (STEM) and the energy dispersive X-ray spectroscopy (EDS). The different growth mechanism can be explained by two reasons: (i) The difference in the diffusivities of indium and gallium adatoms at each facet of 3D GaN structure; and (ii) the difference in the kinetic Wulff plots of polar, semi-polar, and nonpolar GaN planes. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  13. Potentially of using vertical and three dimensional isolation systems in nuclear structures

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Zhiuang [Research Institute of Structural Engineering and Disaster Reduction, Tongji University, Shanghai (China); Wong, Jenna [Lawrence Berkeley National Laboratories, Berkeley (United States); Mahin, Stephen [University of California, Berkeley (United States)

    2016-10-15

    Although the horizontal component of an earthquake response can be significantly reduced through the use of conventional seismic isolators, the vertical component of excitation is still transmitted directly into the structure. Records from instrumented structures, and some recent tests and analyses have actually seen increases in vertical responses in base isolated structures under the combined effects of horizontal and vertical ground motions. This issue becomes a great concern to facilities such as a Nuclear Power Plants (NPP), with specialized equipment and machinery that is not only expensive, but critical to safe operation. As such, there is considerable interest worldwide in vertical and three-dimensional (3D) isolation systems. This paper examines several vertical and 3D isolation systems that have been proposed and their potential application to modern nuclear facilities. In particular, a series of case study analyses of a modern NPP model are performed to examine the benefits and challenges associated with 3D isolation compared with horizontal isolation. It was found that compared with the general horizontal isolators, isolators that have vertical frequencies of no more than 3 Hz can effectively reduce the vertical in-structure responses for the studied NPP model. Among the studied cases, the case that has a vertical isolation frequency of 3 Hz is the one that can keep the horizontal period of the isolators as the first period while having the most flexible vertical isolator properties. When the vertical frequency of isolators reduces to 1 Hz, the rocking effect is obvious and rocking restraining devices are necessary.

  14. Three dimensional simulation of giant magneto-impedance effect in thin film structures

    KAUST Repository

    Li, Bodong

    2011-04-04

    In this paper, a three dimensional model for the giant magneto-impedance (GMI) effect in thin film structures is developed using the finite element method(FEM) with a GMI permeability model embedded. One-layer, three-layer, and five-layer thin film structures are simulated. The GMI effect and the sensitivity are calculated as a function of the external magnetic field, driving frequency, and the thickness of the magnetic layers. The results show that the five-layer structure has the best performance, which is in accordance with experimental results. The GMI ratio and the sensitivity first improve with the increasing thickness of the magnetic layer but reach saturation at a certain value of the thickness. In a five-layer structure,saturation of the GMI effect becomes effective at about 3 μm thickness of the magnetic layers, where a GMI ratio of 1125% was obtained, with a corresponding sensitivity of 0.37%/A/m (29.6%/Oe).

  15. Three-dimensional Nanowire Structures for Ultra-Fast Separation of DNA, Protein and RNA Molecules

    Science.gov (United States)

    Rahong, Sakon; Yasui, Takao; Yanagida, Takeshi; Nagashima, Kazuki; Kanai, Masaki; Meng, Gang; He, Yong; Zhuge, Fuwei; Kaji, Noritada; Kawai, Tomoji; Baba, Yoshinobu

    2015-01-01

    Separation and analysis of biomolecules represent crucial processes for biological and biomedical engineering development; however, separation resolution and speed for biomolecules analysis still require improvements. To achieve separation and analysis of biomolecules in a short time, the use of highly-ordered nanostructures fabricated by top-down or bottom-up approaches have been proposed. Here, we reported on the use of three-dimensional (3D) nanowire structures embedded in microchannels fabricated by a bottom-up approach for ultrafast separation of small biomolecules, such as DNA, protein, and RNA molecules. The 3D nanowire structures could analyze a mixture of DNA molecules (50–1000 bp) within 50 s, a mixture of protein molecules (20–340 kDa) within 5 s, and a mixture of RNA molecules (100–1000 bases) within 25 s. And, we could observe the electrophoretic mobility difference of biomolecules as a function of molecular size in the 3D nanowire structures. Since the present methodology allows users to control the pore size of sieving materials by varying the number of cycles for nanowire growth, the 3D nanowire structures have a good potential for use as alternatives for other sieving materials. PMID:26073192

  16. Three-dimensional fine-scale genetic structure of the neotropical epiphytic orchid, Laelia rubescens.

    Science.gov (United States)

    Trapnell, Dorset W; Hamrick, J L; Nason, John D

    2004-05-01

    Epiphytic plants occupy three-dimensional space, which allows more individuals to be closely clustered spatially than is possible for populations occupying two dimensions. The unique characteristics of epiphytes can act in concert to influence the fine-scale genetic structure of their populations which can, in turn, influence mating patterns and other population phenomena. Three large populations of Laelia rubescens (Orchidaceae) in the Costa Rican seasonal dry forest were sampled at two levels of intensity to determine: (i) whether individual clusters contain more than one genotype, and (ii) the spatial distribution and fine-scale genetic structure of genotypes within populations. Samples were assayed for their multilocus allozyme genotypes and spatial autocorrelation analyses were performed. High levels of genetic diversity, high genotypic diversity and low among-population variation were found. In the larger clusters, multiple genets per cluster were common with discrete clusters containing up to nine genotypes. Spatial autocorrelation analyses indicated significant positive genetic structure at distances of

  17. Three-dimensional glue detection and evaluation based on linear structured light

    Science.gov (United States)

    Xiao, Zhitao; Yang, Ruipeng; Geng, Lei; Liu, Yanbei

    2018-01-01

    During the online glue detection of body in white (BIW), the purpose of traditional glue detection based on machine vision is the localization and segmentation of glue, which is dissatisfactory for estimating the uniformity of glue with complex shape. A three-dimensional glue detection method based on the linear structured light and the movement parameters of robot is proposed. Firstly, the linear structured light and epipolar constraint algorithm are used for sign matching of binocular vision. Then, hand-eye relationship between robot and binocular camera is utilized to unified coordinate system. Finally, a structured light stripe extraction method is proposed to extract the sub-pixel coordinates of the light strip center. Experiments results demonstrate that the propose method can estimate the shape of glue accurately. For three kinds of glue with complex shape and uneven illumination, our method can detect the positions of blemishes. The absolute error of measurement is less than 1.04mm and the relative error is less than 10% respectively, which is suitable for online glue detection in BIW.

  18. Stereo-vision three-dimensional reconstruction of curvilinear structures imaged with a TEM.

    Science.gov (United States)

    Oveisi, Emad; Letouzey, Antoine; De Zanet, Sandro; Lucas, Guillaume; Cantoni, Marco; Fua, Pascal; Hébert, Cécile

    2018-01-01

    Deriving accurate three-dimensional (3-D) structural information of materials at the nanometre level is often crucial for understanding their properties. Tomography in transmission electron microscopy (TEM) is a powerful technique that provides such information. It is however demanding and sometimes inapplicable, as it requires the acquisition of multiple images within a large tilt arc and hence prolonged exposure to electrons. In some cases, prior knowledge about the structure can tremendously simplify the 3-D reconstruction if incorporated adequately. Here, a novel algorithm is presented that is able to produce a full 3-D reconstruction of curvilinear structures from stereo pair of TEM images acquired within a small tilt range that spans from only a few to tens of degrees. Reliability of the algorithm is demonstrated through reconstruction of a model 3-D object from its simulated projections, and is compared with that of conventional tomography. This method is experimentally demonstrated for the 3-D visualization of dislocation arrangements in a deformed metallic micro-pillar. Copyright © 2017. Published by Elsevier B.V.

  19. Three-dimensional structure and evolution of an asymmetric pull-apart basin

    Science.gov (United States)

    Sagy, Amir; Hamiel, Yariv

    2017-07-01

    The structure of a 250-m-long asymmetrical pull-apart basin developed in carbonate rocks at the Galilee heights, Israel, is herein analyzed. The reconstruction of the basin geometry is based on detailed mapping and LiDAR measurements of fault scarps. The architecture of faults is then used as a boundary condition for calculating the stress pattern in the vicinity of the basin, using a dislocation model. The basin is found to be an asymmetrical V-shaped structure bordered by two longitudinal oblique right-lateral strike-slip faults. The strike of one of the faults is bent at the eastern edge of the basin, generating a transverse boundary fault which joins the second boundary fault orthogonally. The overall lateral displacement is smaller than the basin length, and no transverse or diagonal fault is observed in the western end of the basin. The deformation around the basin is mostly displayed by fractures. Yet, folds and fault branches are observed near the tips of the boundary faults and near kink points of fault segments. Stress analysis obtained by the three-dimensional model is in general agreement with the orientation of fractures and location of high deformation regions in and around the basin. Based on our observations, we present a conceptual model which demonstrates the development of asymmetric basins in releasing bends and sheds light on the structures of similar large pull-apart basins.

  20. Three-Dimensional Printing of Complex Structures by Freeform Reversible Embedding of Suspended Hydrogels (FRESH)

    Science.gov (United States)

    Feinberg, Adam

    We demonstrate the additive manufacturing of complex three-dimensional (3D) structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. These structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. This process, termed freeform reversible embedding of suspended hydrogels (FRESH), enables 3D printing of hydrated materials with an elastic modulus less than 500 kPa including alginate, collagen, hyaluronic acid and fibrin. A range of crosslinking mechanisms can be used depending on the polymer being printed, including ionic, enzymatic, pH, thermal and light based approaches. CAD models of 3D optical, computed tomography, and magnetic resonance imaging data can be 3D printed at a resolution of 100 μm and at low cost by leveraging open-source hardware and software tools. Proof-of-concept structures based on femurs, branched coronary arteries, trabeculated embryonic hearts, and human brains are mechanically robust and recreate complex 3D internal and external anatomical architectures. Recent advances have improved the resolution and broadened the range of materials that can be FRESH 3D printed. This work was supported in part by the NIH Director's New Innovator Award (DP2HL117750) and the NSF CAREER Award (1454248).

  1. Prediction of HIV drug resistance from genotype with encoded three-dimensional protein structure.

    Science.gov (United States)

    Yu, Xiaxia; Weber, Irene T; Harrison, Robert W

    2014-01-01

    Drug resistance has become a severe challenge for treatment of HIV infections. Mutations accumulate in the HIV genome and make certain drugs ineffective. Prediction of resistance from genotype data is a valuable guide in choice of drugs for effective therapy. In order to improve the computational prediction of resistance from genotype data we have developed a unified encoding of the protein sequence and three-dimensional protein structure of the drug target for classification and regression analysis. The method was tested on genotype-resistance data for mutants of HIV protease and reverse transcriptase. Our graph based sequence-structure approach gives high accuracy with a new sparse dictionary classification method, as well as support vector machine and artificial neural networks classifiers. Cross-validated regression analysis with the sparse dictionary gave excellent correlation between predicted and observed resistance. The approach of encoding the protein structure and sequence as a 210-dimensional vector, based on Delaunay triangulation, has promise as an accurate method for predicting resistance from sequence for drugs inhibiting HIV protease and reverse transcriptase.

  2. Three-Dimensional Face Recognition in Mild Cognitive Impairment: A Psychophysical and Structural MR Study.

    Science.gov (United States)

    Lemos, Raquel; Santana, Isabel; Caetano, Gina; Bernardino, Inês; Morais, Ricardo; Farivar, Reza; Castelo-Branco, Miguel

    2016-08-01

    Mild cognitive impairment (MCI) has been associated with a high risk of conversion to Alzheimer's dementia. In addition to memory complaints, impairments in the visuospatial domain have been reported in this condition. We have previously shown that deficits in perceiving structure-from-motion (SFM) objects are reflected in functional reorganization of brain activity within the visual ventral stream. Here we aimed to identify structural correlates of psychophysical complex face and object recognition performance in amnestic MCI patients (n=30 vs. n=25 controls). This study was, therefore, motivated by evidence from recent studies showing that a combination of visual information across dorsal and ventral visual streams may be needed for the perception of three-dimensional (3D) SFM objects. In our experimental paradigm, participants had to discriminate 3D SFM shapes (faces and objects) from 3D SFM meaningless (scrambled) shapes. Morphometric analysis established neuroanatomical evidence for impairment in MCI as demonstrated by smaller hippocampal volumes. We found association between cortical thickness and face recognition performance, comprising the occipital lobe and visual ventral stream fusiform regions (overlapping the known location of face fusiform area) in the right hemisphere, in MCI. We conclude that impairment of 3D visual integration exists at the MCI stage involving also the visual ventral stream and contributing to face recognition deficits. The specificity of such observed structure-function correlation for faces suggests a special role of this processing pathway in health and disease. (JINS, 2016, 22, 744-754).

  3. Three-dimensional printing of shape memory hydrogels with internal structure for drug delivery.

    Science.gov (United States)

    Wang, Yongzhou; Miao, Ying; Zhang, Jieling; Wu, Jian Ping; Kirk, Thomas Brett; Xu, Jiake; Ma, Dong; Xue, Wei

    2018-03-01

    Hydrogels with shape memory behavior and internal structure have wide applications in fields ranging from tissue engineering and medical instruments to drug delivery; however, creating the hydrogels has proven to be extremely challenging. This study presents a three-dimensional (3D) printing technology to fabricate the shape memory hydrogels with internal structure (SMHs) by combining sodium alginate (alginate) and pluronic F127 diacrylate macromer (F127DA). SMHs were constituted by a dual network structure. One is a stable network which is formed by F127DA photo-crosslinking; the other one is a reversible network which is formed by Ca 2+ cross-linked alginate. SMHs recovery ratio was 98.15% in 10min after Ca 2+ was removed in the Na 2 CO 3 solution, and the elastic modulus remains essentially stable after the shape memory cycle. It showed that the drug releasing rate is more rapid compared with traditional drug-loaded hydrogels in in vitro experiments. The viability of 3T3 fibroblasts remained intact which revealed its excellent biocompatibility. Therefore, SMHs have a huge prospect for application in drug carriers and tissue engineering scaffold. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Three-dimensional investigation of the two-phase flow structure in a bubbly pipe flow

    International Nuclear Information System (INIS)

    Hassan, Y.A.; Schmidl, W.D.; Ortiz-Villafuerte, J.

    1997-01-01

    Particle Image Velocimetry (PIV) is a non-intrusive measurement technique, which can be used to study the structure of various fluid flows. PIV is used to measure the time varying full field velocity data of a particle-seeded flow field within either a two-dimensional plane or three-dimensional volume. PIV is a very efficient measurement technique since it can obtain both qualitative and quantitative spatial information about the flow field being studied. This information can be further processed into information such as vorticity and pathlines. Other flow measurement techniques (Laser Doppler Velocimetry, Hot Wire Anemometry, etc...) only provide quantitative information at a single point. PIV can be used to study turbulence structures if a sufficient amount of data can be acquired and analyzed, and it can also be extended to study two-phase flows if both phases can be distinguished. In this study, the flow structure around a bubble rising in a pipe filled with water was studied in three-dimensions. The velocity of the rising bubble and the velocity field of the surrounding water was measured. Then the turbulence intensities and Reynolds stresses were calculated from the experimental data. (author)

  5. Computer-aided three-dimensional images of the helical structure in the apical tubule of absorbing epithelia

    International Nuclear Information System (INIS)

    Kawai, Yoshinori; Hatae, Tanenori

    1990-01-01

    Computer-aided three-dimensional models of the helical structure within an apical tubule (AT) of several absorbing epithelia (kidney proximal tubule, visceral yolk sac, and ductuli efferentes) were constructed using ray-tracing graphics software to further understand the highly ordered structural configuration. Our previous electron microscopic studies using thin-section technique have first revealed the helical structure within the AT fixed in situ with a mixture of formaldehyde, glutaraldehyde, and osmium tetroxide. In the present study, we construct a computer-aided three-dimensional model of the helical structure in the AT to explain quantitative data obtained by the electron microscopy. The model could well explain several aspects of electron microscopical images and enables us to understand more clearly the three-dimensional configuration of the unique structure associated with the AT. (author)

  6. Experimental study of soil-structure interaction for proving the three dimensional thin layered element method

    International Nuclear Information System (INIS)

    Kuwabara, Y.; Ogiwara, Y.; Suzuki, T.; Tsuchiya, H.; Nakayama, M.

    1981-01-01

    It is generally recognized that the earthquake response of a structure can be significantly affected by the dynamic interaction between the structure and the surrounding soil. Dynamic soil-structure interaction effects are usually analyzed by using a lumped mass model or a finite element model. In the lumped mass model, the soil is represented by springs and dashpots based on the half-space elastic theory. Each model has its advantages and limitations. The Three Dimensional Thin Layered Element Theory has been developed by Dr. Hiroshi Tajimi based on the combined results of the abovementioned lumped mass model and finite element model. The main characteristic of this theory is that, in consideration and can be applied in the analysis of many problems in soil-structure interaction, such as those involving radiation damping, embedded structures, and multi-layered soil deposits. This paper describes test results on a small scale model used to prove the validity of the computer program based on the Thin Layered Element Theory. As a numerical example, the response analysis of a PWR nuclear power plant is carried out using this program. The vibration test model is simplified and the scale is 1/750 for line. The soil layer of the model is made of congealed gelatine. The test soil layer is 80 cm long, 35 cm wide and 10 cm thick. The super structure is a one mass model made of metal sheet spring and solid mass metal. As fixed inputs, sinusoidal waves (10, 20 gal level) are used. The displacements of the top and base of the super structure, and the accelerations and the displacements of the shaking table are measured. The main parameter of the test is the shear wave velocity of the soil layer. (orig./RW)

  7. Three-dimensional structure of olefinic thermoplastic elastomer blends using electron tomography

    NARCIS (Netherlands)

    Sengupta, P.; Noordermeer, Jacobus W.M.

    2005-01-01

    The present communication reports the first use of electron tomography in reconstructing the three-dimensional morphology in thermoplastic elastomer blends. The blends investigated were dynamically vulcanized blends of ethylene-propylene-diene (EPDM) rubber/poly(propylene)/oil and

  8. Reconstruction of Mammary Gland Structure Using Three-Dimensional Computer-Based Microscopy

    National Research Council Canada - National Science Library

    de

    2003-01-01

    During the administrative funding period of this grant we have developed a system that permits three-dimensional reconstruction of entire the entire murine ductal epithelium from physical tissue sections...

  9. Reconstruction of Mammary Gland Structure Using Three-Dimensional Computer-Based Microscopy

    National Research Council Canada - National Science Library

    De Solorzano, Carlos O

    2004-01-01

    During the administrative funding period of this grant we have developed a system that permits three-dimensional reconstruction of entire the entire murine ductal epithelium from physical tissue sections...

  10. Investigation of three-dimensional turbulent structures in the torsatron TJ-K

    Energy Technology Data Exchange (ETDEWEB)

    Mahdizadeh, N.

    2007-02-14

    In this work, for the first time, the three-dimensional nature of drift waves has been verified experimentally inside the confinement region of the toroidal plasma in TJ-K. The perpendicular dynamics of turbulence has been studied with the focus on the poloidal wavenumber spectra and the scaling of the turbulent structure with the drift scale. To this end, a 64 tip Langmuir probe array has been used, which is poloidally positioned on a flux surface. For the first time, the parallel dynamics of turbulence has been investigated in the core of a toroidally confined plasma. In contrast to previous experiments, multi-probe measurements were carried out to get simultaneous information on the shape and the propagation direction of the turbulent structures. The results for the parallel wave number and the parallel propagation velocity have been compared with results from the simulation code GEM3. It is demonstrated that the propagation in the direction parallel to the magnetic field is affected by Alfven dynamics. Together, these results strongly confirm previous investigations, which have demonstrated the importance of drift-wave turbulence in TJ-K and therefore also in fusion edge plasma. (orig.)

  11. Modeling and numerical analysis of a three-dimensional shape memory alloy shell structure

    Science.gov (United States)

    Zhao, Pengtao; Qiu, Jinhao; Ji, Hongli; Wang, Mingyi; Nie, Rui

    2012-04-01

    In this paper, modeling and numerical analysis of a three dimensional shell structure made of shape memory alloy (SMA) are introduced. As a new smart material, SMA material has been applied in many fields due to two significant macroscopic phenomena which are called the shape memory effect (SME) and pseudoelasticity. The material of SMA exhibits two-way shape memory effect (TWSME) after undergoing especial heat treatment and thermo-mechanical training. This work investigates the numerical simulation and application of the SMA component: SMA strip, which has been pre-curved in the room temperature. The component is expected to extend upon heating and shorten on cooling along the curve. Hence the shape memory effect can be used to change the shape of the structure. The return mapping algorithm of the 3-D SMA thermomechanical constitutive equations based on Boyd-Lagoudas model is used in the finite element analysis to describe the material features of the SMA. In this paper, the ABAQUS finite element program has been utilized with a user material subroutine (UMAT) which is written in the FORTRAN code for the modeling of the SMA strip. The SMA component which has a certain initial transformation strain can emerge considerable deflection during the reverse phase transformation inducing by the temperature.

  12. Effects of lens extirpation with anterior vitrectomy on vitreous three-dimensional mesh structure

    Directory of Open Access Journals (Sweden)

    Yan Zhao

    2017-06-01

    Full Text Available AIM: To investigate the changes in vitreous gel structure after lens extirpation combined with anterior vitrectomy in rabbit eyes. METHODS: Twenty-eight chinchilla rabbits were divided into three groups. The control group (Group I included 16 eyes from eight rabbits who did not receive any treatment. Group II included 20 eyes from 10 rabbits that underwent lens aspiration only. Group III included 20 eyes from 10 rabbits that underwent lens aspiration combined with posterior capsulotomy and anterior vitrectomy. Eyes were harvested on the 30th and 60th day postoperatively, respectively. Changes in vitreous gel stretch length due to gravity and the rate of vitreous liquefaction were observed. The collagen content in the vitreous body was examined using the L-hydroxyproline test. Electronic microscopic images were obtained from each eyeball. RESULTS: On both the 30th and 60th day postoperatively, the vitreous gel length of group III was significantly shorter than group I and group II (P<0.05, while the rate of liquefaction of the vitreous body in group III was significantly higher than group I and group II (P<0.05. The collagen content in group III was also higher than that in group I and group II (P<0.05. CONCLUSION: Loss of vitreous gel mass is more likely to occur in the eyes of rabbits receiving anterior vitrectomy. Lensectomy combined with anterior vitrectomy may damage the stable three-dimensional mesh structure of collagen, which could aggravate vitreous gel liquefaction.

  13. Three-dimensional bioprinting is not only about cell-laden structures

    Directory of Open Access Journals (Sweden)

    Hong-Bo Zhang

    2016-08-01

    Full Text Available In this review, we focused on a few obstacles that hinder three-dimensional (3D bioprinting process in tissue engineering. One of the obstacles is the bioinks used to deliver cells. Hydrogels are the most widely used bioink materials; however, they are mechanically weak in nature and cannot meet the requirements for supporting structures, especially when the tissues, such as cartilage, require extracellular matrix to be mechanically strong. Secondly and more importantly, tissue regeneration is not only about building all the components in a way that mimics the structures of living tissues, but also about how to make the constructs function normally in the long term. One of the key issues is sufficient nutrient and oxygen supply to the engineered living constructs. The other is to coordinate the interplays between cells, bioactive agents and extracellular matrix in a natural way. This article reviews the approaches to improve the mechanical strength of hydrogels and their suitability for 3D bioprinting; moreover, the key issues of multiple cell lines coprinting with multiple growth factors, vascularization within engineered living constructs etc. were also reviewed.

  14. Three-dimensional facial anthropometry of unilateral cleft lip infants with a structured light scanning system.

    Science.gov (United States)

    Li, Guanghui; Wei, Jianhua; Wang, Xi; Wu, Guofeng; Ma, Dandan; Wang, Bo; Liu, Yanpu; Feng, Xinghua

    2013-08-01

    Cleft lip in the presence or absence of a cleft palate is a major public health problem. However, few studies have been published concerning the soft-tissue morphology of cleft lip infants. Currently, obtaining reliable three-dimensional (3D) surface models of infants remains a challenge. The aim of this study was to investigate a new way of capturing 3D images of cleft lip infants using a structured light scanning system. In addition, the accuracy and precision of the acquired facial 3D data were validated and compared with direct measurements. Ten unilateral cleft lip patients were enrolled in the study. Briefly, 3D facial images of the patients were acquired using a 3D scanner device before and after the surgery. Fourteen items were measured by direct anthropometry and 3D image software. The accuracy and precision of the 3D system were assessed by comparative analysis. The anthropometric data obtained using the 3D method were in agreement with the direct anthropometry measurements. All data calculated by the software were 'highly reliable' or 'reliable', as defined in the literature. The localisation of four landmarks was not consistent in repeated experiments of inter-observer reliability in preoperative images (P0.05). The structured light scanning system is proven to be a non-invasive, accurate and precise method in cleft lip anthropometry. Copyright © 2013 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

  15. Viscoelastic polymer flows and elastic turbulence in three-dimensional porous structures.

    Science.gov (United States)

    Mitchell, Jonathan; Lyons, Kyle; Howe, Andrew M; Clarke, Andrew

    2016-01-14

    Viscoelastic polymer solutions flowing through reservoir rocks have been found to improve oil displacement efficiency when the aqueous-phase shear-rate exceeds a critical value. A possible mechanism for this enhanced recovery is elastic turbulence that causes breakup and mobilization of trapped oil ganglia. Here, we apply nuclear magnetic resonance (NMR) pulsed field gradient (PFG) diffusion measurements in a novel way to detect increased motion of disconnected oil ganglia. The data are acquired directly from a three-dimensional (3D) opaque porous structure (sandstone) when viscoelastic fluctuations are expected to be present in the continuous phase. The measured increase in motion of trapped ganglia provides unequivocal evidence of fluctuations in the flowing phase in a fully complex 3D system. This work provides direct evidence of elastic turbulence in a realistic reservoir rock - a measurement that cannot be readily achieved by conventional laboratory methods. We support the NMR data with optical microscopy studies of fluctuating ganglia in simple two-dimensional (2D) microfluidic networks, with consistent apparent rheological behaviour of the aqueous phase, to provide conclusive evidence of elastic turbulence in the 3D structure and hence validate the proposed flow-fluctuation mechanism for enhanced oil recovery.

  16. Investigation of three-dimensional turbulent structures in the torsatron TJ-K

    International Nuclear Information System (INIS)

    Mahdizadeh, N.

    2007-01-01

    In this work, for the first time, the three-dimensional nature of drift waves has been verified experimentally inside the confinement region of the toroidal plasma in TJ-K. The perpendicular dynamics of turbulence has been studied with the focus on the poloidal wavenumber spectra and the scaling of the turbulent structure with the drift scale. To this end, a 64 tip Langmuir probe array has been used, which is poloidally positioned on a flux surface. For the first time, the parallel dynamics of turbulence has been investigated in the core of a toroidally confined plasma. In contrast to previous experiments, multi-probe measurements were carried out to get simultaneous information on the shape and the propagation direction of the turbulent structures. The results for the parallel wave number and the parallel propagation velocity have been compared with results from the simulation code GEM3. It is demonstrated that the propagation in the direction parallel to the magnetic field is affected by Alfven dynamics. Together, these results strongly confirm previous investigations, which have demonstrated the importance of drift-wave turbulence in TJ-K and therefore also in fusion edge plasma. (orig.)

  17. Fully three-dimensional analysis of high-speed train-track-soil-structure dynamic interaction

    Science.gov (United States)

    Galvín, P.; Romero, A.; Domínguez, J.

    2010-11-01

    In this paper, a general and fully three dimensional multi-body-finite element-boundary element model, formulated in the time domain to predict vibrations due to train passage at the vehicle, the track and the free field, is presented. The vehicle is modelled as a multi-body system and, therefore, the quasi-static and the dynamic excitation mechanisms due to train passage can be considered. The track is modelled using finite elements. The soil is considered as a homogeneous half-space by the boundary element method. This methodology could be used to take into account local soil discontinuities, underground constructions such as underpasses, and coupling with nearby structures that break the uniformity of the geometry along the track line. The nonlinear behaviour of the structures could be also considered. In the present paper, in order to test the model, vibrations induced by high-speed train passage are evaluated for a ballasted track. The quasi-static and dynamic load components are studied and the influence of the suspended mass on the vertical loads is analyzed. The numerical model is validated by comparison with experimental records from two HST lines. Finally, the dynamic behaviour of a transition zone between a ballast track and a slab track is analyzed and the obtained results from the proposed model are compared with those obtained from a model with invariant geometry with respect to the track direction.

  18. Three-Dimensional Electronic Structure of the Type-II Weyl Semimetal WTe_{2}.

    Science.gov (United States)

    Di Sante, Domenico; Das, Pranab Kumar; Bigi, C; Ergönenc, Z; Gürtler, N; Krieger, J A; Schmitt, T; Ali, M N; Rossi, G; Thomale, R; Franchini, C; Picozzi, S; Fujii, J; Strocov, V N; Sangiovanni, G; Vobornik, I; Cava, R J; Panaccione, G

    2017-07-14

    By combining bulk sensitive soft-x-ray angular-resolved photoemission spectroscopy and first-principles calculations we explored the bulk electron states of WTe_{2}, a candidate type-II Weyl semimetal featuring a large nonsaturating magnetoresistance. Despite the layered geometry suggesting a two-dimensional electronic structure, we directly observe a three-dimensional electronic dispersion. We report a band dispersion in the reciprocal direction perpendicular to the layers, implying that electrons can also travel coherently when crossing from one layer to the other. The measured Fermi surface is characterized by two well-separated electron and hole pockets at either side of the Γ point, differently from previous more surface sensitive angle-resolved photoemission spectroscopy experiments that additionally found a pronounced quasiparticle weight at the zone center. Moreover, we observe a significant sensitivity of the bulk electronic structure of WTe_{2} around the Fermi level to electronic correlations and renormalizations due to self-energy effects, previously neglected in first-principles descriptions.

  19. Three-dimensional quantitative structure-activity relationships of mazindol analogues at the dopamine transporter.

    Science.gov (United States)

    Kulkarni, Santosh S; Newman, Amy Hauck; Houlihan, William J

    2002-09-12

    A three-dimensional quantitative structure-activity relationship (3D-QSAR) study was performed on a series of mazindol analogues using the comparative molecular field analysis (CoMFA) method with their corresponding binding affinities for the displacement of [(3)H]WIN 35 428 from rat caudate putamen tissue. The cross-validated CoMFA models were derived from a training set of 50 compounds, and the predictive ability of the resulting CoMFA models was evaluated against a test set of 21 compounds. A set of alignment rules was derived to superimpose these compounds onto a template structure, mazindol (1). These CoMFA models yielded significant cross-validated r(2)(cv) values. Inclusion of additional descriptors did not improve the significance of the CoMFA models; thus, steric and electrostatic fields are the relevant descriptors for these compounds. The best QSAR model was selected on the basis of the predictive ability of the activity on the external test set of compounds. The analysis of coefficient contour maps provided further insight into the binding interactions of mazindol analogues with the DAT. The aromatic rings C and D are involved in hydrophobic interactions in which ring D may bind in a large hydrophobic groove. The relative orientation of these two rings is also important for high binding affinity to the DAT.

  20. Matching experimental and three dimensional numerical models for structural vibration problems with uncertainties

    Science.gov (United States)

    Langer, P.; Sepahvand, K.; Guist, C.; Bär, J.; Peplow, A.; Marburg, S.

    2018-03-01

    The simulation model which examines the dynamic behavior of real structures needs to address the impact of uncertainty in both geometry and material parameters. This article investigates three-dimensional finite element models for structural dynamics problems with respect to both model and parameter uncertainties. The parameter uncertainties are determined via laboratory measurements on several beam-like samples. The parameters are then considered as random variables to the finite element model for exploring the uncertainty effects on the quality of the model outputs, i.e. natural frequencies. The accuracy of the output predictions from the model is compared with the experimental results. To this end, the non-contact experimental modal analysis is conducted to identify the natural frequency of the samples. The results show a good agreement compared with experimental data. Furthermore, it is demonstrated that geometrical uncertainties have more influence on the natural frequencies compared to material parameters and material uncertainties are about two times higher than geometrical uncertainties. This gives valuable insights for improving the finite element model due to various parameter ranges required in a modeling process involving uncertainty.

  1. Three-dimensional structure of lectin from Dioclea violacea and comparative vasorelaxant effects with Dioclea rostrata

    Energy Technology Data Exchange (ETDEWEB)

    Rocha, B.A.M.; Bezerra, M.J.B.; Bezerra, G.A.; Alencar, K.L.L.; Nascimento, K.S.; Naganao, C.S.; Sampaio, A.H.; Cavada, B.S. [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil); Delatorre, P. [Universidade Federal da Paraiba (UFPB), Joao Pessoa, PB (Brazil); Rodrigues, N.V.; Pires, A.F.; Assreuy, A.M.S. [Universidade Estadual do Ceara (UECE), Fortaleza, CE (Brazil); Marins, J.L. [Universidade Federal de Pelotas (UFPel), Pelotas, RS (Brazil)

    2012-07-01

    Full text: Lectins are a structural heterogeneous group of proteins possessing at least one non-catalytic domain that binds reversibly to a specific mono or oligosaccharide. Diocleinae lectins exhibit glucose/mannose monosaccharide binding specificity and studies of their chemical and physicochemical properties revealed a high degree of identity in their amino acid sequences and three dimensional structures. This study investigated structural/functional relationships between lectins obtained from Dioclea violacea (DVL) and Dioclea rostrata (DRL). The purified lectin (DVL) was solubilized in 20 mM Tris-HCl pH 7.6 with 5 mM CaCl{sub 2} and MnCl{sub 2} buffer and incubated during one hour before the crystallization experiments with the ligand X-Man (5-bromo-4-chloro-3-indolyl-{alpha}-D-mannose) at 3 mM. Crystals of DVL grew in condition 33 of Crystal Screen I (4M Sodium formate) and belong to the orthorhombic space group I222. The structure of DVL at 2.6 resolution was obtained by molecular replacement using the coordinates of DRL (PDB code 2ZBJ), after the last refinement the structure presented R factor of 0.23 and R free of 0.27. The crystal structures reveal differences between them and could be related to relaxant activity. The conformation of residues HIS51, HIS131 and GLU205 and others positioned at CRD lead to different lectin binding activities. In fact, the pocket in DVL is small and deep and promotes weak interaction with carbohydrates, while DRL pocket is large and shallow, allowing strong interaction between CRD and sugars. This can explain why DVL and DRL elicited different degrees of aorta relaxation showing maximal effects of 43 % and 96 %, respectively. (author)

  2. Three-dimensional structures of human phospholipase A2 from pancreas and synovial fluid by model building

    DEFF Research Database (Denmark)

    Christensen, I T; Jørgensen, Flemming Steen; Svensson, L A

    1993-01-01

    Three-dimensional structures of the enzyme phospholipase A2 (PLA2) from human pancreas and from human synovial fluid were constructed by model building based on high-resolution X-ray crystallographic structures and homology considerations. The structure of the human pancreatic PLA2 was based...

  3. Three-dimensional intracellular structure of a whole rice mesophyll cell observed with FIB-SEM.

    Science.gov (United States)

    Oi, Takao; Enomoto, Sakiko; Nakao, Tomoyo; Arai, Shigeo; Yamane, Koji; Taniguchi, Mitsutaka

    2017-07-01

    Ultrathin sections of rice leaf blades observed two-dimensionally using a transmission electron microscope (TEM) show that the chlorenchyma is composed of lobed mesophyll cells, with intricate cell boundaries, and lined with chloroplasts. The lobed cell shape and chloroplast positioning are believed to enhance the area available for the gas exchange surface for photosynthesis in rice leaves. However, a cell image revealing the three-dimensional (3-D) ultrastructure of rice mesophyll cells has not been visualized. In this study, a whole rice mesophyll cell was observed using a focused ion beam scanning electron microscope (FIB-SEM), which provides many serial sections automatically, rapidly and correctly, thereby enabling 3-D cell structure reconstruction. Rice leaf blades were fixed chemically using the method for conventional TEM observation, embedded in resin and subsequently set in the FIB-SEM chamber. Specimen blocks were sectioned transversely using the FIB, and block-face images were captured using the SEM. The sectioning and imaging were repeated overnight for 200-500 slices (each 50 nm thick). The resultant large-volume image stacks ( x = 25 μm, y = 25 μm, z = 10-25 μm) contained one or two whole mesophyll cells. The 3-D models of whole mesophyll cells were reconstructed using image processing software. The reconstructed cell models were discoid shaped with several lobes around the cell periphery. The cell shape increased the surface area, and the ratio of surface area to volume was twice that of a cylinder having the same volume. The chloroplasts occupied half the cell volume and spread as sheets along the cell lobes, covering most of the inner cell surface, with adjacent chloroplasts in close contact with each other. Cellular and sub-cellular ultrastructures of a whole mesophyll cell in a rice leaf blade are demonstrated three-dimensionally using a FIB-SEM. The 3-D models and numerical information support the hypothesis that rice mesophyll

  4. Non-Linear Three Dimensional Finite Elements for Composite Concrete Structures

    Directory of Open Access Journals (Sweden)

    O. Kohnehpooshi

    Full Text Available Abstract The current investigation focused on the development of effective and suitable modelling of reinforced concrete component with and without strengthening. The modelling includes physical and constitutive models. New interface elements have been developed, while modified constitutive law have been applied and new computational algorithm is utilised. The new elements are the Truss-link element to model the interaction between concrete and reinforcement bars, the interface element between two plate bending elements and the interface element to represent the interfacial behaviour between FRP, steel plates and concrete. Nonlinear finite-element (FE codes were developed with pre-processing. The programme was written using FORTRAN language. The accuracy and efficiency of the finite element programme were achieved by analyzing several examples from the literature. The application of the 3D FE code was further enhanced by carrying out the numerical analysis of the three dimensional finite element analysis of FRP strengthened RC beams, as well as the 3D non-linear finite element analysis of girder bridge. Acceptable distributions of slip, deflection, stresses in the concrete and FRP plate have also been found. These results show that the new elements are effective and appropriate to be used for structural component modelling.

  5. Beacon: A three-dimensional structural analysis code for bowing history of fast breeder reactor cores

    International Nuclear Information System (INIS)

    Miki, K.

    1979-01-01

    The core elements of an LMFBR are bowed due to radial gradients of both temperature and neutron flux in the core. Since all hexagonal elements are multiply supported by adjacent elements or the restraint system, restraint forces and bending stresses are induced. In turn, these forces and stresses are relaxed by irradiation enhanced creep of the material. The analysis of the core bowing behavior requires a three-dimensional consideration of the mechanical interactions among the core elements, because the core consists of different kinds of elements and of fuel assemblies with various burnup histories. A new computational code BEACON has been developed for analyzing the bowing behavior of an LMFBR's core in three dimensions. To evaluate mechanical interactions among core elements, the code uses the analytical method of the earlier SHADOW code. BEACON analyzes the mechanical interactions in three directions, which form angles of 60 0 with one another. BEACON is applied to the 60 0 sector of a typical LMFBR's core for analyzing the bowing history during one equilibrium cycle. 120 core elements are treated, assuming the boundary condition of rotational symmetry. The application confirms that the code can be an effective tool for parametric studies as well as for detailed structural analysis of LMFBR's core. (orig.)

  6. Three-dimensional structure of the two-peptide bacteriocin plantaricin JK.

    Science.gov (United States)

    Rogne, Per; Haugen, Christofer; Fimland, Gunnar; Nissen-Meyer, Jon; Kristiansen, Per Eugen

    2009-09-01

    The three-dimensional structures of the two peptides, PlnJ and PlnK, that constitutes the two-peptide bacteriocin plantaricin JK have been solved in water/TFE and water/DPC-micellar solutions using nuclear magnetic resonance (NMR) spectroscopy. PlnJ, a 25 residue peptide, has an N-terminal amphiphilic alpha-helix between Trp-3 and Tyr-15. The 32 residues long PlnK forms a central amphiphilic alpha-helix between Gly-9 and Leu-24. Measurements of the effect on anti-microbial activity of single glycine replacements in PlnJ and PlnK show that Gly-13 and Gly-17 in both peptides are very sensitive, giving more than a 100-fold reduction in activity when large residues replace glycine. In variants where other glycine residues, Gly-20 in PlnJ and Gly-7, Gly-9, Gly-24 and Gly-25 in PlnK, were replaced, the activity was reduced less than 10-fold. It is proposed that the detrimental effect on activity when exchanging Gly-13 and Gly-17 in PlnJ and PlnK is a result of reduced ability of the two peptides to interact through the GxxxG-motifs constituting Gly-13 and Gly-17.

  7. Altimetric signal and three-dimensional structure of the sea in the Channel of Sicily

    Science.gov (United States)

    Nardelli, Bruno Buongiorno; Santoleri, Rosalia; Iudicone, Daniele; Zoffoli, Simona; Marullo, Salvatore

    1999-09-01

    The 1996 Altimeter/Synoptic Mesoscale Plancton Experiment (ALT/SYMPLEX) was specifically designed to perform in situ measurements simultaneous with the passage of TOPEX/POSEIDON (T/P) and ERS 2 over selected tracks in the central and eastern Sicily Channel. This experiment made it possible to have, for the first time, a validation of altimetry with in situ data over the Mediterranean, where weak dynamics results in a modest sea elevation, rarely exceeding 10 cm. Historical infrared and altimetric satellite data were first analyzed in order to study the variability of the circulation in the area. The comparative and integrative analysis of simultaneous satellite data and in situ measurements permitted investigation of the relation between the altimeter-derived surface topography and the three-dimensional structure of the sea. The Pearson correlation coefficients between altimeter data and dynamic heights along track resulted to be 0.72-0.89 (T/P) and 0.88 (ERS 2) when using conventional repeat track analysis. For T/P, a correlation value of 0.87 was found for time differences computed basing on a collinear analysis technique. This analysis also led to the identification of a strong barotropic component of the velocity field located near the Sicilian continental shelf, where it is responsible for approximately 60% of the signal.

  8. Universal structure conversion method for organic molecules: From atomic connectivity to three-dimensional geometry

    International Nuclear Information System (INIS)

    Kim, Yeon Joon; Kim, Woo Youn

    2015-01-01

    We present a powerful method for the conversion of molecular structures from atomic connectivity to bond orders to three-dimensional (3D) geometries. There are a number of bond orders and 3D geometries corresponding to a given atomic connectivity. To uniquely determine an energetically more favorable one among them, we use general chemical rules without invoking any empirical parameter, which makes our method valid for any organic molecule. Specifically, we first assign a proper bond order to each atomic pair in the atomic connectivity so as to maximize their sum and the result is converted to a SMILES notation using graph theory. The corresponding 3D geometry is then obtained using force field or ab initio calculations. This method successfully reproduced the bond order matrices and 3D geometries of 10 000 molecules randomly sampled from the PubChem database with high success rates of near 100% except a few exceptional cases. As an application, we demonstrate that it can be used to search for molecular isomers efficiently

  9. Three-dimensional structure of the bacterial protein-translocation complex SecYEG.

    Science.gov (United States)

    Breyton, Cécile; Haase, Winfried; Rapoport, Tom A; Kühlbrandt, Werner; Collinson, Ian

    2002-08-08

    Transport and membrane integration of polypeptides is carried out by specific protein complexes in the membranes of all living cells. The Sec transport path provides an essential and ubiquitous route for protein translocation. In the bacterial cytoplasmic membrane, the channel is formed by oligomers of a heterotrimeric membrane protein complex consisting of subunits SecY, SecE and SecG. In the endoplasmic reticulum membrane, the channel is formed from the related Sec61 complex. Here we report the structure of the Escherichia coli SecYEG assembly at an in-plane resolution of 8 A. The three-dimensional map, calculated from two-dimensional SecYEG crystals, reveals a sandwich of two membranes interacting through the extensive cytoplasmic domains. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. In the centre of the dimer we observe a 16 x 25 A cavity closed on the periplasmic side by two highly tilted transmembrane helices. This may represent the closed state of the protein-conducting channel.

  10. Structural dynamic modeling for rotating blades using three dimensional finite elements

    Energy Technology Data Exchange (ETDEWEB)

    Kee, Young Jung; Shin, Sang Joon [Seoul National University, Seoul (Korea, Republic of)

    2015-04-15

    A precise analysis model was developed in this paper to investigate the dynamic characteristics of rotating composite blades. An eighteen-node solid-shell finite element was used to model the blade structures. This study is focused on geometrically nonlinear problems, because the material is assumed linear elastic. Incremental total Lagrangian approach was adopted to allow estimations on arbitrarily large rotations and displacements. The equations of motion for the finite element model were derived by using Hamilton's principle, and the resulting nonlinear equilibrium equations were solved by applying Newton-Raphson method combined with load control. A modified stress-strain relation was adopted to avoid the transverse shear locking problem, and fairly reliable results were obtained with no sign of locking phenomenon. The obtained numerical results were compared to several benchmark problems, and the results show a good correlation with the experimental data and other finite element analysis results. The vibration characteristics of shell- and beam-type blades were investigated. For shell-type blades, the dynamic characteristics may be significantly influenced by blade curvature, pre-twist, and geometric nonlinearity. For beam-type blades, one-dimensional beam and three-dimensional solid models offer comparable predictions for the straight and large aspect ratio blade. As blade aspect ratio decreases, considerable differences appear in the bending and torsion modes. The tip sweep angle tends to decrease the flap bending frequencies, but the torsion frequency increases with the tip sweep angle.

  11. Structural dynamic modeling for rotating blades using three dimensional finite elements

    International Nuclear Information System (INIS)

    Kee, Young Jung; Shin, Sang Joon

    2015-01-01

    A precise analysis model was developed in this paper to investigate the dynamic characteristics of rotating composite blades. An eighteen-node solid-shell finite element was used to model the blade structures. This study is focused on geometrically nonlinear problems, because the material is assumed linear elastic. Incremental total Lagrangian approach was adopted to allow estimations on arbitrarily large rotations and displacements. The equations of motion for the finite element model were derived by using Hamilton's principle, and the resulting nonlinear equilibrium equations were solved by applying Newton-Raphson method combined with load control. A modified stress-strain relation was adopted to avoid the transverse shear locking problem, and fairly reliable results were obtained with no sign of locking phenomenon. The obtained numerical results were compared to several benchmark problems, and the results show a good correlation with the experimental data and other finite element analysis results. The vibration characteristics of shell- and beam-type blades were investigated. For shell-type blades, the dynamic characteristics may be significantly influenced by blade curvature, pre-twist, and geometric nonlinearity. For beam-type blades, one-dimensional beam and three-dimensional solid models offer comparable predictions for the straight and large aspect ratio blade. As blade aspect ratio decreases, considerable differences appear in the bending and torsion modes. The tip sweep angle tends to decrease the flap bending frequencies, but the torsion frequency increases with the tip sweep angle.

  12. A low-profile three-dimensional neural probe array using a silicon lead transfer structure

    Science.gov (United States)

    Cheng, Ming-Yuan; Je, Minkyu; Tan, Kwan Ling; Lim Tan, Ee; Lim, Ruiqi; Yao, Lei; Li, Peng; Park, Woo-Tae; Phua, Eric Jian Rong; Lip Gan, Chee; Yu, Aibin

    2013-09-01

    This paper presents a microassembly method for low-profile three-dimensional probe arrays for neural prosthesis and neuroscience applications. A silicon (Si) lead transfer structure, Si interposer, is employed to form electrical connections between two orthogonal planes—the two dimensional probes and the dummy application-specific integrated circuit (ASIC) chip. In order to hold the probe array and facilitate the alignment of probes during assembly, a Si platform is designed to have through-substrate slots for the insertion of probes and cavities for holding the Si interposers. The electrical interconnections between the probes and the dummy ASIC chip are formed by solder reflow, resulting in greatly improved throughput in the proposed assembly method. Moreover, since the backbone of the probe can be embedded inside the cavity of the Si platform, the profile of the probe array above the cortical surface can be controlled within 750 µm. This low-profile allows the probe array not to touch the skull after it is implanted on the brain. The impedance of the assembled probe is also measured and discussed.

  13. Three-dimensional structural representation of the sleep-wake adaptability.

    Science.gov (United States)

    Putilov, Arcady A

    2016-01-01

    Various characteristics of the sleep-wake cycle can determine the success or failure of individual adjustment to certain temporal conditions of the today's society. However, it remains to be explored how many such characteristics can be self-assessed and how they are inter-related one to another. The aim of the present report was to apply a three-dimensional structural representation of the sleep-wake adaptability in the form of "rugby cake" (scalene or triaxial ellipsoid) to explain the results of analysis of the pattern of correlations of the responses to the initial 320-item list of a new inventory with scores on the six scales designed for multidimensional self-assessment of the sleep-wake adaptability (Morning and Evening Lateness, Anytime and Nighttime Sleepability, and Anytime and Daytime Wakeability). The results obtained for sample consisting of 149 respondents were confirmed by the results of similar analysis of earlier collected responses of 139 respondents to the same list of 320 items and responses of 1213 respondents to the 72 items of one of the earlier established questionnaire tools. Empirical evidence was provided in support of the model-driven prediction of the possibility to identify items linked to as many as 36 narrow (6 core and 30 mixed) adaptabilities of the sleep-wake cycle. The results enabled the selection of 168 items for self-assessment of all these adaptabilities predicted by the rugby cake model.

  14. A Forest Structure Dynamics Model for Driving Three-Dimensional Canopy Radiative Transfer Simulations

    Science.gov (United States)

    Yang, W.; Kobayashi, H.; Kondoh, A.

    2016-12-01

    Three-dimensional (3-D) Monte Carlo (MC)-based radiative transfer (RT) models can simulate highly detailed forest environments, and have produced simulations that agree well with observations; thus, they are routinely used for benchmarking in intercomparisons of RT models. However, MC-based RT models have not been widely applied to the development of inversion algorithms for generating global remote sensing products of forests, due mainly to the difficulties in obtaining realistic forest structures for a variety of forest biomes. In this study, we developed a Forest Structure Dynamics Model (FSDM) to facilitate the application of MC-based RT models to global forests. In this model, the tree architectures are determined based on allometric equations, and the tree locations within a study domain are determined by statistical distributions. The performance of the FSDM was evaluated using field measurements of forest landscapes at two sites located at Järvselja, Estonia and the Poker Flat Research Range (PFRR), USA, respectively. The bidirectional reflectance factor (BRF) for the two study sites was simulated by an MC-based RT model, based on the measured forest stands and modeled stands from the FSDM. A comparison of the results demonstrated that the simulated BRF based on the measured forest stands agreed well with the simulated BRF based on the modeled stands from the FSDM for the two study sites. The applicability of the FSDM to a leaf area index (LAI) retrieval algorithm was also verified using simulations from the MC-based RT model. The results indicate that the FSDM can provide reasonable forest structures to drive 3-D canopy RT models, with no loss of simulation accuracy. When combined with several existing field data sets and satellite products, the FSDM can be used to generate a typical stand structure database for global forest biomes.

  15. Potentiality of Using Vertical and Three-Dimensional Isolation Systems in Nuclear Structures

    Directory of Open Access Journals (Sweden)

    Zhiguang Zhou

    2016-10-01

    Full Text Available Although the horizontal component of an earthquake response can be significantly reduced through the use of conventional seismic isolators, the vertical component of excitation is still transmitted directly into the structure. Records from instrumented structures, and some recent tests and analyses have actually seen increases in vertical responses in base isolated structures under the combined effects of horizontal and vertical ground motions. This issue becomes a great concern to facilities such as a Nuclear Power Plants (NPP, with specialized equipment and machinery that is not only expensive, but critical to safe operation. As such, there is considerable interest worldwide in vertical and three-dimensional (3D isolation systems. This paper examines several vertical and 3D isolation systems that have been proposed and their potential application to modern nuclear facilities. In particular, a series of case study analyses of a modern NPP model are performed to examine the benefits and challenges associated with 3D isolation compared with horizontal isolation. It was found that compared with the general horizontal isolators, isolators that have vertical frequencies of no more than 3 Hz can effectively reduce the vertical in-structure responses for the studied NPP model. Among the studied cases, the case that has a vertical isolation frequency of 3 Hz is the one that can keep the horizontal period of the isolators as the first period while having the most flexible vertical isolator properties. When the vertical frequency of isolators reduces to 1 Hz, the rocking effect is obvious and rocking restraining devices are necessary.

  16. Versatile morphometric analysis and visualization of the three-dimensional structure of neurons.

    Science.gov (United States)

    Aguiar, Paulo; Sousa, Mafalda; Szucs, Peter

    2013-10-01

    The computational properties of a neuron are intimately related to its morphology. However, unlike electrophysiological properties, it is not straightforward to collapse the complexity of the three-dimensional (3D) structure into a small set of measurements accurately describing the structural properties. This strong limitation leads to the fact that many studies involving morphology related questions often rely solely on empirical analysis and qualitative description. It is possible however to acquire hierarchical lists of positions and diameters of points describing the spatial structure of the neuron. While there is a number of both commercially and freely available solutions to import and analyze this data, few are extendable in the sense of providing the possibility to define novel morphometric measurements in an easy to use programming environment. Fewer are capable of performing morphometric analysis where the output is defined over the topology of the neuron, which naturally requires powerful visualization tools. The computer application presented here, Py3DN, is an open-source solution providing novel tools to analyze and visualize 3D data collected with the widely used Neurolucida (MBF) system. It allows the construction of mathematical representations of neuronal topology, detailed visualization and the possibility to define non-standard morphometric analysis on the neuronal structures. Above all, it provides a flexible and extendable environment where new types of analyses can be easily set up allowing a high degree of freedom to formulate and test new hypotheses. The application was developed in Python and uses Blender (open-source software) to produce detailed 3D data representations.

  17. Three-dimensional structure of wind turbine wakes as measured by scanning lidar

    Science.gov (United States)

    Bodini, Nicola; Zardi, Dino; Lundquist, Julie K.

    2017-08-01

    The lower wind speeds and increased turbulence that are characteristic of turbine wakes have considerable consequences on large wind farms: turbines located downwind generate less power and experience increased turbulent loads. The structures of wakes and their downwind impacts are sensitive to wind speed and atmospheric variability. Wake characterization can provide important insights for turbine layout optimization in view of decreasing the cost of wind energy. The CWEX-13 field campaign, which took place between June and September 2013 in a wind farm in Iowa, was designed to explore the interaction of multiple wakes in a range of atmospheric stability conditions. Based on lidar wind measurements, we extend, present, and apply a quantitative algorithm to assess wake parameters such as the velocity deficits, the size of the wake boundaries, and the location of the wake centerlines. We focus on wakes from a row of four turbines at the leading edge of the wind farm to explore variations between wakes from the edge of the row (outer wakes) and those from turbines in the center of the row (inner wakes). Using multiple horizontal scans at different elevations, a three-dimensional structure of wakes from the row of turbines can be created. Wakes erode very quickly during unstable conditions and can in fact be detected primarily in stable conditions in the conditions measured here. During stable conditions, important differences emerge between the wakes of inner turbines and the wakes of outer turbines. Further, the strong wind veer associated with stable conditions results in a stretching of the wake structures, and this stretching manifests differently for inner and outer wakes. These insights can be incorporated into low-order wake models for wind farm layout optimization or for wind power forecasting.

  18. Characteristics of sandwich-type structural elements built of advanced composite materials from three dimensional fabrics

    Directory of Open Access Journals (Sweden)

    Castejón, L.

