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Sample records for 3-d global chemical

  1. Estimation of Atmospheric Methane Surface Fluxes Using a Global 3-D Chemical Transport Model

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Prinn, R.

    2003-12-01

    Accurate determination of atmospheric methane surface fluxes is an important and challenging problem in global biogeochemical cycles. We use inverse modeling to estimate annual, seasonal, and interannual CH4 fluxes between 1996 and 2001. The fluxes include 7 time-varying seasonal (3 wetland, rice, and 3 biomass burning) and 3 steady aseasonal (animals/waste, coal, and gas) global processes. To simulate atmospheric methane, we use the 3-D chemical transport model MATCH driven by NCEP reanalyzed observed winds at a resolution of T42 ( ˜2.8° x 2.8° ) in the horizontal and 28 levels (1000 - 3 mb) in the vertical. By combining existing datasets of individual processes, we construct a reference emissions field that represents our prior guess of the total CH4 surface flux. For the methane sink, we use a prescribed, annually-repeating OH field scaled to fit methyl chloroform observations. MATCH is used to produce both the reference run from the reference emissions, and the time-dependent sensitivities that relate individual emission processes to observations. The observational data include CH4 time-series from ˜15 high-frequency (in-situ) and ˜50 low-frequency (flask) observing sites. Most of the high-frequency data, at a time resolution of 40-60 minutes, have not previously been used in global scale inversions. In the inversion, the high-frequency data generally have greater weight than the weekly flask data because they better define the observational monthly means. The Kalman Filter is used as the optimal inversion technique to solve for emissions between 1996-2001. At each step in the inversion, new monthly observations are utilized and new emissions estimates are produced. The optimized emissions represent deviations from the reference emissions that lead to a better fit to the observations. The seasonal processes are optimized for each month, and contain the methane seasonality and interannual variability. The aseasonal processes, which are less variable, are

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

    PubMed Central

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

    2010-01-01

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

  3. 3-D QSARS FOR RANKING AND PRIORITIZATION OF LARGE CHEMICAL DATASETS: AN EDC CASE STUDY

    EPA Science Inventory

    The COmmon REactivity Pattern (COREPA) approach is a three-dimensional structure activity (3-D QSAR) technique that permits identification and quantification of specific global and local steroelectronic characteristics associated with a chemical's biological activity. It goes bey...

  4. 3D printing of versatile reactionware for chemical synthesis.

    PubMed

    Kitson, Philip J; Glatzel, Stefan; Chen, Wei; Lin, Chang-Gen; Song, Yu-Fei; Cronin, Leroy

    2016-05-01

    In recent decades, 3D printing (also known as additive manufacturing) techniques have moved beyond their traditional applications in the fields of industrial manufacturing and prototyping to increasingly find roles in scientific research contexts, such as synthetic chemistry. We present a general approach for the production of bespoke chemical reactors, termed reactionware, using two different approaches to extrusion-based 3D printing. This protocol describes the printing of an inert polypropylene (PP) architecture with the concurrent printing of soft material catalyst composites, using two different 3D printer setups. The steps of the PROCEDURE describe the design and preparation of a 3D digital model of the desired reactionware device and the preparation of this model for use with fused deposition modeling (FDM) type 3D printers. The protocol then further describes the preparation of composite catalyst-silicone materials for incorporation into the 3D-printed device and the steps required to fabricate a reactionware device. This combined approach allows versatility in the design and use of reactionware based on the specific needs of the experimental user. To illustrate this, we present a detailed procedure for the production of one such reactionware device that will result in the production of a sealed reactor capable of effecting a multistep organic synthesis. Depending on the design time of the 3D model, and including time for curing and drying of materials, this procedure can be completed in ∼3 d. PMID:27077333

  5. 2D-3D MIGRATION AND CONFORMATIONAL MULTIPLICATION OF CHEMICALS IN LARGE CHEMICAL INVENTORIES

    EPA Science Inventory

    Chemical interactions are three-dimensional (3D) in nature and require modeling chemicals as 3D entities. In turn, using 3D models of chemicals leads to the realization that a single 2D structure can have hundreds of different conformations, and the electronic properties of these...

  6. GBS: Global 3D simulation of tokamak edge region

    NASA Astrophysics Data System (ADS)

    Zhu, Ben; Fisher, Dustin; Rogers, Barrett; Ricci, Paolo

    2012-10-01

    A 3D two-fluid global code, namely Global Braginskii Solver (GBS), is being developed to explore the physics of turbulent transport, confinement, self-consistent profile formation, pedestal scaling and related phenomena in the edge region of tokamaks. Aimed at solving drift-reduced Braginskii equations [1] in complex magnetic geometry, the GBS is used for turbulence simulation in SOL region. In the recent upgrade, the simulation domain is expanded into close flux region with twist-shift boundary conditions. Hence, the new GBS code is able to explore global transport physics in an annular full-torus domain from the top of the pedestal into the far SOL. We are in the process of identifying and analyzing the linear and nonlinear instabilities in the system using the new GBS code. Preliminary results will be presented and compared with other codes if possible.[4pt] [1] A. Zeiler, J. F. Drake and B. Rogers, Phys. Plasmas 4, 2134 (1997)

  7. Simulation of 3D Global Wave Propagation Through Geodynamic Models

    NASA Astrophysics Data System (ADS)

    Schuberth, B.; Piazzoni, A.; Bunge, H.; Igel, H.; Steinle-Neumann, G.

    2005-12-01

    This project aims at a better understanding of the forward problem of global 3D wave propagation. We use the spectral element program "SPECFEM3D" (Komatitsch and Tromp, 2002a,b) with varying input models of seismic velocities derived from mantle convection simulations (Bunge et al., 2002). The purpose of this approach is to obtain seismic velocity models independently from seismological studies. In this way one can test the effects of varying parameters of the mantle convection models on the seismic wave field. In order to obtain the seismic velocities from the temperature field of the geodynamical simulations we follow a mineral physics approach. Assuming a certain mantle composition (e.g. pyrolite with CMASF composition) we compute the stable phases for each depth (i.e. pressure) and temperature by system Gibbs free energy minimization. Elastic moduli and density are calculated from the equations of state of the stable mineral phases. For this we use a mineral physics database derived from calorimetric experiments (enthalphy and entropy of formation, heat capacity) and EOS parameters.

  8. MPSalsa 3D Simulations of Chemically Reacting Flows

    DOE Data Explorer

    Many important scientific and engineering applications require a detailed analysis of complex systems with coupled fluid flow, thermal energy transfer, mass transfer and nonequilibrium chemical reactions. Currently, computer simulations of these complex reacting flow problems are limited to idealized systems in one or two spatial dimensions when coupled with a detailed, fundamental chemistry model. The goal of our research is to develop, analyze and implement advanced MP numerical algorithms that will allow high resolution 3D simulations with an equal emphasis on fluid flow and chemical kinetics modeling. In our research, we focus on the development of new, fully coupled, implicit solution strategies that are based on robust MP iterative solution methods (copied from http://www.cs.sandia.gov/CRF/MPSalsa/). These simulations are needed for scientific and technical areas such as: combustion research for transportation, atmospheric chemistry modeling for pollution studies, chemically reacting flow models for analysis and control of manufacturing processes, surface catalytic reactors for methane to methanol conversion and chemical vapor deposition (CVD) process modeling for production of advanced semiconductor materials (http://www.cs.sandia.gov/CRF/MPSalsa/).

    This project website provides six QuickTime videos of these simulations, along with a small image gallery and slideshow animations. A list of related publications and conference presentations is also made available.

  9. 3D Chemical and Elemental Imaging by STXM Spectrotomography

    SciTech Connect

    Wang, J.; Karunakaran, C.; Lu, Y.; Hormes, J.; Hitchcock, A. P.; Prange, A.; Franz, B.; Harkness, T.; Obst, M.

    2011-09-09

    Spectrotomography based on the scanning transmission x-ray microscope (STXM) at the 10ID-1 spectromicroscopy beamline of the Canadian Light Source was used to study two selected unicellular microorganisms. Spatial distributions of sulphur globules, calcium, protein, and polysaccharide in sulphur-metabolizing bacteria (Allochromatium vinosum) were determined at the S 2p, C 1s, and Ca 2p edges. 3D chemical mapping showed that the sulphur globules are located inside the bacteria with a strong spatial correlation with calcium ions (it is most probably calcium carbonate from the medium; however, with STXM the distribution and localization in the cell can be made visible, which is very interesting for a biologist) and polysaccharide-rich polymers, suggesting an influence of the organic components on the formation of the sulphur and calcium deposits. A second study investigated copper accumulating in yeast cells (Saccharomyces cerevisiae) treated with copper sulphate. 3D elemental imaging at the Cu 2p edge showed that Cu(II) is reduced to Cu(I) on the yeast cell wall. A novel needle-like wet cell sample holder for STXM spectrotomography studies of fully hydrated samples is discussed.

  10. Representation of chemical information in OASIS centralized 3D database for existing chemicals.

    PubMed

    Nikolov, Nikolai; Grancharov, Vanio; Stoyanova, Galya; Pavlov, Todor; Mekenyan, Ovanes

    2006-01-01

    The present inventory of existing chemicals in regulatory agencies in North America and Europe, encompassing the chemicals of the European Chemicals Bureau (EINECS, with 61 573 discrete chemicals); the Danish EPA (159 448 chemicals); the U.S. EPA (TSCA, 56 882 chemicals; HPVC, 10 546 chemicals) and pesticides' active and inactive ingredients of the U.S. EPA (1379 chemicals); the Organization for Economic Cooperation and Development (HPVC, 4750 chemicals); Environment Canada (DSL, 10851 chemicals); and the Japanese Ministry of Economy, Trade, and Industry (16811), was combined in a centralized 3D database for existing chemicals. The total number of unique chemicals from all of these databases exceeded 185 500. Defined and undefined chemical mixtures and polymers are handled, along with discrete (hydrolyzing and nonhydrolyzing) chemicals. The database manager provides the storage and retrieval of chemical structures with 2D and 3D data, accounting for molecular flexibility by using representative sets of conformers for each chemical. The electronic and geometric structures of all conformers are quantum-chemically optimized and evaluated. Hence, the database contains over 3.7 million 3D records with hundreds of millions of descriptor data items at the levels of structures, conformers, or atoms. The platform contains a highly developed search subsystem--a search is possible on Chemical Abstracts Service numbers; names; 2D and 3D fragment searches; structural, conformational, or atomic properties; affiliation in other chemical databases; structure similarity; logical combinations; saved queries; and search result exports. Models (collections of logically related descriptors) are supported, including information on a model's author, date, bioassay, organs/tissues, conditions, administration, and so forth. Fragments can be interactively constructed using a visual structure editor. A configurable database browser is designed for the inspection and editing of all types of

  11. Ozone formation during an episode over Europe: A 3-D chemical/transport model simulation

    NASA Technical Reports Server (NTRS)

    Berntsen, Terje; Isaksen, Ivar S. A.

    1994-01-01

    A 3-D regional photochemical tracer/transport model for Europe and the Eastern Atlantic has been developed based on the NASA/GISS CTM. The model resolution is 4x5 degrees latitude and longitude with 9 layers in the vertical (7 in the troposphere). Advective winds, convection statistics and other meteorological data from the NASA/GISS GCM are used. An extensive gas-phase chemical scheme based on the scheme used in our global 2D model has been incorporated in the 3D model. In this work ozone formation in the troposphere is studied with the 3D model during a 5 day period starting June 30. Extensive local ozone production is found and the relationship between the source regions and the downwind areas are discussed. Variations in local ozone formation as a function of total emission rate, as well as the composition of the emissions (HC/NO(x)) ratio and isoprene emissions) are elucidated. An important vertical transport process in the troposphere is by convective clouds. The 3D model includes an explicit parameterization of this process. It is shown that this process has significant influence on the calculated surface ozone concentrations.

