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Sample records for 3d wall structures

  1. Analysis of thin-walled structural elements via 3D standard BEM with generic substructuring

    SciTech Connect

    De Araujo, Francisco Celio; Gray, Leonard J

    2008-01-01

    This paper is concerned with the application of standard 3D Boundary Element Methods to solve thin-walled structural elements (needle-like/shell-like solids). A subregion-by-subregion data structure, incorporating iterative solvers and discontinuous boundary elements, is presented. To efficiently and accurately evaluate the quasi-singular integrals, special quadrature methods are applied. In addition, structured matrix-vector products, designed to avoid the excessive number of conditional tests during solver iterations, are proposed. Numerical results for complex thin-walled BE models are validated by comparison with FEM calculations and previously published BEM analyses.

  2. Experimental Investigation of the Near Wall Flow Structure of a Low Reynolds Number 3-D Turbulent Boundary Layer

    NASA Technical Reports Server (NTRS)

    Fleming, J. L.; Simpson, R. L.

    1997-01-01

    Laser Doppler velocimetry (LDV) measurements and hydrogen bubble flow visualization techniques were used to examine the near-wall flow structure of 2D and 3D turbulent boundary layers (TBLs) over a range of low Reynolds numbers. The goals of this research were (1) an increased understanding of the flow physics in the near wall region of turbulent boundary layers,(2) to observe and quantify differences between 2D and 3D TBL flow structures, and (3) to document Reynolds number effects for 3D TBLs. The LDV data have provided results detailing the turbulence structure of the 2D and 3D TBLs. These results include mean Reynolds stress distributions, flow skewing results, and U and V spectra. Effects of Reynolds number for the 3D flow were also examined. Comparison to results with the same 3D flow geometry but at a significantly higher Reynolds number provided unique insight into the structure of 3D TBLs. While the 3D mean and fluctuating velocities were found to be highly dependent on Reynolds number, a previously defined shear stress parameter was discovered to be invariant with Reynolds number. The hydrogen bubble technique was used as a flow visualization tool to examine the near-wall flow structure of 2D and 3D TBLs. Both the quantitative and qualitative results displayed larger turbulent fluctuations with more highly concentrated vorticity regions for the 2D flow.

  3. A fast technique applied to the analysis of Resistive Wall Modes with 3D conducting structures

    SciTech Connect

    Rubinacci, Guglielmo Liu, Yueqiang

    2009-03-20

    This paper illustrates the development of a 'fast' technique for the analysis of Resistive Wall Modes (RWMs) in fusion devices with three-dimensional conducting structures, by means of the recently developed CarMa code. Thanks to its peculiar features, the computational cost scales almost linearly with the number of discrete unknowns. Some large scale problems are solved in configurations of interest for the International Thermonuclear Experimental Reactor (ITER)

  4. Opportunity at the Wall 3-D

    NASA Image and Video Library

    2004-11-23

    NASA Mars Exploration Rover Opportunity reached the base of Burns Cliff, a portion of the inner wall of Endurance Crater in this anaglyph from the rover 285th martian day Nov. 11, 2004. 3D glasses are necessary to view this image.

  5. Identification of artery wall stiffness: in vitro validation and in vivo results of a data assimilation procedure applied to a 3D fluid-structure interaction model.

    PubMed

    Bertoglio, Cristóbal; Barber, David; Gaddum, Nicholas; Valverde, Israel; Rutten, Marcel; Beerbaum, Philipp; Moireau, Philippe; Hose, Rodney; Gerbeau, Jean-Frédéric

    2014-03-21

    We consider the problem of estimating the stiffness of an artery wall using a data assimilation method applied to a 3D fluid-structure interaction (FSI) model. Recalling previous works, we briefly present the FSI model, the data assimilation procedure and the segmentation algorithm. We present then two examples of the procedure using real data. First, we estimate the stiffness distribution of a silicon rubber tube from image data. Second, we present the estimation of aortic wall stiffness from real clinical data.

  6. 3D-graphite structure

    SciTech Connect

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

    2011-01-15

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

  7. 3D structured illumination microscopy

    NASA Astrophysics Data System (ADS)

    Dougherty, William M.; Goodwin, Paul C.

    2011-03-01

    Three-dimensional structured illumination microscopy achieves double the lateral and axial resolution of wide-field microscopy, using conventional fluorescent dyes, proteins and sample preparation techniques. A three-dimensional interference-fringe pattern excites the fluorescence, filling in the "missing cone" of the wide field optical transfer function, thereby enabling axial (z) discrimination. The pattern acts as a spatial carrier frequency that mixes with the higher spatial frequency components of the image, which usually succumb to the diffraction limit. The fluorescence image encodes the high frequency content as a down-mixed, moiré-like pattern. A series of images is required, wherein the 3D pattern is shifted and rotated, providing down-mixed data for a system of linear equations. Super-resolution is obtained by solving these equations. The speed with which the image series can be obtained can be a problem for the microscopy of living cells. Challenges include pattern-switching speeds, optical efficiency, wavefront quality and fringe contrast, fringe pitch optimization, and polarization issues. We will review some recent developments in 3D-SIM hardware with the goal of super-resolved z-stacks of motile cells.

  8. Enigmatic structures within salt walls of the Santos Basin-Part 1: Geometry and kinematics from 3D seismic reflection and well data

    NASA Astrophysics Data System (ADS)

    Jackson, Christopher A.-L.; Jackson, Martin P. A.; Hudec, Michael R.; Rodriguez, Clara R.

    2015-06-01

    Understanding intrasalt structure may elucidate the fundamental kinematics and, ultimately, the mechanics of diapir growth. However, there have been relatively few studies of the internal structure of salt diapirs outside the mining industry because their cores are only partly exposed in the field and poorly imaged on seismic reflection data. This study uses 3D seismic reflection and borehole data from the São Paulo Plateau, Santos Basin, offshore Brazil to document the variability in intrasalt structural style in natural salt diapirs. We document a range of intrasalt structures that record: (i) initial diapir rise; (ii) rise of lower mobile halite through an arched and thinned roof of denser, layered evaporites, and emplacement of an intrasalt sheet or canopy; (iii) formation of synclinal flaps kinematically linked to emplacement of the intrasalt allochthonous bodies; and (iv) diapir squeezing. Most salt walls contain simple internal anticlines. Only a few salt walls contain allochthonous bodies and breakout-related flaps. The latter occur in an area having a density inversion within the autochthonous salt layer, such that upper, anhydrite-rich, layered evaporites are denser than lower, more halite-rich evaporites. We thus interpret that most diapirs rose through simple fold amplification of internal salt stratigraphy but that locally, where a density inversion existed in the autochthonous salt, Rayleigh-Taylor overturn within the growing diapir resulted in the ascent of less dense evaporites into the diapir crest by breaching of the internal anticline. This resulted in the formation of steep salt-ascension zones or feeders and the emplacement of high-level intrasalt allocthonous sheets underlain by breakout-related flaps. Although regional shortening undoubtedly occurred on the São Paulo Plateau during the Late Cretaceous, we suggest this was only partly responsible for the complex intrasalt deformation. We suggest that, although based on the Santos Basin, our

  9. Microfabricating 3D Structures by Laser Origami

    DTIC Science & Technology

    2011-11-09

    10.1117/2.1201111.003952 Microfabricating 3D structures by laser origami Alberto Piqué, Scott Mathews, Andrew Birnbaum, and Nicholas Charipar A new...folding known as origami allows the transformation of flat patterns into 3D shapes. A similar approach can be used to generate 3D structures com...materials Figure 1. (A–C) Schematic illustrating the steps in the laser origami process and (D) a resulting folded out-of-plane 3D structure. that can

  10. Chest wall segmentation in automated 3D breast ultrasound scans.

    PubMed

    Tan, Tao; Platel, Bram; Mann, Ritse M; Huisman, Henkjan; Karssemeijer, Nico

    2013-12-01

    In this paper, we present an automatic method to segment the chest wall in automated 3D breast ultrasound images. Determining the location of the chest wall in automated 3D breast ultrasound images is necessary in computer-aided detection systems to remove automatically detected cancer candidates beyond the chest wall and it can be of great help for inter- and intra-modal image registration. We show that the visible part of the chest wall in an automated 3D breast ultrasound image can be accurately modeled by a cylinder. We fit the surface of our cylinder model to a set of automatically detected rib-surface points. The detection of the rib-surface points is done by a classifier using features representing local image intensity patterns and presence of rib shadows. Due to attenuation of the ultrasound signal, a clear shadow is visible behind the ribs. Evaluation of our segmentation method is done by computing the distance of manually annotated rib points to the surface of the automatically detected chest wall. We examined the performance on images obtained with the two most common 3D breast ultrasound devices in the market. In a dataset of 142 images, the average mean distance of the annotated points to the segmented chest wall was 5.59 ± 3.08 mm. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Integral Textile Structure for 3-D CMC Turbine Airfoils

    NASA Technical Reports Server (NTRS)

    Marshall, David B. (Inventor); Cox, Brian N. (Inventor); Sudre, Olivier H. (Inventor)

    2017-01-01

    An integral textile structure for 3-D CMC turbine airfoils includes top and bottom walls made from an angle-interlock weave, each of the walls comprising warp and weft fiber tows. The top and bottom walls are merged on a first side parallel to the warp fiber tows into a single wall along a portion of their widths, with the weft fiber tows making up the single wall interlocked through the wall's thickness such that delamination of the wall is inhibited. The single wall suitably forms the trailing edge of an airfoil; the top and bottom walls are preferably joined along a second side opposite the first side and parallel to the radial fiber tows by a continuously curved section in which the weave structure remains continuous with the weave structure in the top and bottom walls, the continuously curved section being the leading edge of the airfoil.

  12. 3D cardiac wall thickening assessment for acute myocardial infarction

    NASA Astrophysics Data System (ADS)

    Khalid, A.; Chan, B. T.; Lim, E.; Liew, Y. M.

    2017-06-01

    Acute myocardial infarction (AMI) is the most severe form of coronary artery disease leading to localized myocardial injury and therefore irregularities in the cardiac wall contractility. Studies have found very limited differences in global indices (such as ejection fraction, myocardial mass and volume) between healthy subjects and AMI patients, and therefore suggested regional assessment. Regional index, specifically cardiac wall thickness (WT) and thickening is closely related to cardiac function and could reveal regional abnormality due to AMI. In this study, we developed a 3D wall thickening assessment method to identify regional wall contractility dysfunction due to localized myocardial injury from infarction. Wall thickness and thickening were assessed from 3D personalized cardiac models reconstructed from cine MRI images by fitting inscribed sphere between endocardial and epicardial wall. The thickening analysis was performed in 5 patients and 3 healthy subjects and the results were compared against the gold standard 2D late-gadolinium-enhanced (LGE) images for infarct localization. The notable finding of this study is the highly accurate estimation and visual representation of the infarct size and location in 3D. This study provides clinicians with an intuitive way to visually and qualitatively assess regional cardiac wall dysfunction due to infarction in AMI patients.

  13. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  14. Switchable field-tuned control of magnetic domain wall pinning along Co microwires by 3D e-beam lithographed structures

    NASA Astrophysics Data System (ADS)

    Blanco-Roldán, C.; Quirós, C.; Rodriguez-Rodriguez, G.; Vélez, M.; Martín, J. I.; Alameda, J. M.

    2016-02-01

    Three-dimensional magnetic circuits composed of Co microwires crossed by elevated Co bridges have been patterned on Si substrate by e-beam lithography and lift-off process. The lithographic procedure includes a double resist procedure that optimizes the shape of the bridge, so that 200 nm air gaps can be routinely achieved in between the wire and bridge elements. Microwire magnetization reversal processes have been analyzed by magneto-optical Kerr effect microscopy with different remanent bridge configurations. When the Co bridge is magnetized along the in-plane direction parallel to the wire axis, its stray field induces a marked pinning effect on domain wall propagation along the wire below it, even without being in contact. Changing the sign of the remanent state of the bridge, domain wall pinning can be selected to occur in either the ascending or descending branches of the wire hysteresis loop. Thus, these wire-bridge 3D circuits provide a simple system for tunable domain wall pinning controllable through the pre-recorded bridge remanent state.

  15. Self assembled structures for 3D integration

    NASA Astrophysics Data System (ADS)

    Rao, Madhav

    Three dimensional (3D) micro-scale structures attached to a silicon substrate have various applications in microelectronics. However, formation of 3D structures using conventional micro-fabrication techniques are not efficient and require precise control of processing parameters. Self assembly is a method for creating 3D structures that takes advantage of surface area minimization phenomena. Solder based self assembly (SBSA), the subject of this dissertation, uses solder as a facilitator in the formation of 3D structures from 2D patterns. Etching a sacrificial layer underneath a portion of the 2D pattern allows the solder reflow step to pull those areas out of the substrate plane resulting in a folded 3D structure. Initial studies using the SBSA method demonstrated low yields in the formation of five different polyhedra. The failures in folding were primarily attributed to nonuniform solder deposition on the underlying metal pads. The dip soldering method was analyzed and subsequently refined. A modified dip soldering process provided improved yield among the polyhedra. Solder bridging referred as joining of solder deposited on different metal patterns in an entity influenced the folding mechanism. In general, design parameters such as small gap-spacings and thick metal pads were found to favor solder bridging for all patterns studied. Two types of soldering: face and edge soldering were analyzed. Face soldering refers to the application of solder on the entire metal face. Edge soldering indicates application of solder only on the edges of the metal face. Mechanical grinding showed that face soldered SBSA structures were void free and robust in nature. In addition, the face soldered 3D structures provide a consistent heat resistant solder standoff height that serve as attachments in the integration of dissimilar electronic technologies. Face soldered 3D structures were developed on the underlying conducting channel to determine the thermo-electric reliability of

  16. 3D Structures of Responsive Nanocompartmentalized Microgels.

    PubMed

    Gelissen, Arjan P H; Oppermann, Alex; Caumanns, Tobias; Hebbeker, Pascal; Turnhoff, Sarah K; Tiwari, Rahul; Eisold, Sabine; Simon, Ulrich; Lu, Yan; Mayer, Joachim; Richtering, Walter; Walther, Andreas; Wöll, Dominik

    2016-11-09

    Compartmentalization in soft matter is important for segregating and coordinating chemical reactions, sequestering (re)active components, and integrating multifunctionality. Advances depend crucially on quantitative 3D visualization in situ with high spatiotemporal resolution. Here, we show the direct visualization of different compartments within adaptive microgels using a combination of in situ electron and super-resolved fluorescence microscopy. We unravel new levels of structural details and address the challenge of reconstructing 3D information from 2D projections for nonuniform soft matter as opposed to monodisperse proteins. Moreover, we visualize the thermally induced shrinkage of responsive core-shell microgels live in water. This strategy opens doors for systematic in situ studies of soft matter systems and their application as smart materials.

  17. Inferential modeling of 3D chromatin structure.

    PubMed

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-04-30

    For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Inferential modeling of 3D chromatin structure

    PubMed Central

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-01-01

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

  19. Exploring DNA Structure with Cn3D

    PubMed Central

    Day, Joseph; McCarty, Richard E.; Shearn, Allen; Shingles, Richard; Fletcher, Linnea; Murphy, Stephanie; Pearlman, Rebecca

    2007-01-01

    Researchers in the field of bioinformatics have developed a number of analytical programs and databases that are increasingly important for advancing biological research. Because bioinformatics programs are used to analyze, visualize, and/or compare biological data, it is likely that the use of these programs will have a positive impact on biology education. Over the past years, we have been working to help biology instructors introduce bioinformatics activities into their curricula by providing them with instructional materials that use bioinformatics programs and databases as educational tools. In this study, we measured the impact of a set of these materials on student learning. The activities in these materials asked students to use the molecular structure visualization program Cn3D to locate, identify, or analyze diverse features in DNA structures. Both the experimental groups of college and high school students showed significant increases in learning relative to control groups. Further, learning gains by the college students were correlated with the number of activities assigned. We conclude that working with Cn3D was important for improving student understanding of DNA structure. This study is one example of how a bioinformatics program for visualization can be used to support student learning. PMID:17339395

  20. Improvements on digital inline holographic PTV for 3D wall-bounded turbulent flow measurements

    NASA Astrophysics Data System (ADS)

    Toloui, Mostafa; Mallery, Kevin; Hong, Jiarong

    2017-04-01

    Three-dimensional (3D) particle image velocimetry (PIV) and particle tracking velocimetry (PTV) provide the most comprehensive flow information for unraveling the physical phenomena in a wide range of fluid problems, from microfluidics to wall-bounded turbulent flows. Compared with other 3D PIV techniques, such as tomographic PIV and defocusing PIV, the digital inline holographic PTV (DIH-PTV) provides 3D flow measurement solution with high spatial resolution, low cost optical setup, and easy alignment and calibration. Despite these advantages, DIH-PTV suffers from major limitations including poor longitudinal resolution, human intervention (i.e. requirement for manually determined tuning parameters during tracer field reconstruction and extraction), limited tracer concentration, small sampling volume and expensive computations, limiting its broad use for 3D flow measurements. In this study, we present our latest developments on minimizing these challenges, which enables high-fidelity DIH-PTV implementation to larger sampling volumes with significantly higher particle seeding densities suitable for wall-bounded turbulent flow measurements. The improvements include: (1) adjustable window thresholding; (2) multi-pass 3D tracking; (3) automatic wall localization; and (4) continuity-based out-of-plane velocity component computation. The accuracy of the proposed DIH-PTV method is validated with conventional 2D PIV and double-view holographic PTV measurements in smooth-wall turbulent channel flow experiments. The capability of the technique in characterization of wall-bounded turbulence is further demonstrated through its application to flow measurements for smooth- and rough-wall turbulent channel flows. In these experiments, 3D velocity fields are measured within sampling volumes of 14.7  ×  50.0  ×  14.4 mm3 (covering the entire depth of the channel) with a velocity resolution of  <1.1 mm/vector. Overall, the presented DIH-PTV method and

  1. Automated modeling of RNA 3D structure.

    PubMed

    Rother, Kristian; Rother, Magdalena; Skiba, Pawel; Bujnicki, Janusz M

    2014-01-01

    This chapter gives an overview over the current methods for automated modeling of RNA structures, with emphasis on template-based methods. The currently used approaches to RNA modeling are presented with a side view on the protein world, where many similar ideas have been used. Two main programs for automated template-based modeling are presented: ModeRNA assembling structures from fragments and MacroMoleculeBuilder performing a simulation to satisfy spatial restraints. Both approaches have in common that they require an alignment of the target sequence to a known RNA structure that is used as a modeling template. As a way to find promising template structures and to align the target and template sequences, we propose a pipeline combining the ParAlign and Infernal programs on RNA family data from Rfam. We also briefly summarize template-free methods for RNA 3D structure prediction. Typically, RNA structures generated by automated modeling methods require local or global optimization. Thus, we also discuss methods that can be used for local or global refinement of RNA structures.

  2. Discovering Structural Regularity in 3D Geometry

    PubMed Central

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

    2010-01-01

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

  3. Numerical 3D flow simulation of ultrasonic horns with attached cavitation structures and assessment of flow aggressiveness and cavitation erosion sensitive wall zones.

    PubMed

    Mottyll, Stephan; Skoda, Romuald

    2016-07-01

    As a contribution to a better understanding of cavitation erosion mechanisms, a compressible inviscid finite volume flow solver with barotropic homogeneous liquid-vapor mixture cavitation model is applied to ultrasonic horn set-ups with and without stationary specimen, that exhibit attached cavitation at the horn tip. Void collapses and shock waves, which are closely related to cavitation erosion, are resolved. The computational results are compared to hydrophone, shadowgraphy and erosion test data. At the horn tip, vapor volume and topology, subharmonic oscillation frequency as well as the amplitude of propagating pressure waves are in good agreement with experimental data. For the evaluation of flow aggressiveness and the assessment of erosion sensitive wall zones, statistical analyses of wall loads and of the multiplicity of distinct collapses in wall-adjacent flow regions are applied to the horn tip and the stationary specimen. An a posteriori projection of load collectives, i.e. cumulative collapse rate vs. collapse pressure, onto a reference grid eliminates the grid dependency effectively for attached cavitation at the horn tip, whereas a significant grid dependency remains at the stationary specimen. The load collectives show an exponential decrease towards higher collapse pressures. Erosion sensitive wall zones are well predicted for both, horn tip and stationary specimen, and load profiles are in good qualitative agreement with measured topography profiles of eroded duplex stainless steel samples after long-term runs. For the considered amplitude and gap width according to ASTM G32-10 standard, the analysis of load collectives reveals that the distinctive erosive ring shape at the horn tip can be attributed to frequent breakdown and re-development of a small portion of the tip-attached cavity. This partial breakdown of the attached cavity repeats at each driving cycle and is associated with relatively moderate collapse peak pressures, whereas the

  4. 3-D plasma boundary and plasma wall interaction research at UW-Madison

    NASA Astrophysics Data System (ADS)

    Schmitz, Oliver; Akerson, Adrian; Bader, Aaron; Barbui, Tullio; Effenberg, Florian; Flesch, Kurt; Frerichs, Heinke; Green, Jonathan; Hinson, Edward; Kremeyer, Thierry; Norval, Ryan; Stephey, Laurie; Waters, Ian; Winters, Victoria

    2016-10-01

    The necessity of considering 3-D effects on the plasma boundary and plasma wall interaction (PWI) in tokamaks, stellarators and reversed field pinches has been highlighted by abundant experimental and numerical results in the recent past. Prominent examples with 3-D boundary situations are numerous: ELM controlled H-modes by RMP fields in tokamaks, research on boundary plasmas and PWI in stellarators in general, quasi-helical states in RFPs, asymmetric fueling situations, and structural and wall elements which are not aligned with the magnetic guiding fields. A systematic approach is being taken at UW-Madison to establish a targeted experimental basis for identifying the most significant effects for plasma edge transport and resulting PWI in such 3-D plasma boundary situations. We deploy advanced 3-D modeling using the EMC3-EIRENE, ERO and MCI codes in combination with laboratory experiments at UW-Madison to investigate the relevance of 3-D effects in large scale devices with a concerted approach on DIII-D, NSTX-U, and Wendelstein 7-X. Highlights of experimental results from the on-site laboratory activities at UW-Madison and the large scale facilities are presented and interlinks will be discussed. This work was supported by US DOE DE-SC0013911, DE-SC00012315 and DE-SC00014210.

  5. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

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

    2015-07-15

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

  6. 3D Structure of Tillage Soils

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  7. FASTR3D: a fast and accurate search tool for similar RNA 3D structures

    PubMed Central

    Lai, Chin-En; Tsai, Ming-Yuan; Liu, Yun-Chen; Wang, Chih-Wei; Chen, Kun-Tze; Lu, Chin Lung

    2009-01-01

    FASTR3D is a web-based search tool that allows the user to fast and accurately search the PDB database for structurally similar RNAs. Currently, it allows the user to input three types of queries: (i) a PDB code of an RNA tertiary structure (default), optionally with specified residue range, (ii) an RNA secondary structure, optionally with primary sequence, in the dot-bracket notation and (iii) an RNA primary sequence in the FASTA format. In addition, the user can run FASTR3D with specifying additional filtering options: (i) the released date of RNA structures in the PDB database, and (ii) the experimental methods used to determine RNA structures and their least resolutions. In the output page, FASTR3D will show the user-queried RNA molecule, as well as user-specified options, followed by a detailed list of identified structurally similar RNAs. Particularly, when queried with RNA tertiary structures, FASTR3D provides a graphical display to show the structural superposition of the query structure and each of identified structures. FASTR3D is now available online at http://bioalgorithm.life.nctu.edu.tw/FASTR3D/. PMID:19435878

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

    PubMed

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

    2015-07-01

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

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

    PubMed Central

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

    2015-01-01

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

  10. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

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

    2016-07-08

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. 3D-GNOME: an integrated web service for structural modeling of the 3D genome

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    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.

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

    PubMed Central

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

    2017-01-01

    Purpose The major problem in producing artificial livers is that primary hepatocytes cannot be cultured for many days. Recently, 3-dimensional (3D) printing technology draws attention and this technology regarded as a useful tool for current cell biology. By using the 3D bio-printing, these problems can be resolved. Methods To generate 3D bio-printed structures (25 mm × 25 mm), cells-alginate constructs were fabricated by 3D bio-printing system. Mouse primary hepatocytes were isolated from the livers of 6–8 weeks old mice by a 2-step collagenase method. Samples of 4 × 107 hepatocytes with 80%–90% viability were printed with 3% alginate solution, and cultured with well-defined culture medium for primary hepatocytes. To confirm functional ability of hepatocytes cultured on 3D alginate scaffold, we conducted quantitative real-time polymerase chain reaction and immunofluorescence with hepatic marker genes. Results Isolated primary hepatocytes were printed with alginate. The 3D printed hepatocytes remained alive for 14 days. Gene expression levels of Albumin, HNF-4α and Foxa3 were gradually increased in the 3D structures. Immunofluorescence analysis showed that the primary hepatocytes produced hepatic-specific proteins over the same period of time. Conclusion Our research indicates that 3D bio-printing technique can be used for long-term culture of primary hepatocytes. It can therefore be used for drug screening and as a potential method of producing artificial livers. PMID:28203553

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  15. RNA Structure: Advances and Assessment of 3D Structure Prediction.

    PubMed

    Miao, Zhichao; Westhof, Eric

    2017-03-30

    Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of current predictions. The assessment metrics used in RNA-Puzzles are briefly described. The detection of RNA 3D modules from sequence data and their automatic implementation belong to the current challenges in RNA 3D structure prediction. Expected final online publication date for the Annual Review of Biophysics Volume 46 is May 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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

    PubMed

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

    2015-07-01

    Protein aggregation underlies an increasing number of disorders and constitutes a major bottleneck in the development of therapeutic proteins. Our present understanding on the molecular determinants of protein aggregation has crystalized in a series of predictive algorithms to identify aggregation-prone sites. A majority of these methods rely only on sequence. Therefore, they find difficulties to predict the aggregation properties of folded globular proteins, where aggregation-prone sites are often not contiguous in sequence or buried inside the native structure. The AGGRESCAN3D (A3D) server overcomes these limitations by taking into account the protein structure and the experimental aggregation propensity scale from the well-established AGGRESCAN method. Using the A3D server, the identified aggregation-prone residues can be virtually mutated to design variants with increased solubility, or to test the impact of pathogenic mutations. Additionally, A3D server enables to take into account the dynamic fluctuations of protein structure in solution, which may influence aggregation propensity. This is possible in A3D Dynamic Mode that exploits the CABS-flex approach for the fast simulations of flexibility of globular proteins. The A3D server can be accessed at http://biocomp.chem.uw.edu.pl/A3D/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    PubMed Central

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

    2015-01-01

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

  18. Synthesis of 3D Mesoporous Wall-Like MnO2 with Improved Electrochemical Performance

    NASA Astrophysics Data System (ADS)

    Wei, Hongmei; Wang, Jinxing; Yang, Shengwei; Wang, Weifang; Hou, Dewen; Li, Tengfei

    2017-03-01

    Manganese dioxide (MnO2) with mesoporous framework self-assembled by ultrathin nanosheets was synthesized via a facile hydrothermal strategy without any binders and substrates. The wall-like structure of this electrode material for supercapacitors can provide more attaching points for active material and shorten the diffusion paths of electrons and ions, leading to a high specific capacitance (SC) of 400 F g-1 at current density of 1 A g-1 and the good cyclic stability up to 3000 cycles. Meanwhile, the relationships among structure, specific surface area, pore size and electrochemical properties have been discussed. It indicated that three-dimensional (3D) wall-like δ-MnO2 is a promising electrochemical electrode candidate for supercapacitors.

  19. Quantitative 3D structured illumination microscopy of nuclear structures.

    PubMed

    Kraus, Felix; Miron, Ezequiel; Demmerle, Justin; Chitiashvili, Tsotne; Budco, Alexei; Alle, Quentin; Matsuda, Atsushi; Leonhardt, Heinrich; Schermelleh, Lothar; Markaki, Yolanda

    2017-05-01

    3D structured illumination microscopy (3D-SIM) is the super-resolution technique of choice for multicolor volumetric imaging. Here we provide a validated sample preparation protocol for labeling nuclei of cultured mammalian cells, image acquisition and registration practices, and downstream image analysis of nuclear structures and epigenetic marks. Using immunostaining and replication labeling combined with image segmentation, centroid mapping and nearest-neighbor analyses in open-source environments, 3D maps of nuclear structures are analyzed in individual cells and normalized to fluorescence standards on the nanometer scale. This protocol fills an unmet need for the application of 3D-SIM to the technically challenging nuclear environment, and subsequent quantitative analysis of 3D nuclear structures and epigenetic modifications. In addition, it establishes practical guidelines and open-source solutions using ImageJ/Fiji and the TANGO plugin for high-quality and routinely comparable data generation in immunostaining experiments that apply across model systems. From sample preparation through image analysis, the protocol can be executed within one week.

  20. Along Endurance Crater's Inner Wall (3-D Anaglyph)

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This stereo view from the base of 'Burns Cliff' in the inner wall of 'Endurance Crater' combines several frames taken by Opportunity's navigation camera during the NASA rover's 280th martian day (Nov. 6, 2004). It is presented in a cylindrical-perspective projection with geometric seam correction. The cliff dominates the left and right portions of the image, while the central portion looks down into the crater. The 'U' shape of this mosaic results from the rover's tilt of about 30 degrees on the sloped ground below the cliff. Rover wheel tracks in the left half of the image show some of the slippage the rover experienced in making its way to this point. The site from which this image was taken has been designated as Opportunity's Site 37.

  1. Numerical integration of structural elements in NIKE3D and DYNA3D

    NASA Astrophysics Data System (ADS)

    Maker, B. N.; Whirley, R. G.; Engelmann, B. E.

    1992-08-01

    The beam and shell elements found in many linear elastic finite element codes accept integrated cross sectional properties as input, and produce solutions using classical beam and shell theory. These theories are built upon the equation of resultant forces and moments with integrals of assumed stress distributions over the cross section. In contrast, the structural elements in NIKE3D and DYNA3D are formulated to represent nonlinear geometric and material behavior. Thus stress distributions may not necessarily be representable by simple functions of cross section variables. In NIKE3D and DYNA3D, the Hughes-Liu beam element and all shell elements accommodate these more general stress distributions by computing stresses at various points in the cross section. The integration of stresses within each element is then performed numerically, using a variety of methods. This report describes these numerical integration procedures in detail, and highlights their application to engineering problems. Several other features of the structural elements are also described, including force and moment resultants, user-defined reference surfaces, and user-defined integration rules. Finally, the shear correction factor is described in a section which relates results from NIKE3D and DYNA3D to those obtained from classical beam theory.

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

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

    RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  3. Differentiating bladder carcinoma from bladder wall using 3D textural features: an initial study

    NASA Astrophysics Data System (ADS)

    Xu, Xiaopan; Zhang, Xi; Liu, Yang; Tian, Qiang; Zhang, Guopeng; Lu, Hongbing

    2016-03-01

    Differentiating bladder tumors from wall tissues is of critical importance for the detection of invasion depth and cancer staging. The textural features embedded in bladder images have demonstrated their potentials in carcinomas detection and classification. The purpose of this study was to investigate the feasibility of differentiating bladder carcinoma from bladder wall using three-dimensional (3D) textural features extracted from MR bladder images. The widely used 2D Tamura features were firstly wholly extended to 3D, and then different types of 3D textural features including 3D features derived from gray level co-occurrence matrices (GLCM) and grey level-gradient co-occurrence matrix (GLGCM), as well as 3D Tamura features, were extracted from 23 volumes of interest (VOIs) of bladder tumors and 23 VOIs of patients' bladder wall. Statistical results show that 30 out of 47 features are significantly different between cancer tissues and wall tissues. Using these features with significant differences between these two types of tissues, classification performance with a supported vector machine (SVM) classifier demonstrates that the combination of three types of selected 3D features outperform that of using only one type of features. All the observations demonstrate that significant textural differences exist between carcinomatous tissues and bladder wall, and 3D textural analysis may be an effective way for noninvasive staging of bladder cancer.

  4. 3D Printing of Hierarchical Silk Fibroin Structures.

    PubMed

    Sommer, Marianne R; Schaffner, Manuel; Carnelli, Davide; Studart, André R

    2016-12-21

    Like many other natural materials, silk is hierarchically structured from the amino acid level up to the cocoon or spider web macroscopic structures. Despite being used industrially in a number of applications, hierarchically structured silk fibroin objects with a similar degree of architectural control as in natural structures have not been produced yet due to limitations in fabrication processes. In a combined top-down and bottom-up approach, we exploit the freedom in macroscopic design offered by 3D printing and the template-guided assembly of ink building blocks at the meso- and nanolevel to fabricate hierarchical silk porous materials with unprecedented structural control. Pores with tunable sizes in the range 40-350 μm are generated by adding sacrificial organic microparticles as templates to a silk fibroin-based ink. Commercially available wax particles or monodisperse polycaprolactone made by microfluidics can be used as microparticle templates. Since closed pores are generated after template removal, an ultrasonication treatment can optionally be used to achieve open porosity. Such pore templating particles can be further modified with nanoparticles to create a hierarchical template that results in porous structures with a defined nanotopography on the pore walls. The hierarchically porous silk structures obtained with this processing technique can potentially be utilized in various application fields from structural materials to thermal insulation to tissue engineering scaffolds.

  5. Modeling resistive wall modes and disruptive instabilities with M3D-C1

    NASA Astrophysics Data System (ADS)

    Ferraro, Nm; Jardin, Sc; Pfefferle, D.

    2016-10-01

    Disruptive instabilities pose a significant challenge to the tokamak approach to magnetic fusion energy, and must be reliably avoided in a successful reactor. These instabilities generally involve rapid, global changes to the magnetic field, and electromagnetic interaction with surrounding conducting structures. Here we apply the extended-MHD code M3D-C1 to calculate the stability and evolution of disruptive modes, including their interaction with external conducting structures. The M3D-C1 model includes the effects of resistivity, equilibrium rotation, and resistive walls of arbitrary thickness, each of which may play important roles in the stability and evolution of disruptive modes. The strong stabilizing effect of rotation on resistive wall modes is explored and compared with analytic theory. The nonlinear evolution of vertical displacement events is also considered, including the evolution of non-axisymmetric instabilities that may arise during the current-quench phase of the disruption. It is found that the non-axisymmetric stability of the plasma during a VDE depends strongly on the thermal history of the plasma. This work is supported by US DOE Grant DE-AC02-09CH11466 and the SciDAC Center for Extended MHD Modeling.

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

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

    data have low explanatory power outside low biomass areas. There is no current capability for repeatable disturbance and regrowth estimates. (2) The science and policy needs for information on vegetation 3D structure can be successfully addressed by a mission capable of producing (i) a first global inventory of forest biomass with a spatial resolution 1km or finer and unprecedented accuracy (ii) annual global disturbance maps at a spatial resolution of 1 ha with subsequent biomass accumulation rates at resolutions of 1km or finer, and (iii) transects of vertical and horizontal forest structure with 30 m along-transect measurements globally at 25 m spatial resolution, essential for habitat characterization. We also show from the literature that lidar profile samples together with wall-to53 wall L-band quad-pol-SAR imagery and ecosystem dynamics models can work together to satisfy these vegetation 3D structure and biomass measurement requirements. Finally we argue that the technology readiness levels of combined pol-SAR and lidar instruments are adequate for space flight. Remaining to be worked out, are the particulars of a lidar/pol-SAR mission design that is feasible and at a minimum satisfies the information and measurement requirement articulated herein.

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

    PubMed

    Luu, Tien-Dao; Rusu, Alin-Mihai; Walter, Vincent; Ripp, Raymond; Moulinier, Luc; Muller, Jean; Toursel, Thierry; Thompson, Julie D; Poch, Olivier; Nguyen, Hoan

    2012-01-01

    The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era. We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model. Major releases of the database are automatically generated and updated regularly in line with the dbSNP (database of Single Nucleotide Polymorphism) and SwissVar releases, by exploiting the extensive Décrypthon computational grid resources. The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in XML or flat file formats. Database URL: http://decrypthon.igbmc.fr/msv3d.

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

    NASA Astrophysics Data System (ADS)

    Jaiswal, Neeru; Kishtawal, C. M.

    2016-05-01

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

  9. Surface modeling and segmentation of the 3D airway wall in MSCT

    NASA Astrophysics Data System (ADS)

    Ortner, Margarete; Fetita, Catalin; Brillet, Pierre-Yves; Pr"teux, Françoise; Grenier, Philippe

    2011-03-01

    Airway wall remodeling in asthma and chronic obstructive pulmonary disease (COPD) is a well-known indicator of the pathology. In this context, current clinical studies aim for establishing the relationship between the airway morphological structure and its function. Multislice computed tomography (MSCT) allows morphometric assessment of airways, but requires dedicated segmentation tools for clinical exploitation. While most of the existing tools are limited to cross-section measurements, this paper develops a fully 3D approach for airway wall segmentation. Such approach relies on a deformable model which is built up as a patient-specific surface model at the level of the airway lumen and deformed to reach the outer surface of the airway wall. The deformation dynamics obey a force equilibrium in a Lagrangian framework constrained by a vector field which avoids model self-intersections. The segmentation result allows a dense quantitative investigation of the airway wall thickness with a deeper insight at bronchus subdivisions than classic cross-section methods. The developed approach has been assessed both by visual inspection of 2D cross-sections, performed by two experienced radiologists on clinical data obtained with various protocols, and by using a simulated ground truth (pulmonary CT image model). The results confirmed a robust segmentation in intra-pulmonary regions with an error in the range of the MSCT image resolution and underlined the interest of the volumetric approach versus purely 2D methods.

  10. Dual multispectral and 3D structured light laparoscope

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  11. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

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

  12. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

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

  13. 3D-Printed Millimeter Wave Structures

    DTIC Science & Technology

    2016-03-14

    Wave Structures Andrew Zai, Michael Lis, Dave Cipolle, John Russo Maxwell Plaut, Theodore Fedynyshyn, and Jennifer Lewis* MIT Lincoln Laboratory...millimeter wave (mmW) components. The dielectric properties of the two materials are characterized at mmW frequencies and show properties comparable...millimeter wave components, filter, dielectric lens Introduction The trend to integrate microwave systems on one chip, such as with a monolithic

  14. 3D Motion Modeling and Reconstruction of Left Ventricle Wall in Cardiac MRI.

    PubMed

    Yang, Dong; Wu, Pengxiang; Tan, Chaowei; Pohl, Kilian M; Axel, Leon; Metaxas, Dimitris

    2017-06-01

    The analysis of left ventricle (LV) wall motion is a critical step for understanding cardiac functioning mechanisms and clinical diagnosis of ventricular diseases. We present a novel approach for 3D motion modeling and analysis of LV wall in cardiac magnetic resonance imaging (MRI). First, a fully convolutional network (FCN) is deployed to initialize myocardium contours in 2D MR slices. Then, we propose an image registration algorithm to align MR slices in space and minimize the undesirable motion artifacts from inconsistent respiration. Finally, a 3D deformable model is applied to recover the shape and motion of myocardium wall. Utilizing the proposed approach, we can visually analyze 3D LV wall motion, evaluate cardiac global function, and diagnose ventricular diseases.

  15. The 3D Structure of the Proton

    NASA Astrophysics Data System (ADS)

    Kaiser, Ralf

    2012-09-01

    When Rutherford, Geiger and Marsden discovered the atomic nucleus in 1909 in Manchester, they at the same time also laid the foundations for the most successful method to study the structure of nuclei and nucleons. They found a point-like scattering centre inside the atom and identified it with the atomic nucleus and the theoretical description of this process has been known as Rutherford scattering ever since. The deviation between the theoretical description for a point-like scattering centre and experimental data has since been used to reveal information about the structure of the nucleus as well as the nucleon. There has been a continuous development from Hofstadters experiments in the 1950s, over the SLAC experiments in the 60s and 70s to the the HERA experiments at DESY and the experimental programme at Jeffersonlab. In this paper I am presenting the most recent results in Deeply Virtual Compton Scattering from the Hermes experiment at DESY, taken with a high density unpolarised target and a recoil detector in 2006/7.

  16. Acetylcholinesterase: From 3D Structure to Function

    PubMed Central

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

    2010-01-01

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

  17. 3D visualization of middle ear structures

    NASA Astrophysics Data System (ADS)

    Vogel, Uwe; Schmitt, Thomas

    1998-06-01

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

  18. Direct 3D Printing of Catalytically Active Structures

    DOE PAGES

    Manzano, J. Sebastian; Weinstein, Zachary B.; Sadow, Aaron D.; ...