    1997-12-01

    Full Text Available Sandwich-type structures have proved to be alternatives of great success for several fields of application, and specially in the building sector. This is due to their outstanding properties of .specific rigidity and strength against bending loads and other range of advantages like fatigue and impact resistance, attainment of flat and smooth surfaces, high electric and thermal insulation, design versatility and some others. However, traditional sandwich structures present problems like their tendency towards delamination, stress concentrations in bores or screwed Joints, and pre resistance. These problems are alleviated thanks to the use of new sandwich structures built using three dimensional structures of advanced composite materials, maintaining the present advantages for more traditional sandwich structures. At this rate, these new structures can be applied in several areas where conventional sandwich structures used to be like walls, partitions, floor and ceiling structures, domes, vaults and dwellings, but with greater success.

    Las estructuras tipo sándwich han demostrado ser alternativas de gran éxito para diversos campos de aplicación y, en concreto, en el sector de la construcción, listo es gracias a sus excelentes propiedades de rigidez y resistencia específica frente a cargas de flexión y otra larga lista de ventajas, a la que pertenecen, por ejemplo, su buena resistencia a fatiga, resistencia al impacto, obtención de superficies lisas y suaves, elevado aislamiento térmico y eléctrico, versatilidad de diseño y otras. Sin embargo, las estructuras sándwich, tradicionales presentan una problemática consistente en su tendencia a la delaminación, concentraciones de tensiones ¿aparecidas ante la existencia de agujeros o uniones atornilladas y resistencia al fuego. Estos problemas son pifiados gracias a la aplicación de estructuras novedosas tipo sándwich, construidas a partir de tejidos tridimensionales de materiales

  19. Theoretical assessment of optical resolution enhancement and background fluorescence reduction by three-dimensional nonlinear structured illumination microscopy using stimulated emission depletion

    Science.gov (United States)

    Dake, Fumihiro

    2016-08-01

    Three-dimensional structured illumination microscopy (SIM) enlarges frequency cutoff laterally and axially by a factor of two, compared with conventional microscopy. However, its optical resolution is still fundamentally limited. It is necessary to introduce nonlinearity to enlarge frequency cutoff further. We propose three-dimensional nonlinear structured illumination microscopy based on stimulated emission depletion (STED) effect, which has a structured excitation pattern and a structured STED pattern, and both three-dimensional illumination patterns have the same lateral pitch and orientation. Theoretical analysis showed that nonlinearity induced by STED effect, which causes harmonics and contributes to enlarging frequency cutoff, depends on the phase difference between two structured illuminations and that the phase difference of π is the most efficient to increase nonlinearity. We also found that undesirable background fluorescence, which degenerates the contrast of structured pattern and limits the ability of SIM, can be reduced by our method. These results revealed that optical resolution improvement and background fluorescence reduction would be compatible. The feasibility study showed that our method will be realized with commercially available laser, having 3.5 times larger frequency cutoff compared with conventional microscopy.

  20. A three-dimensional view of the thermal structure in a super-penumbral canopy

    Energy Technology Data Exchange (ETDEWEB)

    Beck, C. [National Solar Observatory (NSO), 3010 Coronal Loop, Sunspot, NM 88349 (United States); Choudhary, D. P. [Department of Physics and Astronomy, California State University, Northridge (CSUN), CA 91330-8268 (United States); Rezaei, R., E-mail: cbeck@nso.edu [Kiepenheuer Institut für Sonnenphysik (KIS), Schöneckstrasse 6, D-79104 Freiburg (Germany)

    2014-06-20

    We investigate the three-dimensional (3D) thermal topology in a super-penumbral canopy of an active region (AR). We derive temperature stratifications in the AR by an inversion of the Ca II IR line at 854.2 nm, assuming local thermal equilibrium. We find that about half of the radially oriented fibrils in the super-penumbral canopy form short, low-lying (h < 1 Mm) loops in the 3D temperature cube. These closed loops connect from bright grains in or close to the penumbra to the photosphere a few Mms away from the sunspot. The other half of the fibrils monotonically rise with distance from the sunspot. Many of the fibrils show a central dark core and two lateral brightenings in line-core intensity images. The corresponding velocity image shows fibrils that are as wide as the fibrils seen in intensity without a lateral substructure. Additionally, we study a feature from a different class of structures without prominent mass flows. Its 3D topology is formed by two parallel, closed loops that connect patches of opposite polarity. We present evidence that the inverse Evershed flow into the sunspot in the lower chromosphere is the consequence of siphon flows along short loops that connect photospheric foot points. The dark-cored structure of the chromospheric fibrils cannot have a convective origin because of their location above regular granulation. The dark core most likely results from an opacity difference between the central axis and the lateral edges caused by the significant flow speed along the fibrils.

  1. Linkage mechanisms in the vertebrate skull: Structure and function of three-dimensional, parallel transmission systems.

    Science.gov (United States)

    Olsen, Aaron M; Westneat, Mark W

    2016-12-01

    Many musculoskeletal systems, including the skulls of birds, fishes, and some lizards consist of interconnected chains of mobile skeletal elements, analogous to linkage mechanisms used in engineering. Biomechanical studies have applied linkage models to a diversity of musculoskeletal systems, with previous applications primarily focusing on two-dimensional linkage geometries, bilaterally symmetrical pairs of planar linkages, or single four-bar linkages. Here, we present new, three-dimensional (3D), parallel linkage models of the skulls of birds and fishes and use these models (available as free kinematic simulation software), to investigate structure-function relationships in these systems. This new computational framework provides an accessible and integrated workflow for exploring the evolution of structure and function in complex musculoskeletal systems. Linkage simulations show that kinematic transmission, although a suitable functional metric for linkages with single rotating input and output links, can give misleading results when applied to linkages with substantial translational components or multiple output links. To take into account both linear and rotational displacement we define force mechanical advantage for a linkage (analogous to lever mechanical advantage) and apply this metric to measure transmission efficiency in the bird cranial mechanism. For linkages with multiple, expanding output points we propose a new functional metric, expansion advantage, to measure expansion amplification and apply this metric to the buccal expansion mechanism in fishes. Using the bird cranial linkage model, we quantify the inaccuracies that result from simplifying a 3D geometry into two dimensions. We also show that by combining single-chain linkages into parallel linkages, more links can be simulated while decreasing or maintaining the same number of input parameters. This generalized framework for linkage simulation and analysis can accommodate linkages of differing

  2. Three-dimensional structure and stoichiometry of Helmintosporium victoriae190S totivirus

    International Nuclear Information System (INIS)

    Caston, Jose R.; Luque, Daniel; Trus, Benes L.; Rivas, German; Alfonso, Carlos; Gonzalez, Jose M.; Carrascosa, Jose L.; Annamalai, Padmanaban; Ghabrial, Said A.

    2006-01-01

    Most double-stranded RNA viruses have a characteristic capsid consisting of 60 asymmetric coat protein dimers in a so-called T = 2 organization, a feature probably related to their unique life cycle. These capsids organize the replicative complex(es) that is actively involved in genome transcription and replication. Available structural data indicate that their RNA-dependent RNA polymerase (RDRP) is packaged as an integral capsid component, either as a replicative complex at the pentameric vertex (as in reovirus capsids) or as a fusion protein with the coat protein (as in some totivirus). In contrast with members of the family Reoviridae, there are two well-established capsid arrangements for dsRNA fungal viruses, exemplified by the totiviruses L-A and UmV and the chrysovirus PcV. Whereas L-A and UmV have a canonical T = 2 capsid, the PcV capsid is based on a T = 1 lattice composed of 60 capsid proteins. We used cryo-electron microscopy combined with three-dimensional reconstruction techniques and hydrodynamic analysis to determine the structure at 13.8 A resolution of Helminthosporium victoriae 190S virus (Hv190SV), a totivirus isolated from a filamentous fungus. The Hv190SV capsid has a smooth surface and is based on a T = 2 lattice with 60 equivalent dimers. Unlike the RDRP of some other totiviruses, which are expressed as a capsid protein-RDRP fusion protein, the Hv190SV RDRP is incorporated into the capsid as a separate, nonfused protein, free or non-covalently associated to the capsid interior

  3. Dacron graft as replacement to dissected aorta: A three-dimensional fluid-structure-interaction analysis.

    Science.gov (United States)

    Jayendiran, R; Nour, B M; Ruimi, A

    2018-02-01

    Aortic dissection (AD) is a serious medical condition characterized by a tear in the intima, the inner layer of the aortic walls. In such occurrence, blood is being diverted to the media (middle) layer and may result in patient death if not quickly attended. In the case where the diseased portion of the aorta needs to be replaced, one common surgical technique is to use a graft made of Dacron, a synthetic fabric. We investigate the response of a composite human aortic segment-Dacron graft structure subjected to blood flow using the three-dimensional fluid-structure-interaction (FSI) capability in Abaqus. We obtain stress and strain profiles in each of the three layers of the aortic walls as well as in the Dacron graft. Results are compared when elastic and hyperelastic models are used and when isotropy vs. anisotropy is assumed. The more complex case (hyperelastic-anisotropy) is represented by the Holzapfel-Gasser-Ogden (HGO) model which also accounts for the orientation of the fibers present in the tissues. The fluid flow is taken as Newtonian, incompressible, pulsatile and turbulent. The simulation show that for all the cases, the von Mises stress distribution at aorta-Dacron interface is well below the ultimate strength of the aorta. No significant change in radial displacement at the interface of the two materials due to blood flow is observed. Computation cost is also addressed and results show that the hyperelastic-anisotropic model takes about three times longer to run than the elastic isotropic case. Trade-off between accuracy and computational cost has to be weighted. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Impact of data resolution on three-dimensional structure inference methods.

    Science.gov (United States)

    Park, Jincheol; Lin, Shili

    2016-02-06

    Assays that are capable of detecting genome-wide chromatin interactions have produced massive amount of data and led to great understanding of the chromosomal three-dimensional (3D) structure. As technology becomes more sophisticated, higher-and-higher resolution data are being produced, going from the initial 1 Megabases (Mb) resolution to the current 10 Kilobases (Kb) or even 1 Kb resolution. The availability of genome-wide interaction data necessitates development of analytical methods to recover the underlying 3D spatial chromatin structure, but challenges abound. Most of the methods were proposed for analyzing data at low resolution (1 Mb). Their behaviors are thus unknown for higher resolution data. For such data, one of the key features is the high proportion of "0" contact counts among all available data, in other words, the excess of zeros. To address the issue of excess of zeros, in this paper, we propose a truncated Random effect EXpression (tREX) method that can handle data at various resolutions. We then assess the performance of tREX and a number of leading existing methods for recovering the underlying chromatin 3D structure. This was accomplished by creating in-silico data to mimic multiple levels of resolution and submit the methods to a "stress test". Finally, we applied tREX and the comparison methods to a Hi-C dataset for which FISH measurements are available to evaluate estimation accuracy. The proposed tREX method achieves consistently good performance in all 30 simulated settings considered. It is not only robust to resolution level and underlying parameters, but also insensitive to model misspecification. This conclusion is based on observations made in terms of 3D structure estimation accuracy and preservation of topologically associated domains. Application of the methods to the human lymphoblastoid cell line data on chromosomes 14 and 22 further substantiates the superior performance of tREX: the constructed 3D structure from tREX is

  5. Three-dimensional P velocity structure of the crust and upper mantle under Beijing region

    Energy Technology Data Exchange (ETDEWEB)

    Quan, A.; Liu, F.; Sun, Y.

    1980-04-01

    By use of the teleseismic P arrival times at 15 stations of the Beijing network for 120 events distributed over various azimuths, we studied the three-dimensional P velocity structure under the Beijing region. In calculating the theoretic travel time, we adopted the source parameters given in BISC, and used the J-B model as the standard model of earth. On inversion, we adopted singular value decomposition as a generalized inversion package, which can be used for solving very large over-determined systems of equations Gm = t without resorting to normal equations G/sup T/Gm = G/sup T/t. The results are that within the crust and upper mantle under the Beijing region there are clear lateral differences. In the results obtained by use of data from 1972 to 1975, it can be seen that there are three different zones of P-velocity. In the southeast Beijing region, P velocity is lower than that of the normal model by 10 to 14% within the crust, and by 8 to 9% within the upper mantle. The northwest Beijing region is a higher-velocity zone, within which the average P-velocity is faster than that of the normal model by about 9%. It disappears after entering into the upper mantle. The central part of this region is a normal zone. On the surface, the distribution of these P velocity variations corresponds approximately to the distribution of the over-burden. But in the deeper region, the distribution of velocity variation agrees with the distribution of seismicity. It is interesting to note that the hypocenters of several major earthquakes in this region, e.g., the Sanhe-Pinggu earthquake (1679, M = 8), the Shacheng earthquake (1730, M = 6-3/4) and the Tangshan earthquake (1976, M = 7.8), are all located very close to this boundary of these P-velocity variation zones.

  6. Three-Dimensional Elastomeric Scaffolds Designed with Cardiac-Mimetic Structural and Mechanical Features

    Science.gov (United States)

    Neal, Rebekah A.; Jean, Aurélie; Park, Hyoungshin; Wu, Patrick B.; Hsiao, James; Engelmayr, George C.; Langer, Robert

    2013-01-01

    Tissue-engineered constructs, at the interface of material science, biology, engineering, and medicine, have the capacity to improve outcomes for cardiac patients by providing living cells and degradable biomaterials that can regenerate the native myocardium. With an ultimate goal of both delivering cells and providing mechanical support to the healing heart, we designed three-dimensional (3D) elastomeric scaffolds with (1) stiffnesses and anisotropy mimicking explanted myocardial specimens as predicted by finite-element (FE) modeling, (2) systematically varied combinations of rectangular pore pattern, pore aspect ratio, and strut width, and (3) structural features approaching tissue scale. Based on predicted mechanical properties, three scaffold designs were selected from eight candidates for fabrication from poly(glycerol sebacate) by micromolding from silicon wafers. Large 20×20 mm scaffolds with high aspect ratio features (5:1 strut height:strut width) were reproducibly cast, cured, and demolded at a relatively high throughput. Empirically measured mechanical properties demonstrated that scaffolds were cardiac mimetic and validated FE model predictions. Two-layered scaffolds providing fully interconnected pore networks were fabricated by layer-by-layer assembly. C2C12 myoblasts cultured on one-layered scaffolds exhibited specific patterns of cell elongation and interconnectivity that appeared to be guided by the scaffold pore pattern. Neonatal rat heart cells cultured on two-layered scaffolds for 1 week were contractile, both spontaneously and in response to electrical stimulation, and expressed sarcomeric α-actinin, a cardiac biomarker. This work not only demonstrated several scaffold designs that promoted functional assembly of rat heart cells, but also provided the foundation for further computational and empirical investigations of 3D elastomeric scaffolds for cardiac tissue engineering. PMID:23190320

  7. Fluid-structure interaction of three-dimensional magnetic artificial cilia

    NARCIS (Netherlands)

    Khaderi, S. N.; Onck, P. R.

    2012-01-01

    A numerical model is developed to analyse the interaction of artificial cilia with the surrounding fluid in a three-dimensional setting in the limit of vanishing fluid inertia forces. The cilia are modelled using finite shell elements and the fluid is modelled using a boundary element approach. The

  8. Three-dimensional neuroimaging

    International Nuclear Information System (INIS)

    Toga, A.W.

    1990-01-01

    This book reports on new neuroimaging technologies that are revolutionizing the study of the brain be enabling investigators to visualize its structure and entire pattern of functional activity in three dimensions. The book provides a theoretical and practical explanation of the new science of creating three-dimensional computer images of the brain. The coverage includes a review of the technology and methodology of neuroimaging, the instrumentation and procedures, issues of quantification, analytic protocols, and descriptions of neuroimaging systems. Examples are given to illustrate the use of three-dimensional enuroimaging to quantitate spatial measurements, perform analysis of autoradiographic and histological studies, and study the relationship between brain structure and function

  9. Three dimensional flow structures and turbulence distribution in an urban environment

    Science.gov (United States)

    Monnier, Bruno

    Understanding and controlling the dispersion of pollutants and contaminants in urban areas has become a major focus recently. Field measurements, numerical studies, and wind tunnel experiments have increased in number. Specifically, there is a growing need for a spatio-temporal description of such complex flow fields under well-controlled conditions, typically obtained in wind tunnel experiments. The reduced scale model of interest is a 4 by 3 array of cuboid blocks in an experimentally modeled, neutrally stratified, atmospheric boundary-layer. The use of Stereoscopic Particle Image Velocimetry (SPIV) allows for a three-dimensional description of this urban flow. A large amount of SPIV data is collected upstream and in each middle street of the urban environment allowing for a study of the flow evolution from street to street. Valuable information about the flow structures are presented along with the mechanisms responsible for contaminant transport and dispersion. The effects of small incidence angles of the incoming flow with respect to the urban array and the effects of streamwise spacing between streets on the flow characteristics are investigated. A major observation from this work is that a strong channeling effect is observed for incidence angles as small as 4.5° and is found to be comparable in strength to that observed in other investigations for much larger angles. A coupling between this channeling effect and the structures responsible for contaminant transport is revealed. An innovative method using sparse measurements to estimate the continuous temporal evolution of the dominant structures in the flow is investigated. Proper Orthogonal Decomposition is used to obtain a reduced-order representation (ROR) of the flow field. Sparse velocity measurements within the domain serve as input to measurement models that provide an estimation of the ROR of the velocity field. This ROR of the flow field could be regarded as the first that provides a temporal

  10. Pulse-Like Rupture Induced by Three-Dimensional Fault Zone Flower Structures

    KAUST Repository

    Pelties, Christian

    2014-07-04

    © 2014, Springer Basel. Faults are often embedded in low-velocity fault zones (LVFZ) caused by material damage. Previous 2D dynamic rupture simulations (Huang and Ampuero, 2011; Huang et al., 2014) showed that if the wave velocity contrast between the LVFZ and the country rock is strong enough, ruptures can behave as pulses, i.e. with local slip duration (rise time) much shorter than whole rupture duration. Local slip arrest (healing) is generated by waves reflected from the LVFZ–country rock interface. This effect is robust against a wide range of fault zone widths, absence of frictional healing, variation of initial stress conditions, attenuation, and off-fault plasticity. These numerical studies covered two-dimensional problems with fault-parallel fault zone structures. Here, we extend previous work to 3D and geometries that are more typical of natural fault zones, including complexities such as flower structures with depth-dependent velocity and thickness, and limited fault zone depth extent. This investigation requires high resolution and flexible mesh generation, which are enabled here by the high-order accurate arbitrary high-order derivatives discontinuous Galerkin method with an unstructured tetrahedral element discretization (Peltieset al., 2012). We show that the healing mechanism induced by waves reflected in the LVFZ also operates efficiently in such three-dimensional fault zone structures and that, in addition, a new healing mechanism is induced by unloading waves generated when the rupture reaches the surface. The first mechanism leads to very short rise time controlled by the LVFZ width to wave speed ratio. The second mechanism leads to generally longer, depth-increasing rise times, is also conditioned by the existence of an LVFZ, and persists at some depth below the bottom of the LVFZ. Our simulations show that the generation of slip pulses by these two mechanisms is robust to the depth extent of the LVFZ and to the position of the hypocenter

  11. Time-of-Flight Three Dimensional Neutron Diffraction in Transmission Mode for Mapping Crystal Grain Structures

    OpenAIRE

    Cereser, Alberto; Strobl, Markus; Hall, Stephen; Steuwer, Axel; Kiyanagi, Ryoji; Tremsin, Anton; Knudsen, Erik Bergbäck; Shinohara, Takenao; Willendrup, Peter; Fanta, Alice Bastos da Silva; Iyengar, Srinivasan; Larsen, Peter Mahler; Hanashima, Takayasu; Moyoshi, Taketo; Kadletz, Peter M.

    2017-01-01

    The physical properties of polycrystalline materials depend on their microstructure, which is the nano- to centimeter scale arrangement of phases and defects in their interior. Such microstructure depends on the shape, crystallographic phase and orientation, and interfacing of the grains constituting the material. This article presents a new non-destructive 3D technique to study centimeter-sized bulk samples with a spatial resolution of hundred micrometers: time-of-flight three-dimensional ne...

  12. Three-dimensional quantitative structure-activity relationships of steroid aromatase inhibitors

    Science.gov (United States)

    Oprea, Tudor I.; García, Angel E.

    1996-06-01

    Inhibition of aromatase, a cytochrome P450 that converts androgens to estrogens, is relevant in the therapeutic control of breast cancer. We investigate this inhibition using a three-dimensional quantitative structure-activity relationship (3D QSAR) method known as Comparative Molecular Field Analysis, CoMFA [Cramer III, R.D. et al., J. Am. Chem. Soc., 110 (1988) 5959]. We analyzed the data for 50 steroid inhibitors [Numazawa, M. et al., J. Med. Chem., 37 (1994) 2198, and references cited therein] assayed against androstenedione on human placental microsomes. An initial CoMFA resulted in a three-component model for log(1/Ki), with an explained variance r2 of 0.885, and a cross-validated q2 of 0.673. Chemometric studies were performed using GOLPE [Baroni, M. et al., Quant. Struct.-Act. Relatsh., 12 (1993) 9]. The CoMFA/GOLPE model is discussed in terms of robustness, predictivity, explanatory power and simplicity. After randomized exclusion of 25 or 10 compounds (repeated 25 times), the q2 for one component was 0.62 and 0.61, respectively, while r2 was 0.674. We demonstrate that the predictive r2 based on the mean activity (Ym) of the training set is misleading, while the test set Ym-based predictive r2 index gives a more accurate estimate of external predictivity. Using CoMFA, the observed differences in aromatase inhibition among C6-substituted steroids are rationalized at the atomic level. The CoMFA fields are consistent with known, potent inhibitors of aromatase, not included in the model. When positioned in the same alignment, these compounds have distinct features that overlap with the steric and electrostatic fields obtained in the CoMFA model. The presence of two hydrophobic binding pockets near the aromatase active site is discussed: a steric bulk tolerant one, common for C4, C6-alpha and C7-alpha substitutents, and a smaller one at the C6-beta region.

  13. Unmanned aerial vehicle acquisition of three-dimensional digital image correlation measurements for structural health monitoring of bridges

    Science.gov (United States)

    Reagan, Daniel; Sabato, Alessandro; Niezrecki, Christopher

    2017-04-01

    Civil engineering structures such as bridges, buildings, and tunnels continue to be used despite aging and deterioration well past their design life. In 2013, the American Society of Civil Engineers (ASCE) rated the state of the U.S. bridges as mediocre, despite the $12.8 billion USD annually invested. Traditional inspection and monitoring techniques may produce inconsistent results, are labor intensive and too time-consuming to be considered effective for large-scale monitoring. Therefore, new structural health monitoring systems must be developed that are automated, highly accurate, minimally invasive, and cost effective. Three-dimensional (3D) digital image correlation (DIC) systems possess the capability of extracting full-field strain, displacement, and geometry profiles. Furthermore, as this measurement technique is implemented within an Unmanned Aerial Vehicle (UAV) the capability to expedite the optical-based measurement process is increased as well as the infrastructure downtime being reduced. These resulting integrity maps of the structure of interest can be easily interpreted by trained personal. Within this paper, the feasibility of performing DIC measurements using a pair of cameras installed on a UAV is shown. Performance is validated with in-flight measurements. Also, full-field displacement monitoring, 3D measurement stitching, and 3D point-tracking techniques are employed in conjunction with 3D mapping and data management software. The results of these experiments show that the combination of autonomous flight with 3D DIC and other non-contact measurement systems provides a highly valuable and effective civil inspection platform.

  14. Monte Carlo modelling of photodynamic therapy treatments comparing clustered three dimensional tumour structures with homogeneous tissue structures

    Science.gov (United States)

    Campbell, C. L.; Wood, K.; Brown, C. T. A.; Moseley, H.

    2016-07-01

    We explore the effects of three dimensional (3D) tumour structures on depth dependent fluence rates, photodynamic doses (PDD) and fluorescence images through Monte Carlo radiation transfer modelling of photodynamic therapy. The aim with this work was to compare the commonly used uniform tumour densities with non-uniform densities to determine the importance of including 3D models in theoretical investigations. It was found that fractal 3D models resulted in deeper penetration on average of therapeutic radiation and higher PDD. An increase in effective treatment depth of 1 mm was observed for one of the investigated fractal structures, when comparing to the equivalent smooth model. Wide field fluorescence images were simulated, revealing information about the relationship between tumour structure and the appearance of the fluorescence intensity. Our models indicate that the 3D tumour structure strongly affects the spatial distribution of therapeutic light, the PDD and the wide field appearance of surface fluorescence images.

  15. Three-dimensional structure of the surface layer protein of Aquaspirilium serpens VHA determined by electron crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Dickson, M.R.; Downing, K.H.; Wu, W.H.; Glaeser, R.M.

    1986-09-01

    The three-dimensional structure of the protein which forms the S layer of Aquaspirilium serpens strain VHA has been determined by electron microscopy. Structures have been reconstructed to a resolution of about 1.6 nm for single-layered specimens and about 4 nm for two-layered specimens. The structure, which has hexagonal symmetry, consists of a core in the shape of a cup, with six projections arising from the rim of the cup to join adjacent subunits at the threefold symmetry axes. The model is consistent with edge views of the S layer which have been obtained in this and other work. It is now clear from this work and from three-dimensional reconstructions of other bacterial S layers that a wide diversity exists in the morphology of surface layers.

  16. Three-dimensional structure of the surface layer protein of Aquaspirillum serpens VHA determined by electron crystallography.

    Science.gov (United States)

    Dickson, M R; Downing, K H; Wu, W H; Glaeser, R M

    1986-09-01

    The three-dimensional structure of the protein which forms the S layer of Aquaspirillum serpens strain VHA has been determined by electron microscopy. Structures have been reconstructed to a resolution of about 1.6 nm for single-layered specimens and about 4 nm for two-layered specimens. The structure, which has hexagonal symmetry, consists of a core in the shape of a cup, with six projections arising from the rim of the cup to join adjacent subunits at the threefold symmetry axes. The model is consistent with edge views of the S layer which have been obtained in this and other work. It is now clear from this work and from three-dimensional reconstructions of other bacterial S layers that a wide diversity exists in the morphology of surface layers.

  17. Fully three-dimensional analysis of high-speed traintracksoil-structure dynamic interaction

    OpenAIRE

    Galvín, Pedro; Romero Ordoñez, Antonio; Domínguez Abascal, José

    2010-01-01

    In this paper, a general and fully three dimensional multi-body-finite element-boundary element model, formulated in the time domain to predict vibrations due to train passage at the vehicle, the track and the free field, is presented. The vehicle is modelled as a multi-body system and, therefore, the quasi-static and the dynamic excitation mechanisms due to train passage can be considered. The track is modelled using finite elements. The soil is considered as a homogeneous half-space by the ...

  18. Three-dimensional Investigations of Wave Overtopping on Rubble Mound Structures

    DEFF Research Database (Denmark)

    Andersen, Thomas Lykke; Burcharth, Hans F.

    2009-01-01

    To study the influence of wave obliquity and directional spreading on wave overtopping of rubble mound breakwaters a total of 736 three-dimensional model tests were carried out at Aalborg University. The results of these tests are presented and analysed in this paper yielding a new empirical...... reduction factor to describe the influence of wave obliquity and directional spreading on the average wave overtopping discharges. The study shows that perpendicularly incident, long-crested waves result in conservative values of the overtopping discharge for the tested cross-section....

  19. High power microwave source with a three dimensional printed metamaterial slow-wave structure

    International Nuclear Information System (INIS)

    French, David M.; Shiffler, Don

    2016-01-01

    For over the last decade, the concept of metamaterials has led to new approaches for considering the interaction of radiation with complex structures. However, practical manifestations of such a device operating at high power densities have proven difficult to achieve due to the resonant nature of metamaterials and the resultant high electric fields, which place severe constraints on manufacturing the slow wave structures. In this paper, we describe the first experimental manifestation of a high power microwave device utilizing a metallic slow wave structure (metamaterial-like) fabricated using additive manufacturing. The feasibility of utilizing additive manufacturing as a technique for building these relatively complicated structures has thus been demonstrated. The MW class microwave source operates in the C-band and shows frequency tunablility with electron beam voltage. The basic electromagnetic characteristics of this device, the construction using additive manufacturing, and the basic performance as a microwave oscillator are considered. Due to the tunable nature of the device, it shows promise not only as an oscillator but also as a microwave amplifier. Therefore, the dispersive characteristics and a discussion of the anticipated gain is included as it relates to an amplifier configuration.

  20. Three-dimensional dose distribution in contrast-enhanced digital mammography using Gafchromic XR-QA2 films: Feasibility study

    International Nuclear Information System (INIS)

    Hwang, Yi-Shuan; Lin, Yu-Ying; Cheung, Yun-Chung; Tsai, Hui-Yu

    2014-01-01

    This study was aimed to establish three-dimensional dose distributions for contrast-enhanced digital mammography (CEDM) using self-developed Gafchromic XR-QA2 films. Dose calibration and distribution evaluations were performed on a full-field digital mammography unit with dual energy (DE) contrast-enhanced option. Strategy for dose calibration of films in the DE mode was based on the data obtained from common target/filter/kVp combinations used clinically and the dose response model modified from Rampado's model. Dose derived from films were also verified by measured data from an ionization chamber. The average difference of dose was 8.9% in the dose range for clinical uses. Three-dimensional dose distributions were estimated using triangular acrylic phantom equipped with the mammography system. Five pieces of film sheets were separately placed between the acrylic slabs to evaluate the dose distribution at different depths. After normalizing the dose in each pixel to the maximum dose at the top-center position of the acrylic, normalized dose distribution for transverse, coronal and sagittal planes, could thus be obtained. The depth dose distribution evaluated in this study may further serve as a reference for evaluating the patient glandular dose at different depths based on the entrance exposure information. - Highlights: • CEDM techniques can enhance contrast uptake areas and suppress background tissue. • Dose for the dual-energy acquisition is about 20% higher than standard mode. • A new method is proposed to estimate the 3D dose distribution in dual-energy CEDM. • Depth of normalized dose ratio of 0.5 is less than but near 1 cm in the DE mode

  1. The crystal structures of three pyrazine-2,5-dicarb-oxamides: three-dimensional supra-molecular structures.

    Science.gov (United States)

    Cati, Dilovan S; Stoeckli-Evans, Helen

    2017-05-01

    The complete mol-ecules of the title compounds, N 2 , N 5 -bis-(pyridin-2-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (I), 3,6-dimethyl- N 2 , N 5 -bis-(pyridin-2-yl-meth-yl)pyrazine-2,5-dicarboxamide, C 20 H 20 N 6 O 2 (II), and N 2 , N 5 -bis-(pyridin-4-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (III), are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each mol-ecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7)° in (I), 75.83 (8)° in (II) and by 82.71 (6)° in (III). In the crystal of (I), mol-ecules are linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (II), mol-ecules are also linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the (10-1) plane. As in (I), the layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (III), mol-ecules are again linked by N-H⋯N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π-π inter-actions [inter-centroid distance = 3.739 (1) Å]. The sheets are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. Compound (I) crystallizes in the monoclinic space group P 2 1 / c . Another monoclinic polymorph, space group C 2/ c , has been reported on by Cockriel et al. [ Inorg. Chem. Commun. (2008), 11 , 1-4]. The mol-ecular structures of the two polymorphs are compared.

  2. Three dimensional periodic foundations for base seismic isolation

    International Nuclear Information System (INIS)

    Yan, Y; Mo, Y L; Cheng, Z; Shi, Z; Menq, F; Tang, Y

    2015-01-01

    Based on the concept of phononic crystals, periodic foundations made of periodic materials are investigated in this paper. The periodic foundations can provide low frequency band gaps, which cover the main frequency ranges of seismic waves. Therefore, the periodic foundations are able to protect the upper structures during earthquake events. In this paper, the basic theory of three dimensional periodic foundations is studied and the finite element method was used to conduct the sensitivity study. A simplified three-dimensional periodic foundation with a superstructure was tested in the field and the feasibility of three dimensional periodic foundations was proved. The test results showed that the response of the upper structure with the three dimensional periodic foundation was reduced under excitation waves with the main frequency falling in the attenuation zones. The finite element analysis results are consistent with the experimental data, indicating that three dimensional periodic foundations are a feasible way of reducing seismic vibrations. (paper)

  3. Feasibility and Accuracy of Automated Software for Transthoracic Three-Dimensional Left Ventricular Volume and Function Analysis: Comparisons with Two-Dimensional Echocardiography, Three-Dimensional Transthoracic Manual Method, and Cardiac Magnetic Resonance Imaging.

    Science.gov (United States)

    Tamborini, Gloria; Piazzese, Concetta; Lang, Roberto M; Muratori, Manuela; Chiorino, Elisa; Mapelli, Massimo; Fusini, Laura; Ali, Sarah Ghulam; Gripari, Paola; Pontone, Gianluca; Andreini, Daniele; Pepi, Mauro

    2017-11-01

    Recently, a new automated software package (HeartModel) was developed to obtain three-dimensional (3D) left ventricular (LV) volumes using a model-based algorithm (MBA) with a "one-button" simple system and user-adjustable slider. The aims of this study were to verify the feasibility and accuracy of the MBA in comparison with other commonly used imaging techniques in a large unselected population, to evaluate possible accuracy improvements of free operator border adjustments or changes of the slider's default position, and to identify differences in method accuracy related to specific pathologies. This prospective study included consecutive 200 patients. LV volumes and ejection fraction were obtained using the MBA and compared with the two-dimensional biplane method, the 3D full-volume (3DFV) modality, and, in 90 of 200 cases, cardiac magnetic resonance (CMR) measurements. To evaluate the optimal position of the slider with respect to the 3DFV and CMR modalities, a set of threefold cross-validation experiments was performed. Optimized and manually corrected LV volumes obtained using the MBA were also tested. Linear correlation and Bland-Altman analysis were used to assess intertechnique agreement. Automatic volumes were feasible in 194 patients (94.5%), with a mean processing time of 29 ± 10 sec. MBA-derived volumes correlated significantly with all evaluated methods, with slight overestimation of two-dimensional biplane and slight underestimation of CMR measurements. Higher correlations were found between MBA and 3DFV measurements, with negligible differences both in volumes (overestimation) and in LV ejection fraction (underestimation), respectively. Optimization of the user-adjustable slider position improved the correlation and markedly reduced the bias between the MBA and 3DFV or CMR. The accuracy of MBA volumes was lower in some pathologies for incorrect definition of LV endocardium. The MBA is highly feasible, reproducible, and rapid, and it correlates

  4. Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 2. Teaching Units that Utilize an Interactive Web-Accessible Subset of the Cambridge Structural Database

    Science.gov (United States)

    Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

    2010-01-01

    A series of online interactive teaching units have been developed that illustrate the use of experimentally measured three-dimensional (3D) structures to teach fundamental chemistry concepts. The units integrate a 500-structure subset of the Cambridge Structural Database specially chosen for their pedagogical value. The units span a number of key…

  5. Three-dimensional volumetric interpolated breath-hold MR imaging for whole-body tumor staging in less than 15 minutes: a feasibility study.

    Science.gov (United States)

    Lauenstein, Thomas C; Goehde, Susanne C; Herborn, Christoph U; Treder, Wiebke; Ruehm, Stefan G; Debatin, Jörg F; Barkhausen, Jörg

    2002-08-01

    The purpose of our study was to evaluate the feasibility and accuracy of three-dimensional (3D) volumetric interpolated breath-hold whole-body MR imaging using CT and nuclear medicine techniques as the standard of reference in patients with metastases. The 3D volumetric interpolated breath-hold whole-body MR imaging examination for metastases screening correlates well with CT and scintigraphy. The use of the rolling table platform permits rapid whole-body imaging in an average of 11 min. The preliminary results indicate that the described technique has the potential to emerge as an all-encompassing alternative to conventional multimodality tumor staging strategies.

  6. Three Dimensional Structure of the Mars North Polar Basal Unit from MARSIS data

    Science.gov (United States)

    Frigeri, A.; Orosei, R.; Cartacci, M.; Cicchetti, A.; Mitri, G.; Giuppi, S.; Noschese, R.; Picardi, G.; Plaut, J.

    2012-04-01

    Mars Advanced Radar for Subsurface and Ionospheric Sounding (MARSIS) is an orbital subsurface sounder aboard ESA's Mars Express spacecraft . It transmits a low-frequency radar pulse that is capable of penetrating below the surface, and is reflected by subsurface dielectric discontinuities. MARSIS has been used to probe both the south and the north polar caps of Mars, revealing their thickness and structure. We report on the results of a campaign of observations of the north polar ice cap of Mars that took place between May and December 2011 in uniquely favorable conditions and produced data of unprecedented quality. The focus of this work is the so-called Basal Unit, a dark, ice-rich, complexely layered geologic unit lying stratigraphically between the polar layered deposits and the Vastitas Borealis Formation, and extending beneath most of Planum Boreum and Olympia Planitia. The objective of this work is the to study the full three dimensional structure of the Northern Polar Deposit and in particular of the Basal Unit (BU). It was recently found that the BU consists of two markedly different units, called the Rupes Tenuis unit and the Planum Boreum cavi unit. The Rupes Tenuis unit appears to be older, horizontally layered, and lacking erosional contacts. It has been thus interpreted as the result of precipitation and cold-trapping of dust-laden volatiles. The Planum Boreum cavi unit displays cross-bedding, indicating dune accumulation. Bright layers within it are interpreted as being made of ice-cemented dust, while dark layers should consist of weathered basalt fines. It seems likely that, in places, the Planum Boreum cavi unit rests directly on the Vastitas Borealis, without the Rupes Tenuis unit in between. Because the two units in the BU have formed much earlier than the north polar layered deposits, and at some interval from each other, they bear evidence of past climatic conditions that were very different from present, so that they "could potentially be a

  7. Time-of-Flight Three Dimensional Neutron Diffraction in Transmission Mode for Mapping Crystal Grain Structures

    DEFF Research Database (Denmark)

    Cereser, Alberto; Strobl, Markus; Hall, Stephen A.

    2017-01-01

    constituting the material. This article presents a new non-destructive 3D technique to study centimeter-sized bulk samples with a spatial resolution of hundred micrometers: time-of-flight three-dimensional neutron diffraction (ToF 3DND). Compared to existing analogous X-ray diffraction techniques, ToF 3DND......-of-flight neutron beamline. The technique was developed and tested with data collected at the Materials and Life Science Experimental Facility of the Japan Proton Accelerator Complex (J-PARC) for an iron sample. We successfully reconstructed the shape of 108 grains and developed an indexing procedure....... The reconstruction algorithms have been validated by reconstructing two stacked Co-Ni-Ga single crystals, and by comparison with a grain map obtained by post-mortem electron backscatter diffraction (EBSD)....

  8. Designing spatial correlation of quantum dots: towards self-assembled three-dimensional structures

    International Nuclear Information System (INIS)

    Bortoleto, J R R; Zelcovit, J G; Gutierrez, H R; Bettini, J; Cotta, M A

    2008-01-01

    Buried two-dimensional arrays of InP dots were used as a template for the lateral ordering of self-assembled quantum dots. The template strain field can laterally organize compressive (InAs) as well as tensile (GaP) self-assembled nanostructures in a highly ordered square lattice. High-resolution transmission electron microscopy measurements show that the InAs dots are vertically correlated to the InP template, while the GaP dots are vertically anti-correlated, nucleating in the position between two buried InP dots. Finite InP dot size effects are observed to originate InAs clustering but do not affect GaP dot nucleation. The possibility of bilayer formation with different vertical correlations suggests a new path for obtaining three-dimensional pseudocrystals

  9. Structural Analysis of Three-dimensional Human Neural Tissue derived from Induced Pluripotent Stem Cells

    DEFF Research Database (Denmark)

    Terrence Brooks, Patrick; Rasmussen, Mikkel Aabech; Hyttel, Poul

    2016-01-01

    Objective: The present study aimed at establishing a method for production of a three-dimensional (3D) human neural tissue derived from induced pluripotent stem cells (iPSCs) and analyzing the outcome by a combination of tissue ultrastructure and expression of neural markers. Methods: A two......-step cell culture procedure was implemented by subjecting human iPSCs to a 3D scaffoldbased neural differentiation protocol. First, neural fate-inducing small molecules were used to create a neuroepithelial monolayer. Second, the monolayer was trypsinized into single cells and seeded into a porous...... polystyrene scaffold and further cultured to produce a 3D neural tissue. The neural tissue was characterized by a combination of immunohistochemistry and transmission electron microscopy (TEM). Results: iPSCs developed into a 3D neural tissue expressing markers for neural progenitor cells, early neural...

  10. Method for the determination of the three-dimensional structure of ultrashort relativistic electron bunches

    Energy Technology Data Exchange (ETDEWEB)

    Geloni, Gianluca; Ilinski, Petr; Saldin, Evgeni; Schneidmiller, Evgeni; Yurkov, Mikhail

    2009-05-15

    We describe a novel technique to characterize ultrashort electron bunches in Xray Free-Electron Lasers. Namely, we propose to use coherent Optical Transition Radiation to measure three-dimensional (3D) electron density distributions. Our method relies on the combination of two known diagnostics setups, an Optical Replica Synthesizer (ORS) and an Optical Transition Radiation (OTR) imager. Electron bunches are modulated at optical wavelengths in the ORS setup.When these electron bunches pass through a metal foil target, coherent radiation pulses of tens MW power are generated. It is thereafter possible to exploit advantages of coherent imaging techniques, such as direct imaging, diffractive imaging, Fourier holography and their combinations. The proposed method opens up the possibility of real-time, wavelength-limited, single-shot 3D imaging of an ultrashort electron bunch. (orig.)

  11. Posture, speed, and habitat structure: three-dimensional hindlimb kinematics of two species of padless geckos.

    Science.gov (United States)

    Fuller, Patrick O; Higham, Timothy E; Clark, Andrew J

    2011-04-01

    Differences in habitat use are often correlated with differences in morphology and behavior, while animals in similar habitats often exhibit similarities in form and function. However, this has not been tested extensively among lizards, especially geckos. Most studies of gecko locomotion have focused on the ability to adhere to surfaces. However, there are several species of geckos that have either secondarily lost adhesive capabilities or simply lack the capability. We quantified the three-dimensional locomotor kinematics for two desert-dwelling padless geckos, Teratoscincus scincus and Eublepharis macularius, on a level trackway over a range of speeds. Our results indicate that T. scincus landed with a high relative hip height of 48.7 ± 2.4% of total limb length at footfall, while E. macularius exhibited hip heights averaging only 36.0 ± 1.8% of total limb length for footfall. The three-dimensional knee angle of T. scincus averaged 120.6 ± 3.9° at footfall, while E. macularius averaged only 101.6 ± 1.8° at footfall. In addition, the femur of E. macularius was elevated to a much greater extent (i.e., was closer to being perpendicular to the long axis of the body) than that of T. scincus and every other lizard that has been studied, suggesting they move with a "hyper-sprawled" posture. Both of these gecko species live in deserts, but T. scincus is psammophilic while E. macularius inhabits a rocky, more densely vegetated environment. Benefits of the more upright posture of T. scincus on open sandy habitat may include a greater field of view and more efficient locomotion. The more sprawled posture of E. macularius may lower its center of gravity and aid in balance while climbing on rocks or shrubs. Copyright © 2011 Elsevier GmbH. All rights reserved.

  12. DOE THREE-DIMENSIONAL STRUCTURE AND PHYSICAL PROPERTIES OF A METHANE HYDRATE DEPOSIT AND GAS RESERVOIR, BLAKE RIDGE

    Energy Technology Data Exchange (ETDEWEB)

    W. Steven Holbrook

    2004-11-11

    This report contains a summary of work conducted and results produced under the auspices of award DE-FC26-00NT40921, ''DOE Three-Dimensional Structure and Physical Properties of a Methane Hydrate Deposit and Gas Reservoir, Blake Ridge.'' This award supported acquisition, processing, and interpretation of two- and three-dimensional seismic reflection data over a large methane hydrate reservoir on the Blake Ridge, offshore South Carolina. The work supported by this project has led to important new conclusions regarding (1) the use of seismic reflection data to directly detect methane hydrate, (2) the migration and possible escape of free gas through the hydrate stability zone, and (3) the mechanical controls on the maximum thickness of the free gas zone and gas escape.

  13. Observation of three-dimensional internal structure of steel materials by means of serial sectioning with ultrasonic elliptical vibration cutting.

    Science.gov (United States)

    Fujisaki, K; Yokota, H; Nakatsuchi, H; Yamagata, Y; Nishikawa, T; Udagawa, T; Makinouchi, A

    2010-01-01

    A three-dimensional (3D) internal structure observation system based on serial sectioning was developed from an ultrasonic elliptical vibration cutting device and an optical microscope combined with a high-precision positioning device. For bearing steel samples, the cutting device created mirrored surfaces suitable for optical metallography, even for long-cutting distances during serial sectioning of these ferrous materials. Serial sectioning progressed automatically by means of numerical control. The system was used to observe inclusions in steel materials on a scale of several tens of micrometers. Three specimens containing inclusions were prepared from bearing steels. These inclusions could be detected as two-dimensional (2D) sectional images with resolution better than 1 mum. A three-dimensional (3D) model of each inclusion was reconstructed from the 2D serial images. The microscopic 3D models had sharp edges and complicated surfaces.

  14. Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

    Science.gov (United States)

    Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

    2011-01-01

    Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

  15. Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 4. Examples of Discovery-Based Learning Using the Complete Cambridge Structural Database

    Science.gov (United States)

    Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

    2011-01-01

    Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

  16. Three-dimensional metamaterials

    Science.gov (United States)

    Burckel, David Bruce [Albuquerque, NM

    2012-06-12

    A fabrication method is capable of creating canonical metamaterial structures arrayed in a three-dimensional geometry. The method uses a membrane suspended over a cavity with predefined pattern as a directional evaporation mask. Metallic and/or dielectric material can be evaporated at high vacuum through the patterned membrane to deposit resonator structures on the interior walls of the cavity, thereby providing a unit cell of micron-scale dimension. The method can produce volumetric metamaterial structures comprising layers of such unit cells of resonator structures.

  17. The band structures of three-dimensional nonlinear plasma photonic crystals

    Science.gov (United States)

    Zhang, Hai-Feng

    2018-01-01

    In this paper, the properties of the photonic band gaps (PBGs) for three-dimensional (3D) nonlinear plasma photonic crystals (PPCs) are theoretically investigated by the plane wave expansion method, whose equations for calculations also are deduced. The configuration of 3D nonlinear PPCs is the Kerr nonlinear dielectric spheres (Kerr effect is considered) inserted in the plasma background with simple-cubic lattices. The inserted dielectric spheres are Kerr nonlinear dielectrics whose relative permittivities are the functions of the external light intensity. Three different Kerr nonlinear dielectrics are considered, which can be expressed as the functions of space coordinates. The influences of the parameters for the Kerr nonlinear dielectrics on the PBGs also are discussed. The calculated results demonstrate that the locations, bandwidths and number of PBGs can be manipulated with the different Kerr nonlinear dielectrics. Compared with the conventional 3D dielectric PCs and PPCs with simple-cubic lattices, the more PBGs or larger PBG can be achieved in the 3D nonlinear PPCs. Those results provide a new way to design the novel devices based on the PPCs.

  18. The band structures of three-dimensional nonlinear plasma photonic crystals

    Directory of Open Access Journals (Sweden)

    Hai-Feng Zhang

    2018-01-01

    Full Text Available In this paper, the properties of the photonic band gaps (PBGs for three-dimensional (3D nonlinear plasma photonic crystals (PPCs are theoretically investigated by the plane wave expansion method, whose equations for calculations also are deduced. The configuration of 3D nonlinear PPCs is the Kerr nonlinear dielectric spheres (Kerr effect is considered inserted in the plasma background with simple-cubic lattices. The inserted dielectric spheres are Kerr nonlinear dielectrics whose relative permittivities are the functions of the external light intensity. Three different Kerr nonlinear dielectrics are considered, which can be expressed as the functions of space coordinates. The influences of the parameters for the Kerr nonlinear dielectrics on the PBGs also are discussed. The calculated results demonstrate that the locations, bandwidths and number of PBGs can be manipulated with the different Kerr nonlinear dielectrics. Compared with the conventional 3D dielectric PCs and PPCs with simple-cubic lattices, the more PBGs or larger PBG can be achieved in the 3D nonlinear PPCs. Those results provide a new way to design the novel devices based on the PPCs.

  19. Time-of-Flight Three Dimensional Neutron Diffraction in Transmission Mode for Mapping Crystal Grain Structures.

    Science.gov (United States)

    Cereser, Alberto; Strobl, Markus; Hall, Stephen A; Steuwer, Axel; Kiyanagi, Ryoji; Tremsin, Anton S; Knudsen, Erik B; Shinohara, Takenao; Willendrup, Peter K; da Silva Fanta, Alice Bastos; Iyengar, Srinivasan; Larsen, Peter M; Hanashima, Takayasu; Moyoshi, Taketo; Kadletz, Peter M; Krooß, Philipp; Niendorf, Thomas; Sales, Morten; Schmahl, Wolfgang W; Schmidt, Søren

    2017-08-25

    The physical properties of polycrystalline materials depend on their microstructure, which is the nano- to centimeter scale arrangement of phases and defects in their interior. Such microstructure depends on the shape, crystallographic phase and orientation, and interfacing of the grains constituting the material. This article presents a new non-destructive 3D technique to study centimeter-sized bulk samples with a spatial resolution of hundred micrometers: time-of-flight three-dimensional neutron diffraction (ToF 3DND). Compared to existing analogous X-ray diffraction techniques, ToF 3DND enables studies of samples that can be both larger in size and made of heavier elements. Moreover, ToF 3DND facilitates the use of complicated sample environments. The basic ToF 3DND setup, utilizing an imaging detector with high spatial and temporal resolution, can easily be implemented at a time-of-flight neutron beamline. The technique was developed and tested with data collected at the Materials and Life Science Experimental Facility of the Japan Proton Accelerator Complex (J-PARC) for an iron sample. We successfully reconstructed the shape of 108 grains and developed an indexing procedure. The reconstruction algorithms have been validated by reconstructing two stacked Co-Ni-Ga single crystals, and by comparison with a grain map obtained by post-mortem electron backscatter diffraction (EBSD).

  20. Application of equivalent elastic methods in three-dimensional finite element structural analysis

    International Nuclear Information System (INIS)

    Jones, D.P.; Gordon, J.L.; Hutula, D.N.; Holliday, J.E.; Jandrasits, W.G.

    1998-02-01

    This paper describes use of equivalent solid (EQS) modeling to obtain efficient solutions to perforated material problems using three-dimensional finite element analysis (3D-FEA) programs. It is shown that the accuracy of EQS methods in 3D-FEA depends on providing sufficient equivalent elastic properties to allow the EQS material to respond according to the elastic symmetry of the pattern. Peak stresses and ligament stresses are calculated from the EQS stresses by an appropriate 3D-FEA submodel approach. The method is demonstrated on the problem of a transversely pressurized simply supported plate with a central divider lane separating two perforated regions with circular penetrations arranged in a square pattern. A 3D-FEA solution for a model that incorporates each penetration explicitly is used for comparison with results from an EQS solution for the plate. Results for deflection and stresses from the EQS solution are within 3% of results from the explicit 3D-FE model. A solution to the sample problem is also provided using the procedures in the ASME B and PV Code. The ASME B and PV Code formulas for plate deflection were shown to overestimate the stiffening effects of the divider lane and the outer stiffening ring

  1. Three dimensional analysis of turbulent steam jets in enclosed structures: a CFD approach

    International Nuclear Information System (INIS)

    Ishii, M.; NguyenLe, Q.

    1999-01-01

    This paper compares the three-dimensional numerical simulation with the experimental data of a steam blowdown event in a light water reactor containment building. The temperature and pressure data of a steam blowdown event was measured at the Purdue University Multi-Dimensional Integrated Test Assembly (PUMA), a scaled model of the General Electric simplified Boiling Water Reactor. A three step approach was used to analyze the steam jet behavior. First, a 1-Dimensional, system level RELAP5/Mod3.2 model of the steam blowdown event was created and the results used to set the initial conditions for the PUMA blowdown experiments. Second, 2-Dimensional CFD models of the discharged steam jets were computed using PHOENICS, a commercially available CFD package. Finally, 3-Dimensional model of the PUMA drywell was created with the boundary conditions based on experimental measurements. The results of the 1-D and 2-D models were reported in the previous meeting. This paper discusses in detail the formulation and the results of the 3-Dimensional PHOENICS model of the PUMA drywell. It is found that the 3-D CFD solutions compared extremely well with the measured data

  2. Three-dimensional configuration of orientated fibers as guidance structures for cell migration and axonal growth.

    Science.gov (United States)

    Kriebel, Andreas; Rumman, Muhammad; Scheld, Miriam; Hodde, Dorothee; Brook, Gary; Mey, Jörg

    2014-02-01

    Peripheral nerve injuries can be surgically repaired by suturing the transected nerve stumps or, in case of larger lesions, by the transplantation of an autologous nerve graft. To avoid donor site morbidity, the development of artificial implants is desired. Clinically, hollow conduits have been used for this purpose but are inferior to the autograft because they lack internal guidance cues for Schwann cells and regenerating axons. In this article, we describe the design of a three-dimensional (3D) scaffold consisting of parallel fibers embedded in a collagen matrix. For this purpose, an electrospinning device was developed to produce and manipulate a 3D array of aligned poly(ɛ-caprolactone) (PCL) microfibers. This fiber array was then incorporated into biodegradable PCL tubes to serve as artificial nerve bridges. Using primary cultures of embryonic chicken dorsal root ganglia, we show that PCL microfibers in the 3D matrix of our composite scaffold guide the direction of Schwann cell migration and axonal growth. Copyright © 2013 Wiley Periodicals, Inc.

  3. A compact structured light based otoscope for three dimensional imaging of the tympanic membrane

    Science.gov (United States)

    Das, Anshuman J.; Estrada, Julio C.; Ge, Zhifei; Dolcetti, Sara; Chen, Deborah; Raskar, Ramesh

    2015-02-01

    Three dimensional (3D) imaging of the tympanic membrane (TM) has been carried out using a traditional otoscope equipped with a high-definition webcam, a portable projector and a telecentric optical system. The device allows us to project fringe patterns on the TM and the magnified image is processed using phase shifting algorithms to arrive at a 3D description of the TM. Obtaining a 3D image of the TM can aid in the diagnosis of ear infections such as otitis media with effusion, which is essentially fluid build-up in the middle ear. The high resolution of this device makes it possible examine a computer generated 3D profile for abnormalities in the shape of the eardrum. This adds an additional dimension to the image that can be obtained from a traditional otoscope by allowing visualization of the TM from different perspectives. In this paper, we present the design and construction of this device and details of the imaging processing for recovering the 3D profile of the subject under test. The design of the otoscope is similar to that of the traditional device making it ergonomically compatible and easy to adopt in clinical practice.

  4. Three-dimensional structure of P3HT assemblies in organic solvents revealed by cryo-TEM.

    Science.gov (United States)

    Wirix, Maarten J M; Bomans, Paul H H; Friedrich, Heiner; Sommerdijk, Nico A J M; de With, Gijsbertus

    2014-01-01

    Poly(3-hexylthiophene) (P3HT) assemblies in vitrified organic solvents were visualized at nanometer scale resolution by cryo-transmission electron microscopy, low dose electron diffraction, and cryo-tomography revealing a three-dimensional lamellar structure formed by the stacking of the conjugated backbones of P3HT with a distance of 1.7 nm and increased order in the bulk of the nanowire. This combination of techniques reveals local structures in dispersion and the condensed state that play a crucial role in the performance of organic electronic devices.

  5. Characterizing the Three-Dimensional Structure of Block Copolymers via Sequential Infiltration Synthesis and Scanning Transmission Electron Tomography.