  12. Quantitative Reconstructions of 3D Chemical Nanostructures in Nanowires.

    PubMed

    Rueda-Fonseca, P; Robin, E; Bellet-Amalric, E; Lopez-Haro, M; Den Hertog, M; Genuist, Y; André, R; Artioli, A; Tatarenko, S; Ferrand, D; Cibert, J

    2016-03-01

    Energy dispersive X-ray spectrometry is used to extract a quantitative 3D composition profile of heterostructured nanowires. The analysis of hypermaps recorded along a limited number of projections, with a preliminary calibration of the signal associated with each element, is compared to the intensity profiles calculated for a model structure with successive shells of circular, elliptic, or faceted cross sections. This discrete tomographic technique is applied to II-VI nanowires grown by molecular beam epitaxy, incorporating ZnTe and CdTe and their alloys with Mn and Mg, with typical size down to a few nanometers and Mn or Mg content as low as 10%. PMID:26837636

  13. Global stability analysis of turbulent 3D wakes

    NASA Astrophysics Data System (ADS)

    Rigas, Georgios; Sipp, Denis; Juniper, Matthew

    2015-11-01

    At low Reynolds numbers, corresponding to laminar and transitional regimes, hydrodynamic stability theory has aided the understanding of the dynamics of bluff body wake-flows and the application of effective control strategies. However, flows of fundamental importance to many industries, in particular the transport industry, involve high Reynolds numbers and turbulent wakes. Despite their turbulence, such wake flows exhibit organisation which is manifested as coherent structures. Recent work has shown that the turbulent coherent structures retain the shape of the symmetry-breaking laminar instabilities and only those manifest as large-scale structures in the near wake (Rigas et al., JFM vol. 750:R5 2014, JFM vol. 778:R2 2015). Based on the findings of the persistence of the laminar instabilities at high Reynolds numbers, we investigate the global stability characteristics of a turbulent wake generated behind a bluff three-dimensional axisymmetric body. We perform a linear global stability analysis on the experimentally obtained mean flow and we recover the dynamic characteristics and spatial structure of the coherent structures, which are linked to the transitional instabilities. A detailed comparison of the predictions with the experimental measurements will be provided.

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

    PubMed

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

    2013-07-01

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

  15. 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

  16. NEW 3D TECHNIQUES FOR RANKING AND PRIORITIZATION OF CHEMICAL INVENTORIES

    EPA Science Inventory

    New three-dimensional quantitative structure activity (3-D QSAR) techniques for prioritizing chemical inventories for endocrine activity will be presented. The Common Reactivity Pattern (COREPA) approach permits identification of common steric and/or electronic patterns associate...

  17. XEDS STEM Tomography For 3D Chemical Characterization Of Nanoscale Particles

    SciTech Connect

    Genc, Arda; Kovarik, Libor; Gu, Meng; Cheng, Huikai; Plachinda, Pavel; Pullan, Lee; Freitag, Bert; Wang, Chong M.

    2013-08-01

    We present a tomography technique which couples scanning transmission electron microscopy (STEM) and X-ray energy dispersive spectrometry (XEDS) to resolve 3D distribution of elements in nanoscale materials. STEM imaging when combined with a symmetrically arranged XEDS detector design around the specimen overcomes many of the obstacles in 3D spectroscopic tomography of nanoscale materials and successfully elucidate the 3D chemical information in a large field of view of the TEM sample. We employed this technique to investigate 3D distribution of Nickel (Ni), Manganese (Mn) and Oxygen (O) in Li(NiMn)O2 battery cathode material. For this purpose, 2D elemental maps were acquired for a range of tilt angles and reconstructed to obtain 3D elemental distribution in an isolated Li(NiMnO2) nanoparticle. The results highlight the strength of this technique in 3D chemical analysis of nanoscale materials by successfully resolving Ni, Mn and O elemental distributions in 3D and discovering the new phenomenon of Ni surface segregation in this material. Furthermore, the comparison of simultaneously acquired HAADF STEM and XEDS STEM tomography results show that XEDS STEM tomography provides additional 3D chemical information of the material especially when there is low atomic number (Z) contrast in the material of interest.

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

    DOEpatents

    Zemla, Adam T.

    2011-09-20

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

  19. True 3D chemical dosimetry (gels, plastics): Development and clinical role

    NASA Astrophysics Data System (ADS)

    Schreiner, L. J.

    2015-01-01

    Since the introduction of volumetric chemical dosimetry with Fricke gel dosimeters in the 1980s, three-dimensional (3D) dosimetry has been a promising technique for the clinic, since it provides a unique methodology for 3D dose measurement of the complex conformal dose distributions achieved by modern techniques such as Intensity Modulated and Volumetric Arc Radiation Therapy. In the last decade, the potential for improved clinical applicability has been advanced by the development of improved 3D dosimeters such as normoxic polymer gel systems, radiochromic plastics (such as PRESAGE) and, recently, newer radiochromic gel dosimeters. Some of these new 3D dosimetry systems were enabled by the availability of optical computed tomography imaging systems for fast dose readout. However, despite its promise, true 3D dosimetry is still not widely practiced in the community. Its use has been confined primarily to select centres of expertise and to specialised quality assurance or commissioning roles where other dosimetry techniques are difficult to implement. In this paper I review some of the current 3D chemical dosimeters available, discuss the requirements for their use and briefly review the roles that these systems can provide to complement the other dose delivery validation approaches available in the clinic. I conclude by describing two roles that may be uniquely served by 3D chemical dosimetry in end-to-end process testing and validation in the complex environment coming into play with the development of Image Guided Adaptive Radiation Therapy.

  20. 3D SERS Imaging Using Chemically Synthesized Highly Symmetric Nanoporous Silver Microparticles.

    PubMed

    Vantasin, Sanpon; Ji, Wei; Tanaka, Yoshito; Kitahama, Yasutaka; Wang, Mengfan; Wongravee, Kanet; Gatemala, Harnchana; Ekgasit, Sanong; Ozaki, Yukihiro

    2016-07-11

    3D surface-enhanced Raman scattering (SERS) imaging with highly symmetric 3D silver microparticles as a SERS substrate was developed. Although the synthesis method is purely chemical and does not involve lithography, the synthesized nanoporous silver microparticles possess a regular hexapod shape and octahedral symmetry. By using p-aminothiophenol (PATP) as a probe molecule, the 3D enhancement patterns of the particles were shown to be very regular and predictable, resembling the particle shape and exhibiting symmetry. An application to the detection of 3D inhomogeneity in a polymer blend, which relies on the predictable enhancement pattern of the substrate, is presented. 3D SERS imaging using the substrate also provides an improvement in spatial resolution along the Z axis, which is a challenge for Raman measurement in polymers, especially layered polymeric systems. PMID:27240138

  1. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

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

    2016-08-19

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

  2. Global regular solutions for the 3D Kawahara equation posed on unbounded domains

    NASA Astrophysics Data System (ADS)

    Larkin, Nikolai A.; Simões, Márcio Hiran

    2016-08-01

    An initial boundary value problem for the 3D Kawahara equation posed on a channel-type domain was considered. The existence and uniqueness results for global regular solutions as well as exponential decay of small solutions in the H 2-norm were established.

  3. Global regular solutions for the 3D Zakharov-Kuznetsov equation posed on unbounded domains

    NASA Astrophysics Data System (ADS)

    Larkin, N. A.

    2015-09-01

    An initial-boundary value problem for the 3D Zakharov-Kuznetsov equation posed on unbounded domains is considered. Existence and uniqueness of a global regular solution as well as exponential decay of the H2-norm for small initial data are proven.

  4. Dense 3d Point Cloud Generation from Uav Images from Image Matching and Global Optimazation

    NASA Astrophysics Data System (ADS)

    Rhee, S.; Kim, T.

    2016-06-01

    3D spatial information from unmanned aerial vehicles (UAV) images is usually provided in the form of 3D point clouds. For various UAV applications, it is important to generate dense 3D point clouds automatically from over the entire extent of UAV images. In this paper, we aim to apply image matching for generation of local point clouds over a pair or group of images and global optimization to combine local point clouds over the whole region of interest. We tried to apply two types of image matching, an object space-based matching technique and an image space-based matching technique, and to compare the performance of the two techniques. The object space-based matching used here sets a list of candidate height values for a fixed horizontal position in the object space. For each height, its corresponding image point is calculated and similarity is measured by grey-level correlation. The image space-based matching used here is a modified relaxation matching. We devised a global optimization scheme for finding optimal pairs (or groups) to apply image matching, defining local match region in image- or object- space, and merging local point clouds into a global one. For optimal pair selection, tiepoints among images were extracted and stereo coverage network was defined by forming a maximum spanning tree using the tiepoints. From experiments, we confirmed that through image matching and global optimization, 3D point clouds were generated successfully. However, results also revealed some limitations. In case of image-based matching results, we observed some blanks in 3D point clouds. In case of object space-based matching results, we observed more blunders than image-based matching ones and noisy local height variations. We suspect these might be due to inaccurate orientation parameters. The work in this paper is still ongoing. We will further test our approach with more precise orientation parameters.

  5. Compilation of 3D global conductivity model of the Earth for space weather applications

    NASA Astrophysics Data System (ADS)

    Alekseev, Dmitry; Kuvshinov, Alexey; Palshin, Nikolay

    2015-07-01

    We have compiled a global three-dimensional (3D) conductivity model of the Earth with an ultimate goal to be used for realistic simulation of geomagnetically induced currents (GIC), posing a potential threat to man-made electric systems. Bearing in mind the intrinsic frequency range of the most intense disturbances (magnetospheric substorms) with typical periods ranging from a few minutes to a few hours, the compiled 3D model represents the structure in depth range of 0-100 km, including seawater, sediments, earth crust, and partly the lithosphere/asthenosphere. More explicitly, the model consists of a series of spherical layers, whose vertical and lateral boundaries are established based on available data. To compile a model, global maps of bathymetry, sediment thickness, and upper and lower crust thicknesses as well as lithosphere thickness are utilized. All maps are re-interpolated on a common grid of 0.25×0.25 degree lateral spacing. Once the geometry of different structures is specified, each element of the structure is assigned either a certain conductivity value or conductivity versus depth distribution, according to available laboratory data and conversion laws. A numerical formalism developed for compilation of the model, allows for its further refinement by incorporation of regional 3D conductivity distributions inferred from the real electromagnetic data. So far we included into our model four regional conductivity models, available from recent publications, namely, surface conductance model of Russia, and 3D conductivity models of Fennoscandia, Australia, and northwest of the United States.

  6. Combining chemical sequential extractions with 3D fluorescence spectroscopy to characterize sludge organic matter.

    PubMed

    Muller, Mathieu; Jimenez, Julie; Antonini, Maxime; Dudal, Yves; Latrille, Eric; Vedrenne, Fabien; Steyer, Jean-Philippe; Patureau, Dominique

    2014-12-01

    The design and management of anaerobic digestion of sewage sludge (SS) require a relevant characterisation of the sludge organic matter (OM). Methods currently used are time-consuming and often insufficiently informative. A new method combining chemical sequential extractions (CSE) with 3D fluorescence spectroscopy was developed to provide a relevant SS characterisation to assess both OM bioaccessibility and complexity which govern SS biodegradability. CSE fractionates the sludge OM into 5 compartments of decreasing accessibility. First applied on three SS samples with different OM stability, fractionation profiles obtained were in accordance with the latter. 3D fluorescence spectroscopy revealed that the bioaccessible compartments were mainly constituted of simple and easily biodegradable OM while the unaccessible ones were largely made of complex and refractory OM. Then, primary, secondary and anaerobically digested sludge with different biodegradabilities were tested. Complexity revealed by 3D fluorescence spectroscopy was linked with biodegradability and chemical accessibility was correlated with sludge bioaccessibility. PMID:25223440

  7. LigandBox: A database for 3D structures of chemical compounds

    PubMed Central

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

  8. Uncertainty analysis in 3D global models: Aerosol representation in MOZART-4

    NASA Astrophysics Data System (ADS)

    Gasore, J.; Prinn, R. G.

    2012-12-01

    The Probabilistic Collocation Method (PCM) has been proven to be an efficient general method of uncertainty analysis in atmospheric models (Tatang et al 1997, Cohen&Prinn 2011). However, its application has been mainly limited to urban- and regional-scale models and chemical source-sink models, because of the drastic increase in computational cost when the dimension of uncertain parameters increases. Moreover, the high-dimensional output of global models has to be reduced to allow a computationally reasonable number of polynomials to be generated. This dimensional reduction has been mainly achieved by grouping the model grids into a few regions based on prior knowledge and expectations; urban versus rural for instance. As the model output is used to estimate the coefficients of the polynomial chaos expansion (PCE), the arbitrariness in the regional aggregation can generate problems in estimating uncertainties. To address these issues in a complex model, we apply the probabilistic collocation method of uncertainty analysis to the aerosol representation in MOZART-4, which is a 3D global chemical transport model (Emmons et al., 2010). Thereafter, we deterministically delineate the model output surface into regions of homogeneous response using the method of Principal Component Analysis. This allows the quantification of the uncertainty associated with the dimensional reduction. Because only a bulk mass is calculated online in Mozart-4, a lognormal number distribution is assumed with a priori fixed scale and location parameters, to calculate the surface area for heterogeneous reactions involving tropospheric oxidants. We have applied the PCM to the six parameters of the lognormal number distributions of Black Carbon, Organic Carbon and Sulfate. We have carried out a Monte-Carlo sampling from the probability density functions of the six uncertain parameters, using the reduced PCE model. The global mean concentration of major tropospheric oxidants did not show a

  9. Melting points and chemical bonding properties of 3d transition metal elements

    NASA Astrophysics Data System (ADS)

    Takahara, Wataru

    2014-08-01

    The melting points of 3d transition metal elements show an unusual local minimal peak at manganese across Period 4 in the periodic table. The chemical bonding properties of scandium, titanium, vanadium, chromium, manganese, iron, cobalt, nickel and copper are investigated by the DV-Xα cluster method. The melting points are found to correlate with the bond overlap populations. The chemical bonding nature therefore appears to be the primary factor governing the melting points.