    2017-09-22

    3D printing of materials with active functional groups can provide custom-designed structures that promote chemical conversions. Catalytically active architectures were produced by photopolymerizing bifunctional molecules using a commercial stereolithographic 3D printer. Functionalities in the monomers included a polymerizable vinyl group to assemble the 3D structures and a secondary group to provide them with active sites. The 3D-printed architectures containing accessible carboxylic acid, amine, and copper carboxylate functionalities were catalytically active for the Mannich, aldol, and Huisgen cycloaddition reactions, respectively. The functional groups in the 3D-printed structures were also amenable to post-printing chemical modification. And as proof of principle, chemically activemore » cuvette adaptors were 3D printed and used to measure in situ the kinetics of a heterogeneously catalyzed Mannich reaction in a conventional solution spectrophotometer. In addition, 3D-printed millifluidic devices with catalytically active copper carboxylate complexes were used to promote azide-alkyne cycloaddition under flow conditions. The importance of controlling the 3D architecture of the millifluidic devices was evidenced by enhancing reaction conversion upon increasing the complexity of the 3D prints.« less

  19. 3D Animations for Exploring Nucleon Structure

    NASA Astrophysics Data System (ADS)

    Gorman, Waverly; Burkardt, Matthias

    2016-09-01

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

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

    PubMed

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

    2015-08-05

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

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

    NASA Astrophysics Data System (ADS)

    Zhao, Hailong; Dong, Ye; Zhou, Haijing; Zou, Wenkang; Wang, Qiang

    2016-10-01

    Cubic region (34cm × 34cm × 18cm) including the double post-hole convolute (DPHC) structure was chosen to perform a series of fully 3D PIC simulations using NEPTUNE3D codes, massive data ( 200GB) could be acquired and solved in less than 5 hours. Cold-chamber tests were performed during which only cathode electron emission was considered without temperature rise or ion emission, current loss efficiency was estimated by comparisons between output magnetic field profiles with or without electron emission. PIC simulation results showed three stages of current transforming process with election emission in DPHC structure, the maximum ( 20%) current loss was 437kA at 15ns, while only 0.46% 0.48% was lost when driving current reached its peak. DPHC structure proved valuable functions during energy transform process in PTS facility, and NEPTUNE3D provided tools to explore this sophisticated physics. Project supported by the National Natural Science Foundation of China, Grant No. 11571293, 11505172.

  2. 3-D Radiative Transfer Modeling of Structured Winds in Massive Hot Stars with Wind3D

    NASA Astrophysics Data System (ADS)

    Lobel, A.; Toalá, J. A.; Blomme, R.

    2011-01-01

    We develop 3-D models of the structured winds of massive hot stars with the Wind3D radiative transfer (RT) code. We investigate the physical properties of large-scale structures observed in the wind of the B-type supergiant HD 64760 with detailed line profile fits to Discrete Absorption Components (DACs) and rotational modulations observed with IUE in Si IV λ1395. We develop parameterized input models for Wind3D with large-scale equatorial wind density- and velocity-structures, or so-called `Co-rotating Interaction Regions' (CIRs) and `Rotational Modulation Regions' (RMRs). The parameterized models offer important advantages for high-performance RT calculations over ab-initio hydrodynamic input models. The acceleration of the input model calculations permits us to simulate and investigate a wide variety of physical conditions in the extended winds of massive hot stars. The new modeling method is very flexible for constraining the dynamic and geometric wind properties of RMRs in HD 64760. We compute that the modulations are produced by a regular pattern of radial density enhancements that protrude almost linearly into the equatorial wind. We find that the modulations are caused by narrow `spoke-like' wind regions. We present a hydrodynamic model showing that the linearly shaped radial wind pattern can be caused by mechanical wave action at the base of the stellar wind from the blue supergiant.

  3. 3D nanomolding and fluid mixing in micromixers with micro-patterned microchannel walls.

    PubMed

    Farshchian, Bahador; Amirsadeghi, Alborz; Choi, Junseo; Park, Daniel S; Kim, Namwon; Park, Sunggook

    2017-01-01

    Microfluidic devices where the microchannel walls were decorated with micro and nanostructures were fabricated using 3D nanomolding. Using 3D molded microfluidic devices with microchannel walls decorated with microscale gratings, the fluid mixing behavior was investigated through experiments and numerical simulation. The use of microscale gratings in the micromixer was predicated by the fact that large obstacles in a microchannel enhances the mixing performance. Slanted ratchet gratings on the channel walls resulted in a helical flow along the microchannel, thus increasing the interfacial area between fluids and cutting down the diffusion length. Increasing the number of walls decorated with continuous ratchet gratings intensified the strength of the helical flow, enhancing mixing further. When ratchet gratings on the surface of the top cover plate were aligned in a direction to break the continuity of gratings from the other three walls, a stack of two helical flows was formed one above each other. This work concludes that the 3D nanomolding process can be a cost-effective tool for scaling-up the fabrication of microfluidic mixers with improved mixing efficiencies.Graphical abstractIn this paper we show that a micromixer with patterned walls can be fabricated using 3D nanomolding and solvent-assisted bonding to manipulate the flow patterns to improve mixing.

  4. Assessment of dry-stone terrace wall degradation with a 3D approach

    NASA Astrophysics Data System (ADS)

    Djuma, Hakan; Camera, Corrado; Faka, Marina; Bruggeman, Adriana; Hermon, Sorin

    2016-04-01

    In the Mediterranean basin, terracing is a common element of agricultural lands. Terraces retained by dry-stone walls are used to conserve arable soil, delay erosion processes and retain rainfall runoff. Currently, agricultural land abandonment is widespread in the Mediterranean region leading to terrace wall failure due to lack of maintenance and consequently an increase in soil erosion. The objective of this study is to test the applicability of digital 3D documentation on mountainous agricultural areas for assessing changes in terrace wall geometry, including terrace wall failures and associated soil erosion. The study area is located at 800-1100 m above sea level, in the Ophiolite complex of the Troodos Mountains in Cyprus. Average annual precipitation is 750 mm. Two sites with dry-stone terraces were selected for this study. The first site had a sequence of three terrace walls that were surveyed. The uppermost terrace wall was collapsed at several locations; the middle at few locations; and the lowest was still intact. Three fieldwork campaigns were conducted at this site: during the dry season (initial conditions), the middle and end of the wet season. The second site had one terrace wall that was almost completely collapsed. This terrace was restored during a communal terrace rehabilitation event. Two fieldwork campaigns were conducted for this terrace: before and after the terrace wall restoration. Terrace walls were documented with a set of digital images, and transformed into a 3D point cloud (using web-based services and commercial software - Autodesk 123D catch and Menci Software uMap, respectively). A set of points, registered with the total station and geo-referenced with a GPS, enabled the scaling of the 3D model and aligning the terrace walls within the same reference system. The density (distance between each point) of the reconstructed point clouds is 0.005 m by Umap and 0.025 m by 123D Catch. On the first site, the model analysis identified wall

  5. Evaluation of 3D multi-contrast joint intra- and extracranial vessel wall cardiovascular magnetic resonance.

    PubMed

    Zhou, Zechen; Li, Rui; Zhao, Xihai; He, Le; Wang, Xiaole; Wang, Jinnan; Balu, Niranjan; Yuan, Chun

    2015-05-27

    Multi-contrast vessel wall cardiovascular magnetic resonance (CMR) has demonstrated its capability for atherosclerotic plaque morphology measurement and component characterization in different vasculatures. However, limited coverage and partial volume effect with conventional two-dimensional (2D) techniques might cause lesion underestimation. The aim of this work is to evaluate the performance in a) blood suppression and b) vessel wall delineation of three-dimensional (3D) multi-contrast joint intra- and extracranial vessel wall imaging at 3T. Three multi-contrast 3D black blood (BB) sequences with T1, T2 and heavy T1 weighting and a custom designed 36-channel neurovascular coil covering the entire intra- and extracranial vasculature have been used and investigated in this study. Two healthy subjects were recruited for sequence parameter optimization and twenty-five patients were consecutively scanned for image quality and blood suppression assessment. Qualitative image scores of vessel wall delineation as well as quantitative Signal-to-Noise Ratio (SNR) and Contrast-to-Noise Ratio (CNR) were evaluated at five typical locations ranging from common carotid arteries to middle cerebral arteries. The 3D multi-contrast images acquired within 15mins allowed the vessel wall visualization with 0.8 mm isotropic spatial resolution covering intra- and extracranial segments. Quantitative wall and lumen SNR measurements for each sequence showed effective blood suppression at all selected locations (P < 0.0001). Although the wall-lumen CNR varied across measured locations, each sequence provided good or adequate image quality in both intra- and extracranial segments. The proposed 3D multi-contrast vessel wall technique provides isotropic resolution and time efficient solution for joint intra- and extracranial vessel wall CMR.

  6. 3-D visualization of geologic structures and processes

    NASA Astrophysics Data System (ADS)

    Pflug, R.; Klein, H.; Ramshorn, Ch.; Genter, M.; Stärk, A.

    Interactive 3-D computer graphics techniques are used to visualize geologic structures and simulated geologic processes. Geometric models that serve as input to 3-D viewing programs are generated from contour maps, from serial sections, or directly from simulation program output. Choice of viewing parameters strongly affects the perception of irregular surfaces. An interactive 3-D rendering program and its graphical user interface provide visualization tools for structural geology, seismic interpretation, and visual post-processing of simulations. Dynamic display of transient ground-water simulations and sedimentary process simulations can visualize processes developing through time.

  7. Spectral Triangulation: a 3D Method for Locating Single-Walled Carbon Nanotubes in vivo

    PubMed Central

    Lin, Ching-Wei; Bachilo, Sergei M.; Vu, Michael; Beckingham, Kathleen M.; Weisman, R. Bruce

    2016-01-01

    Nanomaterials with luminescence in the short-wave infrared (SWIR) region are of special interest for biological research and medical diagnostics because of favorable tissue transparency and low autofluorescence backgrounds in that region. Single-walled carbon nanotubes (SWCNTs) show well-known sharp SWIR spectral signatures and therefore have the potential for noninvasive detection and imaging of cancer tumours, when linked to selective targeting agents such as antibodies. However, such applications face the challenge of sensitively detecting and localizing the source of SWIR emission from inside tissues. A new method, called spectral triangulation, is presented for three dimensional (3D) localization using sparse optical measurements made at the specimen surface. Structurally unsorted SWCNT samples emitting over a range of wavelengths are excited inside tissue phantoms by an LED matrix. The resulting SWIR emission is sampled at points on the surface by a scanning fibre optic probe leading to an InGaAs spectrometer or a spectrally filtered InGaAs avalanche photodiode detector. Because of water absorption, attenuation of the SWCNT fluorescence in tissues is strongly wavelength-dependent. We therefore gauge the SWCNT-probe distance by analysing differential changes in the measured SWCNT emission spectra. SWCNT fluorescence can be clearly detected through at least 20 mm of tissue phantom, and the 3D locations of embedded SWCNT test samples are found with sub-millimeter accuracy at depths up to 10 mm. Our method can also distinguish and locate two embedded SWCNT sources at distinct positions. PMID:27140495

  8. Spectral triangulation: a 3D method for locating single-walled carbon nanotubes in vivo.

    PubMed

    Lin, Ching-Wei; Bachilo, Sergei M; Vu, Michael; Beckingham, Kathleen M; Bruce Weisman, R

    2016-05-21

    Nanomaterials with luminescence in the short-wave infrared (SWIR) region are of special interest for biological research and medical diagnostics because of favorable tissue transparency and low autofluorescence backgrounds in that region. Single-walled carbon nanotubes (SWCNTs) show well-known sharp SWIR spectral signatures and therefore have potential for noninvasive detection and imaging of cancer tumours, when linked to selective targeting agents such as antibodies. However, such applications face the challenge of sensitively detecting and localizing the source of SWIR emission from inside tissues. A new method, called spectral triangulation, is presented for three dimensional (3D) localization using sparse optical measurements made at the specimen surface. Structurally unsorted SWCNT samples emitting over a range of wavelengths are excited inside tissue phantoms by an LED matrix. The resulting SWIR emission is sampled at points on the surface by a scanning fibre optic probe leading to an InGaAs spectrometer or a spectrally filtered InGaAs avalanche photodiode detector. Because of water absorption, attenuation of the SWCNT fluorescence in tissues is strongly wavelength-dependent. We therefore gauge the SWCNT-probe distance by analysing differential changes in the measured SWCNT emission spectra. SWCNT fluorescence can be clearly detected through at least 20 mm of tissue phantom, and the 3D locations of embedded SWCNT test samples are found with sub-millimeter accuracy at depths up to 10 mm. Our method can also distinguish and locate two embedded SWCNT sources at distinct positions.

  9. Finding Organized Structures in 3-D LADAR Data

    DTIC Science & Technology

    2004-12-01

    work exists also on how to extract planar and linear objects from scattered 3-D point clouds , see for example [5], [6]. Methods were even proposed to...of structure detection and segmentation from 3-D point clouds collected from a single sensor location or integrated from multiple locations. In [2...primitives to point clouds are difficult to use practically for large data sets containing multiple complex structures, in opposition to multiple planar

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

    PubMed

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

    2017-01-01

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

  11. Direct-Write 3D Nanoprinting of Plasmonic Structures.

    PubMed

    Winkler, Robert; Schmidt, Franz-Philipp; Haselmann, Ulrich; Fowlkes, Jason D; Lewis, Brett B; Kothleitner, Gerald; Rack, Philip D; Plank, Harald

    2017-03-08

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. While several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. In this study, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. By that, complex 3D nanostructures composed of highly compact, pure gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.

  12. Direct-Write 3D Nanoprinting of Plasmonic Structures

    SciTech Connect

    Winkler, Robert; Schmidt, Franz-Philipp; Haselmann, Ulrich; Fowlkes, Jason D.; Lewis, Brett B.; Kothleitner, Gerald; Rack, Philip D.; Plank, Harald

    2016-11-23

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. And while several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. Here, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. Furthermore, by that, complex 3D nanostructures composed of highly compact, pure gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.

  13. Direct-Write 3D Nanoprinting of Plasmonic Structures

    DOE PAGES

    Winkler, Robert; Schmidt, Franz-Philipp; Karl-Franzens Univ.; ...

    2016-11-23

    During the past decade, significant progress has been made in the field of resonant optics ranging from fundamental aspects to concrete applications. And while several techniques have been introduced for the fabrication of highly defined metallic nanostructures, the synthesis of complex, free-standing three-dimensional (3D) structures is still an intriguing, but so far intractable, challenge. Here, we demonstrate a 3D direct-write synthesis approach that addresses this challenge. Specifically, we succeeded in the direct-write fabrication of 3D nanoarchitectures via electron-stimulated reactions, which are applicable on virtually any material and surface morphology. Furthermore, by that, complex 3D nanostructures composed of highly compact, puremore » gold can be fabricated, which reveal strong plasmonic activity and pave the way for a new generation of 3D nanoplasmonic architectures that can be printed on-demand.« less

  14. 3D-Fun: predicting enzyme function from structure.

    PubMed

    von Grotthuss, Marcin; Plewczynski, Dariusz; Vriend, Gert; Rychlewski, Leszek

    2008-07-01

    The 'omics' revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be annotated with a putative function by comparing them with proteins of known function. This form of annotation is typically performed with BLAST or similar software. Structural genomics is nowadays also bringing us three dimensional structures of proteins with unknown function. We present here software that can be used when sequence comparisons fail to determine the function of a protein with known structure but unknown function. The software, called 3D-Fun, is implemented as a server that runs at several European institutes and is freely available for everybody at all these sites. The 3D-Fun servers accept protein coordinates in the standard PDB format and compare them with all known protein structures by 3D structural superposition using the 3D-Hit software. If structural hits are found with proteins with known function, these are listed together with their function and some vital comparison statistics. This is conceptually very similar in 3D to what BLAST does in 1D. Additionally, the superposition results are displayed using interactive graphics facilities. Currently, the 3D-Fun system only predicts enzyme function but an expanded version with Gene Ontology predictions will be available soon. The server can be accessed at http://3dfun.bioinfo.pl/ or at http://3dfun.cmbi.ru.nl/.

  15. Complex crustal structures: their 3D grav/mag modelling and 3D printing

    NASA Astrophysics Data System (ADS)

    Götze, Hans-Jürgen; Schmidt, Sabine; Menzel, Peter

    2017-04-01

    Our new techniques for modelling and visualization are user-friendly because they are highly interactive, ideally real-time and topology conserving and can be used for both flat and spherical models in 3D. These are important requirements for joint inversion for gravity and magnetic modelling of fields and their derivatives, constrained by seismic and structural input from independent data sources. A borehole tool for magnetic and gravity modelling will also be introduced. We are already close to satisfying the demand of treating several geophysical methods in a single model for subsurface evaluation purposes and aim now for fulfilling most of the constraints: consistency of modelling results and measurements and geological plausibility as well. For 3D modelling, polyhedrons built by triangles are used. All elements of the gravity and magnetic tensors can be included. In the modelling interface, after geometry changes the effect on the model is quickly updated because only the changed triangles have to be recalculated. Because of the triangular model structure, our approach can handle complex structures very well and flexible (e.g. overhangs of salt domes or plumes). For regional models, the use of spherical geometries and calculations is necessary and available. 3D visualization is performed with a 3D-printer (Ultimaker 2) and gives new insights into even rather complicated Earth subsurface structures. Inversion can either be run over the whole model, but typically it is used in smaller parts of the model, helping to solve local problems and/or proving/disproving local hypotheses. The basic principles behind this interactive approach are high performance optimized algorithms (CMA-ES: Covariance-matrix-adoption-evolution-strategy). The efficiency of the algorithm is rather good in terms of stable convergence due to topological model validity. Potential field modelling is always influenced by edge effects. To avoid this, a simple but very robust method has been

  16. Formal representation of 3D structural geological models

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed

    Earley, Clarke W

    2013-11-18

    While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user's computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/.

  18. Dynamic Characteristics of a Model and Prototype for 3D-RC Structure

    NASA Astrophysics Data System (ADS)

    Moniuddin, Md. Khaja; Vasanthalakshmi, G.; Chethan, K.; Babu, R. Ramesh

    2016-06-01

    Infill walls provide durable and economical partitions that have relatively excellent thermal and sound insulation with high fire resistance. Monolithic infilled walls are provided within RC structures without being analyzed as a combination of concrete and brick elements, although in reality they act as a single unit during earthquakes. The performance of such structures during earthquakes has proved to be superior in comparison to bare frames in terms of stiffness, strength and energy dissipation. To know the dynamic characteristics of monolithic infill wall panels and masonry infill, modal, response spectrum and time history analyses have been carried out on a model and prototype of a 3D RC structure for a comparative study.

  19. Toward mobile 3D visualization for structural biologists.

    PubMed

    Tanramluk, Duangrudee; Akavipat, Ruj; Charoensawan, Varodom

    2013-12-01

    Technological advances in crystallography have led to the ever-rapidly increasing number of biomolecular structures deposited in public repertoires. This undoubtedly shifts the bottleneck of structural biology research from obtaining high-quality structures to data analysis and interpretation. The recently available glasses-free autostereoscopic laptop offers an unprecedented opportunity to visualize and study 3D structures using a much more affordable, and for the first time, portable device. Together with a gamepad re-programmed for 3D structure controlling, we describe how the gaming technologies can deliver the output 3D images for high-quality viewing, comparable to that of a passive stereoscopic system, and can give the user more control and flexibility than the conventional controlling setup using only a mouse and a keyboard.

  20. 3D nanomolding and fluid mixing in micromixers with micro-patterned microchannel walls

    NASA Astrophysics Data System (ADS)

    Farshchian, Bahador; Amirsadeghi, Alborz; Choi, Junseo; Park, Daniel S.; Kim, Namwon; Park, Sunggook

    2017-03-01

    Microfluidic devices where the microchannel walls were decorated with micro and nanostructures were fabricated using 3D nanomolding. Using 3D molded microfluidic devices with microchannel walls decorated with microscale gratings, the fluid mixing behavior was investigated through experiments and numerical simulation. The use of microscale gratings in the micromixer was predicated by the fact that large obstacles in a microchannel enhances the mixing performance. Slanted ratchet gratings on the channel walls resulted in a helical flow along the microchannel, thus increasing the interfacial area between fluids and cutting down the diffusion length. Increasing the number of walls decorated with continuous ratchet gratings intensified the strength of the helical flow, enhancing mixing further. When ratchet gratings on the surface of the top cover plate were aligned in a direction to break the continuity of gratings from the other three walls, a stack of two helical flows was formed one above each other. This work concludes that the 3D nanomolding process can be a cost-effective tool for scaling-up the fabrication of microfluidic mixers with improved mixing efficiencies.[Figure not available: see fulltext.

  1. Preparation of 3D electrode microarrays of multi-walled carbon nanotubes/nafion nanocomposites for microfluidic biofuel cells.

    PubMed

    Choi, Jin Ho; Kim, Young Ho; Choi, Sung Deuk; Kim, Gyu Man

    2014-12-01

    Three-dimensional (3D) electrode microarrays with multi-walled carbon nanotubes (MWCNTs) reinforced Nafion nanocomposites were prepared for microfluidic biofuel cells. The oxidized MWCNTs (ox-MWCNTs) were prepared using chemical reactions with 60% nitric acid solution with pristine MWCNTs at 120 degrees C for 12 hrs with a nitrogen gas flow environment. Ox-MWCNTs in the range of 1 to 20 wt.% based on the Nafion polymer weight were reinforced to Nafion nanocomposites by solution casting. The micro-porous structure of the ox-MWCNTs reinforced Nafion nanocomposites was prepared by plasma etching for 5 to 20 min. The 10 wt.% ox-MWCNTs reinforced Nafion nanocomposite produced stable micro-porous structures of 3D electrodes by 10 min plasma etching. Micro-scale 3D structures of MWCNTs reinforced Nafion nanocomposites in a diameter range of 47 to 300 μm were prepared by the micro-stencil assisted casting. To characterize the 3D electrode microarrays, the physical geometry and the reinforced MWCNT dispersion in the nanocomposite structure were examined using a scanning electron microscope (SEM) and an optical microscope. Thermal property measurements of the ox-MWCNTs reinforced Nafion nanocomposites with 10 min of plasma etching, and without plasma etching were made. Both showed stable thermal properties over 300 degrees C. The proposed 3D electrode microarray of MWCNT/Nafion nanocomposites with micro-porous structures can be applied to miniaturized fuel cell devices.

  2. Culturing and applications of rotating wall vessel bioreactor derived 3D epithelial cell models.

    PubMed

    Radtke, Andrea L; Herbst-Kralovetz, Melissa M

    2012-04-03

    Cells and tissues in the body experience environmental conditions that influence their architecture, intercellular communications, and overall functions. For in vitro cell culture models to accurately mimic the tissue of interest, the growth environment of the culture is a critical aspect to consider. Commonly used conventional cell culture systems propagate epithelial cells on flat two-dimensional (2-D) impermeable surfaces. Although much has been learned from conventional cell culture systems, many findings are not reproducible in human clinical trials or tissue explants, potentially as a result of the lack of a physiologically relevant microenvironment. Here, we describe a culture system that overcomes many of the culture condition boundaries of 2-D cell cultures, by using the innovative rotating wall vessel (RWV) bioreactor technology. We and others have shown that organotypic RWV-derived models can recapitulate structure, function, and authentic human responses to external stimuli similarly to human explant tissues (1-6). The RWV bioreactor is a suspension culture system that allows for the growth of epithelial cells under low physiological fluid shear conditions. The bioreactors come in two different formats, a high-aspect rotating vessel (HARV) or a slow-turning lateral vessel (STLV), in which they differ by their aeration source. Epithelial cells are added to the bioreactor of choice in combination with porous, collagen-coated microcarrier beads (Figure 1A). The cells utilize the beads as a growth scaffold during the constant free fall in the bioreactor (Figure 1B). The microenvironment provided by the bioreactor allows the cells to form three-dimensional (3-D) aggregates displaying in vivo-like characteristics often not observed under standard 2-D culture conditions (Figure 1D). These characteristics include tight junctions, mucus production, apical/basal orientation, in vivo protein localization, and additional epithelial cell-type specific properties

  3. 3D annotation and manipulation of medical anatomical structures

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

  4. 3D visualization of sheath folds in Ancient Roman marble wall coverings from Ephesos, Turkey

    NASA Astrophysics Data System (ADS)

    Wex, Sebastian; Passchier, Cees W.; de Kemp, Eric A.; İlhan, Sinan

    2014-10-01

    Archaeological excavations and restoration of a palatial Roman housing complex in Ephesos, Turkey yielded 40 wall-decorating plates of folded mylonitic marble (Cipollino verde), derived from the internal Hellenides near Karystos, Greece. Cipollino verde was commonly used for decoration purposes in Roman buildings. The plates were serial-sectioned from a single quarried block of 1,25 m3 and provided a research opportunity for detailed reconstruction of the 3D geometry of meterscale folds in mylonitized marble. A GOCAD model is used to visualize the internal fold structures of the marble, comprising curtain folds and multilayered sheath folds. The sheath folds are unusual in that they have their intermediate axis normal to the parent layering. This agrees with regional tectonic studies, which suggest that Cipollino verde structures formed by local constrictional non-coaxial flow. Sheath fold cross-section geometry, exposed on the surface of a plate or outcrop, is found to be independent of the intersection angle of the fold structure with the studied plane. Consequently, a single surface cannot be used as an indicator of the three-dimensional geometry of transected sheath folds.

  5. Reconstruction of 3D structures from protein contact maps.

    PubMed

    Vassura, Marco; Margara, Luciano; Di Lena, Pietro; Medri, Filippo; Fariselli, Piero; Casadio, Rita

    2008-01-01

    The prediction of the protein tertiary structure from solely its residue sequence (the so called Protein Folding Problem) is one of the most challenging problems in Structural Bioinformatics. We focus on the protein residue contact map. When this map is assigned it is possible to reconstruct the 3D structure of the protein backbone. The general problem of recovering a set of 3D coordinates consistent with some given contact map is known as a unit-disk-graph realization problem and it has been recently proven to be NP-Hard. In this paper we describe a heuristic method (COMAR) that is able to reconstruct with an unprecedented rate (3-15 seconds) a 3D model that exactly matches the target contact map of a protein. Working with a non-redundant set of 1760 proteins, we find that the scoring efficiency of finding a 3D model very close to the protein native structure depends on the threshold value adopted to compute the protein residue contact map. Contact maps whose threshold values range from 10 to 18 Angstroms allow reconstructing 3D models that are very similar to the proteins native structure.

  6. 3D Ultrasonic Wave Simulations for Structural Health Monitoring

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  7. Proposed traceable structural resolution protocols for 3D imaging systems

    NASA Astrophysics Data System (ADS)

    MacKinnon, David; Beraldin, J.-Angelo; Cournoyer, Luc; Carrier, Benjamin; Blais, François

    2009-08-01

    A protocol for determining structural resolution using a potentially-traceable reference material is proposed. Where possible, terminology was selected to conform to those published in ISO JCGM 200:2008 (VIM) and ASTM E 2544-08 documents. The concepts of resolvability and edge width are introduced to more completely describe the ability of an optical non-contact 3D imaging system to resolve small features. A distinction is made between 3D range cameras, that obtain spatial data from the total field of view at once, and 3D range scanners, that accumulate spatial data for the total field of view over time. The protocol is presented through the evaluation of a 3D laser line range scanner.

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

    PubMed Central

    2013-01-01

    Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

  9. 3D WHOLE-PROMINENCE FINE STRUCTURE MODELING

    SciTech Connect

    Gunár, Stanislav; Mackay, Duncan H.

    2015-04-20

    We present the first 3D whole-prominence fine structure model. The model combines a 3D magnetic field configuration of an entire prominence obtained from nonlinear force-free field simulations, with a detailed description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Through the use of a novel radiative transfer visualization technique for the Hα line such plasma-loaded magnetic field model produces synthetic images of the modeled prominence comparable with high-resolution observations. This allows us for the first time to use a single technique to consistently study, in both emission on the limb and absorption against the solar disk, the fine structures of prominences/filaments produced by a magnetic field model.

  10. Spectral triangulation: a 3D method for locating single-walled carbon nanotubes in vivo

    NASA Astrophysics Data System (ADS)

    Lin, Ching-Wei; Bachilo, Sergei M.; Vu, Michael; Beckingham, Kathleen M.; Bruce Weisman, R.

    2016-05-01

    Nanomaterials with luminescence in the short-wave infrared (SWIR) region are of special interest for biological research and medical diagnostics because of favorable tissue transparency and low autofluorescence backgrounds in that region. Single-walled carbon nanotubes (SWCNTs) show well-known sharp SWIR spectral signatures and therefore have potential for noninvasive detection and imaging of cancer tumours, when linked to selective targeting agents such as antibodies. However, such applications face the challenge of sensitively detecting and localizing the source of SWIR emission from inside tissues. A new method, called spectral triangulation, is presented for three dimensional (3D) localization using sparse optical measurements made at the specimen surface. Structurally unsorted SWCNT samples emitting over a range of wavelengths are excited inside tissue phantoms by an LED matrix. The resulting SWIR emission is sampled at points on the surface by a scanning fibre optic probe leading to an InGaAs spectrometer or a spectrally filtered InGaAs avalanche photodiode detector. Because of water absorption, attenuation of the SWCNT fluorescence in tissues is strongly wavelength-dependent. We therefore gauge the SWCNT-probe distance by analysing differential changes in the measured SWCNT emission spectra. SWCNT fluorescence can be clearly detected through at least 20 mm of tissue phantom, and the 3D locations of embedded SWCNT test samples are found with sub-millimeter accuracy at depths up to 10 mm. Our method can also distinguish and locate two embedded SWCNT sources at distinct positions.Nanomaterials with luminescence in the short-wave infrared (SWIR) region are of special interest for biological research and medical diagnostics because of favorable tissue transparency and low autofluorescence backgrounds in that region. Single-walled carbon nanotubes (SWCNTs) show well-known sharp SWIR spectral signatures and therefore have potential for noninvasive detection and

  11. The 3D Structure of Some Diarrheal Causing Bacterial Toxins

    DTIC Science & Technology

    1991-07-01

    AD-A242 202 AD THE 3D STRUCTURE OF SOME DIARRHEAL CAUSING BACTERIAL TOXINS ANNUAL REPORT MARTIN SAX JULY 1, 1991 Supported by U.S. ARMY MEDICAL...21702-5012 162787A 162787A8714] AA tDA313380 11. TITLE (Include SeCUrit Clauftcatton) The 3D Structure of Some Diarrheal Causing Bacterial Toxins 12...speculative. 4 RBPRRlINCZB . 1. Marrack, P. T Kappler, J. Science 24.8, 705-711 (1990). 2. Spero et al. In Bacterial Toxins , VI 4, Ed. C Hardegree and A

  12. Automated 3D structure composition for large RNAs.

    PubMed

    Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W

    2012-08-01

    Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.

  13. Automated 3D structure composition for large RNAs

    PubMed Central

    Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J.; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W.

    2012-01-01

    Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues. PMID:22539264

  14. Designing 3D Structure by 5-7 Kirigami

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  15. Coherent structures in 3D viscous time-periodic flow

    NASA Astrophysics Data System (ADS)

    Znaien, J. G.; Speetjens, M. F. M.; Trieling, R. R.; Clercx, H. J. H.

    2010-11-01

    Periodically driven laminar flows occur in many industrial processes from food-mixing devices to micro-mixer in lab-on-a-chip systems. The present study is motivated by better understanding fundamental transport phenomena in three-dimensional viscous time-periodic flows. Both numerical simulation and three-dimensional Particle Tracking Velocimetry measurements are performed to investigate the 3D advection of a passive scalar in a lid-driven cylindrical cavity flow. The flow is forced by a time-periodic in-plane motion of one endwall via a given forcing protocol. We concentrate on the formation and interaction of coherent structures due to fluid inertia, which play an important role in 3D mixing by geometrically determining the tracer transport. The disintegration of these structures by fluid inertia reflects an essentially 3D route to chaos. Data from tracking experiments of small particles will be compared with predictions from numerical simulations on transport of passive tracers.

  16. Prospective 3D Investigation of Bleb Wall after Trabeculectomy Using Anterior-Segment OCT.

    PubMed

    Watanabe-Kitamura, Fumika; Inoue, Toshihiro; Kojima, Sachi; Nakashima, Kei-Ichi; Fukushima, Ayako; Tanihara, Hidenobu

    2017-01-01

    We used three-dimensional anterior-segment optical coherence tomography (3D AS-OCT) to evaluate time-dependent posttrabeculectomy changes in bleb wall volume and intensity. This prospective observational study included patients with open-angle glaucoma who underwent fornix-based trabeculectomy between January 2012 and October 2012. Twenty-nine eyes met inclusion criteria, and the bleb walls of 22 were amenable to three-dimensional analysis by 3D AS-OCT for 1 year after surgery. The high-intensity volume ratio was calculated as the proportion of the high-intensity region in the total bleb wall. Changes in the high-intensity volume ratio were of high intensity, and parameters influencing the ratio were analyzed using 3D AS-OCT. The mean high-intensity volume ratios (±SDs) were 43.5 ± 21.4, 44.1 ± 14.8, 41.5 ± 22.6, and 43.2 ± 19.7% at 0.5, 3, 6, and 12 months after trabeculectomy, respectively. When the volume ratios obtained 0.5 and 12 months posttrabeculectomy were compared, four and five eyes exhibited decreases and increases of over 20%, respectively. The volume ratios at 12 months correlated with the intraocular pressure (IOP) at that time (t = 2.44, P = 0.024) and the bleb wall vascularity score at 12 months (t = 5.44, P < 0.001). The high-intensity bleb wall at 12 months posttrabeculectomy reflected the IOP and the bleb wall vascularity at that time.

  17. 3D printing of nano- and micro-structures

    NASA Astrophysics Data System (ADS)

    Ramasamy, Mouli; Varadan, Vijay K.

    2016-04-01

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

  18. 3D mapping of airway wall thickening in asthma with MSCT: a level set approach

    NASA Astrophysics Data System (ADS)

    Fetita, Catalin; Brillet, Pierre-Yves; Hartley, Ruth; Grenier, Philippe A.; Brightling, Christopher

    2014-03-01

    Assessing the airway wall thickness in multi slice computed tomography (MSCT) as image marker for airway disease phenotyping such asthma and COPD is a current trend and challenge for the scientific community working in lung imaging. This paper addresses the same problem from a different point of view: considering the expected wall thickness-to-lumen-radius ratio for a normal subject as known and constant throughout the whole airway tree, the aim is to build up a 3D map of airway wall regions of larger thickness and to define an overall score able to highlight a pathological status. In this respect, the local dimension (caliber) of the previously segmented airway lumen is obtained on each point by exploiting the granulometry morphological operator. A level set function is defined based on this caliber information and on the expected wall thickness ratio, which allows obtaining a good estimate of the airway wall throughout all segmented lumen generations. Next, the vascular (or mediastinal dense tissue) contact regions are automatically detected and excluded from analysis. For the remaining airway wall border points, the real wall thickness is estimated based on the tissue density analysis in the airway radial direction; thick wall points are highlighted on a 3D representation of the airways and several quantification scores are defined. The proposed approach is fully automatic and was evaluated (proof of concept) on a patient selection coming from different databases including mild, severe asthmatics and normal cases. This preliminary evaluation confirms the discriminative power of the proposed approach regarding different phenotypes and is currently extending to larger cohorts.

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

    PubMed Central

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

    2013-01-01

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

  20. Orbital Wall Reconstruction with Two-Piece Puzzle 3D Printed Implants: Technical Note

    PubMed Central

    Mommaerts, Maurice Y.; Büttner, Michael; Vercruysse, Herman; Wauters, Lauri; Beerens, Maikel

    2015-01-01

    The purpose of this article is to describe a technique for secondary reconstruction of traumatic orbital wall defects using titanium implants that act as three-dimensional (3D) puzzle pieces. We present three cases of large defect reconstruction using implants produced by Xilloc Medical B.V. (Maastricht, the Netherlands) with a 3D printer manufactured by LayerWise (3D Systems; Heverlee, Belgium), and designed using the biomedical engineering software programs ProPlan and 3-Matic (Materialise, Heverlee, Belgium). The smaller size of the implants allowed sequential implantation for the reconstruction of extensive two-wall defects via a limited transconjunctival incision. The precise fit of the implants with regard to the surrounding ledges and each other was confirmed by intraoperative 3D imaging (Mobile C-arm Systems B.V. Pulsera, Philips Medical Systems, Eindhoven, the Netherlands). The patients showed near-complete restoration of orbital volume and ocular motility. However, challenges remain, including traumatic fat atrophy and fibrosis. PMID:26889349

  1. 3D genome structure modeling by Lorentzian objective function.

    PubMed

    Trieu, Tuan; Cheng, Jianlin

    2017-02-17

    The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data. Our method was robust to noise and performed well in comparison with a panel of existing methods on a controlled simulated data set. On a real Hi-C data set of the human genome, our method produced chromosome and genome structures that are consistent with 3D FISH data and known knowledge about the human chromosome and genome, such as, chromosome territories and the cluster of small chromosomes in the nucleus center with the exception of the chromosome 18. The tool and experimental data are available at https://missouri.box.com/v/LorDG.

  2. 3D genome structure modeling by Lorentzian objective function.

    PubMed

    Trieu, Tuan; Cheng, Jianlin

    2016-11-29

    The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data. Our method was robust to noise and performed well in comparison with a panel of existing methods on a controlled simulated data set. On a real Hi-C data set of the human genome, our method produced chromosome and genome structures that are consistent with 3D FISH data and known knowledge about the human chromosome and genome, such as, chromosome territories and the cluster of small chromosomes in the nucleus center with the exception of the chromosome 18. The tool and experimental data are available at https://missouri.box.com/v/LorDG.

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

    PubMed

    Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M

    2016-07-01

    Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.

  4. Correlations of Surface Deformation and 3D Flow Field in a Compliant Wall Turbulent Channel Flow.

    NASA Astrophysics Data System (ADS)

    Wang, Jin; Zhang, Cao; Katz, Joseph

    2015-11-01

    This study focuses on the correlations between surface deformation and flow features, including velocity, vorticity and pressure, in a turbulent channel flow over a flat, compliant Polydimethylsiloxane (PDMS) wall. The channel centerline velocity is 2.5 m/s, and the friction Reynolds number is 2.3x103. Analysis is based on simultaneous measurements of the time resolved 3D velocity and surface deformation using tomographic PIV and Mach-Zehnder Interferometry. The volumetric pressure distribution is calculated plane by plane by spatially integrating the material acceleration using virtual boundary, omni-directional method. Conditional sampling based on local high/low pressure and deformation events reveals the primary flow structures causing the deformation. High pressure peaks appear at the interface between sweep and ejection, whereas the negative deformations peaks (dent) appear upstream, under the sweeps. The persistent phase lag between flow and deformations are presumably caused by internal damping within the PDMS. Some of the low pressure peaks and strong ejections are located under the head of hairpin vortices, and accordingly, are associated with positive deformation (bump). Others bumps and dents are correlated with some spanwise offset large inclined quasi-streamwise vortices that are not necessarily associated with hairpins. Sponsored by ONR.

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

    NASA Astrophysics Data System (ADS)

    Clausen, Anders; Andreassen, Erik; Sigmund, Ole

    2017-08-01

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

  6. RNA and protein 3D structure modeling: similarities and differences.

    PubMed

    Rother, Kristian; Rother, Magdalena; Boniecki, Michał; Puton, Tomasz; Bujnicki, Janusz M

    2011-09-01

    In analogy to proteins, the function of RNA depends on its structure and dynamics, which are encoded in the linear sequence. While there are numerous methods for computational prediction of protein 3D structure from sequence, there have been very few such methods for RNA. This review discusses template-based and template-free approaches for macromolecular structure prediction, with special emphasis on comparison between the already tried-and-tested methods for protein structure modeling and the very recently developed "protein-like" modeling methods for RNA. We highlight analogies between many successful methods for modeling of these two types of biological macromolecules and argue that RNA 3D structure can be modeled using "protein-like" methodology. We also highlight the areas where the differences between RNA and proteins require the development of RNA-specific solutions.

  7. Strain measurement of 3D structured nanodevices by EBSD.

    PubMed

    Osborn, William; Friedman, Lawrence H; Vaudin, Mark

    2017-08-29

    We present a new methodology to accurately measure strain magnitudes from 3D nanodevices using Electron Backscatter Diffraction (EBSD). Because the dimensions of features on these devices are smaller than the interaction volume for backscattered electrons, EBSD patterns from 3D nanodevices will frequently be the superposition of patterns from multiple material regions simultaneously. The effect of this superposition on EBSD strain measurement is demonstrated, along with an approach to separate EBSD patterns from these devices via subtraction. The subtraction procedure is applied to 33 nm wide SiGe lines, and it provides accurate strain magnitudes where the traditional EBSD strain analysis method undervalues the strain magnitude by an order of magnitude. The approach provides a strain measurement technique for nanoscale 3D structures that is high spatial resolution, nondestructive, and accurate. Published by Elsevier B.V.

  8. Strategies to reconstruct 3D Coffea arabica L. plant structure.

    PubMed

    Matsunaga, Fabio Takeshi; Tosti, Jonas Barbosa; Androcioli-Filho, Armando; Brancher, Jacques Duílio; Costes, Evelyne; Rakocevic, Miroslava

    2016-01-01

    Accurate model of structural elements is necessary to model the foliage and fruit distributions in cultivated plants, both of them being key parameters for yield prediction. However, the level of details in architectural data collection could vary, simplifying the data collection when plants get older and because of the high time cost required. In the present study, we aimed at reconstructing and analyzing plant structure, berry distributions and yield in Coffea arabica (Arabica coffee), by using both detailed or partial morphological information and probabilistic functions. Different datasets of coffee plant architectures were available with different levels of detail depending on the tree age. Three scales of decomposition-plant, axes and metamers were used reconstruct the plant architectures. CoffePlant3D, a software which integrates a series of mathematical, computational and statistical methods organized in three newly developed modules, AmostraCafe3D, VirtualCafe3D and Cafe3D, was developed to accurately reconstruct coffee plants in 3D, whatever the level of details available. The number of metamers of the 2nd order axes was shown to be linearly proportional to that of the orthotropic trunk, and the number of berries per metamer was modeled as a Gaussian function within a specific zone along the plagiotropic axes. This ratio of metamer emission rhythm between the orthotropic trunk and plagiotropic axes represents the pillar of botanical events in the C. arabica development and was central in our modeling approach, especially to reconstruct missing data. The methodology proposed for reconstructing coffee plants under the CoffePlant3D was satisfactorily validated across dataset available and could be performed for any other Arabica coffee variety.