    Science.gov (United States)

    Segal-Peretz, Tamar; Winterstein, Jonathan; Doxastakis, Manolis; Ramírez-Hernández, Abelardo; Biswas, Mahua; Ren, Jiaxing; Suh, Hyo Seon; Darling, Seth B; Liddle, J Alexander; Elam, Jeffrey W; de Pablo, Juan J; Zaluzec, Nestor J; Nealey, Paul F

    2015-05-26

    Understanding and controlling the three-dimensional structure of block copolymer (BCP) thin films is critical for utilizing these materials for sub-20 nm nanopatterning in semiconductor devices, as well as in membranes and solar cell applications. Combining an atomic layer deposition (ALD)-based technique for enhancing the contrast of BCPs in transmission electron microscopy (TEM) together with scanning TEM (STEM) tomography reveals and characterizes the three-dimensional structures of poly(styrene-block-methyl methacrylate) (PS-b-PMMA) thin films with great clarity. Sequential infiltration synthesis (SIS), a block-selective technique for growing inorganic materials in BCPs films in an ALD tool and an emerging technique for enhancing the etch contrast of BCPs, was harnessed to significantly enhance the high-angle scattering from the polar domains of BCP films in the TEM. The power of combining SIS and STEM tomography for three-dimensional (3D) characterization of BCP films was demonstrated with the following cases: self-assembled cylindrical, lamellar, and spherical PS-b-PMMA thin films. In all cases, STEM tomography has revealed 3D structures that were hidden underneath the surface, including (1) the 3D structure of defects in cylindrical and lamellar phases, (2) the nonperpendicular 3D surface of grain boundaries in the cylindrical phase, and (3) the 3D arrangement of spheres in body-centered-cubic (BCC) and hexagonal-closed-pack (HCP) morphologies in the spherical phase. The 3D data of the spherical morphologies was compared to coarse-grained simulations and assisted in validating the simulations' parameters. STEM tomography of SIS-treated BCP films enables the characterization of the exact structure used for pattern transfer and can lead to a better understating of the physics that is utilized in BCP lithography.

  6. Phase analysis for three-dimensional surface reconstruction of apples using structured-illumination reflectance imaging

    Science.gov (United States)

    Lu, Yuzhen; Lu, Renfu

    2017-05-01

    Three-dimensional (3-D) shape information is valuable for fruit quality evaluation. This study was aimed at developing phase analysis techniques for reconstruction of the 3-D surface of fruit from the pattern images acquired by a structuredillumination reflectance imaging (SIRI) system. Phase-shifted sinusoidal patterns, distorted by the fruit geometry, were acquired and processed through phase demodulation, phase unwrapping and other post-processing procedures to obtain phase difference maps relative to the phase of a reference plane. The phase maps were then transformed into height profiles and 3-D shapes in a world coordinate system based on phase-to-height and in-plane calibrations. A reference plane-based approach, coupled with the curve fitting technique using polynomials of order 3 or higher, was utilized for phase-to-height calibrations, which achieved superior accuracies with the root-mean-squared errors (RMSEs) of 0.027- 0.033 mm for a height measurement range of 0-91 mm. The 3rd-order polynomial curve fitting technique was further tested on two reference blocks with known heights, resulting in relative errors of 3.75% and 4.16%. In-plane calibrations were performed by solving a linear system formed by a number of control points in a calibration object, which yielded a RMSE of 0.311 mm. Tests of the calibrated system for reconstructing the surface of apple samples showed that surface concavities (i.e., stem/calyx regions) could be easily discriminated from bruises from the phase difference maps, reconstructed height profiles and the 3-D shape of apples. This study has laid a foundation for using SIRI for 3-D shape measurement, and thus expanded the capability of the technique for quality evaluation of horticultural products. Further research is needed to utilize the phase analysis techniques for stem/calyx detection of apples, and optimize the phase demodulation and unwrapping algorithms for faster and more reliable detection.

  7. Three-dimensional structure of clumpy outflow from supercritical accretion flow onto black holes

    Science.gov (United States)

    Kobayashi, Hiroshi; Ohsuga, Ken; Takahashi, Hiroyuki R.; Kawashima, Tomohisa; Asahina, Yuta; Takeuchi, Shun; Mineshige, Shin

    2018-02-01

    We perform global three-dimensional (3D) radiation-hydrodynamic (RHD) simulations of outflow from supercritical accretion flow around a 10 M⊙ black hole. We only solve the outflow part, starting from the axisymmetric 2D simulation data in a nearly steady state but with small perturbations in a sinusoidal form being added in the azimuthal direction. The mass accretion rate onto the black hole is ˜102LE/c2 in the underlying 2D simulation data, and the outflow rate is ˜10 LE/c2 (with LE and c being the Eddington luminosity and speed of light, respectively). We first confirm the emergence of clumpy outflow, which was discovered by the 2D RHD simulations, above the photosphere located at a few hundreds of Schwarzschild radii (rS) from the central black hole. As prominent 3D features we find that the clumps have the shape of a torn sheet, rather than a cut string, and that they are rotating around the central black hole with a sub-Keplerian velocity at a distance of ˜103 rS from the center. The typical clump size is ˜30 rS or less in the radial direction, and is more elongated in the angular directions, ˜ hundreds of rS at most. The sheet separation ranges from 50 to 150 rS. We expect stochastic time variations when clumps pass across the line of the sight of a distant observer. Variation timescales are estimated to be several seconds for a black hole with mass of ten to several tens of M⊙, in rough agreement with the observations of some ultra-luminous X-ray sources.

  8. Rapid fabrication of three-dimensional structures for dielectrophoretic sorting of lipid-containing organisms

    Science.gov (United States)

    Schor, Alisha R.; Buie, Cullen R.

    2016-10-01

    In this work, we demonstrate a microfluidic particle sorter consisting of three-dimensional, conducting microposts. Our sorter uses dielectrophoresis (DEP) to sort high- and low-lipid phenotypes of the yeast Yarrowia lipolytica. Y. lipolytica is one of the many microorganisms being explored as a hydrocarbon source for biodiesel, Omega-3 additives, and other products derived from fatty acids. A rapid, non-destructive, lipid-based sorting tool would accelerate the commercialization of these products. Our device consists of an array of 105, 25 μm wide gold microposts that span the height of a 15 μm channel. This array generates an electric field in a microfluidic device that is uniform through the channel height, but has a custom-shaped non-uniformity in the horizontal directions. This is crucial in order to achieve continuous sorting using DEP, as it ensures all cells are exposed to the same conditions throughout the channel height. By using very low currents (100 μA), we are able to electroplate these post arrays in fewer than 15 min. This is an order of magnitude improvement over previous reports of electroplated microstructures. With an applied signal of 250 MHz, 2.6 V pp in our device, we separate a heterogeneous population with a purity of 97.8% in the low-lipid stream and 71.4% in the high-lipid stream. The high-lipid stream purity can be improved by adjusting the spacing of the array. This unique protocol for the rapid fabrication of 3D microstructures has enabled the creation of a non-invasive sorting tool for genetically engineered, lipid-producing organisms. The ability to screen organisms based on lipid content will alleviate one of the major bottlenecks in commercialization of microbial biofuels.

  9. Learning the Cell Structures with Three-Dimensional Models: Students' Achievement by Methods, Type of School and Questions' Cognitive Level

    Science.gov (United States)

    Lazarowitz, Reuven; Naim, Raphael

    2014-01-01

    The cell topic was taught to 9th-grade students in three modes of instruction: (a) students "hands-on," who constructed three-dimensional cell organelles and macromolecules during the learning process; (b) teacher demonstration of the three-dimensional model of the cell structures; and (c) teaching the cell topic with the regular…

  10. Preliminary study of the application of transthoracic echocardiography-guided three-dimensional printing for the assessment of structural heart disease.

    Science.gov (United States)

    Zhu, Yanbo; Liu, Jianshi; Wang, Lianqun; Guan, Xin; Luo, Yongjuan; Geng, Jie; Geng, Qingguo; Lin, Yunjia; Zhang, Lixia; Li, Xixue; Lu, Yaping

    2017-12-01

    To investigate the feasibility and diagnostic value of a preoperative transthoracic echocardiography-guided three-dimensional printed model (TTE-guided 3DPM) for the assessment of structural heart disease (SHD). Fourty-four patients underwent cardiac surgery at Tianjin Chest Hospital. The patients were preoperatively assessed using TTE-guided 3DPM, which was compared to conventional three-dimensional transthoracic echocardiography (3DTTE) along with direct intraoperative findings, which were considered the "gold standard." Twelve patients had SHD, including four with mitral prolapse, two with partial endocardial cushion defects, two with secondary atrial septal defects, two with rheumatic mitral stenosis, one with tetralogy of Fallot, and one with a ventricular septal defect (VSD). Thirty-two patients who did not have SHDs were designated as the negative control group. The sensitivity and specificity of the TTE-guided 3DPM were greater than or equal to those of the 3DTTE. The P-value of the McNemar test of 3DTTE was >.05, which indicates that the difference was not statistically significant (Kappa = 0.745, P guided 3DPM was >.05, which indicates that the difference was not statistically significant (Kappa = 0.955, P guided 3DPM resulted in a P-value >.05, which indicates that the difference was not statistically significant (Kappa = 0.879, P guided 3DPM displayed the 3D structure of SHDs and cardiac lesions clearly and was consistent with the intra-operative findings. Transthoracic echocardiography-guided three-dimensional printed model (TTE-guided 3DPM) provides essential information for preoperative evaluation and decision making for patients with SHDs. © 2017, Wiley Periodicals, Inc.

  11. Label-free three-dimensional (3D) structural imaging in live cells using intrinsic optical refractive index

    KAUST Repository

    Liu, Chen

    2017-04-14

    Here we report a method for visualization of volumetric structural information of live biological samples with no exogenous contrast agents. The process is made possible through a technique that involves generation, synthesis and analysis of three-dimensional (3D) Fourier components of light diffracted by the sample. This leads to the direct recovery of quantitative cellular morphology with no iterative procedures for reduced computational complexity. Combing with the fact that the technique is easily adaptive to any imaging platform and requires minimum sample preparation, our proposed method is particularly promising for observing fast, volumetric and dynamic events previously only accessible through staining methods.

  12. Three-Dimensional Hysterosalpingo Contrast Sonography with Gel Foam: Methodology and Feasibility to Obtain 3-Dimensional Volumes of Tubal Shape.

    Science.gov (United States)

    Exacoustos, Caterina; Pizzo, Alessandra; Lazzeri, Lucia; Pietropolli, Adalgisa; Piccione, Emilio; Zupi, Errico

    To investigate the feasibility of hysterosalpingo foam sonography (HyFoSy) with automated 3-dimensional (3D) software in the evaluation of tubal patency and visualization of the tubal course by obtaining a 3D volume acquisition of tubes. Prospective observational study (Canadian Task Force classification III). University hospital. A total of 132 infertile females evaluated between October 2013 and February 2015. All patients underwent HyFoSy with the new automated 3D coded contrast imaging (CCI) followed by 2-dimensional (2D) real-time HyFoSy. To evaluate the feasibility of 3D visualization of the tubal course, consecutive volume acquisitions were performed during gel foam contrast agent injection. Conventional 2D real-time hysterosalpingo contrast sonography (HyCoSy) by detection of gel foam moving through the tubes and around the ovaries was finally performed and considered to indicate the final results of tubal status. All the patients underwent 3D CCI HyFoSy, followed by 2D real-time HyFoSy. After both procedures, we observed 108 patients (81.8%) with bilateral tubal patency, 22 patients (16.6%) with unilateral tubal patency, and 2 patients (1.5%) with bilateral tubal occlusion. The concordance rate for tubal status between the first and second 3D volume acquisitions and the final 2D real-time evaluation was 84.8% and 97.0%, respectively. Transvaginal ultrasound HyFoSy with 3D volume reconstruction of the uterus and tubes is an accurate and safe technique that allows complete visualization of tubal shape and patency with high patient compliance. Copyright © 2017 AAGL. Published by Elsevier Inc. All rights reserved.

  13. Mesoscale Eddies in the Northwestern Pacific Ocean: Three-Dimensional Eddy Structures and Heat/Salt Transports

    Science.gov (United States)

    Dong, Di; Brandt, Peter; Chang, Ping; Schütte, Florian; Yang, Xiaofeng; Yan, Jinhui; Zeng, Jisheng

    2017-12-01

    The region encompassing the Kuroshio Extension (KE) in the Northwestern Pacific Ocean (25°N-45°N and 130°E-180°E) is one of the most eddy-energetic regions of the global ocean. The three-dimensional structures and transports of mesoscale eddies in this region are comprehensively investigated by combined use of satellite data and Argo profiles. With the allocation of Argo profiles inside detected eddies, the spatial variations of structures of eddy temperature and salinity anomalies are analyzed. The results show that eddies predominantly have subsurface (near-surface) intensified temperature and salinity anomalies south (north) of the KE jet, which is related to different background stratifications between these regions. A new method based on eddy trajectories and the inferred three-dimensional eddy structures is proposed to estimate heat and salt transports by eddy movements in a Lagrangian framework. Spatial distributions of eddy transports are presented over the vicinity of the KE for the first time. The magnitude of eddy-induced meridional heat (freshwater volume) transport is on the order of 0.01 PW (103 m3/s). The eddy heat transport divergence results in an oceanic heat loss south and heat gain north of the KE, thereby reinforcing and counteracting the oceanic heat loss from air-sea fluxes south and north of the KE jet, respectively. It also suggests a poleward heat transport across the KE jet due to eddy propagation.

  14. Seismic response analysis of soil-structure interactive system using a coupled three-dimensional FE-IE method

    International Nuclear Information System (INIS)

    Ryu, Jeong-Soo; Seo, Choon-Gyo; Kim, Jae-Min; Yun, Chung-Bang

    2010-01-01

    This paper proposes a slightly new three-dimensional radial-shaped dynamic infinite elements fully coupled to finite elements for an analysis of soil-structure interaction system in a horizontally layered medium. We then deal with a seismic analysis technique for a three-dimensional soil-structure interactive system, based on the coupled finite-infinite method in frequency domain. The dynamic infinite elements are simulated for the unbounded domain with wave functions propagating multi-generated wave components. The accuracy of the dynamic infinite element and effectiveness of the seismic analysis technique may be demonstrated through a typical compliance analysis of square surface footing, an L-shaped mat concrete footing on layered soil medium and two kinds of practical seismic analysis tests. The practical analyses are (1) a site response analysis of the well-known Hualien site excited by all travelling wave components (primary, shear, Rayleigh waves) and (2) a generation of a floor response spectrum of a nuclear power plant. The obtained dynamic results show good agreement compared with the measured response data and numerical values of other soil-structure interaction analysis package.

  15. The shikimate pathway: review of amino acid sequence, function and three-dimensional structures of the enzymes.

    Science.gov (United States)

    Mir, Rafia; Jallu, Shais; Singh, T P

    2015-06-01

    The aromatic compounds such as aromatic amino acids, vitamin K and ubiquinone are important prerequisites for the metabolism of an organism. All organisms can synthesize these aromatic metabolites through shikimate pathway, except for mammals which are dependent on their diet for these compounds. The pathway converts phosphoenolpyruvate and erythrose 4-phosphate to chorismate through seven enzymatically catalyzed steps and chorismate serves as a precursor for the synthesis of variety of aromatic compounds. These enzymes have shown to play a vital role for the viability of microorganisms and thus are suggested to present attractive molecular targets for the design of novel antimicrobial drugs. This review focuses on the seven enzymes of the shikimate pathway, highlighting their primary sequences, functions and three-dimensional structures. The understanding of their active site amino acid maps, functions and three-dimensional structures will provide a framework on which the rational design of antimicrobial drugs would be based. Comparing the full length amino acid sequences and the X-ray crystal structures of these enzymes from bacteria, fungi and plant sources would contribute in designing a specific drug and/or in developing broad-spectrum compounds with efficacy against a variety of pathogens.

  16. A simplified description of the three-dimensional structure of agroforestry trees for use with a radiative transfer model

    International Nuclear Information System (INIS)

    Meloni, S.

    1998-01-01

    To simulate transmitted radiation in agroforestry systems, radiative transfer models usually require a detailed three-dimensional description of the tree canopy. We propose here a simplification of the description of the three-dimensional structure of wild cherry trees (Prunus avium). The simplified tree description was tested against the detailed one for five-year-old wild cherry. It allowed accurate simulation of transmitted radiation and avoided tedious measurements of tree structure. The simplified description was then applied to older trees. Allometric relationships were used to compute the parameters not available on free-grown trees. The transmitted radiation in an agroforestry system was simulated at four different ages: 5, 10, 15 and 20 years. The trees were planted on a 5 m square grid. Two row orientations, chosen to provide different transmitted radiation patterns, were tested: north/south and north- east/south-west. The simulations showed that the daily mean transmitted radiation was reduced from 92% of incident radiation under five-year-old trees to 37% under 20-year-old trees. The variability of transmitted radiation increased with tree growth. The row orientation had only small effects on the shaded area at the beginning and end of the day when solar elevation was low. (author)

  17. Use of three-dimensional parameters in the analysis of crystal structures under compression

    DEFF Research Database (Denmark)

    Balic Zunic, Tonci

    2007-01-01

    . For a complete understanding of structural changes, the behaviour of all coordination polyhedra plus the voids that separate them must be investigated. The structural voids in a framework are identified by a Voronoi tessellation. It can be performed e.g. on the anionic framework alone to find the centres...... of the coordination polyhedra of cations and the voids that separate them. Analysis of individual compressional characteristics of structural components gives clues for the strong and weak parts of structures under high pressures and paths for structural transformations. The expected behaviour of distortion...

  18. Structural origin of dynamic heterogeneity in three-dimensional colloidal glass formers and its link to crystal nucleation.

    Science.gov (United States)

    Kawasaki, Takeshi; Tanaka, Hajime

    2010-06-16

    The physical understanding of glass transition remains a major challenge of physics and materials science. Among various glass-forming liquids, a colloidal liquid interacting with hard-core repulsion is now regarded as one of the most ideal model systems. Here we study the structure and dynamics of three-dimensional polydisperse colloidal liquids by Brownian dynamics simulations. We reveal that medium-range crystalline bond orientational order of the hexagonal close packed structure grows in size and lifetime with increasing packing fraction. We show that dynamic heterogeneity may be a direct consequence of this transient structural ordering, which suggests its origin is thermodynamic rather than kinetic. We also reveal that nucleation of crystals preferentially occurs in regions of high medium-range order, reflecting the low crystal-liquid interfacial energy there. These findings may shed new light not only on the fundamental nature of the glass transition, but also the mechanism of crystal nucleation.

  19. 3did: a catalog of domain-based interactions of known three-dimensional structure.

    Science.gov (United States)

    Mosca, Roberto; Céol, Arnaud; Stein, Amelie; Olivella, Roger; Aloy, Patrick

    2014-01-01

    The database of 3D interacting domains (3did, available online for browsing and bulk download at http://3did.irbbarcelona.org) is a catalog of protein-protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural templates of domain-domain interactions in the Protein Data Bank, providing molecular details for such interactions. The current version also includes a pipeline for the discovery and annotation of novel domain-motif interactions. For every interaction, 3did identifies and groups different binding modes by clustering similar interfaces into 'interaction topologies'. By maintaining a constantly updated collection of domain-based structural interaction templates, 3did is a reference source of information for the structural characterization of protein interaction networks. 3did is updated every 6 months.

  20. Canine hippocampal formation composited into three-dimensional structure using MPRAGE.

    Science.gov (United States)

    Jung, Mi-Ae; Nahm, Sang-Soep; Lee, Min-Su; Lee, In-Hye; Lee, Ah-Ra; Jang, Dong-Pyo; Kim, Young-Bo; Cho, Zang-Hee; Eom, Ki-Dong

    2010-07-01

    This study was performed to anatomically illustrate the living canine hippocampal formation in three-dimensions (3D), and to evaluate its relationship to surrounding brain structures. Three normal beagle dogs were scanned on a MR scanner with inversion recovery segmented 3D gradient echo sequence (known as MP-RAGE: Magnetization Prepared Rapid Gradient Echo). The MRI data was manually segmented and reconstructed into a 3D model using the 3D slicer software tool. From the 3D model, the spatial relationships between hippocampal formation and surrounding structures were evaluated. With the increased spatial resolution and contrast of the MPRAGE, the canine hippocampal formation was easily depicted. The reconstructed 3D image allows easy understanding of the hippocampal contour and demonstrates the structural relationship of the hippocampal formation to surrounding structures in vivo.

  1. Three-dimensional fluid-structure interaction case study on cubical fluid cavity with flexible bottom

    Science.gov (United States)

    Ghelardi, Stefano; Rizzo, Cesare; Villa, Diego

    2017-12-01

    In this paper, we report our study on a numerical fluid-structure interaction problem originally presented by Mok et al. (2001) in two dimensions and later studied in three dimensions by Valdés Vazquez (2007), Lombardi (2012), and Trimarchi (2012). We focus on a 3D test case in which we evaluated the sensitivity of several input parameters on the fluid and structural results. In particular, this analysis provides a starting point from which we can look deeper into specific aspects of these simulations and analyze more realistic cases, e.g., in sails design. In this study, using the commercial software ADINA™, we addressed a well-known unsteadiness problem comprising a square box representing the fluid domain with a flexible bottom modeled with structural shell elements. We compared data from previously published work whose authors used the same numerical approach, i.e., a partitioned approach coupling a finite volume solver (for the fluid domain) and a finite element solver (for the solid domain). Specifically, we established several benchmarks and made comparisons with respect to fluid and solid meshes, structural element types, and structural damping, as well as solution algorithms. Moreover, we compared our method with a monolithic finite element solution method. Our comparisons of new and old results provide an outline of best practices for such simulations.

  2. Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.

    Directory of Open Access Journals (Sweden)

    Vidya Mangala Prasad

    2017-06-01

    Full Text Available Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.

  3. Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.

    Science.gov (United States)

    Mangala Prasad, Vidya; Klose, Thomas; Rossmann, Michael G

    2017-06-01

    Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.

  4. Determination of the three-dimensional structure for weakly aligned biomolecules by NMR spectroscopy

    International Nuclear Information System (INIS)

    Shahkhatuni, Astghik A; Shahkhatuni, Aleksan G

    2002-01-01

    The key achievements and the potential of NMR spectroscopy for weakly aligned biomolecules are considered. Due to weak alignment, it becomes possible to determine a number of NMR parameters dependent on the orientation of biomolecules, which are averaged to zero in usual isotropic media. The addition of new orientational constraints to standard procedures of 3D structure determination markedly increases the achievable accuracy. The possibility of structure determination for biomolecules using only orientation-dependent parameters without invoking other NMR data is discussed. The methods of orientation, experimental techniques, and calculation methods are systematised. The main results obtained and the prospects of using NMR spectroscopy of weakly aligned systems to study different classes of biomolecules and to solve various problems of molecular biology are analysed. Examples of biomolecules whose structures have been determined using orientation-dependent parameters are given. The bibliography includes 508 references.

  5. Identification on the three-dimensional vortical structures of impeller flow by a multi-plane stereoscopic PIV method

    International Nuclear Information System (INIS)

    Yoon, Sang Youl; Kim, Kyung Chun

    2003-01-01

    The three-dimensional spatial structures of impeller flow created by a six bladed Rushton turbine have identified based on the volumetric velocity information from multi-plane stereoscopic PIV measurements. A total of 10 planes with 2 mm space and a 50 mm by 64 mm size of the field of view were targeted. To reduce the depth of focus, we adopted an angle offset configuration which satisfied the Scheimpflug condition. The distortion compensation procedure was utilized during the in situ calibration. Phase-locked instantaneous data were ensemble averaged and interpolated in order to obtain mean 3-D, volumetric velocity fields on a 60 degree sector of a cylindrical ring volume enclosing the turbine blade. Using the equi-vorticity surface rendering, the spatial structure of the trailing vortices was clearly demonstrated. Detail flow characteristics of the radial jet reported in previous studies of mixer flows were easily identified

  6. Three-dimensional structure of phosphoribosyl pyrophosphate synthetase from E. coli at 2.71 Å resolution

    Energy Technology Data Exchange (ETDEWEB)

    Timofeev, V. I., E-mail: inna@ns.crys.ras.ru, E-mail: tostars@mail.ru, E-mail: ugama@yandex.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Abramchik, Yu. A. [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Zhukhlistova, N. E. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation); Muravieva, T. I.; Esipov, R. S. [Russian Academy of Sciences, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry (Russian Federation); Kuranova, I. P. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2016-01-15

    Phosphoribosyl pyrophosphate synthetase from Escherichia coli was cloned, purified, and crystallized. Single crystals of the enzyme were grown under microgravity. The X-ray diffraction data set was collected at the Spring-8 synchrotron facility and used to determine the three-dimensional structure of the enzyme by the molecular-replacement method at 2.71 Å resolution. The active and regulatory sites in the molecule of E. coli phosphoribosyl pyrophosphate synthetase were revealed by comparison with the homologous protein from Bacillus subtilis, the structure of which was determined in a complex with functional ligands. The conformations of polypeptide-chain fragments surrounding and composing the active and regulatory sites were shown to be identical in both proteins.

  7. Three-dimensional super-resolution structured illumination microscopy with maximum a posteriori probability image estimation.

    Science.gov (United States)

    Lukeš, Tomáš; Křížek, Pavel; Švindrych, Zdeněk; Benda, Jakub; Ovesný, Martin; Fliegel, Karel; Klíma, Miloš; Hagen, Guy M

    2014-12-01

    We introduce and demonstrate a new high performance image reconstruction method for super-resolution structured illumination microscopy based on maximum a posteriori probability estimation (MAP-SIM). Imaging performance is demonstrated on a variety of fluorescent samples of different thickness, labeling density and noise levels. The method provides good suppression of out of focus light, improves spatial resolution, and allows reconstruction of both 2D and 3D images of cells even in the case of weak signals. The method can be used to process both optical sectioning and super-resolution structured illumination microscopy data to create high quality super-resolution images.

  8. Three-dimensional quantification of structures in trabecular bone using measures of complexity

    DEFF Research Database (Denmark)

    Marwan, Norbert; Kurths, Jürgen; Thomsen, Jesper Skovhus

    2009-01-01

    evaluate different aspects of organization and complexity of 3D structures, such as complexity of its surface or shape variability. We apply these measures to 3D data acquired by high-resolution microcomputed tomography (µCT) from human proximal tibiae and lumbar vertebrae at different stages...... of osteoporotic bone loss. The outcome is compared to the results of conventional static histomorphometry and exhibits clear relationships between the analyzed geometrical features of trabecular bone and loss of bone density, but also indicate that the measures reveal additional information about the structural...

  9. Three-dimensional segmentation and skeletonization to build an airway tree data structure for small animals

    International Nuclear Information System (INIS)

    Chaturvedi, Ashutosh; Lee, Zhenghong

    2005-01-01

    Quantitative analysis of intrathoracic airway tree geometry is important for objective evaluation of bronchial tree structure and function. Currently, there is more human data than small animal data on airway morphometry. In this study, we implemented a semi-automatic approach to quantitatively describe airway tree geometry by using high-resolution computed tomography (CT) images to build a tree data structure for small animals such as rats and mice. Silicon lung casts of the excised lungs from a canine and a mouse were used for micro-CT imaging of the airway trees. The programming language IDL was used to implement a 3D region-growing threshold algorithm for segmenting out the airway lung volume from the CT data. Subsequently, a fully-parallel 3D thinning algorithm was implemented in order to complete the skeletonization of the segmented airways. A tree data structure was then created and saved by parsing through the skeletonized volume using the Python programming language. Pertinent information such as the length of all airway segments was stored in the data structure. This approach was shown to be accurate and efficient for up to six generations for the canine lung cast and ten generations for the mouse lung cast

  10. Large-Pore Mesoporous Silica with Three-Dimensional Wormhole Framework Structures.

    Science.gov (United States)

    Park, In; Pinnavaia, Thomas J

    2009-02-01

    Large-pore mesoporous silica with 3D wormhole framework structures (denoted MSU-J) are prepared through a supramolecular hydrogen-bonding assembly pathway from low-cost sodium silicate as the silica source and commercially available mono- and triamine Jeffamine and Surfonamine surfactants as structure-directing porogens. The calcined mesostructures exhibit large pore sizes (up to 8.2 nm), surface areas (632-1030 m(2)/g) and pore volumes (0.5-2.0 cm(3)/g), depending on the surfactant chain length and synthesis temperature (25-65 °C). The textural properties of these new wormhole mesostructures are comparable to those of hexagonal SBA-15 derivatives and large pore MCM-48. However, unlike the SBA-15 structure type, wherein the 3D pore network is formed by connecting 1D cylindrical mesopores through micropores, MSU-J mesophases have wormhole framework structures containing fully interconnected 3D mesopores that can minimize the diffusion limitations often encountered in adsorption and chemical catalysis. Also, unlike large pore MCM-48, which requires cost-intensive tetraethylorthosilicate as a silica source and the use of a co-surfactant as a pore expander under strong acid conditions, MSU-J mesostructures are assembled from low cost sodium silicate in the presence of a single Jeffamine or Surfonamine porogen at near-neutral pH.

  11. Three-dimensional Morphology and X-ray Scattering Structure of ...

    Indian Academy of Sciences (India)

    Abstract. It is well established that water-alcohol mixtures exhibit anomalous properties at very low as well as at very high alcohol concentrations. Almost all the studies in this regard intend to link these anomalies to the microscopic structural changes as water (or alcohol) concentration increases in the mixture. However, it is.

  12. Three-dimensional solution structure of Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy.

    Science.gov (United States)

    Cai, M; Gong, Y; Kao, J L; Krishnamoorthi, R

    1995-04-18

    The solution structure of Cucurbita maxima trypsin inhibitor-V (CMTI-V), which is also a specific inhibitor of the blood coagulation protein, factor XIIa, was determined by 1H NMR spectroscopy in combination with a distance-geometry and simulated annealing algorithm. Sequence-specific resonance assignments were made for all the main-chain and most of the side-chain hydrogens. Stereospecific assignments were also made for some of the beta-, gamma-, delta-, and epsilon-hydrogens and valine methyl hydrogens. The ring conformations of all six prolines in the inhibitor were determined on the basis of 1H-1H vicinal coupling constant patterns; most of the proline ring hydrogens were stereospecifically assigned on the basis of vicinal coupling constant and intraresidue nuclear Overhauser effect (NOE) patterns. Distance constraints were determined on the basis of NOEs between pairs of hydrogens. Dihedral angle constraints were determined from estimates of scalar coupling constants and intraresidue NOEs. On the basis of 727 interproton distance and 111 torsion angle constraints, which included backbone phi angles and side-chain chi 1, chi 2, chi 3, and chi 4 angles, 22 structures were calculated by a distance geometry algorithm and refined by energy minimization and simulated annealing methods. Both main-chain and side-chain atoms are well-defined, except for a loop region, two terminal residues, and some side-chain atoms located on the molecular surface. The average root mean squared deviation in the position for equivalent atoms between the 22 individual structures and the mean structure obtained by averaging their coordinates is 0.58 +/- 0.06 A for the main-chain atoms and 1.01 +/- 0.07 A for all the non-hydrogen atoms of residues 3-40 and 49-67. These structures were compared to the X-ray crystallographic structure of another protein of the same inhibitor family-chymotrypsin inhibitor-2 from barley seeds [CI-2; McPhalen, C. A., & James, M. N. G. (1987) Biochemistry 26

  13. Three-dimensional structure of the Upper Scorpius association with the Gaia first data release

    Science.gov (United States)

    Galli, Phillip A. B.; Joncour, Isabelle; Moraux, Estelle

    2018-03-01

    Using new proper motion data from recently published catalogs, we revisit the membership of previously identified members of the Upper Scorpius association. We confirmed 750 of them as cluster members based on the convergent point method, compute their kinematic parallaxes and combined them with Gaia parallaxes to investigate the 3D structure and geometry of the association using a robust covariance method. We find a mean distance of 146 ± 3 ± 6 pc and show that the morphology of the association defined by the brightest (and most massive) stars yields a prolate ellipsoid with dimensions of 74 × 38 × 32 pc3, while the faintest cluster members define a more elongated structure with dimensions of 98 × 24 × 18 pc3. We suggest that the different properties of both populations is an imprint of the star formation history in this region.

  14. Three-dimensionality of space in the structure of the periodic table of chemical elements

    International Nuclear Information System (INIS)

    Veremeichik, T. F.

    2006-01-01

    The effect of the dimension of the 3D homogeneous and isotropic Euclidean space, and the electron spin on the self-organization of the electron systems of atoms of chemical elements is considered. It is shown that the finite dimension of space creates the possibility of periodicity in the structure of an electron cloud, while the value of the dimension determines the number of stable systems of electrons at different levels of the periodic table of chemical elements and some characteristics of the systems. The conditions for the stability of systems of electrons and the electron system of an atom as a whole are considered. On the basis of the results obtained, comparison with other hierarchical systems (nanostructures and biological structures) is performed

  15. Three-dimensional stacked structured ASIC devices and methods of fabrication thereof

    Science.gov (United States)

    Shinde, Subhash L.; Teifel, John; Flores, Richard S.; Jarecki Jr., Robert L.; Bauer, Todd

    2015-11-19

    A 3D stacked sASIC is provided that includes a plurality of 2D reconfigurable structured structured ASIC (sASIC) levels interconnected through hard-wired arrays of 3D vias. The 2D sASIC levels may contain logic, memory, analog functions, and device input/output pad circuitry. During fabrication, these 2D sASIC levels are stacked on top of each other and fused together with 3D metal vias. Such 3D vias may be fabricated as through-silicon vias (TSVs). They may connect to the back-side of the 2D sASIC level, or they may be connected to top metal pads on the front-side of the 2D sASIC level.

  16. Three-dimensional Structure of a Viral Genome-delivery Portal Vertex

    Energy Technology Data Exchange (ETDEWEB)

    A Olia; P Prevelige Jr.; J Johnson; G Cingolani

    2011-12-31

    DNA viruses such as bacteriophages and herpesviruses deliver their genome into and out of the capsid through large proteinaceous assemblies, known as portal proteins. Here, we report two snapshots of the dodecameric portal protein of bacteriophage P22. The 3.25-{angstrom}-resolution structure of the portal-protein core bound to 12 copies of gene product 4 (gp4) reveals a {approx}1.1-MDa assembly formed by 24 proteins. Unexpectedly, a lower-resolution structure of the full-length portal protein unveils the unique topology of the C-terminal domain, which forms a {approx}200-{angstrom}-long {alpha}-helical barrel. This domain inserts deeply into the virion and is highly conserved in the Podoviridae family. We propose that the barrel domain facilitates genome spooling onto the interior surface of the capsid during genome packaging and, in analogy to a rifle barrel, increases the accuracy of genome ejection into the host cell.

  17. [Three dimensional structure of the connective tissue papillae of the tongue in Suncus murinus].

    Science.gov (United States)

    Kobayashi, K; Miyata, K; Iwasaki, S; Takahashi, K

    1989-08-01

    The surface structure of the connective tissue papillae (CP) of Suncus murinus tongue was observed by SEM after fixing with Karnovsky's fixative and removal of the epithelial cell layer with 3N or 8N HCl. On the surface of the slender conical tongue, there are densely distributed filiform papillae among which fungiform papillae are seen sporadically. A pair of vallate papillae are situated in the posterior region of the tongue. Filiform papillae appear somewhat different externally depending on the dorsal surface of the anterior tongue. At the tip of the tongue, filiform papillae are of a slender conical shape and have a slight depression in the anterior basal portion. The CP of these is seen as a spherical protrusion on which a shallow groove runs in the anteroposterior direction. In the middle region, somewhat large filiform papillae contain CP having one or two small round head-like structures on each spherical protrusion. These head-like structures are increased in number in the posterior region. In the most posterior region of the anterior tongue, there are distributed large filiform papillae having several slender protrusions that surround a basal anterior depression. These large branched filiform papillae have a glove finger like CP. Small conical filiform papillae are distributed in the posterior marginal region of the anterior tongue which have CP of a horse-shoe like protrusion that opens in the anterior direction. Spherical fungiform papillae have CP which are thick columnar in shape with many lateral thin folds running vertically and having a round depression on the top of each. CP of the vallate papillae appear as a beehive like structure.(ABSTRACT TRUNCATED AT 250 WORDS)

  18. Three-dimensional midwater camouflage from a novel two-component photonic structure in hatchetfish skin.

    Science.gov (United States)

    Rosenthal, Eric I; Holt, Amanda L; Sweeney, Alison M

    2017-05-01

    The largest habitat by volume on Earth is the oceanic midwater, which is also one of the least understood in terms of animal ecology. The organisms here exhibit a spectacular array of optical adaptations for living in a visual void that have only barely begun to be described. We describe a complex pattern of broadband scattering from the skin of Argyropelecus sp., a hatchetfish found in the mesopelagic zone of the world's oceans. Hatchetfish skin superficially resembles the unpolished side of aluminium foil, but on closer inspection contains a complex composite array of subwavelength-scale dielectric structures. The superficial layer of this array contains dielectric stacks that are rectangular in cross-section, while the deeper layer contains dielectric bundles that are elliptical in cross-section; the cells in both layers have their longest dimension running parallel to the dorsal-ventral axis of the fish. Using the finite-difference time-domain approach and photographic radiometry, we explored the structural origins of this scattering behaviour and its environmental consequences. When the fish's flank is illuminated from an arbitrary incident angle, a portion of the scattered light exits in an arc parallel to the fish's anterior-posterior axis. Simultaneously, some incident light is also scattered downwards through the complex birefringent skin structure and exits from the ventral photophores. We show that this complex scattering pattern will provide camouflage simultaneously against the horizontal radially symmetric solar radiance in this habitat, and the predatory bioluminescent searchlights that are common here. The structure also directs light incident on the flank of the fish into the downwelling, silhouette-hiding counter-illumination of the ventral photophores. © 2017 The Authors.

  19. Study of Three-dimensional Magnetic Structure and the Successive Eruptive Nature of Active Region 12371

    Science.gov (United States)

    Vemareddy, P.; Demóulin, P.

    2018-04-01

    We study the magnetic structure of a successively erupting sigmoid in active region 12371 by modeling the quasi-static coronal field evolution with nonlinear force-free field (NLFFF) equilibria. Helioseismic and Magnetic Imager/Solar Dynamic Observatory vector magnetograms are used as input to the NLFFF model. In all eruption events, the modeled structure resembles the observed pre-eruptive coronal sigmoid and the NLFFF core field is a combination of double inverse-J-shaped and inverse-S field lines with dips touching the photosphere. Such field lines are formed by the flux cancellation reconnection of opposite-J field lines at bald-patch locations, which in turn implies the formation of a weakly twisted flux-rope (FR) from large-scale sheared arcade field lines. Later on, this FR undergoes coronal tether-cutting reconnection until a coronal mass ejection is triggered. The modeled structure captured these major features of sigmoid-to-arcade-to-sigmoid transformation, which is reoccuring under continuous photospheric flux motions. Calculations of the field line twist reveal a fractional increase followed by a decrease of the number of pixels having a range of twist. This traces the buildup process of a twisted core field by slow photospheric motions and the relaxation after eruption, respectively. Our study infers that the large eruptivity of this AR is due to a steep decrease of the background coronal field meeting the torus instability criteria at a low height (≈40 Mm) in contrast to noneruptive ARs.

  20. Three-dimensional structure of a schistosome serpin revealing an unusual configuration of the helical subdomain

    Energy Technology Data Exchange (ETDEWEB)

    Granzin, Joachim [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany); Huang, Ying; Topbas, Celalettin [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Huang, Wenying [Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Wu, Zhiping [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Misra, Saurav [Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Hazen, Stanley L. [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Blanton, Ronald E. [Department of Infectious Diseases, Case Western Reserve University, Cleveland, OH 44190 (United States); Lee, Xavier [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Weiergräber, Oliver H., E-mail: o.h.weiergraeber@fz-juelich.de [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany)

    2012-06-01

    The crystal structure of ShSPI, a serpin from the blood fluke S. haematobium, reveals some peculiar features of the helical subdomain which have not been observed previously in the serpin superfamily. Parasitic organisms are constantly challenged by the defence mechanisms of their respective hosts, which often depend on serine protease activities. Consequently, protease inhibitors such as those belonging to the serpin superfamily have emerged as protective elements that support the survival of the parasites. This report describes the crystal structure of ShSPI, a serpin from the trematode Schistosoma haematobium. The protein is exposed on the surface of invading cercaria as well as of adult worms, suggesting its involvement in the parasite–host interaction. While generally conforming to the well established serpin fold, the structure reveals several distinctive features, mostly concerning the helical subdomain of the protein. It is proposed that these peculiarities are related to the unique biological properties of a small serpin subfamily which is conserved among pathogenic schistosomes.

  1. Evaluation of Intrauterine Structural Pathology by Three-Dimensional Sonohysterography Using An Extended Imaging Method

    Directory of Open Access Journals (Sweden)

    Fatemeh Zafarani

    2013-01-01

    Full Text Available Structural intrauterine abnormalities are an important cause of infertility, recurrentpregnancy loss and bleeding or pain associated with a poor reproductive outcome. Variousdiagnostic methods have been applied to detect these lesions such as hysterosalpingography,hysteroscopy and sonohysterography. More recently, three-dimensionalextended imaging (3DXI provides the ability to obtain sequential sections of acquiredvolume scans in A, B and C planes. Here, we briefly discuss the technique of salineinfusion sonography, followed by a review of sonohysterographic characteristics ofintracavitary pathologies with more focus on some definitions and measurements.

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

    Science.gov (United States)

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

    2017-02-01

    The major problem in producing artificial livers is that primary hepatocytes cannot be cultured for many days. Recently, 3-dimensional (3D) printing technology draws attention and this technology regarded as a useful tool for current cell biology. By using the 3D bio-printing, these problems can be resolved. To generate 3D bio-printed structures (25 mm × 25 mm), cells-alginate constructs were fabricated by 3D bio-printing system. Mouse primary hepatocytes were isolated from the livers of 6-8 weeks old mice by a 2-step collagenase method. Samples of 4 × 10 7 hepatocytes with 80%-90% viability were printed with 3% alginate solution, and cultured with well-defined culture medium for primary hepatocytes. To confirm functional ability of hepatocytes cultured on 3D alginate scaffold, we conducted quantitative real-time polymerase chain reaction and immunofluorescence with hepatic marker genes. Isolated primary hepatocytes were printed with alginate. The 3D printed hepatocytes remained alive for 14 days. Gene expression levels of Albumin , HNF-4α and Foxa3 were gradually increased in the 3D structures. Immunofluorescence analysis showed that the primary hepatocytes produced hepatic-specific proteins over the same period of time. Our research indicates that 3D bio-printing technique can be used for long-term culture of primary hepatocytes. It can therefore be used for drug screening and as a potential method of producing artificial livers.

  3. Three-dimensional structure and cyanobacterial activity within a desert biological soil crust.

    Science.gov (United States)

    Raanan, Hagai; Felde, Vincent J M N L; Peth, Stephan; Drahorad, Sylvie; Ionescu, Danny; Eshkol, Gil; Treves, Haim; Felix-Henningsen, Peter; Berkowicz, Simon M; Keren, Nir; Horn, Rainer; Hagemann, Martin; Kaplan, Aaron

    2016-02-01

    Desert biological soil crusts (BSCs) are formed by adhesion of soil particles to polysaccharides excreted by filamentous cyanobacteria, the pioneers and main producers in this habitat. Biological soil crust destruction is a central factor leading to land degradation and desertification. We study the effect of BSC structure on cyanobacterial activity. Micro-scale structural analysis using X-ray microtomography revealed a vesiculated layer 1.5-2.5 mm beneath the surface in close proximity to the cyanobacterial location. Light profiles showed attenuation with depth of 1%-5% of surface light within 1 mm but also revealed the presence of 'light pockets', coinciding with the vesiculated layer, where the irradiance was 10-fold higher than adjacent crust parts at the same depth. Maximal photosynthetic activity, examined by O2 concentration profiles, was observed 1 mm beneath the surface and another peak in association with the 'light pockets'. Thus, photosynthetic activity may not be visible to currently used remote sensing techniques, suggesting that BSCs' contribution to terrestrial productivity is underestimated. Exposure to irradiance higher than 10% full sunlight diminished chlorophyll fluorescence, whereas O2 evolution and CO2 uptake rose, indicating that fluorescence did not reflect cyanobacterial photosynthetic activity. Our data also indicate that although resistant to high illumination, the BSC-inhabiting cyanobacteria function as 'low-light adapted' organisms. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  4. Structure-based approach to pharmacophore identification, in silico screening, and three-dimensional quantitative structure-activity relationship studies for inhibitors of Trypanosoma cruzi dihydrofolate reductase function

    Energy Technology Data Exchange (ETDEWEB)

    Schormann, N.; Senkovich, O.; Walker, K.; Wright, D.L.; Anderson, A.C.; Rosowsky, A.; Ananthan, S.; Shinkre, B.; Velu, S.; Chattopadhyay, D. (UAB); (Connecticut); (Southern Research); (DFCI)

    2009-07-10

    We have employed a structure-based three-dimensional quantitative structure-activity relationship (3D-QSAR) approach to predict the biochemical activity for inhibitors of T. cruzi dihydrofolate reductase-thymidylate synthase (DHFR-TS). Crystal structures of complexes of the enzyme with eight different inhibitors of the DHFR activity together with the structure in the substrate-free state (DHFR domain) were used to validate and refine docking poses of ligands that constitute likely active conformations. Structural information from these complexes formed the basis for the structure-based alignment used as input for the QSAR study. Contrary to indirect ligand-based approaches the strategy described here employs a direct receptor-based approach. The goal is to generate a library of selective lead inhibitors for further development as antiparasitic agents. 3D-QSAR models were obtained for T. cruzi DHFR-TS (30 inhibitors in learning set) and human DHFR (36 inhibitors in learning set) that show a very good agreement between experimental and predicted enzyme inhibition data. For crossvalidation of the QSAR model(s), we have used the 10% leave-one-out method. The derived 3D-QSAR models were tested against a few selected compounds (a small test set of six inhibitors for each enzyme) with known activity, which were not part of the learning set, and the quality of prediction of the initial 3D-QSAR models demonstrated that such studies are feasible. Further refinement of the models through integration of additional activity data and optimization of reliable docking poses is expected to lead to an improved predictive ability.

  5. Three-dimensional thermal-structural analysis of a swept cowl leading edge subjected to skewed shock-shock interference heating

    Science.gov (United States)

    Polesky, Sandra P.; Dechaumphai, Pramote; Glass, Christopher E.; Pandey, Ajay K.

    1990-01-01

    A three-dimensional flux-based thermal analysis method has been developed and its capability is demonstrated by predicting the transient nonlinear temperature response of a swept cowl leading edge subjected to intense three-dimensional aerodynamic heating. The predicted temperature response from the transient thermal analysis is used in a linear elastic structural analysis to determine thermal stresses. Predicted thermal stresses are compared with those obtained from a two-dimensional analysis which represents conditions along the chord where maximum heating occurs. Results indicate a need for a three-dimensional analysis to predict accurately the leading edge thermal stress response.

  6. Three-dimensional resistivity structure of Furnas volcano (Azores archipelago, Portugal) revealed by magnetotelluric data

    Science.gov (United States)

    Kiyan, Duygu; Hogg, Colin; Rath, Volker; Byrdina, Svetlana; Vandemeulebrouck, Jean; Revil, Andre; Silva, Catarina; Viveiros, Fatima; Ferreira, Teresa; Carmo, Rita

    2017-04-01

    The Furnas volcano is the eastern-most of the three active central volcanoes of Sao Miguel Island. The main caldera formed about 30 ka BP, followed by a younger eruption at 10-12 ka BP, which is responsible for the steep topography of more than 200 m in the target area. It contains several very young eruptive centers, and a shallow caldera lake. Tectonic features of varying directions have been identified in the caldera and its vicinity (Carmo et al., 2015). In the northern part of the caldera, containing the fumarole field of Caldeiras das Furnas, a detailed map of surface CO2 emissions was recently made available (Viveiros et al., 2010). Following a pilot survey of 13 AudioMagnetoTelluric soundings (AMT) and Electrical Resistivity Tomography (ERT) data collected along two profiles in the eastern part of Furnas caldera in 2015, a second campaign was completed in June 2016, yielding a total of 39 separate soundings including 15 broad-band magnetotelluric (MT) soundings to image the electrical conductivity of the subsurface. The data quality achieved by both techniques is very good, and initial results indicate a general correlation between regions of elevated conductivity at depth and the mapped surface CO2 emissions, suggesting that they may both be caused by the presence hydrothermal fluids. Dimensionality and directionality analysis using the WALDIM (Marti et al., 2009) approach in conjunction with Phase Tensor (Caldwell et al., 2004) indicate that the geo-electrical structure needs to be inverted in 3-D. Indicators of directionality derived from the analysis follow the general geological, fault dominated structural trend of NE-SW of Sao Miguel Island. A quantitative analysis of the potential influence of the Atlantic Ocean indicates that MT data up to 1 second period can be used in inversions with confidence without including the ocean. The 3-D inversions thus have been performed including only high-resolution topography and the Furnas lake bathymetry data

  7. DHMPIV and Tomo-PIV measurements of three-dimensional structures in a turbulent boundary layer

    Science.gov (United States)

    Amili, O.; Atkinson, C.; Soria, J.

    In turbulent boundary layers, a large portion of total turbulence production happens in the near wall region, y/δ memory intensive reconstruction algorithm. It is based on a multiplicative line-of-sight (MLOS) estimation that determines possible particle locations in the volume, followed by simultaneous iterative correction. Application of MLOS-SART and MART to a turbulent boundary layer at Refθ=2200 using a 4 camera Tomo-PIV system with a volume of 1000×1000×160 voxels is discussed. In addition, near wall velocity measurement attempt made by digital holographic microscopic particle image velocimetry (DHMPIV). The technique provides a solution to overcome the poor axial accuracy and the low spatial resolution which are common problems in digital holography [5]. By reducing the depth of focus by at least one order of magnitude as well as increasing the lateral spatial resolution, DHMPIV provides the opportunity to resolve the small-scale structures existing in near wall layers.

  8. Heritable yeast prions have a highly organized three-dimensional architecture with interfiber structures.

    Science.gov (United States)

    Saibil, Helen R; Seybert, Anja; Habermann, Anja; Winkler, Juliane; Eltsov, Mikhail; Perkovic, Mario; Castaño-Diez, Daniel; Scheffer, Margot P; Haselmann, Uta; Chlanda, Petr; Lindquist, Susan; Tyedmers, Jens; Frangakis, Achilleas S

    2012-09-11

    Yeast prions constitute a "protein-only" mechanism of inheritance that is widely deployed by wild yeast to create diverse phenotypes. One of the best-characterized prions, [PSI(+)], is governed by a conformational change in the prion domain of Sup35, a translation-termination factor. When this domain switches from its normal soluble form to an insoluble amyloid, the ensuing change in protein synthesis creates new traits. Two factors make these traits heritable: (i) the amyloid conformation is self-templating; and (ii) the protein-remodeling factor heat-shock protein (Hsp)104 (acting together with Hsp70 chaperones) partitions the template to daughter cells with high fidelity. Prions formed by several other yeast proteins create their own phenotypes but share the same mechanistic basis of inheritance. Except for the amyloid fibril itself, the cellular architecture underlying these protein-based elements of inheritance is unknown. To study the 3D arrangement of prion assemblies in their cellular context, we examined yeast [PSI(+)] prions in the native, hydrated state in situ, taking advantage of recently developed methods for cryosectioning of vitrified cells. Cryo-electron tomography of the vitrified sections revealed the prion assemblies as aligned bundles of regularly spaced fibrils in the cytoplasm with no bounding structures. Although the fibers were widely spaced, other cellular complexes, such as ribosomes, were excluded from the fibril arrays. Subtomogram image averaging, made possible by the organized nature of the assemblies, uncovered the presence of an additional array of densities between the fibers. We suggest these structures constitute a self-organizing mechanism that coordinates fiber deposition and the regulation of prion inheritance.

  9. Three-dimensional visualization of magnetic domain structure with strong uniaxial anisotropy via scanning hard X-ray microtomography

    Science.gov (United States)

    Suzuki, Motohiro; Kim, Kab-Jin; Kim, Sanghoon; Yoshikawa, Hiroki; Tono, Takayuki; Yamada, Kihiro T.; Taniguchi, Takuya; Mizuno, Hayato; Oda, Kent; Ishibashi, Mio; Hirata, Yuushou; Li, Tian; Tsukamoto, Arata; Chiba, Daichi; Ono, Teruo

    2018-03-01

    An X-ray tomographic technique was developed to investigate the internal magnetic domain structure in a micrometer-sized ferromagnetic sample. The technique is based on a scanning hard X-ray nanoprobe using X-ray magnetic circular dichroism (XMCD). From transmission XMCD images at the Gd L3 edge as a function of the sample rotation angle, the three-dimensional (3D) distribution of a single component of the magnetic vector in a GdFeCo microdisc was reconstructed with a spatial resolution of 360 nm, using a modified algebraic reconstruction algorithm. The method is applicable to practical magnetic materials and can be extended to 3D visualization of the magnetic domain formation process under external magnetic fields.

  10. Radio frequency plasma method for uniform surface processing of RF cavities and other three-dimensional structures

    Energy Technology Data Exchange (ETDEWEB)

    Popovic, Svetozar; Upadhyay, Janardan; Vuskovic, Leposava; Phillips, H. Lawrence; Valente-Feliciano, Anne-Marie

    2017-12-26

    A method for efficient plasma etching of surfaces inside three-dimensional structures can include positioning an inner electrode within the chamber cavity; evacuating the chamber cavity; adding a first inert gas to the chamber cavity; regulating the pressure in the chamber; generating a plasma sheath along the inner wall of the chamber cavity; adjusting a positive D.C. bias on the inner electrode to establish an effective plasma sheath voltage; adding a first electronegative gas to the chamber cavity; optionally readjusting the positive D.C. bias on the inner electrode reestablish the effective plasma sheath voltage at the chamber cavity; etching the inner wall of the chamber cavity; and polishing the inner wall to a desired surface roughness.

  11. Three-dimensional band structure of LaSb and CeSb: Absence of band inversion

    Science.gov (United States)

    Oinuma, H.; Souma, S.; Takane, D.; Nakamura, T.; Nakayama, K.; Mitsuhashi, T.; Horiba, K.; Kumigashira, H.; Yoshida, M.; Ochiai, A.; Takahashi, T.; Sato, T.

    2017-07-01

    We have performed angle-resolved photoemission spectroscopy (ARPES) of LaSb and CeSb, a candidate of topological insulators. Using soft-x-ray photons, we have accurately determined the three-dimensional bulk band structure and revealed that the band inversion at the Brillouin-zone corner, a prerequisite for realizing the topological-insulator phase, is absent in both LaSb and CeSb. Moreover, unlike the ARPES data obtained with soft-x-ray photons, those with VUV photons were found to suffer significant kz broadening. These results suggest that LaSb and CeSb are topologically trivial semimetals, and unusual Dirac-cone-like states observed with VUV photons are not of the topological origin.