  10. Integrated 3D-printed reactionware for chemical synthesis and analysis.

    PubMed

    Symes, Mark D; Kitson, Philip J; Yan, Jun; Richmond, Craig J; Cooper, Geoffrey J T; Bowman, Richard W; Vilbrandt, Turlif; Cronin, Leroy

    2012-05-01

    Three-dimensional (3D) printing has the potential to transform science and technology by creating bespoke, low-cost appliances that previously required dedicated facilities to make. An attractive, but unexplored, application is to use a 3D printer to initiate chemical reactions by printing the reagents directly into a 3D reactionware matrix, and so put reactionware design, construction and operation under digital control. Here, using a low-cost 3D printer and open-source design software we produced reactionware for organic and inorganic synthesis, which included printed-in catalysts and other architectures with printed-in components for electrochemical and spectroscopic analysis. This enabled reactions to be monitored in situ so that different reactionware architectures could be screened for their efficacy for a given process, with a digital feedback mechanism for device optimization. Furthermore, solely by modifying reactionware architecture, reaction outcomes can be altered. Taken together, this approach constitutes a relatively cheap, automated and reconfigurable chemical discovery platform that makes techniques from chemical engineering accessible to typical synthetic laboratories. PMID:22522253

  11. Laser nanolithography and chemical metalization for the manufacturing of 3D metallic interconnects

    NASA Astrophysics Data System (ADS)

    Jonavičius, Tomas; RekštytÄ--, Sima; Žukauskas, Albertas; Malinauskas, Mangirdas

    2014-03-01

    We present a developed method based on direct laser writing (DLW) and chemical metallization (CM) for microfabrication of three-dimensional (3D) metallic structures. Such approach enables manufacturing of free­-form electro conductive interconnects which can be used in integrated electric circuits such micro-opto-electro mechanical systems (MOEMS). The proposed technique employing ultrafast high repetition rate laser enables efficient fabrication of 3D microstructures on dielectric as well as conductive substrates. The produced polymer links out of organic-inorganic composite matrix after CM serve as interconnects of separate metallic contacts, their dimensions are: height 15μm, width 5μm, length 35-45 μm and could provide 300 nΩm resistivity measured in a macroscopic way. This proves the techniques potential for creating integrated 3D electric circuits at microscale.

  12. Global 3-d weather models for the atmospheric correction of gravity time series

    NASA Astrophysics Data System (ADS)

    Klügel, Thomas; Wziontek, Hartmut

    2016-04-01

    The use of 3-dimensional weather models allows for an effective reduction of atmospheric effects in gravity time series. In the past the BKG service Atmacs (Atmospheric Attraction Computation Service) provided 3-d atmospheric correction time series only for European stations of the International Geodynamics and Earth Tide Service (IGETS, formerly Global Geodynamics Project, GGP), which are based on the high resolution regional model COSMO-EU of the German Weather Service (DWD). The provision of 3-d density data from the global weather models GME (20 km resolution) and most recently ICON (13 km resolution) by the DWD now allows the computation of 3-d atmospheric correction time series for all IGETS stations worldwide. Due to the triangular grid structure, a different procedure for mass elements close to the computation point is necessary. By increasing the spatial resolution towards the computation point by linear interpolation of the grid values, the use of a point mass approach became possible with an approximation error below 0.3 nm/s2. This approach also allows to consider horizontal density gradients and a tilted model surface of the innermost cells. By means of a variance reduction at different frequency bands a significant improvement of the atmospheric correction can be demonstrated at many IGETS stations. The limited temporal resolution of recently 3 hours can be improved by the user by including local air pressure records using a remove-restore technique. Atmospheric correction time series are online available at http://atmacs.bkg.bund.de.

  13. A Global Hypothesis Verification Framework for 3D Object Recognition in Clutter.

    PubMed

    Aldoma, Aitor; Tombari, Federico; Stefano, Luigi Di; Vincze, Markus

    2016-07-01

    Pipelines to recognize 3D objects despite clutter and occlusions usually end up with a final verification stage whereby recognition hypotheses are validated or dismissed based on how well they explain sensor measurements. Unlike previous work, we propose a Global Hypothesis Verification (GHV) approach which regards all hypotheses jointly so as to account for mutual interactions. GHV provides a principled framework to tackle the complexity of our visual world by leveraging on a plurality of recognition paradigms and cues. Accordingly, we present a 3D object recognition pipeline deploying both global and local 3D features as well as shape and color. Thereby, and facilitated by the robustness of the verification process, diverse object hypotheses can be gathered and weak hypotheses need not be suppressed too early to trade sensitivity for specificity. Experiments demonstrate the effectiveness of our proposal, which significantly improves over the state-of-art and attains ideal performance (no false negatives, no false positives) on three out of the six most relevant and challenging benchmark datasets. PMID:26485476

  14. 3D Reconstruction of Interplanetary Scintillation (IPS) Remote-Sensing Data: Global Solar Wind Boundaries for Driving 3D-MHD Models

    NASA Astrophysics Data System (ADS)

    Yu, H.-S.; Jackson, B. V.; Hick, P. P.; Buffington, A.; Odstrcil, D.; Wu, C.-C.; Davies, J. A.; Bisi, M. M.; Tokumaru, M.

    2015-09-01

    The University of California, San Diego, time-dependent analyses of the heliosphere provide three-dimensional (3D) reconstructions of solar wind velocities and densities from observations of interplanetary scintillation (IPS). Using data from the Solar-Terrestrial Environment Laboratory, Japan, these reconstructions provide a real-time prediction of the global solar-wind density and velocity throughout the whole heliosphere with a temporal cadence of about one day (ips.ucsd.edu). Updates to this modeling effort continue: in the present article, near-Sun results extracted from the time-dependent 3D reconstruction are used as inner boundary conditions to drive 3D-MHD models ( e.g. ENLIL and H3D-MHD). This allows us to explore the differences between the IPS kinematic-model data-fitting procedure and current 3D-MHD modeling techniques. The differences in these techniques provide interesting insights into the physical principles governing the expulsion of coronal mass ejections (CMEs). Here we detail for the first time several specific CMEs and an induced shock that occurred in September 2011 that demonstrate some of the issues resulting from these analyses.

  15. Chemical Dealloying Derived 3D Porous Current Collector for Li Metal Anodes.

    PubMed

    Yun, Qinbai; He, Yan-Bing; Lv, Wei; Zhao, Yan; Li, Baohua; Kang, Feiyu; Yang, Quan-Hong

    2016-08-01

    A 3D porous Cu current collector is fabricated through chemical dealloying from a commerial Cu-Zn alloy tape. The interlinked porous framework naturally integrated can accommodate Li deposition, suppressing dendrite growth and alleviating the huge volume change during cycling. The Li metal anode combined with such a porous Cu collector demonstrates excellent performance and commerial potentials in Li-based secondary batteries. PMID:27219349

  16. 3-D Spherical modelling of the thermo-chemical evolution of Venus

    NASA Astrophysics Data System (ADS)

    Armann, M.; Tackley, P. J.

    2009-04-01

    Several first-order aspects of the dynamics of Venus' mantle remain poorly understood. These include (i) how Venus' mantle loses its radiogenic heat (presumably about the same as Earth's) despite the presence of stagnant lid convection. Hypotheses that have been advanced (summarised in [1]) are conduction through a thin lithosphere, episodic overturn of the lithosphere, magmatic heat transport, and concentration of almost all heat-producing elements into the crust, but there are problems with all of these taken individually. A thick lithosphere may not be consistent with admittance ratios, magmatic heat transport would require a too-large resurfacing rate, and a large concentration of heat-producing elements in the crust would cause weakness and possibly melting in the deep crust. (ii) The relatively long-wavelength distribution of surface features, which is surprising because numerical models and analogue laboratory experiments of stagnant-lid convection produce relatively short-wavelength convective cells. (iii) The inferred (from crater distributions [2]) relatively uniform surface age of 500-700 Ma. (iv) Whether the highlands are above mantle downwellings as on Earth or above mantle upwellings [3]. (v) How the mantle can have outgassing only 25% of 40Ar [4] but supposedly most of its water [5]. (vi) The cause of coronae and relationship to mantle processes [6]. To study some of these questions, we are performing integrated thermo-chemical convection modelling of Venus' evolution over 4.5 billion years, in 3-D spherical geometry as well as 2-D spherical annulus geometry [7]. These models include realistic ("laboratory") rheological parameters for diffusion creep and dislocation creep based on [8][9], which are also composition-dependent, and plastic yielding based on Byerlee's law, which might cause changes in tectonic regime (e.g., episodic plate tectonics). Crustal formation and the resulting differentiation of the crust and mantle are modelled using a self

  17. 3-D Spherical modelling of the thermo-chemical evolution of Venus' mantle and crust

    NASA Astrophysics Data System (ADS)

    Armann, M.; Tackley, P. J.

    2008-09-01

    Background Several first-order aspects of the dynamics of Venus' mantle remain poorly understood. These include (i) how Venus' mantle loses its radiogenic heat, which is expected to be about the same as Earth's, despite the presence of stagnant lid convection. Hypotheses that have been advanced (summarised in [1]) are conduction through a thin lithosphere, episodic overturn of the lithosphere, magmatic heat transport, and concentration of almost all heat-producing elements into the crust, but there are problems with all of these taken individually. A thick lithosphere may not be consistent with admittance ratios, magmatic heat transport would require a too-large resurfacing rate, and a large concentration of heat-producing elements in the crust would cause weakness and possibly melting in the deep crust. (ii) The relatively long-wavelength distribution of surface features, which is surprising because numerical models and analogue laboratory experiments of stagnant-lid convection produce relatively short-wavelength convective cells. (iii) The inferred (from crater distributions [2]) relatively uniform surface age of 500-700 Ma. (iv) Whether the highlands are above mantle downwellings as on Earth or above mantle upwellings [3]. (v) How the mantle can have outgassing only 25% of 40Ar [4] but supposedly most of its water [5]. (vi) The cause of coronae and relationship to mantle processes [6]. Model To study some of these questions, we take advantage of advances in computational capabilities to perform integrated thermo-chemical convection models of Venus' evolution over 4.5 billion years, in 3-D spherical geometry as well as 2-D spherical annulus geometry [7]. These models include realistic ("laboratory") rheological parameters for diffusion creep and dislocation creep based on [8][9], which are also composition-dependent, and plastic yielding based on Byerlee's law, which might cause changes in tectonic regime (e.g., episodic plate tectonics). Crustal formation and

  18. 3D numerical simulation of the transport of chemical signature compounds from buried landmines

    NASA Astrophysics Data System (ADS)

    Irrazabal, Maik; Borrero, Ernesto; Briano, Julio G.; Castro, Miguel; Hernandez, Samuel P.

    2005-06-01

    The transport of the chemical signature compounds from buried landmines in a three-dimensional (3D) array has been numerically modeled using the finite-volume technique. Compounds such as trinitrotoluene, dinitrotoluene, and their degradation products, are semi volatile and somewhat soluble in water. Furthermore, they can strongly adsorb to the soil and undergo chemical and biological degradation. Consequently, the spatial and temporal concentration distributions of such chemicals depend on the mobility of the water and gaseous phases, their molecular and mechanical diffusion, adsorption characteristics, soil water content, compaction, and environmental factors. A 3D framework is required since two-dimensional (2D) symmetry may easily fade due to terrain topography: non-flat surfaces, soil heterogeneity, or underground fractures. The spatial and temporal distribution of the chemical-signature-compounds, in an inclined grid has been obtained. The fact that the chemicals may migrate horizontally, giving higher surface concentrations at positions not directly on top of the objects, emphasizes the need for understanding the transport mechanism when a chemical detector is used. Deformation in the concentration contours after rainfall is observed in the inclined surface and is attributed to both: the advective flux, and to the water flux at the surface caused by the slope. The analysis of the displacements in the position of the maximum concentrations at the surface, respect to the actual location of the mine, in an inclined system, is presented.