  9. 3-D structure and dynamics of microtubule self-organization

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Ou-Yang, H. Daniel

    2008-03-01

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

  10. 3D digitising using structured illumination: application to mould redesign

    NASA Astrophysics Data System (ADS)

    Granero, L.; Sánchez, J.; Micó, V.; Esteve, J. J.; Hervás, J.; Simón, S.; Pérez, E.

    2007-06-01

    Conventional techniques applied to three dimensional (3D) acquisition of information has significant limitations depending on the features of the piece under test. Thus, complex curvatures, deeper concavities and higher volumes are some examples of critical factors in which contact digitising systems are not suitable to undertake such kind of task. In these cases, the usage of optical 3D digitization systems implies a more appropriate way to obtain 3D information about the sample. In particular, structured illumination by means of white light provides point-to-point object acquisition with accuracy and resolution that are always below the manufactured tolerances. Moreover, when the object under test is too large, structured illumination can be mixed with photogrammetrical techniques in order to avoid errors by means of the delimitation of the overall working volume. This proceeding presents several real cases applied to mould industry in which 3D shape measurement using white light structured illumination is combined with finite element method (FEM) and laser cladding techniques to allow the repair of the mould.

  11. Instability and Wave Propagation in Structured 3D Composites

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    PubMed Central

    van Dijk, Marc; Bonvin, Alexandre M. J. J.

    2009-01-01

    There is a growing interest in structural studies of DNA by both experimental and computational approaches. Often, 3D-structural models of DNA are required, for instance, to serve as templates for homology modeling, as starting structures for macro-molecular docking or as scaffold for NMR structure calculations. The conformational adaptability of DNA when binding to a protein is often an important factor and at the same time a limitation in such studies. As a response to the demand for 3D-structural models reflecting the intrinsic plasticity of DNA we present the 3D-DART server (3DNA-Driven DNA Analysis and Rebuilding Tool). The server provides an easy interface to a powerful collection of tools for the generation of DNA-structural models in custom conformations. The computational engine beyond the server makes use of the 3DNA software suite together with a collection of home-written python scripts. The server is freely available at http://haddock.chem.uu.nl/dna without any login requirement. PMID:19417072

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

    PubMed

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

    2015-07-29

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

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

    PubMed Central

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

    2015-01-01

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

  15. 3D-wall motion tracking: a new tool for myocardial contractility analysis.

    PubMed

    Perez de Isla, Leopoldo; Montes, Cesar; Monzón, Tania; Herrero, José; Saltijeral, Adriana; Balcones, David Vivas; de Agustin, Alberto; Nuñez-Gil, Ivan; Fernández-Golfín, Covadonga; Almería, Carlos; Rodrigo, José Luis; Marcos-Alberca, Pedro; Macaya, Carlos; Zamorano, Jose

    2010-10-16

    BACKGROUND: Left-ventricular ejection fraction (LVEF), the most frequently used parameter to evaluate left ventricular (LV) systolic function, depends not only on LV contractility, but also on different variables such as pre-load and after-load. Three-dimensional wall motion tracking echocardiography (3D-WMT) is a new technique that provides information regarding different new parameters of LV systolic function. Our aim was to evaluate whether the new 3D-WMT-derived LV systolic function parameters are less dependent on load conditions than LVEF. METHODS: In order to modify the load conditions to study the dependence of the different LV systolic function parameters on them, a group of renal failure patients under chronic hemodialysis treatment was selected. The echocardiographic studies, including the 3D-WMT analysis, were performed immediately before and immediately after the hemodialysis session. RESULTS: Thirty-one consecutive patients were enrolled (mean age 65.5 ± 17.0 years; 74.2% men). There was a statistically significant change in predialysis and postdialysis, pre-load and after-load conditions (E/È ratio and systolic blood pressure) and in the LV end-diastolic volume and LVEF. Nevertheless, the findings did not show any significant change before and after dialysis in the 3D-WMT-derived parameters. CONCLUSIONS: LV 3D-wall motion tracking-derived systolic function parameters are less dependent on load conditions than LVEF. They might measure myocardial contractility in a more direct way than LVEF. Thus, hypothetically, they might be useful to detect early and subtle contractility impairments in a wide number of cardiac patients and they could help to optimize the clinical management of such patients.

  16. Tracking variable number of multiple subcellular structures in 3D.

    PubMed

    Wen, Quan; Gao, Jean

    2009-01-01

    With the introduction of sensitive and fast electronic imaging devices and the development of biological methods to tag proteins of interest by green fluorescent proteins (GFP), it has now become critical to develop automatic quantitative data analysis tools to study the live cell dynamics at subcellular level. In this paper, a sequential Monte Carlo (SMC) method to track variable number of multiple 3D subcellular structures is proposed. First, multiple subcellular structures are represented by a joint state. Then the distribution of the dimension changing joint state is sampled efficiently by the reverse jump Markov chain Monte Carlo (RJMCMC) method designed with update move, identity switch move, disappearing move, and appearing move. The experimental results show that the proposed method can successfully track multiple 3D subcellular structures with different motion modalities such as object appearing and disappearing.

  17. Distributed snow and rock temperature modelling in steep rock walls using Alpine3D

    NASA Astrophysics Data System (ADS)

    Haberkorn, Anna; Wever, Nander; Hoelzle, Martin; Phillips, Marcia; Kenner, Robert; Bavay, Mathias; Lehning, Michael

    2017-02-01

    In this study we modelled the influence of the spatially and temporally heterogeneous snow cover on the surface energy balance and thus on rock temperatures in two rugged, steep rock walls on the Gemsstock ridge in the central Swiss Alps. The heterogeneous snow depth distribution in the rock walls was introduced to the distributed, process-based energy balance model Alpine3D with a precipitation scaling method based on snow depth data measured by terrestrial laser scanning. The influence of the snow cover on rock temperatures was investigated by comparing a snow-covered model scenario (precipitation input provided by precipitation scaling) with a snow-free (zero precipitation input) one. Model uncertainties are discussed and evaluated at both the point and spatial scales against 22 near-surface rock temperature measurements and high-resolution snow depth data from winter terrestrial laser scans.In the rough rock walls, the heterogeneously distributed snow cover was moderately well reproduced by Alpine3D with mean absolute errors ranging between 0.31 and 0.81 m. However, snow cover duration was reproduced well and, consequently, near-surface rock temperatures were modelled convincingly. Uncertainties in rock temperature modelling were found to be around 1.6 °C. Errors in snow cover modelling and hence in rock temperature simulations are explained by inadequate snow settlement due to linear precipitation scaling, missing lateral heat fluxes in the rock, and by errors caused by interpolation of shortwave radiation, wind and air temperature into the rock walls.Mean annual near-surface rock temperature increases were both measured and modelled in the steep rock walls as a consequence of a thick, long-lasting snow cover. Rock temperatures were 1.3-2.5 °C higher in the shaded and sunny rock walls, while comparing snow-covered to snow-free simulations. This helps to assess the potential error made in ground temperature modelling when neglecting snow in steep bedrock.

  18. 3D printed components with ultrasonically arranged microscale structure

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  19. 3D endoscopic imaging using structured illumination technique (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Le, Hanh N. D.; Nguyen, Hieu; Wang, Zhaoyang; Kang, Jin U.

    2017-02-01

    Surgeons have been increasingly relying on minimally invasive surgical guidance techniques not only to reduce surgical trauma but also to achieve accurate and objective surgical risk evaluations. A typical minimally invasive surgical guidance system provides visual assistance in two-dimensional anatomy and pathology of internal organ within a limited field of view. In this work, we propose and implement a structure illumination endoscope to provide a simple, inexpensive 3D endoscopic imaging to conduct high resolution 3D imagery for use in surgical guidance system. The system is calibrated and validated for quantitative depth measurement in both calibrated target and human subject. The system exhibits a depth of field of 20 mm, depth resolution of 0.2mm and a relative accuracy of 0.1%. The demonstrated setup affirms the feasibility of using the structured illumination endoscope for depth quantization and assisting medical diagnostic assessments

  20. 3D Nanoporous Anodic Alumina Structures for Sustained Drug Release.

    PubMed

    Porta-I-Batalla, Maria; Xifré-Pérez, Elisabet; Eckstein, Chris; Ferré-Borrull, Josep; Marsal, Lluis F

    2017-08-21

    The use of nanoporous anodic alumina (NAA) for the development of drug delivery systems has gained much attention in recent years. The release of drugs loaded inside NAA pores is complex and depends on the morphology of the pores. In this study, NAA, with different three-dimensional (3D) pore structures (cylindrical pores with several pore diameters, multilayered nanofunnels, and multilayered inverted funnels) were fabricated, and their respective drug delivery rates were studied and modeled using doxorubicin as a model drug. The obtained results reveal optimal modeling of all 3D pore structures, differentiating two drug release stages. Thus, an initial short-term and a sustained long-term release were successfully modeled by the Higuchi and the Korsmeyer-Peppas equations, respectively. This study demonstrates the influence of pore geometries on drug release rates, and further presents a sustained long-term drug release that exceeds 60 days without an undesired initial burst.

  1. 3D Nanoporous Anodic Alumina Structures for Sustained Drug Release

    PubMed Central

    Xifré-Pérez, Elisabet; Eckstein, Chris; Ferré-Borrull, Josep

    2017-01-01

    The use of nanoporous anodic alumina (NAA) for the development of drug delivery systems has gained much attention in recent years. The release of drugs loaded inside NAA pores is complex and depends on the morphology of the pores. In this study, NAA, with different three-dimensional (3D) pore structures (cylindrical pores with several pore diameters, multilayered nanofunnels, and multilayered inverted funnels) were fabricated, and their respective drug delivery rates were studied and modeled using doxorubicin as a model drug. The obtained results reveal optimal modeling of all 3D pore structures, differentiating two drug release stages. Thus, an initial short-term and a sustained long-term release were successfully modeled by the Higuchi and the Korsmeyer–Peppas equations, respectively. This study demonstrates the influence of pore geometries on drug release rates, and further presents a sustained long-term drug release that exceeds 60 days without an undesired initial burst. PMID:28825654

  2. Capabilities of wind tunnels with two-adaptive walls to minimize boundary interference in 3-D model testing

    NASA Technical Reports Server (NTRS)

    Rebstock, Rainer; Lee, Edwin E., Jr.

    1989-01-01

    An initial wind tunnel test was made to validate a new wall adaptation method for 3-D models in test sections with two adaptive walls. First part of the adaptation strategy is an on-line assessment of wall interference at the model position. The wall induced blockage was very small at all test conditions. Lift interference occurred at higher angles of attack with the walls set aerodynamically straight. The adaptation of the top and bottom tunnel walls is aimed at achieving a correctable flow condition. The blockage was virtually zero throughout the wing planform after the wall adjustment. The lift curve measured with the walls adapted agreed very well with interference free data for Mach 0.7, regardless of the vertical position of the wing in the test section. The 2-D wall adaptation can significantly improve the correctability of 3-D model data. Nevertheless, residual spanwise variations of wall interference are inevitable.

  3. Advancements in 3D Structural Analysis of Geothermal Systems

    SciTech Connect

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

    2013-06-23

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

  4. Seismic modeling of Earth's 3D structure: Recent advancements

    NASA Astrophysics Data System (ADS)

    Ritsema, J.

    2008-12-01

    Global models of Earth's seismic structure continue to improve due to the growth of seismic data sets, implementation of advanced wave propagations theories, and increased computational power. In my presentation, I will summarize seismic tomography results from the past 5-10 years. I will compare the most recent P and S velocity models, discuss model resolution and model interpretation, and present an, admittedly biased, list of research directions required to develop the next generation 3D models.

  5. The 3D Structure of Some Diarrheal Causing Bacterial Toxins

    DTIC Science & Technology

    1992-07-23

    of intoxication resulting from food poisoning by •. anreus and for elucidating stereochemical details in the mechanism of superantigencity. The method ...of approach was to use classical methods of protein crystallography to determine the 3D structures of the SEs. Our strategy consisted of solving the...successful. At this stage purification by chromatofocusing was tried. The IEF gel clearly showed two or three bands which we were able to separate

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  7. 3D reconstruction methods of coronal structures by radio observations

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  8. Cancer3D: understanding cancer mutations through protein structures.

    PubMed

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

    2015-01-01

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

  9. Indoor imagery with a 3D through-wall synthetic aperture radar

    NASA Astrophysics Data System (ADS)

    Sévigny, Pascale; DiFilippo, David J.; Laneve, Tony; Fournier, Jonathan

    2012-06-01

    Through-wall radar imaging is an emerging technology with great interest to military and police forces operating in an urban environment. A through-wall imaging radar can potentially provide interior room layouts as well as detection and localization of targets of interest within a building. In this paper, we present our through-wall radar system mounted on the side of a vehicle and driven along a path in front of a building of interest. The vehicle is equipped with a LIDAR (Light Detection and Ranging) and motion sensors that provide auxiliary information. The radar uses an ultra wideband frequency-modulated continuous wave (FMCW) waveform to obtain high range resolution. Our system is composed of a vertical linear receive array to discriminate targets in elevation, and two transmit elements operated in a slow multiple-input multiple output (MIMO) configuration to increase the achievable elevation resolution. High resolution in the along-track direction is obtained through synthetic aperture radar (SAR) techniques. We present experimental results that demonstrate the 3-D capability of the radar. We further demonstrate target detection behind challenging walls, and imagery of internal wall features. Finally, we discuss future work.

  10. Isotropic 3D Black Blood MRI of Abdominal Aortic Aneurysm Wall and Intraluminal Thrombus

    PubMed Central

    Zhu, Chengcheng; Haraldsson, Henrik; Faraji, Farshid; Owens, Christopher; Gasper, Warren; Ahn, Sinyeob; Liu, Jing; Laub, Gerhard; Hope, Michael D.; Saloner, David

    2015-01-01

    Introduction The aortic wall and intraluminal thrombus (ILT) have been increasingly studied as potential markers of progressive disease with abdominal aortic aneurysms (AAAs). Our goal was to develop a high resolution, 3D black blood MR technique for AAA wall and ILT imaging within a clinically acceptable scan time. Methods Twenty two patients with AAAs (maximal diameter 4.3±1.0cm), along with five healthy volunteers, were imaged at 3T with a 3D T1-weighted fast-spin-echo sequence using variable flip angle trains (SPACE) with a preparation pulse (DANTE) for suppressing blood signal. Volunteers and ten patients were also scanned with SPACE alone for comparison purposes. The signal to noise ratio (SNR) and the aortic wall/ILT to lumen contrast to noise ratio (CNR) were measured. Qualitative image scores (1–4 scale) assessing the inner lumen and outer wall boundaries of AAA were performed by two blinded reviewers. In patients with ILT, the ratio of ILT signal intensity (ILTSI) over psoas muscle SI (MuscleSI) was calculated, and the signal heterogeneity of ILT was quantified as standard deviation (SD) over the mean. Results All subjects were imaged successfully with an average scan time of 7.8±0.7 minutes. The DANTE preparation pulse for blood suppression substantially reduced flow artifacts in SPACE with lower lumen SNR (8.8 vs. 21.4, p<0.001) and improved the wall/ILT to lumen CNR (9.9 vs. 6.3, p<0.001) in patients. Qualitative assessment showed improved visualization of lumen boundaries (73% higher scores on average, p=0.01) and comparable visualization of outer wall boundary (p>0.05). ILT was present in ten patients, with relatively high signal and a wide SD (average ILTSI/MuscleSI 1.42±0.48 (range 0.75–2.11) ) and with SD/mean of 27.7%±6.6% (range 19.6% – 39.4%). Conclusion High resolution, 3D black blood MRI of AAAs can be achieved in a clinical accepted scan time with reduction of flow artifacts using the DANTE preparation pulse. Signal characteristics

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

    PubMed

    Chen, Jinxiang; Tuo, Wanyong; Guo, Zhensheng; Yan, Lili

    2017-02-01

    The present paper renewedly expounds upon the characteristics of the 3D lightweight structure of beetle forewings and notes that two biomimetic structures (models) that have appeared in recent years do not comply with these characteristics based on a comparison of the structures of the biological prototypes. The first model features transverse tubules based on observations of circular holes in cross-sectional figures of the Cybister forewing. The second is a biomimetic spherical cavity model with hollow trabeculae that reportedly exhibits superior mechanical properties because its structures are most similar to the biological prototype. Finally, a false biomimetic proposition that the mechanical properties of biomimetic structures with "fiber winding" patterns are superior to those of structures constructed of pure "epoxy" is also noted. Hopefully, the present study can serve to improve the state of research on biomimetic applications of beetle forewing structures.

  12. Prognostic value of Tissue Transition Projection 3D transparent wall CT reconstructions in bowel ischemia.

    PubMed

    Moschetta, Marco; Scardapane, Arnaldo; Telegrafo, Michele; Lucarelli, Nicola Maria; Lorusso, Valentina; Angelelli, Giuseppe; Stabile Ianora, Amato Antonio

    2016-10-01

    Multi-detector computed tomography (MDCT) represents the gold standard in patients with acute abdomen syndrome and suspected bowel ischemia. It provides a correct diagnosis and contributes to appropriate treatment planning. This study aims to evaluate the role of 3D Tissue Transition Projection (TTP) transparent wall CT reconstruction for detecting the degree of bowel dilatation and to correlate this finding with the aetiology and prognosis in patients affected by mesenteric infarction. Forty-seven patients affected by bowel infarction due to vascular obstruction (arterial in 66% of cases, venous in 34%) were assessed by MDCT examination searching for the degree of bowel dilatation (subdivided into 4 groups: entire small bowel (SB); ≥50% of SB; < 50% of SB; large bowel only). Two blinded radiologists evaluated TTP 3D transparent wall and multi-planar reconstructions. Chi square test was used to correlate CT findings with the disease course and the mortality rate. Cohen's kappa statistics was used in order to assess inter-observer agreement. The overall mortality rate was 64%, with a 90% value for arterial forms and 10% in case of venous infarctions. The entire SB (n = 10) or a ≥50% SB dilatation (n = 16) correlated with poor prognosis in all cases (p < 0.05); a <50% SB dilatation (n = 16) correlated with good prognosis in 87.5% of cases (p < 0.05). A large bowel only dilatation (n = 5) did not show a significant prognostic value (p = 0.13). Almost perfect agreement between the two readers was found (k = 0.84). MDCT offers different reconstruction software for diagnosing bowel ischemia. 3D TTP transparent wall reconstructions represent a rapid and automatic tool for identifying loop dilatation, which significantly correlates with an arterial aetiology and poor prognosis. Copyright © 2016. Published by Elsevier Ltd.

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

    PubMed

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

    2014-09-23

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

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

    PubMed Central

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

    2008-01-01

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

  15. Manufacturing of a 3D complex hyperstable Cesic structure

    NASA Astrophysics Data System (ADS)

    Kroedel, Matthias; Courteau, Pascal; Poupinet, Anne; Sarri, Giuseppe

    2007-09-01

    Global astrometry requires extremely stable materials for instrument structures, such as optical benches. Cesic®, developed by ECM and Thales Alenia Space for mirrors and high stability structures, offers an excellent compromise in terms of structural strength, stability and very high lightweight capability, with a coefficient of thermal expansion that is virtually zero at cryogenic T°. The High-Stability Optical Bench (HSOB) GAIA study, realized by Thales Alenia Space under ESA contract, aimed to design, develop and test a full-scale representative of the HSOB bench, made entirely of Cesic®. The bench has been equipped with SAGEIS-CSO laser metrology system MOUSE1, a Michelson interferometer composed of integrated optics with nm-resolution. The HSOB bench has been submitted to a homogeneous T° step under vacuum to characterize 3-D expansion behavior of its two arms. The quite negligible interarm differential, measured with a nm-range reproducibility, demonstrates that a complete 3-D structure made of Cesic® has the same CTE homogeneity as do characterization samples, fully in line with the stringent GAIA requirements (1ppm at 120K). This demonstrates that Cesic® properties at cryogenic temperatures are fully appropriate to the manufacturing of complex highly stable optical structures. This successful study confirms ECM's and Thales Alenia Space's ability to design and manufacture monolithic lightweight highly stable optical structures, based on inner-cell triangular design made possible by the unique Cesic® manufacturing process.

  16. 3-D Flyby of Hurricane Edouard Sees Double Eye-Wall

    NASA Image and Video Library

    On Sept. 17 at 03:39 UTC, the TRMM satellite saw a newer outer eyewall forming around Edouard's original eyewall creating a double eye-wall structure. Red indicates heavy rainfall. Credit: NASA/SSA...

  17. Automatic structural matching of 3D image data

    NASA Astrophysics Data System (ADS)

    Ponomarev, Svjatoslav; Lutsiv, Vadim; Malyshev, Igor

    2015-10-01

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

  18. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

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

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

    PubMed

    Schmalz, Christoph; Forster, Frank; Schick, Anton; Angelopoulou, Elli

    2012-07-01

    We present a new endoscopic 3D scanning system based on Single Shot Structured Light. The proposed design makes it possible to build an extremely small scanner. The sensor head contains a catadioptric camera and a pattern projection unit. The paper describes the working principle and calibration procedure of the sensor. The prototype sensor head has a diameter of only 3.6mm and a length of 14mm. It is mounted on a flexible shaft. The scanner is designed for tubular cavities and has a cylindrical working volume of about 30mm length and 30mm diameter. It acquires 3D video at 30 frames per second and typically generates approximately 5000 3D points per frame. By design, the resolution varies over the working volume, but is generally better than 200μm. A prototype scanner has been built and is evaluated in experiments with phantoms and biological samples. The recorded average error on a known test object was 92μm.

  20. 3-D Attenuation Structure around the SAFOD site, Parkfield, California

    NASA Astrophysics Data System (ADS)

    Harrington, N. L.; Thurber, C. H.; Zhang, H.; Roecker, S.

    2006-12-01

    We are developing models of the 3-D attenuation structure, both Qp and Qs, for a region about 15 km square centered on SAFOD. We are analyzing local earthquake data collected in 2001 and 2002 from the UW/RPI PASO array, the UC-Berkeley HRSN, and USGS seismic network stations around Parkfield. We determine the P- or S-wave t* values for an individual local earthquake for each of the observing stations by fitting observed spectra using a joint inversion for a common corner frequency, low-frequency amplitude, and t*. Within our initial data set, we examine 575 events recorded at up to 111 stations and obtain over 19000 P- wave t* values. We use these t* values in simul2000 and tomoDD to perform the inversion to obtain a 3-D, frequency-independent Qp model of the attenuation structure, using an existing 3-D Vp model and associated event locations. We will use this same procedure to obtain the Qs structure. In our preliminary Qp structure results, we observe a high Qp feature (about 250) at 0-8 km depth on the southwest side of the fault. We associate this feature with the high density, high velocity Salinian basement rocks. We also see a moderate Qp feature (about 150) in the fault zone that encompasses the hypocenters of our events. On the northeast side of the fault, we observe Qp values generally increasing with depth, from 125 at the surface to 200 at 8 km. We will present our final Qp and Qs models, identify major features within the two, and discuss how these features relate to the findings of other geophysical studies in the area (seismic velocity, electrical resistivity, anisotropy). We will discuss how these features relate to the nature of the crust in that area, including the local geology, presence of fluids, fracturing, etc.

  1. Holographic measurement of wall stress distribution and 3D flow over a surface textured by microfibers

    NASA Astrophysics Data System (ADS)

    Bocanegra, Humberto; Gorumlu, Seder; Aksak, Burak; Castillo, Luciano; Sheng, Jian

    2015-11-01

    Understanding how fluid flow interacts with micro-textured surfaces is crucial for a broad range of key biological processes and engineering applications including particle dispersion, pathogenic infections, and drag manipulation by surface topology. Existing methods, such as μPIV, suffers from low spatial resolution and fail to track tracer particle motion very close to a rough surface and within roughness elements. In this paper, we present a technique that combines high speed digital holographic microscopy (DHM) with a correlation based de-noising algorithm to overcome the optical interference generated by surface roughness and to capture a large number of 3D particle trajectories. It allows us to obtain a 3D velocity field with an uncertainty of 0.01% and 2D wall shear stress distribution at the resolution of ~ 65 μPa. Applying the technique to a microfluidics with a surface textured by microfibers, we find that the flow is three-dimensional and complex. While the microfibers affect the velocity flow field locally, their presence is felt globally in terms of wall shear stresses. The study of effect of microfiber patterns and flow characteristics on skin frictions are ongoing and will be reported.

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

    NASA Astrophysics Data System (ADS)

    Singh, Suryabhan; Bhim, Anupam

    2016-12-01

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

  3. Gene3D: modelling protein structure, function and evolution.

    PubMed

    Yeats, Corin; Maibaum, Michael; Marsden, Russell; Dibley, Mark; Lee, David; Addou, Sarah; Orengo, Christine A

    2006-01-01

    The Gene3D release 4 database and web portal (http://cathwww.biochem.ucl.ac.uk:8080/Gene3D) provide a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository for manually deduced protein domains. Amongst the changes from the last publication are: the addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG and GO, and protein-protein interaction data from MINT and BIND. The website has been rebuilt to allow more sophisticated querying and the data returned is presented in a clearer format with greater functionality. Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers.

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

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

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

  5. Microchip-Based Electrochemical Detection using a 3-D Printed Wall-Jet Electrode Device

    PubMed Central

    Munshi, Akash S.; Martin, R. Scott

    2016-01-01

    Three dimensional (3-D) printing technology has evolved dramatically in the last few years, offering the capability of printing objects with a variety of materials. Printing microfluidic devices using this technology offers various advantages such as ease and uniformity of fabrication, file sharing between laboratories, and increased device-to-device reproducibility. One unique aspects of this technology, when used with electrochemical detection, is the ability to produce a microfluidic device as one unit while also allowing the reuse of the device and electrode for multiple analyses. Here we present an alternate electrode configuration for microfluidic devices, a wall-jet electrode (WJE) approach, created by 3-D printing. Using microchip-based flow injection analysis, we compared the WJE design with the conventionally used thin-layer electrode (TLE) design. It was found that the optimized WJE system enhances analytical performance (as compared to the TLE design), with improvements in sensitivity and the limit of detection. Experiments were conducted using two working electrodes – 500 μm platinum and 1 mm glassy carbon. Using the 500 μm platinum electrode the calibration sensitivity was 16 times higher for the WJE device (as compared to the TLE design). In addition, use of the 1 mm glassy carbon electrode led to limit of detection of 500 nM for catechol, as compared to 6 μM for the TLE device. Finally, to demonstrate the versatility and applicability of the 3-D printed WJE approach, the device was used as an inexpensive electrochemical detector for HPLC. The number of theoretical plates was comparable to the use of commercially available UV and MS detectors, with the WJE device being inexpensive to utilize. These results show that 3D-printing can be a powerful tool to fabricate reusable and integrated microfluidic detectors in configurations that are not easily achieved with more traditional lithographic methods. PMID:26649363

  6. Microchip-based electrochemical detection using a 3-D printed wall-jet electrode device.

    PubMed

    Munshi, Akash S; Martin, R Scott

    2016-02-07

    Three dimensional (3-D) printing technology has evolved dramatically in the last few years, offering the capability of printing objects with a variety of materials. Printing microfluidic devices using this technology offers various advantages such as ease and uniformity of fabrication, file sharing between laboratories, and increased device-to-device reproducibility. One unique aspect of this technology, when used with electrochemical detection, is the ability to produce a microfluidic device as one unit while also allowing the reuse of the device and electrode for multiple analyses. Here we present an alternate electrode configuration for microfluidic devices, a wall-jet electrode (WJE) approach, created by 3-D printing. Using microchip-based flow injection analysis, we compared the WJE design with the conventionally used thin-layer electrode (TLE) design. It was found that the optimized WJE system enhances analytical performance (as compared to the TLE design), with improvements in sensitivity and the limit of detection. Experiments were conducted using two working electrodes - 500 μm platinum and 1 mm glassy carbon. Using the 500 μm platinum electrode the calibration sensitivity was 16 times higher for the WJE device (as compared to the TLE design). In addition, use of the 1 mm glassy carbon electrode led to limit of detection of 500 nM for catechol, as compared to 6 μM for the TLE device. Finally, to demonstrate the versatility and applicability of the 3-D printed WJE approach, the device was used as an inexpensive electrochemical detector for HPLC. The number of theoretical plates was comparable to the use of commercially available UV and MS detectors, with the WJE device being inexpensive to utilize. These results show that 3-D-printing can be a powerful tool to fabricate reusable and integrated microfluidic detectors in configurations that are not easily achieved with more traditional lithographic methods.

  7. Direct Observation of Current-Induced Motion of a 3D Vortex Domain Wall in Cylindrical Nanowires.

    PubMed

    Ivanov, Yurii P; Chuvilin, Andrey; Lopatin, Sergei; Mohammed, Hanan; Kosel, Jurgen

    2017-05-24

    The current-induced dynamics of 3D magnetic vortex domain walls in cylindrical Co/Ni nanowires are revealed experimentally using Lorentz microscopy and theoretically using micromagnetic simulations. We demonstrate that a spin-polarized electric current can control the reversible motion of 3D vortex domain walls, which travel with a velocity of a few hundred meters per second. This finding is a key step in establishing fast, high-density memory devices based on vertical arrays of cylindrical magnetic nanowires.

  8. Protein 3D Structure Computed from Evolutionary Sequence Variation

    PubMed Central

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

    2011-01-01

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

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

    PubMed

    Marks, Debora S; Colwell, Lucy J; Sheridan, Robert; Hopf, Thomas A; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2011-01-01

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

  10. Modeling of flow and mixing in 3D rough-walled rock fracture intersections

    NASA Astrophysics Data System (ADS)

    Zou, Liangchao; Jing, Lanru; Cvetkovic, Vladimir

    2017-09-01

    The processes of fluid flow and solute transport through rock fractures are of primary importance in environmental engineering and geosciences. This study presented numerical modeling results of fluid flow and solute transport in a 3D rock fracture-matrix system with an orthogonal intersection of two rough-walled rock fractures. The rough-walled fracture geometry models were built from laser-scanned data of a real rock surface, for a realistic representation of natural rock fracture surface roughness. The fluid flow in the two intersected fractures and solute transport in the fracture-matrix system were simulated by solving the Navier-Stokes equations (NSE) and transport equation in the entire system. The dependence of mixing on Péclet number (Pe) and flow directionality features were analyzed. The results directly visualized important channeling flow patterns that significantly enhanced the solute mixing process at the rough-walled fracture intersection. The illustrated channeling flow and associated impacts on mixing are particularly important in the prediction of solute transport in natural fractured rocks, especially when discrete fracture network (DFN) approach is applied.

  11. Application Of Moldex3D For Thin-wall Injection Moulding Simulation

    NASA Astrophysics Data System (ADS)

    Šercer, Mladen; Godec, Damir; Bujanić, Božo

    2007-05-01

    The benefits associated with decreasing wall thicknesses below their current values are still measurable and desired even if the final wall thickness is nowhere near those of the aggressive portable electronics industry. It is important to note that gains in wall section reduction do not always occur without investment, in this case, in tooling and machinery upgrades. Equally important is the fact that productivity and performance benefits of reduced material usage, fast cycle times, and lighter weight can often outweigh most of the added costs. In order to eliminate unnecessary mould trials, minimize product development cycle, reduce overall costs and improve product quality, polymeric engineers use new CAE technology (Computer Aided Engineering). This technology is a simulation tool, which combines proven theories, material properties and process conditions to generate realistic simulations and produce valuable recommendations. Based on these recommendations, an optional combination of product design, material and process conditions can be identified. In this work, Moldex3D software was used for simulation of injection moulding in order to avoid potential moulding problems. The results gained from the simulation were used for the optimization of an existing product design, for mould development and for optimization of processing parameters, e.g. injection pressure, mould cavity temperature, etc.

  12. Joint segmentation of 3D femoral lumen and outer wall surfaces from MR images.

    PubMed

    Ukwatta, Eranga; Yuan, Jing; Qiu, Wu; Rajchl, Martin; Chiu, Bernard; Shavakh, Shadi; Xu, Jianrong; Fenster, Aaron

    2013-01-01

    We propose a novel algorithm to jointly delineate the femoral artery lumen and outer wall surfaces from 3D black-blood MR images, while enforcing the spatial consistency of the reoriented MR slices along the medial axis of the femoral artery. We demonstrate that the resulting optimization problem of the proposed segmentation can be solved globally and exactly by means of convex relaxation, for which we introduce a novel coupled continuous max-flow (CCOMF) model based on an Ishikawa-type flow configuration and show its duality to the studied convex relaxed optimization problem. Using the proposed CCMF model, the exactness and globalness of its dual convex relaxation problem is proven. Experiment results demonstrate that the proposed method yielded high accuracy (i.e. Dice similarity coefficient > 85%) for both the lumen and outer wall and high reproducibility (intra-class correlation coefficient of 0.95) for generating vessel wall area. The proposed method outperformed the previous method, in terms of computation time, by a factor of pproximately 20.

  13. Diagnosis and control of 3D elastic mechanical structures

    NASA Astrophysics Data System (ADS)

    Krajcin, Idriz; Soeffker, Dirk

    2005-05-01

    In this paper, a model-based approach for fault detection and vibration control of flexible structures is proposed and applied to 3D-structures. Faults like cracks or impacts acting on a flexible structure are considered as unknown inputs acting on the structure. The Proportional-Integral-Observer (PI-Observer) is used to estimate the system states as well as unknown inputs acting on a system. Also the effects of structural changes are understood as external effects (related to the unchanged structure) and are considered as fictitious external forces or moments. The paper deals with the design of the PI-Observer for practical applications when measurement noise and model uncertainties are present and shows its performance in experimental results. As examples, impacts acting upon a one side clamped elastic beam and on a thin plate structure are estimated using displacement or strain measurements. To control the vibration of the flexible plate, two piezoelectric patches bonded on the structure are used as actuators. The control algorithm introduced in this contribution contains a state feedback control and additionally a disturbance rejection. The disturbances are estimated using the PI-Observer. Experimental results show the performance and the robustness properties of the control strategy for the vibration control of a very thin plate.

  14. Four 3D "brick-wall"-like metal-organic frameworks with a flexible ligand of (S,S,R,R)-1,2,3,4-cyclopentanetetracarboxylic acid: crystal structures, luminescent and magnetic properties.

    PubMed

    Cui, Lin; Luan, Xin-Jun; Zhang, Cui-Ping; Kang, Yi-Fan; Zhang, Wen-Tao; Wang, Yao-Yu; Shi, Qi-Zhen

    2013-02-07

    To investigate the conformation of cyclopentanetetracarboxylic acid, four new "brick-wall"-like metal-organic frameworks have been synthesized from hydrothermal reactions with different metal salts, (S,S,R,R)-1,2,3,4-cyclopentanetetracarboxylic acid (H(4)cptc) and auxiliary N-donor ligands, namely, Cu(2)(S,S,R,R-cptc)(bpe)(H(2)O)(2)·2H(2)O (1), Co(2)(S,S,R,R-cptc)(bpe)(0.5)(H(2)O)(2)·2H(2)O (2), Cd(4)(S,S,R,R-cptc)(2)(bpa)(2)(H(2)O)(5)·2H(2)O (3) and Co(2)(S,S,R,R-cptc)(bpy)(0.5)(H(2)O)(2)·2(H(2)O) (4) (bpe = 4-(2-(pyridine-4-yl)vinyl)pyridine, bpa = 4-(2-(pyridine-4-yl)ethyl)pyridine, bpy = 4-(pyridine-4-yl)pyridine). The complexes were further characterized by single-crystal X-ray diffraction, power X-ray diffraction, FT-IR spectra, fluorescent measurements and variable-temperature magnetic susceptibility measurements. The results of the structural investigations show that 1 is a charming (3,3,4)-trinodal architecture, 3 is an interesting trinodal (3,4,5)-connected architecture, and 2 and 4 are isostructural, which are both (4,5)-connected networks. In addition, the magnetic measurements indicate that 2 and 4 show weak antiferromagnetic interactions, and the fluorescent measurement shows the strong solid-state fluorescent emission at room temperature for 3.

  15. Spatial Reasoning and 3D Graphics: A Study of GeoWall-Enhanced Astronomy Instruction

    NASA Astrophysics Data System (ADS)

    Turner, N. E.; Hegarty, M.; Martinez, L. E.

    2006-12-01

    One persistent difficulty many science students face is a lack of accurate, easily manipulated, 3-dimensional mental models of the systems they study. In Introductory Astronomy, students have difficulty conceptualizing the Sun-Earth-Moon system and the geometric relationships that cause the cycle of lunar phases. Advanced computer visualizations exist to alleviate these problems, but they are not equally effective for all students. One factor that might influence their effectiveness is students' existing levels of spatial ability. For example, external visualizations may act as prosthetics for students without well-developed visualization skills or they may favor students who already have highly developed spatial abilities. It is also unclear whether the use of such materials can in any way enhance a student's facility with the creation and manipulation of accurate mental models. We provide analysis of a study of spatial skills in Astronomy students and their relationship to learning about the Moon from a 3D GeoWall animation. We show which spatial skills prove relevant to phases and which students benefit the most from 3D-enhanced instruction.

  16. Band like Electronic Structures in Square Hollow Quantum Dots by 3D-MHFKS Calculation

    NASA Astrophysics Data System (ADS)

    Takizawa, Tokihiro; Okada, Hoshihito; Matsuse, Takehiro

    To find novel aspects of the electronic structures in quantum dots (QD) from a view point of spatial broken symmetry, 3-dimensional-mesh Hartree-Fock-Kohn-Sham (3D-MHFKS) calculations1 are applied to the interacting electron system of electron number N in a symmetry broken hollow QD. For the case of a square hollow quantum dot confined in square hard wall (HW) potential (SSHQD), the magnetic (B) field dependence of the obtained single particle energy levels and chemical potentials in B-N diagram are shown to have a band like electronic structures over the wide B-field range up to 20T. To clarify the origin of the band like electronic structures in SSHQD, 3D-MHFKS calculations are also applied for the mixed symmetry QD's with a circular hollow in square HW potential (SCHQD) and with a square hollow in circular HW potential (CSHQD).

  17. Computerized identification of airway wall in CT examinations using a 3D active surface evolution approach.

    PubMed

    Gu, Suicheng; Fuhrman, Carl; Meng, Xin; Siegfried, Jill M; Gur, David; Leader, Joseph K; Sciurba, Frank C; Pu, Jiantao

    2013-04-01

    Airway diseases (e.g., asthma, emphysema, and chronic bronchitis) are extremely common worldwide. Any morphological variations (abnormalities) of airways may physically change airflow and ultimately affect the ability of the lungs in gas exchange. In this study, we describe a novel algorithm aimed to automatically identify airway walls depicted on CT images. The underlying idea is to place a three-dimensional (3D) surface model within airway regions and thereafter allow this model to evolve (deform) under predefined external and internal forces automatically to the location where these forces reach a state of balance. By taking advantage of the geometric and the density characteristics of airway walls, the evolution procedure is performed in a distance gradient field and ultimately stops at regions with the highest contrast. The performance of this scheme was quantitatively evaluated from several perspectives. First, we assessed the accuracy of the developed scheme using a dedicated lung phantom in airway wall estimation and compared it with the traditional full-width at half maximum (FWHM) method. The phantom study shows that the developed scheme has an error ranging from 0.04 mm to 0.36 mm, which is much smaller than the FWHM method with an error ranging from 0.16 mm to 0.84 mm. Second, we compared the results obtained by the developed scheme with those manually delineated by an experienced (>30 years) radiologist on clinical chest CT examinations, showing a mean difference of 0.084 mm. In particular, the sensitivity of the scheme to different reconstruction kernels was evaluated on real chest CT examinations. For the 'lung', 'bone' and 'standard' kernels, the average airway wall thicknesses computed by the developed scheme were 1.302 mm, 1.333 mm and 1.339 mm, respectively. Our preliminary experiments showed that the scheme had a reasonable accuracy in airway wall estimation. For a clinical chest CT examination, it took around 4 min for this scheme to identify

  18. Superimposé: a 3D structural superposition server

    PubMed Central

    Bauer, Raphael A.; Bourne, Philip E.; Formella, Arno; Frömmel, Cornelius; Gille, Christoph; Goede, Andrean; Guerler, Aysam; Hoppe, Andreas; Knapp, Ernst-Walter; Pöschel, Thorsten; Wittig, Burghardt; Ziegler, Valentin; Preissner, Robert

    2008-01-01

    The Superimposé webserver performs structural similarity searches with a preference towards 3D structure-based methods. Similarities can be detected between small molecules (e.g. drugs), parts of large structures (e.g. binding sites of proteins) and entire proteins. For this purpose, a number of algorithms were implemented and various databases are provided. Superimposé assists the user regarding the selection of a suitable combination of algorithm and database. After the computation on our server infrastructure, a visual assessment of the results is provided. The structure-based in silico screening for similar drug-like compounds enables the detection of scaffold-hoppers with putatively similar effects. The possibility to find similar binding sites can be of special interest in the functional analysis of proteins. The search for structurally similar proteins allows the detection of similar folds with different backbone topology. The Superimposé server is available at: http://bioinformatics.charite.de/superimpose. PMID:18492720

  19. Validation of a Node-Centered Wall Function Model for the Unstructured Flow Code FUN3D

    NASA Technical Reports Server (NTRS)

    Carlson, Jan-Renee; Vasta, Veer N.; White, Jeffery

    2015-01-01

    In this paper, the implementation of two wall function models in the Reynolds averaged Navier-Stokes (RANS) computational uid dynamics (CFD) code FUN3D is described. FUN3D is a node centered method for solving the three-dimensional Navier-Stokes equations on unstructured computational grids. The first wall function model, based on the work of Knopp et al., is used in conjunction with the one-equation turbulence model of Spalart-Allmaras. The second wall function model, also based on the work of Knopp, is used in conjunction with the two-equation k-! turbulence model of Menter. The wall function models compute the wall momentum and energy flux, which are used to weakly enforce the wall velocity and pressure flux boundary conditions in the mean flow momentum and energy equations. These wall conditions are implemented in an implicit form where the contribution of the wall function model to the Jacobian are also included. The boundary conditions of the turbulence transport equations are enforced explicitly (strongly) on all solid boundaries. The use of the wall function models is demonstrated on four test cases: a at plate boundary layer, a subsonic di user, a 2D airfoil, and a 3D semi-span wing. Where possible, different near-wall viscous spacing tactics are examined. Iterative residual convergence was obtained in most cases. Solution results are compared with theoretical and experimental data for several variations of grid spacing. In general, very good comparisons with data were achieved.