  12. Age-Based Comparison of Human Dendritic Spine Structure Using Complete Three-Dimensional Reconstructions

    Science.gov (United States)

    Benavides-Piccione, Ruth; Fernaud-Espinosa, Isabel; Robles, Victor; Yuste, Rafael; DeFelipe, Javier

    2013-01-01

    Dendritic spines of pyramidal neurons are targets of most excitatory synapses in the cerebral cortex. Recent evidence suggests that the morphology of the dendritic spine could determine its synaptic strength and learning rules. However, unfortunately, there are scant data available regarding the detailed morphology of these structures for the human cerebral cortex. In the present study, we analyzed over 8900 individual dendritic spines that were completely 3D reconstructed along the length of apical and basal dendrites of layer III pyramidal neurons in the cingulate cortex of 2 male humans (aged 40 and 85 years old), using intracellular injections of Lucifer Yellow in fixed tissue. We assembled a large, quantitative database, which revealed a major reduction in spine densities in the aged case. Specifically, small and short spines of basal dendrites and long spines of apical dendrites were lost, regardless of the distance from the soma. Given the age difference between the cases, our results suggest selective alterations in spines with aging in humans and indicate that the spine volume and length are regulated by different biological mechanisms. PMID:22710613

  13. Multiscale Pressure-Balanced Structures in Three-dimensional Magnetohydrodynamic Turbulence

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Liping; Zhang, Lei; Feng, Xueshang [SIGMA Weather Group, State Key Laboratory for Space Weather, National Space Science Center, Chinese Academy of Sciences, 100190, Beijing (China); He, Jiansen; Tu, Chuanyi; Wang, Linghua [School of Earth and Space Sciences, Peking University, 100871 Beijing (China); Li, Shengtai [Theoretical Division, MS B284, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Marsch, Eckart [Institute for Experimental and Applied Physics, Christian Albrechts University at Kiel, D-24118 Kiel (Germany); Wang, Xin, E-mail: jshept@gmail.com [School of Space and Environment, Beihang University, 100191 Beijing (China)

    2017-02-10

    Observations of solar wind turbulence indicate the existence of multiscale pressure-balanced structures (PBSs) in the solar wind. In this work, we conduct a numerical simulation to investigate multiscale PBSs and in particular their formation in compressive magnetohydrodynamic turbulence. By the use of the higher-order Godunov code Athena, a driven compressible turbulence with an imposed uniform guide field is simulated. The simulation results show that both the magnetic pressure and the thermal pressure exhibit a turbulent spectrum with a Kolmogorov-like power law, and that in many regions of the simulation domain they are anticorrelated. The computed wavelet cross-coherence spectra of the magnetic pressure and the thermal pressure, as well as their space series, indicate the existence of multiscale PBSs, with the small PBSs being embedded in the large ones. These multiscale PBSs are likely to be related to the highly oblique-propagating slow-mode waves, as the traced multiscale PBS is found to be traveling in a certain direction at a speed consistent with that predicted theoretically for a slow-mode wave propagating in the same direction.

  14. Three-dimensional Imaging Reveals New Compartments and Structural Adaptations in Odontoblasts.

    Science.gov (United States)

    Khatibi Shahidi, M; Krivanek, J; Kaukua, N; Ernfors, P; Hladik, L; Kostal, V; Masich, S; Hampl, A; Chubanov, V; Gudermann, T; Romanov, R A; Harkany, T; Adameyko, I; Fried, K

    2015-07-01

    In organized tissues, the precise geometry and the overall shape are critical for the specialized functions that the cells carry out. Odontoblasts are major matrix-producing cells of the tooth and have also been suggested to participate in sensory transmission. However, refined morphologic data on these important cells are limited, which hampers the analysis and understanding of their cellular functions. We took advantage of fluorescent color-coding genetic tracing to visualize and reconstruct in 3 dimensions single odontoblasts, pulp cells, and their assemblages. Our results show distinct structural features and compartments of odontoblasts at different stages of maturation, with regard to overall cellular shape, formation of the main process, orientation, and matrix deposition. We demonstrate previously unanticipated contacts between the processes of pulp cells and odontoblasts. All reported data are related to mouse incisor tooth. We also show that odontoblasts express TRPM5 and Piezo2 ion channels. Piezo2 is expressed ubiquitously, while TRPM5 is asymmetrically distributed with distinct localization to regions proximal to and within odontoblast processes. © International & American Associations for Dental Research 2015.

  15. Development of a novel starch with a three-dimensional ordered macroporous structure for improving the dissolution rate of felodipine

    Energy Technology Data Exchange (ETDEWEB)

    Hao, Yanna; Wu, Chao, E-mail: wuchao27@126.com; Zhao, Zongzhe; Zhao, Ying; Xu, Jie; Qiu, Yang; Jiang, Jie; Yu, Tong; Ma, Chunyu; Zhou, Buyun

    2016-01-01

    In this study, silica nanospheres with different particle sizes were used as hard template for synthesis of a starch with a novel three-dimensional ordered macroporous structure (3DOMTS). As a pharmaceutical adjuvant, 3DOMTS was used to improve the dissolution rate and oral relative bioavailability of water-insoluble drugs. Felodipine (FDP) was chosen as a model drug and was loaded into the 3DOMTS by solvent evaporation. FDP loading into 3DOMTS with different pore sizes was characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), differential scanning calorimeter (DSC), powder X-ray diffractometer (PXRD) and Fourier-Transform Infrared (FTIR). The results obtained showed that FDP was present in the pores in an amorphic or microcrystalline state. The in vitro dissolution results showed that 3DOMTS could effectively improve the dissolution rate of FDP in comparison with commercial common tablets. Pharmacokinetic results indicated that the oral relative bioavailability of self-made FDP–3DOMTS tablets were 184%, showing that 3DOMTS produced a significantly increased oral absorption of FDP. In conclusion, 3DOMTS exhibits the dual potential of improving the dissolution rate of poorly water soluble drugs and the novel filler produced by direct compression technology confirming that 3DOMTS will be useful for many applications in the field of pharmaceutics. - Highlights: • We successfully prepared a starch with a novel three-dimensional ordered macroporous structure (3DOMTS). • 3DOMTS can suppress the crystallinity of the drug to maintain it at amorphous state. • In vivo and in vitro experiments proved that 3DOMTS can improve the solubility and bioavailability of felodipine.

  16. Using high resolution computed tomography to visualize the three dimensional structure and function of plant vasculature.

    Science.gov (United States)

    McElrone, Andrew J; Choat, Brendan; Parkinson, Dilworth Y; MacDowell, Alastair A; Brodersen, Craig R

    2013-04-05

    High resolution x-ray computed tomography (HRCT) is a non-destructive diagnostic imaging technique with sub-micron resolution capability that is now being used to evaluate the structure and function of plant xylem network in three dimensions (3D) (e.g. Brodersen et al. 2010; 2011; 2012a,b). HRCT imaging is based on the same principles as medical CT systems, but a high intensity synchrotron x-ray source results in higher spatial resolution and decreased image acquisition time. Here, we demonstrate in detail how synchrotron-based HRCT (performed at the Advanced Light Source-LBNL Berkeley, CA, USA) in combination with Avizo software (VSG Inc., Burlington, MA, USA) is being used to explore plant xylem in excised tissue and living plants. This new imaging tool allows users to move beyond traditional static, 2D light or electron micrographs and study samples using virtual serial sections in any plane. An infinite number of slices in any orientation can be made on the same sample, a feature that is physically impossible using traditional microscopy methods. Results demonstrate that HRCT can be applied to both herbaceous and woody plant species, and a range of plant organs (i.e. leaves, petioles, stems, trunks, roots). Figures presented here help demonstrate both a range of representative plant vascular anatomy and the type of detail extracted from HRCT datasets, including scans for coast redwood (Sequoia sempervirens), walnut (Juglans spp.), oak (Quercus spp.), and maple (Acer spp.) tree saplings to sunflowers (Helianthus annuus), grapevines (Vitis spp.), and ferns (Pteridium aquilinum and Woodwardia fimbriata). Excised and dried samples from woody species are easiest to scan and typically yield the best images. However, recent improvements (i.e. more rapid scans and sample stabilization) have made it possible to use this visualization technique on green tissues (e.g. petioles) and in living plants. On occasion some shrinkage of hydrated green plant tissues will cause

  17. Using High Resolution Computed Tomography to Visualize the Three Dimensional Structure and Function of Plant Vasculature

    Science.gov (United States)

    McElrone, Andrew J.; Choat, Brendan; Parkinson, Dilworth Y.; MacDowell, Alastair A.; Brodersen, Craig R.

    2013-01-01

    High resolution x-ray computed tomography (HRCT) is a non-destructive diagnostic imaging technique with sub-micron resolution capability that is now being used to evaluate the structure and function of plant xylem network in three dimensions (3D) (e.g. Brodersen et al. 2010; 2011; 2012a,b). HRCT imaging is based on the same principles as medical CT systems, but a high intensity synchrotron x-ray source results in higher spatial resolution and decreased image acquisition time. Here, we demonstrate in detail how synchrotron-based HRCT (performed at the Advanced Light Source-LBNL Berkeley, CA, USA) in combination with Avizo software (VSG Inc., Burlington, MA, USA) is being used to explore plant xylem in excised tissue and living plants. This new imaging tool allows users to move beyond traditional static, 2D light or electron micrographs and study samples using virtual serial sections in any plane. An infinite number of slices in any orientation can be made on the same sample, a feature that is physically impossible using traditional microscopy methods. Results demonstrate that HRCT can be applied to both herbaceous and woody plant species, and a range of plant organs (i.e. leaves, petioles, stems, trunks, roots). Figures presented here help demonstrate both a range of representative plant vascular anatomy and the type of detail extracted from HRCT datasets, including scans for coast redwood (Sequoia sempervirens), walnut (Juglans spp.), oak (Quercus spp.), and maple (Acer spp.) tree saplings to sunflowers (Helianthus annuus), grapevines (Vitis spp.), and ferns (Pteridium aquilinum and Woodwardia fimbriata). Excised and dried samples from woody species are easiest to scan and typically yield the best images. However, recent improvements (i.e. more rapid scans and sample stabilization) have made it possible to use this visualization technique on green tissues (e.g. petioles) and in living plants. On occasion some shrinkage of hydrated green plant tissues will cause

  18. Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures.

    Science.gov (United States)

    Kosinski, Jan; von Appen, Alexander; Ori, Alessandro; Karius, Kai; Müller, Christoph W; Beck, Martin

    2015-03-01

    Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques. Cross-linking mass spectrometry (XL-MS) identifies proximal protein residues and thus is increasingly used to map protein interactions and determine the relative orientation of subunits within the structure of protein complexes. To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures. Xlink Analyzer enables automatic visualization of cross-links, identifies cross-links violating spatial restraints, calculates violation statistics, maps chemically modified surfaces, and allows interactive manipulations that facilitate analysis of XL-MS data and aid designing new experiments. We demonstrate these features by mapping interaction sites within RNA polymerase I and the Rvb1/2 complex. Xlink Analyzer is implemented as a plugin to UCSF Chimera, a standard structural biology software tool, and thus enables seamless integration of XL-MS data with, e.g. fitting of X-ray structures to EM maps. Xlink Analyzer is available for download at http://www.beck.embl.de/XlinkAnalyzer.html. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  19. Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling

    Directory of Open Access Journals (Sweden)

    Dostie Josée

    2011-10-01

    Full Text Available Abstract Background Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mechanism of gene expression regulation. Chromosome Conformation Capture Carbon Copy (5C and its variant Hi-C are techniques used to measure the interaction frequency (IF between specific regions of the genome. Our goal is to use the IF data generated by these experiments to computationally model and analyze three-dimensional chromatin organization. Results We formulate a probabilistic model linking 5C/Hi-C data to physical distances and describe a Markov chain Monte Carlo (MCMC approach called MCMC5C to generate a representative sample from the posterior distribution over structures from IF data. Structures produced from parallel MCMC runs on the same dataset demonstrate that our MCMC method mixes quickly and is able to sample from the posterior distribution of structures and find subclasses of structures. Structural properties (base looping, condensation, and local density were defined and their distribution measured across the ensembles of structures generated. We applied these methods to a biological model of human myelomonocyte cellular differentiation and identified distinct chromatin conformation signatures (CCSs corresponding to each of the cellular states. We also demonstrate the ability of our method to run on Hi-C data and produce a model of human chromosome 14 at 1Mb resolution that is consistent with previously observed structural properties as measured by 3D-FISH. Conclusions We believe that tools like MCMC5C are essential for the reliable analysis of data from the 3C-derived techniques such as 5C and Hi-C. By integrating complex, high-dimensional and noisy datasets into an easy to interpret ensemble of three-dimensional

  20. Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling.

    Science.gov (United States)

    Rousseau, Mathieu; Fraser, James; Ferraiuolo, Maria A; Dostie, Josée; Blanchette, Mathieu

    2011-10-25

    Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mechanism of gene expression regulation. Chromosome Conformation Capture Carbon Copy (5C) and its variant Hi-C are techniques used to measure the interaction frequency (IF) between specific regions of the genome. Our goal is to use the IF data generated by these experiments to computationally model and analyze three-dimensional chromatin organization. We formulate a probabilistic model linking 5C/Hi-C data to physical distances and describe a Markov chain Monte Carlo (MCMC) approach called MCMC5C to generate a representative sample from the posterior distribution over structures from IF data. Structures produced from parallel MCMC runs on the same dataset demonstrate that our MCMC method mixes quickly and is able to sample from the posterior distribution of structures and find subclasses of structures. Structural properties (base looping, condensation, and local density) were defined and their distribution measured across the ensembles of structures generated. We applied these methods to a biological model of human myelomonocyte cellular differentiation and identified distinct chromatin conformation signatures (CCSs) corresponding to each of the cellular states. We also demonstrate the ability of our method to run on Hi-C data and produce a model of human chromosome 14 at 1Mb resolution that is consistent with previously observed structural properties as measured by 3D-FISH. We believe that tools like MCMC5C are essential for the reliable analysis of data from the 3C-derived techniques such as 5C and Hi-C. By integrating complex, high-dimensional and noisy datasets into an easy to interpret ensemble of three-dimensional conformations, MCMC5C allows researchers to

  1. COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures.

    Science.gov (United States)

    Firdaus-Raih, Mohd; Hamdani, Hazrina Yusof; Nadzirin, Nurul; Ramlan, Effirul Ikhwan; Willett, Peter; Artymiuk, Peter J

    2014-07-01

    Hydrogen bonds are crucial factors that stabilize a complex ribonucleic acid (RNA) molecule's three-dimensional (3D) structure. Minute conformational changes can result in variations in the hydrogen bond interactions in a particular structure. Furthermore, networks of hydrogen bonds, especially those found in tight clusters, may be important elements in structure stabilization or function and can therefore be regarded as potential tertiary motifs. In this paper, we describe a graph theoretical algorithm implemented as a web server that is able to search for unbroken networks of hydrogen-bonded base interactions and thus provide an accounting of such interactions in RNA 3D structures. This server, COGNAC (COnnection tables Graphs for Nucleic ACids), is also able to compare the hydrogen bond networks between two structures and from such annotations enable the mapping of atomic level differences that may have resulted from conformational changes due to mutations or binding events. The COGNAC server can be accessed at http://mfrlab.org/grafss/cognac. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. The three-dimensional structure of the FMO protein from Pelodictyon phaeum and the implications for energy transfer.

    Science.gov (United States)

    Larson, Chadwick R; Seng, Chenda O; Lauman, Lisa; Matthies, Heather J; Wen, Jianzhong; Blankenship, Robert E; Allen, James P

    2011-02-01

    The Fenna-Matthews-Olson (FMO) antenna protein from the green bacterium Pelodictyon phaeum mediates the transfer of energy from the peripheral chlorosome antenna complex to the membrane-bound reaction center. The three-dimensional structure of this protein has been solved using protein crystallography to a resolution limit of 2.0 Å, with R(work) and R(free) values of 16.6 and 19.9%, respectively. The structure is a trimer of three identical subunits related by a threefold symmetry axis. Each subunit has two beta sheets that surround 8 bacteriochlorophylls. The bacteriochlorophylls are all five-coordinated, with the axial ligand being a histidine, serine, backbone carbonyl, or bound water molecule. The arrangement of the bacteriochlorophylls is generally well conserved in comparison to other FMO structures, but differences are apparent in the interactions with the surrounding protein. In this structure the position and orientation of the eighth bacteriochlorophyll is well defined and shows differences in its location and the coordination of the central Mg compared to previous models. The implications of this structure on the ability of the FMO protein to perform energy transfer are discussed in terms of the experimental optical measurements.

  3. A relationship between three-dimensional surface hydration structures and force distribution measured by atomic force microscopy

    Science.gov (United States)

    Miyazawa, Keisuke; Kobayashi, Naritaka; Watkins, Matthew; Shluger, Alexander L.; Amano, Ken-Ichi; Fukuma, Takeshi

    2016-03-01

    Hydration plays important roles in various solid-liquid interfacial phenomena. Very recently, three-dimensional scanning force microscopy (3D-SFM) has been proposed as a tool to visualise solvated surfaces and their hydration structures with lateral and vertical (sub) molecular resolution. However, the relationship between the 3D force map obtained and the equilibrium water density, ρ(r), distribution above the surface remains an open question. Here, we investigate this relationship at an interface of an inorganic mineral, fluorite, and water. The force maps measured in pure water are directly compared to force maps generated using the solvent tip approximation (STA) model and from explicit molecular dynamics simulations. The results show that the simulated STA force map describes the major features of the experimentally obtained force image. The agreement between the STA data and the experiment establishes the correspondence between the water density used as an input to the STA model and the experimental hydration structure and thus provides a tool to bridge the experimental force data and atomistic solvation structures. Further applications of this method should improve the accuracy and reliability of both interpretation of 3D-SFM force maps and atomistic simulations in a wide range of solid-liquid interfacial phenomena.Hydration plays important roles in various solid-liquid interfacial phenomena. Very recently, three-dimensional scanning force microscopy (3D-SFM) has been proposed as a tool to visualise solvated surfaces and their hydration structures with lateral and vertical (sub) molecular resolution. However, the relationship between the 3D force map obtained and the equilibrium water density, ρ(r), distribution above the surface remains an open question. Here, we investigate this relationship at an interface of an inorganic mineral, fluorite, and water. The force maps measured in pure water are directly compared to force maps generated using the solvent

  4. Three-dimensional structure of the Trypanosome flagellum suggests that the paraflagellar rod functions as a biomechanical spring.

    Directory of Open Access Journals (Sweden)

    Louise C Hughes

    Full Text Available Flagellum motility is critical for normal human development and for transmission of pathogenic protozoa that cause tremendous human suffering worldwide. Biophysical principles underlying motility of eukaryotic flagella are conserved from protists to vertebrates. However, individual cells exhibit diverse waveforms that depend on cell-specific elaborations on basic flagellum architecture. Trypanosoma brucei is a uniflagellated protozoan parasite that causes African sleeping sickness. The T. brucei flagellum is comprised of a 9+2 axoneme and an extra-axonemal paraflagellar rod (PFR, but the three-dimensional (3D arrangement of the underlying structural units is poorly defined. Here, we use dual-axis electron tomography to determine the 3D architecture of the T. brucei flagellum. We define the T. brucei axonemal repeating unit. We observe direct connections between the PFR and axonemal dyneins, suggesting a mechanism by which mechanochemical signals may be transmitted from the PFR to axonemal dyneins. We find that the PFR itself is comprised of overlapping laths organized into distinct zones that are connected through twisting elements at the zonal interfaces. The overall structure has an underlying 57 nm repeating unit. Biomechanical properties inferred from PFR structure lead us to propose that the PFR functions as a biomechanical spring that may store and transmit energy derived from axonemal beating. These findings provide insight into the structural foundations that underlie the distinctive flagellar waveform that is a hallmark of T. brucei cell motility.

  5. Constructing Repairable Meta-Structures of Ultra-Broad-Band Electromagnetic Absorption from Three-Dimensional Printed Patterned Shells.

    Science.gov (United States)

    Song, Wei-Li; Zhou, Zhili; Wang, Li-Chen; Cheng, Xiao-Dong; Chen, Mingji; He, Rujie; Chen, Haosen; Yang, Yazheng; Fang, Daining

    2017-12-13

    Ultra-broad-band electromagnetic absorption materials and structures are increasingly attractive for their critical role in competing with the advanced broad-band electromagnetic detection systems. Mechanically soft and weak wax-based materials composites are known to be insufficient to serve in practical electromagnetic absorption applications. To break through such barriers, here we developed an innovative strategy to enable the wax-based composites to be robust and repairable meta-structures by employing a three-dimensional (3D) printed polymeric patterned shell. Because of the integrated merits from both the dielectric loss wax-based composites and mechanically robust 3D printed shells, the as-fabricated meta-structures enable bear mechanical collision and compression, coupled with ultra-broad-band absorption (7-40 and 75-110 GHz, reflection loss  smaller than -10 dB) approaching state-of-the-art electromagnetic absorption materials. With the assistance of experiment and simulation methods, the design advantages and mechanism of employing such 3D printed shells for substantially promoting the electromagnetic absorption performance have been demonstrated. Therefore, such universal strategy that could be widely extended to other categories of wax-based composites highlights a smart stage on which high-performance practical multifunction meta-structures with ultra-broad-band electromagnetic absorption could be envisaged.

  6. Time-Domain Three Dimensional BE-FE Method for Transient Response of Floating Structures Under Unsteady Loads

    Directory of Open Access Journals (Sweden)

    R. E. S. Ismail

    Full Text Available Abstract This paper presents a direct time-domain three dimensional (3D numerical procedure to simulate the transient response of very large floating structures (VLFS subjected to unsteady external loads as well as moving mass. The proposed procedure employs the Boundary Element and Finite Element methods (FEM-BEM. The floating structure and the surrounding fluid are discretized by 4-node isoparametric finite elements (FE and by 4-node constant boundary elements (BE, respectively. Structural analysis is based on Mindlin's plate theory. The equation of motion is constructed taking into account the effect of inertia loading due to the moving mass. In order to obtain the hydrodynamic forces (added mass and radiation damping, the coupled natural frequencies are first obtained by an iterative method, since hydrodynamic forces become frequency-dependent. Then the Newark integration method is employed to solve the equation of motion for structural system. In order to prove the validity of the present method, a FORTRAN program is developed and numerical examples are carried out to compare its results with those of published experimental results of a scale model of VLFS under a weight drop and airplane landing and takeoff in still water condition. The comparisons show very good agreement.

  7. Modelling of three-dimensional structures of cytochromes P450 11B1 and 11B2.

    Science.gov (United States)

    Belkina, N V; Lisurek, M; Ivanov, A S; Bernhardt, R

    2001-12-15

    The final steps of the biosynthesis of glucocorticoids and mineralocorticoids in the adrenal cortex require the action of two different cytochromes P450--CYP11B1 and CYP11B2. Homology modelling of the three-dimensional structures of these cytochromes was performed based on crystallographic coordinates of two bacterial P450s, CYP102 (P450BM-3) and CYP108 (P450terp). Principal attention was given to the modelling of the active sites and a comparison of the active site structures of CYP11B1 and CYP11B2 was performed. It can be demonstrated that key residue contacts within the active site appear to depend on the orientation of the heme. The obtained 3D structures of CYP11B1 and CYP11B2 were used for investigation of structure-function relationships of these enzymes. Previously obtained results on naturally occurring mutants and on mutants obtained by site-directed mutagenesis are discussed.

  8. The Safety and Feasibility of Three-Dimensional Visualization Technology Assisted Right Posterior Lobe Allied with Part of V and VIII Sectionectomy for Right Hepatic Malignancy Therapy.

    Science.gov (United States)

    Hu, Min; Hu, Haoyu; Cai, Wei; Mo, Zhikang; Xiang, Nan; Yang, Jian; Fang, Chihua

    2017-11-27

    Hepatectomy is the optimal method for liver cancer; the virtual liver resection based on three-dimensional visualization technology (3-DVT) could provide better preoperative strategy for surgeon. We aim to introduce right posterior lobe allied with part of V and VIII sectionectomy assisted by 3-DVT as a promising treatment for massive or multiple right hepatic malignancies to retain maximum residual liver volume on the basis of R0 resection. Among 126 consecutive patients who underwent hepatectomy, 9 (7%) underwent right posterior lobe allied with part of V and VIII sectionectomy. 21 (17%) underwent right hemihepatectomy (RH). The virtual RH was performed with 3-DVT, which provided better observation of spatial position relationship between tumor and vessels, and the more accurate estimation of the remnant liver volume. If remnant liver volume was transfusion, operation length, liver function, and postoperative complications, were similar between two groups before and after propensity matching. The postoperative first, third, fifth, and seventh days mean value of aspartate aminotransferase (AST), alanine aminotransferase (ALT), albumin (ALB), and total bilirubin had no significant difference compared with preoperative value. One patient in each group had recurrence six months after surgery. Right posterior lobe allied with part of V and VIII sectionectomy based on 3-DVT is safe and feasible surgery way, and can be a very promising method in massive or multiple right hepatic malignancy therapy.

  9. Utility of a Three-Dimensional Interactive Augmented Reality Program for Balance and Mobility Rehabilitation in the Elderly: A Feasibility Study.

    Science.gov (United States)

    Im, Dal Jae; Ku, Jeunghun; Kim, Yeun Joon; Cho, Sangwoo; Cho, Yun Kyung; Lim, Teo; Lee, Hye Sun; Kim, Hyun Jung; Kang, Youn Joo

    2015-06-01

    To improve lower extremity function and balance in elderly persons, we developed a novel, three-dimensional interactive augmented reality system (3D ARS). In this feasibility study, we assessed clinical and kinematic improvements, user participation, and the side effects of our system. Eighteen participants (age, 56-76 years) capable of walking independently and standing on one leg were recruited. The participants received 3D ARS training during 10 sessions (30-minute duration each) for 4 weeks. Berg Balance Scale (BBS) and the Timed Up and Go (TUG) scores were obtained before and after the exercises. Outcome performance variables, including response time and success rate, and kinematic variables, such as hip and knee joint angle, were evaluated after each session. Participants exhibited significant clinical improvements in lower extremity balance and mobility following the intervention, as shown by improved BBS and TUG scores (pincreased across sessions (p<0.001). All participants completed the program without experiencing any adverse effects. Substantial clinical and kinematic improvements were observed after applying a novel 3D ARS training program, suggesting that this system can enhance lower extremity function and facilitate assessments of lower extremity kinematic capacity.

  10. Accurate facade feature extraction method for buildings from three-dimensional point cloud data considering structural information

    Science.gov (United States)

    Wang, Yongzhi; Ma, Yuqing; Zhu, A.-xing; Zhao, Hui; Liao, Lixia

    2018-05-01

    Facade features represent segmentations of building surfaces and can serve as a building framework. Extracting facade features from three-dimensional (3D) point cloud data (3D PCD) is an efficient method for 3D building modeling. By combining the advantages of 3D PCD and two-dimensional optical images, this study describes the creation of a highly accurate building facade feature extraction method from 3D PCD with a focus on structural information. The new extraction method involves three major steps: image feature extraction, exploration of the mapping method between the image features and 3D PCD, and optimization of the initial 3D PCD facade features considering structural information. Results show that the new method can extract the 3D PCD facade features of buildings more accurately and continuously. The new method is validated using a case study. In addition, the effectiveness of the new method is demonstrated by comparing it with the range image-extraction method and the optical image-extraction method in the absence of structural information. The 3D PCD facade features extracted by the new method can be applied in many fields, such as 3D building modeling and building information modeling.

  11. Formation of a-plane facets in three-dimensional hexagonal GaN structures for photonic devices.

    Science.gov (United States)

    Lim, Seung-Hyuk; Sim, Young Chul; Yoo, Yang-Seok; Choi, Sunghan; Lee, Sangwon; Cho, Yong-Hoon

    2017-08-24

    Control of the growth front in three-dimensional (3D) hexagonal GaN core structures is crucial for increased performance of light-emitting diodes (LEDs), and other photonic devices. This is due to the fact that InGaN layers formed on different growth facets in 3D structures exhibit various band gaps which originate from differences in the indium-incorporation efficiency, internal polarization, and growth rate. Here, a-plane {[Formula: see text] } facets, which are rarely formed in hexagonal pyramid based growth, are intentionally fabricated using mask patterns and adjustment of the core growth conditions. Moreover, the growth area covered by these facets is modified by changing the growth time. The origin of the formation of a-plane {[Formula: see text]} facets is also discussed. Furthermore, due to a growth condition transition from a 3D core structure to an InGaN multi-quantum well, a growth front transformation (i.e., a transformation of a-plane {[Formula: see text]} facets to semi-polar {[Formula: see text]} facets) is directly observed. Based on our understanding and control of this novel growth mechanism, we can achieve efficient broadband LEDs or photovoltaic cells.

  12. Towards large-scale mapping of urban three-dimensional structure using Landsat imagery and global elevation datasets

    Science.gov (United States)

    Wang, P.; Huang, C.

    2017-12-01

    The three-dimensional (3D) structure of buildings and infrastructures is fundamental to understanding and modelling of the impacts and challenges of urbanization in terms of energy use, carbon emissions, and earthquake vulnerabilities. However, spatially detailed maps of urban 3D structure have been scarce, particularly in fast-changing developing countries. We present here a novel methodology to map the volume of buildings and infrastructures at 30 meter resolution using a synergy of Landsat imagery and openly available global digital surface models (DSMs), including the Shuttle Radar Topography Mission (SRTM), ASTER Global Digital Elevation Map (GDEM), ALOS World 3D - 30m (AW3D30), and the recently released global DSM from the TanDEM-X mission. Our method builds on the concept of object-based height profile to extract height metrics from the DSMs and use a machine learning algorithm to predict height and volume from the height metrics. We have tested this algorithm in the entire England and assessed our result using Lidar measurements in 25 England cities. Our initial assessments achieved a RMSE of 1.4 m (R2 = 0.72) for building height and a RMSE of 1208.7 m3 (R2 = 0.69) for building volume, demonstrating the potential of large-scale applications and fully automated mapping of urban structure.

  13. High spatial resolution measurements of large-scale three-dimensional structures in a turbulent boundary layer

    Science.gov (United States)

    Atkinson, Callum; Buchmann, Nicolas; Kuehn, Matthias; Soria, Julio

    2011-11-01

    Large-scale three-dimensional (3D) structures in a turbulent boundary layer at Reθ = 2000 are examined via the streamwise extrapolation of time-resolved stereo particle image velocimetry (SPIV) measurements in a wall-normal spanwise plane using Taylor's hypothesis. Two overlapping SPIV systems are used to provide a field of view similar to that of direct numerical simulations (DNS) on the order of 50 δ × 1 . 5 δ × 3 . 0 δ in the streamwise, wall-normal and spanwise directions, respectively, with an interrogation window size of 40+ ×20+ ×60+ wall units. Velocity power spectra are compared with DNS to examine the effective resolution of these measurements and two-point correlations are performed to investigate the integral length scales associated with coherent velocity and vorticity fluctuations. Individual coherent structures are detected to provide statistics on the 3D size, spacing, and angular orientation of large-scale structures, as well as their contribution to the total turbulent kinetic energy and Reynolds shear stress. The support of the ARC through Discovery (and LIEF) grants is gratefully acknowledged.

  14. Direct-Write, Self-Aligned Electrospinning on Paper for Controllable Fabrication of Three-Dimensional Structures.

    Science.gov (United States)

    Luo, Guoxi; Teh, Kwok Siong; Liu, Yumeng; Zang, Xining; Wen, Zhiyu; Lin, Liwei

    2015-12-23

    Electrospinning, a process that converts a solution or melt droplet into an ejected jet under a high electric field, is a well-established technique to produce one-dimensional (1D) fibers or two-dimensional (2D) randomly arranged fibrous meshes. Nevertheless, the direct electrospinning of fibers into controllable three-dimensional (3D) architectures is still a nascent technology. Here, we apply near-field electrospinning (NFES) to directly write arbitrarily shaped 3D structures through consistent and spatially controlled fiber-by-fiber stacking of polyvinylidene fluoride (PVDF) fibers. An element central to the success of this 3D electrospinning is the use of a printing paper placed on the grounded conductive plate and acting as a fiber collector. Once deposited on the paper, residual solvents from near-field electrospun fibers can infiltrate the paper substrate, enhancing the charge transfer between the deposited fibers and the ground plate via the fibrous network within the paper. Such charge transfer grounds the deposited fibers and turns them into locally fabricated electrical poles, which attract subsequent in-flight fibers to deposit in a self-aligned manner on top of each other. This process enables the design and controlled fabrication of electrospun 3D structures such as grids, walls, hollow cylinders, and other 3D logos. As such, this technique has the potential to advance the existing electrospinning technologies in constructing 3D structures for biomedical, microelectronics, and MEMS/NMES applications.

  15. IDENTIFICATION OF WIND LOAD APPLIED TO THREE-DIMENSIONAL STRUCTURES BY VIRTUE OF ITS SIMULATION IN THE WIND TUNNEL

    Directory of Open Access Journals (Sweden)

    Doroshenko Sergey Aleksandrovich

    2012-10-01

    Full Text Available The authors discuss wind loads applied to a set of two buildings. The wind load is simulated with the help of the wind tunnel. In the Russian Federation, special attention is driven to the aerodynamics of high-rise buildings and structures. According to the Russian norms, identification of aerodynamic coefficients for high-rise buildings, as well as the influence of adjacent buildings and structures, is performed on the basis of models of structures exposed to wind impacts simulated in the wind tunnel. This article deals with the results of the wind tunnel test of buildings. The simulation was carried out with the involvement of a model of two twenty-three storied buildings. The experiment was held in a wind tunnel of the closed type at in the Institute of Mechanics of Moscow State University. Data were compared at the zero speed before and after the experiment. LabView software was used to process the output data. Graphs and tables were developed in the Microsoft Excel package. GoogleSketchUp software was used as a visualization tool. The three-dimensional flow formed in the wind tunnel can't be adequately described by solving the two-dimensional problem. The aerodynamic experiment technique is used to analyze the results for eighteen angles of the wind attack.

  16. Fine structure of modal focusing effect in a three dimensional plasma-sheath-lens formed by disk electrodes

    DEFF Research Database (Denmark)

    Stamate, Eugen; Yamaguchi, Masahito

    2015-01-01

    Modal and discrete focusing effects associated with three-dimensional plasma-sheath-lenses show promising potential for applications in ion beam extraction, mass spectrometry, plasma diagnostics and for basic studies of plasma sheath. The ion focusing properties can be adjusted by controlling the...... to the sheath thickness and can be used to monitor very small changes in plasma parameters. Three dimensional simulations are found to be in very good agreement with experiments....

  17. System input-output theoretic three-dimensional measurement based on circular-shaped structured light patterns

    Science.gov (United States)

    Lee, Deokwoo; Krim, Hamid

    2017-07-01

    Alternative approaches to three-dimensional (3-D) reconstruction by employing the concepts of "system identification" and "communication systems" based on structured light patterns are proposed. In addition, a sampling criterion of the light source is derived in the case of using multiple projectors because 3-D reconstruction sometimes employs multiple viewpoints (cameras) and multiple structured light sources (or projectors). To reformulate a reconstruction problem, an input-output (I/O) system theoretic is adopted, and camera(s) and light source(s) that are located at different positions are defined as the output and the input, respectively. Akin to the system identification problem, the ratio of an output to an input, the "system function," is defined as a 3-D measurement result. Alternatively, the reconstruction work can employ the concept of the "modulation and demodulation theory," and the reconstruction work can be reinterpreted as an "input estimation problem." This contribution chiefly deals with approximate reconstruction results that are sufficient for practical applications, such as 3-D object detection, clarification, recognition, and classification, rather than a perfect 3-D reconstruction itself. To that end, the development of an efficient and fast 3-D imaging system framework is proposed.

  18. Three-dimensional architectural and structural analysis--a transition in concept and design from Delaire's cephalometric analysis.

    Science.gov (United States)

    Lee, S-H; Kil, T-J; Park, K-R; Kim, B C; Kim, J-G; Piao, Z; Corre, P

    2014-09-01

    The aim of this study was to present a systematic sequence for three-dimensional (3D) measurement and cephalometry, provide the norm data for computed tomography-based 3D architectural and structural cephalometric analysis, and validate the 3D data through comparison with Delaire's two-dimensional (2D) lateral cephalometric data for the same Korean adults. 2D and 3D cephalometric analyses were performed for 27 healthy subjects and the measurements of both analyses were then individually and comparatively analyzed. Essential diagnostic tools for 3D cephalometry with modified definitions of the points, planes, and measurements were set up based on a review of the conceptual differences between two and three dimensions. Some 2D and 3D analysis results were similar, though significant differences were found with regard to craniofacial angle (C1-F1), incisal axis angles, cranial base length (C2), and cranial height (C3). The discrepancy in C2 and C3 appeared to be directly related to the magnification of 2D cephalometric images. Considering measurement discrepancies between 2D and 3D Delaire's analyses due to differences in concept and design, 3D architectural and structural analysis needs to be conducted based on norms and a sound 3D basis for the sake of its accurate application and widespread adoption. Copyright © 2014 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

  19. Three-Dimensional Modeling of Quasicrystal Structures from X-ray Diffraction: An Icosahedral Al-Cu-Fe Alloy.

    Science.gov (United States)

    Hong, Seung-Tae

    2017-07-03

    Quasicrystals (QCs) are well-ordered but aperiodic crystals with classically forbidden symmetries (such as 5-fold). High-dimensional (HD) crystallography is a standard method to locate atom positions explicitly. However, in practice, it is still challenging because of its complexity. Here, we report a new simple approach to three-dimensional (3D) atomic modeling derived from X-ray diffraction data, and apply it to the icosahedral QC Al 0.63 Cu 0.25 Fe 0.12 . Electron density maps were calculated directly from 3D diffraction data indexed with noninteger (fractional) numbers as measured, with proper phases; each of 2 5 = 32 possible phase assignments for the five strongest reflections was used for Fourier synthesis. This resulted in an initial phasing model based on chemically sensible electron density maps. The following procedure was exactly the same as that used to determine ordinary crystal structures, except that fractional indices were assigned to the reciprocal vectors relative to the three orthogonal 2-fold axes in icosahedral (I h ) symmetry to which the observed diffraction data conformed. Finally, ∼30 000 atoms were located within a sphere of a ∼48 Å radius. Structural motifs or basic repeating units with a hierarchical nature can be found. Isolated icosahedral clusters are surrounded by a concentric dodecahedron, beyond which there is a concentric truncated icosahedron. These are strikingly similar to those obtained via HD crystallography, but show very clear real-space relationships between the clusters.

  20. The three-dimensional structure of CFA/I adhesion pili: traveler's diarrhea bacteria hang on by a spring.

    Science.gov (United States)

    Mu, Xiang-Qi; Savarino, Stephen J; Bullitt, Esther

    2008-02-22

    To survive the harsh environment of a churning intestinal tract, bacteria attach to the host epithelium via thin fibers called pili (or fimbriae). Enterotoxigenic Escherichia coli bacteria expressing colonization factor antigen I (CFA/I) pili and related pili are the most common known bacterial cause of diarrheal disease, including traveler's diarrhea. CFA/I pili, assembled via the alternate chaperone pathway, are essential for binding and colonization of the small bowel by these pathogenic bacteria. Herein, we elucidate unique structural features of CFA/I pili that appear to optimize their function as bacterial tethers in the intestinal tract. Using transmission electron microscopy of negatively stained samples in combination with iterative three-dimensional helical reconstruction methods for image processing, we determined the structure of the CFA/I pilus filament. Our results indicate that strong end-to-end protein interactions and weak interactions between the coils of a sturdy spring-like helix provide the combination of strength, stability, and flexibility required to sustain bacterial adhesion and incite intestinal disease. We propose that CFA/I pili behave like a spring to maintain attachment to the gut lining during vortex mixing and downward flow of the intestinal contents, thereby persisting long enough for these bacteria to colonize the host epithelium and cause enteric disease.

  1. RECONSTRUCTING THE SUBSURFACE THREE-DIMENSIONAL MAGNETIC STRUCTURE OF A SOLAR ACTIVE REGION USING SDO/HMI OBSERVATIONS

    International Nuclear Information System (INIS)

    Chintzoglou, Georgios; Zhang Jie

    2013-01-01

    A solar active region (AR) is a three-dimensional (3D) magnetic structure formed in the convection zone, whose property is fundamentally important for determining the coronal structure and solar activity when emerged. However, our knowledge of the detailed 3D structure prior to its emergence is rather poor, largely limited by the low cadence and sensitivity of previous instruments. Here, using the 45 s high-cadence observations from the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory, we are able for the first time to reconstruct a 3D data cube and infer the detailed subsurface magnetic structure of NOAA AR 11158, and to characterize its magnetic connectivity and topology. This task is accomplished with the aid of the image-stacking method and advanced 3D visualization. We find that the AR consists of two major bipoles or four major polarities. Each polarity in 3D shows interesting tree-like structure, i.e., while the root of the polarity appears as a single tree-trunk-like tube, the top of the polarity has multiple branches consisting of smaller and thinner flux tubes which connect to the branches of the opposite polarity that is similarly fragmented. The roots of the four polarities align well along a straight line, while the top branches are slightly non-coplanar. Our observations suggest that an active region, even appearing highly complicated on the surface, may originate from a simple straight flux tube that undergoes both horizontal and vertical bifurcation processes during its rise through the convection zone.

  2. Characterization of coherent structures in three-dimensional turbulent flows using the finite-size Lyapunov exponent

    International Nuclear Information System (INIS)

    Bettencourt, João H; López, Cristóbal; Hernández-García, Emilio

    2013-01-01

    In this paper, we use the finite-size Lyapunov exponent (FSLE) to characterize Lagrangian coherent structures in three-dimensional (3D) turbulent flows. Lagrangian coherent structures act as the organizers of transport in fluid flows and are crucial to understand their stirring and mixing properties. Generalized maxima (ridges) of the FSLE fields are used to locate these coherent structures. 3D FSLE fields are calculated in two phenomenologically distinct turbulent flows: a wall-bounded flow (channel flow) and a regional oceanic flow obtained by the numerical solution of the primitive equations where two-dimensional (2D) turbulence dominates. In the channel flow, autocorrelations of the FSLE field show that the structure is substantially different from the near wall to the mid-channel region and relates well to the more widely studied Eulerian coherent structure of the turbulent channel flow. The ridges of the FSLE field have complex shapes due to the 3D character of the turbulent fluctuations. In the oceanic flow, strong horizontal stirring is present and the flow regime is similar to that of 2D turbulence where the domain is populated by coherent eddies that interact strongly. This in turn results in the presence of high FSLE lines throughout the domain leading to strong non-local mixing. The ridges of the FSLE field are quasi-vertical surfaces, indicating that the horizontal dynamics dominates the flow. Indeed, due to rotation and stratification, vertical motions in the ocean are much less intense than horizontal ones. This suppression is absent in the channel flow, as the 3D character of the FSLE ridges shows. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Lyapunov analysis: from dynamical systems theory to applications’. (paper)

  3. Enhanced photocatalytic properties of hierarchical three-dimensional TiO{sub 2} grown on femtosecond laser structured titanium substrate

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Ting, E-mail: huangting@bjut.edu.cn; Lu, Jinlong; Xiao, Rongshi; Wu, Qiang; Yang, Wuxiong

    2017-05-01

    Highlights: • The hierarchical 3D-TiO{sub 2} is fabricated on femtosecond laser structured Ti substrate. • The formation mechanism of hierarchical 3D-TiO{sub 2} is proposed. • The structure-induced improvement of photocatalytic activity is reported. - Abstract: Three-dimensional micro-/nanostructured TiO{sub 2} (3D-TiO{sub 2}) fabricated on titanium substrate effectively improves its performance in photocatalysis, dye-sensitized solar cell and lithium-ion battery applications. In this study, the hierarchical 3D-TiO{sub 2} with anatase phase directly grown on femtosecond laser structured titanium substrate is reported. First, the primary columnar arrays were fabricated on the surface of titanium substrate by femtosecond laser structuring. Next, the secondary nano-sheet substructures were grown on the primary columnar arrays by NaOH hydrothermal treatment. Followed by ion-exchange process in HCl and annealing in the air, the hierarchical anatase 3D-TiO{sub 2} was achieved. The hierarchical anatase 3D-TiO{sub 2} exhibited enhanced performances in light harvesting and absorption ability compared to that of nano-sheet TiO{sub 2} grown on flat titanium surface without femtosecond laser structuring. The photocatalytic degradation of methyl orange reveals that photocatalytic efficiency of the hierarchical anatase 3D-TiO{sub 2} was improved by a maximum of 57% compared to that of nano-sheet TiO{sub 2} (55% vs 35%). Meanwhile, the hierarchical anatase 3D-TiO{sub 2} remained mechanically stable and constant in consecutive degradation cycles, which promises significance in practical application.

  4. Preliminary study of visualizing membrane structures of spiculated pulmonary nodules in three-dimensional thoracic CT images

    Science.gov (United States)

    Kawata, Y.; Niki, N.; Ohmatsu, H.; Aokage, K.; Kusumoto, M.; Tsuchida, T.; Eguchi, K.; Kaneko, M.

    2016-03-01

    Research results from the National Lung Screening Trial revealed that screening for lung cancer with low-dose CT (LDCT) reduces lung cancer mortality in heavy smokers by 20% compared to radiography. While this study does show the efficacy of CT-based screening, radiologists often face the problem of estimating the malignant likelihoods of pulmonary nodules detected on LDCT screening for maximizing patient survival and for preserving lung function. Spiculation is considered as one of the indicators of nodule malignancy and an important feature to assess requirements on a patient-tailored follow-up procedure. However, the spiculation is also observed in some benign nodules, particularly in tuberculoma. The elucidation of the spliculation morphology in 3D thoracic CT images is an important preliminary step towards developing the malignant discrimination strategies from benign nodules. In this study, we present a visualization method to reveal a spatial configuration of spiculation of pulmonary nodules in three-dimensional thoracic CT images. Applying the method to an example of malignant nodule with the spiculated margins, the visualizing preliminary result of the spatial configuration reveals the presence of membrane structures of spiculation.

  5. Band structure of a three-dimensional topological insulator quantum wire in the presence of a magnetic field.

    Science.gov (United States)

    Liu, Zhe; Jiang, Liwei; Zheng, Yisong

    2016-07-13

    By means of a numerical diagonalization approach, we calculate the electronic structure of a three-dimensional topological insulator (3DTI) quantum wire (QW) in the presence of a magnetic field. The QW can be viewed as a 3DTI film with lateral surfaces, when its rectangular cross section has a large aspect ratio. Our calculation indicates that nonchiral edge states emerge because of the confined states at the lateral surfaces. These states completely cover the valence band region among the Landau levels, which reasonably account for the absence of the [Formula: see text] quantum Hall effect in the relevant experimental works. In an ultrathin 3DTI film, inversion between the electron-type and hole-type bands occurs, which leads to the so-called pseudo-spin Hall effect. In a 3DTI QW with a square cross section, a tilting magnetic field can establish well-defined Landau levels in all four surfaces. In such a case, the quantum Hall edge states are localized at the square corners, characterized by the linearly crossing one-dimensional band profile. And they can be shifted between the adjacent corners by simply rotating the magnetic field.

  6. Resolving the deep electrical resistivity structure at Central Pontides, Northern Turkey by three-dimensional magnetotelluric modeling

    Science.gov (United States)

    Özaydın, Sinan; Bülent Tank, Sabri; Karaş, Mustafa; Sandvol, Eric

    2017-04-01

    Wide-band magnetotelluric (MT) (360 Hz - 1860 sec) data were acquired at 25 sites along a north - south aligned profile cutting across the Central Pontides, which are made up of highly metamorphosed formations and their tectonic boundaries including: a Lower Cretaceous-aged turbidite sequence, Central Pontides Metamorphic Supercomplex (CPMS), North Anatolian Fault Zone (NAFZ) and Izmir-Ankara-Erzincan Suture Zone (IAESZ). Dimensionality analyses over all observation points demonstrated high electrical anisotropy, which indicates complex geological and tectonic structures. This dimensional complexity and presence of the electrically conductive Black Sea augmented the requirement for a three-dimensional analysis. Inverse modeling routines, ModEM (Egbert and Kelbert, 2012) and WSINV3DMT (Siripunvaraporn et al., 2005) were utilized to reveal the geo-electrical implications over this unusually complicated region. Interpretations of the resultant models are summarized as follows: (i) Çangaldaǧ and Domuzdaǧ complexes appear as highly resistive bodies bounded by north dipping faults. (ii) Highly conductive Tosya Basin sediments overlain the ophiolitic materials as a thin cover located at the south of the NAFZ. (iii) North Anatolian Fault and some auxiliary faults within the system exhibit conductive-resistive interfaces that reach to lower crustal levels. (iv) IAESZ is a clear feature marked by the resistivity contrast between NAFZ-related sedimentary basins and Neo-Tethyan ophiolites.

  7. Syntheses, structures, and photoluminescence of three-dimensional lanthanide coordination polymers with 2,5-pyridinedicarboxylic acid

    International Nuclear Information System (INIS)

    Huang Yan; Song Yishan; Yan, Bing; Shao Min

    2008-01-01

    Four new open-framework coordination polymers of lanthanide 2,5-pyridinedicarboxylates, with the formulas Pr2(pydc) 3 (H 2 O) 2 (1), Ln(pydc)(Hpydc) (Ln=Tb (2), Er (3), Eu (5)), and Gd(pydc)(nic)(H 2 O) (4) (H 2 pydc=2,5-pyridinedicarboxylic acid, Hnic=nicotinic acid), have been hydrothermally synthesized and four of them (except Eu (5)) have been structurally characterized. Complex 1 consists of two types of ligand-binding modes contributing to link the PrO 7 N(H 2 O) polyhedral chains to three-dimensional (3D) open-framework architecture. Complexes 2 and 3 are isostructural and feature unique 3D cage-like supramolecular frameworks remarkably different from that of 1, owing to the different ligand-bridging pattern. Complex 4, however, has the distinct 3D open-framework architecture due to the presence of unexpected nicotinate ligands, which may be derived from pydc ligands via in-situ decarboxylation under the hydrothermal condition. - Graphical abstract: Four new lanthanide coordination polymers have been hydrothermally synthesized by the reaction of 2,5-pyridinedicarboxylic acid with the corresponding lanthanide nitrates, and they show three types of 3D open-framework architecture. Complexes 2 and 5 show strong characteristic green (or red) luminescence and long lifetimes

  8. Three-Dimensional Dendritic Structures of NiCoMo as Efficient Electrocatalysts for the Hydrogen Evolution Reaction.

    Science.gov (United States)

    Gao, Di; Guo, Jiangna; Cui, Xun; Yang, Lin; Yang, Yang; He, Huichao; Xiao, Peng; Zhang, Yunhuai

    2017-07-12

    First-row (3d) transition-metal catalysts, such as bimetallic Ni-Co, represent an emerging class of electrocatalysts for HER, but they usually suffer from a large overpotential significantly above thermodynamic demands. Here, we doped NiCo catalyst with non3d metals molybdenum (Mo) for improvement in catalyzing the hydrogen evolution reaction. The ternary catalyst was readily obtained by a one-pot process via the sequential electrodeposition of Ni, Co, and Mo precursors on titanium (Ti) support. By tailing the deposition conditions, we fabricated NiCoMo catalysts with three-dimensional dendritic structures, exhibiting large amounts of electrochemically active sites. To attain the benchmark HER current density of -10 mA cm -2 , an overpotential of ∼132 mV is required in 0.1 M KOH for the Mo-doped NiCo (5 atom % Mo in bath), and they produced the decreasing in Tafel slope of ∼108 mV decade -1 exceeding those of binary NiCo alloy catalysts and other contents of Mo doping. In a synergistic effect, dopant incorporation of Mo element may provide near-optimal adsorption energies for HER intermediates promoting the process of water dissociation and hydrogen intermediates production and binding into molecular hydrogen.

  9. Evaluation of Artificial Caudal Fin for Fish Robot with Two Joints by Using Three-Dimensional Fluid-Structure Simulation

    Directory of Open Access Journals (Sweden)

    Yogo Takada

    2013-01-01

    Full Text Available A fish robot with image sensors is useful to research for underwater creatures such as fish. However, the propulsion velocity of a fish robot is very slow compared with live fish. It is necessary to swim at a speed several times faster than the speed of the current robots for various usages. Therefore, we are searching for the method of making the robot swim fast. The simulation before making the robot is important. We have made the computational simulation program of three-dimensional fluid-structure analysis. The flow around the caudal fin can be examined by analyzing the fin as an elastic body. We compared the results of numerical analysis with the results of PIV measurement. Both were agreed well. Because the performance of a fish robot with two joints is better than that of a fish robot with one joint, we searched for an excellent fin for the fish robot with two joints by using CFD. We confirmed that the swimming performance of a fish robot becomes very good when the caudal fin is rigid except for the root of the fin which is comparatively flexible.

  10. New Three-Dimensional Porous Electrode Concept: Vertically-Aligned Carbon Nanotubes Directly Grown on Embroidered Copper Structures

    Directory of Open Access Journals (Sweden)

    Noemí Aguiló-Aguayo

    2017-12-01

    Full Text Available New three-dimensional (3D porous electrode concepts are required to overcome limitations in Li-ion batteries in terms of morphology (e.g., shapes, dimensions, mechanical stability (e.g., flexibility, high electroactive mass loadings, and electrochemical performance (e.g., low volumetric energy densities and rate capabilities. Here a new electrode concept is introduced based on the direct growth of vertically-aligned carbon nanotubes (VA-CNTs on embroidered Cu current collectors. The direct growth of VA-CNTs was achieved by plasma-enhanced chemical vapor deposition (PECVD, and there was no application of any post-treatment or cleaning procedure. The electrochemical behavior of the as-grown VA-CNTs was analyzed by charge/discharge cycles at different specific currents and with electrochemical impedance spectroscopy (EIS measurements. The results were compared with values found in the literature. The as-grown VA-CNTs exhibit higher specific capacities than graphite and pristine VA-CNTs found in the literature. This together with the possibilities that the Cu embroidered structures offer in terms of specific surface area, total surface area, and designs provide a breakthrough in new 3D electrode concepts.

  11. Three-dimensional spatial structures of solar wind turbulence from 10 000-km to 100-km scales

    Directory of Open Access Journals (Sweden)

    Y. Narita

    2011-10-01

    Full Text Available Using the four Cluster spacecraft, we have determined the three-dimensional wave-vector spectra of fluctuating magnetic fields in the solar wind. Three different solar wind intervals of Cluster data are investigated for this purpose, representing three different spatial scales: 10 000 km, 1000 km, and 100 km. The spectra are determined using the wave telescope technique (k-filtering technique without assuming the validity of Taylor's frozen-in-flow hypothesis nor are any assumptions made as to the symmetry properties of the fluctuations. We find that the spectra are anisotropic on all the three scales and the power is extended primarily in the directions perpendicular to the mean magnetic field, as might be expected of two-dimensional turbulence, however, the analyzed fluctuations are not axisymmetric. The lack of axisymmetry invalidates some earlier techniques using single spacecraft observations that were used to estimate the percentage of magnetic energy residing in quasi-two-dimensional power. However, the dominance of two-dimensional turbulence is consistent with the relatively long mean free paths of cosmic rays in observed in the heliosphere. On the other hand, the spectra also exhibit secondary extended structures oblique from the mean magnetic field direction. We discuss possible origins of anisotropy and asymmetry of solar wind turbulence spectra.

  12. Three-dimensional electromagnetic strong turbulence. II. Wave packet collapse and structure of wave packets during strong turbulence

    Science.gov (United States)

    Graham, D. B.; Robinson, P. A.; Cairns, Iver H.; Skjaeraasen, O.