  19. 3D simulation and analytical model of chemical heating during silicon wet etching in microchannels

    NASA Astrophysics Data System (ADS)

    Konakov, S. A.; Krzhizhanovskaya, V. V.

    2016-02-01

    We investigate chemical heating of a Silicon-on-Glass (SOG) chip during a highly exothermic reaction of silicon etching in potassium hydroxide (KOH) solution in a microchannel of 100-micron width inside a 1x1 cm SOG chip. Two modeling approaches have been developed, implemented and compared. (1) A detailed 3D model is based on unsteady Navier-Stokes equations, heat and mass transfer equations of a laminar flow of viscous incompressible fluid in microchannel, coupled to the heat transfer equation in the solid chip. 3D simulation results predicted temperature distributions for different KOH flow rates and silicon etching areas. Microchannels of a small diameter do not heat the chip due to the insufficient chemical heating of the cold fluid, whereas large-area etching (large channel diameter and/or length) leads to local overheating that may have negative effects on the device performance and durability. (2) A simplified analytical model solves a thermal balance equation describing the heating by chemical reactions inside the microchannel and energy loss by free convection of air around the chip. Analytical results compare well with the 3D simulations of a single straight microchannel, therefore the analytical model is suitable for quick estimation of process parameters. For complex microstructures, this simplified approach may be used as the first approximation.

  20. The global 3-D distribution of tropospheric aerosols as characterized by CALIOP

    NASA Astrophysics Data System (ADS)

    Winker, D. M.; Tackett, J. L.; Getzewich, B. J.; Liu, Z.; Vaughan, M. A.; Rogers, R. R.

    2013-03-01

    The CALIOP lidar, carried on the CALIPSO satellite, has been acquiring global atmospheric profiles since June 2006. This dataset now offers the opportunity to characterize the global 3-D distribution of aerosol as well as seasonal and interannual variations, and confront aerosol models with observations in a way that has not been possible before. With that goal in mind, a monthly global gridded dataset of daytime and nighttime aerosol extinction profiles has been constructed, available as a Level 3 aerosol product. Averaged aerosol profiles for cloud-free and all-sky conditions are reported separately. This 6-yr dataset characterizes the global 3-dimensional distribution of tropospheric aerosol. Vertical distributions are seen to vary with season, as both source strengths and transport mechanisms vary. In most regions, clear-sky and all-sky mean aerosol profiles are found to be quite similar, implying a lack of correlation between high semi-transparent cloud and aerosol in the lower troposphere. An initial evaluation of the accuracy of the aerosol extinction profiles is presented. Detection limitations and the representivity of aerosol profiles in the upper troposphere are of particular concern. While results are preliminary, we present evidence that the monthly-mean CALIOP aerosol profiles provide quantitative characterization of elevated aerosol layers in major transport pathways. Aerosol extinction in the free troposphere in clean conditions, where the true aerosol extinction is typically 0.001 km-1 or less, is generally underestimated, however. The work described here forms an initial global 3-D aerosol climatology which we plan to extend and improve over time.

  1. Global gyrokinetic models for energetic particle driven Alfvén instabilities in 3D equilibria

    NASA Astrophysics Data System (ADS)

    Spong, Don; Holod, Ihor

    2015-11-01

    The GTC global gyrokinetic PIC model has been adapted to 3D VMEC equilibria and provides a new method for the analysis of Alfvénic instabilities in stellarators, 3D tokamaks, and helical RFP states. The gyrokinetic orderings (k||/k⊥ << 1, ω/Ωci << 1, ρEP/L << 1) are applicable to a range of energetic particle driven instabilities that have been observed in 3D configurations. Applications of this model to stellarators have indicated that a variety of different Alfvén instabilities can be excited, depending on the toroidal mode number, fast ion average energy and fast ion density profile. Both an LHD discharge where bursting n = 1 Alfvén activity in the TAE gap was observed and a W7-X case have been examined. TAE,/EAE/GAE modes have been found in the simulations, depending on the mode family and fast ion profiles used. The dynamical evolution of the instabilities shows the field period coupling between n and n + Nfp expected for a stellarator. The development of gyrofluid reduced models that can capture relevant physics aspects of the gyrokinetic models will also be discussed. Research sponsored by the U.S. Department of Energy under Contract DE-AC05-00OR22725 with UT-Battelle, LLC and the GSEP SciDAC Center.

  2. A Real-time 3D Visualization of Global MHD Simulation for Space Weather Forecasting

    NASA Astrophysics Data System (ADS)

    Murata, K.; Matsuoka, D.; Kubo, T.; Shimazu, H.; Tanaka, T.; Fujita, S.; Watari, S.; Miyachi, H.; Yamamoto, K.; Kimura, E.; Ishikura, S.

    2006-12-01

    Recently, many satellites for communication networks and scientific observation are launched in the vicinity of the Earth (geo-space). The electromagnetic (EM) environments around the spacecraft are always influenced by the solar wind blowing from the Sun and induced electromagnetic fields. They occasionally cause various troubles or damages, such as electrification and interference, to the spacecraft. It is important to forecast the geo-space EM environment as well as the ground weather forecasting. Owing to the recent remarkable progresses of super-computer technologies, numerical simulations have become powerful research methods in the solar-terrestrial physics. For the necessity of space weather forecasting, NICT (National Institute of Information and Communications Technology) has developed a real-time global MHD simulation system of solar wind-magnetosphere-ionosphere couplings, which has been performed on a super-computer SX-6. The real-time solar wind parameters from the ACE spacecraft at every one minute are adopted as boundary conditions for the simulation. Simulation results (2-D plots) are updated every 1 minute on a NICT website. However, 3D visualization of simulation results is indispensable to forecast space weather more accurately. In the present study, we develop a real-time 3D webcite for the global MHD simulations. The 3-D visualization results of simulation results are updated every 20 minutes in the following three formats: (1)Streamlines of magnetic field lines, (2)Isosurface of temperature in the magnetosphere and (3)Isoline of conductivity and orthogonal plane of potential in the ionosphere. For the present study, we developed a 3-D viewer application working on Internet Explorer browser (ActiveX) is implemented, which was developed on the AVS/Express. Numerical data are saved in the HDF5 format data files every 1 minute. Users can easily search, retrieve and plot past simulation results (3D visualization data and numerical data) by using

  3. CheS-Mapper - Chemical Space Mapping and Visualization in 3D

    PubMed Central

    2012-01-01

    Analyzing chemical datasets is a challenging task for scientific researchers in the field of chemoinformatics. It is important, yet difficult to understand the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. To that respect, visualization tools can help to better comprehend the underlying correlations. Our recently developed 3D molecular viewer CheS-Mapper (Chemical Space Mapper) divides large datasets into clusters of similar compounds and consequently arranges them in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kind of features, like structural fragments as well as quantitative chemical descriptors. These features can be highlighted within CheS-Mapper, which aids the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. As a final function, the tool can also be used to select and export specific subsets of a given dataset for further analysis. PMID:22424447

  4. 3D Global Two-Fluid Simulations of Turbulence in LAPD

    NASA Astrophysics Data System (ADS)

    Fisher, Dustin; Rogers, Barrett; Ricci, Paolo

    2012-10-01

    3D global two-fluid simulations are presented in an ongoing effort to identify and understand the physics of instabilities that arise in the Large Plasma Device (LAPD) at UCLA's Basic Science Facility. The LAPD, with its wide range of tunable parameters and device configurations, is ideally suited for studying space and laboratory plasmas. Moreover, the highly detailed and reproducible measurements of the LAPD lend themselves amicably to comparisons with simulations. Ongoing modeling is done using a modified version of the Global Braginskii Solver (GBS) [1] that models the plasma from source to edge region in a fully 3D two-fluid code. The reduced Braginskii equations are solved on a field-aligned grid using a finite difference method and 4th order Runge-Kutta time stepping and are parallelized on Dartmouth's Discovery cluster. Recent progress has been made to account for the thermionic cathode emission of fast electrons at the source, the axial dependence of the plasma source, and it is now possible to vary the potential on the front and side walls. Preliminary results, seen from the density and temperature profiles, show that the low frequency Kelvin Helmholtz instability still dominates the turbulence in the device.[4pt] [1] B. Rogers and P. Ricci. Phys. Rev. Lett. 104:225002, 2010

  5. 3D Global Magnetohydrodynamic Simulations of the Solar Wind/Earth's Magnetosphere Interaction

    NASA Astrophysics Data System (ADS)

    Yalim, M. S.; Poedts, S.

    2014-09-01

    In this paper, we present results of real-time 3D global magnetohydrodynamic (MHD) simulations of the solar wind interaction with the Earth's magnetosphere using time-varying data from the NASA Advanced Composition Explorer (ACE) satellite during a few big magnetic storm events of the previous and current solar cycles, namely the 06 April 2000, 20 November 2003 and 05 April 2010 storms. We introduce a numerical magnetic storm index and compare the geo-effectiveness of these events in terms of this storm index which is a measure for the resulting global perturbation of the Earth's magnetic field. Steady simulations show that the upstream solar wind plasma parameters enter the low-β switch-on regime for some time intervals during a magnetic storm causing a complex dimpled bow shock structure. We also investigate the traces of such bow shock structures during time-dependent simulations of the events. We utilize a 3D, implicit, parallel, unstructured grid, compressible finite volume ideal MHD solver with an anisotropic grid adaptation technique for the computer simulations.

  6. Global Structure of Idealized Stream Interaction Regions Using 3D MHD Simulations

    NASA Astrophysics Data System (ADS)

    Pahud, D. M.; Hughes, W. J.; Merkin, V. G.

    2014-12-01

    The global structure of the heliosphere during solar cycles (SC) 23 and 24 differed significantly in many ways, for example in terms of global magnetic field strength, velocity structure and the observed properties of Stream Interaction Region (SIR) and associated shocks. The differences considered in this study focus primarily on the effects of the three-dimensional (3D) structure of SIRs. During the minimum of SC 24, equatorial coronal holes were prevalent as sources of low-latitude high-speed solar wind. In contrast, the canonical depiction of SC 23's minimum wind configuration is of a band of slow wind undulating about the heliographic equator. Using the heliospheric adaptation of the Lyon-Fedder-Mobarry magnetohydrodynamic (MHD) model (LFM-helio), we have run simulations for two idealized global solar wind conditions. The first simulation approximates the classical tilted dipole, with fast solar wind at high latitudes and a band of slow wind tilted with respect to the heliographic equator, and the second consists of global slow solar wind with equatorial circular sources of high-speed streams. The evolution of the SIRs from 0.1 AU to 2.0 AU is characterized using the amplitude and location of the maximum compressions of the plasma and the magnetic field as well as the largest deflection of solar wind flow. The relation between plasma and magnetic field compressions differs between the two cases considered. The SIRs produced by the equatorial coronal holes have similar maximum densities to those of the tilted dipole case, but the magnetic field magnitude is larger and the plasma is hotter. This suggests that evolution depends on the 3D structure of the SIR and its effects on the competitive roles of the growth of the structure, driven by compression from dynamic pressure, and and relaxation from the plasma flow and magnetic field deflections occurring in the region. Magnetic field threading SIRs and tracing plasma parcels are examined.

  7. Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

    SciTech Connect

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy

    2015-10-14

    Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), {sup 1}H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong {sup 1}H–{sup 1}H homonuclear dipolar couplings and narrow {sup 1}H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) {sup 1}H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about {sup 1}H–{sup 1}H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic

  8. 3D dynamics of hydrous thermal-chemical plumes in subduction zones

    NASA Astrophysics Data System (ADS)

    Zhu, G.; Gerya, T.; Yuen, D.; Connolly, J. A. D.

    2009-04-01

    Mantle wedges are identified as sites of intense thermal convection and thermal-chemical Rayleigh-Taylor instabilities ("cold plumes") controlling distribution and intensity of magmatic activity in subduction zones. To investigate 3D hydrous partially molten cold plumes forming in the mantle wedge in response to slab dehydration, we perform 3D petrological-thermomechanical numerical simulations of the intraoceanic one-sided subduction with spontaneously bending retreating slab characterized by weak hydrated upper interface. I3ELVIS code is used which is developed based on multigrid approach combined with marker-in-cell method with conservative finite-difference schemes. We investigated regional 800 km wide and 200 km deep 3D subduction models with variable 200 to 800 km lateral dimension along the trench using uniform numerical staggered grid with 405x101x101 nodal points and up to 50 million markers. Our results show three patterns (roll(sheet)-, zig-zag- and finger-like) of Rayleigh-Taylor instabilities can develop above the subducting slab, which are controlled by effective viscosity of partially molten rocks. Spatial and temporal periodicity of plumes correlate well with that of volcanic activity in natural intraoceanic arcs such as Japan. High laterally variable surface heat flow predicted in the arc region in response to thermal-chemical plumes activity is also consistent with natural observations.