  20. 3D GeoWall Analysis System for Shuttle External Tank Foreign Object Debris Events

    NASA Technical Reports Server (NTRS)

    Brown, Richard; Navard, Andrew; Spruce, Joseph

    2010-01-01

    An analytical, advanced imaging method has been developed for the initial monitoring and identification of foam debris and similar anomalies that occur post-launch in reference to the space shuttle s external tank (ET). Remote sensing technologies have been used to perform image enhancement and analysis on high-resolution, true-color images collected with the DCS 760 Kodak digital camera located in the right umbilical well of the space shuttle. Improvements to the camera, using filters, have added sharpness/definition to the image sets; however, image review/analysis of the ET has been limited by the fact that the images acquired by umbilical cameras during launch are two-dimensional, and are usually nonreferenceable between frames due to rotation translation of the ET as it falls away from the space shuttle. Use of stereo pairs of these images can enable strong visual indicators that can immediately portray depth perception of damaged areas or movement of fragments between frames is not perceivable in two-dimensional images. A stereoscopic image visualization system has been developed to allow 3D depth perception of stereo-aligned image pairs taken from in-flight umbilical and handheld digital shuttle cameras. This new system has been developed to augment and optimize existing 2D monitoring capabilities. Using this system, candidate sequential image pairs are identified for transformation into stereo viewing pairs. Image orientation is corrected using control points (similar points) between frames to place the two images in proper X-Y viewing perspective. The images are then imported into the WallView stereo viewing software package. The collected control points are used to generate a transformation equation that is used to re-project one image and effectively co-register it to the other image. The co-registered, oriented image pairs are imported into a WallView image set and are used as a 3D stereo analysis slide show. Multiple sequential image pairs can be used

  1. POISs3: A 3D poisson smoother of structured grids

    NASA Astrophysics Data System (ADS)

    Lehtimaeki, R.

    Flow solvers based on solving Navier-Stokes or Euler equations generally need a computational grid to represent the domain of the flow. A structured computational grid can be efficiently produced by algebraic methods like transfinite interpolation. Unfortunately, algebraic methods propagate all kinds of unsmoothness of the boundary into the field. Unsmoothness of the grid, in turn, can result in inaccuracy in the flow solver. In the present work a 3D elliptic grid smoother was developed. The smoother is based on solving three Poisson equations, one for each curvilinear direction. The Poisson equations formed in the physical region are first transformed to the computational (rectilinear) region. The resulting equations form a system of three coupled elliptic quasi-linear partial differential equations in the computational domain. A short review of the Poisson method is presented. The regularity of a grid cell is studied and a skewness value is developed.

  2. Multifunctional 3D printing of heterogeneous hydrogel structures.

    PubMed

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

    2016-09-15

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing.

  3. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

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

  4. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

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

  5. Multifunctional 3D printing of heterogeneous hydrogel structures

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing.

  6. Multifunctional 3D printing of heterogeneous hydrogel structures

    PubMed Central

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

    2016-01-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing. PMID:27630079

  7. 3D Wilson cycle: structural inheritance and subduction polarity reversals

    NASA Astrophysics Data System (ADS)

    Beaussier, Stephane; Gerya, Taras; Burg, Jean-Pierre

    2016-04-01

    Many orogenies display along-strike variations in their orogenic wedge geometry. For instance, the Alps is an example of lateral changes in the subducting lithosphere polarity. High resolution tomography has shown that the southeast dipping European lithosphere is separated from the northeast dipping Adriatic lithosphere by a narrow transition zone at about the "Judicarian" line (Kissling et al. 2006). The formation of such 3D variations remains conjectural. We investigate the conditions that can spontaneously induce such lithospheric structures, and intend to identify the main parameters controlling their formation and geometry. Using the 3D thermo-mechanical code, I3ELVIS (Gerya and Yuen 2007) we modelled a Wilson cycle starting from a continental lithosphere in an extensional setting resulting in continental breakup and oceanic spreading. At a later stage, divergence is gradually reversed to convergence, which induce subduction of the oceanic lithosphere formed during oceanic spreading. In this model, all lateral and longitudinal structures of the lithospheres are generated self-consistently, and are consequences of the initial continental structure, tectono-magmatic inheritance, and material rheology. Our numerical simulations point out the control of rheological parameters defining the brittle/plastic yielding conditions for the lithosphere. Formation of several opposing domains of opposing subduction polarity is facilitated by wide and weak oceanic lithospheres. Furthermore, contrasts of strength between the continental and oceanic lithosphere, as well as the angle between the plate suture and the shortening direction have a second order effect on the lateral geometry of the subduction zone. In our numerical experiments systematic lateral changes in the subduction lithosphere polarity during subduction initiation form spontaneously suggesting intrinsic physical origin of this phenomenon. Further studies are necessary to understand why this feature, observed

  8. Use and Evaluation of 3D GeoWall Visualizations in Undergraduate Space Science Classes

    NASA Astrophysics Data System (ADS)

    Turner, N. E.; Hamed, K. M.; Lopez, R. E.; Mitchell, E. J.; Gray, C. L.; Corralez, D. S.; Robinson, C. A.; Soderlund, K. M.

    2005-12-01

    One persistent difficulty many astronomy students face is the lack of 3- dimensional mental model of the systems being studied, in particular the Sun-Earth-Moon system. Students without such a mental model can have a very hard time conceptualizing the geometric relationships that cause, for example, the cycle of lunar phases or the pattern of seasons. The GeoWall is a recently developed and affordable projection mechanism for three-dimensional stereo visualization which is becoming a popular tool in classrooms and research labs for use in geology classes, but as yet very little work has been done involving the GeoWall for astronomy classes. We present results from a large study involving over 1000 students of varied backgrounds: some students were tested at the University of Texas at El Paso, a large public university on the US-Mexico border and other students were from the Florida Institute of Technology, a small, private, technical school in Melbourne Florida. We wrote a lecture tutorial-style lab to go along with a GeoWall 3D visual of the Earth-Moon system and tested the students before and after with several diagnostics. Students were given pre and post tests using the Lunar Phase Concept Inventory (LPCI) as well as a separate evaluation written specifically for this project. We found the lab useful for both populations of students, but not equally effective for all. We discuss reactions from the students and their improvement, as well as whether the students are able to correctly assess the usefullness of the project for their own learning.

  9. 3D Imaging with Structured Illumination for Advanced Security Applications

    SciTech Connect

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

    2015-09-01

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

  10. 3D printing technology using high viscous materials - Synthesis of functional materials and fabrication of 3D metal structure

    NASA Astrophysics Data System (ADS)

    Hong, Seongik

    In the 3D printing technology, the research for using various materials has been performing. In this research work, 3D printable high viscous materials are suggested as one of the solutions for problems in the traditional 3D printing technology. First, Cu-Ag coreshell was synthesized as a functional material. In terms of the reaction rate, reaction rate limiting step was defined as a fundamental research, and then prepared Cu-Ag coreshell was printed and analyzed. Second, the high viscous Cu paste was prepared and then metal 3D printed structure was fabricated by using new printing method. In the synthesis of Cu-Ag coreshell, different sizes of Cu particle, 2μm and 100nm were used, and when 2μm Cu was applied, the reaction rate was limited by film diffusion control. However, when 100nm Cu was applied, reaction rate was controlled by CuO film and the rate of the reaction, which includes removing CuO film in the solution, is limited by chemical reaction control. The shape of Cu-Ag particle is spherical in the 2μm Cu condition and dendrite shape in the 100nm Cu condition respectively. The conductivity of Cu-Ag coreshell paste increased as increasing content of coreshell particle in the paste and sintering temperature. In order to print high viscous metal paste, the high viscous Cu paste was printed by using screw extruder, and the viscosity of Cu paste was measured as a fundamental research. As increasing wt.% of Cu in the paste, the viscosity also increased. In addition, the shrinkage factor was reduced by increasing wt.% of Cu in the paste. An optimized printing condition for the high viscous material was obtained, and by using this condition, 3D metal structure was fabricated. The final product was heat treated and polished. Through these processes, a fine quality of metal 3D structure was printed.

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

    PubMed

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

    2014-07-01

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

  12. Parameterization of 3D brain structures for statistical shape analysis

    NASA Astrophysics Data System (ADS)

    Zhu, Litao; Jiang, Tianzi

    2004-05-01

    Statistical Shape Analysis (SSA) is a powerful tool for noninvasive studies of pathophysiology and diagnosis of brain diseases. It also provides a shape constraint for the segmentation of brain structures. There are two key problems in SSA: the representation of shapes and their alignments. The widely used parameterized representations are obtained by preserving angles or areas and the alignments of shapes are achieved by rotating parameter net. However, representations preserving angles or areas do not really guarantee the anatomical correspondence of brain structures. In this paper, we incorporate shape-based landmarks into parameterization of banana-like 3D brain structures to address this problem. Firstly, we get the triangulated surface of the object and extract two landmarks from the mesh, i.e. the ends of the banana-like object. Then the surface is parameterized by creating a continuous and bijective mapping from the surface to a spherical surface based on a heat conduction model. The correspondence of shapes is achieved by mapping the two landmarks to the north and south poles of the sphere and using an extracted origin orientation to select the dateline during parameterization. We apply our approach to the parameterization of lateral ventricle and a multi-resolution shape representation is obtained by using the Discrete Fourier Transform.

  13. The 3D structure of Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Patsourakos, Spiros

    2016-07-01

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

  14. Stratigraphic and structural interpretation with 3-D seismic coherence

    SciTech Connect

    Bahorich, M.; Lopez, J.; Haskell, N.

    1996-12-31

    3-D seismic discontinuity is useful for identifying faults, stratigraphic features and the relationship between them. This paper covers the application of coherence technology to three basins; the Gulf of Mexico, the North Sea, aid the Ardmore Basin of Oklahoma. In the Gulf of Mexico, 3-D coherence data may be used to simultaneously view faults and stratigraphic features and therefore see the relationship between them. Coherence data reveal channels that avoid a structural high generated by a salt dome, Channels that change direction as they cross faults, radial faults adjacent to a salt dome, and complex and en-echelon faults. Since the coherence process is applied to non- interpreted seismic data, these features are available for viewing without the time or bias of interpretation. Coherence time slices from the Ardmore Basin of Oklahoma were compared with a horizon-dip map and a discrepancy in the fault patterns was noted. Further analysis revealed that subtle errors in the autopicking had created a false bend in a fault trace seen on the horizon-dip map. After correction, the horizon-dip map and coherence time slice indicated similar fault patterns. Since the coherence method is run on the raw seismic data, it provides a view of the faults that is not biased by the interpreter or horizon autopicker. In the North Sea, faults may exhibit meandering patterns that are easy to interpret on traditional time-slices where they cut perpendicular to stratigraphic bedding but are difficult to recognize where they cut parallel to bedding. The coherence technique images faults in any orientation equally well.

  15. Stratigraphic and structural interpretation with 3-D seismic coherence

    SciTech Connect

    Bahorich, M.; Lopez, J.; Haskell, N.; Nissen, S.; Poole, A.

    1996-06-01

    3-D seismic discontinuity is useful for identifying faults, stratigraphic features and the relationship between them. This paper covers the application of coherence technology to three basins; the Gulf of Mexico, the North Sea, and the Ardmore Basin of Oklahoma. In the Gulf of Mexico, 3-D coherence data may be used to simultaneously view faults and stratigraphic features and therefore see the relationship between them. Coherence data reveal channels that avoid a structural high generated by a salt dome, channels that change direction as they cross faults, radial faults adjacent to a salt dome, and complex and en-echelon faults. Since the coherence process is applied to non-interpreted seismic data, these features are available for viewing without the time or bias of interpretation. Coherence time slices from the Ardmore Basin of Oklahoma were compared with a horizon-dip map and a discrepancy in the fault patterns was noted. Further analysis revealed that subtle errors in the autopicking had created a false bend in a fault trace seen on the horizon-dip map. After correction, the horizon-dip map and coherence time slice indicated similar fault patterns. Since the coherence method is run on the raw seismic data, it provides a view of the faults that is not biased by the interpreter or horizon autopicker. In the North Sea, faults may exhibit meandering patterns that are easy to interpret on traditional time-slices where they cut perpendicular to stratigraphic bedding but are difficult to recognize where they cut parallel to bedding. The coherence technique images faults in any orientation equally well.

  16. 3D Seismic Imaging over a Potential Collapse Structure

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

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

    2014-01-01

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

  18. ConvNet-Based Localization of Anatomical Structures in 3D Medical Images.

    PubMed

    de Vos, Bob; Wolterink, Jelmer; de Jong, Pim; Leiner, Tim; Viergever, Max; Isgum, Ivana

    2017-02-23

    Localization of anatomical structures is a prerequisite for many tasks in medical image analysis. We propose a method for automatic localization of one or more anatomical structures in 3D medical images through detection of their presence in 2D image slices using a convolutional neural network (ConvNet). A single ConvNet is trained to detect presence of the anatomical structure of interest in axial, coronal, and sagittal slices extracted from a 3D image. To allow the ConvNet to analyze slices of different sizes, spatial pyramid pooling is applied. After detection, 3D bounding boxes are created by combining the output of the ConvNet in all slices. In the experiments 200 chest CT, 100 cardiac CT angiography (CTA), and 100 abdomen CT scans were used. The heart, ascending aorta, aortic arch, and descending aorta were localized in chest CT scans, the left cardiac ventricle in cardiac CTA scans, and the liver in abdomen CT scans. Localization was evaluated using the distances between automatically and manually defined reference bounding box centroids and walls. The best results were achieved in localization of structures with clearly defined boundaries (e.g. aortic arch) and the worst when the structure boundary was not clearly visible (e.g. liver). The method was more robust and accurate in localization multiple structures.

  19. The 3D Attenuation Structure of Deception Island (Antarctica)

    NASA Astrophysics Data System (ADS)

    Prudencio, J.; De Siena, L.; Ibáñez, J. M.; Del Pezzo, E.; García-Yeguas, A.; Díaz-Moreno, A.

    2015-05-01

    The seismic and volcanological structure of Deception Island (Antarctica) is an intense focus topic in Volcano Geophysics. The interpretations given by scientists on the origin, nature, and location of the structures buried under the island strongly diverge. We present a high-resolution 3D P-wave attenuation tomography model obtained by using the coda normalization method on 20,293 high-quality waveforms produced by active sources. The checkerboard and synthetic anomaly tests guarantee the reproduction of the input anomalies under the island down to a depth of 4 km. The results, once compared with our current knowledge on the geological, geochemical, and geophysical structure of the region, depict Deception as a piecemeal caldera structure coming out of the Bransfield Trough. High-attenuation anomalies contouring the northeastern emerged caldera rim correlate with the locations of sediments. In our interpretation, the main attenuation contrast, which appears under the collapsed southeastern caldera rim, is related to the deeper feeding systems. A unique P-wave high-attenuation spherical-like anomaly in the inner bay extends between depths of 1 and 3 km. The northern contour of the anomaly coincides with the calderic rim both at 1 and 2 km, while smaller anomalies connect it with deeper structures below 3 km, dipping toward the Bransfield Trough. In our interpretation, the large upper anomaly is caused by a high-temperature shallow (1-3 km deep) geothermal system, located beneath the sediment-filled bay in the collapsed blocks and heated by smaller, deeper contributions of molten materials (magma) rising from southeast.

  20. 3D structures of membrane proteins from genomic sequencing

    PubMed Central

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

    2012-01-01

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

  1. Pack Aluminization Synthesis of Superalloy 3D Woven and 3D Braided Structures

    NASA Astrophysics Data System (ADS)

    Erdeniz, Dinc; Levinson, Amanda J.; Sharp, Keith W.; Rowenhorst, David J.; Fonda, Richard W.; Dunand, David C.

    2015-01-01

    Micro-architectured, precipitation-strengthened structures were created in a new process combining weaving, gas-phase alloying, diffusion, and precipitation. First, high-ductility Ni-20 wt pct Cr wires with 202 μm diameter were braided, or non-crimp orthogonal woven, into three-dimensional structures. Second, these structures were vapor-phase alloyed with Al at 1273 K (1000 °C) by pack cementation, creating uniform NiAl coatings on the wires when using a retort. Also, solid-state bonding was achieved at wire intersections, where two wires were sufficiently close to each other, as determined via optical and X-ray tomographic microscopy. Third, the NiAl-coated wires were fully homogenized and aged to form γ' precipitates distributed in a γ matrix phase, the same microstructure providing strength in nickel-based superalloys. The resulting structures—consisting of wires (i) woven in a controlled three-dimensional architecture, (ii) bonded at contact points and (iii) strengthened by γ' precipitates—are expected to show high strength at ambient and elevated temperatures, low density, and high permeability which is useful for active cooling.

  2. Cellular uptake mechanisms of functionalised multi-walled carbon nanotubes by 3D electron tomography imaging

    NASA Astrophysics Data System (ADS)

    Al-Jamal, Khuloud T.; Nerl, Hannah; Müller, Karin H.; Ali-Boucetta, Hanene; Li, Shouping; Haynes, Peter D.; Jinschek, Joerg R.; Prato, Maurizio; Bianco, Alberto; Kostarelos, Kostas; Porter, Alexandra E.

    2011-06-01

    Carbon nanotubes (CNTs) are being investigated for a variety of biomedical applications. Despite numerous studies, the pathways by which carbon nanotubes enter cells and their subsequent intracellular trafficking and distribution remain poorly determined. Here, we use 3-D electron tomography techniques that offer optimum enhancement of contrast between carbon nanotubes and the plasma membrane to investigate the mechanisms involved in the cellular uptake of shortened, functionalised multi-walled carbon nanotubes (MWNT-NH3+). Both human lung epithelial (A549) cells, that are almost incapable of phagocytosis and primary macrophages, capable of extremely efficient phagocytosis, were used. We observed that MWNT-NH3+ were internalised in both phagocytic and non-phagocytic cells by any one of three mechanisms: (a) individually via membrane wrapping; (b) individually by direct membrane translocation; and (c) in clusters within vesicular compartments. At early time points following intracellular translocation, we noticed accumulation of nanotube material within various intracellular compartments, while a long-term (14-day) study using primary human macrophages revealed that MWNT-NH3+ were able to escape vesicular (phagosome) entrapment by translocating directly into the cytoplasm.Carbon nanotubes (CNTs) are being investigated for a variety of biomedical applications. Despite numerous studies, the pathways by which carbon nanotubes enter cells and their subsequent intracellular trafficking and distribution remain poorly determined. Here, we use 3-D electron tomography techniques that offer optimum enhancement of contrast between carbon nanotubes and the plasma membrane to investigate the mechanisms involved in the cellular uptake of shortened, functionalised multi-walled carbon nanotubes (MWNT-NH3+). Both human lung epithelial (A549) cells, that are almost incapable of phagocytosis and primary macrophages, capable of extremely efficient phagocytosis, were used. We observed

  3. 3D Protein structure prediction with genetic tabu search algorithm

    PubMed Central

    2010-01-01

    -climbing capability in the conventional genetic algorithm by using the flexible memory functions of TS. Compared with some previous algorithms, GATS algorithm has better performance in global optimization and can predict 3D protein structure more effectively. PMID:20522256

  4. 3D protein structure prediction with genetic tabu search algorithm.

    PubMed

    Zhang, Xiaolong; Wang, Ting; Luo, Huiping; Yang, Jack Y; Deng, Youping; Tang, Jinshan; Yang, Mary Qu

    2010-05-28

    algorithm by using the flexible memory functions of TS. Compared with some previous algorithms, GATS algorithm has better performance in global optimization and can predict 3D protein structure more effectively.

  5. Micro structured coupling elements for 3D silicon optical interposer

    NASA Astrophysics Data System (ADS)

    Charania, Sujay; Lüngen, Sebastian; Al-Husseini, Zaid; Killge, Sebastian; Nieweglowski, Krzysztof; Neumann, Niels; Plettemeier, Dirk; Bock, Karlheinz; Bartha, Johann W.

    2017-05-01

    Current trends in electronic industry, such as Internet of Things (IoT) and Cloud Computing call for high interconnect bandwidth, increased number of active devices and high IO count. Hence the integration of on silicon optical waveguides becomes an alternative approach to cope with the performance demands. The application and fabrication of horizontal (planar) and vertical (Through Silicon Vias - TSVs) optical waveguides are discussed here. Coupling elements are used to connect both waveguide structures. Two micro-structuring technologies for integration of coupling elements are investigated: μ-mirror fabrication by nanoimprint (i) and dicing technique (ii). Nanoimprint technology creates highly precise horizontal waveguides with polymer (refractive index nC = 1.56 at 650 nm) as core. The waveguide ends in reflecting facets aligned to the optical TSVs. To achieve Total Internal Reflection (TIR), SiO2 (nCl = 1.46) is used as cladding. TSVs (diameter 20-40μm in 200-380μm interposer) are realized by BOSCH process1, oxidation and SU-8 filling techniques. To carry out the imprint, first a silicon structure is etched using a special plasma etching process. A polymer stamp is then created from the silicon template. Using this polymer stamp, SU-8 is imprinted aligned to vertical TSVs over Si surface.Waveguide dicing is presented as a second technology to create coupling elements on polymer waveguides. The reflecting mirror is created by 45° V-shaped dicing blade. The goal of this work is to develop coupling elements to aid 3D optical interconnect network on silicon interposer, to facilitate the realization of the emerging technologies for the upcoming years.

  6. 3D Soil Images Structure Quantification using Relative Entropy

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  7. Slat Cove Unsteadiness Effect of 3D Flow Structures

    NASA Technical Reports Server (NTRS)

    Choudhari, Meelan M.; Khorrami, Mehdi R.

    2006-01-01

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

  8. Chest-wall segmentation in automated 3D breast ultrasound images using thoracic volume classification

    NASA Astrophysics Data System (ADS)

    Tan, Tao; van Zelst, Jan; Zhang, Wei; Mann, Ritse M.; Platel, Bram; Karssemeijer, Nico

    2014-03-01

    Computer-aided detection (CAD) systems are expected to improve effectiveness and efficiency of radiologists in reading automated 3D breast ultrasound (ABUS) images. One challenging task on developing CAD is to reduce a large number of false positives. A large amount of false positives originate from acoustic shadowing caused by ribs. Therefore determining the location of the chestwall in ABUS is necessary in CAD systems to remove these false positives. Additionally it can be used as an anatomical landmark for inter- and intra-modal image registration. In this work, we extended our previous developed chestwall segmentation method that fits a cylinder to automated detected rib-surface points and we fit the cylinder model by minimizing a cost function which adopted a term of region cost computed from a thoracic volume classifier to improve segmentation accuracy. We examined the performance on a dataset of 52 images where our previous developed method fails. Using region-based cost, the average mean distance of the annotated points to the segmented chest wall decreased from 7.57±2.76 mm to 6.22±2.86 mm.art.

  9. Measurement of the 3D arterial wall strain tensor using intravascular B-mode ultrasound images: a feasibility study

    NASA Astrophysics Data System (ADS)

    Liang, Yun; Zhu, Hui; Friedman, Morton H.

    2010-11-01

    Intravascular ultrasound (IVUS) elastography is a promising tool for studying atherosclerotic plaque composition and assessing plaque vulnerability. Current IVUS elastography techniques can measure the 1D or 2D strain of the vessel wall using various motion tracking algorithms. Since biological soft tissue tends to deform non-uniformly in 3D, measurement of the complete 3D strain tensor is desirable for more rigorous analysis of arterial wall mechanics. In this paper, we extend our previously developed method of 2D arterial wall strain measurement based on non-rigid image registration into 3D strain measurement. The new technique registers two image volumes acquired from the same vessel segment under different levels of luminal pressure and longitudinal stress. The 3D displacement field obtained from the image registration is used to calculate the local 3D strain tensor. From the 3D strain tensor, radial, circumferential and longitudinal strain distributions can be obtained and displayed. This strain tensor measurement method is validated and evaluated using IVUS images of healthy porcine carotid arteries subjected to a luminal pressure increase and longitudinal stretch. The ability of the algorithm to overcome systematic noise was tested, as well as the consistency of the results under different longitudinal frame resolutions.

  10. 3D analysis of vortical structures in an abdominal aortic aneurysm by stereoscopic PIV

    NASA Astrophysics Data System (ADS)

    Deplano, Valérie; Guivier-Curien, Carine; Bertrand, Eric

    2016-11-01

    The present work presents an experimental in vitro three-dimensional analysis of the flow dynamics in an abdominal aortic aneurysm (AAA) through stereoscopic particle image velocimetry (SPIV) measurements. The experimental set-up mimics the pathophysiological context involving a shear thinning blood analogue fluid, compliant AAA and aorto-iliac bifurcation walls and controlled inlet and outlet flow rate and pressure waveforms as well as working fluid temperature. SPIV was carefully calibrated and conducted to assess the three velocity components in the AAA volume. For the first time in the literature, the 3D vortex ring genesis, propagation, and vanishing in the AAA bulge are experimentally described and quantified. In comparison with classical 2-component PIV measurements (2C PIV), the third component of the velocity vector was shown to be of importance in such a geometry, especially, during the deceleration phase of the flow rate. The 3D velocity magnitude reached up more than 20 % of the 2D one showing that 2C PIV are definitively not accurate enough to provide a complete description of flow behaviour in an AAA. In addition to potential clinical implications of a full 3D vortex ring description in AAA evolution, the 3D in vitro experimental quantification of the flow dynamics carried out in the present study offers an interesting tool for the validation of fluid-structure interaction numerical studies dealing with AAA.

  11. Construction of Extended 3D Field of Views of the Internal Bladder Wall Surface: A Proof of Concept

    NASA Astrophysics Data System (ADS)

    Ben-Hamadou, Achraf; Daul, Christian; Soussen, Charles

    2016-09-01

    3D extended field of views (FOVs) of the internal bladder wall facilitate lesion diagnosis, patient follow-up and treatment traceability. In this paper, we propose a 3D image mosaicing algorithm guided by 2D cystoscopic video-image registration for obtaining textured FOV mosaics. In this feasibility study, the registration makes use of data from a 3D cystoscope prototype providing, in addition to each small FOV image, some 3D points located on the surface. This proof of concept shows that textured surfaces can be constructed with minimally modified cystoscopes. The potential of the method is demonstrated on numerical and real phantoms reproducing various surface shapes. Pig and human bladder textures are superimposed on phantoms with known shape and dimensions. These data allow for quantitative assessment of the 3D mosaicing algorithm based on the registration of images simulating bladder textures.

  12. 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures

    PubMed Central

    Wang, Jian; Zhao, Yunjie; Zhu, Chunyan; Xiao, Yi

    2015-01-01

    Model evaluation is a necessary step for better prediction and design of 3D RNA structures. For proteins, this has been widely studied and the knowledge-based statistical potential has been proved to be one of effective ways to solve this problem. Currently, a few knowledge-based statistical potentials have also been proposed to evaluate predicted models of RNA tertiary structures. The benchmark tests showed that they can identify the native structures effectively but further improvements are needed to identify near-native structures and those with non-canonical base pairs. Here, we present a novel knowledge-based potential, 3dRNAscore, which combines distance-dependent and dihedral-dependent energies. The benchmarks on different testing datasets all show that 3dRNAscore are more efficient than existing evaluation methods in recognizing native state from a pool of near-native states of RNAs as well as in ranking near-native states of RNA models. PMID:25712091

  13. Pedestal-to-Wall 3D Fluid Transport Simulations on DIII-D

    DOE PAGES

    Lore, Jeremy D.; Wolfmeister, Alexis Briesemeister; Ferraro, Nathaniel M.; ...

    2017-03-30

    The 3D fluid-plasma edge transport code EMC3-EIRENE is used to test several magnetic field models with and without plasma response against DIII-D experimental data for even and odd-parity n=3 magnetic field perturbations. The field models include ideal and extended MHD equilibria, and the vacuum approximation. Plasma response is required to reduce the stochasticity in the pedestal region for even-parity fields, however too much screening suppresses the measured splitting of the downstream Te profile. Odd-parity perturbations result in weak tearing and only small additional peaks in the downstream measurements. In this case plasma response is required to increase the size ofmore » the lobe structure. Finally, no single model is able to simultaneously reproduce the upstream and downstream characteristics for both odd and even-parity perturbations.« less

  14. Pedestal-to-wall 3D fluid transport simulations on DIII-D

    NASA Astrophysics Data System (ADS)

    Lore, J. D.; Briesemeister, A. R.; Ferraro, N. M.; Frerichs, H.; Lyons, B.; McLean, A.; Park, J.-K.; Shafer, M. W.

    2017-05-01

    The 3D fluid-plasma edge transport code EMC3-EIRENE is used to test several magnetic field models with and without plasma response against DIII-D experimental data for even and odd-parity n  =  3 magnetic field perturbations. The field models include ideal and extended MHD equilibria, and the vacuum approximation. Plasma response is required to reduce the stochasticity in the pedestal region for even-parity fields, however too much screening suppresses the measured splitting of the downstream T e profile. Odd-parity perturbations result in weak tearing and only small additional peaks in the downstream measurements. In this case plasma response is required to increase the size of the lobe structure. No single model is able to simultaneously reproduce the upstream and downstream characteristics for both odd and even-parity perturbations. ).

  15. 3-D segmentation and quantitative analysis of inner and outer walls of thrombotic abdominal aortic aneurysms

    NASA Astrophysics Data System (ADS)

    Lee, Kyungmoo; Yin, Yin; Wahle, Andreas; Olszewski, Mark E.; Sonka, Milan

    2008-03-01

    An abdominal aortic aneurysm (AAA) is an area of a localized widening of the abdominal aorta, with a frequent presence of thrombus. A ruptured aneurysm can cause death due to severe internal bleeding. AAA thrombus segmentation and quantitative analysis are of paramount importance for diagnosis, risk assessment, and determination of treatment options. Until now, only a small number of methods for thrombus segmentation and analysis have been presented in the literature, either requiring substantial user interaction or exhibiting insufficient performance. We report a novel method offering minimal user interaction and high accuracy. Our thrombus segmentation method is composed of an initial automated luminal surface segmentation, followed by a cost function-based optimal segmentation of the inner and outer surfaces of the aortic wall. The approach utilizes the power and flexibility of the optimal triangle mesh-based 3-D graph search method, in which cost functions for thrombus inner and outer surfaces are based on gradient magnitudes. Sometimes local failures caused by image ambiguity occur, in which case several control points are used to guide the computer segmentation without the need to trace borders manually. Our method was tested in 9 MDCT image datasets (951 image slices). With the exception of a case in which the thrombus was highly eccentric, visually acceptable aortic lumen and thrombus segmentation results were achieved. No user interaction was used in 3 out of 8 datasets, and 7.80 +/- 2.71 mouse clicks per case / 0.083 +/- 0.035 mouse clicks per image slice were required in the remaining 5 datasets.

  16. Computerized 3-D reconstruction of complicated anatomical structure

    NASA Astrophysics Data System (ADS)

    Andreasen, Arne; Drewes, Asbjorn M.; Assentoft, Joergen E.

    1992-06-01

    In the study of the rabbit hippocampal region, images of 430 serial sections were aligned by a `parameter-shift' algorithm. The resulting 3-D matrix represents a fixed and stained but `whole' rabbit brain. From this virtual object the slice procedure, displacement, and re- alignment could be computer simulated and the artifacts associated with these procedures estimated.

  17. Postprocessing techniques for 3D non-linear structures

    NASA Technical Reports Server (NTRS)

    Gallagher, Richard S.

    1987-01-01

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

  18. Stratigraphic and structural interpretation with 3-D coherence

    SciTech Connect

    Bahorich, M.S.; Lopez, J.; Haskell, N.L.

    1995-12-31

    3-D seismic coherence is useful for identifying faults, stratigraphic features and the relationship between them (Bahorich, and Farmer, 1994). This paper documents the use of this technology in three basins; the Gulf of Mexico, the North Sea, and the Ardmore Basin of Oklahoma.

  19. Extremely high resolution 3D electrical resistivity tomography to depict archaeological subsurface structures

    NASA Astrophysics Data System (ADS)

    Al-Saadi, Osamah; Schmidt, Volkmar; Becken, Michael; Fritsch, Thomas

    2017-04-01

    Electrical resistivity tomography (ERT) methods have been increasingly used in various shallow depth archaeological prospections in the last few decades. These non-invasive techniques are very useful in saving time, costs, and efforts. Both 2D and 3D ERT techniques are used to obtain detailed images of subsurface anomalies. In two surveyed areas near Nonnweiler (Germany), we present the results of the full 3D setup with a roll-along technique and of the quasi-3D setup (parallel and orthogonal profiles in dipole-dipole configuration). In area A, a dipole-dipole array with 96 electrodes in a uniform rectangular survey grid has been used in full 3D to investigate a presumed Roman building. A roll-along technique has been utilized to cover a large part of the archaeological site with an electrode spacing of 1 meter and with 0.5 meter for a more detailed image. Additional dense parallel 2D profiles have been carried out in dipole-dipole array with 0.25 meter electrode spacing and 0.25 meter between adjacent profiles in both direction for higher- resolution subsurface images. We have designed a new field procedure, which used an electrode array fixed in a frame. This facilitates efficient field operation, which comprised 2376 electrode positions. With the quasi 3D imaging, we confirmed the full 3D inversion model but at a much better resolution. In area B, dense parallel 2D profiles were directly used to survey the second target with also 0.25 meter electrode spacing and profiles separation respectively. The same field measurement design has been utilized and comprised 9648 electrode positions in total. The quasi-3D inversion results clearly revealed the main structures of the Roman construction. These ERT inversion results coincided well with the archaeological excavation, which has been done in some parts of this area. The ERT result successfully images parts from the walls and also smaller internal structures of the Roman building.

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

    NASA Astrophysics Data System (ADS)

    Gheorghe, Radu; Tchouprakov, Andrei; Sokolov, Roman

    2013-02-01

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

  1. A negative correlation between human carotid atherosclerotic plaque progression and plaque wall stress: in vivo MRI-based 2D/3D FSI models.

    PubMed

    Tang, Dalin; Yang, Chun; Mondal, Sayan; Liu, Fei; Canton, Gador; Hatsukami, Thomas S; Yuan, Chun

    2008-01-01

    It is well accepted that atherosclerosis initiation and progression correlate positively with low and oscillating flow wall shear stresses (FSS). However, this mechanism cannot explain why advanced plaques continue to grow under elevated FSS conditions. In vivo magnetic resonance imaging (MRI)-based 2D/3D multi-component models with fluid-structure interactions (FSI, 3D only) for human carotid atherosclerotic plaques were introduced to quantify correlations between plaque progression measured by wall thickness increase (WTI) and plaque wall (structure) stress (PWS) conditions. A histologically validated multi-contrast MRI protocol was used to acquire multi-year in vivo MRI images. Our results using 2D models (200-700 data points/patient) indicated that 18 out of 21 patients studied showed significant negative correlation between WTI and PWS at time 2 (T2). The 95% confidence interval for the Pearson correlation coefficient is (-0.443,-0.246), p<0.0001. Our 3D FSI model supported the 2D correlation results and further indicated that combining both plaque structure stress and flow shear stress gave better approximation results (PWS, T2: R(2)=0.279; FSS, T1: R(2)=0.276; combining both: R(2)=0.637). These pilot studies suggest that both lower PWS and lower FSS may contribute to continued plaque progression and should be taken into consideration in future investigations of diseases related to atherosclerosis.

  2. A Negative Correlation between Human Carotid Atherosclerotic Plaque Progression and Plaque Wall Stress: In Vivo MRI-Based 2D/3D FSI Models

    PubMed Central

    Tang, Dalin; Yang, Chun; Mondal, Sayan; Liu, Fei; Canton, Gador; Hatsukami, Thomas S.; Yuan, Chun

    2008-01-01

    It is well accepted that atherosclerosis initiation and progression correlate positively with low and oscillating flow wall shear stresses (FSS). However, this mechanism cannot explain why advanced plaques continue to grow under elevated FSS conditions. In vivo magnetic resonance imaging (MRI)-based 2D/3D multi-component models with fluid-structure interactions (FSI, 3D only) for human carotid atherosclerotic plaques were introduced to quantify correlations between plaque progression measured by wall thickness increase (WTI) and plaque wall (structure) stress (PWS) conditions. A histologically validated multi-contrast MRI protocol was used to acquire multi-year in vivo MRI images. Our results using 2D models (200–700 data points/patient) indicated that 18 out of 21 patients studied showed significant negative correlation between WTI and PWS at time 2 (T2). The 95% confidence interval for the Pearson correlation coefficient is (−0.443, −0.246), p < 0.0001. Our 3D FSI model supported the 2D correlation results and further indicated that combining both plaque structure stress and flow shear stress gave better approximation results (PWS, T2: R2 = 0.279; FSS, T1: R2 = 0.276; Combining both: R2 = 0.637). These pilot studies suggest that both lower PWS and lower FSS may contribute to continued plaque progression and should be taken into consideration in future investigations of diseases related to atherosclerosis. PMID:18191138

  3. Construction and histological analysis of a 3D human arterial wall model containing vasa vasorum using a layer-by-layer technique.

    PubMed

    Shima, Fumiaki; Narita, Hirokazu; Hiura, Ayami; Shimoda, Hiroshi; Akashi, Mitsuru

    2017-03-01

    There is considerable global demand for three-dimensional (3D) functional tissues which mimic our native organs and tissues for use as in vitro drug screening systems and in regenerative medicine. In particular, there has been an increasing number of patients who suffer from arterial diseases such as arteriosclerosis. As such, in vitro 3D arterial wall models that can evaluate the effects of novel medicines and a novel artificial graft for the treatment are required. In our previous study, we reported the rapid construction of 3D tissues by employing a layer-by-layer (LbL) technique and revealed their potential applications in the pharmaceutical fields and tissue engineering. In this study, we successfully constructed a 3D arterial wall model containing vasa vasorum by employing a LbL technique for the first time. The cells were coated with extracellular matrix nanofilms and seeded into a culture insert using a cell accumulation method. This model had a three-layered hierarchical structure: a fibroblast layer, a smooth muscle layer, and an endothelial layer, which resembled the native arterial wall. Our method could introduce vasa vasorum into a fibroblast layer in vitro and the 3D arterial wall model showed barrier function which was evaluated by immunostaining and transendothelial electrical resistance measurement. Furthermore, electron microscopy observations revealed that the vasa vasorum was composed of single-layered endothelial cells, and the endothelial tubes were surrounded by the basal lamina, which are known to promote maturation and stabilization in native blood capillaries. These models should be useful for tissue engineering, regenerative medicine, and pharmaceutical applications. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 814-823, 2017. © 2016 Wiley Periodicals, Inc.

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

    PubMed Central

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

    The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics. PMID:28054558

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

    PubMed

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-05

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

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

    NASA Astrophysics Data System (ADS)

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

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

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

    PubMed Central

    Rezania, Vahid; Tuszynski, Jack

    2016-01-01

    In this paper, we develop a spatio-temporal modeling approach to describe blood and drug flow, as well as drug uptake and elimination, on an approximation of the liver. Extending on previously developed computational approaches, we generate an approximation of a liver, which consists of a portal and hepatic vein vasculature structure, embedded in the surrounding liver tissue. The vasculature is generated via constrained constructive optimization, and then converted to a spatial grid of a selected grid size. Estimates for surrounding upscaled lobule tissue properties are then presented appropriate to the same grid size. Simulation of fluid flow and drug metabolism (hepatic clearance) are completed using discretized forms of the relevant convective-diffusive-reactive partial differential equations for these processes. This results in a single stage, uniformly consistent method to simulate equations for blood and drug flow, as well as drug metabolism, on a 3D structure representative of a liver. PMID:27649537

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

    PubMed

    White, Diana; Coombe, Dennis; Rezania, Vahid; Tuszynski, Jack

    2016-01-01

    In this paper, we develop a spatio-temporal modeling approach to describe blood and drug flow, as well as drug uptake and elimination, on an approximation of the liver. Extending on previously developed computational approaches, we generate an approximation of a liver, which consists of a portal and hepatic vein vasculature structure, embedded in the surrounding liver tissue. The vasculature is generated via constrained constructive optimization, and then converted to a spatial grid of a selected grid size. Estimates for surrounding upscaled lobule tissue properties are then presented appropriate to the same grid size. Simulation of fluid flow and drug metabolism (hepatic clearance) are completed using discretized forms of the relevant convective-diffusive-reactive partial differential equations for these processes. This results in a single stage, uniformly consistent method to simulate equations for blood and drug flow, as well as drug metabolism, on a 3D structure representative of a liver.