    2011-07-01

    Large-scale simulations of wave packet collapse are performed by numerically solving the three-dimensional (3D) electromagnetic Zakharov equations, focusing on individual wave packet collapses and on wave packets that form in continuously driven strong turbulence. The collapse threshold is shown to decrease as the electron thermal speed νe/c increases and as the temperature ratio Ti/Te of ions to electrons decreases. Energy lost during wave packet collapse and dissipation is shown to depend on νe/c. The dynamics of density perturbations after collapse are studied in 3D electromagnetic strong turbulence for a range of Ti/Te. The structures of the Langmuir, transverse, and total electric field components of wave packets during strong turbulence are investigated over a range of νe/c. For νe/c ≲0.17, strong turbulence is approximately electrostatic and wave packets have very similar structure to purely electrostatic wave packets. For νe/c ≳0.17, transverse modes become trapped in density wells and contribute significantly to the structure of the total electric field. At all νe/c, the Langmuir energy density contours of wave packets are predominantly oblate (pancake shaped). The transverse energy density contours of wave packets are predominantly prolate (sausage shaped), with the major axis being perpendicular to the major axes of the Langmuir component. This results in the wave packet becoming more nearly spherical as νe/c increases, and in turn generates more spherical density wells during collapse. The results obtained are compared with previous 3D electrostatic results and 2D electromagnetic results.

  13. Four Mixed-Ligand Zn(II Three-Dimensional Metal-Organic Frameworks: Synthesis, Structural Diversity, and Photoluminescent Property

    Directory of Open Access Journals (Sweden)

    Chih-Chieh Wang

    2017-11-01

    Full Text Available Assemblies of four three-dimensional (3D mixed-ligand coordination polymers (CPs having formulas, {[Zn2(bdc2(4-bpdh]·C2H5OH·2H2O}n (1, [Zn(bdc(4-bpdh]n (2, {[Zn2(bdc2(4-bpdh2]·(4-bpdh}n (3, and {[Zn(bdc(4-bpdh]·C2H5OH}n (4 (bdc2− = dianion of 1,4-benzenedicarboxylic acid, 4-bpdh = 2,5-bis(4-pyridyl-3,4-diaza-2,4-hexadiene have been synthesized and structurally characterized by single-crystal X-ray diffraction method. Structural determination reveals that the coordination numbers (geometry of Zn(II ions in 1, 2, 3, and 4 are five (distorted square-pyramidal (SP, six (distorted octahedral (Oh, five (trigonal-bipyramidal (TBP, and four (tetrahedral (Td, respectively, and are bridged by 4-bpdh with bis-monodentate coordination mode and bdc2− ligands with bis-bidentate in 1, chelating/bidentate in 2, bis-monodentate and bis-bidentate in 3, and bis-monodentate in 4, to generate two-fold interpenetrating 3D cube-like metal-organic framework (MOF with pcu topology, non-interpenetrating 3D MOF, two-fold interpenetrating 3D rectangular-box-like MOF with pcu topology and five-fold interpenetrating diamondoid-like MOF with dia topology, respectively. These different intriguing architectures indicate that the coordination numbers and geometries of Zn(II ions, coordination modes of bdc2− ligand, and guest molecules play important roles in the construction of MOFs and the formation of the structural topologies and interpenetrations. Thermal stabilities, and photoluminescence study of 1–4 were also studied in detail. The complexes exhibit ligands based photoluminescence properties at room temperature.

  14. Study of structural attachments of a pool type LMFBR vessel through seismic analysis of a simplified three dimensional finite element model

    International Nuclear Information System (INIS)

    Ahmed, H.; Ma, D.

    1979-01-01

    A simplified three dimensional finite element model of a pool type LMFBR in conjunction with the computer program ANSYS is developed and scoping results of seismic analysis are produced. Through this study various structural attachments of a pool type LMFBR like the reactor vessel skirt support, the pump support and reactor shell-support structure interfaces are studied. This study also provides some useful results on equivalent viscous damping approach and some improvements to the treatment of equivalent viscous damping are recommended. This study also sets forth pertinent guidelines for detailed three dimensional finite element seismic analysis of pool type LMFBR

  15. Feasibility of three-dimensional magnetic resonance angiography-fluoroscopy image fusion technique in guiding complex endovascular aortic procedures in patients with renal insufficiency.

    Science.gov (United States)

    Schwein, Adeline; Chinnadurai, Ponraj; Shah, Dipan J; Lumsden, Alan B; Bechara, Carlos F; Bismuth, Jean

    2017-05-01

    Three-dimensional image fusion of preoperative computed tomography (CT) angiography with fluoroscopy using intraoperative noncontrast cone-beam CT (CBCT) has been shown to improve endovascular procedures by reducing procedure length, radiation dose, and contrast media volume. However, patients with a contraindication to CT angiography (renal insufficiency, iodinated contrast allergy) may not benefit from this image fusion technique. The primary objective of this study was to evaluate the feasibility of magnetic resonance angiography (MRA) and fluoroscopy image fusion using noncontrast CBCT as a guidance tool during complex endovascular aortic procedures, especially in patients with renal insufficiency. All endovascular aortic procedures done under MRA image fusion guidance at a single-center were retrospectively reviewed. The patients had moderate to severe renal insufficiency and underwent diagnostic contrast-enhanced magnetic resonance imaging after gadolinium or ferumoxytol injection. Relevant vascular landmarks electronically marked in MRA images were overlaid on real-time two-dimensional fluoroscopy for image guidance, after image fusion with noncontrast intraoperative CBCT. Technical success, time for image registration, procedure time, fluoroscopy time, number of digital subtraction angiography (DSA) acquisitions before stent deployment or vessel catheterization, and renal function before and after the procedure were recorded. The image fusion accuracy was qualitatively evaluated on a binary scale by three physicians after review of image data showing virtual landmarks from MRA on fluoroscopy. Between November 2012 and March 2016, 10 patients underwent endovascular procedures for aortoiliac aneurysmal disease or aortic dissection using MRA image fusion guidance. All procedures were technically successful. A paired t-test analysis showed no difference between preimaging and postoperative renal function (P = .6). The mean time required for MRA-CBCT image

  16. Three Dimensional Lithospheric Electrical Structure of the Tibetan Plateau as Revealed by SinoProbe Long Period Magnetotelluric Array Data

    Science.gov (United States)

    Wei, Wenbo; Zhang, Letian; Jin, Sheng; Ye, Gaofeng; Jing, Jianen; Dong, Hao; Xie, Chengliang; Yin, Yaotian

    2017-04-01

    The on-going continent-continent collision between the Indian and Eurasian plates since 55 Ma has created the spectacular topography of the Tibetan plateau. However, many first order questions remain to be answered as to the mechanisms behind this young orogenic process. Under the auspices of the SinoProbe Project, a three dimensional (3-D) Magnetotelluric (MT) array have been deployed on the Tibetan Plateau from 2010 to 2013 to better understand this orogeny. By the end of 2013, 1099 MT stations have been completed, including 102 combined broadband MT (BBMT) and long period MT (LMT) stations. In this study, MT data of these 102 combined stations have been used to investigate the deep lithospheric electrical structure of the Tibetan Plateau. MT impedances within the period range of 10 - 50000 s were extracted to be used for 3-D inversions with the ModEM code using the standard NLCG algorithm. The resulting lithospheric electrical structure of the Tibetan Plateau shows a distinct pattern of strong variation not only vertically, but also horizontally. Conductors are found to be widespread in the middle to lower crust. But their geometries are quite complex, and not obviously consistent with the hypothesis of continuous eastward channel flow. Instead, most crustal conductors in central and southern Tibet display a pattern of N-S extension. In the depth range of the upper mantle, two more conductive regions can be identified in the southern Qiangtang Terrane and in the central Lhasa Terrane. Resistor associated with the underthrust Inidan plate can be traced beneath the Bangong-Nujiang suture in western Tibet, but only beneath the central Lhasa terrane in central Tibet. * This work was jointly supported by the grants from Project SinoProbe-01 and National Natural Science Foundation of China (41404060).

  17. Three-dimensional velocity model of crustal structure in the southern Korean Peninsula and its full-waveform validations

    Science.gov (United States)

    Rhie, J.; Kim, S.; Woo, J. U.; Song, J. H.

    2016-12-01

    To obtain a high-resolution crustal three-dimensional (3-D) model, we incorporate multiple regional ambient noise datasets in different scales, which consist of 150 accelerometer stations (1-6 s group velocity), 37 regional broadband stations (5-30 s group and phase velocity), and longer period phase velocity maps from previous study (25-40 s phase velocity). A 3-D structure of shear wave velocity is constrained by integrating one-dimensional depth profiles from inversions of surface wave dispersions. The model estimation is carried out thoroughly in a trans-dimensional and hierarchical Bayesian inversion framework, such that the resulting model is less biased by arbitrary assumptions in the inversion process. To obtain P-wave velocity structure, then, a previous estimation of the variation of Vp/Vs ratio is applied. A 1-D velocity model will be replaced by this new 3-D model for determining accurate hypocenters and source processes of local earthquakes in the region. In addition, the new model will make more reliable seismic hazard analysis for scenario earthquakes possible. Before adopting the new model for various applications, it is necessary to validate it. To verify the validity of the model, full-waveform simulations for recent local earthquakes are performed. Two well observed moderate earthquakes occurred at NE and SW of the southern Korean Peninsula are considered for waveform simulations. The comparison between synthetic and observed waveforms shows that the new model reasonably well represents the seismic wave propagation characteristics in the southern Korean Peninsula.

  18. NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

    Science.gov (United States)

    Dunn, Michael F.

    2013-01-01

    Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR

  19. Two and three dimensional characterization of Zucchini Yellow Mosaic Virus induced structural alterations in Cucurbita pepo L. plants.

    Science.gov (United States)

    Zellnig, Günther; Pöckl, Michael Herbert; Möstl, Stefan; Zechmann, Bernd

    2014-05-01

    Infection of plants by Zucchini Yellow Mosaic Virus (ZYMV) induces severe ultrastructural changes. The aim of this study was to investigate ultrastructural changes during ZYMV-infection in Cucurbita pepo L. plants on the two and three dimensional (2D and 3D) level and to correlate these changes with the spread of ZYMV throughout the plant by transmission electron microscopy (TEM) and image analysis. This study revealed that after inoculation of the cotyledons ZYMV moved into roots [3 days post inoculation (dpi)], then moved upwards into the stem and apical meristem (5 dpi), then into the first true leaf (7 dpi) and could finally be found in all plant parts (9 dpi). ZYMV-infected cells contained viral inclusion bodies in the form of cylindrical inclusions (CIs). These CIs occurred in four different forms throughout the cytosol of roots and leaves: scrolls and pinwheels when cut transversely and long tubular structures and bundles of filaments when cut longitudinally. 3D reconstruction of ZYMV-infected cells containing scrolls revealed that they form long tubes throughout the cytosol. The majority has a preferred orientation and an average length and width of 3 μm and 120 nm, respectively. Image analysis revealed an increased size of cells and vacuoles (107% and 447%, respectively) in younger ZYMV-infected leaves leading to a similar ratio of cytoplasm to vacuole (about 1:1) in older and younger ZYMV-infected leaves which indicates advanced cell growth in younger tissues. The collected data advances the current knowledge about ZYMV-induced ultrastructural changes in Cucurbita pepo. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  20. Matrix architecture dictates three-dimensional migration modes of human macrophages: differential involvement of proteases and podosome-like structures.

    Science.gov (United States)

    Van Goethem, Emeline; Poincloux, Renaud; Gauffre, Fabienne; Maridonneau-Parini, Isabelle; Le Cabec, Véronique

    2010-01-15

    Tissue infiltration of macrophages, although critical for innate immunity, is also involved in pathologies, such as chronic inflammation and cancer. In vivo, macrophages migrate mostly in a constrained three-dimensional (3D) environment. However, in vitro studies, mainly focused on two dimensions, do not provide meaningful clues about the mechanisms involved in 3D macrophage migration. In contrast, tumor cell 3D migration is well documented. It comprises a protease-independent and Rho kinase (ROCK)-dependent amoeboid migration mode and a protease-dependent and ROCK-independent mesenchymal migration mode. In this study, we examined the influence of extracellular matrix (composition, architecture, and stiffness) on 3D migration of human macrophages derived from blood monocytes (MDMs). We show that: 1) MDMs use either the amoeboid migration mode in fibrillar collagen I or the mesenchymal migration mode in Matrigel and gelled collagen I, whereas HT1080 tumor cells only perform mesenchymal migration; 2) when MDMs use the mesenchymal migratory mode, they form 3D collagenolytic structures at the tips of cell protrusions that share several markers with podosomes as described in two dimensions; 3) in contrast to tumor cells, matrix metalloproteinase inhibitors do not impair protease-dependent macrophage 3D migration, suggesting the involvement of other proteolytic systems; and 4) MDMs infiltrating matrices of similar composition but with variable stiffness adapt their migration mode primarily to the matrix architecture. In conclusion, although it is admitted that leukocytes 3D migration is restricted to the amoeboid mode, we show that human macrophages also perform the mesenchymal mode but in a distinct manner than tumor cells, and they naturally adapt their migration mode to the environmental constraints.

  1. Two- and three-dimensional reformatted computed tomography imaging analysis of the lumbosacropelvic structure in degenerative anterolisthesis

    Energy Technology Data Exchange (ETDEWEB)

    Ergun, T., E-mail: tarkanergun@yahoo.co [Department of Radiology, Baskent University, Alanya Teaching and Medical Research Center, Alanya (Turkey); Sahin, M.S. [Department of Orthopaedics and Traumatology, Baskent University, Alanya Teaching and Medical Research Center, Alanya (Turkey); Lakadamyali, H. [Department of Radiology, Baskent University, Alanya Teaching and Medical Research Center, Alanya (Turkey)

    2010-11-15

    Aim: To evaluate the differences in the lumbosacropelvic structure between normal individuals and those with pseudospondylolisthesis. Materials and methods: The renal stone protocol abdominal CT images of 452 patients were retrospectively analysed. Twenty individuals who had degenerative anterolisthesis at the L5-S1 level were included in the study. Moreover, a control group of individuals was formed, similar in age and gender to the study group. A number of linear and angular lumbosacral morphological parameters were evaluated using two- and three-dimensionally reformatted CT images. The data of the two groups were compared using the t-test and Mann-Whitney U-test. Results: There was an association between spondylolisthesis and decreased thickness of the transverse process (p = 0.01), the height of the iliac crest (p = 0.028), lumbar angle (p = 0.041), sacral table angle (p = 0.033), sacral table index (p = 0.0001), sacral kyphosis (p = 0.025), sacral slope (p = 0.007), and width of the transverse process (p = 0.038), and increased transverse articular dimension of the facet joint (p = 0.003), axial angle of the facet joint (p = 0.002), sagittal angle of the facet joint (p = 0.012), S1 vertebra interfacet index (p = 0.003), the distance between the L5 vertebral transverse process and the iliac crest (p = 0.003), pelvic incidence (p = 0.016), L5 vertebra posterior angle (p = 0.001), and intersacroiliac joint angle (p = 0.024). Conclusion: The lumbosacropelvic morphology in patients with degenerative spondylolisthesis is quite different from that of normal individuals. These abnormalities should be revealed using imaging methods as they can be defining for pseudospondylolisthesis development and have important effects on therapy planning.

  2. Three-dimensional grain structure of sintered bulk strontium titanate from X-ray diffraction contrast tomography

    DEFF Research Database (Denmark)

    Syha, M.; Rheinheimer, W.; Bäurer, M.

    2012-01-01

    The three-dimensional grain boundary network of sintered bulk strontium titanate is reconstructed using X-ray diffraction contrast tomography, a non-destructive technique for determining the grain shape and crystallographic orientation in polycrystals that is ideally suited for detailed studies...

  3. Three-dimensional fine structure of the lingual papillae and their connective tissue cores in the human tongue.

    Science.gov (United States)

    Kobayashi, K; Kumakura, M; Shinkai, H; Ishii, K

    1994-10-01

    The three-dimensional structure of the four types of lingual papillae and their connective tissue cores (CTCs) in the human tongue was studied by scanning electron microscopy after removal of the epithelial cell layer, and was compared to those of other mammalian species. Filiform papillae are densely distributed on the dorsal surface of the anterior two-thirds of the tongue. Each filiform papilla has numerous slender protrusions on the top. After removal of the epithelium, the CTC of the filiform papilla has a columnar primary core with 10-30 rod-shaped small secondary cores surrounding an upper central depression. A few long spine-like protrusions are frequently found in the center of this upper depression. The number, thickness and length of each secondary protrusion of the filiform CTC show some variations at the region distributed on the tongue. Fungiform papillae with spherical heads are scattered among these filiform papillae and are numerous at the anterior margin of the tongue. The CTC of the fungiform papilla shows a coralliform structure with numerous small rod-shaped protrusions on the lateral surface, and its branched top has flat areas with a few small round depressions harboring taste buds. It must be emphasized that human fungiform papilla has some taste buds not only in the young, but also in the adult age. Several to 12 vallate papillae are distributed in front of the terminal groove and had the CTC of pinecone-like structure with numerous small thorns (secondary connective tissue cores). Foliate papillae consist of 10-15 parallel folds at the posterior margin of the tongue. The CTC of the foliate papillae appears as ridges and grooves. Small protrusions are scattered on the surface of the ridges. The underside view of the exfoliated epithelium of the vallate as well as the foliate papillae revealed numerous taste buds arranged in single file in the lateral epithelium. The dorsal surface of the root of the tongue has evenly distributed short rod

  4. Modelling the drying of three-dimensional pulp moulded structures. Part II, Drying data obtained from flat panels using virgin and recycled paper fibre

    Science.gov (United States)

    John F. Hunt; Margit. Tamasy-Bano; Heike. Nyist

    1999-01-01

    A three-dimensional structural panel, called FPL Spaceboard, was developed at the USDA Forest Products Laboratory. Spaceboard panels have been formed using a variety of fibrous materials using either a wet- or dry-forming process. Geometrically, the panel departs from the traditional two-dimensional flat panel by integrally forming an array of perpendicular ribs and...

  5. Feasibility of in vivo three-dimensional T2*mapping using dicarboxy-PROXYL and CW-EPR-based single-point imaging.

    Science.gov (United States)

    Kubota, Harue; Komarov, Denis A; Yasui, Hironobu; Matsumoto, Shingo; Inanami, Osamu; Kirilyuk, Igor A; Khramtsov, Valery V; Hirata, Hiroshi

    2017-06-01

    The aim of this study was to demonstrate the feasibility of in vivo three-dimensional (3D) relaxation time T 2 * mapping of a dicarboxy-PROXYL radical using continuous-wave electron paramagnetic resonance (CW-EPR) imaging. Isotopically substituted dicarboxy-PROXYL radicals, 3,4-dicarboxy-2,2,5,5-tetra( 2 H 3 )methylpyrrolidin-(3,4- 2 H 2 )-(1- 15 N)-1-oxyl ( 2 H, 15 N-DCP) and 3,4-dicarboxy-2,2,5,5-tetra( 2 H 3 )methylpyrrolidin-(3,4- 2 H 2 )-1-oxyl ( 2 H-DCP), were used in the study. A clonogenic cell survival assay was performed with the 2 H-DCP radical using squamous cell carcinoma (SCC VII) cells. The time course of EPR signal intensities of intravenously injected 2 H, 15 N-DCP and 2 H-DCP radicals were determined in tumor-bearing hind legs of mice (C3H/HeJ, male, n = 5). CW-EPR-based single-point imaging (SPI) was performed for 3D T 2 * mapping. 2 H-DCP radical did not exhibit cytotoxicity at concentrations below 10 mM. The in vivo half-life of 2 H, 15 N-DCP in tumor tissues was 24.7 ± 2.9 min (mean ± standard deviation [SD], n = 5). The in vivo time course of the EPR signal intensity of the 2 H, 15 N-DCP radical showed a plateau of 10.2 ± 1.2 min (mean ± SD) where the EPR signal intensity remained at more than 90% of the maximum intensity. During the plateau, in vivo 3D T 2 * maps with 2 H, 15 N-DCP were obtained from tumor-bearing hind legs, with a total acquisition time of 7.5 min. EPR signals of 2 H, 15 N-DCP persisted long enough after bolus intravenous injection to conduct in vivo 3D T 2 * mapping with CW-EPR-based SPI.

  6. Characterization and estimation of three-dimensional structure in unforced and forced blunt trailing edge wake flows

    Science.gov (United States)

    Clark, Heather

    Blunt trailing edge airfoils offer structural and aerodynamic advantages in modern wind turbine and aircraft applications. However, penalties are introduced concurrently by vortex shedding at separation. In particular, the adverse effects of increased drag and unsteady loading motivate the development of a control strategy for the blunt trailing edge wake. Closed-loop control is pursued for its potentially greater effectiveness and efficiency, relative to open-loop forcing. Toward this aim, the thesis addresses the need for estimation of the state from limited measurements. The wake of a blunt trailing edge body is investigated experimentally through simultaneous measurements of velocity and the spanwise distribution of fluctuating surface pressure. Passive forcing is implemented with an array of vortex generators that are arranged according to the characteristic wavelength of the dominant small-scale instability. The guiding considerations for the analysis and discussion are physical characterization and the development of estimation strategies based on surface pressure. Joint examination of the measured variables through reduced-order modelling, wavelet analysis, and conditional averaging yields insight regarding the unsteady, three-dimensional nature of the flow. The investigation of forcing is focused upon the influence of the perturbation on the surface pressure and the performance of estimation models in the modified wake. It is found that low-frequency amplitude modulation of the pressure results from variation of both the magnitude of velocity fluctuations and the vortex formation length. The forcing regularizes the shedding in time and space, as evidenced by the attenuated modulation and enhanced spanwise coherence of the amplitude and phase. Examination of this behaviour confirms the connection between amplitude modulation and vortex dislocations in bluff body wakes. Several properties of the estimation approaches hold in general. It is shown that the

  7. The Use of Molecular Modeling and VSEPR Theory in the Undergraduate Curriculum to Predict the Three-Dimensional Structure of Molecules

    Science.gov (United States)

    Pfennig, Brian W.; Frock, Richard L.

    1999-07-01

    This paper illustrates how valence shell electron pair repulsion (VSEPR) theory and molecular modeling can be used in a complimentary fashion in the undergraduate curriculum to predict the three-dimensional structure of molecules. Students use the familiar VSEPR model to sketch the three-dimensional structures of molecules predicted by a comparison of the relative magnitudes of electrostatic repulsion between electron pair domains on the central atom. Despite the simplicity and elegance of the VSEPR model, however, students often have difficulty visualizing the three-dimensional shapes of molecules and learning the more subtle features of the model, such as the bond length and bond angle deviations from ideal geometry that accompany the presence of lone pair or multiple bond domains or that result from differences in the electronegativity of the bonded atoms, partial charges and molecular dipole moments, and site preferences in the trigonal bipyramidal electron geometry. Students therefore also employ a molecular modeling approach to predict the three-dimensional shapes of molecules by performing both molecular mechanics and semiempirical quantum mechanical calculations to minimize the structures of these molecules. A major strength of the molecular modeling approach is that it allows students to quantitatively explore the more subtle implications of VSEPR theory using an alternative model. Student responses on end-of-the-semester evaluations ranked this exercise highly among the seven projects performed during the semester, commenting specifically on how the software allowed them to visualize the three-dimensional aspects of molecules more effectively than simple ball-and-stick models and on how the molecular modeling helped them to explore the more detailed structural features predicted by VSEPR theory.

  8. A high-spatial-resolution three-dimensional detector array for 30-200 keV X-rays based on structured scintillators

    DEFF Research Database (Denmark)

    Olsen, Ulrik Lund; Schmidt, Søren; Poulsen, Henning Friis

    2008-01-01

    A three-dimensional X-ray detector for imaging 30-200 keV photons is described. It comprises a set of semi-transparent structured scintillators, where each scintillator is a regular array of waveguides in silicon, and with pores filled with CsI. The performance of the detector is described theore...... in efficiency by a factor of 5-15 is obtainable. The cross-talk between screens in the three-dimensional detector is shown to be negligible. The three-dimensional concept enables ray-tracing and super-resolution algorithms to be applied.......A three-dimensional X-ray detector for imaging 30-200 keV photons is described. It comprises a set of semi-transparent structured scintillators, where each scintillator is a regular array of waveguides in silicon, and with pores filled with CsI. The performance of the detector is described...... theoretically and explored in detail through simulations. Based on available hardware, a spatial resolution of 1 mm is obtainable. The resolution of a single screen is shown to be determined only by the pitch, at least up to 100 keV. In comparison with conventional homogeneous screens, an improvement...

  9. Three-dimensional quantitative structure-activity relationships and docking studies of some structurally diverse flavonoids and design of new aldose reductase inhibitors

    Directory of Open Access Journals (Sweden)

    Utpal Chandra De

    2015-01-01

    Full Text Available Aldose reductase (AR plays an important role in the development of several long-term diabetic complications. Inhibition of AR activities is a strategy for controlling complications arising from chronic diabetes. Several AR inhibitors have been reported in the literature. Flavonoid type compounds are shown to have significant AR inhibition. The objective of this study was to perform a computational work to get an idea about structural insight of flavonoid type compounds for developing as well as for searching new flavonoid based AR inhibitors. The data-set comprising 68 flavones along with their pIC 50 values ranging from 0.44 to 4.59 have been collected from literature. Structure of all the flavonoids were drawn in Chembiodraw Ultra 11.0, converted into corresponding three-dimensional structure, saved as mole file and then imported to maestro project table. Imported ligands were prepared using LigPrep option of maestro 9.6 version. Three-dimensional quantitative structure-activity relationships and docking studies were performed with appropriate options of maestro 9.6 version installed in HP Z820 workstation with CentOS 6.3 (Linux. A model with partial least squares factor 5, standard deviation 0.2482, R 2 = 0.9502 and variance ratio of regression 122 has been found as the best statistical model.

  10. Equilibrium: three-dimensional configurations

    International Nuclear Information System (INIS)

    Anon.

    1987-01-01

    This chapter considers toroidal MHD configurations that are inherently three-dimensional. The motivation for investigation such complicated equilibria is that they possess the potential for providing toroidal confinement without the need of a net toroidal current. This leads to a number of advantages with respect to fusion power generation. First, the attractive feature of steady-state operation becomes more feasible since such configurations no longer require a toroidal current transformer. Second, with zero net current, one potentially dangerous class of MHD instabilities, the current-driven kink modes, is eliminated. Finally, three-dimensional configurations possess nondegenerate flux surfaces even in the absence of plasma pressure and plasma current. Although there is an enormous range of possible three-dimensional equilibria, the configurations of interest are accurately described as axisymmetric tori with superimposed helical fields; furthermore, they possess no net toroidal current. Instead, two different and less obvious restoring forces are developed: the helical sideband force and the toroidal dipole current force. Each is discussed in detail in Chapter 7. A detailed discussion of the parallel current constraint, including its physical significance, is given in section 7.2. A general analysis of helical sideband equilibria, along with a detailed description of the Elmo bumpy torus, is presented in sections 7.3 and 7.4. A general description of toroidal dipole-current equilibria, including a detailed discussion of stellarators, heliotrons, and torsatrons, is given in sections 7.5 and 7.6

  11. Fabrication of triple-layered bifurcated vascular scaffold with a certain degree of three-dimensional structure

    Science.gov (United States)

    Liu, Yuanyuan; Jiang, Weijian; Yang, Yang; Pu, Huayan; Peng, Yan; Xin, Liming; Zhang, Yi; Sun, Yu

    2018-01-01

    Constructing vascular scaffolds is important in tissue engineering. However, scaffolds with characteristics such as multiple layers and a certain degree of spatial morphology still cannot be readily constructed by current vascular scaffolds fabrication techniques. This paper presents a three-layered bifurcated vascular scaffold with a curved structure. The technique combines 3D printed molds and casting hydrogel and fugitive ink to create vessel-mimicking constructs with customizable structural parameters. Compared with other fabrication methods, the technique can create more native-like 3D geometries. The diameter and wall thickness of the fabricated constructs can be independently controlled, providing a feasible approach for vascular scaffold construction. Enzymatically-crosslinked gelatin was used as the scaffold material. The morphology and mechanical properties were evaluated. Human umbilical cord derived endothelial cells (HUVECs) were seeded on the scaffolds and cultured for 72 h. Cell viability and morphology were assessed. The results showed that the proposed process had good application potentials, and will hopefully provide a feasible approach for constructing vascular scaffolds.

  12. X-Ray Crystallography as a Tool to Determine Three-Dimensional Structures of Commercial Enzymes Subjected to Treatment in Pressurized Fluids.

    Science.gov (United States)

    Feiten, Mirian Cristina; Di Luccio, Marco; Santos, Karine F; de Oliveira, Débora; Oliveira, J Vladimir

    2017-06-01

    The study of enzyme function often involves a multi-disciplinary approach. Several techniques are documented in the literature towards determining secondary and tertiary structures of enzymes, and X-ray crystallography is the most explored technique for obtaining three-dimensional structures of proteins. Knowledge of three-dimensional structures is essential to understand reaction mechanisms at the atomic level. Additionally, structures can be used to modulate or improve functional activity of enzymes by the production of small molecules that act as substrates/cofactors or by engineering selected mutants with enhanced biological activity. This paper presentes a short overview on how to streamline sample preparation for crystallographic studies of treated enzymes. We additionally revise recent developments on the effects of pressurized fluid treatment on activity and stability of commercial enzymes. Future directions and perspectives on the the role of crystallography as a tool to access the molecular mechanisms underlying enzymatic activity modulation upon treatment in pressurized fluids are also addressed.

  13. The structure of a three-dimensional boundary layer subjected to streamwise-varying spanwise-homogeneous pressure gradient

    International Nuclear Information System (INIS)

    Bentaleb, Y.; Leschziner, M.A.

    2013-01-01

    Highlights: • We study a spatially-evolving three-dimensional boundary layer. • We impose a streamwise-varying spanwise-homogeneous pressure gradient. • A collateral flow is formed close to the wall, and this is investigated alongside the skewed upper part of the boundary layer. • A wide range of flow-physical properties have been studied. -- Abstract: A spatially-evolving three-dimensional boundary layer, subjected to a streamwise-varying spanwise-homogeneous pressure gradient, equivalent to a body force, is investigated by way of direct numerical simulation. The pressure gradient, prescribed to change its sign half-way along the boundary layer, provokes strong skewing of the velocity vector, with a layer of nearly collateral flow forming close to the wall up to the position of maximum spanwise velocity. A wide range of flow-physical properties have been studied, with particular emphasis on the near-wall layer, including second-moments, major budget contributions and wall-normal two-point correlations of velocity fluctuations and their angles, relative to wall-shear fluctuations. The results illustrate the complexity caused by skewing, including a damping in turbulent mixing and a significant lag between strains and stresses. The study has been undertaken in the context of efforts to develop and test novel hybrid LES–RANS schemes for non-equilibrium near-wall flows, with an emphasis on three-dimensional near-wall straining. Fundamental flow-physical issues aside, the data derived should be of particular relevance to a priori studies of second-moment RANS closure and the development and validation of RANS-type near-wall approximations implemented in LES schemes for high-Reynolds-number complex flows

  14. Three-dimensional structure of Wza, the protein required for translocation of group 1 capsular polysaccharide across the outer membrane of Escherichia coli.

    Science.gov (United States)

    Beis, Konstantinos; Collins, Richard F; Ford, Robert C; Kamis, Alhaji B; Whitfield, Chris; Naismith, James H

    2004-07-02

    Wza is a highly conserved multimeric outer membrane protein complex required for the surface expression of the serotype K30 group 1 capsular polysaccharide in Escherichia coli. Here we present the first three-dimensional structure of this type of polysaccharide exporter at a 15.5-A resolution obtained using single particle averaging on a dataset of cryo-negatively stained protein. Previous structural studies on purified Wza have revealed a homo-oligomeric ring structure that is most probably composed of eight subunits. Symmetry analysis of the three-dimensional structure combined with biochemical two- and three-dimensional crystallographic data strongly suggest that Wza is an octameric complex with a C4 quasi-rotational symmetry and is organized as a tetramer of dimeric subunits. Wza is best described as a stack of two 4-A high rings with differing diameters providing a mushroom-like aspect from the side. The larger ring has a distinctive square shape with a diameter of 115 A, whereas the smaller is almost circular with a diameter of 90 A. In the center of the complex and enclosed by the four symmetrical arms is a small elliptical cagelike cavity of approximately 40 A in diameter. The central cavity is effectively sealed at the top and bottom of the complex but has small inter-arm holes when viewed from the side. We discuss the structure of this complex and implications in the surface translocation of cell-surface polysaccharide.

  15. Feasibility of three-dimensional ultrashort echo time magnetic resonance imaging at 1.5 T for the diagnosis of skull fractures

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Hao; Zhong, Yu-min; Zhang, Hong; Lin, Yi; Zhu, Ming [Shanghai Jiao Tong University School of Medicine, Department of Radiology, Shanghai Children' s Medical Center, Shanghai (China); Nie, Quan-min; Guo, Lie-mei; Yang, Xi [Shanghai Jiao Tong University School of Medicine, Department of Neurosurgery Ren Ji Hospital, Shanghai (China); Chen, Wei-bo; Dai, Yong-ming [Philips Healthcare, Shanghai (China); Xu, Jian-rong [Shanghai Jiao Tong University School of Medicine, Department of Radiology, Ren Ji Hospital, Shanghai (China)

    2016-01-15

    To investigate the feasibility of ultrashort echo time (UTE) magnetic resonance imaging (MRI) for the diagnosis of skull fractures. The skull fracture models of ten Bama pigs and 364 patients with craniocerebral trauma were subjected to computed tomography (CT), UTE and conventional MRI sequences. The accuracy of UTE imaging in skull fracture diagnosis was analysed using receiver operating characteristic (ROC) curve analysis, McNemar's test and Kappa values. Differences among CT, UTE imaging and anatomical measurement (AM) values for linear fractures (LFs) and depressed fractures (DFs) were compared using one-way ANOVA and a paired-samples t-test. UTE imaging clearly demonstrated skull structures and fractures. The accuracy, validity and reliability of UTE MRI were excellent, with no significant differences between expert readings (P > 0.05; Kappa, 0.899). The values obtained for 42 LFs and 13 DFs in the ten specimens were not significantly different among CT, UTE MRI and AMs, while those obtained for 55 LFs and ten DFs in 44 patients were not significantly different between CT and UTE MRI (P > 0.05). UTE MRI sequences are feasible for the evaluation of skull structures and fractures, with no radiation exposure, particularly for paediatric and pregnant patients. (orig.)

  16. Determination of Three-Dimensional Morphology and Inner Structure of Second-Phase Inclusions in Metals by Non-Aqueous Solution Electrolytic and Room Temperature Organic Methods

    OpenAIRE

    Jing Guo; Keming Fang; Hanjie Guo; Yiwa Luo; Shengchao Duan; Xiao Shi; Wensheng Yang

    2018-01-01

    The secondary-phase particles in metals, particularly those composed of non-metallic materials, are often detrimental to the mechanical properties of metals; thus, it is crucial to control inclusion formation and growth. One of the challenges is determining the three-dimensional morphology and inner structures of such inclusions. In this study, a non-aqueous solution electrolytic method and a room-temperature organic technique were developed based on the principle of electrochemistry to deter...

  17. Elastocapillary fabrication of three-dimensional microstructures

    NARCIS (Netherlands)

    van Honschoten, J.W.; Berenschot, Johan W.; Ondarcuhu, T.; Sanders, Remco G.P.; Sundaram, J.; Elwenspoek, Michael Curt; Tas, Niels Roelof

    2010-01-01

    We describe the fabrication of three-dimensional microstructures by means of capillary forces. Using an origami-like technique, planar silicon nitride structures of various geometries are folded to produce three-dimensional objects of 50–100 m. Capillarity is a particularly effective mechanism since

  18. Analyses of magnetic structures and nuclear-density distribution by the structure-refinement and three-dimensional visualization systems RIETAN-FP-VENUS

    International Nuclear Information System (INIS)

    Izumi, Fujio; Momma, Koichi

    2010-01-01

    We have been developing a multi-purpose pattern-fitting system RIETAN-FP and a three-dimensional visualization system VENUS, which have been extensively used for structure refinements of various metal and inorganic materials from neutron powder diffraction data. At first, their outlines and the history of their developments are shortly looked back. The second part describes procedures for analyzing collinear magnetic structures with the combination of VESTA in the VENUS system and RIETAN-FP by taking BiCoO 3 for instance. Finally, a new C++ program, Dysnomia, for the maximum entropy method is introduced with emphasis on its new features. Dysnomia excels its predecessor, PRIMA, in computation speed, memory efficiency, scalability, and reliability. In particular, addition of a normal-distribution constraint is effective in obtaining nuclear-density distribution that is physically and chemically reasonable. (author)

  19. Experimental observations of the three-dimensional wake structures and dynamics generated by a rigid, bioinspired pitching panel

    Science.gov (United States)

    King, Justin T.; Kumar, Rajeev; Green, Melissa A.

    2018-03-01

    The effects of changing Strouhal number on the three-dimensional wake produced by a rigid, bioinspired trapezoidal pitching panel are analyzed through the use of stereoscopic particle image velocimetry over a Strouhal number range of 0.17-0.56. The results show that for all cases, at least some section of the wake comprises an alternating series of interacting vortex rings. The behavior of the flows induced by these vortex rings is consistent with the wake phenomena of spanwise compression and transverse expansion. Increases in Strouhal number correspond to an increased rate of spanwise compression, a greater amount of transverse expansion, and the movement of the location of wake breakdown onset upstream.

  20. A nonlinear, implicit, three-dimensional finite element code for solid and structural mechanics - User`s Manual

    Energy Technology Data Exchange (ETDEWEB)

    Maker, B.N.

    1995-04-14

    This report provides a user`s manual for NIKE3D, a fully implicit three-dimensional finite element code for analyzing the finite strain static and dynamic response of inelastic solids, shells, and beams. Spatial discretization is achieved by the use of 8-node solid elements, 2-node truss and beam elements, and 4-node membrane and shell elements. Over twenty constitutive models are available for representing a wide range of elastic, plastic, viscous, and thermally dependent material behavior. Contact-impact algorithms permit gaps, frictional sliding, and mesh discontinuities along material interfaces. Several nonlinear solution strategies are available, including Full-, Modified-, and Quasi-Newton methods. The resulting system of simultaneous linear equations is either solved iteratively by an element-by-element method, or directly by a factorization method, for which case bandwidth minimization is optional. Data may be stored either in or out of core memory to allow for large analyses.

  1. Three dimensional system integration

    CERN Document Server

    Papanikolaou, Antonis; Radojcic, Riko

    2010-01-01

    Three-dimensional (3D) integrated circuit (IC) stacking is the next big step in electronic system integration. It enables packing more functionality, as well as integration of heterogeneous materials, devices, and signals, in the same space (volume). This results in consumer electronics (e.g., mobile, handheld devices) which can run more powerful applications, such as full-length movies and 3D games, with longer battery life. This technology is so promising that it is expected to be a mainstream technology a few years from now, less than 10-15 years from its original conception. To achieve thi

  2. Three-Dimensional Flows

    CERN Document Server

    Araujo, Vitor; Viana, Marcelo

    2010-01-01

    In this book, the authors present the elements of a general theory for flows on three-dimensional compact boundaryless manifolds, encompassing flows with equilibria accumulated by regular orbits. The book aims to provide a global perspective of this theory and make it easier for the reader to digest the growing literature on this subject. This is not the first book on the subject of dynamical systems, but there are distinct aspects which together make this book unique. Firstly, this book treats mostly continuous time dynamical systems, instead of its discrete counterpart, exhaustively treated

  3. Butterfly Wings Are Three-Dimensional: Pupal Cuticle Focal Spots and Their Associated Structures in Junonia Butterflies.

    Science.gov (United States)

    Taira, Wataru; Otaki, Joji M

    2016-01-01

    Butterfly wing color patterns often contain eyespots, which are developmentally determined at the late larval and early pupal stages by organizing activities of focal cells that can later form eyespot foci. In the pupal stage, the focal position of a future eyespot is often marked by a focal spot, one of the pupal cuticle spots, on the pupal surface. Here, we examined the possible relationships of the pupal focal spots with the underneath pupal wing tissues and with the adult wing eyespots using Junonia butterflies. Large pupal focal spots were found in two species with large adult eyespots, J. orithya and J. almana, whereas only small pupal focal spots were found in a species with small adult eyespots, J. hedonia. The size of five pupal focal spots on a single wing was correlated with the size of the corresponding adult eyespots in J. orithya. A pupal focal spot was a three-dimensional bulge of cuticle surface, and the underside of the major pupal focal spot exhibited a hollowed cuticle in a pupal case. Cross sections of a pupal wing revealed that the cuticle layer shows a curvature at a focal spot, and a positional correlation was observed between the cuticle layer thickness and its corresponding cell layer thickness. Adult major eyespots of J. orithya and J. almana exhibited surface elevations and depressions that approximately correspond to the coloration within an eyespot. Our results suggest that a pupal focal spot is produced by the organizing activity of focal cells underneath the focal spot. Probably because the focal cell layer immediately underneath a focal spot is thicker than that of its surrounding areas, eyespots of adult butterfly wings are three-dimensionally constructed. The color-height relationship in adult eyespots might have an implication in the developmental signaling for determining the eyespot color patterns.

  4. Microlaser-based three-dimensional display

    Science.gov (United States)

    Takeuchi, Eric B.; Bergstedt, Robert; Hargis, David E.; Higley, Paul D.

    1999-08-01

    Three dimensional (3D) displays are critical for viewing complex multi-dimensional information and for viewing representations of the three dimensional real world. A teaming arrangement between Laser Power Corporation (LPC) and Specialty Devices, Inc. (SDI) has led to the feasibility demonstration of a directly-viewed three dimensional volumetric display. LPC has developed red, green, and blue (RGB) diode pumped solid state microlaser display technology for use as a high resolution, high brightness display engine for the three dimensional display. Concurrently, SDI has developed a unique technology for viewing high resolution three dimensional volumetric images without external viewing aids (eye wear). When coupled to LPC's display engine, the resultant all solid state three dimensional display presets a true, physical three dimensionality which is directly viewable from all angles by multiple viewers without additional viewing equipment (eye wear). The resultant volumetric display will further enable applications such as the 'virtual sandbox,' visualization of radar and sonar data, air traffic control, remote surgery and diagnostics, and CAD workstations.

  5. Seismic-geodynamic constraints on three-dimensional structure, vertical flow, and heat transfer in the mantle

    Science.gov (United States)

    Forte, A.M.; Woodward, R.L.

    1997-01-01

    Joint inversions of seismic and geodynamic data are carried out in which we simultaneously constrain global-scale seismic heterogeneity in the mantle as well as the amplitude of vertical mantle flow across the 670 km seismic discontinuity. These inversions reveal the existence of a family of three-dimensional (3-D) mantle models that satisfy the data while at the same time yielding predictions of layered mantle flow. The new 3-D mantle models we obtain demonstrate that the buoyancy forces due to the undulations of the 670 km phase-change boundary strongly inhibit the vertical flow between the upper and lower mantle. The strong stabilizing effect of the 670 km topography also has an important impact on the predicted dynamic topography of the Earth's solid surface and on the surface gravity anomalies. The new 3-D models that predict strongly or partially layered mantle flow provide essentially identical fits to the global seismic data as previous models that have, until now, predicted only whole-mantle flow. The convective vertical transport of heat across the mantle predicted on the basis of the new 3-D models shows that the heat flow is a minimum at 1000 km depth. This suggests the presence at this depth of a globally defined horizon across which the pattern of lateral heterogeneity changes rapidly. Copyright 1997 by the American Geophysical Union.

  6. THE OUTFLOWS AND THREE-DIMENSIONAL STRUCTURE OF NGC 6337: A PLANETARY NEBULA WITH A CLOSE BINARY NUCLEUS

    International Nuclear Information System (INIS)

    Garcia-Diaz, Ma. T.; Clark, D. M.; Lopez, J. A.; Steffen, W.; Richer, M. G.

    2009-01-01

    NGC 6337 is a member of the rare group of planetary nebulae where a close binary nucleus has been identified. The nebula's morphology and emission line profiles are both unusual, particularly the latter. We present a thorough mapping of spatially resolved, long-slit echelle spectra obtained over the nebula that allows a detailed characterization of its complex kinematics. This information, together with narrowband imagery, is used to produce a three-dimensional (3D) model of the nebula using the code SHAPE. The 3D model yields a slowly expanding toroid with large density fluctuations in its periphery that are observed as cometary knots. A system of bipolar expanding caps of low ionization is located outside the toroid. In addition, an extended high velocity and tenuous bipolar collimated outflow is found emerging from the core and sharply bending in opposite directions, a behavior that cannot be accounted for by pure magnetic launching and collimation unless the source of the outflow is precessing or rotating, as could be expected from a close binary nucleus.

  7. Construction of a Novel Three-Dimensional PEDOT/RVC Electrode Structure for Capacitive Deionization: Testing and Performance.

    Science.gov (United States)

    Aldalbahi, Ali; Rahaman, Mostafizur; Govindasami, Periyasami; Almoiqli, Mohammed; Altalhi, Tariq; Mezni, Amine

    2017-07-24

    This article discusses the deposition of different amount of microstuctured poly(3,4-ethylenedioxythiophene) (PEDOT) on reticulated vitreous carbon (RVC) by electrochemical method to prepare three-dimensional (3D) PEDOT/RVC electrodes aimed to be used in capacitive deionization (CDI) technology. A CDI unit cell has been constructed here in this study. The performance of CDI cell in the ion removal of NaCl onto the sites of PEDOT/RVC electrode has been systematically investigated in terms of flow-rate, applied electrical voltage, and increasing PEDOT loading on PEDOT/RVC electrodes. It is observed that the increase in flow-rate, electric voltage, and PEDOT loading up to a certain level improve the ion removal performance of electrode in the CDI cell. The result shows that these electrodes can be used effectively for desalination technology, as the electrosorption capacity/desalination performance of these electrodes is quite high compared to carbon materials. Moreover, the stability of the electrodes has been tested and it is reported that these electrodes are regenerative. The effect of increasing NaCl concentration on the electrosorption capacity has also been investigated for these electrodes. Finally, it has been shown that 1 m³ PEDOT-120 min/RVC electrodes from 75 mg/L NaCl feed solution produce 421, 978 L water per day of 20 mg/L NaCl final concentration.

  8. Coherent optical nonlinearities and phase relaxation of quasi-three-dimensional and quasi-two-dimensional excitons in ZnSxSe1 - x/ZnSe structures

    DEFF Research Database (Denmark)

    Wagner, Hans Peter; Schätz, A.; Maier, R.

    1997-01-01

    We investigate the dephasing of heavy-hole excitons in different free-standing ZnSxSe1-x/ZnSe layer structures by spectrally resolved transient four-wave mixing. ZnSe layers of 80, 8, and 4 nm thickness with ternary barriers are studied, representing the crossover from quasi-three-dimensional to ......We investigate the dephasing of heavy-hole excitons in different free-standing ZnSxSe1-x/ZnSe layer structures by spectrally resolved transient four-wave mixing. ZnSe layers of 80, 8, and 4 nm thickness with ternary barriers are studied, representing the crossover from quasi...

  9. Structure-based and multiple potential three-dimensional quantitative structure-activity relationship (SB-MP-3D-QSAR) for inhibitor design.

    Science.gov (United States)

    Du, Qi-Shi; Gao, Jing; Wei, Yu-Tuo; Du, Li-Qin; Wang, Shu-Qing; Huang, Ri-Bo

    2012-04-23

    The inhibitions of enzymes (proteins) are determined by the binding interactions between ligands and targeting proteins. However, traditional QSAR (quantitative structure-activity relationship) is a one-side technique, only considering the structures and physicochemical properties of inhibitors. In this study, the structure-based and multiple potential three-dimensional quantitative structure-activity relationship (SB-MP-3D-QSAR) is presented, in which the structural information of host protein is involved in the QSAR calculations. The SB-MP-3D-QSAR actually is a combinational method of docking approach and QSAR technique. Multiple docking calculations are performed first between the host protein and ligand molecules in a training set. In the targeting protein, the functional residues are selected, which make the major contribution to the binding free energy. The binding free energy between ligand and targeting protein is the summation of multiple potential energies, including van der Waals energy, electrostatic energy, hydrophobic energy, and hydrogen-bond energy, and may include nonthermodynamic factors. In the foundational QSAR equation, two sets of weighting coefficients {aj} and {bp} are assigned to the potential energy terms and to the functional residues, respectively. The two coefficient sets are solved by using iterative double least-squares (IDLS) technique in the training set. Then, the two sets of weighting coefficients are used to predict the bioactivities of inquired ligands. In an application example, the new developed method obtained much better results than that of docking calculations.

  10. Development of a High-Order Navier-Stokes Solver Using Flux Reconstruction to Simulate Three-Dimensional Vortex Structures in a Curved Artery Model

    Science.gov (United States)

    Cox, Christopher

    Low-order numerical methods are widespread in academic solvers and ubiquitous in industrial solvers due to their robustness and usability. High-order methods are less robust and more complicated to implement; however, they exhibit low numerical dissipation and have the potential to improve the accuracy of flow simulations at a lower computational cost when compared to low-order methods. This motivates our development of a high-order compact method using Huynh's flux reconstruction scheme for solving unsteady incompressible flow on unstructured grids. We use Chorin's classic artificial compressibility formulation with dual time stepping to solve unsteady flow problems. In 2D, an implicit non-linear lower-upper symmetric Gauss-Seidel scheme with backward Euler discretization is used to efficiently march the solution in pseudo time, while a second-order backward Euler discretization is used to march in physical time. We verify and validate implementation of the high-order method coupled with our implicit time stepping scheme using both steady and unsteady incompressible flow problems. The current implicit time stepping scheme is proven effective in satisfying the divergence-free constraint on the velocity field in the artificial compressibility formulation. The high-order solver is extended to 3D and parallelized using MPI. Due to its simplicity, time marching for 3D problems is done explicitly. The feasibility of using the current implicit time stepping scheme for large scale three-dimensional problems with high-order polynomial basis still remains to be seen. We directly use the aforementioned numerical solver to simulate pulsatile flow of a Newtonian blood-analog fluid through a rigid 180-degree curved artery model. One of the most physiologically relevant forces within the cardiovascular system is the wall shear stress. This force is important because atherosclerotic regions are strongly correlated with curvature and branching in the human vasculature, where the

  11. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

    Directory of Open Access Journals (Sweden)

    Wasik Szymon

    2010-05-01

    Full Text Available Abstract Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA

  12. The analysis of three-dimensional effects of nitanium palatal expander 2 and hyrax maxillary expansion appliances on craniofacial structures: A finite element study

    Directory of Open Access Journals (Sweden)

    Avinash Kumar

    2017-01-01

    Full Text Available Objectives: To analyze three-dimensional effects of stress distribution and displacement on the craniofacial structures, following the application of forces from Nitanium Palatal Expander 2 (NPE2 and Hyrax appliance in early mixed dentition period using finite element analysis. Materials and Methods: Three-dimensional finite element models of the young dried human skull, NPE2 and Hyrax were constructed, and the initial activation of the expanders was simulated to carry out the analysis and to evaluate the von misses stresses and displacement on the craniofacial structures. Results: Both the models demonstrated the highest stresses at the mid-palatal suture, with maximum posterior dislocation. The inferior nasal floor showed highest downward displacement and point A showed outward, backward, and upward displacement in both the models. The pattern of stress distribution was almost similar in both the groups, but NPE2 revealed lower magnitude stresses than Hyrax. The cusp of the erupting canine and the mesiobuccal cusp of the second molar showed outward, backward, and downward displacement signifying eruption pattern following maxillary expansion. Conclusions: Nickel titanium palatal expander-2 and Hyrax produced similar stress pattern in early mixed dentition period finite element model. We conclude from this finite element method study that NPE2 is equally effective as Hyrax when used in early mixed dentition period as it exhibits orthopedic nature of expansion with minimal residual stresses in the craniofacial structures.

  13. Three dimensional energy profile:

    International Nuclear Information System (INIS)

    Kowsari, Reza; Zerriffi, Hisham

    2011-01-01

    The provision of adequate, reliable, and affordable energy has been considered as a cornerstone of development. More than one-third of the world's population has a very limited access to modern energy services and suffers from its various negative consequences. Researchers have been exploring various dimensions of household energy use in order to design strategies to provide secure access to modern energy services. However, despite more than three decades of effort, our understanding of household energy use patterns is very limited, particularly in the context of rural regions of the developing world. Through this paper, the past and the current trends in the field of energy analysis are investigated. The literature on rural energy and energy transition in developing world has been explored and the factors affecting households' decisions on energy use are listed. The and the factors affecting households' decisions on energy use are listed. The gaps identified in the literature on rural household energy analysis provide a basis for developing an alternative model that can create a more realistic view of household energy use. The three dimensional energy profile is presented as a new conceptual model for assessment of household energy use. This framework acts as a basis for building new theoretical and empirical models of rural household energy use. - Highlights: ► Reviews literature on household energy, energy transitions and decision-making in developing countries. ► Identifies gaps in rural household energy analysis and develops a new conceptual framework. ► The 3-d energy profile provides a holistic view of household energy system characteristics. ► Illustrates the use of the framework for understanding household energy transitions.

  14. Three-dimensional echocardiography

    International Nuclear Information System (INIS)

    Buck, Thomas

    2011-01-01

    Presents tips and tricks for beginners and experts Provides educational material for 3D training courses Features comprehensively illustrated cases Includes an accompanying DVD with video clips of all sample cases Three-dimensional echocardiography is the most recent fundamental advancement in echocardiography. Since real-time 3D echocardiography became commercially available in 2002, it has rapidly been accepted in echo labs worldwide. This book covers all clinically relevant aspects of this fascinating new technology, including a comprehensive explanation of its basic principles, practical aspects of clinical application, and detailed descriptions of specific uses in the broad spectrum of clinically important heart disease. The book was written by a group of well-recognized international experts in the field, who have not only been involved in the scientific and clinical evolution of 3D echocardiography since its inception but are also intensively involved in expert training courses. As a result, the clear focus of this book is on the practical application of 3D echocardiography in daily clinical routine with tips and tricks for both beginners and experts, accompanied by more than 150 case examples comprehensively illustrated in more than 800 images and more than 500 videos provided on a DVD. In addition to an in-depth review of the most recent literature on real-time 3D echocardiography, this book represents an invaluable reference work for beginners and expert users of 3D echocardiography. - Tips and tricks for beginners and experts - Educational material for 3D training courses - Comprehensively illustrated cases - DVD with video clips of all sample cases.

  15. Multilocality and fusion rules on the generalized structure functions in two-dimensional and three-dimensional Navier-Stokes turbulence.

    Science.gov (United States)

    Gkioulekas, Eleftherios

    2016-09-01

    Using the fusion-rules hypothesis for three-dimensional and two-dimensional Navier-Stokes turbulence, we generalize a previous nonperturbative locality proof to multiple applications of the nonlinear interactions operator on generalized structure functions of velocity differences. We call this generalization of nonperturbative locality to multiple applications of the nonlinear interactions operator "multilocality." The resulting cross terms pose a new challenge requiring a new argument and the introduction of a new fusion rule that takes advantage of rotational symmetry. Our main result is that the fusion-rules hypothesis implies both locality and multilocality in both the IR and UV limits for the downscale energy cascade of three-dimensional Navier-Stokes turbulence and the downscale enstrophy cascade and inverse energy cascade of two-dimensional Navier-Stokes turbulence. We stress that these claims relate to nonperturbative locality of generalized structure functions on all orders and not the term-by-term perturbative locality of diagrammatic theories or closure models that involve only two-point correlation and response functions.