  9. Facile synthesis 3D flexible core-shell graphene/glass fiber via chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Yang, Cheng; Xu, Yuanyuan; Zhang, Chao; Sun, Zhencui; Chen, Chuansong; Li, Xiuhua; Jiang, Shouzhen; Man, Baoyuan

    2014-08-01

    Direct deposition of graphene layers on the flexible glass fiber surface to form the three-dimensional (3D) core-shell structures is offered using a two-heating reactor chemical vapor deposition system. The two-heating reactor is utilized to offer sufficient, well-proportioned floating C atoms and provide a facile way for low-temperature deposition. Graphene layers, which are controlled by changing the growth time, can be grown on the surface of wire-type glass fiber with the diameter from 30 nm to 120 um. The core-shell graphene/glass fiber deposition mechanism is proposed, suggesting that the 3D graphene films can be deposited on any proper wire-type substrates. These results open a facile way for direct and high-efficiency deposition of the transfer-free graphene layers on the low-temperature dielectric wire-type substrates.

  10. Towards the next generation of global 3D upper mantle Q models

    NASA Astrophysics Data System (ADS)

    Gung, Y.; Romanowicz, B.; Capdeville, Y.

    2003-12-01

    Global anelastic tomography can bring important constraints on the thermal structure of the mantle and therefore is dynamics, complementing those provided by elastic tomography. Progress in anelastic tomography has been slow, because of the inherent technical difficulties encountered in discriminating anelastic signal from elastic effects on amplitude data. It has been shown that while the elastic focusing/defocusing effects are not significant at low degrees ( ˜ 8) (e.g. Selby and Woodhouse, 2002; Gung and Romanowicz, 2003), they need to be included to achieve a higher resolution Q model. Ideally, one would use an exact method, such as the Spectral Element Method (SEM) for predicting the focusing effects. SEM is however very heavy computationally. We present a procedure to better constrain the 3D upper mantle Q from 3 component long-period seismic waveforms. In this procedure, the amplitude and phase perturbations due to the 3D elastic structure are corrected for using higher order normal mode asymptotic theory, and applying it to current elastic models. We first evaluate the normal mode asymptotic approach by comparing the corresponding 3D synthetics with those computed using the coupled spectral element/normal mode method (CSEM). 3 normal mode based asymptotic approaches are compared: path average approximation (PAVA), non-linear asymptotic coupling theory (NACT) and NACT+F, an extension of NACT with focusing terms computed using higher order asymptotic theory. Systematic waveform comparison and inversion experiments are implemented. We find that (1) when the anomaly lies on the source-receiver great circle path, the 3 techniques are fairly accurate for fundamental mode surface waves, but NACT and NACT+F provide much better fit for overtone phases and are therefore more powerful in resolving 3D structure in the mid and lower mantle; and (2) the off-great-circle effects, which result in focusing/defocusing and not seen by PAVA or NACT, are well explained by NACT

  11. SALSA3D: Validating a Global 3D P-Velocity Model of the Earth's Crust and Mantle for Improved Event Location

    NASA Astrophysics Data System (ADS)

    Begnaud, M. L.; Ballard, S.; Young, C. J.; Hipp, J. R.; Encarnacao, A.; Phillips, W. S.; Chael, E. P.; Rowe, C. A.

    2012-12-01

    We are developing a global 3D P wave velocity model of the Earth's crust and mantle using seismic tomography to assess improvement to seismic event locations obtained using high quality 3D Earth models in lieu of 1D and 2/2.5D models. We present the most recent version of SALSA3D (SAndia LoS Alamos 3D) version 1.9, and demonstrate its ability to reduce mislocations for a large set of realizations derived from a carefully chosen set of globally-distributed ground truth (GT) events. Our model is derived from the latest version of the GT catalog of P/Pn travel-time picks assembled by Los Alamos National Laboratory. For this current version, we employ more robust data quality control measures than previously used, as well as additional global GT data sources. To prevent over-weighting due to ray path redundancy and to reduce the computational burden, we cluster rays into representative rays. The model is represented using the triangular tessellation system described by Ballard et al. (2009), which incorporates variable resolution in both the geographic and radial dimensions. For our starting model, we use a simplified layer crustal model derived from the NNSA Unified model in Eurasia and Crust 2.0 model everywhere else, overlying a uniform ak135 mantle. Sufficient damping is used to reduce velocity adjustments so that ray path changes between iterations are small. We obtain proper model smoothness by using progressive grid refinement, refining the grid only in areas where the data warrant such a refinement. In previous versions, we based this refinement on velocity changes from previous model iterations. For the current version, we utilize the diagonal of the model resolution matrix to control where grid refinement occurs, resulting in more consistent and continuous areas of refinement than before. In addition to the changes in grid refinement, we also employ a more robust convergence criterion between successive grid refinements, allowing a better fit to first broader

  12. A global 3-D CTM evaluation of black carbon in the Tibetan Plateau

    NASA Astrophysics Data System (ADS)

    He, C.; Li, Q. B.; Liou, K. N.; Zhang, J.; Qi, L.; Mao, Y.; Gao, M.; Lu, Z.; Streets, D. G.; Zhang, Q.; Sarin, M. M.; Ram, K.

    2014-07-01

    We systematically evaluate the black carbon (BC) simulations for 2006 over the Tibetan Plateau by a global 3-D chemical transport model (CTM) (GEOS-Chem) driven by GEOS-5 assimilated meteorological fields, using in situ measurements of BC in surface air, BC in snow, and BC absorption aerosol optical depth (AAOD). Using improved anthropogenic BC emission inventories for Asia that account for rapid technology renewal and energy consumption growth (Zhang et al., 2009; Lu et al., 2011) and improved global biomass burning emission inventories that account for small fires (van der Werf et al., 2010; Randerson et al., 2012), we find that model results of both BC in surface air and in snow are statistically in good agreement with observations (biases < 15%) away from urban centers. Model results capture the seasonal variations of the surface BC concentrations at rural sites in the Indo-Gangetic Plain, but the observed elevated values in winter are absent. Modeled surface-BC concentrations are within a factor of 2 of the observations at remote sites. Part of the discrepancy is explained by the deficiencies of the meteorological fields over the complex Tibetan terrain. We find that BC concentrations in snow computed from modeled BC deposition and GEOS-5 precipitation are spatiotemporally consistent with observations (r = 0.85). The computed BC concentrations in snow are a factor of 2-4 higher than the observations at several Himalayan sites because of excessive BC deposition. The BC concentrations in snow are biased low by a factor of 2 in the central plateau, which we attribute to the absence of snow aging in the CTM and strong local emissions unaccounted for in the emission inventories. Modeled BC AAOD is more than a factor of 2 lower than observations at most sites, particularly to the northwest of the plateau and along the southern slopes of the Himalayas in winter and spring, which is attributable in large part to underestimated emissions and the assumption of external

  13. Improved time-space method for 3-D heat transfer problems including global warming

    SciTech Connect

    Saitoh, T.S.; Wakashima, Shinichiro

    1999-07-01

    In this paper, the Time-Space Method (TSM) which has been proposed for solving general heat transfer and fluid flow problems was improved in order to cover global and urban warming. The TSM is effective in almost all-transient heat transfer and fluid flow problems, and has been already applied to the 2-D melting problems (or moving boundary problems). The computer running time will be reduced to only 1/100th--1/1000th of the existing schemes for 2-D and 3-D problems. However, in order to apply to much larger-scale problems, for example, global warming, urban warming and general ocean circulation, the SOR method (or other iterative methods) in four dimensions is somewhat tedious and provokingly slow. Motivated by the above situation, the authors improved the speed of iteration of the previous TSM by introducing the following ideas: (1) Timewise chopping: Time domain is chopped into small peaches to save memory requirement; (2) Adaptive iteration: Converged region is eliminated for further iteration; (3) Internal selective iteration: Equation with slow iteration speed in iterative procedure is selectively iterated to accelerate entire convergence; and (4) False transient integration: False transient term is added to the Poisson-type equation and the relevant solution is regarded as a parabolic equation. By adopting the above improvements, the higher-order finite different schemes and the hybrid mesh, the computer running time for the TSM is reduced to some 1/4600th of the conventional explicit method for a typical 3-D natural convection problem in a closed cavity. The proposed TSM will be more efficacious for large-scale environmental problems, such as global warming, urban warming and general ocean circulation, in which a tremendous computing time would be required.

  14. Capabilities of a Global 3D MHD Model for Monitoring Extremely Fast CMEs

    NASA Astrophysics Data System (ADS)

    Wu, C. C.; Plunkett, S. P.; Liou, K.; Socker, D. G.; Wu, S. T.; Wang, Y. M.

    2015-12-01

    Since the start of the space era, spacecraft have recorded many extremely fast coronal mass ejections (CMEs) which have resulted in severe geomagnetic storms. Accurate and timely forecasting of the space weather effects of these events is important for protecting expensive space assets and astronauts and avoiding communications interruptions. Here, we will introduce a newly developed global, three-dimensional (3D) magnetohydrodynamic (MHD) model (G3DMHD). The model takes the solar magnetic field maps at 2.5 solar radii (Rs) and intepolates the solar wind plasma and field out to 18 Rs using the algorithm of Wang and Sheeley (1990, JGR). The output is used as the inner boundary condition for a 3D MHD model. The G3DMHD model is capable of simulating (i) extremely fast CME events with propagation speeds faster than 2500 km/s; and (ii) multiple CME events in sequence or simultaneously. We will demonstrate the simulation results (and comparison with in-situ observation) for the fastest CME in record on 23 July 2012, the shortest transit time in March 1976, and the well-known historic Carrington 1859 event.

  15. 3D global estimation and augmented reality visualization of intra-operative X-ray dose.

    PubMed

    Rodas, Nicolas Loy; Padoy, Nicolas

    2014-01-01

    The growing use of image-guided minimally-invasive surgical procedures is confronting clinicians and surgical staff with new radiation exposure risks from X-ray imaging devices. The accurate estimation of intra-operative radiation exposure can increase staff awareness of radiation exposure risks and enable the implementation of well-adapted safety measures. The current surgical practice of wearing a single dosimeter at chest level to measure radiation exposure does not provide a sufficiently accurate estimation of radiation absorption throughout the body. In this paper, we propose an approach that combines data from wireless dosimeters with the simulation of radiation propagation in order to provide a global radiation risk map in the area near the X-ray device. We use a multi-camera RGBD system to obtain a 3D point cloud reconstruction of the room. The positions of the table, C-arm and clinician are then used 1) to simulate the propagation of radiation in a real-world setup and 2) to overlay the resulting 3D risk-map onto the scene in an augmented reality manner. By using real-time wireless dosimeters in our system, we can both calibrate the simulation and validate its accuracy at specific locations in real-time. We demonstrate our system in an operating room equipped with a robotised X-ray imaging device and validate the radiation simulation on several X-ray acquisition setups. PMID:25333145

  16. Global 3-D Hybrid Simulations of Mars and the Effect of Crustal Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Brecht, S. H.; Ledvina, S. A.; Luhmann, J. G.

    2001-12-01

    Mars is not protected from the solar wind by a strong intrinsic magnetic field. Further, Mars is a very small planet. These two aspects of Mars mean that the solar wind interaction with the planet is both direct and kinetic in behavior. The large gyroradius of the incoming solar wind and the large gyroradius of the pick up ions make the solar wind interaction with Mars very unique. Over the years the authors using a 3-D kinetic hybrid particle code have studied this planet. Mars Global Surveyor has produced many exciting discoveries. Probably the most significant and unexpected was the presence of the crustal magnetic fields on the surface of the planet. The presence of these strong crustal fields suggests that the solar wind interaction with Mars will be altered. In fact, it suggests that the loss rate of pick up ions and the shape of the Martian magnetosphere will be substantially changed. Results will be presented from our latest 3-D hybrid particle code simulations of Mars where models for the crustal magnetic field have been inserted into the simulations. Particular emphasis will be placed on changes to the magnetic field topology and the change in the rate of pick up ions.