  9. The magnetotelluric response over a 3D polarizable structure

    NASA Astrophysics Data System (ADS)

    Esposito, R.; Troiano, A.; Di Giuseppe, M. G.; Patella, D.; Castelo Branco, R. M.

    2017-06-01

    This paper analyses the 3D magnetotelluric (MT) response in the presence of resistivity frequency dispersion. The aim is to give further insight into this topic, already approached in previous papers dedicated to 1D and 2D cases. We show the MT diagrams along three parallel profiles, normal to the longitudinal axis of a dispersive conductive prism of finite horizontal and vertical extent, buried in a non-dispersive resistive half-space. The Cole-Cole dispersion law has been assumed to represent the dispersion features of the prism. The MT responses along the same profiles in the complete absence of dispersion effects are also provided for reference. The results confirm that the TE mode, as in the 2D case, is mostly affected by dispersion. Compared with the non-dispersive responses, a notable increase in the amplitude of the anomaly is observed along the profile passing through the center of the prism, while an increase in its width is the effect along the profile above the edge of the prism. As a field example, the MT profile in the eastern Snake River Plain geothermal area is considered. The profile was already dealt with in a previous paper by a 2D dispersive MT modeling approach, by which a dispersive slab of infinite length in the direction normal to the MT profile, immersed in a 1D layered host, was modeled. A finite length of the dispersive conductive slab is now derived, validated by the increased goodness of fit between the field TM and TE pseudosections and the synthetic ones from the 3D model compared with the misfit previously obtained by the 2D approach. Finally, an explanation of the chargeability and main values of the time constant assumed to fit the field data is attempted in terms of the abundance of hydrothermal alteration products and temperature, respectively, inside the dispersive slab.

  10. Implementation of wall boundary conditions for transpiration in F3D thin-layer Navier-Stokes code

    NASA Technical Reports Server (NTRS)

    Kandula, M.; Martin, F. W., Jr.

    1991-01-01

    Numerical boundary conditions for mass injection/suction at the wall are incorporated in the thin-layer Navier-Stokes code, F3D. The accuracy of the boundary conditions and the code is assessed by a detailed comparison of the predictions of velocity distributions and skin-friction coefficients with exact similarity solutions for laminar flow over a flat plate with variable blowing/suction, and measurements for turbulent flow past a flat plate with uniform blowing. In laminar flow, F3D predictions for friction coefficient compare well with exact similarity solution with and without suction, but produces large errors at moderate-to-large values of blowing. A slight Mach number dependence of skin-friction coefficient due to blowing in turbulent flow is computed by F3D code. Predicted surface pressures for turbulent flow past an airfoil with mass injection are in qualitative agreement with measurements for a flat plate.

  11. On the correlation among surface chemistry, 3D structure, morphology, electrochemical and impedance behavior of various lithiated carbon electrodes

    NASA Astrophysics Data System (ADS)

    Aurbach, D.; Gnanaraj, J. S.; Levi, M. D.; Levi, E. A.; Fischer, J. E.; Claye, A.

    This work relates to a rigorous study of the correlation among surface chemistry (FTIR, XPS), 3D structure (X-ray and neutron scattering), morphology (SEM, AFM), and electrochemical and impedance behavior of lithiated carbon electrodes in commonly used liquid electrolyte solutions. Four different types of carbons were explored in a single study. These included, for comparison, two types of disordered carbons, single-wall carbon nanotubes (SWNT), and synthetic graphite powder as a reference system. All four types of carbons develop a similar surface chemistry in alkyl carbonate solutions which is dominated by solvent reduction. The differences in the 3D structure of these carbons leads to pronounced differences in the mechanisms of Li-insertion into them. The effect of the carbons' 3D structure on the solid-state diffusion of Li-ions is demonstrated and discussed.

  12. 3D Printing: 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles (Adv. Mater. 19/2016).

    PubMed

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

    2016-05-01

    On page 3712, E. Fantino, A. Chiappone, and co-workers fabricate conductive 3D hybrid structures by coupling the photo-reduction of metal precursors with 3D printing technology. The generated structures consist of metal nanoparticles embedded in a polymer matrix shaped into complex multilayered architectures. 3D conductive structures are fabricated with a digital light-processing printer incorporating silver salt into photocurable formulations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Reconstructing White Walls: Multi-View Multi-Shot 3d Reconstruction of Textureless Surfaces

    NASA Astrophysics Data System (ADS)

    Ley, Andreas; Hänsch, Ronny; Hellwich, Olaf

    2016-06-01

    The reconstruction of the 3D geometry of a scene based on image sequences has been a very active field of research for decades. Nevertheless, there are still existing challenges in particular for homogeneous parts of objects. This paper proposes a solution to enhance the 3D reconstruction of weakly-textured surfaces by using standard cameras as well as a standard multi-view stereo pipeline. The underlying idea of the proposed method is based on improving the signal-to-noise ratio in weakly-textured regions while adaptively amplifying the local contrast to make better use of the limited numerical range in 8-bit images. Based on this premise, multiple shots per viewpoint are used to suppress statistically uncorrelated noise and enhance low-contrast texture. By only changing the image acquisition and adding a preprocessing step, a tremendous increase of up to 300% in completeness of the 3D reconstruction is achieved.

  14. Three dimensional level set based semiautomatic segmentation of atherosclerotic carotid artery wall volume using 3D ultrasound imaging

    NASA Astrophysics Data System (ADS)

    Hossain, Md. Murad; AlMuhanna, Khalid; Zhao, Limin; Lal, Brajesh K.; Sikdar, Siddhartha

    2014-03-01

    3D segmentation of carotid plaque from ultrasound (US) images is challenging due to image artifacts and poor boundary definition. Semiautomatic segmentation algorithms for calculating vessel wall volume (VWV) have been proposed for the common carotid artery (CCA) but they have not been applied on plaques in the internal carotid artery (ICA). In this work, we describe a 3D segmentation algorithm that is robust to shadowing and missing boundaries. Our algorithm uses distance regularized level set method with edge and region based energy to segment the adventitial wall boundary (AWB) and lumen-intima boundary (LIB) of plaques in the CCA, ICA and external carotid artery (ECA). The algorithm is initialized by manually placing points on the boundary of a subset of transverse slices with an interslice distance of 4mm. We propose a novel user defined stopping surface based energy to prevent leaking of evolving surface across poorly defined boundaries. Validation was performed against manual segmentation using 3D US volumes acquired from five asymptomatic patients with carotid stenosis using a linear 4D probe. A pseudo gold-standard boundary was formed from manual segmentation by three observers. The Dice similarity coefficient (DSC), Hausdor distance (HD) and modified HD (MHD) were used to compare the algorithm results against the pseudo gold-standard on 1205 cross sectional slices of 5 3D US image sets. The algorithm showed good agreement with the pseudo gold standard boundary with mean DSC of 93.3% (AWB) and 89.82% (LIB); mean MHD of 0.34 mm (AWB) and 0.24 mm (LIB); mean HD of 1.27 mm (AWB) and 0.72 mm (LIB). The proposed 3D semiautomatic segmentation is the first step towards full characterization of 3D plaque progression and longitudinal monitoring.

  15. Third generation anthropomorphic physical phantom for mammography and DBT: incorporating voxelized 3D printing and uniform chest wall QC region

    NASA Astrophysics Data System (ADS)

    Zhao, Christine; Solomon, Justin; Sturgeon, Gregory M.; Gehm, Michael E.; Catenacci, Matthew; Wiley, Benjamin J.; Samei, Ehsan; Lo, Joseph Y.

    2017-03-01

    Physical breast phantoms provide a standard method to test, optimize, and develop clinical mammography systems, including new digital breast tomosynthesis (DBT) systems. In previous work, we produced an anthropomorphic phantom based on 500x500x500 μm breast CT data using commercial 3D printing. We now introduce an improved phantom based on a new cohort of virtual models with 155x155x155 μm voxels and fabricated through voxelized 3D printing and dithering, which confer higher resolution and greater control over contrast. This new generation includes a uniform chest wall extension for evaluating conventional QC metrics. The uniform region contains a grayscale step wedge, chest wall coverage markers, fiducial markers, spheres, and metal ink stickers of line pairs and edges to assess contrast, resolution, artifact spread function, MTF, and other criteria. We also experimented with doping photopolymer material with calcium, iodine, and zinc to increase our current contrast. In particular, zinc was discovered to significantly increase attenuation beyond 100% breast density with a linear relationship between zinc concentration and attenuation or breast density. This linear relationship was retained when the zinc-doped material was applied in conjunction with 3D printing. As we move towards our long term goal of phantoms that are indistinguishable from patients, this new generation of anthropomorphic physical breast phantom validates our voxelized printing process, demonstrates the utility of a uniform QC region with features from 3D printing and metal ink stickers, and shows potential for improved contrast via doping.

  16. High fidelity digital inline holographic PTV for 3D flow measurements: from microfluidics to wall-bounded turbulence

    NASA Astrophysics Data System (ADS)

    Hong, Jiarong; Toloui, Mostafa; Mallery, Kevin

    2016-11-01

    Three-dimensional PIV and PTV provides the most comprehensive flow information for unraveling the physical phenomena in a wide range of fluid problems, from microfluidics to wall-bounded turbulent flows. Compared with other commercialized 3D PIV techniques, such as tomographic PIV and defocusing PIV, the digital inline holographic PTV (namely DIH-PTV) provides 3D flow measurement solution with high spatial resolution, low cost optical setup, and easy alignment and calibration. Despite these advantages, DIH-PTV suffers from major limitations including poor longitudinal resolution, human intervention (i.e. requirement for manually determined tuning parameters during tracer field reconstruction and extraction), limited tracer concentration, small sampling volume and expensive computations, limiting its broad use for 3D flow measurements. Here we will report our latest work on improving DIH-PTV method through an integration of deconvolution algorithm, iterative removal method and GPU computation to overcome some of abovementioned limitations. We will also present the application of our DIH-PTV for measurements in the following sample cases: (i) flows in bio-filmed microchannel with 50-60 μm vector spacing within sampling volumes of 1 mm (streamwise) x 1 mm (wall-normal) x 1 mm (spanwise); (ii) turbulent flows over smooth and rough surfaces (1.1 mm vector spacing within 15 mm x 50 mm x 15 mm); (iii) 3D distribution and kinematics of inertial particles in turbulent air duct flow.

  17. Lightweight NiFe2O4 with controllable 3D network structure and enhanced microwave absorbing properties

    NASA Astrophysics Data System (ADS)

    Wang, Fen; Wang, Xing; Zhu, Jianfeng; Yang, Haibo; Kong, Xingang; Liu, Xiao

    2016-11-01

    3D network structure NiFe2O4 was successfully synthesized by a templated salt precipitation method using PMMA colloid crystal as templates. The morphology, phase composition and microwave absorbing properties of as-prepared samples were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), vector network analyzer (VNA), and so on. The results revealed that the 3D network structure was configurated with smooth spherical walls composed of NiFe2O4 nanocrystals and their pore diameters being in the range of 80–250 nm. The microwave absorption properties of the 3D network structure NiFe2O4 were crucially determined by the special structure. The synergy of intrinsic magnetic loss of magnetic NiFe2O4 and the interfacial polarization enhanced by 3D network structure and the interaction of multiple mechanisms endowed the sample with the feature of strong absorption, broad bandwidth and lightweight. There is more than one valley in the reflection loss curves and the maximum reflection loss is 27.5 dB with a bandwidth of 4 GHz. Moreover, the 3D network structure NiFe2O4 show a greater reflection loss with the same thickness comparing to the ordinary NiFe2O4 nanoparticles, which could achieve the feature of lightweight of the microwave absorbing materials.

  18. Lightweight NiFe2O4 with controllable 3D network structure and enhanced microwave absorbing properties

    PubMed Central

    Wang, Fen; Wang, Xing; Zhu, Jianfeng; Yang, Haibo; Kong, Xingang; Liu, Xiao

    2016-01-01

    3D network structure NiFe2O4 was successfully synthesized by a templated salt precipitation method using PMMA colloid crystal as templates. The morphology, phase composition and microwave absorbing properties of as-prepared samples were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), vector network analyzer (VNA), and so on. The results revealed that the 3D network structure was configurated with smooth spherical walls composed of NiFe2O4 nanocrystals and their pore diameters being in the range of 80–250 nm. The microwave absorption properties of the 3D network structure NiFe2O4 were crucially determined by the special structure. The synergy of intrinsic magnetic loss of magnetic NiFe2O4 and the interfacial polarization enhanced by 3D network structure and the interaction of multiple mechanisms endowed the sample with the feature of strong absorption, broad bandwidth and lightweight. There is more than one valley in the reflection loss curves and the maximum reflection loss is 27.5 dB with a bandwidth of 4 GHz. Moreover, the 3D network structure NiFe2O4 show a greater reflection loss with the same thickness comparing to the ordinary NiFe2O4 nanoparticles, which could achieve the feature of lightweight of the microwave absorbing materials. PMID:27897209

  19. Lightweight NiFe2O4 with controllable 3D network structure and enhanced microwave absorbing properties.

    PubMed

    Wang, Fen; Wang, Xing; Zhu, Jianfeng; Yang, Haibo; Kong, Xingang; Liu, Xiao

    2016-11-29

    3D network structure NiFe2O4 was successfully synthesized by a templated salt precipitation method using PMMA colloid crystal as templates. The morphology, phase composition and microwave absorbing properties of as-prepared samples were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), vector network analyzer (VNA), and so on. The results revealed that the 3D network structure was configurated with smooth spherical walls composed of NiFe2O4 nanocrystals and their pore diameters being in the range of 80-250 nm. The microwave absorption properties of the 3D network structure NiFe2O4 were crucially determined by the special structure. The synergy of intrinsic magnetic loss of magnetic NiFe2O4 and the interfacial polarization enhanced by 3D network structure and the interaction of multiple mechanisms endowed the sample with the feature of strong absorption, broad bandwidth and lightweight. There is more than one valley in the reflection loss curves and the maximum reflection loss is 27.5 dB with a bandwidth of 4 GHz. Moreover, the 3D network structure NiFe2O4 show a greater reflection loss with the same thickness comparing to the ordinary NiFe2O4 nanoparticles, which could achieve the feature of lightweight of the microwave absorbing materials.

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

    NASA Astrophysics Data System (ADS)

    Lun, Huijie; Li, Xuefei; Wang, Xiao; Li, Haiyan; Li, Yamin; Bai, Yan

    2017-01-01

    A new coordination polymer, {[Mn(HPIDC)(H2O)]·2H2O}n (1) (H3PIDC = 2-(pyridin-4-yl)-1H-imidazole-4,5-dicarboxylic acid), has been obtained by hydrothermal method and structurally characterized by X-ray single crystal diffraction, elemental analysis and thermogravimetric analysis (TGA). X-ray single crystal diffraction reveals that compound 1 crystallizing in acentric Pna21 space group, exhibits an ultimate racemic three-dimension framework with rare noninterpenetrated (10,3)-d (or utp) topology due to the alternate array of left- and right-handed helixes. Moreover, compound 1 also features ferroelectric, nonlinear optical (NLO) and antiferromagnetic behaviors.

  1. Superpose3D: A Local Structural Comparison Program That Allows for User-Defined Structure Representations

    PubMed Central

    Gherardini, Pier Federico; Ausiello, Gabriele; Helmer-Citterich, Manuela

    2010-01-01

    Local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. The outcome of such analyses is critically dependent on the representation used to describe the structure. Indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. We have therefore developed superpose3D, a novel structural comparison software that lets users specify, with a powerful and flexible syntax, the structure description most suited to the requirements of their analysis. Input proteins are processed according to the user's directives and the program identifies sets of residues (or groups of atoms) that have a similar 3D position in the two structures. The advantages of using such a general purpose program are demonstrated with several examples. These test cases show that no single representation is appropriate for every analysis, hence the usefulness of having a flexible program that can be tailored to different needs. Moreover we also discuss how to interpret the results of a database screening where a known structural motif is searched against a large ensemble of structures. The software is written in C++ and is released under the open source GPL license. Superpose3D does not require any external library, runs on Linux, Mac OSX, Windows and is available at http://cbm.bio.uniroma2.it/superpose3D. PMID:20700534

  2. Ex Vivo 3D Diffusion Tensor Imaging and Quantification of Cardiac Laminar Structure

    PubMed Central

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

    2007-01-01

    A three-dimensional (3D) diffusion-weighted imaging (DWI) method for measuring cardiac fiber structure at high spatial resolution is presented. The method was applied to the ex vivo reconstruction of the fiber architecture of seven canine hearts. A novel hypothesis-testing method was developed and used to show that distinct populations of secondary and tertiary eigenvalues may be distinguished at reasonable confidence levels (P ≤ 0.01) within the canine ventricle. Fiber inclination and sheet angles are reported as a function of transmural depth through the anterior, lateral, and posterior left ventricle (LV) free wall. Within anisotropic regions, two consistent and dominant orientations were identified, supporting published results from histological studies and providing strong evidence that the tertiary eigenvector of the diffusion tensor (DT) defines the sheet normal. PMID:16149057

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

    PubMed

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

    2016-11-04

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

  4. DYNA3D Finite Element Analysis of Steam Explosion Loads on a Pedestal Wall Design

    SciTech Connect

    Noble, C R

    2007-01-18

    The objective of this brief report is to document the ESBWR pedestal wall finite element analyses that were performed as a quick turnaround effort in July 2005 at Lawrence Livermore National Laboratory and describe the assumptions and failure criteria used for these analyses [Ref 4]. The analyses described within are for the pedestal wall design that included an internal steel liner. The goal of the finite element analyses was to assist in determining the load carrying capacity of the ESBWR pedestal wall subjected to an impulsive pressure generated by a steam explosion.

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

    PubMed Central

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W.A.; Chothia, Cyrus; Cozzetto, Domenico; Dana, José M.; Filippis, Ioannis; Gough, Julian; Jones, David T.; Kelley, Lawrence A.; Kleywegt, Gerard J.; Minneci, Federico; Mistry, Jaina; Murzin, Alexey G.; Ochoa-Montaño, Bernardo; Oates, Matt E.; Punta, Marco; Rackham, Owen J.L.; Stahlhacke, Jonathan; Sternberg, Michael J.E.; Velankar, Sameer; Orengo, Christine

    2015-01-01

    Genome3D (http://www.genome3d.eu) is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the resource. We have annotated representatives from Pfam families to improve coverage of diverse sequences and added a fast sequence search to the website to allow users to find Genome3D-annotated sequences similar to their own. We have improved and extended the Genome3D data, enlarging the source data set from three model organisms to 10, and adding VIVACE, a resource new to Genome3D. We have analysed and updated Genome3D's SCOP/CATH mapping. Finally, we have improved the superposition tools, which now give users a more powerful interface for investigating similarities and differences between structural models. PMID:25348407

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

    PubMed Central

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

    2012-01-01

    Structure and composition at the nanoscale determine the behavior of biological systems and engineered materials. The drive to understand and control this behavior has placed strong demands on developing methods for high resolution imaging. In general, the improvement of three-dimensional (3D) resolution is accomplished by tightening constraints: reduced manageable specimen sizes, decreasing analyzable volumes, degrading contrasts, and increasing sample preparation efforts. Aiming to overcome these limitations, we present a non-destructive and multiple-contrast imaging technique, using principles of X-ray laminography, thus generalizing tomography towards laterally extended objects. We retain advantages that are usually restricted to 2D microscopic imaging, such as scanning of large areas and subsequent zooming-in towards a region of interest at the highest possible resolution. Our technique permits correlating the 3D structure and the elemental distribution yielding a high sensitivity to variations of the electron density via coherent imaging and to local trace element quantification through X-ray fluorescence. We demonstrate the method by imaging a lithographic nanostructure and an aluminum alloy. Analyzing a biological system, we visualize in lung tissue the subcellular response to toxic stress after exposure to nanotubes. We show that most of the nanotubes are trapped inside alveolar macrophages, while a small portion of the nanotubes has crossed the barrier to the cellular space of the alveolar wall. In general, our method is non-destructive and can be combined with different sample environmental or loading conditions. We therefore anticipate that correlative X-ray nano-laminography will enable a variety of in situ and in operando 3D studies. PMID:23185554

  7. In Vivo/Ex Vivo MRI-Based 3D Non-Newtonian FSI Models for Human Atherosclerotic Plaques Compared with Fluid/Wall-Only Models.

    PubMed

    Yang, Chun; Tang, Dalin; Yuan, Chun; Hatsukami, Thomas S; Zheng, Jie; Woodard, Pamela K

    2007-01-01

    It has been recognized that fluid-structure interactions (FSI) play an important role in cardiovascular disease initiation and development. However, in vivo MRI multi-component FSI models for human carotid atherosclerotic plaques with bifurcation and quantitative comparisons of FSI models with fluid-only or structure-only models are currently lacking in the literature. A 3D non-Newtonian multi-component FSI model based on in vivo/ex vivo MRI images for human atherosclerotic plaques was introduced to investigate flow and plaque stress/strain behaviors which may be related to plaque progression and rupture. Both artery wall and plaque components were assumed to be hyperelastic, isotropic, incompressible and homogeneous. Blood flow was assumed to be laminar, non-Newtonian, viscous and incompressible. In vivo/ex vivo MRI images were acquired using histologically-validated multi-spectral MRI protocols. The 3D FSI models were solved and results were compared with those from a Newtonian FSI model and wall-only/fluid-only models. A 145% difference in maximum principal stresses (Stress-P(1)) between the FSI and wall-only models and 40% difference in flow maximum shear stress (MSS) between the FSI and fluid-only models were found at the throat of the plaque using a severe plaque sample (70% severity by diameter). Flow maximum shear stress (MSS) from the rigid wall model is much higher (20-40% in maximum MSS values, 100-150% in stagnation region) than those from FSI models.

  8. Semiautomatic approaches to account for 3-D distortion of the electric field from local, near-surface structures in 3-D resistivity inversions of 3-D regional magnetotelluric data

    USGS Publications Warehouse

    Rodriguez, Brian D.

    2017-03-31

    This report summarizes the results of three-dimensional (3-D) resistivity inversion simulations that were performed to account for local 3-D distortion of the electric field in the presence of 3-D regional structure, without any a priori information on the actual 3-D distribution of the known subsurface geology. The methodology used a 3-D geologic model to create a 3-D resistivity forward (“known”) model that depicted the subsurface resistivity structure expected for the input geologic configuration. The calculated magnetotelluric response of the modeled resistivity structure was assumed to represent observed magnetotelluric data and was subsequently used as input into a 3-D resistivity inverse model that used an iterative 3-D algorithm to estimate 3-D distortions without any a priori geologic information. A publicly available inversion code, WSINV3DMT, was used for all of the simulated inversions, initially using the default parameters, and subsequently using adjusted inversion parameters. A semiautomatic approach of accounting for the static shift using various selections of the highest frequencies and initial models was also tested. The resulting 3-D resistivity inversion simulation was compared to the “known” model and the results evaluated. The inversion approach that produced the lowest misfit to the various local 3-D distortions was an inversion that employed an initial model volume resistivity that was nearest to the maximum resistivities in the near-surface layer.

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

    PubMed

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

    2016-07-01

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

  10. Holographic microscopy and microfluidics platform for measuring wall stress and 3D flow over surfaces textured by micro-pillars.

    PubMed

    Bocanegra Evans, Humberto; Gorumlu, Serdar; Aksak, Burak; Castillo, Luciano; Sheng, Jian

    2016-06-29

    Understanding how fluid flow interacts with micro-textured surfaces is crucial for a broad range of key biological processes and engineering applications including particle dispersion, pathogenic infections, and drag manipulation by surface topology. We use high-speed digital holographic microscopy (DHM) in combination with a correlation based de-noising algorithm to overcome the optical interference generated by surface roughness and to capture a large number of 3D particle trajectories in a microfluidic channel with one surface patterned with micropillars. It allows us to obtain a 3D ensembled velocity field with an uncertainty of 0.06% and 2D wall shear stress distribution at the resolution of ~65 μPa. Contrary to laminar flow in most microfluidics, we find that the flow is three-dimensional and complex for the textured microchannel. While the micropillars affect the velocity flow field locally, their presence is felt globally in terms of wall shear stresses at the channel walls. These findings imply that micro-scale mixing and wall stress sensing/manipulation can be achieved through hydro-dynamically smooth but topologically rough micropillars.

  11. Holographic microscopy and microfluidics platform for measuring wall stress and 3D flow over surfaces textured by micro-pillars

    PubMed Central

    Bocanegra Evans, Humberto; Gorumlu, Serdar; Aksak, Burak; Castillo, Luciano; Sheng, Jian

    2016-01-01

    Understanding how fluid flow interacts with micro-textured surfaces is crucial for a broad range of key biological processes and engineering applications including particle dispersion, pathogenic infections, and drag manipulation by surface topology. We use high-speed digital holographic microscopy (DHM) in combination with a correlation based de-noising algorithm to overcome the optical interference generated by surface roughness and to capture a large number of 3D particle trajectories in a microfluidic channel with one surface patterned with micropillars. It allows us to obtain a 3D ensembled velocity field with an uncertainty of 0.06% and 2D wall shear stress distribution at the resolution of ~65 μPa. Contrary to laminar flow in most microfluidics, we find that the flow is three-dimensional and complex for the textured microchannel. While the micropillars affect the velocity flow field locally, their presence is felt globally in terms of wall shear stresses at the channel walls. These findings imply that micro-scale mixing and wall stress sensing/manipulation can be achieved through hydro-dynamically smooth but topologically rough micropillars. PMID:27353632

  12. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    PubMed

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

    2016-05-01

    Coupling the photoreduction of a metal precursor with 3D-printing technology is shown to allow the fabrication of conductive 3D hybrid structures consisting of metal nanoparticles and organic polymers shaped in complex multilayered architectures. 3D conductive structures are fabricated incorporating silver nitrate into a photocurable oligomer in the presence of suitable photoinitiators and exposing them to a digital light system. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    PubMed

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

    2015-09-01

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

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

    NASA Technical Reports Server (NTRS)

    Huang, T. S.

    1982-01-01

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

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  17. Using "click-e-bricks" to make 3D elastomeric structures.

    PubMed

    Morin, Stephen A; Shevchenko, Yanina; Lessing, Joshua; Kwok, Sen Wai; Shepherd, Robert F; Stokes, Adam A; Whitesides, George M

    2014-09-10

    Soft, 3D elastomeric structures and composite structures are easy to fabricate using click-e-bricks, and the internal architecture of these structures together with the capabilities built into the bricks themselves provide mechanical, optical, electrical, and fluidic functions.

  18. The 3D Structure of the Galactic Bulge

    NASA Astrophysics Data System (ADS)

    Zoccali, Manuela; Valenti, Elena

    2016-06-01

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

  19. Cooperative Wall-climbing Robots in 3D Environments for Surveillance and Target Tracking

    DTIC Science & Technology

    2009-02-08

    distribution of impeller vanes, volume of the chamber, and sealing effect , etc. Fig. 5 and 6 show some exemplary simulation results. In paper [11], we...Environments for Surveillance and Target Tracking 11 multiple nonholonomic mobile robots using Cartesian coordinates. Based on the special feature...gamma-ray or x-ray cargo inspection system. Three-dimensional (3D) measurements of the objects inside a cargo can be obtained by effectively

  20. The 3D structures of VDAC represent a native conformation

    PubMed Central

    Hiller, Sebastian; Abramson, Jeff; Mannella, Carmen; Wagner, Gerhard; Zeth, Kornelius

    2010-01-01

    The most abundant protein of the mitochondrial outer membrane is the voltage-dependent anion channel (VDAC), which facilitates the exchange of ions and molecules between mitochondria and cytosol and is regulated by interactions with other proteins and small molecules. VDAC has been extensively studied for more than three decades, and last year three independent investigations revealed a structure of VDAC-1 exhibiting 19 transmembrane β-strands, constituting a unique structural class of β-barrel membrane proteins. Here, we provide a historical perspective on VDAC research and give an overview of the experimental design used to obtain these structures. Furthermore, we validate the protein refolding approach and summarize biochemical and biophysical evidence that links the 19-stranded structure to the native form of VDAC. PMID:20708406

  1. 3-D Structure of Molecules of Biological Significance

    ERIC Educational Resources Information Center

    Bennett, Alice S.; Schwenk, Karl

    1974-01-01

    Describes how to use the distinctive properties of osazone formation in conjunction with molecular model construction to demonstrate the relationship between the three-dimensional structures of simple sugars and the shapes of crystals they form. (BR)

  2. The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database.

    PubMed

    Garavelli, J S; Hou, Z; Pattabiraman, N; Stephens, R M

    2001-01-01

    The RESID Database is a comprehensive collection of annotations and structures for protein post-translational modifications including N-terminal, C-terminal and peptide chain cross-link modifications. The RESID Database includes systematic and frequently observed alternate names, Chemical Abstracts Service registry numbers, atomic formulas and weights, enzyme activities, taxonomic range, keywords, literature citations with database cross-references, structural diagrams and molecular models. The NRL-3D Sequence-Structure Database is derived from the three-dimensional structure of proteins deposited with the Research Collaboratory for Structural Bioinformatics Protein Data Bank. The NRL-3D Database includes standardized and frequently observed alternate names, sources, keywords, literature citations, experimental conditions and searchable sequences from model coordinates. These databases are freely accessible through the National Cancer Institute-Frederick Advanced Biomedical Computing Center at these web sites: http://www. ncifcrf.gov/RESID, http://www.ncifcrf.gov/NRL-3D; or at these National Biomedical Research Foundation Protein Information Resource web sites: http://pir.georgetown.edu/pirwww/dbinfo/resid .html, http://pir.georgetown.edu/pirwww/dbinfo/nrl3d .html

  3. Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database

    PubMed Central

    Buchan, Daniel W.A.; Shepherd, Adrian J.; Lee, David; Pearl, Frances M.G.; Rison, Stuart C.G.; Thornton, Janet M.; Orengo, Christine A.

    2002-01-01

    We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies. PMID:11875040

  4. On 3D flow-structures behind an inclined plate

    NASA Astrophysics Data System (ADS)

    Uruba, Václav; Pavlík, David; Procházka, Pavel; Skála, Vladislav; Kopecký, Václav

    Stereo PIV measurements has been performed behind the inclined plate, angle of attack 5 and 10 deg. Occurrence and dynamics of streamwise structures behind the plate trailing edge have been studied in details using POD method. The streamwise structures are represented by vortices and low- and highvelocity regions, probably streaks. The obtained results support the hypothesis of an airfoil-flow force interaction by Hoffman and Johnson [1,2].

  5. MUFOLD: A new solution for protein 3D structure prediction.

    PubMed

    Zhang, Jingfen; Wang, Qingguo; Barz, Bogdan; He, Zhiquan; Kosztin, Ioan; Shang, Yi; Xu, Dong

    2010-04-01

    There have been steady improvements in protein structure prediction during the past 2 decades. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. First, a systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein. Then, an efficient process was applied for iterative coarse-grain model generation and evaluation at the Calpha or backbone level. In this process, we construct models using interresidue spatial restraints derived from alignments by multidimensional scaling, evaluate and select models through clustering and static scoring functions, and iteratively improve the selected models by integrating spatial restraints and previous models. Finally, the full-atom models were evaluated using molecular dynamics simulations based on structural changes under simulated heating. We have continuously improved the performance of MUFOLD by using a benchmark of 200 proteins from the Astral database, where no template with >25% sequence identity to any target protein is included. The average root-mean-square deviation of the best models from the native structures is 4.28 A, which shows significant and systematic improvement over our previous methods. The computing time of MUFOLD is much shorter than many other tools, such as Rosetta. MUFOLD demonstrated some success in the 2008 community-wide experiment for protein structure prediction CASP8.

  6. Comparison between 2D and 3D high-resolution black-blood techniques for carotid artery wall imaging in clinically significant atherosclerosis.

    PubMed

    Balu, Niranjan; Chu, Baocheng; Hatsukami, Thomas S; Yuan, Chun; Yarnykh, Vasily L

    2008-04-01

    To compare two- (2D) and three-dimensional (3D) black-blood imaging methods for morphological measurements of the carotid artery wall and atherosclerotic plaque. A total of 18 subjects with 50% to 79% carotid stenosis were scanned with 2D (2-mm slice thickness) and 3D (1-mm/0.5-mm actual/interpolated slice thickness) T1-weighted fast spin-echo (FSE) black-blood imaging sequences with double inversion-recovery (DIR) blood suppression. Morphological measurements (lumen area, wall area, vessel area, mean wall thickness, and maximal wall thickness), signal-to-noise ratio (SNR) in the wall and lumen, and wall-lumen contrast-to-noise ratio (CNR) were compared between 2D and 3D images. The effect of improved slice resolution in 3D imaging was evaluated for visualization of small plaque components. Lumen SNR (P = 0.16), wall SNR (P = 0.65), and CNR (P = 0.94) were comparable between 2D/3D. There was no difference in average lumen area (P = 0.16), average wall area (P = 0.99), average vessel area (P = 0.0.58), mean wall thickness (P = 0.09), and maximum wall thickness (P = 0.06) between 2D/3D. Distributions of small plaque components such as calcification were better characterized by the 3D acquisition. There was a higher sensitivity to motion artifacts with 3D imaging, resulting in three examinations with low image quality. 2D and 3D protocols provided comparable morphometric measurements of the carotid artery. The major advantage of 3D imaging is improved small plaque component visualization, while the 2D technique provides higher reliability for image quality. (c) 2008 Wiley-Liss, Inc.

  7. Comparison Between 2D and 3D High-Resolution Black-Blood Techniques for Carotid Artery Wall Imaging in Clinically Significant Atherosclerosis

    PubMed Central

    Balu, Niranjan; Chu, Baocheng; Hatsukami, Thomas S.; Yuan, Chun; Yarnykh, Vasily L.

    2010-01-01

    Purpose To compare two- (2D) and three-dimensional (3D) black-blood imaging methods for morphological measurements of the carotid artery wall and atherosclerotic plaque. Materials and Methods A total of 18 subjects with 50% to 79% carotid stenosis were scanned with 2D (2-mm slice thickness) and 3D (1-mm/0.5-mm actual/interpolated slice thickness) T1-weighted fast spin-echo (FSE) black-blood imaging sequences with double inversion-recovery (DIR) blood suppression. Morphological measurements (lumen area, wall area, vessel area, mean wall thickness, and maximal wall thickness), signal-to-noise ratio (SNR) in the wall and lumen, and wall-lumen contrast-to-noise ratio (CNR) were compared between 2D and 3D images. The effect of improved slice resolution in 3D imaging was evaluated for visualization of small plaque components. Results Lumen SNR (P = 0.16), wall SNR (P = 0.65), and CNR (P = 0.94) were comparable between 2D/3D. There was no difference in average lumen area (P = 0.16), average wall area (P = 0.99), average vessel area (P = 0.0.58), mean wall thickness (P = 0.09), and maximum wall thickness (P = 0.06) between 2D/3D. Distributions of small plaque components such as calcification were better characterized by the 3D acquisition. There was a higher sensitivity to motion artifacts with 3D imaging, resulting in three examinations with low image quality. Conclusion 2D and 3D protocols provided comparable morphometric measurements of the carotid artery. The major advantage of 3D imaging is improved small plaque component visualization, while the 2D technique provides higher reliability for image quality. PMID:18383253

  8. 3D multi-directional sensor with pyramid mirror and structured light

    NASA Astrophysics Data System (ADS)

    Xu, Jing; Wang, Peng; Yao, Youyou; Liu, Shuntao; Zhang, Guanglie

    2017-06-01

    Structured-light-based 3D multi-directional sensors are widely used due to their flexible field of view (FOV), which is a significant benefit. Nevertheless, existing 3D multi-directional sensors based on linear lasers are only capable of measuring a slice of a 3D scene at low resolution. In addition, other 3D multi-directional sensors are capable of measuring 3D scenes by shooting 2D structured light patterns in different directions through curved mirrors. However, the projected and captured structured light patterns are blurred due to the optical aberration property of curved mirrors, resulting in inaccurate 3D reconstruction. This paper proposes a 3D, high-resolution, high-accuracy, real-time multi-directional sensor that utilizes pyramid mirrors to decompose the FOVs into different directions and reduce the optical aberration phenomenon. The mathematical model of the 3D sensor is presented, and the FOV is analyzed. A dual-frequency phase-shifting fringe pattern is used for 3D reconstruction in real time. Moreover, the sensor is calibrated using a planar circle calibration gauge and the Householder reflection constraint. Finally, the experimental results demonstrate that the measurement error of the 3D multi-directional sensor is less than 1 mm and 0.03 rad, thus verifying the method's feasibility.

  9. Subtractive 3D Printing of Optically Active Diamond Structures

    NASA Astrophysics Data System (ADS)

    Martin, Aiden A.; Toth, Milos; Aharonovich, Igor

    2014-05-01

    Controlled fabrication of semiconductor nanostructures is an essential step in engineering of high performance photonic and optoelectronic devices. Diamond in particular has recently attracted considerable attention as a promising platform for quantum technologies, photonics and high resolution sensing applications. Here we demonstrate the fabrication of optically active, functional diamond structures using gas-mediated electron beam induced etching (EBIE). The technique achieves dry chemical etching at room temperature through the dissociation of surface-adsorbed H2O molecules by energetic electrons in a water vapor environment. Parallel processing is possible by electron flood exposure and the use of an etch mask, while high resolution, mask-free, iterative editing is demonstrated by direct write etching of inclined facets of diamond microparticles. The realized structures demonstrate the potential of EBIE for the fabrication of optically active structures in diamond.

  10. Structured light imaging system for structural and optical characterization of 3D tissue-simulating phantoms

    NASA Astrophysics Data System (ADS)

    Liu, Songde; Smith, Zach; Xu, Ronald X.

    2016-10-01

    There is a pressing need for a phantom standard to calibrate medical optical devices. However, 3D printing of tissue-simulating phantom standard is challenged by lacking of appropriate methods to characterize and reproduce surface topography and optical properties accurately. We have developed a structured light imaging system to characterize surface topography and optical properties (absorption coefficient and reduced scattering coefficient) of 3D tissue-simulating phantoms. The system consisted of a hyperspectral light source, a digital light projector (DLP), a CMOS camera, two polarizers, a rotational stage, a translation stage, a motion controller, and a personal computer. Tissue-simulating phantoms with different structural and optical properties were characterized by the proposed imaging system and validated by a standard integrating sphere system. The experimental results showed that the proposed system was able to achieve pixel-level optical properties with a percentage error of less than 11% for absorption coefficient and less than 7% for reduced scattering coefficient for phantoms without surface curvature. In the meanwhile, 3D topographic profile of the phantom can be effectively reconstructed with an accuracy of less than 1% deviation error. Our study demonstrated that the proposed structured light imaging system has the potential to characterize structural profile and optical properties of 3D tissue-simulating phantoms.

  11. 3D engineered fiberboard : a new structural building product

    Treesearch

    John F. Hunt; Jerrold E. Winandy

    2002-01-01

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

  12. Delineation of nuclear structures in 3D multicellular systems

    SciTech Connect

    2013-09-13

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

  13. Analysis of Metrics for Human Detection behind Walls Using Experimental 3-D Synthetic Aperture Radar Imagery

    DTIC Science & Technology

    2014-12-01

    layouts and to detect targets of interest behind walls such as humans, arms caches , and furniture. This situational awareness capability can be...characterize a document and could be helpful in cataloguing the document. They should be selected so that no security classification is required. Identifiers

  14. Estimation of Solar Energy on Vertical 3D Building Walls on City Quarter Scale

    NASA Astrophysics Data System (ADS)

    Jaugsch, F.; Löwner, M.-O.

    2016-10-01

    In urban areas, solar energy is one promising source of renewable energy to achieve the EU parliament's goal of reducing CO2 emissions by 20 % compared to 1990. Although annual radiation on vertical walls is lower than that on roof surfaces, they are larger in area and, therefore may contribute to energy production. On the other hand, the modelling of shadowing effects is cost intensive in an complex urban environment. Here we present a method for the calculation of solar potential on vertical walls for simple 2D maps with additional building height information. We introduced observer point columns that enable a fast decision whether a whole vertical set of observer points is illuminated or not. By the introduction of a maximum shade length, we reduce processing time in ArcGIS. 206,291 points of 130 buildings have been analysed in time steps of 15 minutes resulting in 15 769 pairs of solar angles. Results disprove the potential of vertical walls serving to fill the winter gap of roof mounted solar energy plants. Best wall orientation for the deployment of solar panels are west and east in summer, whereas it is southeast in winter.