  16. Three-dimensional analysis of the magnetic structure in Hokkaido, Japan; Hokkaido no sanjigen jiki kozo kaiseki

    Energy Technology Data Exchange (ETDEWEB)

    Makino, M. [Geological Survey of Japan, Tsukuba (Japan)

    1996-10-01

    The magnetic structure in Hokkaido was quantitatively analyzed by the magnetic anomaly distribution. This paper describes its characteristics. Detection of structural boundaries and 3-D analysis of double-layer structure were conducted for the regional magnetic data in a region with about 500 km square. There was not so large difference in patterns of magnetic anomaly distribution between the case that the direction of magnetization was set at 45{degree} to the west during the geomagnetic conversion according to Segawa and Oshima and the case that it was set as same as the current geomagnetic direction. The method of Blakely and Simpson was useful to detect the boundaries of magnetic structures. The structural boundaries obtained were more linear than the iso-magnetic contour lines. A new method has been conceived in which the approximation of 3-D magnetic structure analysis can be deduced, and the irregularity of magnetic basement can be determined by the repeated calculation. In practice, this method was applied to the magnetic data in the whole Hokkaido. The calculation was stably converged. It was found that the magnetic structure obtained in the Kamuikotan/Ishikari-Kitakami magnetic belt exhibited a fault structure having steep slopes accompanied by the basin structure in the western boundaries. 19 refs., 6 figs.

  17. Elastocapillary folding of three dimensional micro-structures using water pumped through the wafer via a silicon nitride tube

    NARCIS (Netherlands)

    Legrain, A.B.H.; Berenschot, Johan W.; Sanders, Remco G.P.; Ma, Kechun; Tas, Niels Roelof; Abelmann, Leon

    2011-01-01

    In this paper we present the first investigation of a batch method for folding of threedimensional micrometer-sized silicon nitride structures by capillary forces. Silicon nitride tubes have been designed and fabricated using DRIE at the center of the planar origami patterns of the structures. Water

  18. Three-dimensional structural damage localization system and method using layered two-dimensional array of capacitance sensors

    Science.gov (United States)

    Curry, Mark A (Inventor); Senibi, Simon D (Inventor); Banks, David L (Inventor)

    2010-01-01

    A system and method for detecting damage to a structure is provided. The system includes a voltage source and at least one capacitor formed as a layer within the structure and responsive to the voltage source. The system also includes at least one sensor responsive to the capacitor to sense a voltage of the capacitor. A controller responsive to the sensor determines if damage to the structure has occurred based on the variance of the voltage of the capacitor from a known reference value. A method for sensing damage to a structure involves providing a plurality of capacitors and a controller, and coupling the capacitors to at least one surface of the structure. A voltage of the capacitors is sensed using the controller, and the controller calculates a change in the voltage of the capacitors. The method can include signaling a display system if a change in the voltage occurs.

  19. The three-dimensional solution structure of mini-M conotoxin BtIIIA reveals a disconnection between disulfide connectivity and peptide fold.

    Science.gov (United States)

    Akcan, Muharrem; Cao, Ying; Chongxu, Fan; Craik, David J

    2013-06-15

    Conotoxins are bioactive peptides from the venoms of marine snails and have been divided into several superfamilies based on homologies in their precursor sequences. The M-superfamily conotoxins can be further divided into five branches based on the number of residues in the third loop of the peptide sequence. Recently two M-1 branch conotoxins (tx3a and mr3e) with a C1-C5, C2-C4, C3-C6 disulfide connectivity and one M-2 branch conotoxin (mr3a) with a C1-C6, C2-C4, C3-C5 disulfide connectivity were described. Here we report the disulfide connectivity, chemical synthesis and the three-dimensional NMR structure of the novel 14-residue conotoxin BtIIIA, extracted from the venom of Conus betulinus. It has the same disulfide connectivity as mr3a, which puts it in the M-2 branch conotoxins but has a distinctly different structure from other M-2 branch conotoxins. 105 NOE distance restraints and seven dihedral angle restraints were used for the structure calculations. The three-dimensional structure was determined with CYANA based on torsion angle dynamics and refinement in a water solvent box was carried out with CNS. Fifty structures were calculated and the 20 lowest energy structures superimposed with a RMSD of 0.49±0.16 Å. Even though it has the M-2 branch disulfide connectivity, BtIIIA was found to have a 'flying bird' backbone motif depiction that is found in the M-1 branch conotoxin mr3e. This study shows that conotoxins with the same cysteine framework can have different disulfide connectivities and different peptide folds. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Hybrid finite-element/rigorous coupled wave analysis for scattering from three-dimensional doubly periodic structures.

    Science.gov (United States)

    Kuloglu, Mustafa; Lee, Robert

    2012-07-01

    A new hybrid finite-element/rigorous coupled wave analysis formulation is presented for the modeling of electromagnetic wave interactions with doubly periodic structures. The structures under investigation are periodic in two dimensions and have a finite extent in the third dimension. The proposed model can handle structures that have material properties varying arbitrarily in any of the dimensions within the unit cell. Employment of Fourier series expansion and Floquet's theory in one of the periodic dimensions helps to reduce the dimension of the mesh. Results obtained from alternative methods are used to verify the proposed method's validity.

  1. Three-dimensional ICT reconstruction

    International Nuclear Information System (INIS)

    Zhang Aidong; Li Ju; Chen Fa; Sun Lingxia

    2005-01-01

    The three-dimensional ICT reconstruction method is the hot topic of recent ICT technology research. In the context, qualified visual three-dimensional ICT pictures are achieved through multi-piece two-dimensional images accumulation by, combining with thresholding method and linear interpolation. Different direction and different position images of the reconstructed pictures are got by rotation and interception respectively. The convenient and quick method is significantly instructive to more complicated three-dimensional reconstruction of ICT images. (authors)

  2. Three-dimensional ICT reconstruction

    International Nuclear Information System (INIS)

    Zhang Aidong; Li Ju; Chen Fa; Sun Lingxia

    2004-01-01

    The three-dimensional ICT reconstruction method is the hot topic of recent ICT technology research. In the context qualified visual three-dimensional ICT pictures are achieved through multi-piece two-dimensional images accumulation by order, combining with thresholding method and linear interpolation. Different direction and different position images of the reconstructed pictures are got by rotation and interception respectively. The convenient and quick method is significantly instructive to more complicated three-dimensional reconstruction of ICT images. (authors)

  3. Polarimetric and Interferometric Synthetic Aperture Radar ; a new way to quantify three-dimensional structure of Earth and planetary surfaces

    Data.gov (United States)

    National Aeronautics and Space Administration — The PolInSAR technique is designed to greatly improve estimates of forest biomass and ecosystem 3D structure . This application is also of special interest in the...

  4. Three-Dimensional Structure of Thermohaline Staircases in the Tropical North Atlantic and Their Effect on Acoustic Propagation

    Science.gov (United States)

    2012-12-01

    STRUCTURE OF THERMOHALINE STAIRCASES IN THE TROPICAL NORTH ATLANTIC AND THEIR EFFECT ON ACOUSTIC PROPAGATION by Amy C. Bulters December... THERMOHALINE STAIRCASES IN THE TROPICAL NORTH ATLANTIC AND THEIR EFFECT ON ACOUSTIC PROPAGATION 5. FUNDING NUMBERS 6. AUTHOR(S) Amy C. Bulters 7...overlies cold, fresh fluid). The formation of staircases in the thermohaline structure of the ocean has been observed since the late 1960s, with

  5. Comparison of Commercial Structure-From Photogrammety Software Used for Underwater Three-Dimensional Modeling of Coral Reef Environments

    Science.gov (United States)

    Burns, J. H. R.; Delparte, D.

    2017-02-01

    Structural complexity in ecosystems creates an assortment of microhabitat types and has been shown to support greater diversity and abundance of associated organisms. The 3D structure of an environment also directly affects important ecological parameters such as habitat provisioning and light availability and can therefore strongly influence ecosystem function. Coral reefs are architecturally complex 3D habitats, whose structure is intrinsically linked to the ecosystem biodiversity, productivity, and function. The field of coral ecology has, however, been primarily limited to using 2-dimensional (2D) planar survey techniques for studying the physical structure of reefs. This conventional approach fails to capture or quantify the intricate structural complexity of corals that influences habitat facilitation and biodiversity. A 3-dimensional (3D) approach can obtain accurate measurements of architectural complexity, topography, rugosity, volume, and other structural characteristics that affect biodiversity and abundance of reef organisms. Structurefrom- Motion (SfM) photogrammetry is an emerging computer vision technology that provides a simple and cost-effective method for 3D reconstruction of natural environments. SfM has been used in several studies to investigate the relationship between habitat complexity and ecological processes in coral reef ecosystems. This study compared two commercial SfM software packages, Agisoft Photoscan Pro and Pix4Dmapper Pro 3.1, in order to assess the cpaability and spatial accuracy of these programs for conducting 3D modeling of coral reef habitats at three spatial scales.

  6. Three-dimensional reconstructions for asymptomatic and cerebral palsy children's lower limbs using a biplanar X-ray system: A feasibility study

    Energy Technology Data Exchange (ETDEWEB)

    Assi, Ayman, E-mail: ayman.assi@gmail.com [Laboratoire de Biomécanique, Arts et Métiers ParisTech, Paris (France); Laboratory of Biomechanics, Faculty of Medicine, University of Saint-Joseph, Beirut (Lebanon); Gait and Motion Analysis Lab, SESOBEL, Beirut (Lebanon); Chaibi, Yasmina, E-mail: yasmina.chaibi@gmail.com [Laboratoire de Biomécanique, Arts et Métiers ParisTech, Paris (France); Presedo, Ana, E-mail: a.presedo@gmail.com [Laboratoire de Biomécanique, Arts et Métiers ParisTech, Paris (France); Hôpital Robert Debré, Paris (France); Dubousset, Jean, E-mail: jean.dubousset@wanadoo.fr [Laboratoire de Biomécanique, Arts et Métiers ParisTech, Paris (France); Ghanem, Ismat, E-mail: ghanem.i@dm.net.lb [Laboratory of Biomechanics, Faculty of Medicine, University of Saint-Joseph, Beirut (Lebanon); Gait and Motion Analysis Lab, SESOBEL, Beirut (Lebanon); Hôpital Hôtel Dieu de France, Beirut (Lebanon); Skalli, Wafa, E-mail: wafa.skalli@ensam.eu [Laboratoire de Biomécanique, Arts et Métiers ParisTech, Paris (France)

    2013-12-01

    The aim of this study is to explore the feasibility of 3D subject-specific skeletal reconstructions of lower limb in children using stereoradiography, and to assess uncertainty of clinical and anatomical parameters for children with cerebral palsy and for healthy children. The stereoradiography technique, using the EOS{sup ®} system (Eos-imaging{sup ®}), is based on the acquisition of two simultaneous digital anteroposterior and lateral X-rays, from head to feet in standing position and at low radiation dose. This technique allows subject-specific skeletal 3D reconstructions. Five children with cerebral palsy (CP) and 5 typically developing children (TD) were included in the study. Two operators performed the lower limb reconstructions twice. Tridimensional reconstructions were feasible for children over the age of 5 years. The study of reproducibility of anatomical parameters defining skeletal alignment showed uncertainties under 3° for the neck shaft angle, the femoral mechanical angle, and for the femoral and tibial torsions. The maximum degree of uncertainty was obtained for the femoral tibial rotation (4° for healthy children and 3.5° for children with CP)

  7. Diffuser-aided diffuse optical imaging for breast tumor: a feasibility study based on time-resolved three-dimensional Monte Carlo modeling.

    Science.gov (United States)

    Chuang, Ching-Cheng; Lee, Chia-Yen; Chen, Chung-Ming; Hsieh, Yao-Sheng; Liu, Tsan-Chi; Sun, Chia-Wei

    2012-05-01

    This study proposed diffuser-aided diffuse optical imaging (DADOI) as a new approach to improve the performance of the conventional diffuse optical tomography (DOT) approach for breast imaging. The 3-D breast model for Monte Carlo simulation is remodeled from clinical MRI image. The modified Beer-Lambert's law is adopted with the DADOI approach to substitute the complex algorithms of inverse problem for mapping of spatial distribution, and the depth information is obtained based on the time-of-flight estimation. The simulation results demonstrate that the time-resolved Monte Carlo method can be capable of performing source-detector separations analysis. The dynamics of photon migration with various source-detector separations are analyzed for the characterization of breast tissue and estimation of optode arrangement. The source-detector separations should be less than 4 cm for breast imaging in DOT system. Meanwhile, the feasibility of DADOI was manifested in this study. In the results, DADOI approach can provide better imaging contrast and faster imaging than conventional DOT measurement. The DADOI approach possesses great potential to detect the breast tumor in early stage and chemotherapy monitoring that implies a good feasibility for clinical application.

  8. Three-dimensional reconstructions for asymptomatic and cerebral palsy children's lower limbs using a biplanar X-ray system: A feasibility study

    International Nuclear Information System (INIS)

    Assi, Ayman; Chaibi, Yasmina; Presedo, Ana; Dubousset, Jean; Ghanem, Ismat; Skalli, Wafa

    2013-01-01

    The aim of this study is to explore the feasibility of 3D subject-specific skeletal reconstructions of lower limb in children using stereoradiography, and to assess uncertainty of clinical and anatomical parameters for children with cerebral palsy and for healthy children. The stereoradiography technique, using the EOS ® system (Eos-imaging ® ), is based on the acquisition of two simultaneous digital anteroposterior and lateral X-rays, from head to feet in standing position and at low radiation dose. This technique allows subject-specific skeletal 3D reconstructions. Five children with cerebral palsy (CP) and 5 typically developing children (TD) were included in the study. Two operators performed the lower limb reconstructions twice. Tridimensional reconstructions were feasible for children over the age of 5 years. The study of reproducibility of anatomical parameters defining skeletal alignment showed uncertainties under 3° for the neck shaft angle, the femoral mechanical angle, and for the femoral and tibial torsions. The maximum degree of uncertainty was obtained for the femoral tibial rotation (4° for healthy children and 3.5° for children with CP)

  9. Combined particle-image velocimetry and force analysis of the three-dimensional fluid-structure interaction of a natural owl wing.

    Science.gov (United States)

    Winzen, A; Roidl, B; Schröder, W

    2016-04-01

    Low-speed aerodynamics has gained increasing interest due to its relevance for the design process of small flying air vehicles. These small aircraft operate at similar aerodynamic conditions as, e.g. birds which therefore can serve as role models of how to overcome the well-known problems of low Reynolds number flight. The flight of the barn owl is characterized by a very low flight velocity in conjunction with a low noise emission and a high level of maneuverability at stable flight conditions. To investigate the complex three-dimensional flow field and the corresponding local structural deformation in combination with their influence on the resulting aerodynamic forces, time-resolved stereoscopic particle-image velocimetry and force and moment measurements are performed on a prepared natural barn owl wing. Several spanwise positions are measured via PIV in a range of angles of attack [Formula: see text] 6° and Reynolds numbers 40 000 [Formula: see text] 120 000 based on the chord length. Additionally, the resulting forces and moments are recorded for -10° ≤ α ≤ 15° at the same Reynolds numbers. Depending on the spanwise position, the angle of attack, and the Reynolds number, the flow field on the wing's pressure side is characterized by either a region of flow separation, causing large-scale vortical structures which lead to a time-dependent deflection of the flexible wing structure or wing regions showing no instantaneous deflection but a reduction of the time-averaged mean wing curvature. Based on the force measurements the three-dimensional fluid-structure interaction is assumed to considerably impact the aerodynamic forces acting on the wing leading to a strong mechanical loading of the interface between the wing and body. These time-depending loads which result from the flexibility of the wing should be taken into consideration for the design of future small flying air vehicles using flexible wing structures.

  10. Two and three dimensional simulation of disk-loaded travelling-wave output structures for high-power klystrons

    International Nuclear Information System (INIS)

    Eppley, K.R.

    1994-01-01

    The authors have developed algorithms for designing disk-loaded travelling-wave output structures for X-band klystrons to be used in the SLAC NLC. They use either a four or five cell structure in a π/2 mode. The disk radii are tapered to produce an approximately constant gradient. The matching calculation is not performed on the tapered structure, but rather on a coupler whose input and output cells are the same as the final cell of the tapered structure, and whose interior cells are the same as the penultimate cell in the tapered structure. 2-D calculations using CONDOR model the waveguide as a radial transmission line of adjustable impedance. 3-D calculations with MAFIA model the actual rectangular waveguide and coupling slot. A good match is obtained by adjusting the impedance of the final cell. In 3-D, this requires varying both the radius of the cell and the width of the aperture. When the output cell with the best match is inserted in the tapered structure, they obtain excellent cold-test agreement between the 2-D and 3-D models. They use hot-test simulations with CONDOR to design the structure with maximum efficiency and minimum surface fields. The azimuthal asymmetry due to the coupling iris can increase the peak fields by 20 to 30 percent. They can reduce this problem by making the final cavity with a non-circular cross section. With proper dimensions, they can keep a good match while reducing the azimuthal asymmetry to 6 percent. They have designed circuits at 11.424 Ghz for several different perveances. At 440 kV, microperveance 1.2, they calculate 83 MW, 54 percent efficiency, peak surface field 76 MV/m. At microperveance 0.8, they calculate 60 MW, 58 percent efficiency, peak field 67 MV/m. At 465 kV, microperveance 0.6, they calculate 55 MW, 62 percent efficiency, peak field 63 MV/m

  11. Three-dimensional structures in the design of therapeutics targeting parasitic protozoa: reflections on the past, present and future.

    Science.gov (United States)

    Hol, Wim G J

    2015-05-01

    Parasitic protozoa cause a range of diseases which threaten billions of human beings. They are responsible for tremendous mortality and morbidity in the least-developed areas of the world. Presented here is an overview of the evolution over the last three to four decades of structure-guided design of inhibitors, leads and drug candidates aiming at targets from parasitic protozoa. Target selection is a crucial and multi-faceted aspect of structure-guided drug design. The major impact of advances in molecular biology, genome sequencing and high-throughput screening is touched upon. The most advanced crystallographic techniques, including XFEL, have already been applied to structure determinations of drug targets from parasitic protozoa. Even cryo-electron microscopy is contributing to our understanding of the mode of binding of inhibitors to parasite ribosomes. A number of projects have been selected to illustrate how structural information has assisted in arriving at promising compounds that are currently being evaluated by pharmacological, pharmacodynamic and safety tests to assess their suitability as pharmaceutical agents. Structure-guided approaches are also applied to incorporate properties into compounds such that they are less likely to become the victim of resistance mechanisms. A great increase in the number of novel antiparasitic compounds will be needed in the future. These should then be combined into various multi-compound therapeutics to circumvent the diverse resistance mechanisms that render single-compound, or even multi-compound, drugs ineffective. The future should also see (i) an increase in the number of projects with a tight integration of structural biology, medicinal chemistry, parasitology and pharmaceutical sciences; (ii) the education of more `medicinal structural biologists' who are familiar with the properties that compounds need to have for a high probability of success in the later steps of the drug-development process; and (iii) the

  12. UV-A photocatalytic treatment of Legionella pneumophila bacteria contaminated airflows through three-dimensional solid foam structured photocatalytic reactors

    Energy Technology Data Exchange (ETDEWEB)

    Josset, Sebastien; Hajiesmaili, Shabnam; Begin, Dominique; Edouard, David; Pham-Huu, Cuong [Laboratoire des Materiaux, Surfaces et Procedes pour la Catalyse (LMSPC), European Laboratory for Catalysis and Surface Sciences (ELCASS), CNRS, Strasbourg University, 25 rue Becquerel 67087 Strasbourg (France); Lett, Marie-Claire [Laboratoire de Genetique Moleculaire, Genomique, Microbiologie, CNRS, Strasbourg University, 28, rue Goethe 67083 Strasbourg Cedex (France); Keller, Nicolas, E-mail: nkeller@chimie.u-strasbg.fr [Laboratoire des Materiaux, Surfaces et Procedes pour la Catalyse (LMSPC), European Laboratory for Catalysis and Surface Sciences (ELCASS), CNRS, Strasbourg University, 25 rue Becquerel 67087 Strasbourg (France); Keller, Valerie [Laboratoire des Materiaux, Surfaces et Procedes pour la Catalyse (LMSPC), European Laboratory for Catalysis and Surface Sciences (ELCASS), CNRS, Strasbourg University, 25 rue Becquerel 67087 Strasbourg (France)

    2010-03-15

    A 3D-structured photocatalytic media was designed for allowing a tubular reactor to work in a traversing-flow mode at low pressure drops with a strong increase in the surface area-to-volume ratio inside the reactor. A protective polysiloxane coating was performed for protecting a structured polyurethane foam and anchoring the active TiO{sub 2} particles. Filled with the 3D-structured solid foam supporting TiO{sub 2} photocatalyst, the reactor could thus take advantages from the static mixer effect and from the low pressure drop resulting from the reticulated foam support. Very efficient decontamination levels towards airborne Legionella pneumophila bacteria were reached in a single-pass test mode.

  13. UV-A photocatalytic treatment of Legionella pneumophila bacteria contaminated airflows through three-dimensional solid foam structured photocatalytic reactors.

    Science.gov (United States)

    Josset, Sébastien; Hajiesmaili, Shabnam; Begin, Dominique; Edouard, David; Pham-Huu, Cuong; Lett, Marie-Claire; Keller, Nicolas; Keller, Valérie

    2010-03-15

    A 3D-structured photocatalytic media was designed for allowing a tubular reactor to work in a traversing-flow mode at low pressure drops with a strong increase in the surface area-to-volume ratio inside the reactor. A protective polysiloxane coating was performed for protecting a structured polyurethane foam and anchoring the active TiO(2) particles. Filled with the 3D-structured solid foam supporting TiO(2) photocatalyst, the reactor could thus take advantages from the static mixer effect and from the low pressure drop resulting from the reticulated foam support. Very efficient decontamination levels towards airborne Legionella pneumophila bacteria were reached in a single-pass test mode. (c) 2009 Elsevier B.V. All rights reserved.

  14. Three-dimensional structure of porcine pancreatic carboxypeptidase B with an acetate ion and two zinc atoms in the active site

    Energy Technology Data Exchange (ETDEWEB)

    Akparov, V. Kh., E-mail: valery@akparov.ru [State Research Institute for Genetics and Selection of Industrial Microorganisms (Russian Federation); Timofeev, V. I., E-mail: tostars@mail.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” (Russian Federation); Maghsoudi, N. N., E-mail: maghsudi@yahoo.com [Shahid Beheshti University of Medical Sciences, Neuroscience Research Center (Iran, Islamic Republic of); Kuranova, I. P. [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” (Russian Federation)

    2017-03-15

    Crystals of porcine pancreatic carboxypeptidase B (CPB) were grown by the capillary counter-diffusion method in the presence of polyethylene glycol and zinc acetate. The three-dimensional structure of CPB was determined at 1.40 Å resolution using the X-ray diffraction data set collected from the crystals of the enzyme at the SPring 8 synchrotron facility and was refined to R{sub fact} = 17.19%, R{sub free} = 19.78%. The structure contains five zinc atoms, two of which are present in the active site of the enzyme, and an acetate ion. The arrangement of an additional zinc atom in the active site and the acetate ion is different from that reported by Yoshimoto et al.

  15. Shape evolution of three-dimensional periodic structure fabricated by direct-write assembly of concentrated colloidal gels

    Science.gov (United States)

    Zhu, Cheng

    Scope and Method of Study. 3D periodic structures were fabricated by direct-write assembly of concentrated colloidal gels with self-supporting features. The rheological behavior of the gel was characterized in linear viscoelastic regions. The flow behavior of the gel was modeled by using structural kinetics theory. Based on this model, the dynamic extrusion process of the gel was simulated by incorporating slip wall boundary conditions. A viscoelastic catenary model was developed to describe span shape and compare the results to previous results that used a simple elastic beam theory. The shape evolution (i.e., spanning behavior) of spanning filaments observed was related to shear stress conditions and a limited set of rheological parameters. Findings and Conclusions. The rate and magnitude of microstructure change within a colloidal gel ink are crucial factors for shape evolution of 3D structures assembled by direct write techniques. The events that set the equilibrium shape of 3D structure occur within the initial few seconds after deposition and gels microstructure recovery within this period is critical to geometric fidelity. The shape evolution of 3D structures may be predicted by knowledge of the rheological behavior of the colloidal gel in shear loading. Rheological behavior can be related to the structural recovery time of the colloidal gel and this may be measured with a series of equilibrium flow measurements. Successful completion of this research advances science-based ink design methods and optimization of deposition variables. Better control of shape evolution will lead to improvements in advanced applications such as photonic band gap structures, artificial bone structures, and metal-ceramic composites. The improved connections between time-dependent shear behavior and shape evolution in an extrusion process will also impact other industries (e.g., clay extrusion for catalytic converter substrates) and improve industrial productivity through better

  16. Three-dimensional Geological and Geo-mechanical Modelling of Repositories for Nuclear Waste Disposal in Deep Geological Structures

    International Nuclear Information System (INIS)

    Fahland, Sandra; Hofmann, Michael; Bornemann, Otto; Heusermann, Stefan

    2008-01-01

    To prove the suitability and safety of underground structures for the disposal of radioactive waste extensive geo-scientific research and development has been carried out by BGR over the last decades. Basic steps of the safety analysis are the geological modelling of the entire structure including the host rock, the overburden and the repository geometry as well as the geo-mechanical modelling taking into account the 3-D modelling of the underground structure. The geological models are generated using the special-construction openGEO TM code to improve the visualisation an d interpretation of the geological data basis, e.g. borehole, mine, and geophysical data. For the geo-mechanical analysis the new JIFE finite-element code has been used to consider large 3-D structures with complex inelastic material behaviour. To establish the finite-element models needed for stability and integrity calculations, the geological models are simplified with respect to homogenous rock layers with uniform material behaviour. The modelling results are basic values for the evaluation of the stability of the repository mine and the long-term integrity of the geological barrier. As an example of application, the results of geological and geo-mechanical investigations of the Morsleben repository based on 3-D modelling are presented. (authors)

  17. Three-dimensional printing and deformation behavior of low-density target structures by two-photon polymerization

    Science.gov (United States)

    Liu, Ying; Stein, Ori; Campbell, John H.; Jiang, Lijia; Petta, Nicole; Lu, Yongfeng

    2017-08-01

    Two-photon polymerization (2PP), a 3D nano to microscale additive manufacturing process, is being used for the first time to fabricate small custom experimental packages ("targets") to support laser-driven high-energy-density (HED) physics research. Of particular interest is the use of 2PP to deterministically print low-density, low atomic-number (CHO) polymer matrices ("foams") at millimeter scale with sub-micrometer resolution. Deformation during development and drying of the foam structures remains a challenge when using certain commercial photo-resins; here we compare use of acrylic resins IP-S and IP-Dip. The mechanical strength of polymeric beam and foam structures is examined particularly the degree of deformation that occurs during the development and drying processes. The magnitude of the shrinkage in the two resins in quantified by printing sample structures and by use of FEA to simulate the deformation. Capillary drying forces are shown to be small and likely below the elastic limit of the core foam structure. In contrast the substantial shrinkage in IP-Dip ( 5-10%) cause large shear stresses and associated plastic deformation particularly near constrained boundaries such as the substrate and locations with sharp density variation. The inherent weakness of stitching boundaries is also evident and in certain cases can lead to delamination. Use of IP-S shows marked reduction in deformation with a minor loss of print resolution

  18. Observations on structural features and characteristics of biological apatite crystals. 5. Three-dimensional observation on ultrastructure of human enamel crystals.

    Science.gov (United States)

    Ichijo, T; Yamashita, Y; Terashima, T

    1993-09-01

    In a series of studies to investigate the structural features of the biological crystals, such as the tooth and bone, using an electron microscope, we examined the ultrastructure of the enamel, dentin, and bone crystals at near atomic resolution and showed the configuration of the hydroxyapatite structure through the cross and longitudinal sections of the crystals. Thereafter, based on the results of the observations by the authors of the ultrastructure of the tooth and bone crystals, thinking that it might be possible to conduct direct three-dimensional observation of the configuration composing the unit cell of the hydroxyapatite crystals, we conducted a study on this. These results indicated that it was possible to sterically observe the configuration of the hydroxyapatite structure composing the enamel crystal. The materials used for this study were the middle layer of the noncarious enamel from the freshly extracted human erupted permanent molars. The small cubes of the enamel were fixed in glutaraldehyde and osmium tetroxide and embedded in epoxy resin using the routine methods. The ultrathin sections were cut with a diamond knife without decalcification and were examined with the HITACHI H-9000 H type transmission electron microscope operated at 300 kV. Each crystal was observed at an initial magnification of 500,000 times and at the final magnification of 10,000,000 times and over. We sincerely believe that the electron micrographs shown in this report are the first to show three-dimensionally the configuration of the hydroxyapatite structure composing the crystal in the cross and longitudinal sections of an enamel crystal.

  19. Finite-element formulations for the thermal stress analysis of two- and three-dimensional thin reactor structures

    International Nuclear Information System (INIS)

    Kulak, R.F.; Kennedy, J.M.; Belytschko, T.B.; Schoeberle, D.F.

    1977-01-01

    This paper describes finite-element formulations for the thermal stress analysis of LMFBR structures. The first formulation is applicable to large displacement rotation problems in which the strains are small. For this formulation, a general temperature-dependent constituent relationship is derived from a Gibbs potential and a temperature dependent surface. A second formulation is presented for problems characterized by both large displacement-rotations and large strains. Here a set of large strain hypoelastic-plastic relationships are developed to linearly relate the rate of stress to the rate of deformation. These developments were incorporated into two ANL developed finite-element computer codes: the implicit version of STRAW and the 3D Implicit Structural Analaysis code. A set of problems is presented to validate both the 3D and 2D programs and to illustrate their applicability to a variety of problems. (Auth.)

  20. Combined, nonlinear aerodynamic and structural method for the aeroelastic design of a three-dimensional wing in supersonic flow

    Science.gov (United States)

    Pittman, J. L.; Giles, G. L.

    1986-01-01

    An iterative procedure for the static aeroelastic design of a flexible wing at supersonic speeds has been developed. The procedure combines a nonlinear, full-potential solver (NCOREL) with an equivalent plate structural analysis method. The NCOREL method yields significantly improved aerodynamic estimates compared to linear theory. The equivalent plate structural analysis method demonstrates an order of magnitude reduction in computer memory and execution time compared to finite-element methods. A highly swept wing is analyzed at high lift using this aeroelastic procedure. The results indicate that the wing deforms favorably due to aerodynamic loading and, consequently, that the inviscid drag levels do not vary at the required lift coefficient although the angle of attack varies significantly. A sensitivity analysis of the type required for optimization studies was also performed with the aeroelastic design procedure.

  1. Resolving Point Defects in the Hydration Structure of Calcite (10.4) with Three-Dimensional Atomic Force Microscopy

    Science.gov (United States)

    Söngen, Hagen; Reischl, Bernhard; Miyata, Kazuki; Bechstein, Ralf; Raiteri, Paolo; Rohl, Andrew L.; Gale, Julian D.; Fukuma, Takeshi; Kühnle, Angelika

    2018-03-01

    It seems natural to assume that defects at mineral surfaces critically influence interfacial processes such as the dissolution and growth of minerals in water. The experimental verification of this claim, however, is challenging and requires real-space methods with utmost spatial resolution, such as atomic force microscopy (AFM). While defects at mineral-water interfaces have been resolved in 2D AFM images before, the perturbation of the surrounding hydration structure has not yet been analyzed experimentally. In this Letter, we demonstrate that point defects on the most stable and naturally abundant calcite (10.4) surface can be resolved using high-resolution 3D AFM—even within the fifth hydration layer. Our analysis of the hydration structure surrounding the point defect shows a perturbation of the hydration with a lateral extent of approximately one unit cell. These experimental results are corroborated by molecular dynamics simulations.

  2. Characterization of iron ferromagnetism by the local atomic volume: from three-dimensional structures to isolated atoms

    Czech Academy of Sciences Publication Activity Database

    Zhang, L.; Šob, Mojmír; Wu, Z.; Zhang, Y.; Lu, G-H.

    2014-01-01

    Roč. 26, č. 8 (2014), 086002-1-086002-17 ISSN 0953-8984 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068; GA ČR(CZ) GAP108/12/0311; GA AV ČR IAA100100920 Institutional support: RVO:68081723 Keywords : electronic structure * magnetism * iron * ab initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.346, year: 2014

  3. Correlation between magnetic spin structure and the three-dimensional geometry in chemically synthesized nanoscale magnetite rings

    DEFF Research Database (Denmark)

    Eltschka, M.; Klaui, M.; Rudiger, U

    2008-01-01

    The correlation between magnetic spin structure and geometry in nanoscale chemically synthesized Fe3O4 rings has been investigated by transmission electron microscopy. We find primarily the flux closure vortex states but in rings with thickness variations, an effective stray field occurs. Using t....... The interaction between exchange coupled rings leads to antiparallel vortex states and extended onion states. (c) 2008 American Institute of Physics....

  4. Three-dimensional structure of peripheral exocrine gland in rat pancreas: reconstruction using transmission electron microscopic examination of serial sections.

    Science.gov (United States)

    Ashizawa, Nobuo; Sakai, Toshio; Yoneyama, Tsunao; Naora, Hiroyuki; Kinoshita, Yoshikazu

    2005-11-01

    The purpose of this study was to elucidate the 3-dimensional structure of the peripheral pancreatic exocrine gland. We observed serial sections of rat pancreatic tissue using a transmission electron microscope and traced the intercalated duct lumina, intra-acinar secretory canaliculi, intercalated duct cells or centroacinar cells, and basement membranes of acini onto a transparent sheet. These traced diagrams were reconstructed. The intra-acinar secretory canaliculus had branches but no anastomosis. The intercellular secretory canaliculus was extended from the central lumen through the space between the lateral surfaces of the acinar cells to the acinar base. Furthermore, the cytoplasmic process of each centroacinar cell was extended along the central lumen and connected to an intercalated duct cell; thus, centroacinar cells with the same structure as intercalated duct cells were not isolated from the intercalated duct cells. In this study, we elucidated the normal 3-dimensional structure of the peripheral pancreatic exocrine gland. To understand the pathogenesis of chronic pancreatitis, in the future we intend to examine the morphologic changes of pancreatic tissue during the onset and advancement of chronic pancreatitis using animal models.

  5. Small-tilt micromirror-device-based multiwavelength three-dimensional 2X2 fiber optic switch structures

    Science.gov (United States)

    Riza, Nabeel A.; Sumriddetchkajorn, Sarun

    2000-02-01

    Small-tilt micromirror-based 2 X 2 fiber optic switch array structures are proposed using fixed mirrors and fiber interconnections. A multiwavelength 2 X 2 fiber optic switch based on this small-tilt micromirror is experimentally demonstrated. The key innovation in this architecture is the use of a specially located fixed mirror to form a symmetric 2 X 2 retrorefractive switching structure. These 2 X 2 fiber optic switch structures can also provide a fault-tolerant design using a macropixel approach. A 2D digital micromirror device (2D-DMD) from Texas Instruments (TI) designed to operate in the visible band is used to represent the small-tilt micromirrors in our experimental demonstration. Multiwavelength switch operation is characterized by changing the operating wavelength of the tunable laser. The measured average optical coherent crosstalk is -22 dB with +/- 0.9 dB fluctuation over 40 nm, limited by the on-off ratio of the 2D-DMD. The measured average optical loss is 14.8 dB at a 1.55-micrometers operating wavelength, limited by the visible wavelength design TI 2D- DMD, three-port optical circulators, fiber adapters, and free-space-to-fiber coupling efficiency.

  6. Electromagnetic and thermal properties of three-dimensional printed multilayered nano-carbon/poly(lactic) acid structures

    International Nuclear Information System (INIS)

    Paddubskaya, A.; Valynets, N.; Batrakov, K.; Kuzhir, P.; Maksimenko, S.; Kotsilkova, R.; Velichkova, H.; Petrova, I.; Biró, I.; Kertész, K.; Márk, G. I.; Horváth, Z. E.; Biró, L. P.

    2016-01-01

    A new type of light-weight material produced by 3D printing consisting of nano-carbon doped polymer layer followed by a dielectric polymer layer is proposed. We performed temperature dependent characterization and measured the electromagnetic (EM) response of the samples in the GHz and THz range. The temperature dependent structural characteristics, crystallization, and melting were observed to be strongly affected by the presence and the number of nano-carbon doped layers in the sandwich structure. The electromagnetic measurements show a great potential of such a type of periodic material for electromagnetic compatibility applications in microwave frequency range. Sandwich structures containing only two nano-carbon layers already become not transparent to the microwaves, giving an electromagnetic interference shielding efficiency at the level of 8–15 dB. A sandwich consisting of one nano-carbon doped and one polymer layer is opaque for THz radiation, because of 80% of absorption. These studies serve as a basis for design and realization of specific optimal geometries of meta-surface type with the 3D printing technique, in order to reach a high level of electromagnetic interference shielding performance for real world EM cloaking and EM ecology applications.

  7. [Modeling of a three-dimensional structure of cytochrome P-450 1A2 and search for its new ligands].

    Science.gov (United States)

    Belkina, N V; Skvortsov, V S; Ivanov, A S; Archakov, A I

    1998-01-01

    The substances inhibiting cytochrome P450 1A2 (CYP1A2) represent a perspective class of new drugs, which application in clinical practice can become the important part in preventive maintenance in oncology. The present work is devoted to computer modelling of 3-D structure of CYP1A2 and searching of new inhibitors by database mining. The modelling of CYP1A2 was done based on homology with 4 bacterial cytochromes P450 with known 3-D structure. For optimization of CYP1A2 active site structure the models of its complexes with characteristic substrates (caffeine and 7-ethoxyresorufin) were designed. These complexes were optimized by molecular dynamics simulation in water. The models of 24 complexes of CYP1A2 with known ligands with known Kd were designed by means of DockSearch and LeapFrog programs. 3D-QSAR model with good predictive force was created based on these complexes. On a final stage the search of knew CYP1A2 ligands in testing database (more than 23.000 substances from database Maybridge and 112 known CYP1A2 ligands from database Metabolite, MDL) was executed. 680 potential ligands of CYP1A2 with Kd values, comparable with known ones were obtained. This number has included 73 compounds from 112 known ligands, introduced in tested database as the internal control.

  8. Electromagnetic and thermal properties of three-dimensional printed multilayered nano-carbon/poly(lactic) acid structures

    Energy Technology Data Exchange (ETDEWEB)

    Paddubskaya, A. [Research Institute for Nuclear Problems, Belarusian State University, Bobruiskaya Str. 11, 220030 Minsk (Belarus); Center for Physical Sciences and Technology, A. Goštauto 11, LT-01108 Vilnius (Lithuania); Valynets, N.; Batrakov, K. [Research Institute for Nuclear Problems, Belarusian State University, Bobruiskaya Str. 11, 220030 Minsk (Belarus); Kuzhir, P., E-mail: polina.kuzhir@gmail.com; Maksimenko, S. [Research Institute for Nuclear Problems, Belarusian State University, Bobruiskaya Str. 11, 220030 Minsk (Belarus); Tomsk State University, Tomsk 634050 (Russian Federation); Kotsilkova, R.; Velichkova, H.; Petrova, I. [Open Laboratory on Experimental Micro and Nano Mechanics, Institute of Mechanics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 4, Sofia (Bulgaria); Biró, I. [3D Wishes, Bíró u. 44/a/2, Érd (Hungary); Kertész, K.; Márk, G. I.; Horváth, Z. E.; Biró, L. P. [Institute of Technical Physics and Materials Science, Centre for Energy Research, PO Box 49, 1525 Budapest (Hungary)

    2016-04-07

    A new type of light-weight material produced by 3D printing consisting of nano-carbon doped polymer layer followed by a dielectric polymer layer is proposed. We performed temperature dependent characterization and measured the electromagnetic (EM) response of the samples in the GHz and THz range. The temperature dependent structural characteristics, crystallization, and melting were observed to be strongly affected by the presence and the number of nano-carbon doped layers in the sandwich structure. The electromagnetic measurements show a great potential of such a type of periodic material for electromagnetic compatibility applications in microwave frequency range. Sandwich structures containing only two nano-carbon layers already become not transparent to the microwaves, giving an electromagnetic interference shielding efficiency at the level of 8–15 dB. A sandwich consisting of one nano-carbon doped and one polymer layer is opaque for THz radiation, because of 80% of absorption. These studies serve as a basis for design and realization of specific optimal geometries of meta-surface type with the 3D printing technique, in order to reach a high level of electromagnetic interference shielding performance for real world EM cloaking and EM ecology applications.

  9. Three-dimensional structure of carboxypeptidase T from Thermoactinomyces vulgaris in complex with N-BOC-L-leucine.

    Science.gov (United States)

    Timofeev, V I; Kuznetsov, S A; Akparov, V Kh; Chestukhina, G G; Kuranova, I P

    2013-03-01

    The 3D structure of recombinant bacterial carboxypeptidase T (CPT) in complex with N-BOC-L-leucine was determined at 1.38 Å resolution. Crystals for the X-ray study were grown in microgravity using the counter-diffusion technique. N-BOC-L-leucine and SO4(2-) ion bound in the enzyme active site were localized in the electron density map. Location of the leucine side chain in CPT-N-BOC-L-leucine complex allowed identification of the S1 subsite of the enzyme, and its structure was determined. Superposition of the structures of CPT-N-BOC-L-leucine complex and complexes of pancreatic carboxypeptidases A and B with substrate and inhibitors was carried out, and similarity of the S1 subsites in these three carboxypeptidases was revealed. It was found that SO4(2-) ion occupies the same position in the S1' subsite as the C-terminal carboxy group of the substrate.

  10. SNP2Structure: A Public and Versatile Resource for Mapping and Three-Dimensional Modeling of Missense SNPs on Human Protein Structures.

    Science.gov (United States)

    Wang, Difei; Song, Lei; Singh, Varun; Rao, Shruti; An, Lin; Madhavan, Subha

    2015-01-01

    One of the long-standing challenges in biology is to understand how non-synonymous single nucleotide polymorphisms (nsSNPs) change protein structure and further affect their function. While it is impractical to solve all the mutated protein structures experimentally, it is quite feasible to model the mutated structures in silico. Toward this goal, we built a publicly available structure database resource (SNP2Structure, https://apps.icbi.georgetown.edu/snp2structure) focusing on missense mutations, msSNP. Compared with web portals with similar aims, SNP2Structure has the following major advantages. First, our portal offers direct comparison of two related 3D structures. Second, the protein models include all interacting molecules in the original PDB structures, so users are able to determine regions of potential interaction changes when a protein mutation occurs. Third, the mutated structures are available to download locally for further structural and functional analysis. Fourth, we used Jsmol package to display the protein structure that has no system compatibility issue. SNP2Structure provides reliable, high quality mapping of nsSNPs to 3D protein structures enabling researchers to explore the likely functional impact of human disease-causing mutations.

  11. SNP2Structure: A Public and Versatile Resource for Mapping and Three-Dimensional Modeling of Missense SNPs on Human Protein Structures

    Directory of Open Access Journals (Sweden)

    Difei Wang

    2015-01-01

    Full Text Available One of the long-standing challenges in biology is to understand how non-synonymous single nucleotide polymorphisms (nsSNPs change protein structure and further affect their function. While it is impractical to solve all the mutated protein structures experimentally, it is quite feasible to model the mutated structures in silico. Toward this goal, we built a publicly available structure database resource (SNP2Structure, https://apps.icbi.georgetown.edu/snp2structure focusing on missense mutations, msSNP. Compared with web portals with similar aims, SNP2Structure has the following major advantages. First, our portal offers direct comparison of two related 3D structures. Second, the protein models include all interacting molecules in the original PDB structures, so users are able to determine regions of potential interaction changes when a protein mutation occurs. Third, the mutated structures are available to download locally for further structural and functional analysis. Fourth, we used Jsmol package to display the protein structure that has no system compatibility issue. SNP2Structure provides reliable, high quality mapping of nsSNPs to 3D protein structures enabling researchers to explore the likely functional impact of human disease-causing mutations.

  12. THE THREE-DIMENSIONAL STRUCTURE OF THE M31 SATELLITE SYSTEM; STRONG EVIDENCE FOR AN INHOMOGENEOUS DISTRIBUTION OF SATELLITES

    International Nuclear Information System (INIS)

    Conn, A. R.; Parker, Q. A.; Zucker, D. B.; Lewis, G. F.; Ibata, R. A.; Martin, N. F.; McConnachie, A. W.; Valls-Gabaud, D.; Tanvir, N.; Irwin, M. J.; Ferguson, A. M. N.; Chapman, S. C.

    2013-01-01

    We undertake an investigation into the spatial structure of the M31 satellite system utilizing the distance distributions presented in a previous publication. These distances make use of the unique combination of depth and spatial coverage of the Pan-Andromeda Archaeological Survey to provide a large, homogeneous sample consisting of 27 of M31's satellites, as well as M31 itself. We find that the satellite distribution, when viewed as a whole, is no more planar than one would expect from a random distribution of equal size. A disk consisting of 15 of the satellites is however found to be highly significant, and strikingly thin, with an rms thickness of just 12.34 +0.75 -0.43 kpc. This disk is oriented approximately edge-on with respect to the Milky Way and almost perpendicular to the Milky Way disk. It is also roughly orthogonal to the disk-like structure regularly reported for the Milky Way satellite system and in close alignment with M31's Giant Stellar Stream. A similar analysis of the asymmetry of the M31 satellite distribution finds that it is also significantly larger than one would expect from a random distribution. In particular, it is remarkable that 20 of the 27 satellites most likely lie on the Milky Way side of the galaxy, with the asymmetry being most pronounced within the satellite subset forming the aforementioned disk. This lopsidedness is all the more intriguing in light of the apparent orthogonality observed between the satellite disk structures of the Milky Way and M31.

  13. Three dimensional reconstruction of the human skeletal muscle mitochondrial network as a tool to assess mitochondrial content and structural organization

    DEFF Research Database (Denmark)

    Dahl, Rannvá; Larsen, Steen; Dohlmann, Tine L

    2015-01-01

    with 3D reconstruction was used as a tool to analyze mitochondrial morphology and measure mitochondrial fractional volume. Results: Most type I and type II muscle fibers have tubular highly interconnected profusion mitochondria, which are thicker and more structured in type I muscle fibers (Figure 1...... mitochondrial dynamics in response to life-style interventions and/or in certain pathologies. Our results question the classification of mitochondria into subsarcolemmal and intermyofibrillar pools, since they are physically interconnected. This article is protected by copyright. All rights reserved....

  14. Effect of the three-dimensional structure of laser emission on the dynamics of low-threshold optical breakdown plasmas

    Science.gov (United States)

    Anisimov, V. N.; Arutiunian, R. V.; Bol'Shov, L. A.; Derkach, O. N.; Kanevskii, M. F.

    1989-03-01

    The effect of the transverse structure of pulsed CO2 laser emission on the dynamics of laser-induced detonation waves propagating from a metal surface and on plasma transparency recovery is investigated theoretically and experimentally. Particular attention is given to breakdown initiation near the surface. It is suggested that the inclusion of refraction in the plasma into a self-consistent numerical mode is essential for the adequate quantitative description of experimental data on the interaction of laser emission with low-threshold optical breakdown plasmas.

  15. Determination of Three-Dimensional Morphology and Inner Structure of Second-Phase Inclusions in Metals by Non-Aqueous Solution Electrolytic and Room Temperature Organic Methods

    Directory of Open Access Journals (Sweden)

    Jing Guo

    2018-01-01

    Full Text Available The secondary-phase particles in metals, particularly those composed of non-metallic materials, are often detrimental to the mechanical properties of metals; thus, it is crucial to control inclusion formation and growth. One of the challenges is determining the three-dimensional morphology and inner structures of such inclusions. In this study, a non-aqueous solution electrolytic method and a room-temperature organic technique were developed based on the principle of electrochemistry to determine the three-dimensional morphologies and inner structures of non-metallic inclusions in Al-killed steel, Si-killed steel, and ductile cast iron. The inclusions were first extracted without any damage to the inclusions, and then the collected inclusions were wrapped and cut through Cu ion deposition. The results revealed that the inclusions in Al-killed steel had an irregular morphology, that those in the Si-killed steel were mainly spherical, and that almost all the spheroidal graphite in the ductile cast iron featured a uniform globular morphology. In addition, nucleation was not observed in the inner structures of the inclusions in the Al-killed steel, while some dendritic or rod-like MnS phase precipitates appeared on the silicate inclusion surfaces, and some silicate-rich phases were detected in their inner matrix. For spheroidal graphite, rare-earth oxides (one particle or more were observed as nuclei in the center of almost every graphite particle. The formation and evolution of inclusions in these types of metals can be better understood by means of the two developed methods.

  16. Precise prediction of activators for the human constitutive androstane receptor using structure-based three-dimensional quantitative structure-activity relationship methods.

    Science.gov (United States)

    Kato, Harutoshi; Yamaotsu, Noriyuki; Iwazaki, Norihiko; Okamura, Shigeaki; Kume, Toshiyuki; Hirono, Shuichi

    2017-06-01

    The constitutive androstane receptor (CAR, NR1I3) regulates the expression of numerous drug-metabolizing enzymes and transporters. The upregulation of various enzymes, including CYP2B6, by CAR activators is a critical problem leading to clinically severe drug-drug interactions (DDIs). To date, however, few effective computational approaches for identifying CAR activators exist. In this study, we aimed to develop three-dimensional quantitative structure-activity relationship (3D-QSAR) models to predict the CAR activating potency of compounds emerging in the drug-discovery process. Models were constructed using comparative molecular field analysis (CoMFA) based on the molecular alignments of ligands binding to CAR, which were obtained from ensemble ligand-docking using 28 compounds as a training set. The CoMFA model, modified by adding a lipophilic parameter with calculated logD 7.4 (S+logD 7.4 ), demonstrated statistically good predictive ability (r 2  = 0.99, q 2  = 0.74). We also confirmed the excellent predictability of the 3D-QSAR model for CAR activation (r 2 pred  = 0.71) using seven compounds as a test set for external validation. Collectively, our results indicate that the 3D-QSAR model developed in this study provides precise prediction of CAR activating potency and, thus, should be useful for selecting drug candidates with minimized DDI risk related to enzyme-induction in the early drug-discovery stage. Copyright © 2017 The Japanese Society for the Study of Xenobiotics. Published by Elsevier Ltd. All rights reserved.

  17. Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

    International Nuclear Information System (INIS)

    Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D.

    2017-01-01

    This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

  18. Focused-ion-beam overlay-patterning of three-dimensional diamond structures for advanced single-photon properties

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Qianqing; Liu, Dongqi; Liu, Gangqin; Chang, Yanchun; Li, Wuxia, E-mail: liwuxia@aphy.iphy.ac.cn, E-mail: czgu@aphy.iphy.ac.cn [Beijing National Laboratory of Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Pan, Xinyu; Gu, Changzhi, E-mail: liwuxia@aphy.iphy.ac.cn, E-mail: czgu@aphy.iphy.ac.cn [Beijing National Laboratory of Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Collaborative Innovation Center of Quantum Matter, Beijing 100190 (China)

    2014-07-28

    Sources of single photons are of fundamental importance in many applications as to provide quantum states for quantum communication and quantum information processing. Color centers in diamond are prominent candidates to generate and manipulate quantum states of light, even at room temperature. However, the efficiency of photon collection of the color centers in bulk diamond is greatly reduced by refraction at the diamond/air interface. To address this issue, diamond structuring has been investigated by various methods. Among them, focused-ion-beam (FIB) direct patterning has been recognized as the most favorable technique. But it has been noted that diamond tends to present significant challenges in FIB milling, e.g., the susceptibility of forming charging related artifacts and topographical features. In this work, periodically-positioned-rings and overlay patterning with stagger-superimposed-rings were proposed to alleviate some problems encountered in FIB milling of diamond, for improved surface morphology and shape control. Cross-scale network and uniform nanostructure arrays have been achieved in single crystalline diamond substrates. High quality diamond solid immersion lens and nanopillars were sculptured with a nitrogen-vacancy center buried at the desired position. Compared with the film counterpart, an enhancement of about ten folds in single photon collection efficiency was achieved with greatly improved signal to noise ratio. All these results indicate that FIB milling through over-lay patterning could be an effective approach to fabricate diamond structures, potentially for quantum information studies.

  19. Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

    Energy Technology Data Exchange (ETDEWEB)

    Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D., E-mail: jdfv2009@gmail.com [Instituto Militar de Engenharia (IME), Rio de Janeiro, RJ (Brazil). Grupo de Ressonância Magnética Nuclear e Química Medicinal

    2017-07-01

    This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

  20. Postnatal width changes in the internal structures of the human mandible: a longitudinal three-dimensional cephalometric study using implants.

    Science.gov (United States)

    Baumrind, S; Korn, E L

    1992-12-01

    This paper presents case-specific quantitative evidence of the systematic lateral displacement of metallic implants in the mandibles of treated and untreated human subjects between the ages of 8.5 and 15.5 years. This evidence appears to be consistent with the inference of small, but systematic increases in distance between the internal structures of the two sides of the osseous mandible during growth. Such a conclusion, however, is inconsistent with traditional beliefs that the internal structures of the mandibular symphysis fuse at the midline during the first post-natal year and remain dimensionally constant thereafter. We recently published evidence of statistically significant transverse displacement of metallic implants in the mandibular body region for 12 of 28 subjects for whom longitudinal data were available. Of the twelve subjects for whom statistically significant changes were observed, widening occurred in eleven cases and narrowing in one. Matching data are now available on concurrent ramus changes for 22 of the same 28 subjects, including 11 of the 12 for whom statistically significant width changes had previously been noted in the body region. In eight of these 11 subjects, statistically significant widening in the ramus region was also observed. No subject had statistically significant widening in the ramus region without also having statistically significant widening in the body region. No subject had statistically significant trans-ramus narrowing.

  1. Three-Dimensional Rheological Structure of North China Craton Determined by Integration of Multiple observations: Controlling Role for Lithospheric Rifting

    Science.gov (United States)

    Xiong, X.; Shan, B.; Li, Y.