  17. Dynamic 3D micropatterned cell co-cultures within photocurable and chemically degradable hydrogels

    PubMed Central

    Sugiura, Shinji; Cha, Jae Min; Yanagawa, Fumiki; Zorlutuna, Pinar; Bae, Hojae; Khademhosseini, Ali

    2014-01-01

    In this paper we report on the development of dynamically controlled 3D micropatterned cellular co-cultures within photocurable and chemically degradable hydrogels. Specifically, we generated dynamic co-cultures of micropatterned murine embryonic stem (mES) cells with human hepatocellular carcinoma (HepG2) cells within 3D hydrogels. HepG2 cells were used due to their ability to direct the differentiation of mES cells through secreted paracrine factors. To generate dynamic co-cultures, mES cells were first encapsulated within micropatterned photocurable poly(ethylene glycol) (PEG) hydrogels. These micropatterned cell-laden PEG hydrogels were subsequently surrounded by calcium alginate (Ca-Alg) hydrogels containing HepG2 cells. After 4 days, the co-culture step was halted by exposing the system to sodium citrate solution, which removed the alginate gels and the encapsulated HepG2 cells. The encapsulated mES cells were then maintained in the resulting cultures for 16 days and cardiac differentiation was analyzed. We observed that the mES cells that were exposed to HepG2 cells in the co-cultures, generated cells with higher expression of cardiac genes and proteins as well as increased spontaneous beating. Due to its ability to control the 3D microenvironment of cells in a spatially and temporally regulated manner the method presented in this study is useful for a range of cell culture applications related to tissue engineering and regenerative medicine. PMID:24170301

  18. Ray tracing technique for global 3-D modeling of ionospheric electron density using GNSS measurements

    NASA Astrophysics Data System (ADS)

    Alizadeh, Mohamad Mahdi; Schuh, Harald; Schmidt, Michael

    2015-06-01

    For space geodetic techniques, operating in microwave band, ionosphere is a dispersive medium; thus, signals traveling through this medium are in the first approximation, affected proportional to the inverse of the square of their frequencies. This effect allows gaining information about the parameters of the ionosphere in terms of total electron content (TEC) or the electron density (Ne). Making use of this phenomenon, space geodetic techniques have turned into a capable tool for studying the ionosphere in the last decades. Up to now, two-dimensional (2-D) models of Vertical TEC (VTEC) have been widely developed and used by different communities; however, due to the fact that these models provide information about the integral of the whole electron content along the vertical or slant raypath, these maps are not useful when information about the ionosphere at different altitude is required. This paper presents a recent study which aims at developing a global 3-D model of the electron density, using measurements from Global Navigation Satellite Systems and by applying the ray tracing technique to the upper atmosphere. The developed modeling approach represents the horizontal variations of the electron density, with two sets of spherical harmonic expansions of degree and order 15. The height dependency of the electron density is represented by a multilayered Chapman profile function for the bottomside and topside ionosphere, and an appropriate model for the plasmasphere. In addition to the geodetic applications of the developed models, within this study, the 3-D models of electron density can include geophysical parameters like maximum electron density and its corresponding height. High-resolution modeling of these parameters allows an improved geophysical interpretation, which is essential in all studies of the upper atmosphere, space weather, and for the solar-terrestrial environment.

  19. SALSA3D - Improving Event Locations Using a Global 3D P-Velocity Model of the Earth's Crust and Mantle

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    To test the hypothesis that high quality 3D Earth models will produce seismic event locations that are more accurate and more precise than currently used 1D and 2/2.5D models, we are developing a global 3D P wave velocity model of the Earth's crust and mantle using seismic tomography. In this paper, we present the most recent version of our model, SALSA3D (SAndia LoS Alamos 3D) version 1.7, and demonstrate its ability to reduce mislocations for a large set of realizations derived from a carefully chosen set of globally-distributed ground truth (GT) events, compared to existing models and/or systems. Our model is derived from the latest version of the GT catalog of P and Pn travel time picks assembled by Los Alamos National Laboratory. To prevent over-weighting due to ray path redundancy and to reduce the computational burden, we cluster rays to produce representative rays. Reduction in the total number of ray paths is ~50%. The model is represented using the triangular tessellation system described by Ballard et al. (2009), which incorporates variable resolution in both the geographic and radial dimensions. For our starting model, we use a simplified layer crustal model derived from the NNSA Unified model in Eurasia and Crust 2.0 model elsewhere, over a uniform ak135 mantle. Sufficient damping is used to reduce velocity adjustments so that ray path changes between iterations are small. We obtain proper model smoothness by using progressive grid refinement, refining the grid only in areas where the data warrant it. In previous versions of SALSA3D, we based this refinement on velocity changes from previous model iterations. For version 1.7, we utilize the diagonal of the model resolution matrix to control where grid refinement occurs, resulting in more consistent and continuous areas of refinement than before. Our approach produces a smooth, multi-resolution model with node density appropriate to both ray coverage and the velocity gradients required by the data. We

  20. 3-D Spherical modelling of the thermo-chemical evolution of Venus' mantle and crust

    NASA Astrophysics Data System (ADS)

    Armann, M.; Tackley, P. J.

    2008-09-01

    Background Several first-order aspects of the dynamics of Venus' mantle remain poorly understood. These include (i) how Venus' mantle loses its radiogenic heat, which is expected to be about the same as Earth's, despite the presence of stagnant lid convection. Hypotheses that have been advanced (summarised in [1]) are conduction through a thin lithosphere, episodic overturn of the lithosphere, magmatic heat transport, and concentration of almost all heat-producing elements into the crust, but there are problems with all of these taken individually. A thick lithosphere may not be consistent with admittance ratios, magmatic heat transport would require a too-large resurfacing rate, and a large concentration of heat-producing elements in the crust would cause weakness and possibly melting in the deep crust. (ii) The relatively long-wavelength distribution of surface features, which is surprising because numerical models and analogue laboratory experiments of stagnant-lid convection produce relatively short-wavelength convective cells. (iii) The inferred (from crater distributions [2]) relatively uniform surface age of 500-700 Ma. (iv) Whether the highlands are above mantle downwellings as on Earth or above mantle upwellings [3]. (v) How the mantle can have outgassing only 25% of 40Ar [4] but supposedly most of its water [5]. (vi) The cause of coronae and relationship to mantle processes [6]. Model To study some of these questions, we take advantage of advances in computational capabilities to perform integrated thermo-chemical convection models of Venus' evolution over 4.5 billion years, in 3-D spherical geometry as well as 2-D spherical annulus geometry [7]. These models include realistic ("laboratory") rheological parameters for diffusion creep and dislocation creep based on [8][9], which are also composition-dependent, and plastic yielding based on Byerlee's law, which might cause changes in tectonic regime (e.g., episodic plate tectonics). Crustal formation and

  1. 3-D Spherical modelling of the thermo-chemical evolution of Venus

    NASA Astrophysics Data System (ADS)

    Armann, M.; Tackley, P. J.

    2009-04-01

    Several first-order aspects of the dynamics of Venus' mantle remain poorly understood. These include (i) how Venus' mantle loses its radiogenic heat (presumably about the same as Earth's) despite the presence of stagnant lid convection. Hypotheses that have been advanced (summarised in [1]) are conduction through a thin lithosphere, episodic overturn of the lithosphere, magmatic heat transport, and concentration of almost all heat-producing elements into the crust, but there are problems with all of these taken individually. A thick lithosphere may not be consistent with admittance ratios, magmatic heat transport would require a too-large resurfacing rate, and a large concentration of heat-producing elements in the crust would cause weakness and possibly melting in the deep crust. (ii) The relatively long-wavelength distribution of surface features, which is surprising because numerical models and analogue laboratory experiments of stagnant-lid convection produce relatively short-wavelength convective cells. (iii) The inferred (from crater distributions [2]) relatively uniform surface age of 500-700 Ma. (iv) Whether the highlands are above mantle downwellings as on Earth or above mantle upwellings [3]. (v) How the mantle can have outgassing only 25% of 40Ar [4] but supposedly most of its water [5]. (vi) The cause of coronae and relationship to mantle processes [6]. To study some of these questions, we are performing integrated thermo-chemical convection modelling of Venus' evolution over 4.5 billion years, in 3-D spherical geometry as well as 2-D spherical annulus geometry [7]. These models include realistic ("laboratory") rheological parameters for diffusion creep and dislocation creep based on [8][9], which are also composition-dependent, and plastic yielding based on Byerlee's law, which might cause changes in tectonic regime (e.g., episodic plate tectonics). Crustal formation and the resulting differentiation of the crust and mantle are modelled using a self

  2. Exploring 3D structural influences of aliphatic and aromatic chemicals on α-cyclodextrin binding.

    PubMed

    Linden, Lukas; Goss, Kai-Uwe; Endo, Satoshi

    2016-04-15

    Binding of solutes to macromolecules is often influenced by steric effects caused by the 3D structures of both binding partners. In this study, the 1:1 α-cyclodextrin (αCD) binding constants (Ka1) for 70 organic chemicals were determined to explore the solute-structural effects on the αCD binding. Ka1 was measured using a three-part partitioning system with either a headspace or a passive sampler serving as the reference phase. The Ka1 values ranged from 1.08 to 4.97 log units. The results show that longer linear aliphatic chemicals form more stable complexes than shorter ones, and that the position of the functional group has a strong influence on Ka1, even stronger than the type of the functional group. Comparison of linear and variously branched aliphatic chemicals indicates that having a sterically unhindered alkyl chain is favorable for binding. These results suggest that only one alkyl chain can enter the binding cavity. Relatively small aromatic chemicals such as 1,3-dichlorobenzene bind to αCD well, while larger ones like tetrachlorobenzene and 3-ring aromatic chemicals show only a weak interaction with αCD, which can be explained by cavity exclusion. The findings of this study help interpret cyclodextrin binding data and facilitate the understanding of binding processes to macromolecules. PMID:26826354

  3. 3D Global Braginskii Simulations of Plasma Dynamics and Turbulence in LAPD

    NASA Astrophysics Data System (ADS)

    Fisher, Dustin; Rogers, Barrett

    2013-10-01

    3D global two-fluid simulations are presented in an ongoing effort to identify and understand the plasma dynamics in the Large Plasma Device (LAPD) at UCLA's Basic Science Facility. Modeling is done using a modified version of the Global Braginskii Solver (GBS) that models the plasma from source to edge region on a field-aligned grid using a finite difference method and 4th order Runge-Kutta time stepping. Progress has been made to account for the thermionic cathode emission of fast electrons at the source, the axial dependence of the plasma source, and biasing the front and side walls. Along with trying to understand the effect sheath's and neutrals have in setting the plasma potential, work is being done to model the biasable limiter recently used by colleagues at UCLA to better understand flow shear and particle transport in the LAPD. Comparisons of the zero bias case are presented along with analysis of the growth and dynamics of turbulent structures (such as drift waves) seen in the simulations. Supported through CICART under the auspices of the DOE's EPSCoR Grant No. DE-FG02-10ER46372.

  4. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  5. Development of metal-assisted chemical etching of silicon as a 3D nanofabrication platform

    NASA Astrophysics Data System (ADS)

    Hildreth, Owen James

    The considerable interest in nanomaterials and nanotechnology over the last decade is attributed to Industry's desire for lower cost, more sophisticated devices and the opportunity that nanotechnology presents for scientists to explore the fundamental properties of nature at near atomic levels. In pursuit of these goals, researchers around the world have worked to both perfect existing technologies and also develop new nano-fabrication methods; however, no technique exists that is capable of producing complex, 2D and 3D nano-sized features of arbitrary shape, with smooth walls, and at low cost. This in part is due to two important limitations of current nanofabrication methods. First, 3D geometry is difficult if not impossible to fabricate, often requiring multiple lithography steps that are both expensive and do not scale well to industrial level fabrication requirements. Second, as feature sizes shrink into the nano-domain, it becomes increasingly difficult to accurately maintain those features over large depths and heights. The ability to produce these structures affordably and with high precision is critically important to a number of existing and emerging technologies such as metamaterials, nano-fluidics, nano-imprint lithography, and more. To overcome these limitations, this study developed a novel and efficient method to etch complex 2D and 3D geometry in silicon with controllable sub-micron to nano-sized features with aspect ratios in excess of 500:1. This study utilized Metal-assisted Chemical Etching (MaCE) of silicon in conjunction with shape-controlled catalysts to fabricate structures such as 3D cycloids, spirals, sloping channels, and out-of-plane rotational structures. This study focused on taking MaCE from a method to fabricate small pores and silicon nanowires using metal catalyst nanoparticles and discontinuous thin films, to a powerful etching technology that utilizes shaped catalysts to fabricate complex, 3D geometry using a single lithography

  6. Modelling 3D Chemical Weathering Evolution Using Dissolving and Moving Clasts in a Landscape Evolution Model

    NASA Astrophysics Data System (ADS)

    Carretier, S.; Martinez, J.; Martinod, P.; Reich, M.; Godderis, Y.