  15. Imaging solar coronal magnetic structures in 3D

    NASA Astrophysics Data System (ADS)

    Cartledge, N. P.

    The study of solar coronal structures and, in particular prominences, is a key part of understanding the highly complex physical mechanisms occurring in the Sun's atmosphere. Solar prominences are important in their own right and some of the most puzzling questions in solar theory have arisen through their study. For example, how do they form and how is their mass continuously replenished? How can the magnetic field provide their continuous support against gravity over time periods of several months? How can such cool, dense material exist in thermal equilibrium in the surrounding coronal environment? Why do they erupt? A study of their structure and that of the surrounding medium is important in determining the nature of the coronal plasma and magnetic field. Also, prominences are closely associated with other key phenomena such as coronal mass ejections and eruptive solar flares which occur as a prominence loses equilibrium and rises from the solar surface. Our current understanding of these fascinating structures is extremely limited and we know very little about their basic global structure. In fact, recent prominence observations have caused our basic paradigms to be challenged (Priest, 1996) and so we must set up new models in order to gain even a fundamental understanding. Prominences are highly nonlinear, three-dimensional structures. Large feet (or barbs) reach out from the main body of a prominence and reach down to the photosphere where the dense material continuously drains away. These provide a real clue to the three-dimensional nature of the coronal field and its relation to the photospheric field. It is important, therefore, to make stereographic observations of prominences in order to gain a basic understanding of their essentially three-dimensional nature and attempt to formulate new paradigms for their structure and evolution. There is no doubt that the study of prominences in three dimensions is a crucial exercise if we are to develop a better

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

    NASA Astrophysics Data System (ADS)

    Li, Ruiya; Tan, Yuegang; Zhou, Zude; Fang, Liang; Chen, Yiyang

    2016-10-01

    3D printing technology is a rapidly developing manufacturing technology, which is known as a core technology in the third industrial revolution. With the continuous improvement of the application of 3D printing products, the health monitoring of the 3D printing structure is particularly important. Fiber Bragg grating (FBG) sensing technology is a new type of optical sensing technology with unique advantages comparing to traditional sensing technology, and it has great application prospects in structural health monitoring. In this paper, the FBG sensors embedded in the internal structure of the 3D printing were used to monitor the static and dynamic strain variation of 3D printing structure during loading process. The theoretical result and experimental result has good consistency and the characteristic frequency detected by FBG sensor is consistent with the testing results of traditional accelerator in the dynamic experiment. The results of this paper preliminary validate that FBG embedded in the 3D printing structure can effectively detecting the static and dynamic stain change of the 3D printing structure, which provide some guidance for the health monitoring of 3D printing structure.

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

    PubMed

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

    2016-08-01

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

  18. The 3D Structures of Some Diarrheal Causing Bacterial Toxins

    DTIC Science & Technology

    1990-01-02

    The determination of the crystal and molecular structure of diarrzeal causing enterotoxin produced by S. aureus is the overall goal of this research...mitogenic and antigenic properties and activities of S. aureus toxins and enterotoxins have been studied extensively during t,-4 last two decades...interest in S. aureus enterotoxins has resurfaced because of their ability to stimulatj -T6 -proliferation. The arzswer to the question of how this

  19. The 3D Structure of Some Diarrheal Causing Bacterial Toxins

    DTIC Science & Technology

    1988-07-01

    structure analysis were grown by methods which we published recently (1). X-ray data have been collected from the native protein and from heavy atom...by chromatofocusing into individual bands which could be crystallized. Later on better separation was attained with isoelectric focusing. Two of the...Three possibl-a methods are under consideration: SIRAS, ISIR, and the direct ixthod with single isomorphous replacement. (2) Work -n the other toxins

  20. 3D Printing for Spacecraft Multi-Functional Structures

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    SciTech Connect

    ANDERSON, C. A.

    1999-11-22

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

  2. Non-Newtonian models for molecular viscosity and wall shear stress in a 3D reconstructed human left coronary artery.

    PubMed

    Soulis, Johannes V; Giannoglou, George D; Chatzizisis, Yiannis S; Seralidou, Kypriani V; Parcharidis, George E; Louridas, George E

    2008-01-01

    The capabilities and limitations of various molecular viscosity models, in the left coronary arterial tree, were analyzed via: molecular viscosity, local and global non-Newtonian importance factors, wall shear stress (WSS) and wall shear stress gradient (WSSG). The vessel geometry was acquired using geometrically correct 3D intravascular ultrasound (3D IVUS). Seven non-Newtonian molecular viscosity models, plus the Newtonian one, were compared. The WSS distribution yielded a consistent LCA pattern for nearly all non-Newtonian models. High molecular viscosity, low WSS and low WSSG values occurred at the outer walls of the major bifurcation in proximal LCA regions. The Newtonian blood flow was found to be a good approximation at mid- and high-strain rates. The non-Newtonian Power Law, Generalized Power Law, Carreau and Casson and Modified Cross blood viscosity models gave comparable molecular viscosity, WSS and WSSG values. The Power Law and Walburn-Schneck models over-estimated the non-Newtonian global importance factor I(G) and under-estimated the area averaged WSS and WSSG values. The non-Newtonian Power Law and the Generalized Power Law blood viscosity models were found to approximate the molecular viscosity and WSS calculations in a more satisfactory way.

  3. A 3-D Finite Element Model of Anterior Vaginal Wall Support to Evaluate Mechanisms Underlying Cystocele Formation

    PubMed Central

    Chen, Luyun; Ashton-Miller, James A.; DeLancey, John O.L.

    2009-01-01

    Objectives To develop a 3D computer model of the anterior vaginal wall and its supports, validate that model, and then use it to determine the combinations of muscle and connective tissue impairments that result in cystocele formation, as observed on dynamic magnetic resonance imaging (MRI). Methods A subject-specific 3D model of the anterior vaginal wall and its supports was developed based on MRI geometry from a healthy nulliparous woman. It included simplified representations of the anterior vaginal wall, levator muscle, cardinal and uterosacral ligaments, arcus tendineus fascia pelvis and levator ani, paravaginal attachments, and the posterior compartment. This model was then imported into ABAQUS™ and tissue properties were assigned from the literature. An iterative process was used to refine anatomical assumptions until convergence was obtained between model behavior under increases of abdominal pressure up to 168 cmH2O and deformations observed on dynamic MRI. Results Cystocele size was sensitive to abdominal pressure and impairment of connective tissue and muscle. Larger cystocele formed in the presence of impairments in muscular and apical connective tissue support compared to either support element alone. Apical impairment resulted in a larger cystocele than paravaginal impairment. Levator ani muscle impairment caused a larger urogenital hiatus size, longer length of the distal vagina exposed to a pressure differential, larger apical descent and resulted in a larger cystocele size. Conclusions Development of a cystocele requires a levator muscle impairment, an increase in abdominal pressure, and apical and paravaginal support defects. PMID:19481208

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  5. Small-angle scattering and 3D structure interpretation.

    PubMed

    Trewhella, Jill

    2016-10-01

    This review focuses on advances in the application of solution small-angle scattering (SAS) in structural analysis of biomolecules and the complexes they form. Examples highlighted illustrate the unique contribution of SAS, using both X-rays and neutrons, in hybrid or integrative modelling methods. The increased information content when neutron scattering with contrast variation is used is a particular focus. Finally, progress toward an agreed reporting framework, the development of open data and model archives, and the importance of these initiatives is covered.

  6. Electronic structure of 3d metals at finite temperatures

    SciTech Connect

    Delgadillo, I.; Gollisch, H.; Feder, R.

    1996-07-01

    A theoretical approach to the electronic structure of crystalline solids at finite temperature has been developed on the basis of the adiabatic approximation. For any given temperature, correlated ion core displacement configurations on large clusters with periodic boundary conditions are determined such that they are consistent with experimental phonon dispersion relations. Total and {ital k}{searrow}-resolved densities of states are obtained by a tight-binding recursion method for each configuration followed by a configurational average. In the case of ferromagnetic crystals, the above treatment is augmented by including the influence of spin fluctuations. The local magnetic moments associated with the atomic sites are assumed to fluctuate subject to an average magnetization and a short-range order specific for the given temperature. The spin-resolved electronic structure for temperatures up to the Curie temperature and beyond can thus be obtained. Numerical calculations are performed on Cu and Ni and the results compared to experimental photoemission data. {copyright} {ital 1996 American Institute of Physics.}

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

    PubMed Central

    Wang, Jianwei; Zhang, Yong

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Wang, Jianwei; Zhang, Yong

    2016-04-01

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

  9. a 3d GIS Method Applied to Cataloging and Restoring: the Case of Aurelian Walls at Rome

    NASA Astrophysics Data System (ADS)

    Canciani, M.; Ceniccola, V.; Messi, M.; Saccone, M.; Zampilli, M.

    2013-07-01

    The project involves architecture, archaeology, restoration, graphic documentation and computer imaging. The objective is development of a method for documentation of an architectural feature, based on a three-dimensional model obtained through laser scanning technologies, linked to a database developed in GIS environment. The case study concerns a short section of Rome's Aurelian walls, including the Porta Latina. The city walls are Rome's largest single architectural monument, subject to continuous deterioration, modification and maintenance since their original construction beginning in 271 AD. The documentation system provides a flexible, precise and easily-applied instrument for recording the full appearance, materials, stratification palimpsest and conservation status, in order to identify restoration criteria and intervention priorities, and to monitor and control the use and conservation of the walls over time. The project began with an analysis and documentation campaign integrating direct, traditional recording methods with indirect, topographic instrument and 3D laser scanning recording. These recording systems permitted development of a geographic information system based on three-dimensional modelling of separate, individual elements, linked to a database and related to the various stratigraphic horizons, the construction techniques, the component materials and their state of degradation. The investigations of the extant wall fabric were further compared to historic documentation, from both graphic and descriptive sources. The resulting model constitutes the core of the GIS system for this specific monument. The methodology is notable for its low cost, precision, practicality and thoroughness, and can be applied to the entire Aurelian wall and to other monuments.

  10. 3D nano-structures for laser nano-manipulation

    PubMed Central

    Seniutinas, Gediminas; Gervinskas, Gediminas; Brasselet, Etienne; Juodkazis, Saulius

    2013-01-01

    Summary The resputtering of gold films from nano-holes defined in a sacrificial PMMA mask, which was made by electron beam lithography, was carried out with a dry plasma etching tool in order to form well-like structures with a high aspect ratio (height/width ≈ 3–4) at the rims of the nano-holes. The extraordinary transmission through the patterns of such nano-wells was investigated experimentally and numerically. By doing numerical simulations of 50-nm and 100-nm diameter polystyrene beads in water and air, we show the potential of such patterns for self-induced back-action (SIBA) trapping. The best trapping conditions were found to be a trapping force of 2 pN/W/μm2 (numerical result) exerted on a 50-nm diameter bead in water. The simulations were based on the analytical Lorentz force model. PMID:24062979

  11. 3-D Structure of Sunspots using Imaging Spectroscopy

    NASA Technical Reports Server (NTRS)

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

    2006-01-01

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

  12. 2D and 3D reconstruction and geomechanical characterization of kilometre-scale complex folded structures

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    PubMed Central

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

    2013-01-01

    Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence–structure–function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker’s yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs). PMID:23203986

  14. 2D and 3D GPR imaging of structural ceilings in historic and existing constructions

    NASA Astrophysics Data System (ADS)

    Colla, Camilla

    2014-05-01

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

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

    NASA Technical Reports Server (NTRS)

    Riggs, H. R.

    2000-01-01

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

  16. The 3D velocity structure beneath Iceland: Identifying melt pathways

    NASA Astrophysics Data System (ADS)

    Allen, R.

    2003-04-01

    The integration of various seismic datasets, recorded by the broadband HOTSPOT network deployed across Iceland, provides one of the highest resolution studies of the crust and mantle structure associated with a plume-ridge system. The mantle P- and S-velocity models (ICEMAN), derived from teleseismic body-wave and surface wave analysis, show a vertical, cylindrical low velocity anomaly ˜200 km in diameter extending from ˜400 km, the maximum depth of resolution, up to ˜200 km above which low velocity material is present beneath all of Iceland. The maximum P- and S-velocity anomalies of -2% and -4% respectively are found beneath the northwestern edge of Vatnajokull. The crustal S-velocity model (ICECRTb) is constrained by local surface waves, refraction experiments and receiver functions, and shows significant variation in crustal thickness. The thinnest, ˜15 km, crust is found around coastal regions, the thickest crust is beneath northwestern Vatnajokull where it reaches a thickness of 45 km. Within this thick crustal root is a vertical low velocity anomaly connecting the core of the mantle anomaly to horizontal low velocity regions that extend along the western and eastern volcanic zones but not the northern volcanic zone. These crustal low velocity zones are interpreted as regions through which melt is fed from the mantle to shallow magma chambers beneath the rift zones, where crustal formation occurs. The pipework between the core of the mantle anomaly and the southern rift zones is responsible for ˜30 km thick crust. Its absence to the north results in relatively thin, ˜20 km thick, crust.

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

    NASA Astrophysics Data System (ADS)

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

    2010-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Gaso, P.; Jandura, D.; Pudis, D.

    2016-12-01

    In this paper we demonstrate possibilities of three-dimensional (3D) printing technology based on two photon polymerization. We used three-dimensional dip-in direct-laser-writing (DLW) optical lithography to fabricate 2D and 3D optical structures for optoelectronics and for optical sensing applications. DLW lithography allows us use a non conventional way how to couple light into the waveguide structure. We prepared ring resonator and we investigated its transmission spectral characteristic. We present 3D inverse opal structure from its design to printing and scanning electron microscope (SEM) imaging. Finally, SEM images of some prepared photonic crystal structures were performed.

  19. Using 3D visualization and seismic attributes to improve structural and stratigraphic resolution of reservoirs

    SciTech Connect

    Kerr, J. ); Jones, G.L. )

    1996-01-01

    Recent advances in hardware and software have given the interpreter and engineer new ways to view 3D seismic data and well bore information. Recent papers have also highlighted the use of various statistics and seismic attributes. By combining new 3D rendering technologies with recent trends in seismic analysis, the interpreter can improve the structural and stratigraphic resolution of hydrocarbon reservoirs. This paper gives several examples using 3D visualization to better define both the structural and stratigraphic aspects of several different structural types from around the world. Statistics, 3D visualization techniques and rapid animation are used to show complex faulting and detailed channel systems. These systems would be difficult to map using either 2D or 3D data with conventional interpretation techniques.

  20. Using 3D visualization and seismic attributes to improve structural and stratigraphic resolution of reservoirs

    SciTech Connect

    Kerr, J.; Jones, G.L.

    1996-12-31

    Recent advances in hardware and software have given the interpreter and engineer new ways to view 3D seismic data and well bore information. Recent papers have also highlighted the use of various statistics and seismic attributes. By combining new 3D rendering technologies with recent trends in seismic analysis, the interpreter can improve the structural and stratigraphic resolution of hydrocarbon reservoirs. This paper gives several examples using 3D visualization to better define both the structural and stratigraphic aspects of several different structural types from around the world. Statistics, 3D visualization techniques and rapid animation are used to show complex faulting and detailed channel systems. These systems would be difficult to map using either 2D or 3D data with conventional interpretation techniques.

  1. Searching protein 3-D structures for optimal structure alignment using intelligent algorithms and data structures.

    PubMed

    Novosád, Tomáš; Snášel, Václav; Abraham, Ajith; Yang, Jack Y

    2010-11-01

    In this paper, we present a novel algorithm for measuring protein similarity based on their 3-D structure (protein tertiary structure). The algorithm used a suffix tree for discovering common parts of main chains of all proteins appearing in the current research collaboratory for structural bioinformatics protein data bank (PDB). By identifying these common parts, we build a vector model and use some classical information retrieval (IR) algorithms based on the vector model to measure the similarity between proteins--all to all protein similarity. For the calculation of protein similarity, we use term frequency × inverse document frequency ( tf × idf ) term weighing schema and cosine similarity measure. The goal of this paper is to introduce new protein similarity metric based on suffix trees and IR methods. Whole current PDB database was used to demonstrate very good time complexity of the algorithm as well as high precision. We have chosen the structural classification of proteins (SCOP) database for verification of the precision of our algorithm because it is maintained primarily by humans. The next success of this paper would be the ability to determine SCOP categories of proteins not included in the latest version of the SCOP database (v. 1.75) with nearly 100% precision.

  2. Salt as a 3D element in structural modelling - example from the Central European Basin System

    NASA Astrophysics Data System (ADS)

    Maystrenko, Y. P.; Scheck-Wenderoth, M.; Bayer, U.

    2010-12-01

    The Central European Basin System (CEBS) covers the northern part of Central and Western Europe and contains up to 12 km of Permian to Cenozoic deposits. Initiated in the Early Permian, the Central European Basin System accumulated Lower Permian clastics overlain by significant amount of Upper Permian (Zechstein) salt. Post-Permian differentiation of the basin system was controlled by several phases of tectonic activity. These tectonic phases not only provoked regional shifts in subsidence and erosion but also triggered movements of the Upper Permian (Zechstein) salt. Salt rise strongly influenced the Meso-Cenozoic structural evolution in terms of mechanical decoupling of the sedimentary cover from its basement. As a result of several phases of salt tectonics, the CEBS displays a wide variety of salt structures (walls, diapirs and pillows). In order to investigate the interaction of salt movements, deposition and tectonics, the 3D structural model of the CEBS has been constructed covering the entire salt basin (Northern and Southern Permian basins). Seismic interpretation and 3D backstripping have been used to investigate both the present-day structure and the evolution of the CEBS. 3D backstripping includes 3D salt redistribution in response to the changing load conditions in the salt cover. The results of 3D modelling of salt movements and seismic data indicate that the primary initiation of salt movements occurred during the Triassic. The Triassic regional extensional event initiated a phase of salt movements within the coeval depocenters of the CEBS, such as the Glueckstadt Graben, the Horn Graben, the Fjerritslev Trough and the adjacent Himmerland Graben in Denmark, as well as the Polish Basin. The Early Triassic (Buntsandstein) and the Late Triassic (Middle-Late Keuper) extensional events triggered strongest salt movements within the central part of the Glueckstadt Graben. During the Late Jurassic-Early Cretaceous, major erosion regionally truncated the study

  3. Electrodeposition-based 3D Printing of Metallic Microarchitectures with Controlled Internal Structures.

    PubMed

    Seol, Seung Kwon; Kim, Daeho; Lee, Sanghyeon; Kim, Jung Hyun; Chang, Won Suk; Kim, Ji Tae

    2015-08-26

    3D printing of metallic microarchitectures with controlled internal structures is realized at room temperature in ambient air conditions by the manipulation of metal ion concentration and pulsed electric potentials in the electrolyte meniscus during the meniscus-guided electrodeposition. Precise control of the printing nozzle enables the drawing of complex 3D microarchitectures with well-defined geometries and positions.

  4. Qualitative Evaluation of a High-Resolution 3D Multi-Sequence Intracranial Vessel Wall Protocol at 3 Tesla MRI.

    PubMed

    Dieleman, Nikki; Yang, Wenjie; van der Kolk, Anja G; Abrigo, Jill; Lee, Ka Lok; Chu, Winnie Chiu Wing; Zwanenburg, Jaco J M; Siero, Jeroen C W; Wong, Ka Sing; Hendrikse, Jeroen; Chen, Fiona Xiang Yan

    2016-01-01

    Intracranial vessel wall imaging using MRI has great potential as a clinical method for assessing intracranial atherosclerosis. The purpose of the current study was to compare three 3T MRI vessel wall sequences with different contrast weightings (T1w, PD, T2w) and dedicated sagittal orientation perpendicular to the middle cerebral artery, to the reconstructed sagittal image from a transverse 3D T1w volumetric isotropically reconstructed turbo spin-echo acquisition (VIRTA), and provide a clinical recommendation. The above-mentioned sequences were acquired in 10 consecutive Chinese ischemic stroke or TIA patients (age: 68 years, sex: 4 females) with angiographic-confirmed MCA stenosis at 3T. Institutional review board approval was obtained. Two raters qualitatively scored all images on overall image quality, presence of artifacts, and visibility of plaques. Data were compared using Repeated measures ANOVA and Sidak's adjusted post hoc tests. All sequences except the T2w sequence were able to depict the walls of the large vessels of the Circle of Willis (p<0.05). T1w sagittal oblique VIRTA showed significantly more artifacts (p<0.01). Peripherally located plaques were sometimes missed on the sagittal sequences, but could be appreciated on the transverse T1w VIRTA. With the 3T multi-sequence vessel wall protocol we were able to assess the intracranial plaque with two different image contrast weightings. The sequence of preference to include in a clinical protocol would be the transverse 3D T1w VIRTA based on absence of artifacts, larger coverage including the whole Circle of Willis, and excellent lesion depiction.

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

    PubMed

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

    2016-03-01

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

  6. Optimal 3-D culture of primary articular chondrocytes for use in the Rotating Wall Vessel Bioreactor

    PubMed Central

    Mellor, Liliana F.; Baker, Travis L.; Brown, Raquel J.; Catlin, Lindsey W.; Oxford, Julia Thom

    2014-01-01

    INTRODUCTION Reliable culturing methods for primary articular chondrocytes are essential to study the effects of loading and unloading on joint tissue at the cellular level. Due to the limited proliferation capacity of primary chondrocytes and their tendency to dedifferentiate in conventional culture conditions, long-term culturing conditions of primary chondrocytes can be challenging. The goal of this study was to develop a suspension culturing technique that not only would retain the cellular morphology but also maintain gene expression characteristics of primary articular chondrocytes. METHODS Three-dimensional culturing methods were compared and optimized for primary articular chondrocytes in the rotating wall vessel bioreactor, which changes the mechanical culture conditions to provide a form of suspension culture optimized for low shear and turbulence. We performed gene expression analysis and morphological characterization of cells cultured in alginate beads, Cytopore-2 microcarriers, primary monolayer culture, and passaged monolayer cultures using reverse transcription-PCR and laser scanning confocal microscopy. RESULTS Primary chondrocytes grown on Cytopore-2 microcarriers maintained the phenotypical morphology and gene expression pattern observed in primary bovine articular chondrocytes, and retained these characteristics for up to 9 days. DISCUSSION Our results provide a novel and alternative culturing technique for primary chondrocytes suitable for studies that require suspension such as those using the rotating wall vessel bioreactor. In addition, we provide an alternative culturing technique for primary chondrocytes that can impact future mechanistic studies of osteoarthritis progression, treatments for cartilage damage and repair, and cartilage tissue engineering. PMID:25199120

  7. Dynamic 3D reconstructions of the heart wall from tomographic imaging

    NASA Astrophysics Data System (ADS)

    Lange, Joerg; von Smekal, Alexander

    1994-05-01

    We present a dynamic reconstruction of the left ventricle (LV) of the human heart. LV surface is represented by a set of points. The coordinates of these points are iterated by an artificial neural network while optimizing the match between the reconstruction based on these coordinates and the signal data. The input for the network are the segment's positions which represent the surface within the original data. The output is a set of real-valued coordinates quantifying the location of the LV surface points. The reconstruction is simultaneously developed in 3-D space and temporal domain. A topological constraint during training of the network gives corresponding vertices in space and time with global correctness. At any phase of the heart beat the network develops a map among the surface points which is highly ordered. This results in very regular wire-frames, that can be displayed rapidly on even small graphic workstations. Without time and third dimension this is very similar to Durbin's algorithm for solving the traveling salesman problem (TSP). To achieve a smooth representation we keep our network from developing the full TSP optimal solution.

  8. 3D lidar imaging for detecting and understanding plant responses and canopy structure.

    PubMed

    Omasa, Kenji; Hosoi, Fumiki; Konishi, Atsumi

    2007-01-01

    Understanding and diagnosing plant responses to stress will benefit greatly from three-dimensional (3D) measurement and analysis of plant properties because plant responses are strongly related to their 3D structures. Light detection and ranging (lidar) has recently emerged as a powerful tool for direct 3D measurement of plant structure. Here the use of 3D lidar imaging to estimate plant properties such as canopy height, canopy structure, carbon stock, and species is demonstrated, and plant growth and shape responses are assessed by reviewing the development of lidar systems and their applications from the leaf level to canopy remote sensing. In addition, the recent creation of accurate 3D lidar images combined with natural colour, chlorophyll fluorescence, photochemical reflectance index, and leaf temperature images is demonstrated, thereby providing information on responses of pigments, photosynthesis, transpiration, stomatal opening, and shape to environmental stresses; these data can be integrated with 3D images of the plants using computer graphics techniques. Future lidar applications that provide more accurate dynamic estimation of various plant properties should improve our understanding of plant responses to stress and of interactions between plants and their environment. Moreover, combining 3D lidar with other passive and active imaging techniques will potentially improve the accuracy of airborne and satellite remote sensing, and make it possible to analyse 3D information on ecophysiological responses and levels of various substances in agricultural and ecological applications and in observations of the global biosphere.

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  10. Direct Ink Write (DIW) 3D Printed Cellulose Nanocrystal Aerogel Structures.

    PubMed

    Li, Vincent Chi-Fung; Dunn, Conner K; Zhang, Zhe; Deng, Yulin; Qi, H Jerry

    2017-08-14

    Pure cellulose nanocrystal (CNC) aerogels with controlled 3D structures and inner pore architecture are printed using the direct ink write (DIW) technique. While traditional cellulosic aerogel processing approaches lack the ability to easily fabricate complete aerogel structures, DIW 3D printing followed by freeze drying can overcome this shortcoming and can produce CNC aerogels with minimal structural shrinkage or damage. The resultant products have great potential in applications such as tissue scaffold templates, drug delivery, packaging, etc., due to their inherent sustainability, biocompatibility, and biodegradability. Various 3D structures are successfully printed without support material, and the print quality can be improved with increasing CNC concentration and printing resolution. Dual pore CNC aerogel scaffolds are also successfully printed, where the customizable 3D structure and inner pore architecture can potentially enable advance CNC scaffold designs suited for specific cell integration requirements.

  11. Online interactive analysis of protein structure ensembles with Bio3D-web.

    PubMed

    Skjærven, Lars; Jariwala, Shashank; Yao, Xin-Qiu; Grant, Barry J

    2016-11-15

    Bio3D-web is an online application for analyzing the sequence, structure and conformational heterogeneity of protein families. Major functionality is provided for identifying protein structure sets for analysis, their alignment and refined structure superposition, sequence and structure conservation analysis, mapping and clustering of conformations and the quantitative comparison of their predicted structural dynamics. Bio3D-web is based on the Bio3D and Shiny R packages. All major browsers are supported and full source code is available under a GPL2 license from http://thegrantlab.org/bio3d-web CONTACT: bjgrant@umich.edu or lars.skjarven@uib.no. © The Author 2016. Published by Oxford University Press.

  12. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  13. Development of a 3D finite element acoustic model to predict the sound reduction index of stud based double-leaf walls

    NASA Astrophysics Data System (ADS)

    Arjunan, A.; Wang, C. J.; Yahiaoui, K.; Mynors, D. J.; Morgan, T.; Nguyen, V. B.; English, M.

    2014-11-01

    Building standards incorporating quantitative acoustical criteria to ensure adequate sound insulation are now being implemented. Engineers are making great efforts to design acoustically efficient double-wall structures. Accordingly, efficient simulation models to predict the acoustic insulation of double-leaf wall structures are needed. This paper presents the development of a numerical tool that can predict the frequency dependent sound reduction index R of stud based double-leaf walls at one-third-octave band frequency range. A fully vibro-acoustic 3D model consisting of two rooms partitioned using a double-leaf wall, considering the structure and acoustic fluid coupling incorporating the existing fluid and structural solvers are presented. The validity of the finite element (FE) model is assessed by comparison with experimental test results carried out in a certified laboratory. Accurate representation of the structural damping matrix to effectively predict the R values are studied. The possibilities of minimising the simulation time using a frequency dependent mesh model was also investigated. The FEA model presented in this work is capable of predicting the weighted sound reduction index Rw along with A-weighted pink noise C and A-weighted urban noise Ctr within an error of 1 dB. The model developed can also be used to analyse the acoustically induced frequency dependent geometrical behaviour of the double-leaf wall components to optimise them for best acoustic performance. The FE modelling procedure reported in this paper can be extended to other building components undergoing fluid-structure interaction (FSI) to evaluate their acoustic insulation.

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

    PubMed

    Markaki, Yolanda; Smeets, Daniel; Cremer, Marion; Schermelleh, Lothar

    2013-01-01

    Fluorescence in situ hybridization on three-dimensionally preserved cells (3D-FISH) is an efficient tool to analyze the subcellular localization and spatial arrangement of targeted DNA sequences and RNA transcripts at the single cell level. 3D reconstructions from serial optical sections obtained by confocal laser scanning microscopy (CLSM) have long been considered the gold standard for 3D-FISH analyses. Recent super-resolution techniques circumvent the diffraction-limit of optical resolution and have defined a new state-of-the-art in bioimaging. Three-dimensional structured illumination microscopy (3D-SIM) represents one of these technologies. Notably, 3D-SIM renders an eightfold improved volumetric resolution over conventional imaging, and allows the simultaneous visualization of differently labeled target structures. These features make this approach highly attractive for the analysis of spatial relations and substructures of nuclear targets that escape detection by conventional light microscopy. Here, we focus on the application of 3D-SIM for the visualization of subnuclear 3D-FISH preparations. In comparison with conventional fluorescence microscopy, the quality of 3D-SIM data is dependent to a much greater extent on the optimal sample preparation, labeling and acquisition conditions. We describe typical problems encountered with super-resolution imaging of in situ hybridizations in mammalian tissue culture cells and provide optimized DNA-/(RNA)-FISH protocols including combinations with immunofluorescence staining (Immuno-FISH) and DNA replication labeling using click chemistry.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    ERIC Educational Resources Information Center

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

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

  17. 3D structure of individual nanocrystals in solution by electron microscopy

    SciTech Connect

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

    2015-07-17

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

  18. 3D structure of individual nanocrystals in solution by electron microscopy

    DOE PAGES

    Park, Jungwok; Elmlund, Hans; Ercius, Peter; ...

    2015-07-17

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

  19. A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures

    PubMed Central

    Li, Haotian; Huang, Yangyu

    2017-01-01

    Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets. PMID:28358834

  20. A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures.

    PubMed

    Li, Haotian; Huang, Yangyu; Xiao, Yi

    2017-01-01

    Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets.

  1. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    ERIC Educational Resources Information Center

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

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

  2. Complex anatomy surrounding the left atrial posterior wall: analysis with 3D computed tomography.

    PubMed

    Maeda, Shingo; Iesaka, Yoshito; Uno, Kikuya; Otomo, Kiyoshi; Nagata, Yasutoshi; Suzuki, Kenji; Hachiya, Hitoshi; Goya, Masahiko; Takahashi, Atsushi; Fujiwara, Hideomi; Hiraoka, Masayasu; Isobe, Mitsuaki

    2012-01-01

    Few studies have explored the topographic anatomy of the esophagus, posterior wall of the left atrium (LA), or fat pads using multidetector computed tomography (MDCT) to prevent the risk of esophageal injury during atrial fibrillation (AF) ablation. MDCT was performed in 110 consecutive patients with paroxysmal or persistent AF before the ablation procedure to understand the anatomic relationship of the esophagus. Two major types of esophagus routes were demonstrated. Leftward (type A) and rightward (type B) routes were found in 90 and 10% of the patients, respectively. A type A route had a larger mean size of the LA than type B. The fat pad was identifiable at the level of the inferior pulmonary vein in 91% of the patients without any predominance of either type. The thickness of the fat pad was thinner in the patients with a dilated LA (>42 mm) than in those with a normal LA size (≤42 mm) (p = 0.01). The results demonstrated that the majority of cases had a leftward route of the esophagus. There was a close association between the LA dilatation and fat pad thinning. With a dilated LA, the esophagus may become easily susceptible to direct thermal injury during AF ablation. Visualization of the anatomic relationship may contribute to the prevention of the potential risk of an esophageal injury.

  3. GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function.

    PubMed

    Pietal, Michal J; Bujnicki, Janusz M; Kozlowski, Lukasz P

    2015-11-01

    To date, only a few distinct successful approaches have been introduced to reconstruct a protein 3D structure from a map of contacts between its amino acid residues (a 2D contact map). Current algorithms can infer structures from information-rich contact maps that contain a limited fraction of erroneous predictions. However, it is difficult to reconstruct 3D structures from predicted contact maps that usually contain a high fraction of false contacts. We describe a new, multi-step protocol that predicts protein 3D structures from the predicted contact maps. The method is based on a novel distance function acting on a fuzzy residue proximity graph, which predicts a 2D distance map from a 2D predicted contact map. The application of a Multi-Dimensional Scaling algorithm transforms that predicted 2D distance map into a coarse 3D model, which is further refined by typical modeling programs into an all-atom representation. We tested our approach on contact maps predicted de novo by MULTICOM, the top contact map predictor according to CASP10. We show that our method outperforms FT-COMAR, the state-of-the-art method for 3D structure reconstruction from 2D maps. For all predicted 2D contact maps of relatively low sensitivity (60-84%), GDFuzz3D generates more accurate 3D models, with the average improvement of 4.87 Å in terms of RMSD. GDFuzz3D server and standalone version are freely available at http://iimcb.genesilico.pl/gdserver/GDFuzz3D/. iamb@genesilico.pl Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Building the 3D Geological Model of Wall Rock of Salt Caverns Based on Integration Method of Multi-source data

    NASA Astrophysics Data System (ADS)

    Yongzhi, WANG; hui, WANG; Lixia, LIAO; Dongsen, LI

    2017-02-01

    In order to analyse the geological characteristics of salt rock and stability of salt caverns, rough three-dimensional (3D) models of salt rock stratum and the 3D models of salt caverns on study areas are built by 3D GIS spatial modeling technique. During implementing, multi-source data, such as basic geographic data, DEM, geological plane map, geological section map, engineering geological data, and sonar data are used. In this study, the 3D spatial analyzing and calculation methods, such as 3D GIS intersection detection method in three-dimensional space, Boolean operations between three-dimensional space entities, three-dimensional space grid discretization, are used to build 3D models on wall rock of salt caverns. Our methods can provide effective calculation models for numerical simulation and analysis of the creep characteristics of wall rock in salt caverns.

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

    NASA Astrophysics Data System (ADS)

    Sun, Changku; Tao, Li; Wang, Peng; He, Li

    2006-05-01

    A robust and accurate three dimensional (3D) acquisition system is presented, which is a combination of structured-light scanning and shape from silhouette. Using common world coordinate system, two groups of point data can be integrated into the final complete 3D model without any integration and registration algorithm. The mathematics model of structured-light scanning is described in detail, and the shape from silhouette algorithm is introduced as well. The complete 3D model of a cup with a handle is obtained successfully by the proposed technique. At last the measurement on a ball bearing is performed, with the measurement precision better than 0.15 mm.

  6. In Vivo/Ex Vivo MRI-Based 3D Non-Newtonian FSI Models for Human Atherosclerotic Plaques Compared with Fluid/Wall-Only Models

    PubMed Central

    Yang, Chun; Tang, Dalin; Yuan, Chun; Hatsukami, Thomas S.; Zheng, Jie; Woodard, Pamela K.

    2009-01-01

    It has been recognized that fluid-structure interactions (FSI) play an important role in cardiovascular disease initiation and development. However, in vivo MRI multi-component FSI models for human carotid atherosclerotic plaques with bifurcation and quantitative comparisons of FSI models with fluid-only or structure-only models are currently lacking in the literature. A 3D non-Newtonian multi-component FSI model based on in vivo/ex vivo MRI images for human atherosclerotic plaques was introduced to investigate flow and plaque stress/strain behaviors which may be related to plaque progression and rupture. Both artery wall and plaque components were assumed to be hyperelastic, isotropic, incompressible and homogeneous. Blood flow was assumed to be laminar, non-Newtonian, viscous and incompressible. In vivo/ex vivo MRI images were acquired using histologically-validated multi-spectral MRI protocols. The 3D FSI models were solved and results were compared with those from a Newtonian FSI model and wall-only/fluid-only models. A 145% difference in maximum principal stresses (Stress-P1) between the FSI and wall-only models and 40% difference in flow maximum shear stress (MSS) between the FSI and fluid-only models were found at the throat of the plaque using a severe plaque sample (70% severity by diameter). Flow maximum shear stress (MSS) from the rigid wall model is much higher (20–40% in maximum MSS values, 100–150% in stagnation region) than those from FSI models. PMID:19784387

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

    SciTech Connect

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

    2012-04-25

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

  8. RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

    PubMed Central

    Theis, Corinna; Zirbel, Craig L.; zu Siederdissen, Christian Höner; Anthon, Christian; Hofacker, Ivo L.; Nielsen, Henrik; Gorodkin, Jan

    2015-01-01

    Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution. These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D module prediction tools and apply them on a 13-way vertebrate sequence-based alignment. We find that RNA 3D modules predicted by metaRNAmodules and JAR3D are significantly enriched in the screened windows compared to their shuffled counterparts. The initially estimated FDR of 47.0% is lowered to below 25% when certain 3D module predictions are present in the window of the 2D prediction. We discuss the implications and prospects for further development of computational strategies for detection of RNA 2D structure in genomic sequence. PMID:26509713

  9. 3D structure and conductive thermal field of the sea of Marmara

    NASA Astrophysics Data System (ADS)

    Gholamrezaie, Ershad; Scheck-Wenderoth, Magdalena; Heidbach, Oliver

    2017-04-01

    The Sea of Marmara and its basins mainly evolved due to the activities of the Thrace-Eskisehir Fault Zone (TEFZ) in Neogene and the North Anatolian Fault Zone (NAFZ) in Quaternary. At present-day, the Sea of Marmara is still evolving due to the NAFZ and the Marmara region is an earthquake danger zone while hosting around 20 million of inhabitants. For a better understanding of the tectonic processes and geodynamic evolution, it is important to model the geological structure and the thermal field of this region. The aim of this study is to build a 3D lithospheric-scale structural model and a 3D conductive thermal model for the Sea of Marmara and including its adjacent onshore areas. Therefore, we integrate different geological and geophysical data such as existing structural models, well data, seismic observations and gravity to build a new 3D lithospheric-scale structural model which is additionally constrained by 3D gravity modeling. The final 3D structural model differentiates various sedimentary, crustal and mantle units and is the base for the 3D thermal field calculation. The 3D conductive thermal model is a numerical solution to the Fourier's law equation in steady-state condition and considering the thermal properties of the corresponding structural model. Our 3D lithospheric-scale models of the geological structure and the conductive thermal field are the key points for further general research and useful particularly for mechanical modeling, considering variations in rheology and strength of the lithosphere in the Marmara region. In addition, our results have application in geo-resources exploration and would be helpful in risk management and hazard mitigation.

  10. Analysis of wall shear stress around a competitive swimmer using 3D Navier-Stokes equations in CFD.

    PubMed

    Popa, C V; Zaidi, H; Arfaoui, A; Polidori, G; Taiar, R; Fohanno, S

    2011-01-01

    This paper deals with the flow dynamics around a competitive swimmer during underwater glide phases occurring at the start and at every turn. The influence of the head position, namely lifted up, aligned and lowered, on the wall shear stress and the static pressure distributions is analyzed. The problem is considered as 3D and in steady hydrodynamic state. Three velocities (1.4 m/s, 2.2 m/s and 3.1 m/s) that correspond to inter-regional, national and international swimming levels are studied. The flow around the swimmer is assumed turbulent. The Reynolds-averaged Navier-Stokes (RANS) equations are solved with the standard k-ω turbulent model by using the CFD (computational fluid dynamics) numerical method based on a volume control approach. Numerical simulations are carried out with the ANSYS FLUENT® CFD code. The results show that the wall shear stress increases with the velocity and consequently the drag force opposing the movement of the swimmer increases as well. Also, high wall shear stresses are observed in the areas where the body shape, globally rigid in form, presents complex surface geometries such as the head, shoulders, buttocks, heel and chest.

  11. Structure of axionic domain walls

    NASA Astrophysics Data System (ADS)

    Huang, M. C.; Sikivie, P.

    1985-09-01

    The structure of axionic domain walls is investigated using the low-energy effective theory of axions and pions. We derive the spatial dependence of the phases of the Peccei-Quinn scalar field and the QCD quark-antiquark condensates inside an axionic domain wall. Thence an accurate estimate of the wall surface energy density is obtained. The equations of motion for axions, photons, leptons, and baryons in the neighborhood of axionic domain walls are written down and estimates are given for the wall reflection and transmission coefficients of these particles. Finally, we discuss the energy dissipation by axionic domain walls oscillating in the early universe due to the reflection of particles in the primordial soup.

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

    PubMed Central

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

    2012-01-01

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

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

    SciTech Connect

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

    2004-04-28

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

  14. Deformable 2D-3D registration of vascular structures in a one view scenario.

    PubMed

    Groher, Martin; Zikic, Darko; Navab, Nassir

    2009-06-01

    Alignment of angiographic 3D scans to 2D projections is an important issue for 3D depth perception and navigation during interventions. Currently, in a setting where only one 2D projection is available, methods employing a rigid transformation model present the state of the art for this problem. In this work, we introduce a method capable of deformably registering 3D vessel structures to a respective single projection of the scene. Our approach addresses the inherent ill-posedness of the problem by incorporating a priori knowledge about the vessel structures into the formulation. We minimize the distance between the 2D points and corresponding projected 3D points together with regularization terms encoding the properties of length preservation of vessel structures and smoothness of deformation. We demonstrate the performance and accuracy of the proposed method by quantitative tests on synthetic examples as well as real angiographic scenes.