    2017-12-01

    The North China Craton (NCC) has undergone significant lithospheric rejuvenation in late Mesozoic and Cenozoic, one feature of which is the widespread extension and rifting. The extension is distinct between the two parts of NCC: widespread rifting in the eastern NCC and localized narrow rifting in the west. The mechanism being responsible for this difference is uncertain and highly debated. Since lithospheric deformation can be regarded as the response of lithosphere to various dynamic actions, the rheological properties of lithosphere must have a fundamental influence on its tectonics and deformation behavior. In this study, we investigated the 3D thermal and rheological structure of NCC by developing a model integrating several geophysical observables (such as surface heatflow, regional elevation, gravity and geoid anomalies, and seismic tomography models). The results exhibit obvious lateral variation in rheological structure between the eastern and western NCC. The overall lithospheric strength is higher in the western NCC than in the east. Despite of such difference in rheology, both parts of NCC are characterized by mantle dominated strength regime, which facilitates the development of narrow rifting. Using ancient heatflow derived from mantle xenoliths studies, and taking the subduction-related dehydration reactions during Mesozoic into account, we constructed the thermal and rheological structure of NCC in Ordovician, early Cretaceous and early Cenozoic. Combining the evidence from numerical simulations, we proposed an evolution path of the rifting in NCC. The lithosphere of NCC in Ordovician was characterized by a normal craton features: low geotherm, high strength and mantle dominated regime. During Jurassic and Cretaceous, the mantle lithosphere in the eastern NCC was hydrated by fluid released by the suduction of the Pacific plate, resulting in weakening of the lithosphere and a transition from mantle dominated to crust dominated regime, which

  2. Using Second Harmonic Generation Microscopy to Study the Three-Dimensional Structure of Collagen and its Degradation Mechanism

    Science.gov (United States)

    Mega, Yair

    Collagen is one of the most abundant proteins found in the human body. Its crystalline structure possesses no centrosymmetry, allowing it to emit second-harmonic waves. Second harmonic generation (SHG) microscopy utilizes the latter quality to produce high-resolution images of collagen rich tissues and therefore become a key research tool in the biomedical field. We developed a new model, intended to be used together with second harmonic generation (SHG) microscopy, to thoroughly investigate collagen-based tissues. We use our SHG model to reveal information in real time from enzymatic biochemical processes. We also present a novel method used to measure quantitatively the direction of the fibers within the tissue, from SHG images. Using this method, we were able to reconstruct an angular map of the orientation of collagen fibers from multiple sections across the entire area of a human cornea. The structure we obtained demonstrates the criss-crossing structure of the human cornea, previously suggested in the literature. In addition, we also report work on a unique step-wise three-photon fluorescence excitation discovered in melanin. This unique fluorescence mechanism was exploited to discriminate melanin on a small-size, low-cost and low laser power setup which was used as a prototype for a handheld device. The latter study is a part of a larger on-going effort in our group to explore new diagnosis methods to be used for early skin cancer screening. Finally, this work demonstrates a spectroscopy-based method to correct for blood vessel thickness effect. The method analyzes spectral shift from a molecular imaging agent and correlate the shifts to the length of the optical path in blood. The correction method described in this work is intended to be implemented on a guided catheter near infrared fluorescence (NIRF) intra-vascular imaging system. In this imaging system, this study's results will used to correct for the radial distance between the imaging tip of the

  3. Three-dimensional structure of a protozoal double-stranded RNA virus that infects the enteric pathogen Giardia lamblia.

    Science.gov (United States)

    Janssen, Mandy E W; Takagi, Yuko; Parent, Kristin N; Cardone, Giovanni; Nibert, Max L; Baker, Timothy S

    2015-01-15

    Giardia lamblia virus (GLV) is a small, nonenveloped, nonsegmented double-stranded RNA (dsRNA) virus infecting Giardia lamblia, the most common protozoan pathogen of the human intestine and a major agent of waterborne diarrheal disease worldwide. GLV (genus Giardiavirus) is a member of family Totiviridae, along with several other groups of protozoal or fungal viruses, including Leishmania RNA viruses and Trichomonas vaginalis viruses. Interestingly, GLV is more closely related than other Totiviridae members to a group of recently discovered metazoan viruses that includes penaeid shrimp infectious myonecrosis virus (IMNV). Moreover, GLV is the only known protozoal dsRNA virus that can transmit efficiently by extracellular means, also like IMNV. In this study, we used transmission electron cryomicroscopy and icosahedral image reconstruction to examine the GLV virion at an estimated resolution of 6.0 Å. Its outermost diameter is 485 Å, making it the largest totivirus capsid analyzed to date. Structural comparisons of GLV and other totiviruses highlighted a related "T=2" capsid organization and a conserved helix-rich fold in the capsid subunits. In agreement with its unique capacity as a protozoal dsRNA virus to survive and transmit through extracellular environments, GLV was found to be more thermoresistant than Trichomonas vaginalis virus 1, but no specific protein machinery to mediate cell entry, such as the fiber complexes in IMNV, could be localized. These and other structural and biochemical findings provide a basis for future work to dissect the cell entry mechanism of GLV into a "primitive" (early-branching) eukaryotic host and an important enteric pathogen of humans. Numerous pathogenic bacteria, including Corynebacterium diphtheriae, Salmonella enterica, and Vibrio cholerae, are infected with lysogenic bacteriophages that contribute significantly to bacterial virulence. In line with this phenomenon, several pathogenic protozoa, including Giardia lamblia

  4. Three dimensional moire pattern alignment

    Science.gov (United States)

    Juday, Richard D. (Inventor)

    1991-01-01

    An apparatus is disclosed for determining three dimensional positioning relative to a predetermined point utilizing moire interference patterns such that the patterns are complementary when viewed on axis from the predetermined distance. Further, the invention includes means for determining rotational positioning in addition to three dimensional translational positioning.

  5. The Three-Dimensional Sign.

    Science.gov (United States)

    Davis, Daniel R.

    1997-01-01

    Discusses the implications of the three-dimensional sign proposed by Harris (1990) for general linguistic theory and the philosophy of language. The article places the principal characteristics of the three-dimensional sign (contextuality, cotemporality, communicational relevance, and experiential grounding) against those of the two-dimensional…

  6. Insight into the three-dimensional structure of maize chlorotic mottle virus revealed by Cryo-EM single particle analysis.

    Science.gov (United States)

    Wang, Chun-Yan; Zhang, Qin-Fen; Gao, Yuan-Zhu; Zhou, Xue-Ping; Ji, Gang; Huang, Xiao-Jun; Hong, Jian; Zhang, Chuan-Xi

    2015-11-01

    Maize chlorotic mottle virus (MCMV) is the only member of the Machlomovirus genus in the family Tombusviridae. Here, we obtained the Cryo-EM structure of MCMV by single particle analysis with most local resolution at approximately 4 Å. The Cα backbone was built based on residues with bulky side chains. The resolved C-terminus of the capsid protein subunit and obvious openings at the 2-fold axis demonstrated the compactness of the asymmetric unit, which indicates an important role in the stability of MCMV. The Asp116 residue from each subunit around the 5-fold and 3-fold axes contributed to the negative charges in the centers of the pentamers and hexamers, which might serve as a solid barrier against the leakage of genomic RNA. Finally, the loops most exposed on the surface were analyzed and are proposed to be potential functional sites related to MCMV transmission. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Finite-element formulations for the thermal stress analysis of two- and three-dimensional thin ractor structures

    International Nuclear Information System (INIS)

    Kulak, R.F.; Kennedy, J.M.; Belytschko, T.B.; Schoeberle, D.F.

    1977-01-01

    This paper describes finite-element formulations for the thermal stress analysis of LMFBR structures. The first formulation is applicable to large displacement rotation problems in which the strains are small. For this formulation, a general temperature-dependent constituent relationship is derived from a Gibbs potential function and a temperature dependent yield surface. The temperature dependency of the yield surface is based upon a temperature-dependent, material-hardening model. The model uses a temperature-equivalent stress-plastic strain diagram which is generated from isothermal uniaxial stress-strain data. A second formulation is presented for problems characterized by both large displacement-rotations and large strains. Here a set of large strain hypoelastic-plastic relationships are developed to linearly relate the rate of stress to the rate of deformation. The temperature field is described through time-dependent values at mesh node points; the temperature fields in each element are then obtained by interpolation formulas. Hence, problems with both spatial and temporal dependent temperature fields can easily be treated. The above developments were incorporated into two ANL developed finite-element computer codes: the implicit version of STRAW and the 3D Implicit Structural Analysis Code. STRAW is a two-dimensional code with a plane stress/plane strain beam element. The 3D Implicit code has a triangular flat plate element which is capable of sustaining both membrane and bending loads. To insure numerical stability both codes are based on an iterative-incremental solution procedure with equilibrium checks based on an error in energy

  8. The Three-Dimensional Solution Structure of the Src Homology Domain-2 of the Growth Factor Receptor-Bound Protein-2

    International Nuclear Information System (INIS)

    Senior, Mary M.; Frederick, Anne F.; Black, Stuart; Murgolo, Nicholas J.; Perkins, Louise M.; Wilson, Oswald; Snow, Mark E.; Wang Yusen

    1998-01-01

    A set of high-resolution three-dimensional solution structures of the Src homology region-2 (SH2) domain of the growth factor receptor-bound protein-2 was determined using heteronuclear NMR spectroscopy. The NMR data used in this study were collected on a stable monomeric protein solution that was free of protein aggregates and proteolysis. The solution structure was determined based upon a total of 1439 constraints, which included 1326 nuclear Overhauser effect distance constraints, 70 hydrogen bond constraints, and 43 dihedral angle constraints. Distance geometry-simulated annealing calculations followed by energy minimization yielded a family of 18 structures that converged to a root-mean-square deviation of 1.09 A for all backbone atoms and 0.40 A for the backbone atoms of the central β-sheet. The core structure of the SH2 domain contains an antiparallel β-sheet flanked by two parallel α-helices displaying an overall architecture that is similar to other known SH2 domain structures. This family of NMR structures is compared to the X-ray structure and to another family of NMR solution structures determined under different solution conditions

  9. Three-dimensionally modulated anisotropic structure for diffractive optical elements created by one-step three-beam polarization holographic photoalignment

    International Nuclear Information System (INIS)

    Kawai, Kotaro; Sakamoto, Moritsugu; Noda, Kohei; Sasaki, Tomoyuki; Ono, Hiroshi; Kawatsuki, Nobuhiro

    2016-01-01

    A diffractive optical element with a three-dimensional liquid crystal (LC) alignment structure for advanced control of polarized beams was fabricated by a highly efficient one-step photoalignment method. This study is of great significance because different two-dimensional continuous and complex alignment patterns can be produced on two alignment films by simultaneously irradiating an empty glass cell composed of two unaligned photocrosslinkable polymer LC films with three-beam polarized interference beam. The polarization azimuth, ellipticity, and rotation direction of the diffracted beams from the resultant LC grating widely varied depending on the two-dimensional diffracted position and the polarization states of the incident beams. These polarization diffraction properties are well explained by theoretical analysis based on Jones calculus.

  10. Production of three-dimensional structures of PHB using selective laser sintering; Producao de estruturas tridimensionais de PHB utilizando sinterizacao seletiva a laser

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Tatiana F.; Costa, Marysilvia F.; Thire, Rossana M.S.M., E-mail: tatianaf@metalmat.ufrj.br [Programa de Engenharia Metalurgica e de Materiais/COPPE, Universidade Federal do Rio de Janeiro - UFRJ, RJ (Brazil); Oliveira, Marcelo F.; Maia, Izaque A.; Silva, Jorge V.L. [Divisao de Tecnologias Tridimensionais, Centro de Tecnologia da Informacao Renato Archer, Campinas, SP (Brazil)

    2011-07-01

    Selective Laser Sintering (SLS) is a technology of layer-by-layer fabrication of three-dimensional physical models directly from their computational design. The poly(3-hydroxybutyrate) (PHB) is a microbial, biodegradable and semicrystalline polyester. The objective of this work was to produce PHB parts, evaluating the reuse of material in the production of the new parts. Images of SEM of part surface showed the formation of neck that indicates sintering between PHB particles during processing. Analysis of NMR and DSC of the reused polymer showed no changes in the chemical structure and thermal properties of PHB. The parts produced from virgin and reused PHB showed no significant difference in their thermal properties. This could suggest that the reuse of raw material did not influence the process reproducibility. (author)

  11. Investigation of electronic band structure and charge transfer mechanism of oxidized three-dimensional graphene as metal-free anodes material for dye sensitized solar cell application

    Science.gov (United States)

    Loeblein, Manuela; Bruno, Annalisa; Loh, G. C.; Bolker, Asaf; Saguy, Cecile; Antila, Liisa; Tsang, Siu Hon; Teo, Edwin Hang Tong

    2017-10-01

    Dye-sensitized solar cells (DSSCs) offer an optimal trade-off between conversion-efficiency and low-cost fabrication. However, since all its electrodes need to fulfill stringent work-function requirements, its materials have remained unchanged since DSSC's first report early-90s. Here we describe a new material, oxidized-three-dimensional-graphene (o-3D-C), with a band gap of 0.2 eV and suitable electronic band-structure as alternative metal-free material for DSSCs-anodes. o-3D-C/dye-complex has a strong chemical bonding via carboxylic-group chemisorption with full saturation after 12 sec at capacity of ∼450 mg/g (600x faster and 7x higher than optimized metal surfaces). Furthermore, fluorescence quenching of life-time by 28-35% was measured demonstrating charge-transfer from dye to o-3D-C.

  12. A new insight into the three-dimensional architecture of the Golgi complex: Characterization of unusual structures in epididymal principal cells.

    Science.gov (United States)

    Martínez-Martínez, Narcisa; Martínez-Alonso, Emma; Tomás, Mónica; Neumüller, Josef; Pavelka, Margit; Martínez-Menárguez, José A

    2017-01-01

    Principal epididymal cells have one of the largest and more developed Golgi complex of mammalian cells. In the present study, we have used this cell as model for the study of the three-dimensional architecture of the Golgi complex of highly secretory and endocytic cells. Electron tomography demonstrated the presence in this cell type of some unknown or very unusual Golgi structures such as branched cisternae, pocket-like cisternal invaginations or tubular connections. In addition, we have used this methodology and immunoelectron microscopy to analyze the close relationship between this organelle and both the endoplasmic reticulum and microtubules, and to describe in detail how these elements interact with compact and non-compact regions of the ribbon.

  13. Coastwide Reference Monitoring System (CRMS) Vegetation Volume Index: An assessment tool for marsh habitat focused on the three-dimensional structure at CRMS vegetation monitoring stations

    Science.gov (United States)

    Wood, William B.; Visser, Jenneke M.; Piazza, Sarai C.; Sharp, Leigh A.; Hundy, Laura C.; McGinnis, Tommy E.

    2015-12-04

    A Vegetation Volume (VV) variable and Vegetation Volume Index (VVI) have been developed for the Coastwide Reference Monitoring System (CRMS). The VV is a measure of the amount of three-dimensional vegetative structure present at each CRMS site and is based on vegetation data collected annually. The VV uses 10 stations per CRMS site to quantify four vegetation layers: carpet, herbaceous, shrub, and tree. For each layer an overall live vegetation percent cover and height are collected to create a layer volume; the individual layer volumes are then summed to generate a site vegetation volume profile. The VV uses the two-dimensional area of live vegetative cover (in square meters) multiplied by the height (in meters) of each layer to produce a volume (in cubic meters) for each layer present in a 2-meter by 2-meter station. These layers are additive, yielding a total volume for each of the 10 herbaceous vegetation stations and an overall CRMS marsh site average.

  14. RGO-RGONRs-Zn2SnO4 Composite with Three-Dimensional Hierarchical Structure for Use in Lithium-Ion Batteries

    Science.gov (United States)

    Hou, Zhaohui; Chen, Zhengu; Jing, Mingjun; Yang, Hang; Li, Gangyong; Zhou, Minjie

    2018-01-01

    RGO-RGONRs-Zn2SnO4 composite with three-dimensional (3D) hierarchical structure has been formed from Zn2SnO4 nanoparticles grown on conducting reduced graphene oxide (RGO) and reduced graphene oxide nanoribbons (RGONRs) via a chemical co-reduction process. The presence of the RGONRs in this unique hybrid nanostructure prevents restacking of the graphene sheets and provides additional electron transport paths. Lithium-ion batteries using this 3D RGO-RGONRs-Zn2SnO4 composite as anode material displayed enhanced rate capability (510.6 mA h g-1 even at 1600 mA g-1) and cycling properties (779.8 mA h g-1 after 50 cycles at current density of 200 mA g-1).

  15. Three-dimensional density structure of La Soufrière de Guadeloupe lava dome from simultaneous muon radiographies and gravity data

    Science.gov (United States)

    Rosas-Carbajal, M.; Jourde, Kevin; Marteau, Jacques; Deroussi, Sébastien; Komorowski, Jean-Christophe; Gibert, Dominique

    2017-07-01

    Muon imaging has recently emerged as a powerful method to complement standard geophysical tools in the understanding of the Earth's subsurface. Muon measurements yield a "radiography" of the average density along the muon path, allowing to image large volumes of a geological body from a single observation point. Here we jointly invert muon data from three simultaneous telescope acquisitions together with gravity data to estimate the three-dimensional density structure of the La Soufrière de Guadeloupe lava dome. Our unique data set allows us to achieve an unprecedented spatial resolution with this novel technique. The retrieved density model reveals an extensive, low-density anomaly where the most active part of the volcanic hydrothermal system is located, supporting previous studies that indicate this region as the most likely to be involved in a partial edifice collapse.

  16. Tree crown structural characterization: A study using terrestrial laser scanning and three-dimensional radiative transfer modeling

    Science.gov (United States)

    Moorthy, Inian

    Spectroscopic observational data for vegetated environments, have been coupled with 3D physically-based radiative transfer models for retrievals of biochemical and biophysical indicators of vegetation health and condition. With the recent introduction of Terrestrial Laser Scanning (TLS) units, there now exists a means of rapidly measuring intricate structural details of vegetation canopies, which can also serve as input into 3D radiative transfer models. In this investigation, Intelligent Laser Ranging and Imaging System (ILRIS-3D) data was acquired of individual tree crowns in laboratory, and field-based experiments. The ILRIS-3D uses the Time-Of-Flight (TOF) principle to measure the distances of objects based on the time interval between laser pulse exitance and return, upon reflection from an object. At the laboratory-level, this exploratory study demonstrated and validated innovative approaches for retrieving crown-level estimates of Leaf Area Index (LAI) (r2 = 0.98, rmse = 0.26m2/m2), a critical biophysical parameter for vegetation monitoring and modeling. These methods were implemented and expanded in field experiments conducted in olive (Olea europaea L.) orchards in Cordoba, Spain, where ILRIS-3D observations for 24 structurally-variable trees were made. Robust methodologies were developed to characterize diagnostic architectural parameters, such as tree height (r2 = 0.97, rmse = 0.21m), crown width (r 2 = 0.98, rmse = 0.12m), crown height (r2 = 0.81, rmse = 0.11m), crown volume (r2 = 0.99, rmse = 2.6m3), and LAI (r2 = 0.76, rmse = 0.27m2/ m2). These parameters were subsequently used as direct inputs into the Forest LIGHT (FLIGHT) 3D ray tracing model for characterization of the spectral behavior of the olive crowns. Comparisons between FLIGHT-simulated spectra and measured data showed small differences in the visible (measurements were significantly correlated to TLS-derived tree crown complexity metrics. The specific implications of internal crown

  17. The Three-Dimensional Structure of Transatlantic African Dust Transport: A New Perspective from CALIPSO LIDAR Measurements

    Directory of Open Access Journals (Sweden)

    Dong Liu

    2012-01-01

    Full Text Available The lack of information on the vertical distribution of dust, in turn, results in large uncertainties when attempting to evaluate the impacts of dust on climate processes. We analyzed over two years of LIDAR measurements from NASA’s CALIPSO and CloudSat satellites to document the vertical pathways of transatlantic transport of Saharan dust. Our analysis overcomes the limitations of quantitative dust detections with passive satellite measurements over land and low clouds and provides the fine vertical resolved structures. The results show the strong seasonal shift in dust source regions and transportation pathways due to the meteorological and thermodynamical conditions, which also control the dust vertical distribution as well as the depth of the dust layer. The dust layer top descending rates of 35 m/degree in summer, 25 m/degree in autumn and spring, and 10 m/degree in winter are found, respectively, while the dust is being transported across the Atlantic. Comparison with the model simulation highlights the potentials of dust observations using CALIPSO LIDAR. The observed seasonal dependence of these pathways gives new insights into the transport of the Saharan dust and provides important guidance for simulations of the production and transport of the global dust aerosol.

  18. Boundary Inheritance Codec for high-accuracy structured light three-dimensional reconstruction with comparative performance evaluation.

    Science.gov (United States)

    Bui, Lam Quang; Lee, Sukhan

    2013-08-01

    This paper presents a new method of structured light-based 3D reconstruction, referred to here as Boundary Inheritance Codec, that provides high accuracy and low noise in projector-camera correspondence. The proposed method features (1) real-boundary recovery: the exact locations of region boundaries, defined by a coded pattern, are identified in terms of their real coordinates on the image plane. To this end, a radiance independent recovery of accurate boundaries and a disambiguation of true and false boundaries are presented. (2) Boundary inheritance: the consistency among the same boundaries of different layers in pattern hierarchy is exploited to further enhance the accuracy of region correspondence and boundary estimation. Extensive experimentations are carried out to verify the performance of the proposed Boundary Inheritance Codec, especially, in comparison with a number of well-known methods currently available, including Gray-code (GC) plus line/phase shift (LS/PS). The results indicate that the proposed method of recovering real boundaries with boundary inheritance is superior in accuracy and robustness to Gray-code inverse (GCI), GC+LS/PS. For instance, the error standard deviation and the percentile of outliers of the proposed method were 0.152 mm and 0.089%, respectively, while those of GCI were 0.312 mm and 3.937%, respectively, and those of GC+LS/PS were 0.280/0.321 mm and 0.159/7.074%, respectively.

  19. Application of VRML for three-dimensional interactive real-time comparison of OCT structures with standard histology

    Science.gov (United States)

    Tadrous, Paul J.; Podoleanu, Adrian Gh.; Dobre, George M.; Stamp, Gordon W. H.

    2003-07-01

    Optical coherence tomography (OCT) is a potentially useful 'optical biopsy' tool in medicine. To realize this potential doctors must be able to interpret OCT images with at least the same accuracy as conventional histology. It is therefore important that some accurate method of comparing OCT images with conventional histology be found. Despite numerous OCT vs. conventional histology studies in the literature the methods used for comparison have, by necessity, been approximate because it is not possible to cut a physical tissue section in the same plane as the OCT optical section (partly due to histology processing artefacts). In this paper we present a method of rendering solid tissue volumes with semi-transparency using the Virtual Reality Modelling Language (VRML) and devise a VRML script which allows any two volume data sets to be manipulated within the same region of virtual space. This allows the structure of a whole volume of tissue imaged with OCT to be directly compared with the serial section reconstruction of the conventionally stained histology. As the whole volume is visualized any corresponding tissue regions can be more easily identified despite tissue processing artefacts. We demonstrate the effectiveness of our method usng an ex vivo biopsy of human breast carcinoma.

  20. Numerical estimation of structure constants in the three-dimensional Ising conformal field theory through Markov chain uv sampler

    Science.gov (United States)

    Herdeiro, Victor

    2017-09-01

    Herdeiro and Doyon [Phys. Rev. E 94, 043322 (2016), 10.1103/PhysRevE.94.043322] introduced a numerical recipe, dubbed uv sampler, offering precise estimations of the conformal field theory (CFT) data of the planar two-dimensional (2D) critical Ising model. It made use of scale invariance emerging at the critical point in order to sample finite sublattice marginals of the infinite plane Gibbs measure of the model by producing holographic boundary distributions. The main ingredient of the Markov chain Monte Carlo sampler is the invariance under dilation. This paper presents a generalization to higher dimensions with the critical 3D Ising model. This leads to numerical estimations of a subset of the CFT data—scaling weights and structure constants—through fitting of measured correlation functions. The results are shown to agree with the recent most precise estimations from numerical bootstrap methods [Kos, Poland, Simmons-Duffin, and Vichi, J. High Energy Phys. 08 (2016) 036, 10.1007/JHEP08(2016)036].

  1. Synthesis, growth, structural and optical studies of a new organic three dimensional framework: 4-(aminocarbonyl)pyridine 4-(aminocarbonyl)pyridinium hydrogen L-malate

    Energy Technology Data Exchange (ETDEWEB)

    Vijayalakshmi, A. [Department of Chemistry, RMK. Engineering College, Kavaraipettai 601206 (India); Vidyavathy, B., E-mail: vidyavathybalraj@gmail.com [Department of Chemistry,Velammal Engineering College, Chennai 600066 (India); Peramaiyan, G. [Institute of Physics, Academia Sinica, Taipei 11529, Taiwan (China); Vinitha, G. [Department of Physics, VIT University, Chennai 600127 (India)

    2017-02-15

    4-(aminocarbonyl)pyridine 4-(aminocarbonyl)pyridinium hydrogen L-malate [(4ACP)(4ACP).(LM)] a new organic nonlinear optical (NLO) crystal was grown by the slow evaporation method. Single crystal X-ray diffraction analysis revealed that the [(4ACP)(4ACP).(LM)] crystal belongs to monoclinic crystal system, space group P2{sub 1}/n, with a three dimensional network. Thermogravimetry (TG) and differential thermal (DT) analyses showed that [(4ACP)(4ACP).(LM)] is thermally stable up to 165 °C. The optical transmittance window and the lower cut-off wavelength of [(4ACP)(4ACP).(LM)] were found out by UV–vis–NIR spectral study. The molecular structure of [(4ACP)(4ACP).(LM)] was further confirmed by FTIR spectral studies. The relative dielectric permittivity and dielectric loss were determined as function of frequency and temperature. The third order nonlinear optical property of [(4ACP)(4ACP).(LM)] was studied by the Z-scan technique using a 532 nm diode pumped CW Nd:YAG laser. Nonlinear refractive index, nonlinear absorption coefficient and third order nonlinear susceptibility of the grown crystal were found to be 7.38×10{sup −8} cm{sup 2}/W, 0.08×10{sup −4} cm/W and 5.36×10{sup −6} esu, respectively. The laser damage threshold value is found to be 1.75 GW/cm{sup 2} - Graphical abstract: In the crystal structure of the title complex, the asymmetric unit contains one hydrogen L-malate anion, 4-(aminocarbonyl)pyridinium cation and a neutral isonicotinamide molecule. It is stabilized by intermolecular N-H…O, C-H…O and O-H…O hydrogen bonds which generate a three dimensional network.

  2. Three-dimensional structures of Plasmodium falciparum spermidine synthase with bound inhibitors suggest new strategies for drug design

    Energy Technology Data Exchange (ETDEWEB)

    Sprenger, Janina [Lund University, SE-221 00 Lund (Sweden); Lund University, SE-221 84 Lund (Sweden); Svensson, Bo [Lund University, SE-221 00 Lund (Sweden); SARomics Biostructures AB, Box 724, SE-220 07 Lund (Sweden); Hålander, Jenny [Lund University, SE-221 00 Lund (Sweden); Carey, Jannette [Princeton University, Princeton, New Jersey (United States); Persson, Lo [Lund University, SE-221 84 Lund (Sweden); Al-Karadaghi, Salam, E-mail: salam.al-karadaghi@biochemistry.lu.se [Lund University, SE-221 00 Lund (Sweden)

    2015-03-01

    In this work, X-ray crystallography was used to examine ligand complexes of spermidine synthase from the malaria parasite Plasmodium falciparum (PfSpdS). The enzymes of the polyamine-biosynthesis pathway have been proposed to be promising drug targets in the treatment of malaria. Spermidine synthase (SpdS; putrescine aminopropyltransferase) catalyzes the transfer of the aminopropyl moiety from decarboxylated S-adenosylmethionine to putrescine, leading to the formation of spermidine and 5′-methylthioadenosine (MTA). In this work, X-ray crystallography was used to examine ligand complexes of SpdS from the malaria parasite Plasmodium falciparum (PfSpdS). Five crystal structures were determined of PfSpdS in complex with MTA and the substrate putrescine, with MTA and spermidine, which was obtained as a result of the enzymatic reaction taking place within the crystals, with dcAdoMet and the inhibitor 4-methylaniline, with MTA and 4-aminomethylaniline, and with a compound predicted in earlier in silico screening to bind to the active site of the enzyme, benzimidazol-(2-yl)pentan-1-amine (BIPA). In contrast to the other inhibitors tested, the complex with BIPA was obtained without any ligand bound to the dcAdoMet-binding site of the enzyme. The complexes with the aniline compounds and BIPA revealed a new mode of ligand binding to PfSpdS. The observed binding mode of the ligands, and the interplay between the two substrate-binding sites and the flexible gatekeeper loop, can be used in the design of new approaches in the search for new inhibitors of SpdS.

  3. Feasibility of real-time three-dimensional echocardiography for the assessment of distorted biventricular systolic function in patients with cor pulmonale.

    Science.gov (United States)

    Cho, Jung Sun; Youn, Ho-Joong; Cho, Eun-Joo; Her, Sung-Ho; Park, Mahn-Won; Lee, Jae Beum; Choi, Min Seok; Park, Chan Seok

    2013-06-01

    This study was to investigate the feasibility of real-time 3-dimensional echocardiography (RT3DE) for the analysis of biventricular ejection fractions and volume measurements in patients with cor pulmonale and the correlations of RT3DE results with 64-slice multi-detector cardiac computed tomography (64-MDCT) results. This study included a total of 22 patients (59.3 ± 16.6 years of age; 10 males and 12 females) who showed flattening or reverse curvature of the interventricular septum and severe pulmonary hypertension [mean right ventricular (RV) systolic pressure = 66.8 ± 19.7 mmHg] on 2-dimensional transthoracic echocardiography due to cor pulmonale. Biventricular end-diastolic and end-systolic volumes were measured by RT3DE and 64-MDCT. The severity of D-shaped deformation was evaluated by using left ventricular (LV) eccentricity index (ratio of diameters parallel/perpendicular to the interventricular septum on parasternal short axis images of the papillary muscle level). There were moderate correlations between biventricular volumes measured by RT3DE and 64-MDCT except for LV end-systolic volume (59.8 ± 17.1 vs. 73.2 ± 20.2 mL, r = 0.652, p = 0.001 for LV end-diastolic volume; 30.6 ± 9.1 vs. 30.8 ± 12.5 mL, r = 0.361, p = 0.099 for LV end-systolic volume; 110.1 ± 42.9 vs. 171.1 ± 55.3 mL, r = 0.545, p = 0.009 for RV end-diastolic volume; and 80.9 ± 35.0 vs. 128.7 ± 45.1 mL, r = 0.549, p = 0.005 for RV end-systolic volume respectively). This study suggests that RT3DE may be a modest method for measuring distorted biventricular end-systolic and end-diastolic volumes in patients with cor pulmonale.

  4. Three-dimensional model of plate geometry and velocity model for Nankai Trough seismogenic zone based on results from structural studies

    Science.gov (United States)

    Nakanishi, A.; Shimomura, N.; Kodaira, S.; Obana, K.; Takahashi, T.; Yamamoto, Y.; Yamashita, M.; Takahashi, N.; Kaneda, Y.

    2012-12-01

    In the Nankai Trough subduction seismogenic zone, the Nankai and Tonankai earthquakes had often occurred simultaneously, and caused a great event. In order to reduce a great deal of damage to coastal area from both strong ground motion and tsunami generation, it is necessary to understand rupture synchronization and segmentation of the Nankai megathrust earthquake. For a precise estimate of the rupture zone of the Nankai megathrust event based on the knowledge of realistic earthquake cycle and variation of magnitude, it is important to know the geometry and property of the plate boundary of the subduction seismogenic zone. To improve a physical model of the Nankai Trough seismogenic zone, the large-scale high-resolution wide-angle and reflection (MCS) seismic study, and long-term observation has been conducted since 2008. Marine active source seismic data have been acquired along grid two-dimensional profiles having the total length of ~800km every year. A three-dimensional seismic tomography using active and passive seismic data observed both land and ocean bottom stations have been also performed. From those data, we found that several strong lateral variations of the subducting Philippine Sea plate and overriding plate corresponding to margins of coseismic rupture zone of historical large event occurred along the Nankai Trough. Particularly a possible prominent reflector for the forearc Moho is recently imaged in the offshore side in the Kii channel at the depth of ~18km which is shallower than those of other area along the Nankai Trough. Such a drastic variation of the overriding plate might be related to the existence of the segmentation of the Nankai megathrust earthquake. Based on our results derived from seismic studies, we have tried to make a geometrical model of the Philippine Sea plate and a three-dimensional velocity structure model of the Nankai Trough seismogenic zone. In this presentation, we will summarize major results of out seismic studies, and

  5. Three-dimensional hydrogen-bonded structures in the hydrated proton-transfer salts of isonipecotamide with the dicarboxylic oxalic and adipic acid homologues.

    Science.gov (United States)

    Smith, Graham; Wermuth, Urs D

    2013-10-01

    The structures of the 1:1 hydrated proton-transfer compounds of isonipecotamide (piperidine-4-carboxamide) with oxalic acid, 4-carbamoylpiperidinium hydrogen oxalate dihydrate, C6H13N2O(+)·C2HO4(-)·2H2O, (I), and with adipic acid, bis(4-carbamoylpiperidinium) adipate dihydrate, 2C6H13N2O(+)·C6H8O4(2-)·2H2O, (II), are three-dimensional hydrogen-bonded constructs involving several different types of enlarged water-bridged cyclic associations. In the structure of (I), the oxalate monoanions give head-to-tail carboxylic acid O-H···O(carboxyl) hydrogen-bonding interactions, forming C(5) chain substructures which extend along a. The isonipecotamide cations also give parallel chain substructures through amide N-H···O hydrogen bonds, the chains being linked across b and down c by alternating water bridges involving both carboxyl and amide O-atom acceptors and amide and piperidinium N-H···O(carboxyl) hydrogen bonds, generating cyclic R4(3)(10) and R3(2)(11) motifs. In the structure of (II), the asymmetric unit comprises a piperidinium cation, half an adipate dianion, which lies across a crystallographic inversion centre, and a solvent water molecule. In the crystal structure, the two inversion-related cations are interlinked through the two water molecules, which act as acceptors in dual amide N-H···O(water) hydrogen bonds, to give a cyclic R4(2)(8) association which is conjoined with an R4(4)(12) motif. Further N-H···O(water), water O-H···O(amide) and piperidinium N-H···O(carboxyl) hydrogen bonds give the overall three-dimensional structure. The structures reported here further demonstrate the utility of the isonipecotamide cation as a synthon for the generation of stable hydrogen-bonded structures. The presence of solvent water molecules in these structures is largely responsible for the non-occurrence of the common hydrogen-bonded amide-amide dimer, promoting instead various expanded cyclic hydrogen-bonding motifs.

  6. Comparative analysis of three-dimensional structures of homodimers of uridine phosphorylase from Salmonella typhimurium in the unligated state and in a complex with potassium ion

    Energy Technology Data Exchange (ETDEWEB)

    Lashkov, A. A.; Zhukhlistova, N. E.; Gabdulkhakov, A. G.; Mikhailov, A. M., E-mail: amm@ns.crys.ras.ru [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2009-03-15

    The spatial organization of the homodimer of unligated uridine phosphorylase from Salmonella typhimurium (St UPh) was determined with high accuracy. The structure was refined at 1.80 A resolution to R{sub work} = 16.1% and R{sub free} = 20.0%. The rms deviations for the bond lengths, bond angles, and chiral angles are 0.006 A, 1.042{sup o}, and 0.071{sup o}, respectively. The coordinate error estimated by the Luzzati plot is 0.166 A. The coordinate error based on the maximum likelihood is 0.199 A. A comparative analysis of the spatial organization of the homodimer in two independently refined structures and the structure of the homodimer St UPh in the complex with a K{sup +} ion was performed. The substrate-binding sites in the homodimers StUPhs in the unligated state were found to act asynchronously. In the presence of a potassium ion, the three-dimensional structures of the subunits in the homodimer are virtually identical, which is apparently of importance for the synchronous action of both substrate-binding sites. The atomic coordinates of the refined structure of the homodimer and structure factors have been deposited in the Protein Data Bank (PDB ID code 3DPS).

  7. Comparative analysis of three-dimensional structures of homodimers of uridine phosphorylase from Salmonella typhimurium in the unligated state and in a complex with potassium ion

    International Nuclear Information System (INIS)

    Lashkov, A. A.; Zhukhlistova, N. E.; Gabdulkhakov, A. G.; Mikhailov, A. M.

    2009-01-01

    The spatial organization of the homodimer of unligated uridine phosphorylase from Salmonella typhimurium (St UPh) was determined with high accuracy. The structure was refined at 1.80 A resolution to R work = 16.1% and R free = 20.0%. The rms deviations for the bond lengths, bond angles, and chiral angles are 0.006 A, 1.042 o , and 0.071 o , respectively. The coordinate error estimated by the Luzzati plot is 0.166 A. The coordinate error based on the maximum likelihood is 0.199 A. A comparative analysis of the spatial organization of the homodimer in two independently refined structures and the structure of the homodimer St UPh in the complex with a K + ion was performed. The substrate-binding sites in the homodimers StUPhs in the unligated state were found to act asynchronously. In the presence of a potassium ion, the three-dimensional structures of the subunits in the homodimer are virtually identical, which is apparently of importance for the synchronous action of both substrate-binding sites. The atomic coordinates of the refined structure of the homodimer and structure factors have been deposited in the Protein Data Bank (PDB ID code 3DPS).

  8. Three-Dimensional Packing Structure and Electronic Properties of Biaxially Oriented Poly(2,5-bis(3-alkylthiophene-2-yl)thieno[3,2- b ]thiophene) Films

    KAUST Repository

    Cho, Eunkyung

    2012-04-11

    We use a systematic approach that combines experimental X-ray diffraction (XRD) and computational modeling based on molecular mechanics and two-dimensional XRD simulations to develop a detailed model of the molecular-scale packing structure of poly(2,5-bis (3-tetradecylthiophene-2-yl) thieno[3,2-b]thiophene) (PBTTT-C 14) films. Both uniaxially and biaxially aligned films are used in this comparison and lead to an improved understanding of the molecular-scale orientation and crystal structure. We then examine how individual polymer components (i.e., conjugated backbone and alkyl side chains) contribute to the complete diffraction pattern, and how modest changes to a particular component orientation (e.g., backbone or side-chain tilt) influence the diffraction pattern. The effects on the polymer crystal structure of varying the alkyl side-chain length from C 12 to C 14 and C 16 are also studied. The accurate determination of the three-dimensional polymer structure allows us to examine the PBTTT electronic band structure and intermolecular electronic couplings (transfer integrals) as a function of alkyl side-chain length. This combination of theoretical and experimental techniques proves to be an important tool to help establish the relationship between the structural and electronic properties of polymer thin films. © 2012 American Chemical Society.

  9. Study on three dimensional seismic isolation system

    International Nuclear Information System (INIS)

    Morishita, Masaki; Kitamura, Seiji

    2003-01-01

    Japan Nuclear Cycle Development Institute (JNC) and Japan Atomic Power Company (JAPC) launched joint research programs on structural design and three-dimensional seismic isolation technologies, as part of the supporting R and D activities for the feasibility studies on commercialized fast breeder reactor cycle systems. A research project by JAPC under the auspices of the Ministry of Economy, Trade, and Industry (METI) with technical support by JNC is included in this joint study. This report contains the results of the research on the three-dimensional seismic isolation technologies, and the results of this year's study are summarized in the following five aspects. (1) Study on Earthquake Condition for Developing 3-dimensional Base Isolation System. The case study S2 is one of the maximum ground motions, of which the records were investigated up to this time. But a few observed near the fault exceed the case study S2 in the long period domain, depending on the fault length and conditions. Generally it is appropriate that the response spectra ratio (vertical/horizontal) is 0.6. (2) Performance Requirement for 3-dimensional Base Isolation System and Devices. Although the integrity map of main equipment/piping dominate the design criteria for the 3-dimensional base isolation system, the combined integrity map is the same as those of FY 2000, which are under fv=1Hz and over hv=20%. (3) Developing Targets and Schedule for 3-dimensional Isolation Technology. The target items for 3-dimensional base isolation system were rearranged into a table, and developing items to be examined concerning the device were also adjusted. A development plan until FY 2009 was made from the viewpoint of realization and establishment of a design guideline on 3-dimensional base isolation system. (4) Study on 3-dimensional Entire Building Base Isolation System. Three ideas among six ideas that had been proposed in FY2001, i.e., '3-dimensional base isolation system incorporating hydraulic

  10. Three-dimensional multiscale analysis of degradation of nano- and micro-structure in direct methanol fuel cell electrodes after methanol starvation

    Science.gov (United States)

    Netzeband, Christian; Arlt, Tobias; Wippermann, Klaus; Lehnert, Werner; Manke, Ingo

    2016-09-01

    This study investigates the ageing effects on the microstructure of the anode catalyst layer of direct methanol fuel cells (DMFC) after complete methanol starvation. To this end the samples of two methanol-depleted membrane electrode assemblies (MEA) have been compared with a pristine reference sample. A three-dimensional characterization of the anode catalyst layer (ACL) structure on a nanometer scale has been conducted by focused ion beam (FIB)/scanning electron microscope (SEM) tomography. The FIB/SEM tomography allows for a detailed analysis of statistic parameters of micro-structured materials, such as porosity, tortuosity and pore size distributions. Furthermore, the SEM images displayed a high material contrast between the heavy catalyst metals (Pt/Ru) and the relatively light carbon support, which made it possible to map the catalyst distribution in the acquired FIB/SEM tomographies. Additional synchrotron X-ray tomographies have been conducted in order to obtain an overview of the structural changes of all the components of a section of the MEAs after methanol depletion.

  11. Interplay between cellular activity and three-dimensional scaffold-cell constructs with different foam structure processed by electron beam melting.

    Science.gov (United States)

    Nune, Krishna C; Misra, R Devesh K; Gaytan, Sara M; Murr, Lawrence E

    2015-05-01

    The cellular activity, biological response, and consequent integration of scaffold-cell construct in the physiological system are governed by the ability of cells to adhere, proliferate, and biomineralize. In this regard, we combine cellular biology and materials science and engineering to fundamentally elucidate the interplay between cellular activity and interconnected three-dimensional foamed architecture obtained by a novel process of electron beam melting and computational tools. Furthermore, the organization of key proteins, notably, actin, vinclulin, and fibronectin, involved in cellular activity and biological functions and relationship with the structure was explored. The interconnected foamed structure with ligaments was favorable to cellular activity that includes cell attachment, proliferation, and differentiation. The primary rationale for favorable modulation of cellular functions is that the foamed structure provided a channel for migration and communication between cells leading to highly mineralized extracellular matrix (ECM) by the differentiating osteoblasts. The filopodial interaction amongst cells on the ligaments was a governing factor in the secretion of ECM, with consequent influence on maturation and mineralization. © 2014 Wiley Periodicals, Inc.

  12. A High Precision Approach to Calibrate a Structured Light Vision Sensor in a Robot-Based Three-Dimensional Measurement System

    Directory of Open Access Journals (Sweden)

    Defeng Wu

    2016-08-01

    Full Text Available A robot-based three-dimensional (3D measurement system is presented. In the presented system, a structured light vision sensor is mounted on the arm of an industrial robot. Measurement accuracy is one of the most important aspects of any 3D measurement system. To improve the measuring accuracy of the structured light vision sensor, a novel sensor calibration approach is proposed to improve the calibration accuracy. The approach is based on a number of fixed concentric circles manufactured in a calibration target. The concentric circle is employed to determine the real projected centres of the circles. Then, a calibration point generation procedure is used with the help of the calibrated robot. When enough calibration points are ready, the radial alignment constraint (RAC method is adopted to calibrate the camera model. A multilayer perceptron neural network (MLPNN is then employed to identify the calibration residuals after the application of the RAC method. Therefore, the hybrid pinhole model and the MLPNN are used to represent the real camera model. Using a standard ball to validate the effectiveness of the presented technique, the experimental results demonstrate that the proposed novel calibration approach can achieve a highly accurate model of the structured light vision sensor.

  13. Stress orientation and fracturing during three-dimensional buckling: Numerical simulation and application to chocolate-tablet structures in folded turbidites, SW Portugal

    Science.gov (United States)

    Reber, J. E.; Schmalholz, S. M.; Burg, J.-P.

    2010-10-01

    Two orthogonal sets of veins, both orthogonal to bedding, form chocolate tablet structures on the limbs of folded quartzwackes of Carboniferous turbidites in SW Portugal. Structural observations suggest that (1) mode 1 fractures transverse to the fold axes formed while fold amplitudes were small and limbs were under layer-subparallel compression and (2) mode 1 fractures parallel to the fold axes formed while fold amplitudes were large and limbs were brought to be under layer-subparallel tension. We performed two- and three-dimensional numerical simulations investigating the evolution of stress orientations during viscous folding to test whether and how these two successive sets of fractures were related to folding. We employed ellipses and ellipsoids for the visualization and quantification of the local stress field. The numerical simulations show a change in the orientation of the local σ1 direction by almost 90° with respect to the bedding plane in the fold limbs. The coeval σ3 direction rotates from parallel to the fold axis at low fold amplitudes to orthogonal to the fold axis at high fold amplitudes. The stress orientation changes faster in multilayers than in single-layers. The numerical simulations are consistent with observation and provide a mechanical interpretation for the formation of the chocolate tablet structures through consecutive sets of fractures on rotating limbs of folded competent layers.

  14. Reactivity differences of combined and free amino acids: quantifying the relationship between three-dimensional protein structure and singlet oxygen reaction rates.

    Science.gov (United States)

    Lundeen, Rachel A; McNeill, Kristopher

    2013-12-17

    It has long been appreciated that the photooxidation kinetics of amino acid (AA) residues in an intact protein differ from those of free AAs due to differences in the local steric microenvironment, such as its location in the three-dimensional structure. Yet there are only a few studies that have quantified the effect of protein structure on the photochemical reactivity of its residues. This is important for predicting phototransformation rates of AAs in aquatic environments where AAs in combined forms (e.g., oligopeptides and proteins) are more abundant than free AAs. In this work, the photochemical reactivity differences between free and combined AAs were assessed. Singlet oxygen ((1)O2) reaction kinetics of individual photooxidizable residues in the protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were examined. The results suggest that the (1)O2 accessibility of residues in intact GAPDH has a profound effect on their photodegradation kinetics and for histidine residues can explain most of the variation in (1)O2 reactivity. Additionally, (1)O2-accessibile surface area values of residues calculated from protein crystal structure data are useful in predicting their reaction rates in GAPDH. This work illustrates a new approach to assess the differential photochemical reactivity of AA-based biomolecules in natural environments or engineered applications.

  15. Digital three-dimensional model of lumbar region 4-5 and its adjacent structures based on a virtual Chinese human.

    Science.gov (United States)

    Yang, Bo; Fang, Shi-bing; Li, Chang-shu; Yin, Biao; Wang, Le; Wan, Sheng-yu; Xie, Jing-kai; Ding, Qiang; Tang, Lei; Zhong, Shi-zhen

    2013-05-01

    To study the methods for constructing a digitized three-dimensional (3D) model of a virtual lumbar region and its adjacent structures in order to assist anatomical study and virtual surgery. Images of DSCF5375-p1 to DSCF5745-p1 were taken from the database of the digitized Virtual Chinese human of Southern Medical University in Guangzhou. This region encompasses the superior facet joint of L4 to the inferior edge of the intervertebral body of L5. The regions of interest were interactively segmented from the images utilizing Adobe Photoshop software. The images were further processed using format conversion and segmentation. Finally, a 3D model of the L4-5 region and its neighboring structures was reconstructed with the assistance of Mimics 10.01 software. A digitized 3D model of this part of the virtual lumbar spine and its adjacent structures was reconstructed. This model allows all constructed structures to be displayed individually or jointly, moved or rotated arbitrarily, setting of different transparencies and convenient measurement of the diameters and angles of the reconstructed structures. The 3D model precisely displays the anatomical relationships between all structures and provides a reliable 3D model for a spinal endoscopic surgery simulation system. Visualization of the digitized 3D reconstruction of the virtual lower lumbar region displays this region and its adjacent structures stereoscopically and in actuality, thus providing morphological data concerning anatomy, image diagnosis and virtual operations in this region. © 2013 Chinese Orthopaedic Association and Wiley Publishing Asia Pty Ltd.

  16. Towards three-dimensional optical metamaterials

    Science.gov (United States)

    Tanaka, Takuo; Ishikawa, Atsushi

    2017-12-01

    Metamaterials have opened up the possibility of unprecedented and fascinating concepts and applications in optics and photonics. Examples include negative refraction, perfect lenses, cloaking, perfect absorbers, and so on. Since these metamaterials are man-made materials composed of sub-wavelength structures, their development strongly depends on the advancement of micro- and nano-fabrication technologies. In particular, the realization of three-dimensional metamaterials is one of the big challenges in this research field. In this review, we describe recent progress in the fabrication technologies for three-dimensional metamaterials, as well as proposed applications.

  17. Towards three-dimensional optical metamaterials.

    Science.gov (United States)

    Tanaka, Takuo; Ishikawa, Atsushi

    2017-01-01

    Metamaterials have opened up the possibility of unprecedented and fascinating concepts and applications in optics and photonics. Examples include negative refraction, perfect lenses, cloaking, perfect absorbers, and so on. Since these metamaterials are man-made materials composed of sub-wavelength structures, their development strongly depends on the advancement of micro- and nano-fabrication technologies. In particular, the realization of three-dimensional metamaterials is one of the big challenges in this research field. In this review, we describe recent progress in the fabrication technologies for three-dimensional metamaterials, as well as proposed applications.

  18. Three-dimensional sandwich-structured NiMn2O4@reduced graphene oxide nanocomposites for highly reversible Li-ion battery anodes

    Science.gov (United States)

    Huang, Jiarui; Wang, Wei; Lin, Xirong; Gu, Cuiping; Liu, Jinyun

    2018-02-01

    A sandwich-structured NiMn2O4@reduced graphene oxide (NiMn2O4@rGO) nanocomposite consisting of ultrathin NiMn2O4 sheets uniformly anchored on both sides of a three-dimensional (3D) porous rGO is presented. The NiMn2O4@rGO nanocomposites prepared through a dipping process combining with a hydrothermal method show a good electrochemical performance including a high reversible capability of 1384 mAh g-1 at 1000 mA g-1 over 1620 cycles, and an superior rate performance. Thus, a full cell consisting of a commercial LiCoO2 cathode and the NiMn2O4@rGO anode delivers a stable capacity of about 1046 mAh g-1 (anode basis) after cycling at 50 mA g-1 for 60 times. It is demonstrated that the 3D porous composite structure accommodates the volume change during the Li+ insertion/extraction process and facilitates the rapid transport of ions and electrons. The high performance would enable the presented NiMn2O4@rGO nanocomposite a promising anode candidate for practical applications in Li-ion batteries.

  19. Three-dimensional structures of unligated uridine phosphorylase from Yersinia pseudotuberculosis at 1.4 Å resolution and its complex with an antibacterial drug

    Science.gov (United States)

    Balaev, V. V.; Lashkov, A. A.; Gabdulkhakov, A. G.; Dontsova, M. V.; Mironov, A. S.; Betzel, C.; Mikhailov, A. M.

    2015-07-01

    Uridine phosphorylases play an essential role in the cellular metabolism of some antibacterial agents. Acute infectious diseases (bubonic plague, yersiniosis, pseudotuberculosis, etc., caused by bacteria of the genus Yersinia) are treated using both sulfanilamide medicines and antibiotics, including trimethoprim. The action of an antibiotic on a bacterial cell is determined primarily by the character of its interactions with cellular components, including those which are not targets (for example, with pyrimidine phosphorylases). This type of interaction should be taken into account in designing drugs. The three-dimensional structure of uridine phosphorylase from the bacterium Yersinia pseudotuberculosis ( YptUPh) with the free active site was determined for the first time by X-ray crystallography and refined at 1.40 Å resolution (DPI = 0.062 Å; ID PDB: 4OF4). The structure of the complex of YptUPh with the bacteriostatic drug trimethoprim was studied by molecular docking and molecular dynamics methods. The trimethoprim molecule was shown to be buffered by the enzyme YptUPh, resulting in a decrease in the efficiency of the treatment of infectious diseases caused by bacteria of the genus Yersinia with trimethoprim.

  20. Deconstructing three-dimensional (3D) structure of absorptive glass mat (AGM) separator to tailor pore dimensions and amplify electrolyte uptake

    Science.gov (United States)

    Rawal, Amit; Rao, P. V. Kameswara; Kumar, Vijay

    2018-04-01

    Absorptive glass mat (AGM) separator is a vital technical component in valve regulated lead acid (VRLA) batteries that can be tailored for a desired application. To selectively design and tailor the AGM separator, the intricate three-dimensional (3D) structure needs to be unraveled. Herein, a toolkit of 3D analytical models of pore size distribution and electrolyte uptake expressed via wicking characteristics of AGM separators under unconfined and confined states is presented. 3D data of fiber orientation distributions obtained previously through X-ray micro-computed tomography (microCT) analysis are used as key set of input parameters. The predictive ability of pore size distribution model is assessed through the commonly used experimental set-up that usually apply high level of compressive stresses. Further, the existing analytical model of wicking characteristics of AGM separators has been extended to account for 3D characteristics, and subsequently, compared with the experimental results. A good agreement between the theory and experiments pave the way to simulate the realistic charge-discharge modes of the battery by applying cyclic loading condition. A threshold criterion describing the invariant behavior of pore size and wicking characteristics in terms of maximum permissible limit of key structural parameters during charge-discharge mode of the battery has also been proposed.

  1. IGF-1 Signaling Plays an Important Role in the Formation of Three-Dimensional Laminated Neural Retina and Other Ocular Structures From Human Embryonic Stem Cells.

    Science.gov (United States)

    Mellough, Carla B; Collin, Joseph; Khazim, Mahmoud; White, Kathryn; Sernagor, Evelyne; Steel, David H W; Lako, Majlinda

    2015-08-01

    We and others have previously demonstrated that retinal cells can be derived from human embryonic stem cells (hESCs) and induced pluripotent stem cells under defined culture conditions. While both cell types can give rise to retinal derivatives in the absence of inductive cues, this requires extended culture periods and gives lower overall yield. Further understanding of this innate differentiation ability, the identification of key factors that drive the differentiation process, and the development of clinically compatible culture conditions to reproducibly generate functional neural retina is an important goal for clinical cell based therapies. We now report that insulin-like growth factor 1 (IGF-1) can orchestrate the formation of three-dimensional ocular-like structures from hESCs which, in addition to retinal pigmented epithelium and neural retina, also contain primitive lens and corneal-like structures. Inhibition of IGF-1 receptor signaling significantly reduces the formation of optic vesicle and optic cups, while exogenous IGF-1 treatment enhances the formation of correctly laminated retinal tissue composed of multiple retinal phenotypes that is reminiscent of the developing vertebrate retina. Most importantly, hESC-derived photoreceptors exhibit advanced maturation features such as the presence of primitive rod- and cone-like photoreceptor inner and outer segments and phototransduction-related functional responses as early as 6.5 weeks of differentiation, making these derivatives promising candidates for cell replacement studies and in vitro disease modeling. © 2015 AlphaMed Press.

  2. Design, synthesis, antiviral bioactivity and three-dimensional quantitative structure-activity relationship study of novel ferulic acid ester derivatives containing quinazoline moiety.

    Science.gov (United States)

    Wu, Zengxue; Zhang, Jian; Chen, Jixiang; Pan, Jianke; Zhao, Lei; Liu, Dengyue; Zhang, Awei; Chen, Jin; Hu, Deyu; Song, Baoan

    2017-10-01

    Ferulic acid and quinazoline derivatives possess good antiviral activities. In order to develop novel compounds with high antiviral activities, a series of ferulic acid ester derivatives containing quinazoline were synthesized and evaluated for their antiviral activities. Bioassays indicated that some of the compounds exhibited good antiviral activities in vivo against tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV). One of the compounds demonstrated significant curative and protective activities against TMV and CMV, with EC 50 values of 162.14, 114.61 and 255.49, 138.81 mg L -1 , respectively, better than those of ningnanmycin (324.51, 168.84 and 373.88, 272.70 mg L -1 ). The values of q 2 and r 2 for comparative molecular field analysis and comparative molecular similarity index analysis in the TMV (0.508, 0.663 and 0.992, 0.930) and CMV (0.530, 0.626 and 0.997, 0.981) models presented good predictive abilities. Some of the title compounds demonstrated good antiviral activities. Three-dimensional quantitative structure-activity relationship models revealed that the antiviral activities depend on steric and electrostatic properties. These results could provide significant structural insights for the design of highly active ferulic acid derivatives. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  3. Three dimensional imaging of otoliths

    International Nuclear Information System (INIS)

    Barry, B.; Markwitz, A.; David, B.