    2014-12-01

    During mountain uplift, fresh silicate rocks are exhumed and broken into small pieces, potentially increasing their chemical weathering rate and thus the consumption of atmospheric CO2. This process remains debated because although erosion provides fresh rocks, it may also decrease their residence time near Earth's surface where clasts weather. Several recent publications also emphasized the key role of forelands in the weathering of clasts exported from the mountains by erosion. Predicting the chemical outflux of mountains requires to account for the chemical evolution of these rocks from their source to outlet. Powerful chemical models based on diffusion-advection of species between rocks and water have been developed at pedon scale, and recently at hillslope scale. In order to track the weathered material, we have developed a different approach based on the introduction into a 3D landscape evolution model (CIDRE) of dissolving discrete spherical clasts that move downslope. In CIDRE, local erosion and deposition depend on slope and water discharge which adapt dynamically during the topographical evolution. On a cell, bedrock is converted to soil at a rate depending on soil thickness. Clasts are initially spread at specified depths. They have a specified initial size and mineralogical composition. Once they enter the soil, they begins to dissolve at a rate depending on their minerals, temperature and exposed area, which decreases the clast size. Clasts move downstream according to probabilities depending on the ratio between the calculated local deposition and erosion fluxes. Chemical outflux is calculated for each clast during its life. At pedon scale, the model predicts chemical depleted fractions close to that obtained with advection-diffusion models and in agreement with measurements. An integrated chemical flux is estimated for the whole landscape from the clast dissolution rates. This flux reaches a stable solution using a suitable number of initial clasts

  7. 3D thermo-chemical-mechanical simulation of power ramps with ALCYONE fuel code

    NASA Astrophysics Data System (ADS)

    Baurens, B.; Sercombe, J.; Riglet-Martial, C.; Desgranges, L.; Trotignon, L.; Maugis, P.

    2014-09-01

    This paper presents the coupling of the fuel performance code ALCYONE with the thermochemical code ANGE and its application to Iodine-Stress Corrosion Cracking (I-SCC). The coupling is illustrated by a 3D simulation of a power ramp. The release of chemically active gases (CsI(g), Tex(13D simulation, the definition of a stress corrosion initiation criterion is discussed. The combination of the hoop stress and of the quantity of reactive iodine (I(g), I2(g) and TeI2(g) only) released by the pellet is used to show that the necessary conditions for Pellet Cladding Interaction-Stress Corrosion Cracking (PCI-SCC) initiation, based on out-of-pile I-SCC laboratory tests criteria, are met during the simulated power transient.

  8. Creating 3D chemical gradients with self-folding microfluidic networks

    NASA Astrophysics Data System (ADS)

    Jamal, Mustapha; Kalinin, Yevgeniy; Zarafshar, Aasiyeh; Gracias, David

    2012-02-01

    We describe the reversible self-folding of polymeric films into intricate three-dimensional (3D) microfluidic networks and investigate their utility as bio-inspired synthetic vasculature for in vitro tissue culture models. Our fabrication methodology relies on patterning of channels inside the films at the planar microfabrication stage followed by programmable self-folding of the two-dimensional patterned structures. Here self-folding action is enabled by stress gradients which develop in the films due to differential ultraviolet cross-linking and subsequent solvent conditioning. We achieved wafer-scale assembly of micropatterned geometries including helices, polyhedra and corrugated sheets. To demonstrate utility of such self-folded microfluidic devices we present localized chemical delivery of biochemicals in 3D to discrete regions of cells cultured on the curved self-assembled surfaces and in a thick, surrounding hydrogel. We believe that the devices can be used to mimic such natural self-assembled systems as leaves and tissues. Reference: M. Jamal et al., Nature Communications (2011; in press).

  9. SALSA3D - A Global 3D P-Velocity Model of the Earth's Crust and Mantle for Improved Event Location

    NASA Astrophysics Data System (ADS)

    Ballard, S.; Begnaud, M. L.; Young, C. J.; Hipp, J. R.; Chang, M.; Encarnacao, A. V.; Rowe, C. A.; Phillips, W. S.; Steck, L.

    2010-12-01

    To test the hypothesis that high quality 3D Earth models will produce seismic event locations which are more accurate and more precise, we are developing a global 3D P wave velocity model of the Earth’s crust and mantle using seismic tomography. In this paper, we present the most recent version of our model, SALSA3D version 1.5, and demonstrate its ability to reduce mislocations for a large set of realizations derived from a carefully chosen set of globally-distributed ground truth events. Our model is derived from the latest version of the Ground Truth (GT) catalog of P and Pn travel time picks assembled by Los Alamos National Laboratory. To prevent over-weighting due to ray path redundancy and to reduce the computational burden, we cluster rays to produce representative rays. Reduction in the total number of ray paths is ~50%. The model is represented using the triangular tessellation system described by Ballard et al. (2009), which incorporates variable resolution in both the geographic and radial dimensions.. For our starting model, we use a simplified two layer crustal model derived from the Crust 2.0 model over a uniform AK135 mantle. Sufficient damping is used to reduce velocity adjustments so that ray path changes between iterations are small. We obtain proper model smoothness by using progressive grid refinement, refining the grid only around areas with significant velocity changes from the starting model. At each grid refinement level except the last one we limit the number of iterations to prevent convergence thereby preserving aspects of broad features resolved at coarser resolutions. Our approach produces a smooth, multi-resolution model with node density appropriate to both ray coverage and the velocity gradients required by the data. This scheme is computationally expensive, so we use a distributed computing framework based on the Java Parallel Processing Framework, providing us with ~400 processors. Resolution of our model is assessed using a

  10. Dynamic 3-D chemical agent cloud mapping using a sensor constellation deployed on mobile platforms

    NASA Astrophysics Data System (ADS)

    Cosofret, Bogdan R.; Konno, Daisei; Rossi, David; Marinelli, William J.; Seem, Pete

    2014-05-01

    The need for standoff detection technology to provide early Chem-Bio (CB) threat warning is well documented. Much of the information obtained by a single passive sensor is limited to bearing and angular extent of the threat cloud. In order to obtain absolute geo-location, range to threat, 3-D extent and detailed composition of the chemical threat, fusion of information from multiple passive sensors is needed. A capability that provides on-the-move chemical cloud characterization is key to the development of real-time Battlespace Awareness. We have developed, implemented and tested algorithms and hardware to perform the fusion of information obtained from two mobile LWIR passive hyperspectral sensors. The implementation of the capability is driven by current Nuclear, Biological and Chemical Reconnaissance Vehicle operational tactics and represents a mission focused alternative of the already demonstrated 5-sensor static Range Test Validation System (RTVS).1 The new capability consists of hardware for sensor pointing and attitude information which is made available for streaming and aggregation as part of the data fusion process for threat characterization. Cloud information is generated using 2-sensor data ingested into a suite of triangulation and tomographic reconstruction algorithms. The approaches are amenable to using a limited number of viewing projections and unfavorable sensor geometries resulting from mobile operation. In this paper we describe the system architecture and present an analysis of results obtained during the initial testing of the system at Dugway Proving Ground during BioWeek 2013.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  13. 3D kinetic simulations of the global interaction between the solar wind and the magnetosphere

    NASA Astrophysics Data System (ADS)

    Amaya, Jorge; Maneva, Yana; Deca, Jan; Lapenta, Giovanni

    2015-04-01

    We performed three dimensional simulations of the interaction between the solar wind and the magnetosphere, using the self-consistent fully kinetic code iPic3D. The main objective of our simulations is to link the global interaction phenomena to the local turbulence and reconnection processes in the magnetosphere. Other numerical approaches have been used before to study this problem, including MHD, hybrid and Vlasov codes. However, only particle-in-cell codes offer the possibility to study the kinetic effects of the diffusion regions of the Earth environment that drive the energy transfer from the solar wind to the magnetosphere. Previous attempts to perform such kinds of simulations were limited to unphysical thermal velocities of the ion and electron species, small simulation boxes or cell sizes that do not capture the local kinetic effects at the magnetopause. Using the implicit moment Particle-in-Cell approach we performed simulations that can capture these small scale effects and, at the same time, allow to study large scale phenomena such as the bow shock and the development of the magnetotail. We expect that these results will be used to maximize the impact of future space missions, such as THOR, MMS and BepiColombo, by improving our understanding of the planetary environment, from the conditions observed in the solar wind to the turbulence and reconnection processes downstream of the bow shock.

  14. Sulfur in the early martian atmosphere revisited: Experiments with a 3-D Global Climate Model

    NASA Astrophysics Data System (ADS)

    Kerber, Laura; Forget, François; Wordsworth, Robin

    2015-11-01

    Volcanic SO2 in the martian atmosphere has been invoked as a way to create a sustained or transient greenhouse during early martian history. Many modeling studies have been performed to test the feasibility of this hypothesis, resulting in a range of conclusions, from highly feasible to highly improbable. In this study we perform a wide range of simulations using the 3-D Laboratoire de Météorologie Dynamique Generic Global Climate Model (GCM) in order to place earlier results into context and to explore the sensitivity of model outcomes to parameters such as SO2 mixing ratio, atmospheric H2O content, background atmospheric pressure, and aerosol size, abundance, and composition. We conclude that SO2 is incapable of creating a sustained greenhouse on early Mars, and that even in the absence of aerosols, local and daily temperatures rise above 273 K for only for limited periods with favorable background CO2 pressures. In the presence of even small amounts of aerosols, the surface is dramatically cooled for realistic aerosol sizes. Brief, mildly warm conditions require the co-occurrence of many improbable factors, while cooling is achieved for a wide range of model parameters. Instead of causing warming, sulfur in the martian atmosphere may have caused substantial cooling, leading to the end of clement climate conditions on early Mars.

  15. Sulfur in the Early Martian Atmosphere Revisited: Experiments with a 3-D Global Climate Model

    NASA Astrophysics Data System (ADS)

    Kerber, L.; Forget, F.; Wordsworth, R.

    2013-09-01

    [8]. A successful working model for the early Martian atmosphere and hydrosphere must be able not only to produce conditions suitable for liquid water at the surface, but also to explain how the nature of this aqueous activity changed over time and eventually diminished. There are two major end-member hypotheses: first, that early Mars was wet and warm, with a sustained greenhouse that made it possible for liquid water to be stable on the surface for extended periods [e.g., 2, 12-14], and second, that early Mars was generally cold, and that most of the aqueous alteration took place underground [3,5] or during transient warm periods tied to impact cratering [15], or volcanism [16]. In both of these scenarios it is generally agreed that in order to make valley networks and sulfate deposits, a hydrological cycle is needed which is able to recycle water from the lowlands back to the highlands (i.e., the one-time emptying of a regional aquifer would not be sufficient to create the observed features) [4,17]. This would require some precipitation to fall on the southern highlands, either flowing overland or filtering into groundwater aquifers. In both cases, volcanic gases (especially SO2) have been suggested as a possible way of creating either a sustained or transient greenhouse. Several researchers have tested the addition of SO2 to climate models in order to assess whether it would provide an adequate amount of greenhouse warming to allow liquid water to flow across the surface [18-21], with differing results. Postawko and Kuhn [18] found a warming effect of 14 K in a 0.1 bar atmosphere with an SO2 abundance of 1000 ppm. Johnson et al. [20] used a 3-D global circulation model and found a warming of 15-25 K for 245 ppm of SO2 in a dry 0.5 bar atmosphere. Tian et al. [21] used a 1-D model to explore a wide range of SO2 mixing values and CO2 partial pressures, finding a warming of around ~25 K for 100 ppm in a 0.5 bar atmosphere with a fully saturated troposphere (~40 K

  16. A Chemical Approach to 3-D Lithographic Patterning of Si and GeNanocrystals

    SciTech Connect

    Sharp, I.D.; Xu, Q.; Yi, D.O.; Liao, C.Y.; Ager III, J.W.; Beeman, J.W.; Yu, K.M.; Robinson, J.T.; Dubon, O.D.; Chrzan, D.C.; Haller, E.E.