  15. Deformable registration of 3D vessel structures to a single projection image

    NASA Astrophysics Data System (ADS)

    Zikic, Darko; Groher, Martin; Khamene, Ali; Navab, Nassir

    2008-03-01

    Alignment of angiographic preoperative 3D scans to intraoperative 2D projections is an important issue for 3D depth perception and navigation during interventions. Currently, in a setting where only one 2D projection is available, methods employing a rigid transformation model present the state of the art for this problem. In this work, we introduce a method capable of deformably registering 3D vessel structures to a respective single projection of the scene. Our approach addresses the inherent ill-posedness of the problem by incorporating a priori knowledge about the vessel structures into the formulation. We minimize the distance between the 2D points and corresponding projected 3D points together with regularization terms encoding the properties of length preservation of vessel structures and smoothness of deformation. We demonstrate the performance and accuracy of the proposed method by quantitative tests on synthetic examples as well as real angiographic scenes.

  16. A comparison of multi-view 3D reconstruction of a rock wall using several cameras and a laser scanner

    NASA Astrophysics Data System (ADS)

    Thoeni, K.; Giacomini, A.; Murtagh, R.; Kniest, E.

    2014-06-01

    This work presents a comparative study between multi-view 3D reconstruction using various digital cameras and a terrestrial laser scanner (TLS). Five different digital cameras were used in order to estimate the limits related to the camera type and to establish the minimum camera requirements to obtain comparable results to the ones of the TLS. The cameras used for this study range from commercial grade to professional grade and included a GoPro Hero 1080 (5 Mp), iPhone 4S (8 Mp), Panasonic Lumix LX5 (9.5 Mp), Panasonic Lumix ZS20 (14.1 Mp) and Canon EOS 7D (18 Mp). The TLS used for this work was a FARO Focus 3D laser scanner with a range accuracy of ±2 mm. The study area is a small rock wall of about 6 m height and 20 m length. The wall is partly smooth with some evident geological features, such as non-persistent joints and sharp edges. Eight control points were placed on the wall and their coordinates were measured by using a total station. These coordinates were then used to georeference all models. A similar number of images was acquired from a distance of between approximately 5 to 10 m, depending on field of view of each camera. The commercial software package PhotoScan was used to process the images, georeference and scale the models, and to generate the dense point clouds. Finally, the open-source package CloudCompare was used to assess the accuracy of the multi-view results. Each point cloud obtained from a specific camera was compared to the point cloud obtained with the TLS. The latter is taken as ground truth. The result is a coloured point cloud for each camera showing the deviation in relation to the TLS data. The main goal of this study is to quantify the quality of the multi-view 3D reconstruction results obtained with various cameras as objectively as possible and to evaluate its applicability to geotechnical problems.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed Central

    Kaltdorf, Kristin Verena; Schulze, Katja; Helmprobst, Frederik; Kollmannsberger, Philip; Stigloher, Christian

    2017-01-01

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

  19. 3D high-resolution two-photon crosslinked hydrogel structures for biological studies.

    PubMed

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

    2017-03-25

    Hydrogels are widely used as matrices for cell growth due to the their tuneable chemical and physical properties, which mimic the extracellular matrix of natural tissue. The microfabrication of hydrogels into arbitrarily complex 3D structures is becoming essential for numerous biological applications, and in particular for investigating the correlation between cell shape and cell function in a 3D environment. Micrometric and sub-micrometric resolution hydrogel scaffolds are required to deeply investigate molecular mechanisms behind cell-matrix interaction and downstream cellular processes. We report the design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking. Hydrated structures of lateral linewidth down to 0.5 µm, lateral and axial resolution down to a few µm are demonstrated. According to the processing parameters, different degrees of polymerization are obtained, resulting in hydrated scaffolds of variable swelling and deformation. The 3D hydrogels are biocompatible and promote cell adhesion and migration. Interestingly, according to the polymerization degree, 3D hydrogel woodpile structures show variable extent of cell adhesion and invasion. Human BJ cell lines show capability of deforming 3D micrometric resolved hydrogel structures.

  20. High-resolution 3D coronary vessel wall imaging with near 100% respiratory efficiency using epicardial fat tracking: reproducibility and comparison with standard methods.

    PubMed

    Scott, Andrew D; Keegan, Jennifer; Firmin, David N

    2011-01-01

    To quantitatively assess the performance and reproducibility of 3D spiral coronary artery wall imaging with beat-to-beat respiratory-motion-correction (B2B-RMC) compared to navigator gated 2D spiral and turbo-spin-echo (TSE) acquisitions. High-resolution (0.7 × 0.7 mm) cross-sectional right coronary wall acquisitions were performed in 10 subjects using four techniques (B2B-RMC 3D spiral with alternate (2RR) and single (1RR) R-wave gating, navigator-gated 2D spiral (2RR) and navigator-gated 2D TSE (2RR)) on two occasions. Wall thickness measurements were compared with repeated measures analysis of variance (ANOVA). Reproducibility was assessed with the intraclass correlation coefficient (ICC). In all, 91% (73/80) of acquisitions were successful (failures: four TSE, two 3D spiral (1RR) and one 3D spiral (2RR)). Respiratory efficiency of the B2B-RMC was less variable and substantially higher than for navigator gating (99.6 ± 1.2% vs. 39.0 ± 7.5%, P < 0.0001). Coronary wall thicknesses (± standard deviation [SD]) were not significantly different: 1.10 ± 0.14 mm (3D spiral (2RR)), 1.20 ± 0.16 mm (3D spiral (1RR)), 1.14 ± 0.15 mm (2D spiral), and 1.21 ± 0.17 mm (TSE). Wall thickness reproducibility ranged from good (ICC = 0.65, 3D spiral (1RR)) to excellent (ICC = 0.87, 3D spiral (2RR)). High-resolution 3D spiral imaging with B2B-RMC permits coronary vessel wall assessment over multiple thin contiguous slices in a clinically feasible duration. Excellent reproducibility of the technique potentially enables studies of disease progression/regression. Copyright © 2010 Wiley-Liss, Inc.

  1. Edge structure preserving 3D image denoising by local surface approximation.

    PubMed

    Qiu, Peihua; Mukherjee, Partha Sarathi

    2012-08-01

    In various applications, including magnetic resonance imaging (MRI) and functional MRI (fMRI), 3D images are becoming increasingly popular. To improve the reliability of subsequent image analyses, 3D image denoising is often a necessary preprocessing step, which is the focus of the current paper. In the literature, most existing image denoising procedures are for 2D images. Their direct extensions to 3D cases generally cannot handle 3D images efficiently because the structure of a typical 3D image is substantially more complicated than that of a typical 2D image. For instance, edge locations are surfaces in 3D cases which would be much more challenging to handle compared to edge curves in 2D cases. We propose a novel 3D image denoising procedure in this paper, based on local approximation of the edge surfaces using a set of surface templates. An important property of this method is that it can preserve edges and major edge structures (e.g., intersections of two edge surfaces and pointed corners). Numerical studies show that it works well in various applications.

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

    NASA Technical Reports Server (NTRS)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

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

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

    PubMed

    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/.

  6. Gas anti-solvent precipitation assisted salt leaching for generation of micro- and nano-porous wall in bio-polymeric 3D scaffolds.

    PubMed

    Flaibani, Marina; Elvassore, Nicola

    2012-08-01

    The mass transport through biocompatible and biodegradable polymeric 3D porous scaffolds may be depleted by non-porous impermeable internal walls. As consequence the concentration of metabolites and growth factors within the scaffold may be heterogeneous leading to different cell fate depending on spatial cell location, and in some cases it may compromise cell survival. In this work, we fabricated polymeric scaffolds with micro- and nano-scale porosity by developing a new technique that couples two conventional scaffold production methods: solvent casting-salt leaching and gas antisolvent precipitation. 10-15 w/w solutions of a hyaluronic benzyl esters (HYAFF11) and poly-(lactic acid) (PLA) were used to fill packed beds of 0.177-0.425 mm NaCl crystals. The polymer precipitation in micro and nano-porous structures between the salt crystals was induced by high-pressure gas, then its flushing extracted the residual solvent. The salt was removed by water-wash. Morphological analysis by scanning electron microscopy showed a uniform porosity (~70%) and a high interconnectivity between porous. The polymeric walls were porous themselves counting for 30% of the total porosity. This wall porosity did not lead to a remarkable change in compressive modulus, deformation, and rupture pressure. Scaffold biocompatibility was tested with murine muscle cell line C2C12 for 4 and 7 days. Viability analysis and histology showed that micro- and nano-porous scaffolds are biocompatible and suitable for 3D cell culture promoting cell adhesion on the polymeric wall and allowing their proliferation in layers. Micro- and nano-scale porosities enhance cell migration and growth in the inner part of the scaffold.

  7. Protecting ITER walls: fast ion power loads in 3D magnetic field

    NASA Astrophysics Data System (ADS)

    Kurki-Suonio, T.; Särkimäki, K.; Äkäslompolo, S.; Varje, J.; Liu, Y.; Sipilä, S.; Asunta, O.; Hirvijoki, E.; Snicker, A.; Terävä, J.; Cavinato, M.; Gagliardi, M.; Parail, V.; Saibene, G.

    2017-01-01

    The fusion alpha and beam ion with steady-state power loads in all four main operating scenarios of ITER have been evaluated by the ASCOT code. For this purpose, high-fidelity magnetic backgrounds were reconstructed, taking into account even the internal structure of the ferritic inserts and tritium breeding modules (TBM). The beam ions were found to be almost perfectly confined in all scenarios, and only the so-called hybrid scenario featured alpha loads reaching 0.5 MW due to its more triangular plasma. The TBMs were not found to jeopardize the alpha confinement, nor cause any hot spots. Including plasma response did not bring dramatic changes to the load. The ELM control coils (ECC) were simulated in the baseline scenario and found to seriously deteriorate even the beam confinement. However, the edge perturbation in this case is so large that the sources have to be re-evaluated with plasma profiles that take into account the ECC perturbation.

  8. A 3-D Puzzle Approach to Building Protein-DNA Structures.

    PubMed

    Hinton, Deborah M

    2017-02-02

    Despite recent advances in structural analysis, it is still challenging to obtain a high resolution structure for a complex of RNA polymerase, transcriptional factors, and DNA. However, using biochemical constraints, 3-D printed models of available structures, and computer modeling, one can build biologically relevant models of such supramolecular complexes.

  9. From SHAPE Signatures to 3-D Structures | Center for Cancer Research

    Cancer.gov

    RNAs undergo extensive folding to form sophisticated based-paired secondary structures that are, in part, indicators of more complex three-dimensional structures.  These 3-D shapes are an integral part of the cellular gene-expression machinery. Deconstructing these structures is no small matter, yet it is critical to understanding their function.

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

    PubMed

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

    2010-09-27

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

  11. Cryogenic optical localization provides 3D protein structure data with Angstrom resolution.

    PubMed

    Weisenburger, Siegfried; Boening, Daniel; Schomburg, Benjamin; Giller, Karin; Becker, Stefan; Griesinger, Christian; Sandoghdar, Vahid

    2017-02-01

    We introduce Cryogenic Optical Localization in 3D (COLD), a method to localize multiple fluorescent sites within a single small protein with Angstrom resolution. We demonstrate COLD by determining the conformational state of the cytosolic Per-ARNT-Sim domain from the histidine kinase CitA of Geobacillus thermodenitrificans and resolving the four biotin sites of streptavidin. COLD provides quantitative 3D information about small- to medium-sized biomolecules on the Angstrom scale and complements other techniques in structural biology.

  12. 3D and 4D atlas system of living human body structure.

    PubMed

    Suzuki, N; Takatsu, A; Hattori, A; Ezumi, T; Oda, S; Yanai, T; Tominaga, H

    1998-01-01

    A reference system for accessing anatomical information from a complete 3D structure of the whole body "living human", including 4D cardiac dynamics, was reconstructed with 3D and 4D data sets obtained from normal volunteers. With this system, we were able to produce a human atlas in which sectional images can be accessed from any part of the human body interactively by real-time image generation.

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

    PubMed Central

    2010-01-01

    Background Two biomolecular 3-D structures are said to be similar if the RMSD (root mean square deviation) between the two molecules' sequences of 3-D coordinates is less than or equal to some given constant bound. Tools for searching for similar structures in biomolecular 3-D structure databases are becoming increasingly important in the structural biology of the post-genomic era. Results We consider an important, fundamental problem of reporting all substructures in a 3-D structure database of chain molecules (such as proteins) which are similar to a given query 3-D structure, with consideration of indels (i.e., insertions and deletions). This problem has been believed to be very difficult but its exact computational complexity has not been known. In this paper, we first prove that the problem in unbounded dimensions is NP-hard. We then propose a new algorithm that dramatically improves the average-case time complexity of the problem in 3-D in case the number of indels k is bounded by a constant. Our algorithm solves the above problem for a query of size m and a database of size N in average-case O(N) time, whereas the time complexity of the previously best algorithm was O(Nmk+1). Conclusions Our results show that although the problem of searching for similar structures in a database based on the RMSD measure with indels is NP-hard in the case of unbounded dimensions, it can be solved in 3-D by a simple average-case linear time algorithm when the number of indels is bounded by a constant. PMID:20047663

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

    PubMed Central

    Warmuth, Franziska; Körner, Carolin

    2015-01-01

    The static and dynamic mechanical behaviour of cellular materials can be designed by the architecture of the underlying unit cell. In this paper, the phononic band structure of 2D and 3D cellular structures is investigated. It is shown how the geometry of the unit cell influences the band structure and eventually leads to full band gaps. The mechanism leading to full band gaps is elucidated. Based on this knowledge, a 3D cellular structure with a broad full band gap is identified. Furthermore, the dependence of the width of the gap on the geometry parameters of the unit cell is presented. PMID:28793713

  15. Tailored complex 3D vortex lattice structures by perturbed multiples of three-plane waves.

    PubMed

    Xavier, Jolly; Vyas, Sunil; Senthilkumaran, Paramasivam; Joseph, Joby

    2012-04-20

    As three-plane waves are the minimum number required for the formation of vortex-embedded lattice structures by plane wave interference, we present our experimental investigation on the formation of complex 3D photonic vortex lattice structures by a designed superposition of multiples of phase-engineered three-plane waves. The unfolding of the generated complex photonic lattice structures with higher order helical phase is realized by perturbing the superposition of a relatively phase-encoded, axially equidistant multiple of three noncoplanar plane waves. Through a programmable spatial light modulator assisted single step fabrication approach, the unfolded 3D vortex lattice structures are experimentally realized, well matched to our computer simulations. The formation of higher order intertwined helices embedded in these 3D spiraling vortex lattice structures by the superposition of the multiples of phase-engineered three-plane waves interference is also studied.

  16. UV laser direct writing of 2D/3D structures using photo-curable polydimethylsiloxane (PDMS)

    NASA Astrophysics Data System (ADS)

    Obata, Kotaro; Slobin, Shayna; Schonewille, Adam; Hohnholz, Arndt; Unger, Claudia; Koch, Jürgen; Suttmann, Oliver; Overmeyer, Ludger

    2017-07-01

    Additive manufacturing with UV curable polydimethylsiloxane (PDMS) was achieved using UV laser direct writing. In these experiments, UV curable PDMS was locally polymerized to fabricate 1D and 2D single layer structures, as well as 3D multilayer structures. Line arrays with line widths between 18 and 47 µm were produced, and it was observed that good stability and repeatability of the photo-polymerization in the UV curable PDMS was possible. The 3D structures demonstrated the absorption depth of the UV curable PDMS, which was deeper than 3 mm, and enabled the fabrication of 3.1 mm tall structures with an aspect ratio of 2 in only a single layer. The 3D structures were sufficiently strong to show elastic properties. All surfaces were smooth and transparent. In addition, UV laser direct writing of UV curable PDMS realized patterning with uniform resolutions at each layer.

  17. Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy.

    PubMed

    Punjani, Ali; Brubaker, Marcus A; Fleet, David J

    2017-04-01

    Discovering the 3D atomic-resolution structure of molecules such as proteins and viruses is one of the foremost research problems in biology and medicine. Electron Cryomicroscopy (cryo-EM) is a promising vision-based technique for structure estimation which attempts to reconstruct 3D atomic structures from a large set of 2D transmission electron microscope images. This paper presents a new Bayesian framework for cryo-EM structure estimation that builds on modern stochastic optimization techniques to allow one to scale to very large datasets. We also introduce a novel Monte-Carlo technique that reduces the cost of evaluating the objective function during optimization by over five orders of magnitude. The net result is an approach capable of estimating 3D molecular structure from large-scale datasets in about a day on a single CPU workstation.

  18. Near-wall 3D velocity measurements above biomimetic shark skin denticles using Digital In-line Holographic Microscopy

    NASA Astrophysics Data System (ADS)

    Toloui, Mostafa; Brajkovic, David; Hong, Jiarong

    2014-11-01

    Digital In-line Holography is employed to image 3D flow structures in the vicinity of a transparent rough surface consisting of closely packed biomimetic shark skin denticles as roughness elements. The 3D printed surface replicates the morphological features of real shark skin, and the denticles have a geometrical scale of 2 mm, i.e. 10 times of the real ones. In order to minimize optical aberrations near the fluid-roughness interface and enable flow measurements around denticles, the optical refractive index of the fluid medium is maintained the same as that of the denticle model in an index-matched flow facility using NaI solution as the working fluid. The experiment is conducted in a 1.2 m long test section with 50 mm × 50 mm cross section. The sampling volume is located in the downstream region of a shark skin replica of 12'' stretch where the turbulent flow is fully-developed and the transitional effect from smooth to the rough surface becomes negligible. Several instantaneous realizations of the 3D velocity field are obtained and are used to illustrate turbulent coherent structures induced by shark-skin denticles. This information will provide insights on the hydrodynamic function of shark's unique surface ornamentation.

  19. Single cell detection using 3D magnetic rolled-up structures.

    PubMed

    Ger, Tzong-Rong; Huang, Hao-Ting; Huang, Chen-Yu; Lai, Mei-Feng

    2013-11-07

    A 3D rolled-up structure made of a SiO2 layer and a fishbone-like magnetic thin film was proposed here as a biosensor. The magnetoresistance (MR) measurement results of the sensor suggest that the presence of the stray field, which is induced by the magnetic nanoparticles, significantly increased the switching field. Comparing the performance of the 2D sensor and 3D sensor designed in this study, the response in switching field variation was 12.14% in the 2D sensor and 62.55% in the 3D sensor. The response in MR ratio variation was 4.55% in the 2D sensor and 82.32% in the 3D sensor. In addition, the design of the 3D sensor structure also helped to attract and trap a single magnetic cell due to its stronger stray field compared with the 2D structure. The 3D magnetic biosensor designed here can provide important information for future biochip research and applications.

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

    PubMed Central

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

    2015-01-01

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

  1. Quasi 3D imaging of DNA-gold nanoparticle tetrahedral structures.

    PubMed

    Stern, Avigail; Rotem, Dvir; Popov, Inna; Porath, Danny

    2012-04-25

    Verification by imaging of the structure of 3D DNA constructs, both bare and conjugated to metal nanoparticles, is challenging. We demonstrate here two transmission electron microscopy (TEM) based methods to distinguish between fully formed tetrahedra, synthesized from DNA conjugated with gold nanoparticles (GNPs) at their vertices, and structures which are only partially formed. When deposited on a surface, fully formed tetrahedra are expected to retain their 3D pyramidal structure, while partially formed structures are expected to form a 2D structure. The first method by which 3D and 2D structures were distinguished was imaging them at different defocusing values. While for 2D structures all the four GNPs acquire Fresnel fringes at the same defocusing value, for 3D structures at least one particle is at a different plane with respect to the others, and so it acquires Fresnel fringes at a different defocusing value. The second method we show is imaging of the structures at different angles. While a single TEM image gives only a 2D projection of the structure, by combining information achieved from imaging at several tilting angles one may verify the structural construct.

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

    NASA Astrophysics Data System (ADS)

    Ge, Zhaoyang; Hu, Hong; Liu, Yanping

    2013-08-01

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

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

    NASA Astrophysics Data System (ADS)

    Leng, Kuangdai; Nissen-Meyer, Tarje; van Driel, Martin

    2016-12-01

    We present a new, computationally efficient numerical method to simulate global seismic wave propagation in realistic 3-D Earth models. We characterize the azimuthal dependence of 3-D wavefields in terms of Fourier series, such that the 3-D equations of motion reduce to an algebraic system of coupled 2-D meridian equations, which is then solved by a 2-D spectral element method (SEM). Computational efficiency of such a hybrid method stems from lateral smoothness of 3-D Earth models and axial singularity of seismic point sources, which jointly confine the Fourier modes of wavefields to a few lower orders. We show novel benchmarks for global wave solutions in 3-D structures between our method and an independent, fully discretized 3-D SEM with remarkable agreement. Performance comparisons are carried out on three state-of-the-art tomography models, with seismic period ranging from 34 s down to 11 s. It turns out that our method has run up to two orders of magnitude faster than the 3-D SEM, featured by a computational advantage expanding with seismic frequency.

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

    PubMed Central

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

    2003-01-01

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

  5. Mechanical Simulation of the Localized Deformation in the Aluminum Foams: A Three-dimensional (3D) Structure Based Study

    NASA Astrophysics Data System (ADS)

    Kai, Zhu; Enyu, Guo; Wenqian, Zhou; Sansan, Shuai; Tao, Jing; Hongliang, Hou; Yanjin, Xu

    2015-06-01

    Metal-foam materials have been used increasingly in industry for their low-density, high-toughness and high impact resistance properties. Understanding the macro-scale mechanical properties of these materials is essential to evaluate their actual performance and thus to optimize the structures and properties accordingly. Synchrotron radiation X-ray microtomographytechnique is a promising method to study 3D structures at small length scales, which provides high spatial resolution and allows the researchers to observe the change of structures/features in situ without destroying the original objects. In this work, the real 3D structure of closed-cell aluminum foam was obtained by using synchrotron radiation X-ray microtomography. The reconstructed 3D model of the foam was further utilized as input for the subsequent mechanical study to investigate the localized deformation behaviors and evolution process of the foam under longitudinal quasi-static uniaxial compressive loading. By analyzing the simulated results, it is demonstrated that the deformation bands always initiate and propagate along the cell walls which are finally folded upon loading. And the large spherical cells are more susceptible to yielding, as well as to the stress concentration than the cells with other shapes. This finding is consistent with the experimental results.

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

    PubMed

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

    2017-09-01

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

  7. 3-D seismic velocity and attenuation structures in the geothermal field

    SciTech Connect

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

    2013-09-09

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

  8. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

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

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

    PubMed

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

    2016-04-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  11. Fabrication, Characterization, And Deformation of 3D Structural Meta-Materials

    NASA Astrophysics Data System (ADS)

    Montemayor, Lauren C.

    Current technological advances in fabrication methods have provided pathways to creating architected structural meta-materials similar to those found in natural organisms that are structurally robust and lightweight, such as diatoms. Structural meta-materials are materials with mechanical properties that are determined by material properties at various length scales, which range from the material microstructure (nm) to the macro-scale architecture (mum -- mm). It is now possible to exploit material size effect, which emerge at the nanometer length scale, as well as structural effects to tune the material properties and failure mechanisms of small-scale cellular solids, such as nanolattices. This work demonstrates the fabrication and mechanical properties of 3-dimensional hollow nanolattices in both tension and compression. Hollow gold nanolattices loaded in uniaxial compression demonstrate that strength and stiffness vary as a function of geometry and tube wall thickness. Structural effects were explored by increasing the unit cell angle from 30° to 60° while keeping all other parameters constant; material size effects were probed by varying the tube wall thickness, t, from 200nm to 635nm, at a constant relative density and grain size. In-situ uniaxial compression experiments reveal an order-of-magnitude increase in yield stress and modulus in nanolattices with greater lattice angles, and a 150% increase in the yield strength without a concomitant change in modulus in thicker-walled nanolattices for fixed lattice angles. These results imply that independent control of structural and material size effects enables tunability of mechanical properties of 3-dimensional architected meta-materials and highlight the importance of material, geometric, and microstructural effects in small-scale mechanics. This work also explores the flaw tolerance of 3D hollow-tube alumina kagome nanolattices with and without pre-fabricated notches, both in experiment and simulation

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  13. 3D printing of weft knitted textile based structures by selective laser sintering of nylon powder

    NASA Astrophysics Data System (ADS)

    Beecroft, M.

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-01-01

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

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

    PubMed

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

    2016-07-19

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

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

    PubMed Central

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

    2016-01-01

    Polymer nanocomposites have always attracted the interest of researchers and industry because of their potential combination of properties from both the nanofillers and the hosting matrix. Gathering nanomaterials and 3D printing could offer clear advantages and numerous new opportunities in several application fields. Embedding nanofillers in a polymeric matrix could improve the final material properties but usually the printing process gets more difficult. Considering this drawback, in this paper we propose a method to obtain polymer nanocomposites by in situ generation of nanoparticles after the printing process. 3D structures were fabricated through a Digital Light Processing (DLP) system by disolving metal salts in the starting liquid formulation. The 3D fabrication is followed by a thermal treatment in order to induce in situ generation of metal nanoparticles (NPs) in the polymer matrix. Comprehensive studies were systematically performed on the thermo-mechanical characteristics, morphology and electrical properties of the 3D printed nanocomposites. PMID:28773716

  17. Observation of Dynamic Structure Using Ultrasound 3D Imaging System with Encoded Wave Front

    NASA Astrophysics Data System (ADS)

    Ishigami, Satoshi; Yanagida, Hirotaka; Tamura, Yasutaka; Ishihara, Chiaki; Okada, Nagaya

    2003-05-01

    Dynamic ultrasound three-dimensional (3D) imaging using coded transmission is described. A sequence of 3D images of moving objects is reconstructed for each transmission of pulses modulated by Walsh functions. Then, the dynamic structure of the objects is extracted from the image sequence. In this paper, we discuss the relationship of the system performance to the parameters of the transmitting code such as duration time, repetition period, and total transmission length. A Doppler shift estimation and motion compensated image reconstruction method is described. The computer simulation for the motion compensation image reconstruction was carried out. Ultrasound 3D stroboscopic photography was demonstrated by a preliminary experiment utilizing the evaluation system in a 3D medical diagnostic scanner which has 32 transmitters and 32 receivers.

  18. Definition of subsurface stratigraphy, structure and rock properties from 3-D seismic data

    NASA Astrophysics Data System (ADS)

    Hart, Bruce S.

    1999-10-01

    This paper summarizes how three-dimensional (3-D) seismic technology is being used, primarily in the petroleum industry, to define subsurface structure, stratigraphy and rock properties. A 3-D seismic data volume: (a) provides a more accurate image of the subsurface than can be obtained with 2-D seismic methods; (b) is continuous, and so has a much greater spatial sampling than is obtained with 2-D seismic or other subsurface data (e.g., wells); and (c) can be viewed and interpreted interactively from a variety of perspectives, thus enhancing the interpreter's ability to generate an accurate description of subsurface features of interest. Seismic interpretation was once the almost exclusive realm of geophysicists, however, most 3-D seismic interpretation today is conducted by multidisciplinary teams that integrate geophysical, geological, petrophysical and engineering data and concepts into the 3-D seismic interpretation. These factors, plus proper survey design, help to increase the chances of success of a 3-D seismic interpretation project. Although there are cases where the technology is not appropriate or cannot be applied (for economic reasons or otherwise), the general success of 3-D seismic has led it to become a mainstay of the petroleum industry. The approach and technology, first developed in that industry, have potential applications in other applied and fundamental earth science disciplines, including mining, environmental geology, structural geology and stratigraphy.

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

    PubMed

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

    2017-06-21

    Development of a 3D printable material system possessing inherent piezoelectric properties to fabricate integrable sensors in a single-step printing process without poling is of importance to the creation of a wide variety of smart structures. Here, we study the effect of addition of barium titanate nanoparticles in nucleating piezoelectric β-polymorph in 3D printable polyvinylidene fluoride (PVDF) and fabrication of the layer-by-layer and self-supporting piezoelectric structures on a micro- to millimeter scale by solvent evaporation-assisted 3D printing at room temperature. The nanocomposite formulation obtained after a comprehensive investigation of composition and processing techniques possesses a piezoelectric coefficient, d31, of 18 pC N(-1), which is comparable to that of typical poled and stretched commercial PVDF film sensors. A 3D contact sensor that generates up to 4 V upon gentle finger taps demonstrates the efficacy of the fabrication technique. Our one-step 3D printing of piezoelectric nanocomposites can form ready-to-use, complex-shaped, flexible, and lightweight piezoelectric devices. When combined with other 3D printable materials, they could serve as stand-alone or embedded sensors in aerospace, biomedicine, and robotic applications.

  20. Photogrammetry in 3d Modelling of Human Bone Structures from Radiographs

    NASA Astrophysics Data System (ADS)

    Hosseinian, S.; Arefi, H.

    2017-05-01

    Photogrammetry can have great impact on the success of medical processes for diagnosis, treatment and surgeries. Precise 3D models which can be achieved by photogrammetry improve considerably the results of orthopedic surgeries and processes. Usual 3D imaging techniques, computed tomography (CT) and magnetic resonance imaging (MRI), have some limitations such as being used only in non-weight-bearing positions, costs and high radiation dose(for CT) and limitations of MRI for patients with ferromagnetic implants or objects in their bodies. 3D reconstruction of bony structures from biplanar X-ray images is a reliable and accepted alternative for achieving accurate 3D information with low dose radiation in weight-bearing positions. The information can be obtained from multi-view radiographs by using photogrammetry. The primary step for 3D reconstruction of human bone structure from medical X-ray images is calibration which is done by applying principles of photogrammetry. After the calibration step, 3D reconstruction can be done using efficient methods with different levels of automation. Because of the different nature of X-ray images from optical images, there are distinct challenges in medical applications for calibration step of stereoradiography. In this paper, after demonstrating the general steps and principles of 3D reconstruction from X-ray images, a comparison will be done on calibration methods for 3D reconstruction from radiographs and they are assessed from photogrammetry point of view by considering various metrics such as their camera models, calibration objects, accuracy, availability, patient-friendly and cost.

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

    PubMed

    Koga, Daisuke; Ushiki, Tatsuo; Watanabe, Tsuyoshi

    2017-01-01

    The structure of the Golgi apparatus has been extensively examined by light and electron microscopy, but details of its three-dimensional (3D) structure have remained unclear because of the technical limitations of conventional microscopy techniques. To overcome this problem, we have developed several novel scanning electron microscopy (SEM) methods for observing the 3D structure of subcellular organelles including the Golgi apparatus: (1) an osmium maceration method that facilitates SEM observation of membranous organelles, including the Golgi apparatus, by selectively removing soluble cytoplasmic proteins, (2) an osmium impregnation/maceration method that combines an osmium impregnation method with the osmium maceration method to determine the polarity of the Golgi apparatus by SEM, (3) a correlative light and SEM method that combines a cryosectioning technique with the osmium maceration method to enable correlation of the immunocytochemical distribution of molecules with the 3D ultrastructure of the Golgi apparatus, and (4) array tomography based on the systematic collection and integration of SEM images of serial ultrathin sections on glass slides for revealing the 3D ultrastructure of the entire Golgi apparatus. Together, the novel SEM techniques listed above can reveal the complete 3D structure of the Golgi apparatus in different cell types.

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

    PubMed

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

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Kunii, Y.; Sakamoto, R.

    2016-06-01

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

  5. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.

    PubMed

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

    2017-02-27

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

  6. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

    PubMed Central

    2017-01-01

    3D-e-Chem-VM is an open source, freely available Virtual Machine (http://3d-e-chem.github.io/3D-e-Chem-VM/) that integrates cheminformatics and bioinformatics tools for the analysis of protein–ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein–ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb). PMID:28125221

  7. Structure and properties of small clusters of transition 3d-element oxides

    SciTech Connect

    Popov, A. V.

    2011-03-15

    The results of calculations of the parameters of the equilibrium structures of small clusters of transition 3d-element oxides are presented. The calculations are performed by the spin-unrestricted Hartree-Fock method. The properties of the most stable structures, i.e., those with the lowest total energies among all those obtained, are discussed.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Hayat, Sikander; Sander, Chris; Marks, Debora S; Elofsson, Arne

    2015-04-28

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

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

    PubMed Central

    Choi, Dong-Geol; Bok, Yunsu; Kim, Jun-Sik; Shim, Inwook; Kweon, In So

    2017-01-01

    This paper presents a novel structure-from-motion methodology using 2D lidars (Light Detection And Ranging). In 3D space, 2D lidars do not provide sufficient information for pose estimation. For this reason, additional sensors have been used along with the lidar measurement. In this paper, we use a sensor system that consists of only 2D lidars, without any additional sensors. We propose a new method of estimating both the 6D pose of the system and the surrounding 3D structures. We compute the pose of the system using line segments of scan data and their corresponding planes. After discarding the outliers, both the pose and the 3D structures are refined via nonlinear optimization. Experiments with both synthetic and real data show the accuracy and robustness of the proposed method. PMID:28165372

  11. 3D topography of biologic tissue by multiview imaging and structured light illumination

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Zhang, Shiwu; Xu, Ronald

    2014-02-01

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

  12. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  13. Enhanced genome annotation using structural profiles in the program 3D-PSSM.

    PubMed

    Kelley, L A; MacCallum, R M; Sternberg, M J

    2000-06-02

    A method (three-dimensional position-specific scoring matrix, 3D-PSSM) to recognise remote protein sequence homologues is described. The method combines the power of multiple sequence profiles with knowledge of protein structure to provide enhanced recognition and thus functional assignment of newly sequenced genomes. The method uses structural alignments of homologous proteins of similar three-dimensional structure in the structural classification of proteins (SCOP) database to obtain a structural equivalence of residues. These equivalences are used to extend multiply aligned sequences obtained by standard sequence searches. The resulting large superfamily-based multiple alignment is converted into a PSSM. Combined with secondary structure matching and solvation potentials, 3D-PSSM can recognise structural and functional relationships beyond state-of-the-art sequence methods. In a cross-validated benchmark on 136 homologous relationships unambiguously undetectable by position-specific iterated basic local alignment search tool (PSI-Blast), 3D-PSSM can confidently assign 18 %. The method was applied to the remaining unassigned regions of the Mycoplasma genitalium genome and an additional 13 regions were assigned with 95 % confidence. 3D-PSSM is available to the community as a web server: http://www.bmm.icnet.uk/servers/3dpssm

  14. 3D multi-layered fibrous cellulose structure using an electrohydrodynamic process for tissue engineering.

    PubMed

    Kim, Minseong; Kim, GeunHyung

    2015-11-01

    Micro/nanofibrous structures have been applied widely in various tissue-engineering applications because the topological structures are similar to the extracellular matrix (ECM), which encourages a high degree of cell adhesion and growth. However, it has been difficult to produce a three-dimensional (3D) fibrous structure using controllable macro-pores. Recently, cellulose has been considered a high-potential natural-origin biomaterial, but its use in 3D biomedical structures has been limited due to its narrow processing window. Here, we suggest a new 3D cellulose scaffold consisting of multi-layered struts made of submicron-sized entangled fibers that were fabricated using an electrohydrodynamic direct jet (EHDJ) process that is spin-printing. By optimizing processing conditions (electric field strength, cellulose feeding rate, and distance between nozzle and target), we can achieve a multi-layered cellulose structure consisting of the cylindrically entangled cellulose fibers. To compare the properties of the fabricated 3D cellulose structure, we used a PCL fibrous scaffold, which has a similar fibrous morphology and pore geometry, as a control. The physical and in vitro biocompatibilities of both fibrous scaffolds were assessed using human dermal fibroblasts, and the cellulose structure showed higher cell adhesion and metabolic activities compared with the control. These results suggest the EHDJ process to be an effective fabricating tool for tissue engineering and the cellulose scaffold has high potential as a tissue regenerative material.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Mei, Qing; Gao, Jian; Lin, Hui; Chen, Yun; Yunbo, He; Wang, Wei; Zhang, Guanjin; Chen, Xin

    2016-11-01

    We designed a new three-dimensional (3D) measurement system for micro components: a structure light telecentric stereoscopic vision 3D measurement system based on the Scheimpflug condition. This system creatively combines the telecentric imaging model and the Scheimpflug condition on the basis of structure light stereoscopic vision, having benefits of a wide measurement range, high accuracy, fast speed, and low price. The system measurement range is 20 mm×13 mm×6 mm, the lateral resolution is 20 μm, and the practical vertical resolution reaches 2.6 μm, which is close to the theoretical value of 2 μm and well satisfies the 3D measurement needs of micro components such as semiconductor devices, photoelectron elements, and micro-electromechanical systems. In this paper, we first introduce the principle and structure of the system and then present the system calibration and 3D reconstruction. We then present an experiment that was performed for the 3D reconstruction of the surface topography of a wafer, followed by a discussion. Finally, the conclusions are presented.

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

    PubMed Central

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

    2012-01-01

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

  18. Seismic moment tensor inversion using a 3-D structural model: applications for the Australian region

    NASA Astrophysics Data System (ADS)

    Hingee, Myall; Tkalčić, Hrvoje; Fichtner, Andreas; Sambridge, Malcolm

    2011-02-01

    There is significant seismic activity in the region around Australia, largely due to the plate boundaries to the north and to the east of the mainland. This activity results in serious seismic and tsunami hazard in the coastal areas of Australia. Hence seismicity is and will be monitored in real time by Geoscience Australia (GA), which uses a network of permanent broadband seismometers. Seismic moment tensor (MT) solutions are currently determined using 1-D, radially symmetric models of Earth and this requires augmentation by recording stations located outside of Australia. A 3-D model of the Australian continent developed recently using full waveform tomography now offers the opportunity to significantly improve the determination of MT solutions of earthquakes from tectonically active regions. A complete-waveform, time-domain MT inversion method has been developed using a point-source approximation. A series of synthetic tests using first a 1-D and then a 3-D structural model has been performed. The feasibility of deploying 3-D versus 1-D Earth structure for the inversion of seismic data has been studied and the advantages of using the 3-D structural model were illustrated with examples. The 3-D model is superior to the 1-D model, as a number of sensitivity tests show. The ultimate goal of this work is an automated MT inversion system in Australia relying on GA and other international stations, although more work remains to be done before the full implementation of such a scheme in real time.

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

    NASA Astrophysics Data System (ADS)

    Bhavanam, Sharada

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

  20. Towards an efficient compression of 3D coordinates of macromolecular structures

    PubMed Central

    Valasatava, Yana; Bradley, Anthony R.; Rose, Alexander S.; Duarte, Jose M.; Prlić, Andreas

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format. PMID:28362865

  1. Towards an efficient compression of 3D coordinates of macromolecular structures.

    PubMed

    Valasatava, Yana; Bradley, Anthony R; Rose, Alexander S; Duarte, Jose M; Prlić, Andreas; Rose, Peter W

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format.

  2. Simulation approach of atomic layer deposition in large 3D structures

    NASA Astrophysics Data System (ADS)

    Schwille, Matthias C.; Barth, Jonas; Schössler, Timo; Schön, Florian; Bartha, Johann W.; Oettel, Martin

    2017-04-01

    We present a new simulation method predicting thicknesses of thin films obtained by atomic layer deposition in high aspect ratio 3D geometries as they appear in MEMS manufacturing. The method features a Monte-Carlo computation of film deposition in free molecular flow, as well as in the Knudsen and diffusive gas regime, applicable for large structures. We compare our approach to analytic and simulation results from the literature. The capability of the method is demonstrated by a comparison to experimental film thicknesses in a large 3D structure. Finally, the feasability to extract process parameters, i.e. sticking coefficients is shown.

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

    DOEpatents

    Zemla, Adam T [Brentwood, CA

    2011-09-20

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

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

    PubMed

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-10-01

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

  5. Efficacy of 3D conforming nickel titanium rotary instruments in eliminating canal wall bacteria from oval-shaped root canals.