    2008-01-01

    Otoliths are small structures in fish ears made of calcium carbonate which carry a record of the environment in which the fish live. Traditionally, in order to study their microchemistry by a scanning technique such as PIXE the otoliths have been either ground down by hand or thin sectioned to expose the otolith core. However this technique is subject to human error in judging the core position. In this study we have scanned successive layers of otoliths 50 and 100 μm apart by removing the otolith material in a lapping machine which can be set to a few μm precision. In one study by comparing data from otoliths from the two ears of a freshwater species we found that polishing by hand could miss the core and thus give misleading results as to the life cycle of the fish. In another example we showed detail in a marine species which could be used to build a three dimensional picture of the Sr distribution. (author)

  4. Three dimensional electrochemical system for neurobiological studies

    DEFF Research Database (Denmark)

    Vazquez, Patricia; Dimaki, Maria; Svendsen, Winnie Edith

    2009-01-01

    In this work we report a novel three dimensional electrode array for electrochemical measurements in neuronal studies. The main advantage of working with these out-of-plane structures is the enhanced sensitivity of the system in terms of measuring electrochemical changes in the environment...

  5. Electron crystallography of three dimensional protein crystals

    NARCIS (Netherlands)

    Georgieva, Dilyana

    2008-01-01

    This thesis describes an investigation of the potential of electron diffraction for studying three dimensional sub-micro-crystals of proteins and pharmaceuticals. A prerequisite for using electron diffraction for structural studies is the predictable availability of tiny crystals. A method for

  6. Three-dimensional structures of the mammalian multidrug resistance P-glycoprotein demonstrate major conformational changes in the transmembrane domains upon nucleotide binding.

    Science.gov (United States)

    Rosenberg, Mark F; Kamis, Alhaji Bukar; Callaghan, Richard; Higgins, Christopher F; Ford, Robert C

    2003-03-07

    P-glycoprotein is an ATP-binding cassette transporter that is associated with multidrug resistance and the failure of chemotherapy in human patients. We have previously shown, based on two-dimensional projection maps, that P-glycoprotein undergoes conformational changes upon binding of nucleotide to the intracellular nucleotide binding domains. Here we present the three-dimensional structures of P-glycoprotein in the presence and absence of nucleotide, at a resolution limit of approximately 2 nm, determined by electron crystallography of negatively stained crystals. The data reveal a major reorganization of the transmembrane domains throughout the entire depth of the membrane upon binding of nucleotide. In the absence of nucleotide, the two transmembrane domains form a single barrel 5-6 nm in diameter and about 5 nm deep with a central pore that is open to the extracellular surface and spans much of the membrane depth. Upon binding nucleotide, the transmembrane domains reorganize into three compact domains that are each 2-3 nm in diameter and 5-6 nm deep. This reorganization opens the central pore along its length in a manner that could allow access of hydrophobic drugs (transport substrates) directly from the lipid bilayer to the central pore of the transporter.

  7. Numerical integration of gravitational field for general three-dimensional objects and its application to gravitational study of grand design spiral arm structure

    Science.gov (United States)

    Fukushima, Toshio

    2016-12-01

    We present a method to integrate the gravitational field for general three-dimensional objects. By adopting the spherical polar coordinates centred at the evaluation point as the integration variables, we numerically compute the volume integral representation of the gravitational potential and of the acceleration vector. The variable transformation completely removes the algebraic singularities of the original integrals. The comparison with exact solutions reveals around 15 digits accuracy of the new method. Meanwhile, the six digit accuracy of the integrated gravitational field is realized by around 106 evaluations of the integrand per evaluation point, which costs at most a few seconds at a PC with Intel Core i7-4600U CPU running at 2.10 GHz clock. By using the new method, we show the gravitational field of a grand design spiral arm structure as an example. The computed gravitational field shows not only spiral shaped details but also a global feature composed of a thick oblate spheroid and a thin disc. The developed method is directly applicable to the electromagnetic field computation by means of Coulomb's law, the Biot-Savart law, and their retarded extensions. Sample FORTRAN 90 programs and test results are electronically available.

  8. From two-dimensional graphene oxide to three-dimensional honeycomb-like Ni3S2@graphene oxide composite: insight into structure and electrocatalytic properties

    Science.gov (United States)

    Wei, Xinting; Li, Yueqiang; Xu, Wenli; Zhang, Kaixuan; Yin, Jie; Shi, Shaozhen; Wei, Jiazhen; Di, Fangfang; Guo, Junxue; Wang, Can; Chu, Chaofan; Sui, Ning; Chen, Baoli; Zhang, Yingtian; Hao, Hongguo; Zhang, Xianxi; Zhao, Jinsheng; Zhou, Huawei; Wang, Shuhao

    2017-12-01

    Three-dimensional (3D) graphene composites have drawn increasing attention in energy storage/conversion applications due to their unique structures and properties. Herein, we synthesized 3D honeycomb-like Ni3S2@graphene oxide composite (3D honeycomb-like Ni3S2@GO) by a one-pot hydrothermal method. We found that positive charges of Ni2+ and negative charges of NO3- in Ni(NO3)2 induced a transformation of graphene oxide with smooth surface into graphene oxide with wrinkled surface (w-GO). The w-GO in the mixing solution of Ni(NO3)2/thioacetamide/H2O evolved into 3D honeycomb-like Ni3S2@GO in solvothermal process. The GO effectively inhibited the aggregation of Ni3S2 nanoparticles. Photoelectrochemical cells based on 3D Ni3S2@GO synthesized at 60 mM l-1 Ni(NO3)2 exhibited the best energy conversion efficiency. 3D Ni3S2@GO had smaller charge transfer resistance and larger exchange current density than pure Ni3S2 for iodine reduction reaction. The cyclic stability of 3D honeycomb-like Ni3S2@GO was good in the iodine electrolyte. Results are of great interest for fundamental research and practical applications of 3D GO and its composites in solar water-splitting, artificial photoelectrochemical cells, electrocatalysts and Li-S or Na-S batteries.

  9. Measurement of three-dimensional perioral soft tissue changes in dentoalveolar protrusion patients after orthodontic treatment using a structured light scanner.

    Science.gov (United States)

    Ahn, Hyo-Won; Chang, Ye-Jin; Kim, Kyung-A; Joo, Sang-Hwan; Park, Young-Guk; Park, Ki-Ho

    2014-09-01

    To evaluate the three-dimensional (3D) perioral soft tissue changes after orthodontic treatment in patients with dentoalveolar protrusion using structured light-based scanners. Forty-four Korean adults (19 men and 25 women, 21.4 ± 3.4 years) with dentoalveolar protrusion treated by extraction of all four first premolars and then en masse retraction with maximum anchorage were evaluated. Lateral cephalograms and 3D facial scans were obtained before treatment (T1) and immediately after debonding (T2). Superimposition was performed, and 27 perioral landmarks were identified. The 3D changes in the landmarks and ratio of movement of the soft tissue relative to the horizontal incisal tip were evaluated. A paired t-test and one-way analysis of variance were performed. The upper incisors were retracted 5.76 mm and the lower incisors were retracted 4.62 mm (P scanners efficiently evaluated 3D perioral soft tissue in dentoalveolar protrusion patients. Backward movement and significant vertical movement of the lip were observed. The nasal and lip angle areas showed considerable changes.

  10. Comparative Study of the Three-Dimensional Thermodynamical Structure of the Inner Corona of Solar Minimum Carrington Rotations 1915 and 2081

    Science.gov (United States)

    Lloveras, Diego G.; Vásquez, Alberto M.; Nuevo, Federico A.; Frazin, Richard A.

    2017-10-01

    Using differential emission measure tomography (DEMT) based on time series of EUV images, we carry out a quantitative comparative analysis of the three-dimensional (3D) structure of the electron density and temperature of the inner corona (rarticles). They are characterized by plasma β≳1, and may be the result of the efficient dissipation of Alfvén waves at low coronal heights. The comparative analysis reveals that the low latitudes of the equatorial streamer belt of CR-1915 exhibit higher densities than for CR-2081. This cannot be explained by the systematic uncertainties. In addition, the southern hemisphere of the streamer belt of CR-1915 is characterized by higher temperatures and density scale heights than for CR-2081. On the other hand, the coronal hole region of CR-1915 shows lower temperatures than for CR-2081. The reported differences are in the range ≈ 10 - 25%, depending on the specific physical quantity and region that is compared, as fully detailed in the analysis. For other regions and/or physical quantities, the uncertainties do not allow assessing the thermodynamical differences between the two rotations. Future investigation will involve a DEMT analysis of other Carrington rotations selected from both epochs, and also a comparison of their tomographic reconstructions with magnetohydrodynamical simulations of the inner corona.

  11. Growth of three dimensional flower-like molybdenum disulfide hierarchical structures on graphene/carbon nanotube network: An advanced heterostructure for energy storage devices

    Science.gov (United States)

    Lingappan, Niranjanmurthi; Van, Ngoc Huynh; Lee, Suok; Kang, Dae Joon

    2015-04-01

    We report the design and synthesis of three dimensional flower-like molybdenum disulphide (f-MoS2) hierarchical structures, on reduced graphene oxide (RGO)/oxidized multi-walled carbon nanotube (o-MWCNT) backbone (f-MoS2/RGO/o-MWCNT), through one-pot hydrothermal method. Control experiments reveal that the homogenously distributed o-MWCNTs on RGO play an essential role for the formation of such morphology. As an anode for lithium ion batteries, the f-MoS2/RGO/o-MWCNT hybrid delivers a high reversible capacity of 1275 mAh g-1 at the current density of 100 mA g-1, superior rate capability and excellent long cycle life, with capacity retention of 93% after 100 cycles. The outstanding electrochemical performance can be attributed to the large surface area, short diffusion length and continuous electron transport pathway, as a consequence of the intimate contact between f-MoS2, graphene, and o-MWCNTs.

  12. Three dimensional contact/impact methodology

    International Nuclear Information System (INIS)

    Kulak, R.F.

    1987-01-01

    The simulation of three-dimensional interface mechanics between reactor components and structures during static contact or dynamic impact is necessary to realistically evaluate their structural integrity to off-normal loads. In our studies of postulated core energy release events, we have found that significant structure-structure interactions occur in some reactor vessel head closure designs and that fluid-structure interactions occur within the reactor vessel. Other examples in which three-dimensional interface mechanics play an important role are: (1) impact response of shipping casks containing spent fuel, (2) whipping pipe impact on reinforced concrete panels or pipe-to-pipe impact after a pipe break, (3) aircraft crash on secondary containment structures, (4) missiles generated by turbine failures or tornados, and (5) drops of heavy components due to lifting accidents. The above is a partial list of reactor safety problems that require adequate treatment of interface mechanics and are discussed in this paper

  13. Sulfur-nitrogen co-doped three-dimensional carbon foams with hierarchical pore structures as efficient metal-free electrocatalysts for oxygen reduction reactions

    Science.gov (United States)

    Liu, Zheng; Nie, Huagui; Yang, Zhi; Zhang, Jing; Jin, Zhiping; Lu, Yanqi; Xiao, Zhubing; Huang, Shaoming

    2013-03-01

    Despite the good progress in developing doped carbon catalysts for oxygen-reduction reaction (ORR), the current metal-free carbon catalysts are still far from satisfactory for large-scale applications of fuel cell. Developing new metal free doped carbon materials with abundance active sites as well as excellent electron transfer and reactant transport rate towards ORR may be a potential solution. Herein, we develop a novel three-dimensional (3D) sulfur-nitrogen co-doped carbon foams (S-N-CF) with hierarchical pore structures, using a convenient, economical, and scalable method. The experimental results have demonstrated that the obtained 3D S-N-CF exhibited better catalytic activity, longer-term stability and higher methanol tolerance than a commercial Pt/C catalyst. Such excellent performances may be attributed to the synergistic effect, which includes high catalytic sites for ORR provided by high S-N heteroatom loading, excellent reactant transport caused by hierarchical pore structures and high electron transfer rate provided by 3D continuous networks. Our results not only develop a new type of catalysts with excellent electrocatalytic performance by a commercially valid route, but also provide useful information for further clarification of the relationship between the microstructures of metal-free carbon materials and catalyst properties for ORR. More importantly, the idea to design hierarchical pore structures could be applied to other catalytic materials and serve as a general strategy for improving the activity of various ORR catalysts.Despite the good progress in developing doped carbon catalysts for oxygen-reduction reaction (ORR), the current metal-free carbon catalysts are still far from satisfactory for large-scale applications of fuel cell. Developing new metal free doped carbon materials with abundance active sites as well as excellent electron transfer and reactant transport rate towards ORR may be a potential solution. Herein, we develop a novel

  14. An insight into the general relationship between the three dimensional structures of enzymes and their electronic wave functions: Implication for the prediction of functional sites of enzymes.

    Science.gov (United States)

    Fukushima, K; Wada, M; Sakurai, M

    2008-06-01

    In this study, we explored the general relationship between the three-dimensional (3D) structures of enzymes and their electronic wave functions. Furthermore, we developed a method for the prediction of their functionally important sites. For this purpose, we first performed linear-scaling molecular orbital calculations for 112 nonredundant, non-homologous enzymes with known structure and function. In consequence, we showed that the canonical molecular orbitals (MOs) of the enzymes could be classified into three groups according to the degree of electron delocalization: highly localized orbitals (Group A), highly delocalized orbitals whose electrons are distributed over almost the whole molecule (Group B), and moderately delocalized orbitals (Group C). The MOs belonging to Group A are located near the HOMO-LUMO band gap, and thereby include the frontier orbitals of a given enzyme. We inferred that the MOs of Group B play a role in stabilizing the 3D structure of the enzyme, while those of Group C contribute to constructing the covalent bond framework of the enzyme. Next, we investigated whether the frontier orbitals of enzymes could be used for identifying their potential functional sites. As a result, we found that the frontier orbitals of the 112 enzymes have a high propensity to be colocalized with the known functional sites, especially when the enzymes are hydrated. Such a propensity is shown to be remarkable when Glu or Asp is a functional site residue. On the basis of these results, we finally propose a protocol for the prediction of functional sites of enzymes. (c) 2008 Wiley-Liss, Inc.

  15. Three-dimensional Inversion of High Resolution Ground-penetrating Radar for the Stochastic Structure of Velocity Heterogeneity of a Fluvial Aquifer

    Science.gov (United States)

    Lindsay, K. M.; Irving, J.; Bradford, J. H.

    2014-12-01

    Knowledge of the spatial correlation structure of the hydraulic properties in the shallow subsurface is critical for the detailed characterization of near surface aquifers and realistic simulation of flow and transport processes. While the vertical correlation structure is often well constrained by borehole analysis, the lateral correlation structure is often poorly estimated, due to unreliable interpolation between sparsely spaced boreholes and methods that only capture bulk aquifer properties (e.g. pump tests, slug injections). Ground-penetrating radar (GPR) velocity measurements are highly sensitive to changes in water content. In the saturated zone, water content is equivalent to porosity, making ground-penetrating radar a promising tool for extraction of lateral correlation lengths of important hydrologic properties in the near surface. Previous work has shown that there is a simple relationship relating the 2D autocorrelation of a GPR reflection image and the underlying velocity field, allowing for a Monte Carlo inversion strategy to generate sets of parameters describing the autocorrelation of the velocity field, that are consistent with recorded GPR reflection data. We extend this method to the three-dimensional case and apply it to a realistic synthetic GPR dataset. Results obtained from applying this inversion strategy to the 3-D case are similar to the results from previous work done on the 2-D case, and indicate that the inverse solution is non-unique. Multiple combinations of vertical and lateral correlation parameters describing the velocity heterogeneity can generate GPR reflection images with the same 3-D autocorrelations. Despite the non-uniqueness, the aspect ratios of the extracted parameter pairs are the same, indicating that the aspect ratios of the velocity heterogeneity can be reliably extracted. We are currently applying this method to a densely sampled GPR dataset collected at the Boise Hydrogeophysical Research Site (BHRS). The BHRS is an

  16. Nucleotide sequence of Phaseolus vulgaris L. alcohol dehydrogenase encoding cDNA and three-dimensional structure prediction of the deduced protein.

    Science.gov (United States)

    Amelia, Kassim; Khor, Chin Yin; Shah, Farida Habib; Bhore, Subhash J

    2015-01-01

    Common beans (Phaseolus vulgaris L.) are widely consumed as a source of proteins and natural products. However, its yield needs to be increased. In line with the agenda of Phaseomics (an international consortium), work of expressed sequence tags (ESTs) generation from bean pods was initiated. Altogether, 5972 ESTs have been isolated. Alcohol dehydrogenase (AD) encoding gene cDNA was a noticeable transcript among the generated ESTs. This AD is an important enzyme; therefore, to understand more about it this study was undertaken. The objective of this study was to elucidate P. vulgaris L. AD (PvAD) gene cDNA sequence and to predict the three-dimensional (3D) structure of deduced protein. positive and negative strands of the PvAD cDNA clone were sequenced using M13 forward and M13 reverse primers to elucidate the nucleotide sequence. Deduced PvAD cDNA and protein sequence was analyzed for their basic features using online bioinformatics tools. Sequence comparison was carried out using bl2seq program, and tree-view program was used to construct a phylogenetic tree. The secondary structures and 3D structure of PvAD protein were predicted by using the PHYRE automatic fold recognition server. The sequencing results analysis showed that PvAD cDNA is 1294 bp in length. It's open reading frame encodes for a protein that contains 371 amino acids. Deduced protein sequence analysis showed the presence of putative substrate binding, catalytic Zn binding, and NAD binding sites. Results indicate that the predicted 3D structure of PvAD protein is analogous to the experimentally determined crystal structure of s-nitrosoglutathione reductase from an Arabidopsis species. The 1294 bp long PvAD cDNA encodes for 371 amino acid long protein that contains conserved domains required for biological functions of AD. The predicted deduced PvAD protein's 3D structure reflects the analogy with the crystal structure of Arabidopsis thaliana s-nitrosoglutathione reductase. Further study is required

  17. Fusion of three-dimensional X-ray angiography and three-dimensional echocardiography

    International Nuclear Information System (INIS)

    Rasche, Volker; Mansour, Moussa; Reddy, Vivek; Singh, Jagmeet P.; Ruskin, Jeremy; Qureshi, Answer; Manzke, Robert; Sokka, Sham

    2008-01-01

    Cardiovascular intervention guidance requires knowledge of heart function relative to its blood supply or venous drainage. Functional and vascular anatomic data are usually generated on different imaging systems, so fusion of the data is necessary to simultaneously visualize the results for intervention planning and guidance. The objective of this work is to establish the feasibility of fusing volumetric ultrasound (U/S) data with three-dimensional (3D) X-ray imaging data for visualization of cardiac morphology, function and coronary venous drainage. Temporally resolved U/S volume data was registered with the 3D reconstruction of vascular structures derived from X-ray modeling and reconstruction. U/S image registration was obtained by optical tracking fiducial markers with simultaneous X-ray imaging. The proposed technique was applied to phantom data for accuracy assessment of the registration process and to biventricular pacemaker implantation as clinical example. Fusion of U/S data with 3D X-ray reconstruction data produced an RMS registration error below 2 mm. Preliminary clinical feasibility of U/S-derived data synchronously with X-ray derived 3D coronary venography was established. This technique can be applied for fusion of functional U/S data with 3D anatomic X-ray data of the coronary veins during a biventricular pacemaker implantation procedures. (orig.)

  18. VLBA DETERMINATION OF THE DISTANCE TO NEARBY STAR-FORMING REGIONS. III. HP TAU/G2 AND THE THREE-DIMENSIONAL STRUCTURE OF TAURUS

    International Nuclear Information System (INIS)

    Torres, Rosa M.; Loinard, Laurent; Rodriguez, Luis F.; Mioduszewski, Amy J.

    2009-01-01

    Using multiepoch Very Long Baseline Array (VLBA) observations, we have measured the trigonometric parallax of the weak-line T Tauri star HP Tau/G2 in Taurus. The best fit yields a distance of 161.2 ± 0.9 pc, suggesting that the eastern portion of Taurus (where HP Tau/G2 is located) corresponds to the far side of the complex. Previous VLBA observations have shown that T Tau, to the south of the complex, is at an intermediate distance of about 147 pc, whereas the region around L1495 corresponds to the near side at roughly 130 pc. Our observations of only four sources are still too coarse to enable a reliable determination of the three-dimensional structure of the entire Taurus star-forming complex. They do demonstrate, however, that VLBA observations of multiple sources in a given star-forming region have the potential not only to provide a very accurate estimate of its mean distance, but also to reveal its internal structure. The proper motion measurements obtained simultaneously with the parallax allowed us to study the kinematics of the young stars in Taurus. Combining the four observations available so far, we estimate the peculiar velocity of Taurus to be about 10.6 km s -1 almost completely in a direction parallel to the Galactic plane. Using our improved distance measurement, we have refined the determination of the position on the H-R diagram of HP Tau/G2, and of two other members of the HP Tau group (HP Tau itself and HP Tau/G3). Most pre-main-sequence evolutionary models predict significantly discrepant ages (by 5 Myr) for those three stars-expected to be coeval. Only in the models of Palla and Stahler do they fall on a single isochrone (at 3 Myr).

  19. Comparison of the three-dimensional structures of a human Bence-Jones dimer crystallized on Earth and aboard US Space Shuttle Mission STS-95.

    Science.gov (United States)

    Terzyan, Simon S; Bourne, Christina R; Ramsland, Paul A; Bourne, Philip C; Edmundson, Allen B

    2003-01-01

    Crystals of a human (Sea) Bence-Jones dimer were produced in a capillary by vapor diffusion under microgravity conditions in the 9 day US Space Shuttle Mission STS-95. In comparison to ground-based experiments, nucleation was facile and spontaneous in space. Appearance of a very large (8 x 1.6 x 1.0 mm) crystal in a short time period is a strong endorsement for the use of microgravity to produce crystals sufficiently large for neutron diffraction studies. The Sea dimer crystallized in the orthorhombic space group P2(1)2(1)2(1), with a = 48.9 A, b = 85.2 A, and c = 114.0 A. The crystals grown in microgravity exhibited significantly lower mosaicities than those of ground-based crystals and the X-ray diffraction data had a lower overall B factor. Three-dimensional structures determined by X-ray analysis at two temperatures (100 and 293 K) were indistinguishable from those obtained from ground-based crystals. However, both the crystallographic R factor and the free R factor were slightly lower in the models derived from crystals produced in microgravity. The major difference between the two crystal growth systems is a lack of convection and sedimentation in a microgravity environment. This environment resulted in the growth of much larger, higher-quality crystals of the Sea Bence-Jones protein. Structurally, heretofore unrecognized grooves on the external surfaces of the Sea and other immunoglobulin-derived fragments are regular features and may offer supplementary binding regions for super antigens and other elongated ligands in the bloodstream and perivascular tissues. Copyright 2003 John Wiley & Sons, Ltd.

  20. Three-dimensional accelerating electromagnetic waves.

    Science.gov (United States)

    Bandres, Miguel A; Alonso, Miguel A; Kaminer, Ido; Segev, Mordechai

    2013-06-17

    We present a general theory of three-dimensional non-paraxial spatially-accelerating waves of the Maxwell equations. These waves constitute a two-dimensional structure exhibiting shape-invariant propagation along semicircular trajectories. We provide classification and characterization of possible shapes of such beams, expressed through the angular spectra of parabolic, oblate and prolate spheroidal fields. Our results facilitate the design of accelerating beams with novel structures, broadening scope and potential applications of accelerating beams.

  1. Fabrication of All-Solid-State Lithium-ion Cells using Three-Dimensionally Structured Solid Electrolyte Li7La3Zr2O12 Pellets

    Directory of Open Access Journals (Sweden)

    MAO SHOJI

    2016-08-01

    Full Text Available All-solid-state lithium-ion batteries using Li+-ion conducting ceramic electrolytes have been focused on as attractive future batteries for electric vehicles and renewable energy conversion systems because high safety can be realized due to non-flammability of ceramic electrolytes. In addition, a higher volumetric energy density than that of current lithium-ion batteries is expected since the all-solid-state lithium-ion batteries can be made in bipolar cell configurations. However, the special ideas and techniques based on ceramic processing are required to construct the electrochemical interface for all-solid-state lithium-ion batteries since the battery development has been done so far based on liquid electrolyte system over 100 years. As one of promising approaches to develop practical all-solid-state batteries, we have been focusing on three-dimensionally (3D structured cell configurations such as an interdigitated combination of 3D pillars of cathode and anode, which can be realized by using solid electrolyte membranes with hole-array structures. The application of such kinds of 3D structures effectively increases the interface between solid electrode and solid electrolyte per unit volume, lowering the internal resistance of all-solid-state lithium-ion batteries. In this study, Li6.25Al0.25La3Zr2O12 (LLZAl, which is a Al-doped Li7La3Zr2O12 (LLZ with Li+-ion conductivity of ~10–4 S cm–1 at room temperature and high stability against lithium-metal, was used as a solid electrolyte, and its pellets with 700 um depth holes in 700 x 700 um2 area were fabricated to construct 3D-structured all-solid-state batteries with LiCoO2 / LLZAl / lithium-metal configuration. It is expected that the LiCoO2-LLZAl interface is formed by point to point contact even when the LLZAl pellet with 3D hole-array structure is applied. Therefore, the application of mechanically soft Li3BO3 with a low melting point at around 700 °C was also performed as a supporting

  2. Processing of three-dimensional structures of Nuclear Medicine in PET modality; Processamento de estruturas tridimensionais de medicina nuclear na modalidade PET

    Energy Technology Data Exchange (ETDEWEB)

    Pacheco, Edward Florez; Furuie, Sergio Shiguemi, E-mail: edward.florez@usp.br [Universidade de Sao Paulo (EP/USP), SP (Brazil). Dept. de Engenharia de Telecomunicacoes e Controle. Lab. de Engenharia Biomedica

    2013-03-15

    The nuclear medicine, as a specialty to obtain medical images is very important, and it has became one of the main procedures utilized in health care centers to analyze the metabolic behavior of the patient. This project was based on medical images obtained by the PET modality (Positron Emission Tomography). Thus, we developed a framework for processing Nuclear Medicine three-dimensional images of the PET modality, which is composed of consecutive steps that start with the generation of standard images (gold standard) by using simulated images of the Left Ventricular Heart, such as phantoms obtained from the NCAT-4D software. Then, Poisson quantum noise was introduced into the whole volume to simulate the characteristic noises in PET images. Subsequently, the pre-processing step was executed by using specific 3D filters, such as the median filter, the weighted Gaussian filter, and the Anscombe/Wiener filter. Then the segmentation process, which is based on the fuzzy connectedness theory, was implemented. For that purpose four different 3D approaches were implemented: Generic, LIFO, kTetaFOEMS, and dynamic weight algorithm. Finally, an assessment procedure was used as a measurement tool to quantify three parameters (true positive, false positive and maximum distance) that determined the level of efficiency and precision of our process. It was found that the pair filter - segmenter formed by the Anscombe/Wiener filter together with the Fuzzy segmenter based on dynamic weights provided the best results, with VP and FP rates of 98.49 {+-}0.27% and 2.19 {+-}0.19%, respectively, for the simulation of the left ventricular volume. Along with the set of choices made during the processing structure, the project was finished with the analysis of a small number of volumes that belonged to a real PET test, thus the quantification of the volumes was obtained. (author)

  3. Three-Dimensional Reconstruction of Sandpile Interiors

    Science.gov (United States)

    Seidler, G. T.

    2001-03-01

    The granular bed, or sandpile, has become one of the condensed matter physicist's favorite systems. In addition to conceptual appeal, the simplest sandpile of monodisperse hard spheres is a valuable model system for understanding powders, liquids, and metallic glasses. Any fundamental approach to the transport and mechanical properties of three-dimensional mesoscale disordered materials must follow from a thorough understanding of their structure. However, in the overwhelming majority of cases, structure measurements have been limited to the mean filling fraction and the structural autocorrelation function. This is particularly unfortunate in the ongoing sandpile renaissance, where some of the most interesting questions concern structure and the relationship between structure and dynamics. I will discuss the combination of synchrotron x-ray microtomography and computer vision algorithms to perform three-dimensional virtual reconstructions of real sandpiles. This technique is rapid and noninvasive, and is applicable to samples large enough to separate bulk and boundary properties. The resulting complete knowledge of structure can be used to calculate otherwise inaccessible correlation functions. I will present results for several measures of the bond-orientational order in three-dimensional sandpiles, including fabric tensors and nematic order parameters.

  4. Arching in three-dimensional clogging

    Directory of Open Access Journals (Sweden)

    Török János

    2017-01-01

    Full Text Available Arching in dry granular material is a long established concept, however it remains still an open question how three-dimensional orifices clog. We investigate by means of numerical simulations and experimental data how the outflow creates a blocked configuration of particles. We define the concave surface of the clogged dome by two independent methods (geometric and density based. The average shape of the cupola for spheres is almost a hemisphere but individual samples have large holes in the structure indicating a blocked state composed of two-dimensional force chains rather than three-dimensional objects. The force chain structure justifies this assumption. For long particles the clogged configurations display large variations, and in certain cases the empty region reaches a height of 5 hole diameters. These structures involve vertical walls consisting of horizontally placed stable stacking of particles.

  5. Arching in three-dimensional clogging

    Science.gov (United States)

    Török, János; Lévay, Sára; Szabó, Balázs; Somfai, Ellák; Wegner, Sandra; Stannarius, Ralf; Börzsönyi, Tamás

    2017-06-01

    Arching in dry granular material is a long established concept, however it remains still an open question how three-dimensional orifices clog. We investigate by means of numerical simulations and experimental data how the outflow creates a blocked configuration of particles. We define the concave surface of the clogged dome by two independent methods (geometric and density based). The average shape of the cupola for spheres is almost a hemisphere but individual samples have large holes in the structure indicating a blocked state composed of two-dimensional force chains rather than three-dimensional objects. The force chain structure justifies this assumption. For long particles the clogged configurations display large variations, and in certain cases the empty region reaches a height of 5 hole diameters. These structures involve vertical walls consisting of horizontally placed stable stacking of particles.

  6. The Structure and Dynamics of An Active Galactic Nucleus Torus : CO Line Predictions for ALMA from Three-dimensional Hydrodynamical Simulations with X-ray-driven Chemistry

    NARCIS (Netherlands)

    Perez Beaupuits, J.P.; Wada, K.; Spaans, M.

    2011-01-01

    Several attempts have been made to model the mass distribution and dynamical evolution of the circumnuclear gas in active galactic nuclei (AGNs). However, chemical evolution is not included in detail in three-dimensional (3D) hydrodynamic simulations. The X-ray radiation from the AGN can drive the

  7. The contrast-source stress-velocity integral-equation formulation of three-dimensional time-domain elastodynamic scattering problems : A structured approach using tensor partitioning

    NARCIS (Netherlands)

    De Hoop, A.T.; Abubakar, A.; Habashy, T.M.

    2009-01-01

    The contrast-source stress-velocity integral-equation formulation of three-dimensional time-domain elastodynamic scattering problems is discussed. A novel feature of the formulation is a tensor partitioning of the relevant dynamic stress and the contrast source volume density of deformation rate.

  8. A vein display system based on three-dimensional reconstruction

    Science.gov (United States)

    Wang, Danting; Zhou, Ya; Hu, Xiaoming; Wu, Zhaoguo; Dai, Xiaobin

    2014-10-01

    Venipuncture is the most common way of all invasive medical procedures. A vein display system can make vein access easier by capturing the vein information and projecting a visible vein image onto the skin, which is correctly aligned with the subject's vein. The existing systems achieve correct alignment by the design of coaxial structure. Such a structure causes complex optical and mechanical design and big physical dimensions inevitably. In this paper, we design a stereovision- based vein display system, which consists of a pair of cameras, a DLP projector and a near-infrared light source. We recover the three-dimensional venous structure from image pair acquired from two near-infrared cameras. Then the vein image from the viewpoint of projector is generated from the three-dimensional venous structure and projected exactly onto skin by the DLP projector. Since the stereo cameras get the depth information of vessels, the system can make sure the alignment of projected veins and the real veins without a coaxial structure. The experiment results prove that we propose a feasible solution for a portable and low-cost vein display device.

  9. The Three-dimensional Digital Factory for Shipbuilding Technology Research

    Directory of Open Access Journals (Sweden)

    Xu Wei

    2016-01-01

    Full Text Available The three-dimensional digital factory technology research is the hotspot in shipbuilding recently. The three-dimensional digital factory technology not only focus on design the components of the product, but also discuss on the simulation and analyses of the production process.Based on the three-dimensional model, the basic data layer, application control layer and the presentation layer of hierarchical structure are established in the three-dimensional digital factory of shipbuilding in this paper. And the key technologies of three-dimensional digital factory of shipbuilding are analysed. Finally, a case study is applied and the results show that the three-dimensional digital factory will play an important role in the future.

  10. Prediction of cross-recognition of peptide-HLA A2 by Melan-A-specific cytotoxic T lymphocytes using three-dimensional quantitative structure-activity relationships.

    Science.gov (United States)

    Fagerberg, Theres; Zoete, Vincent; Viatte, Sebastien; Baumgaertner, Petra; Alves, Pedro M; Romero, Pedro; Speiser, Daniel E; Michielin, Olivier

    2013-01-01

    The cross-recognition of peptides by cytotoxic T lymphocytes is a key element in immunology and in particular in peptide based immunotherapy. Here we develop three-dimensional (3D) quantitative structure-activity relationships (QSARs) to predict cross-recognition by Melan-A-specific cytotoxic T lymphocytes of peptides bound to HLA A*0201 (hereafter referred to as HLA A2). First, we predict the structure of a set of self- and pathogen-derived peptides bound to HLA A2 using a previously developed ab initio structure prediction approach [Fagerberg et al., J. Mol. Biol., 521-46 (2006)]. Second, shape and electrostatic energy calculations are performed on a 3D grid to produce similarity matrices which are combined with a genetic neural network method [So et al., J. Med. Chem., 4347-59 (1997)] to generate 3D-QSAR models. The models are extensively validated using several different approaches. During the model generation, the leave-one-out cross-validated correlation coefficient (q (2)) is used as the fitness criterion and all obtained models are evaluated based on their q (2) values. Moreover, the best model obtained for a partitioned data set is evaluated by its correlation coefficient (r = 0.92 for the external test set). The physical relevance of all models is tested using a functional dependence analysis and the robustness of the models obtained for the entire data set is confirmed using y-randomization. Finally, the validated models are tested for their utility in the setting of rational peptide design: their ability to discriminate between peptides that only contain side chain substitutions in a single secondary anchor position is evaluated. In addition, the predicted cross-recognition of the mono-substituted peptides is confirmed experimentally in chromium-release assays. These results underline the utility of 3D-QSARs in peptide mimetic design and suggest that the properties of the unbound epitope are sufficient to capture most of the information to determine the

  11. Prediction of cross-recognition of peptide-HLA A2 by Melan-A-specific cytotoxic T lymphocytes using three-dimensional quantitative structure-activity relationships.

    Directory of Open Access Journals (Sweden)

    Theres Fagerberg

    Full Text Available The cross-recognition of peptides by cytotoxic T lymphocytes is a key element in immunology and in particular in peptide based immunotherapy. Here we develop three-dimensional (3D quantitative structure-activity relationships (QSARs to predict cross-recognition by Melan-A-specific cytotoxic T lymphocytes of peptides bound to HLA A*0201 (hereafter referred to as HLA A2. First, we predict the structure of a set of self- and pathogen-derived peptides bound to HLA A2 using a previously developed ab initio structure prediction approach [Fagerberg et al., J. Mol. Biol., 521-46 (2006]. Second, shape and electrostatic energy calculations are performed on a 3D grid to produce similarity matrices which are combined with a genetic neural network method [So et al., J. Med. Chem., 4347-59 (1997] to generate 3D-QSAR models. The models are extensively validated using several different approaches. During the model generation, the leave-one-out cross-validated correlation coefficient (q (2 is used as the fitness criterion and all obtained models are evaluated based on their q (2 values. Moreover, the best model obtained for a partitioned data set is evaluated by its correlation coefficient (r = 0.92 for the external test set. The physical relevance of all models is tested using a functional dependence analysis and the robustness of the models obtained for the entire data set is confirmed using y-randomization. Finally, the validated models are tested for their utility in the setting of rational peptide design: their ability to discriminate between peptides that only contain side chain substitutions in a single secondary anchor position is evaluated. In addition, the predicted cross-recognition of the mono-substituted peptides is confirmed experimentally in chromium-release assays. These results underline the utility of 3D-QSARs in peptide mimetic design and suggest that the properties of the unbound epitope are sufficient to capture most of the information to

  12. Three-dimensional broadband tunable terahertz metamaterials

    DEFF Research Database (Denmark)

    Fan, Kebin; Strikwerda, Andrew; Zhang, Xin

    2013-01-01

    We present optically tunable magnetic three-dimensional (3D) metamaterials at terahertz (THz) frequencies which exhibit a tuning range of ~30% of the resonance frequency. This is accomplished by fabricating 3D array structures consisting of double-split-ring resonators (DSRRs) on silicon on sapph...... as verified through electromagnetic simulations and parameter retrieval. Our approach extends dynamic metamaterial tuning to magnetic control, and may find applications in switching and modulation, polarization control, or tunable perfect absorbers....

  13. Cylindrical Three-Dimensional Porous Anodic Alumina Networks

    Directory of Open Access Journals (Sweden)

    Pedro M. Resende

    2016-11-01

    Full Text Available The synthesis of a conformal three-dimensional nanostructure based on porous anodic alumina with transversal nanopores on wires is herein presented. The resulting three-dimensional network exhibits the same nanostructure as that obtained on planar geometries, but with a macroscopic cylindrical geometry. The morphological analysis of the nanostructure revealed the effects of the initial defects on the aluminum surface and the mechanical strains on the integrity of the three-dimensional network. The results evidence the feasibility of obtaining 3D porous anodic alumina on non-planar aluminum substrates.

  14. Study on prestressed concrete reactor vessel structures. II-5: Crack analysis by three dimensional finite elements method of 1/20 multicavity type PCRV subjected to internal pressure

    Science.gov (United States)

    1978-01-01

    A three-dimensional finite elements analysis is reported of the nonlinear behavior of PCRV subjected to internal pressure by comparing calculated results with test results. As the first stage, an analysis considering the nonlinearity of cracking in concrete was attempted. As a result, it is found possible to make an analysis up to three times the design pressure (50 kg/sqcm), and calculated results agree well with test results.

  15. Real three-dimensional biquadrics

    Energy Technology Data Exchange (ETDEWEB)

    Krasnov, Vyacheslav A [P.G. Demidov Yaroslavl State University, Yaroslavl (Russian Federation)

    2010-09-07

    We find the topological types of biquadrics (complete intersections of two real four-dimensional quadrics). The rigid isotopy classes of real three-dimensional biquadrics were described long ago: there are nine such classes. We find the correspondence between the topological types of real biquadrics and their rigid isotopy classes, and show that only two rigid isotopy classes have the same topological type. One of these classes consists of real GM-varieties and the other contains no GM-varieties. We also study the sets of real lines on real biquadrics.

  16. The Relationship Between the Growth Shape of Three-Dimensional Pb Islands on Cu(100) and the Domain Orientation of the Underlying c(5v2xv2)R45 Degree Structure

    Energy Technology Data Exchange (ETDEWEB)

    KELLOGG,GARY LEE; PLASS,RICHARD A.

    2000-06-12

    The authors use low energy electron microscopy to identify a correlation between the growth shape of three-dimensional Pb islands on Cu(100)and the domain structure of the underlying Pb overlayer. Deposition of 0.6 monolayer Pb on Cu(100) produces a compressed c(2x2) overlayer, designated c(5{radical}2x{radical}2)R45{degree}, with periodic rows of anti-phase boundaries. They found that heating the surface to temperatures above 100 C coarsens the orientational domains of this structure to sizes that are easily resolved in the low energy electron microscope. Three-dimensional Pb islands, grown on the coarsened domains, are found to be asymmetric with orientations that correlate with the domain structure. Once nucleated with a preferred growth orientation, islands continue to grow with the same preferred orientation, even across domain boundaries.

  17. Relationship between spectral reflectance and leaf area index in needleleaf forest: The effect of three-dimensional forest structure and clumping

    International Nuclear Information System (INIS)

    Kobayashi, H.

    2008-01-01

    Toward the reliable estimation of leaf area index (LAI) and fraction of absorbed photosynthetically active radiation (FAPAR), the relationship between LAI/FAPAR and bidirectional reflectance factor (BRF) at the top of canopy should be accurately modeled by the radiation transfer models. These relationships vary with the forest landscape due to its horizontal heterogeneity and needles clumping within shoot. In this study, the effect of the forest heterogeneity on the relationships between BRF and LAI, and NDVI and LAI/FAPAR were examined through the three-dimensional radiative transfer simulation, and were compared with the results from one-dimensional radiative transfer simulation. In addition to the simulation, limitation of one-dimensional radiative transfer simulation was evaluated. The results showed that BRF at red and near infrared, and NDVI had large variations with different forest landscape under the same LAI conditions. However the relationship between NDVI and LAI, and NDVI and FAPAR derived from dense canopy condition were quite similar to the results from one-dimensional model. If we add the shoot clumping effect in one dimensional radiative transfer model as a universal parameter for three-dimensional effect of the forest, one dimensional radiative transfer model can work well for the BRF simulation in spatially heterogeneous landscape except higher LAI conditions

  18. Crystal structure of a mixed-ligand terbium(III coordination polymer containing oxalate and formate ligands, having a three-dimensional fcu topology

    Directory of Open Access Journals (Sweden)

    Chainok Kittipong

    2016-01-01

    Full Text Available The title compound, poly[(μ3-formato(μ4-oxalatoterbium(III], [Tb(CHO2(C2O4]n, is a three-dimensional coordination polymer, and is isotypic with the LaIII, CeIII and SmIII analogues. The asymmetric unit contains one TbIII ion, one formate anion (CHO2− and half of an oxalate anion (C2O42−, the latter being completed by application of inversion symmetry. The TbIII ion is nine-coordinated in a distorted tricapped trigonal–prismatic manner by two chelating carboxylate groups from two C2O42− ligands, two carboxylate oxygen atoms from another two C2O42− ligands and three oxygen atoms from three CHO2− ligands, with the Tb—O bond lengths and the O—Tb—O bond angles ranging from 2.4165 (19 to 2.478 (3 Å and 64.53 (6 to 144.49 (4°, respectively. The CHO2− and C2O42− anions adopt μ3-bridging and μ4-chelating-bridging coordination modes, respectively, linking adjacent TbIII ions into a three-dimensional 12-connected fcu topology with point symbol (324.436.56. The title compound exhibits thermal stability up to 623 K, and also displays strong green photoluminescence in the solid state at room temperature.

  19. 1.42 A crystal structure of mini-IGF-1(2): an analysis of the disulfide isomerization property and receptor binding property of IGF-1 based on the three-dimensional structure

    International Nuclear Information System (INIS)

    Yun Caihong; Tang Yuehua; Feng Youmin; An Xiaomin; Chang Wenrui; Liang Dongcai

    2004-01-01

    Insulin and insulin-like growth factor 1 (IGF-1) share a homologous sequence, a similar three-dimensional structure and weakly overlapping biological activity, but IGF-1 folds into two thermodynamically stable disulfide isomers, while insulin folds into one unique stable tertiary structure. This is a very interesting phenomenon in which one amino acid sequence encodes two three-dimensional structures, and its molecular mechanism has remained unclear for a long time. In this study, the crystal structure of mini-IGF-1(2), a disulfide isomer of an artificial analog of IGF-1, was solved by the SAD/SIRAS method using our in-house X-ray source. Evidence was found in the structure showing that the intra-A-chain/domain disulfide bond of some molecules was broken; thus, it was proposed that disulfide isomerization begins with the breakdown of this disulfide bond. Furthermore, based on the structural comparison of IGF-1 and insulin, a new assumption was made that in insulin the several hydrogen bonds formed between the N-terminal region of the B-chain and the intra-A-chain disulfide region of the A-chain are the main reason for the stability of the intra-A-chain disulfide bond and for the prevention of disulfide isomerization, while Phe B1 and His B5 are very important for the formation of these hydrogen bonds. Moreover, the receptor binding property of IGF-1 was analyzed in detail based on the structural comparison of mini-IGF-1(2), native IGF-1, and small mini-IGF-1

  20. Three-dimensional structural engineering of nanoporous alumina by controlled sprinkling of an electrolyte on a porous anodic alumina (PAA) template

    Science.gov (United States)

    Moradi, M.; Noormohammadi, M.; Behzadi, F.

    2011-02-01

    The significant effect of anodization current on the morphology of nanopores encourages us to consider a novel method for engineering these nanostructures. In this paper we study a controlled anodization process using controlled electrolyte stirring. This is done using an electrical pump with variable speed for sprinkling an electrolyte on a membrane. The variable voltage applied to the pump can control the temperature gradient and diffusion of the ions which produce the anodization current. Here we show the significant role of pumping and how this effect can be used in the engineering of nanopores as a three-dimensional nanostructure. These experiments are carried out for a variety of anodization voltages and various electrolyte concentrations, and thus we investigate how these parameters in the vicinity of pumping can control the porosity of the template in three dimensions.

  1. An Introduction of Three-dimensional Grammar

    Directory of Open Access Journals (Sweden)

    Fan Xiao

    2017-12-01

    Full Text Available This paper introduces some key points of Three-dimensional Grammar. As for the structure, it can be distinguished into syntactic structure, semantic structure and pragmatic structure from the perspectives of syntax, semantics and pragmatics. And the same is true with the followings, such as grammatical constituents, grammatical functions, grammatical meanings, grammatical focuses. Sentence types which is called sentence pattern, sentence model and sentence types respectively, and analysis methods. This paper proposes that grammatical researches should be done in accordance with the four principles, that is form and meaning co-verified, static and dynamic co-referenced, structure and function co-testified and description and interpretation co-promoted.

  2. Three dimensional magnetic abacus memory.

    Science.gov (United States)

    Zhang, ShiLei; Zhang, JingYan; Baker, Alexander A; Wang, ShouGuo; Yu, GuangHua; Hesjedal, Thorsten

    2014-08-22

    Stacking nonvolatile memory cells into a three-dimensional matrix represents a powerful solution for the future of magnetic memory. However, it is technologically challenging to access the data in the storage medium if large numbers of bits are stacked on top of each other. Here we introduce a new type of multilevel, nonvolatile magnetic memory concept, the magnetic abacus. Instead of storing information in individual magnetic layers, thereby having to read out each magnetic layer separately, the magnetic abacus adopts a new encoding scheme. It is inspired by the idea of second quantisation, dealing with the memory state of the entire stack simultaneously. Direct read operations are implemented by measuring the artificially engineered 'quantised' Hall voltage, each representing a count of the spin-up and spin-down layers in the stack. This new memory system further allows for both flexible scaling of the system and fast communication among cells. The magnetic abacus provides a promising approach for future nonvolatile 3D magnetic random access memory.

  3. Three-Dimensional Laser Microvision

    Science.gov (United States)

    Shimotahira, Hiroshi; Iizuka, Keigo; Chu, Sun-Chun; Wah, Christopher; Costen, Furnie; Yoshikuni, Yuzo

    2001-04-01

    A three-dimensional (3-D) optical imaging system offering high resolution in all three dimensions, requiring minimum manipulation and capable of real-time operation, is presented. The system derives its capabilities from use of the superstructure grating laser source in the implementation of a laser step frequency radar for depth information acquisition. A synthetic aperture radar technique was also used to further enhance its lateral resolution as well as extend the depth of focus. High-speed operation was made possible by a dual computer system consisting of a host and a remote microcomputer supported by a dual-channel Small Computer System Interface parallel data transfer system. The system is capable of operating near real time. The 3-D display of a tunneling diode, a microwave integrated circuit, and a see-through image taken by the system operating near real time are included. The depth resolution is 40 m; lateral resolution with a synthetic aperture approach is a fraction of a micrometer and that without it is approximately 10 m.

  4. Three dimensional magnetic abacus memory

    Science.gov (United States)

    Zhang, Shilei; Zhang, Jingyan; Baker, Alexander; Wang, Shouguo; Yu, Guanghua; Hesjedal, Thorsten

    2015-03-01

    Stacking nonvolatile memory cells into a three-dimensional matrix represents a powerful solution for the future of magnetic memory. However, it is technologically challenging to access the individual data in the storage medium if large numbers of bits are stacked on top of each other. Here we introduce a new type of multilevel, nonvolatile magnetic memory concept, the magnetic abacus. Instead of storing information in individual magnetic layers, thereby having to read out each magnetic layer separately, the magnetic abacus adopts a new encoding scheme which envisages a classical abacus with the beads operated by electron spins. It is inspired by the idea of second quantization, dealing with the memory state of the entire stack simultaneously. Direct read operations are implemented by measuring the artificially engineered `quantized' Hall voltage, representing a count of the spin-up and spin-down layers in the stack. This concept of `second quantization of memory' realizes the 3D memory architecture with superior reading and operation efficiency, thus is a promising approach for future nonvolatile magnetic random access memory.

  5. Three dimensional animated images of anorectal malformations

    International Nuclear Information System (INIS)

    Ueno, Shigeru; Yanagimachi, Noriharu; Muro, Isao; Komiya, Taizo; Yokoyama, Seishichi; Hirakawa, Hitoshi; Tajima, Tomoo; Mitomi, Toshio; Suto, Yasuzo.

    1996-01-01

    Accurate reconstruction of the pelvic structures is a most important factor in obtaining a desirable result after anorectoplasty for a patient with anorectal malformation. Preoperative evaluation of the anatomy is indispensable for choosing an appropriate operative method in each case. To facilitate preoperative evaluation, three dimensional animated images of the pelvic structure of patients with anorectal malformations were constructed by computer graphics based upon tomographic images obtained from magnetic resonance imaging. Axial 1-mm thick images of the pelvic portion were generated with spoiling pulse gradient echo sequences using short repetition times (13 msec TR) and short echo times (6 msec TE) with a flip angle of 25 degrees with the patient in the jack-knife position. Graphic data from MR images were transferred to a graphic work station and processed on it. The skin surface, the ano-rectum, the lower urinary tract and the sphincter musculature were segmented by thresholding images by the signal intensity. Three dimensional images were displayed by surface rendering method using the segmented data of each organ and then animation images of these organs were obtained. The anatomy of each type of anomaly was easily recognized by 3-D visualization, and animation of the pelvic viscera and the sphincter musculature made the images more realistic. Animated images of the musculature were especially useful for simulating surgical procedures and could be helpful for reviewing surgical results. (author)

  6. Preparation, structural characterization, and in vitro cell studies of three-dimensional SiO2-CaO binary glass scaffolds built ofultra-small nanofibers.

    Science.gov (United States)

    Luo, Honglin; Li, Wei; Ao, Haiyong; Li, Gen; Tu, Junpin; Xiong, Guangyao; Zhu, Yong; Wan, Yizao

    2017-07-01

    Three-dimensional (3D) nanofibrous scaffolds hold great promises in tissue engineering and regenerative medicine. In this work, for the first time, 3D SiO 2 -CaO binary glass nanofibrous scaffolds have been fabricated via a combined method of template-assisted sol-gel and calcination by using bacterial cellulose as the template. SEM with EDS, TEM, and AFM confirm that the molar ratio of Ca to Si and fiber diameter of the resultant SiO 2 -CaO nanofibers can be controlled by immersion time in the solution of tetraethyl orthosilicate and ethanol. The optimal immersion time was 6h which produced the SiO 2 -CaO binary glass containing 60at.% Si and 40at.% Ca (named 60S40C). The fiber diameter of 60S40C scaffold is as small as 29nm. In addition, the scaffold has highly porous 3D nanostructure with dominant mesopores at 10.6nm and macropores at 20μm as well as a large BET surface area (240.9m 2 g -1 ), which endow the 60S40C scaffold excellent biocompatibility and high ALP activity as revealed by cell studies using osteoblast cells. These results suggest that the 60S40C scaffold has great potential in bone tissue regeneration. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Investigation of the three-dimensional thermoelastic deformation of the core structure of a fast breeder reactor under stationary working conditions

    International Nuclear Information System (INIS)

    Yong-Su, Hoang.

    1976-12-01

    In this study a method is described which has been developed in order to calculate three-dimensional deformation of the reactor core, taking into account thermal expansion. Two problem areas are of particular importance: 1) The spatial deflection of subassemblies in specified flexible supports and with specified clearances; 2) The investigation of the equilibrium configurations of the subassemblies in the planes of clamping (problem of clamping plane). - The elementary theory of beam deflection has been used to calculate the deformation of subassemblies. However, particular problems have been encountered as a result of flexibly designed support configurations having some spatial clearances. The problem has essentially been solved in two steps: a) Uniqueness analysis of the beam-support configuration; b) Calculation of the support loads and bending line for the unique beam-support configuration. - Basic difficulties currently prevent the problem of clamping plane being solved in a satisfactory manner. Therefore, a simplified clamping model was used for supports without spatial clearance and a parametric study was performed for supports having spatial clearance. The computation method developed is applied to the MARK I core of SNR 300. Core deformations are calculated under different support conditions for the subassemblies in the grid plate and in the upper clamping plane. (orig./HR) [de

  8. Heat Shock Protein Genes Undergo Dynamic Alteration in Their Three-Dimensional Structure and Genome Organization in Response to Thermal Stress.

    Science.gov (United States)

    Chowdhary, Surabhi; Kainth, Amoldeep S; Gross, David S

    2017-12-15

    Three-dimensional (3D) chromatin organization is important for proper gene regulation, yet how the genome is remodeled in response to stress is largely unknown. Here, we use a highly sensitive version of chromosome conformation capture in combination with fluorescence microscopy to investigate Heat Shock Protein ( HSP ) gene conformation and 3D nuclear organization in budding yeast. In response to acute thermal stress, HSP genes undergo intense intragenic folding interactions that go well beyond 5'-3' gene looping previously described for RNA polymerase II genes. These interactions include looping between upstream activation sequence (UAS) and promoter elements, promoter and terminator regions, and regulatory and coding regions (gene "crumpling"). They are also dynamic, being prominent within 60 s, peaking within 2.5 min, and attenuating within 30 min, and correlate with HSP gene transcriptional activity. With similarly striking kinetics, activated HSP genes, both chromosomally linked and unlinked, coalesce into discrete intranuclear foci. Constitutively transcribed genes also loop and crumple yet fail to coalesce. Notably, a missense mutation in transcription factor TFIIB suppresses gene looping, yet neither crumpling nor HSP gene coalescence is affected. An inactivating promoter mutation, in contrast, obviates all three. Our results provide evidence for widespread, transcription-associated gene crumpling and demonstrate the de novo assembly and disassembly of HSP gene foci. Copyright © 2017 American Society for Microbiology.

  9. Computer-assisted structure elucidation from 13C-NMR-Spectra. I. The development of a three-dimensional structure code. II. The development of an isomer generating program

    International Nuclear Information System (INIS)

    Schuetz, V.

    1999-05-01

    The presented thesis consists of two separate programs which both aid the automated structure elucidation in the CSEARCH database system. A successful utilization of a large collection of NMR reference spectra for the prediction of chemical shift values is dependent on a strong correlation between the spectral data and the structural information via unique coding. By now, this was done using the two-dimensional HOSE code, which turned out to be insufficient whenever stereochemical effects other than cis/trans-isomerism contribute to the chemical shift values. Therefore, this new algorithm has been developed to derive the demanded three-dimensional descriptors. The calculatio