    PubMed

    Bortoluzzi, Eduardo A; Carlon, Daniel; Meghil, Mohamed M; El-Awady, Ahmed R; Niu, Lina; Bergeron, Brian E; Susin, Lisiane; Cutler, Christopher W; Pashley, David H; Tay, Franklin R

    2015-05-01

    To evaluate the effectiveness of TRUShape® 3D Conforming Files, compared with Twisted Files, in reducing bacteria load from root canal walls, in the presence or absence of irrigant agitation. Extracted human premolars with single oval-shaped canals were infected with Enterococcus faecalis. Teeth in Group I (N=10; NaOCl and QMix® 2in1 as respective initial and final irrigants) were subdivided into 4 subgroups: (A) TRUShape® instrumentation without irrigant activation; (B) TRUShape® instrumentation with sonic irrigant agitation; (C) Twisted Files without irrigant agitation; (D) Twisted Files with sonic irrigant agitation. To remove confounding factor (antimicrobial irrigants), teeth in Group II (N=10) were irrigated with sterile saline, using the same subgroup designations. Specimens before and after chemomechanical débridement were cultured for quantification of colony-forming units (CFUs). Data from each group were analyzed separately using two-factor ANOVA and Holm-Sidak multiple comparison (α=0.05). Canal wall bacteria were qualitatively examined using scanning electron microscopy (SEM) and light microscopy of Taylor-modified Brown and Brenn-stained demineralised sections. CFUs from subgroups in Group I were not significantly different (P=0.935). For Group II, both file type (P<0.001) and irrigant agitation (P<0.001) significantly affected log-reduction in CFU concentrations. The interaction of these two factors was not significant (P=0.601). Although SEM showed reduced canal wall bacteria, bacteria were present within dentinal tubules after rotary instrumentation, as revealed by light microscopy of longitudinal root sections. TRUShape® files removed significantly more canal wall bacteria than Twisted Files when used without an antibacterial irrigant; the latter is required to decontaminate dentinal tubules. Root canal disinfection should not be focused only on a mechanistic approach. Rather, the rational choice of a rotary instrumentation system should be

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed

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

    2016-07-08

    RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    NASA Astrophysics Data System (ADS)

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

    2004-05-01

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

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

    PubMed Central

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

    2016-01-01

    RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb. PMID:27095203

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  11. Detailed Measurement of Wall Strain with 3D Speckle Tracking in the Aortic Root: A Case of Bionic Support for Clinical Decision Making

    PubMed Central

    Vogt, Sebastian; Karatolios, Konstantinos; Wittek, Andreas; Blasé, Christopher; Ramaswamy, Anette; Mirow, Nikolas; Moosdorf, Rainer

    2016-01-01

    Three-dimensional (3D) wall motion tracking (WMT) based on ultrasound imaging enables estimation of aortic wall motion and deformation. It provides insights into changes in vascular compliance and vessel wall properties essential for understanding the pathogenesis and progression of aortic diseases. In this report, we employed the novel 3D WMT analysis on the ascending aorta aneurysm (AA) to estimate local aortic wall motion and strain in case of a patient scheduled for replacement of the aortic root. Although progression of the diameter indicates surgical therapy, at present we addressed the question for optimal surgical time point. According to the data, AA in our case has enlarged diameter and subsequent reduced circumferential wall strain, but area tracking data reveals almost normal elastic properties. Virtual remodeling of the aortic root opens a play list for different loading conditions to determine optimal surgical intervention in time. PMID:28018834

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

    NASA Astrophysics Data System (ADS)

    Simutė, S.; Fichtner, A.

    2015-12-01

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

  13. Element-Specific X-Ray Phase Tomography of 3D Structures at the Nanoscale

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

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

  15. Angular reconstitution-based 3D reconstructions of nanomolecular structures from superresolution light-microscopy images.

    PubMed

    Salas, Desirée; Le Gall, Antoine; Fiche, Jean-Bernard; Valeri, Alessandro; Ke, Yonggang; Bron, Patrick; Bellot, Gaetan; Nollmann, Marcelo

    2017-08-29

    Superresolution light microscopy allows the imaging of labeled supramolecular assemblies at a resolution surpassing the classical diffraction limit. A serious limitation of the superresolution approach is sample heterogeneity and the stochastic character of the labeling procedure. To increase the reproducibility and the resolution of the superresolution results, we apply multivariate statistical analysis methods and 3D reconstruction approaches originally developed for cryogenic electron microscopy of single particles. These methods allow for the reference-free 3D reconstruction of nanomolecular structures from two-dimensional superresolution projection images. Since these 2D projection images all show the structure in high-resolution directions of the optical microscope, the resulting 3D reconstructions have the best possible isotropic resolution in all directions.

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

    PubMed Central

    Jacob, J. Augustin; Kumar, N. Senthil

    2015-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  18. Protein-protein interaction networks studies and importance of 3D structure knowledge.

    PubMed

    Lu, Hui-Chun; Fornili, Arianna; Fraternali, Franca

    2013-12-01

    Protein-protein interaction networks (PPINs) are a powerful tool to study biological processes in living cells. In this review, we present the progress of PPIN studies from abstract to more detailed representations. We will focus on 3D interactome networks, which offer detailed information at the atomic level. This information can be exploited in understanding not only the underlying cellular mechanisms, but also how human variants and disease-causing mutations affect protein functions and complexes' stability. Recent studies have used structural information on PPINs to also understand the molecular mechanisms of binding partner selection. We will address the challenges in generating 3D PPINs due to the restricted number of solved protein structures. Finally, some of the current use of 3D PPINs will be discussed, highlighting their contribution to the studies in genotype-phenotype relationships and in the optimization of targeted studies to design novel chemical compounds for medical treatments.

  19. 3D watershed-based segmentation of internal structures within MR brain images

    NASA Astrophysics Data System (ADS)

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

    2000-06-01

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

  20. Voxel-coding method for quantification of vascular structure from 3D images

    NASA Astrophysics Data System (ADS)

    Soltanian-Zadeh, Hamid; Shahrokni, Ali; Zoroofi, Reza A.

    2001-05-01

    This paper presents an image processing method for information extraction from 3D images of vasculature. It automates the study of vascular structures by extracting quantitative information such as skeleton, length, diameter, and vessel-to- tissue ratio for different vessels as well as their branches. Furthermore, it generates 3D visualization of vessels based on desired anatomical characteristics such as vessel diameter or 3D connectivity. Steps of the proposed approach are as follows. (1) Preprocessing, in which intensity adjustment, optimal thresholding, and median filtering are done. (2) 3D thinning, in which medial axis and skeleton of the vessels are found. (3) Branch labeling, in which different branches are identified and each voxel is assigned to the corresponding branch. (4) Quantitation, in which length of each branch is estimated, based on the number of voxels assigned to it, and its diameter is calculated using the medial axis direction. (5) Visualization, in which vascular structure is shown in 3D, using color coding and surface rendering methods. We have tested and evaluated the proposed algorithms using simulated images of multi-branch vessels and real confocal microscopic images of the vessels in rat brains. Experimental results illustrate performance of the methods and usefulness of the results for medical image analysis applications.

  1. 3D shape shearography with integrated structured light projection for strain inspection of curved objects

    NASA Astrophysics Data System (ADS)

    Anisimov, Andrei G.; Groves, Roger M.

    2015-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-08-01

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

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

    DOE PAGES

    Zhang, Xing; Zhang, Lei; Tong, Huimin; ...

    2015-05-05

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

  4. Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

    PubMed Central

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

    2015-01-01

    A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a three-bead coarse-grained predictive model with implicit salt/solvent potentials. In this study, we further develop the model by improving the implicit-salt electrostatic potential and including a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in divalent/monovalent ion solutions. The model presented here can predict 3D structures of RNA hairpins with bulges/internal loops (<77 nucleotides) from their sequences at the corresponding experimental ion conditions with an overall improved accuracy compared to the experimental data; the model also makes reliable predictions for the flexibility of RNA hairpins with bulge loops of different lengths at several divalent/monovalent ion conditions. In addition, the model successfully predicts the stability of RNA hairpins with various loops/stems in divalent/monovalent ion solutions. PMID:26682822

  5. 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography

    PubMed Central

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

    2015-01-01

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

  6. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

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

    2015-05-05

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

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

    PubMed

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

    2015-07-01

    Nowadays, various methodologies can be applied to model RNA 3D structure. Thus, the plausible quality assessment of 3D models has a fundamental impact on the progress of structural bioinformatics. Here, we present RNAssess server, a novel tool dedicated to visual evaluation of RNA 3D models in the context of the known reference structure for a wide range of accuracy levels (from atomic to the whole molecule perspective). The proposed server is based on the concept of local neighborhood, defined as a set of atoms observed within a sphere localized around a central atom of a particular residue. A distinctive feature of our server is the ability to perform simultaneous visual analysis of the model-reference structure coherence. RNAssess supports the quality assessment through delivering both static and interactive visualizations that allows an easy identification of native-like models and/or chosen structural regions of the analyzed molecule. A combination of results provided by RNAssess allows us to rank analyzed models. RNAssess offers new route to a fast and efficient 3D model evaluation suitable for the RNA-Puzzles challenge. The proposed automated tool is implemented as a free and open to all users web server with an user-friendly interface and can be accessed at: http://rnassess.cs.put.poznan.pl/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    SciTech Connect

    Tung, Chang-Shung

    1997-09-01

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

  9. Picture Wall (Glass Structures)

    NASA Technical Reports Server (NTRS)

    1978-01-01

    Photo shows a subway station in Toronto, Ontario, which is entirely glass-enclosed. The all-glass structure was made possible by a unique glazing concept developed by PPG Industries, Pittsburgh, Pennsylvania, one of the largest U.S. manufacturers of flat glass. In the TVS glazing system, transparent glass "fins" replace conventional vertical support members used to provide support for wind load resistance. For stiffening, silicone sealant bonds the fins to adjacent glass panels. At its glass research center near Pittsburgh, PPG Industries uses the NASTRAN computer program to analyze the stability of enclosures made entirely of glass. The company also uses NASTRAN to simulate stresses on large containers of molten glass and to analyze stress effects of solar heating on flat glass.

  10. Treatment techniques for 3D conformal radiation to breast and chest wall including the internal mammary chain

    SciTech Connect

    Sonnik, Deborah; Selvaraj, Raj N. . E-mail: selvarajrn@upmc.edu; Faul, Clare; Gerszten, Kristina; Heron, Dwight E.; King, Gwendolyn C.

    2007-04-01

    Breast, chest wall, and regional nodal irradiation have been associated with an improved outcome in high-risk breast cancer patients. Complex treatment planning is often utilized to ensure complete coverage of the target volume while minimizing the dose to surrounding normal tissues. The 2 techniques evaluated in this report are the partially wide tangent fields (PWTFs) and the 4-field photon/electron combination (the modified 'Kuske Technique'). These 2 techniques were evaluated in 10 consecutive breast cancer patients. All patients had computerized tomographic (CT) scans for 3D planning supine on a breast board. The breast was defined clinically by the physician and confirmed radiographically with radiopaque bebes. The resulting dose-volume histograms (DVHs) of normal and target tissues were then compared. The deep tangent field with blocks resulted in optimal coverage of the target and the upper internal mammary chain (IMC) while sparing of critical and nontarget tissues. The wide tangent technique required less treatment planning and delivery time. We compared the 2 techniques and their resultant DVHs and feasibility in a busy clinic.

  11. Critical speed and free vibration analysis of spinning 3D single-walled carbon nanotubes resting on elastic foundations

    NASA Astrophysics Data System (ADS)

    Barooti, Mohammad Mostafa; Safarpour, Hamed; Ghadiri, Majid

    2017-01-01

    In this article, the influences of critical speed on the free vibration behavior of spinning 3D single-walled carbon nanotubes (SWCNT) are investigated using modified couple stress theory (MCST). Moreover, the surrounding elastic medium of SWCNT has been considered as a model of Winkler, characterized by the spring. Taking into consideration the first-order shear deformation theory (FSDT), the rotating SWCNT is modeled and its equations of motion are derived using the Hamilton principle. The formulations include Coriolis, centrifugal and initial hoop tension effects due to rotation of the SWCNT. The accuracy of the presented model is validated by some cases in the literature. The novelty of this study is considering the effects of rotation and MCST, in addition to considering the various boundary conditions of SWCNT. The generalized differential quadrature method (GDQM) is used to discretize the model and to approximate the equation of motion. Then investigation has been made on critical speed and natural frequency of the rotating SWCNT due to the influence of initial hoop tension, material length scale parameter, constant of spring, frequency mode number, angular velocity, length-to-radius ratio, radius-to-thickness ratio and boundary conditions.

  12. Treatment techniques for 3D conformal radiation to breast and chest wall including the internal mammary chain.

    PubMed

    Sonnik, Deborah; Selvaraj, Raj N; Faul, Clare; Gerszten, Kristina; Heron, Dwight E; King, Gwendolyn C

    2007-01-01

    Breast, chest wall, and regional nodal irradiation have been associated with an improved outcome in high-risk breast cancer patients. Complex treatment planning is often utilized to ensure complete coverage of the target volume while minimizing the dose to surrounding normal tissues. The 2 techniques evaluated in this report are the partially wide tangent fields (PWTFs) and the 4-field photon/electron combination (the modified "Kuske Technique"). These 2 techniques were evaluated in 10 consecutive breast cancer patients. All patients had computerized tomographic (CT) scans for 3D planning supine on a breast board. The breast was defined clinically by the physician and confirmed radiographically with radiopaque bebes. The resulting dose-volume histograms (DVHs) of normal and target tissues were then compared. The deep tangent field with blocks resulted in optimal coverage of the target and the upper internal mammary chain (IMC) while sparing of critical and nontarget tissues. The wide tangent technique required less treatment planning and delivery time. We compared the 2 techniques and their resultant DVHs and feasibility in a busy clinic.

  13. Graphene originated 3D structures grown on the assembled nickel particles

    NASA Astrophysics Data System (ADS)

    Paronyan, Tereza; Harutyunyan, Avetik; Honda Research Institute USA Inc. Team

    2013-03-01

    Recently, the fabrication of various morphologies of graphene originated structures became very important due to the perspective of wide range of new applications. Particularly, free standing 3D structured graphene foams could be imperative in energy related areas . Here, we present the new approach of the CVD growth of 3D graphene network by using primarily sintered Ni particle's (~40 μm size) assembles as a template-catalyst via decomposition of low rate of CH4 at 1100° C based on synthesis method described earlier. SEM and Raman spectra analysis revealed the formation of graphene structure containing a single up to few layers grown on the sintered metal particles served as a catalyst-template. After etching the metal frame without using any support polymer, 3D free-standing graphene microporous structure was formed demonstrating high BET surface area. Two probe measurements of frame resistance were ~2-8 Ω. Our approach allows controllable tune the pore size and thereby the surface area of 3D graphene network through the variation of the template-catalyst particles size.

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

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

    SciTech Connect

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

    2009-03-10

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

  17. Nitrogen and sulfur co-doping of partially exfoliated MWCNTs as 3-D structured electrocatalysts for the oxygen reduction reaction

    SciTech Connect

    Wang, Jie; Wu, Zexing; Han, Lili; Lin, Ruoqian; Xiao, Weiping; Xuan, Cuijuan; Xin, Huolin. L.; Wang, Deli

    2016-03-14

    Preventing the stacking of graphene sheets is of vital importance for highly efficient and stable fuel cell electrocatalysts. Here, we report a 3-D structured carbon nanotube intercalated graphene nanoribbon with N/S co-doping. The nanocomposite is obtained by using high temperature heat-treated thiourea with partially unzipped multi-walled carbon nanotubes. This unique structure preserves both the properties of carbon nanotubes and graphene, exhibiting excellent catalytic performance for the ORR with similar onset and half-wave potentials to those of Pt/C electrocatalysts. Furthermore, the stereo structured composite exhibits distinct advantages in long-term stability and methanol poisoning tolerance in comparison to Pt/C.

  18. Nitrogen and sulfur co-doping of partially exfoliated MWCNTs as 3-D structured electrocatalysts for the oxygen reduction reaction

    DOE PAGES

    Wang, Jie; Wu, Zexing; Han, Lili; ...

    2016-03-14

    Preventing the stacking of graphene sheets is of vital importance for highly efficient and stable fuel cell electrocatalysts. Here, we report a 3-D structured carbon nanotube intercalated graphene nanoribbon with N/S co-doping. The nanocomposite is obtained by using high temperature heat-treated thiourea with partially unzipped multi-walled carbon nanotubes. This unique structure preserves both the properties of carbon nanotubes and graphene, exhibiting excellent catalytic performance for the ORR with similar onset and half-wave potentials to those of Pt/C electrocatalysts. Furthermore, the stereo structured composite exhibits distinct advantages in long-term stability and methanol poisoning tolerance in comparison to Pt/C.

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Meng, Hui; Hussain, Fazle

    1991-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

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

    SciTech Connect

    Avakian, Harut

    2016-07-01

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

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

    SciTech Connect

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

    2010-11-09

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

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

    SciTech Connect

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

    2016-07-11

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

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

    PubMed

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

    2016-06-01

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

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

    PubMed Central

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

    2016-01-01

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

  8. Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction.

    PubMed

    Tang, Binhua; Cheng, Xiaolong; Xi, Yunlong; Chen, Zixin; Zhou, Yufan; Jin, Victor X

    2017-09-08

    Recent sequence-based profiling technologies such as high-throughput sequencing to detect fragment nucleotide sequence (Hi-C) and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) have revolutionized the field of three-dimensional (3D) chromatin architecture. It is now recognized that human genome functions as folded 3D chromatin units and looping paradigm is the basic principle of gene regulation. To better interpret the 3D data dramatically accumulating in past five years and to gain deep biological insights, huge efforts have been made in developing novel quantitative analysis methods. However, the full understanding of genome regulation requires thorough knowledge in both genomic technologies and their related data analyses. We summarize the recent advances in genomic technologies in identifying the 3D chromatin structure and interaction, and illustrate the quantitative analysis methods to infer functional domains and chromatin interactions, and further elucidate the emerging single-cell Hi-C technique and its computational analysis, and finally discuss the future directions such as advances of 3D chromatin techniques in diseases.

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

    PubMed Central

    Zenou, M.; Sa’ar, A.; Kotler, Z.

    2015-01-01

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

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

    PubMed

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

    2015-11-25

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

  11. 3D shape measurement of shoeprint impression with structured illumination and fringe pattern analysis

    NASA Astrophysics Data System (ADS)

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

    2002-06-01

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

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

    PubMed

    Calway, Andrew

    2005-04-01

    A recursive structure from motion algorithm based on optical flow measurements taken from an image sequence is described. It provides estimates of surface normals in addition to 3D motion and depth. The measurements are affine motion parameters which approximate the local flow fields associated with near-planar surface patches in the scene. These are integrated over time to give estimates of the 3D parameters using an extended Kalman filter. This also estimates the camera focal length and, so, the 3D estimates are metric. The use of parametric measurements means that the algorithm is computationally less demanding than previous optical flow approaches and the recursive filter builds in a degree of noise robustness. Results of experiments on synthetic and real image sequences demonstrate that the algorithm performs well.

  13. 3D electrical structure of porphyry copper deposit: A case study of Shaxi copper deposit

    NASA Astrophysics Data System (ADS)

    Chen, Xiang-Bin; Lü, Qing-Tian; Yan, Jia-Yong

    2012-06-01

    Located in Lu-Zong ore concentration area, middle-lower Yangtze metallogenic belt, ShaXi porphyry copper deposit is a typical hydrothermal deposit. To investigate the distribution of deep ore bodies and spatial characteristics of host structures, an AMT survey was conducted in mining area. Eighteen pseudo-2D resistivity sections were constructed through careful processing and inversion. These sections clearly show resistivity difference between the Silurian sandstones formation and quartz diorite porphyry and this porphyry copper formation was controlled by the highly resistive anticlines. Using 3D block Kriging interpolation method and 3D visualization techniques, we constructed a detailed 3D resistivity model of quartz diorite porphyry which shows the shape and spatial distribution of deep ore bodies. This case study can serve as a good example for future ore prospecting in and around this mining area.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  15. Improving structural brain images acquired with the 3D FLASH sequence.

    PubMed

    Wang, Jinghua; He, Lili; Zheng, Hairong; Lu, Zhong-Lin

    2017-05-01

    The three-dimension Fast Low Angle SHot Magnetic Resonance Imaging (3D FLASH) sequence has been widely adopted in medical diagnostic imaging because of its availability, simplicity, and high spatial resolution. To improve the quality of structural brain images acquired with the 3D FLASH sequence, we developed a parameter optimization scheme and image inhomogeneity correction methods. The optimal imaging parameters were determined by maximizing gray-matter and white-matter CNR efficiency. Compared to protocols based on published parameters, applying the proposed optimal imaging parameters increased CNR efficiency by >10%. Image inhomogeneity, including signal and CNR inhomogeneity, was corrected by the choice of an optimal flip angle, estimated transmit function, and estimated receive sensitivity. As a result, our optimization and image inhomogeneity correction greatly improved the quality of images acquired with the 3D FLASH sequence. Published by Elsevier Inc.

  16. 3D printed low-loss THz waveguide based on Kagome photonic crystal structure.

    PubMed

    Yang, Jing; Zhao, Jiayu; Gong, Cheng; Tian, Haolin; Sun, Lu; Chen, Ping; Lin, Lie; Liu, Weiwei

    2016-10-03

    A low-loss hollow core terahertz waveguide based on Kagome photonic crystal structure has been designed and fabricated by 3D printing. The 3D printed waveguide has been characterized by using THz time-domain spectroscopy. The results demonstrate that the obtained waveguide features average power propagation loss of 0.02 cm-1 for 0.2-1.0 THz (the minimum is about 0.002 cm-1 at 0.75 THz). More interesting, it could be simply mechanically spliced without any additional alignment, while maintaining the excellent performance. The 3D printing technique will be a promising solution to fabricate Kagome THz waveguide with well controllable characteristics and low cost.

  17. Human Sinoatrial Node Structure: 3D Microanatomy of Sinoatrial Conduction Pathways

    PubMed Central

    Csepe, Thomas A.; Zhao, Jichao; Hansen, Brian J.; Li, Ning; Sul, Lidiya V.; Lim, Praise; Wang, Yufeng; Simonetti, Orlando P.; Kilic, Ahmet; Mohler, Peter J.; Janssen, Paul ML.; Fedorov, Vadim V.

    2016-01-01

    Introduction Despite a century of extensive study on the human sinoatrial node (SAN), the structure-to-function features of specialized SAN conduction pathways (SACP) are still unknown and debated. We report a new method for direct analysis of the SAN microstructure in optically-mapped human hearts with and without clinical history of SAN dysfunction. Methods Two explanted donor human hearts were coronary-perfused and optically-mapped. Structural analyses of histological sections parallel to epicardium (~13-21μm intervals) were integrated with optical maps to create 3D computational reconstructions of the SAN complex. High-resolution fiber fields were obtained using 3D Eigen-analysis of the structure tensor, and used to analyze SACP microstructure with a fiber-tracking approach. Results Optical mapping revealed normal SAN activation of the atria through a lateral SACP proximal to the crista terminalis in Heart #1 but persistent SAN exit block in diseased Heart #2. 3D structural analysis displayed a functionally-observed SAN border composed of fibrosis, fat, and/or discontinuous fibers between SAN and atria, which was only crossed by several branching myofiber tracts in SACP regions. Computational 3D fiber-tracking revealed that myofiber tracts of SACPs created continuous connections between SAN #1 and atria, but in SAN #2, SACP region myofiber tracts were discontinuous due to fibrosis and fat. Conclusions We developed a new integrative functional, structural and computational approach that allowed for the resolution of the specialized 3D microstructure of human SACPs for the first time. Application of this integrated approach will shed new light on the role of the specialized SAN microanatomy in maintaining sinus rhythm. PMID:26743207

  18. Effects of 3D Earth structure on W-phase CMT parameters

    NASA Astrophysics Data System (ADS)

    Morales, Catalina; Duputel, Zacharie; Rivera, Luis; Kanamori, Hiroo

    2017-04-01

    The source inversion of the W-phase has demonstrated a great potential to provide fast and reliable estimates of the centroid moment tensor (CMT) for moderate to large earthquakes. It has since been implemented in different operational environments (NEIC-USGS, PTWC, etc.) with the aim of providing rapid CMT solutions. These solutions are in particular useful for tsunami warning purposes. Computationally, W-phase waveforms are usually synthetized by summation of normal modes at long period (100 - 1000 s) for a spherical Earth model (e.g., PREM). Although the energy of these modes mainly stays in the mantle where lateral structural variations are relatively small, the impact of 3D heterogeneities on W-phase solutions have not yet been quantified. In this study, we investigate possible bias in W-phase source parameters due to unmodeled lateral structural heterogeneities. We generate a simulated dataset consisting of synthetic seismograms of large past earthquakes that accounts for the Earth's 3D structure. The W-phase algorithm is then used to invert the synthetic dataset for earthquake CMT parameters with and without added noise. Results show that the impact of 3D heterogeneities is generally larger for surface-waves than for W-phase waveforms. However, some discrepancies are noted between inverted W-phase parameters and target values. Particular attention is paid to the possible bias induced by the unmodeled 3D structure into the location of the W-phase centroid. Preliminary results indicate that the parameter that is most susceptible to 3D Earth structure seems to be the centroid depth.

  19. Study of materials and machines for 3D printed large-scale, flexible electronic structures using fused deposition modeling

    NASA Astrophysics Data System (ADS)

    Hwang, Seyeon

    The 3 dimensional printing (3DP), called to additive manufacturing (AM) or rapid prototyping (RP), is emerged to revolutionize manufacturing and completely transform how products are designed and fabricated. A great deal of research activities have been carried out to apply this new technology to a variety of fields. In spite of many endeavors, much more research is still required to perfect the processes of the 3D printing techniques especially in the area of the large-scale additive manufacturing and flexible printed electronics. The principles of various 3D printing processes are briefly outlined in the Introduction Section. New types of thermoplastic polymer composites aiming to specified functional applications are also introduced in this section. Chapter 2 shows studies about the metal/polymer composite filaments for fused deposition modeling (FDM) process. Various metal particles, copper and iron particles, are added into thermoplastics polymer matrices as the reinforcement filler. The thermo-mechanical properties, such as thermal conductivity, hardness, tensile strength, and fracture mechanism, of composites are tested to figure out the effects of metal fillers on 3D printed composite structures for the large-scale printing process. In Chapter 3, carbon/polymer composite filaments are developed by a simple mechanical blending process with an aim of fabricating the flexible 3D printed electronics as a single structure. Various types of carbon particles consisting of multi-wall carbon nanotube (MWCNT), conductive carbon black (CCB), and graphite are used as the conductive fillers to provide the thermoplastic polyurethane (TPU) with improved electrical conductivity. The mechanical behavior and conduction mechanisms of the developed composite materials are observed in terms of the loading amount of carbon fillers in this section. Finally, the prototype flexible electronics are modeled and manufactured by the FDM process using Carbon/TPU composite filaments and

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

    PubMed Central

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

    2017-01-01

    Abstract Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale. PMID:28025317

  1. 3D printing PLA and silicone elastomer structures with sugar solution support material

    NASA Astrophysics Data System (ADS)

    Hamidi, Armita; Jain, Shrenik; Tadesse, Yonas

    2017-04-01

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

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

    PubMed

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

    2016-12-26

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

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

    PubMed Central

    Bai, Xiao-chen; Martin, Thomas G.; Scheres, Sjors H. W.; Dietz, Hendrik

    2012-01-01

    A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback. PMID:23169645

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

    PubMed Central

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

    2013-01-01

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

  6. Modeling and characterization of 2-D and 3-D textile structural composites

    SciTech Connect

    Yang, J.M.

    1986-01-01

    This dissertation studies the analytical modeling and experimental characterization of various two-dimensional and three-dimensional textile structure composites. In the analytical approach, various theoretical models were established to predict the stiffness, strength, nonlinear deformation, and failure behavior of triaxial woven-fabric composites, 3-D braided composites, and multilayer multidirectional warp knit fabric composites in polymer and metal matrices. The structure performance maps of various textile structural composites were also established, based upon these analytical methods. In the experimental approach, extensive mechanical testing and microstructural characterization were performed to investigate the thermomechanical properties and failure behavior of 3-D braided FP/Al composites. Results of this research will serve as the basis for assessing the potential of textile composites for structural applications.

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

    PubMed

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

    2013-02-01

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

  8. Integrating protein structural dynamics and evolutionary analysis with Bio3D.

    PubMed

    Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

    2014-12-10

    Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

  9. 3D scanning of internal structure in gel engineering materials with visual scanning microscopic light scattering

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  10. ModeRNA: a tool for comparative modeling of RNA 3D structure

    PubMed Central

    Rother, Magdalena; Rother, Kristian; Puton, Tomasz; Bujnicki, Janusz M.

    2011-01-01

    RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative modeling of RNA 3D structures. As an input, ModeRNA requires a 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template. It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post-translational modifications in proteins. ModeRNA can also model DNA structures or use them as templates. It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available. PMID:21300639

  11. 3D Scanning Cloud Radar Observations at Azores during the ARM AMF field campaign: Reconstruction and study of 3D cloud structures and properties

    NASA Astrophysics Data System (ADS)

    Bowley, K.; Jo, I.; Tatarevic, A.; Kollias, P.

    2010-12-01

    The U.S. Department of Energy Atmospheric Radiation Measurement (ARM) Mobile Facility (AMF) has been operating at Graciosa Island (Azores) since May 2009. This 21-month field campaign focuses on the study of marine stratus clouds. The ARM/AMF instrumentation and location provides a unique opportunity to observe the cloud properties of marine stratocumulus utilizing a variety of active and passive remote sensors. In addition to the standard profiling instrumentation, the first scanning W-band (94-GHz) ARM Cloud Radar (SWACR) was deployed for a short two-month period (October-November 2009). Several scan strategies were tested during the SWACR deployment. The scan strategies were designed specifically to provide the ability to reconstruct the 3D cloud structure. The raw radar observations are quality controlled with the identification of radar volumes with significant detections, water vapor attenuation and unfolding of the radar Doppler velocity. The observations are also transformed from the original radar coordinate system (spherical) to a Cartesian coordinate system using an adaptive gridding algorithm. The 3D gridding of the radar observables, along with spatial data analysis, allow us to evaluate important issues, specifically spatial variability of cloud and drizzle structures. Column profiles of SWACR observables are used in combination with Liquid Water Path measurements from the collocated Microwave Radiometer (MWR) to develop new relationships to compute Liquid Water Content (LWC). The best possible estimate of the 3D LWC structure is reconstructed by assessing both our relationship and other known relationships between radar reflectivity and LWC. This is required in order to use the 3D cloud observations for radiative transfer modeling. Additional drizzle-identification techniques are also being developed to allow the isolation of 3D cloud-only or liquid-only fields. These types of variables have a key impact on the understanding of the radiative budget

  12. New 3D structuring process for non-integrated circuit related technologies (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Nouri, Lamia; Possémé, Nicolas; Landis, Stéfan; Milesi, Frédéric; Gaillard, Frédéric-Xavier

    2017-04-01

    Fabrication processes that microelectronic developed for Integrated circuit (IC) technologies for decades, do not meet the new emerging structuration's requirements, in particular non-IC related technologies one, such as MEMS/NEMS, Micro-Fluidics, photovoltaics, lenses. Actually complex 3D structuration requires complex lithography patterning approaches such as gray-scale electron beam lithography, laser ablation, focused ion beam lithography, two photon polymerization. It is now challenging to find cheaper and easiest technique to achieve 3D structures. In this work, we propose a straightforward process to realize 3D structuration, intended for silicon based materials (Si, SiN, SiOCH). This structuration technique is based on nano-imprint lithography (NIL), ion implantation and selective wet etching. In a first step a pattern is performed by lithography on a substrate, then ion implantation is realized through a resist mask in order to create localized modifications in the material, thus the pattern is transferred into the subjacent layer. Finally, after the resist stripping, a selective wet etching is carried out to remove selectively the modified material regarding the non-modified one. In this paper, we will first present results achieved with simple 2D line array pattern processed either on Silicon or SiOCH samples. This step have been carried out to demonstrate the feasibility of this new structuration process. SEM pictures reveals that "infinite" selectivity between the implanted areas versus the non-implanted one could be achieved. We will show that a key combination between the type of implanted ion species and wet etching chemistries is required to obtain such results. The mechanisms understanding involved during both implantation and wet etching processes will also be presented through fine characterizations with Photoluminescence, Raman and Secondary Ion Mass Spectrometry (SIMS) for silicon samples, and ellipso-porosimetry and Fourier Transform Infra

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

    NASA Technical Reports Server (NTRS)

    Burks, B. L.; Rowe, J. C.; Dinkins, M. A.; Christensen, B.; Selleck, C.; Jacoboski, D.; Markus, R.

    1992-01-01

    Surface contours inside the large waste storage tanks typical of the Department of Energy (DOE) complex are, in general, highly irregular. In addition to pipes and other pieces of equipment in the tanks, the surfaces may have features such as mounds, fissures, crystalline structures, and mixed solid and liquid forms. Prior to remediation activities, it will be necessary to characterize the waste to determine the most effective remediation approaches. Surface contour data will be required both prior to and during remediation. The use is described of a structured light source to generate 3-D surface contour maps of the interior of waste storage silos at the Feed Materials Production Center at Fernald, OH. The landscape inside these large waste storage tanks bears a strong resemblance to some of the landscapes that might be encountered during lunar or planetary exploration. Hence, these terrestrial 3-D mapping techniques may be directly applicable to extraterrestrial exploration. In further development, it will be demonstrated that these 3-D data can be used for robotic task planning just as 3-D surface contour data of a satellite could be used to plan maintenance tasks for a space-based servicing robot.

  14. Structural and functional imaging of 3D microfluidic mixers using optical coherence tomography.

    PubMed

    Xi, Chuanwu; Marks, Daniel L; Parikh, Devang S; Raskin, Lutgarde; Boppart, Stephen A

    2004-05-18

    To achieve high mixing efficiency in microfluidic devices, complex designs are often required. Microfluidic devices have been evaluated with light and confocal microscopy, but fluid-flow characteristics at different depths are difficult to separate from the en face images produced. By using optical coherence tomography (OCT), an imaging modality capable of imaging 3D microstructures at micrometer-scale resolutions over millimeter-size scales, we obtained 3D dynamic functional and structural data for three representative microfluidic mixers: a Y channel mixer, a 3D serpentine mixer, and a vortex mixer. In the serpentine mixer, OCT image analysis revealed that the mixing efficiency was linearly dependent on the Reynolds number, whereas it appeared to have exponential dependence when imaged with light microscopy. The visual overlap of fluid flows in light-microscopy images leads to an overestimation of the mixing efficiency, an effect that was eliminated with OCT imaging. Doppler OCT measurements determined velocity profiles at various points in the serpentine mixer. Mixing patterns in the vortex mixer were compared with light-microscopy and OCT image analysis. These results demonstrate that OCT can significantly improve the characterization of 3D microfluidic device structure and function.

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

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications.

  16. Novel 3D bismuth-based coordination polymers: Synthesis, structure, and second harmonic generation properties

    NASA Astrophysics Data System (ADS)

    Wibowo, Arief C.; Smith, Mark D.; Yeon, Jeongho; Halasyamani, P. Shiv; zur Loye, Hans-Conrad

    2012-11-01

    Two new 3D bismuth containing coordination polymers are reported along with their single crystal structures and SHG properties. Compound 1: Bi2O2(pydc) (pydc=pyridine-2, 5-dicarboxylate), crystallizes in the monoclinic, polar space group, P21 (a=9.6479(9) Å, b=4.2349(4) Å, c=11.9615(11) Å, β=109.587(1)°), which contains Bi2O2 chains that are connected into a 3D structure via the pydc ligands. Compound 2: Bi4Na4(1R3S-cam)8(EtOH)3.1(H2O)3.4 (1R3S cam=1R3S-camphoric acid) crystallizes in the monoclinic, polar space group, P21 (a=19.0855(7) Å, b=13.7706(5) Å, c=19.2429(7) Å, β=90.701(1)°) and is a true 3D coordination polymer. These are two example of SHG compounds prepared using unsymmetric ligands (compound 1) or chiral ligands (compound 2), together with metals that often exhibit stereochemically-active lone pairs, such as Bi3+, a synthetic approach that resulted in polar, non-centrosymmetric, 3D metal-organic coordination polymer.

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

    NASA Technical Reports Server (NTRS)

    Burks, B. L.; Rowe, J. C.; Dinkins, M. A.; Christensen, B.; Selleck, C.; Jacoboski, D.; Markus, R.

    1992-01-01

    Surface contours inside the large waste storage tanks typical of the Department of Energy (DOE) complex are, in general, highly irregular. In addition to pipes and other pieces of equipment in the tanks, the surfaces may have features such as mounds, fissures, crystalline structures, and mixed solid and liquid forms. Prior to remediation activities, it will be necessary to characterize the waste to determine the most effective remediation approaches. Surface contour data will be required both prior to and during remediation. The use is described of a structured light source to generate 3-D surface contour maps of the interior of waste storage silos at the Feed Materials Production Center at Fernald, OH. The landscape inside these large waste storage tanks bears a strong resemblance to some of the landscapes that might be encountered during lunar or planetary exploration. Hence, these terrestrial 3-D mapping techniques may be directly applicable to extraterrestrial exploration. In further development, it will be demonstrated that these 3-D data can be used for robotic task planning just as 3-D surface contour data of a satellite could be used to plan maintenance tasks for a space-based servicing robot.

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

    NASA Astrophysics Data System (ADS)

    Liu, Yahui; Yao, Jian; Liu, Kang; Lu, Xiaohu; Xia, Menghan

    2016-06-01

    Crack detection for bridge bottom surfaces via remote sensing techniques is undergoing a revolution in the last few years. For such applications, a large amount of images, acquired with high-resolution industrial cameras close to the bottom surfaces with some mobile platform, are required to be stitched into a wide-view single composite image. The conventional idea of stitching a panorama with the affine model or the homographic model always suffers a series of serious problems due to poor texture and out-of-focus blurring introduced by depth of field. In this paper, we present a novel method to seamlessly stitch these images aided by 3D structure lines of bridge bottom surfaces, which are extracted from 3D camera data. First, we propose to initially align each image in geometry based on its rough position and orientation acquired with both a laser range finder (LRF) and a high-precision incremental encoder, and these images are divided into several groups with the rough position and orientation data. Secondly, the 3D structure lines of bridge bottom surfaces are extracted from the 3D cloud points acquired with 3D cameras, which impose additional strong constraints on geometrical alignment of structure lines in adjacent images to perform a position and orientation optimization in each group to increase the local consistency. Thirdly, a homographic refinement between groups is applied to increase the global consistency. Finally, we apply a multi-band blending algorithm to generate a large-view single composite image as seamlessly as possible, which greatly eliminates both the luminance differences and the color deviations between images and further conceals image parallax. Experimental results on a set of representative images acquired from real bridge bottom surfaces illustrate the superiority of our proposed approaches.

  19. Singularities of 3D laminar boundary layer equations and flow structure in their vicinity on conical bodies

    NASA Astrophysics Data System (ADS)

    Shalaev, V. I.

    2016-10-01

    Singularities appearing in solutions of 3D laminar boundary layer (BL) equations, when two streamline families are collided, are discussed. For conical bodies, equations are investigated using asymptotic methods. Analytical solutions are obtained for the outer BL region; their singularities in the runoff plane are studied. The asymptotic flow structure near the singularity is constructed on the base of Navier-Stokes equations at large Reynolds numbers. For different flow regions analytical solutions are found and are matched with BL equation solutions. Properties of BL equations for the near-wall region in the runoff plane are investigated and a criterion of the solution disappearing is found. It is shown that this criterion separates two different topological flow structures and corresponds to the singularity appearance in this plane in solutions of full equations. Calculations confirmed obtained results are presented.

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

    NASA Astrophysics Data System (ADS)

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

    Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other structures. Proteopedia ( http://www.proteopedia.org ) presents 3D biomolecule structures in a broadly accessible manner to a diverse scientific audience through easy-to-use molecular visualization tools integrated into a wiki environment that anyone with a user account can edit. We describe recent advances in the web resource in the areas of content and software. In terms of content, we describe a large growth in user-added content as well as improvements in automatically-generated content for all PDB entry pages in the resource. In terms of software, we describe new features ranging from the capability to create pages hidden from public view to the capability to export pages for offline viewing. New software features also include an improved file-handling system and availability of biological assemblies of protein structures alongside their asymmetric units.

  1. The crystal structure of Aspergillus fumigatus cyclophilin reveals 3D domain swapping of a central element.

    PubMed

    Limacher, Andreas; Kloer, Daniel P; Flückiger, Sabine; Folkers, Gerd; Crameri, Reto; Scapozza, Leonardo

    2006-02-01

    The crystal structure of Aspergillus fumigatus cyclophilin (Asp f 11) was solved by the multiwavelength anomalous dispersion method and was refined to a resolution of 1.85 A with R and R(free) values of 18.9% and 21.4%, respectively. Many cyclophilin structures have been solved to date, all showing the same monomeric conformation. In contrast, the structure of A. fumigatus cyclophilin reveals dimerization by 3D domain swapping and represents one of the first proteins with a swapped central domain. The domain-swapped element consists of two beta strands and a subsequent loop carrying a conserved tryptophan. The tryptophan binds into the active site, inactivating cis-trans isomerization. This might be a means of biological regulation. The two hinge loops leave the protein prone to misfolding. In this context, alternative forms of 3D domain swapping that can lead to N- or C-terminally swapped dimers, oligomers, and aggregates are discussed.

  2. FILTREST3D: discrimination of structural models using restraints from experimental data.

    PubMed

    Gajda, Michal J; Tuszynska, Irina; Kaczor, Marta; Bakulina, Anastasia Yu; Bujnicki, Janusz M

    2010-12-01

    Automatic methods for macromolecular structure prediction (fold recognition, de novo folding and docking programs) produce large sets of alternative models. These large model sets often include many native-like structures, which are often scored as false positives. Such native-like models can be more easily identified based on data from experimental analyses used as structural restraints (e.g. identification of nearby residues by cross-linking, chemical modification, site-directed mutagenesis, deuterium exchange coupled with mass spectrometry, etc.). We present a simple server for scoring and ranking of models according to their agreement with user-defined restraints. FILTREST3D is freely available for users as a web server and standalone software at: http://filtrest3d.genesilico.pl/ iamb@genesilico.pl Supplementary data are availa