    2005-12-12

    Ion implantation into silica followed by thermal annealingis an established growth method for Si and Ge nanocrystals. Wedemonstrate that growth of Group IV semiconductor nanocrystals can besuppressed by co-implantation of oxygen prior to annealing. For Sinanocrystals, at low Si/O dose ratios, oxygen co-implantation leads to areduction of the average nanocrystal size and a blue-shift of thephotoluminescence emission energy. For both Si and Ge nanocrystals, atlarger Si/O or Ge/O dose ratios, the implanted specie is oxidized andnanocrystals do not form. This chemical deactivation was utilized toachieve patterned growth of Si and Ge nanocrystals. Si was implanted intoa thin SiO2 film on a Si substrate followed by oxygen implantationthrough an electron beam lithographically defined stencil mask. Thermalannealing of the co-implanted structure yields two-dimensionallypatterned growth of Si nanocrystals under the masked regions. We applieda previously developed process to obtain exposed nanocrystals byselective HF etching of the silica matrix to these patterned structures.Atomic force microscopy (AFM) of etched structures revealed that exposednanocrystals are not laterally displaced from their original positionsduring the etching process. Therefore, this process provides a means ofachieving patterned structures of exposed nanocrystals. The possibilitiesfor scaling this chemical-based lithography process to smaller featuresand for extending it to 3-D patterning is discussed.

  17. Combined global 2D-local 3D modeling of the industrial Czochralski silicon crystal growth process

    NASA Astrophysics Data System (ADS)

    Jung, T.; Seebeck, J.; Friedrich, J.

    2013-04-01

    A global, axisymmetric thermal model of a Czochralski furnace is coupled to an external, local, 3D, time-dependent flow model of the melt via the inclusion of turbulent heat fluxes, extracted from the 3D melt model, into the 2D furnace model. Boundary conditions of the 3D model are updated using results from the 2D model. In the 3D model the boundary layers are resolved by aggressive mesh refinement towards the walls, and the Large Eddy Simulation approach is used to model the turbulent flow in the melt volume on a relatively coarse mesh to minimize calculation times. It is shown that by using this approach it is possible to reproduce fairly good results from Direct Numerical Simulations obtained on much finer meshes, as well as experimental results for interface shape and oxygen concentration in the case of growth of silicon crystals with 210 mm diameter for photovoltaics by the Czochralski method.

  18. A Global Model Simulation for 3-D Radiative Transfer Impact on Surface Hydrology over Sierra Nevada and Rocky Mountains

    NASA Astrophysics Data System (ADS)

    Lee, W. L.; Gu, Y.; Liou, K. N.; Leung, L. R.; Hsu, H. H.

    2014-12-01

    We investigate 3-D mountain effects on solar flux distributions and their impact on surface hydrology over the Western United States, specifically the Rocky Mountains and Sierra-Nevada using the CCSM4 (CAM4/CLM) global model with a 0.25 degree resolution for a 6-year climate run. In 3-D radiative transfer parameterization, we have updated surface topography data from a resolution of 1 km to 90 meters using the Shuttle Radar Topography Mission (SRTM) global dataset to improve parameterization accuracy. In addition, we have also modified the upward-flux deviation (3D - PP) adjustment to ensure that energy balance at the top of the atmosphere is conserved in climate simulations involving the 3-D radiation parameterization in a global model. We show that deviations of the net surface fluxes are not only affected by 3-D mountains, but also influenced by cloud feedback in association with the long-term simulations. Deviations in sensible heat and surface temperature generally follow the patterns of net surface solar flux. The monthly SWE deviations averaged over the entire domain show an increase in lower elevations due to reduced snowmelt, leading to a reduction in cumulative runoff. Over higher elevation areas, negative SWE deviations are found because of increased solar radiation available at the surface. Simulated precipitation increases for lower elevations, while decreases for higher elevations with a minimum in April. Liquid runoff significantly decreases in higher elevations after April due to reduced SWE and precipitation.

  19. Multi-scale self-organisation of edge plasma turbulent transport in 3D global simulations

    NASA Astrophysics Data System (ADS)

    Tamain, P.; Ghendrih, Ph; Bufferand, H.; Ciraolo, G.; Colin, C.; Fedorczak, N.; Nace, N.; Schwander, F.; Serre, E.

    2015-05-01

    The 3D global edge turbulence code TOKAM3X is used to study the properties of edge particle turbulent transport in circular limited plasmas, including both closed and open flux surfaces. Turbulence is driven by an incoming particle flux from the core plasma and no scale separation between the equilibrium and the fluctuations is assumed. Simulations show the existence of a complex self-organization of turbulence transport coupling scales ranging from a few Larmor radii up to the machine scale. Particle transport is largely dominated by small scale turbulence with fluctuations forming quasi field-aligned filaments. Radial particle transport is intermittent and associated with the propagation of coherent structures on long distances via avalanches. Long range correlations are also found in the poloidal and toroidal direction. The statistical properties of fluctuations vary with the radial and poloidal directions, with larger fluctuation levels and intermittency found in the outboard scrape-off layer (SOL). Radial turbulent transport is strongly ballooned, with 90% of the flux at the separatrix flowing through the low-field side. One of the main consequences is the existence of quasi-sonic asymmetric parallel flows driving a net rotation of the plasma. Simulations also show the spontaneous onset of an intermittent E × B rotation characterized by a larger shear at the separatrix. Strong correlation is found between the turbulent particle flux and the E × B flow shear in a phenomenology reminiscent of H-mode physics. The poloidal position of the limiter is a key player in the observed dynamics.

  20. Trapping solids at the inner edge of the dead zone: 3-D global MHD simulations

    NASA Astrophysics Data System (ADS)

    Dzyurkevich, N.; Flock, M.; Turner, N. J.; Klahr, H.; Henning, Th.

    2010-06-01

    Context. The poorly-ionized interior of the protoplanetary disk or “dead zone” is the location where dust coagulation processes may be most efficient. However even here, planetesimal formation may be limited by the loss of solid material through radial drift, and by collisional fragmentation of the particles. Both depend on the turbulent properties of the gas. Aims: Our aim here is to investigate the possibility that solid particles are trapped at local pressure maxima in the dynamically evolving disk. We perform the first 3-D global non-ideal magnetohydrodynamical (MHD) calculations of a section of the disk treating the turbulence driven by the magneto-rotational instability (MRI). Methods: We use the ZeusMP code with a fixed Ohmic resistivity distribution. The domain contains an inner MRI-active region near the young star and an outer midplane dead zone, with the transition between the two modeled by a sharp increase in the magnetic diffusivity. Results: The azimuthal magnetic fields generated in the active zone oscillate over time, changing sign about every 150 years. We thus observe the radial structure of the “butterfly pattern” seen previously in local shearing-box simulations. The mean magnetic field diffuses from the active zone into the dead zone, where the Reynolds stress nevertheless dominates, giving a residual α between 10-4 and 10-3. The greater total accretion stress in the active zone leads to a net reduction in the surface density, so that after 800 years an approximate steady state is reached in which a local radial maximum in the midplane pressure lies near the transition radius. We also observe the formation of density ridges within the active zone. Conclusions: The dead zone in our models possesses a mean magnetic field, significant Reynolds stresses and a steady local pressure maximum at the inner edge, where the outward migration of planetary embryos and the efficient trapping of solid material are possible.

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

  2. Combination of spaceborne sensor(s) and 3-D aerosol models to assess global daily near-surface air quality

    NASA Astrophysics Data System (ADS)

    Kacenelenbogen, M.; Redemann, J.; Russell, P. B.

    2009-12-01

    Aerosol Particulate Matter (PM), measured by ground-based monitoring stations, is used as a standard by the EPA (Environmental Protection Agency) to evaluate daily air quality. PM monitoring is particularly important for human health protection because the exposure to suspended particles can contribute, among others, to lung and respiratory diseases and even premature death. However, most of the PM monitoring stations are located close to cities, leaving large areas without any operational data. Satellite remote sensing is well suited for a global coverage of the aerosol load and can provide an independent and supplemental data source to in situ monitoring. Nevertheless, PM at the ground cannot easily be determined from satellite AOD (Aerosol Optical Depth) without additional information on the optical/microphysical properties and vertical distribution of the aerosols. The objective of this study is to explore the efficacy and accuracy of combining a 3-D aerosol transport model and satellite remote sensing as a cost-effective approach for estimating ground-level PM on a global and daily basis. The estimation of the near-surface PM will use the vertical distribution (and, if possible, the physicochemical properties) of the aerosols inferred from a transport model and the measured total load of particles in the atmospheric column retrieved by satellite sensor(s). The first step is to select a chemical transport model (CTM) that provides “good” simulated aerosol vertical profiles. A few global (e.g., WRF-Chem-GOCART) or regional (e.g., MM5-CMAQ, PM-CAMx) CTM will be compared during selected airborne campaigns like ARCTAS-CARB (Arctic Research of the Composition of the Troposphere from Aircraft and Satellites- California Air Resources Board). The next step will be to devise an algorithm that combines the satellite and model data to infer PM mass estimates at the ground, after evaluating different spaceborne instruments and possible multi-sensor combinations.

  3. Data-fusion of high resolution X-ray CT, SEM and EDS for 3D and pseudo-3D chemical and structural characterization of sandstone.

    PubMed

    De Boever, Wesley; Derluyn, Hannelore; Van Loo, Denis; Van Hoorebeke, Luc; Cnudde, Veerle

    2015-07-01

    When dealing with the characterization of the structure and composition of natural stones, problems of representativeness and choice of analysis technique almost always occur. Since feature-sizes are typically spread over the nanometer to centimeter range, there is never one single technique that allows a rapid and complete characterization. Over the last few decades, high resolution X-ray CT (μ-CT) has become an invaluable tool for the 3D characterization of many materials, including natural stones. This technique has many important advantages, but there are also some limitations, including a tradeoff between resolution and sample size and a lack of chemical information. For geologists, this chemical information is of importance for the determination of minerals inside samples. We suggest a workflow for the complete chemical and structural characterization of a representative volume of a heterogeneous geological material. This workflow consists of combining information derived from CT scans at different spatial resolutions with information from scanning electron microscopy and energy-dispersive X-ray spectroscopy. PMID:25939085

  4. (Bio)Chemical Tailoring of Biogenic 3-D Nanopatterned Templates with Energy-Relevant Functionalities

    SciTech Connect

    Sandhage, Kenneth H; Kroger, Nils

    2014-09-08

    The overall aim of this research has been to obtain fundamental understanding of (bio)chemical methodologies that will enable utilization of the unique 3-D nanopatterned architectures naturally produced by diatoms for the syntheses of advanced functional materials attractive for applications in energy harvesting/conversion and storage. This research has been conducted in three thrusts: Thrust 1 (In vivo immobilization of proteins in diatom biosilica) is directed towards elucidating the fundamental mechanism(s) underlying the cellular processes of in vivo immobilization of proteins in diatom silica. Thrust 2 (Shape-preserving reactive conversion of diatom biosilica into porous, high-surface area inorganic replicas) is aimed at understanding the fundamental mechanisms of shape preservation and nanostructural evolution associated with the reactive conversion and/or coating-based conversion of diatom biosilica templates into porous inorganic replicas. Thrust 3 (Immobilization of energy-relevant enzymes in diatom biosilica and onto diatom biosilica-derived inorganic replicas) involves use of the results from both Thrust 1 and 2 to develop strategies for in vivo and in vitro immobilization of enzymes in/on diatom biosilica and diatom biosilica-derived inorganic replicas, respectively. This Final Report describes progress achieved in all 3 of these thrusts.

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

    PubMed

    Montes-Grajales, Diana; Olivero-Verbel, Jesus

    2015-01-01

    Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co. PMID:25451822

  6. 3D Visualization of Monte-Carlo Simulation's of HZE Track Structure and Initial Chemical Species

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francis A.

    2009-01-01

    Heavy ions biophysics is important for space radiation risk assessment [1] and hadron-therapy [2]. The characteristic of heavy ions tracks include a very high energy deposition region close to the track (<20 nm) denoted as the track core, and an outer penumbra region consisting of individual secondary electrons (6-rays). A still open question is the radiobiological effects of 6- rays relative to the track core. Of importance is the induction of double-strand breaks (DSB) [3] and oxidative damage to the biomolecules and the tissue matrix, considered the most important lesions for acute and long term effects of radiation. In this work, we have simulated a 56Fe26+ ion track of 1 GeV/amu with our Monte-Carlo code RITRACKS [4]. The simulation results have been used to calculate the energy depiction and initial chemical species in a "voxelized" space, which is then visualized in 3D. Several voxels with dose >1000 Gy are found in the penumbra, some located 0.1 mm from the track core. In computational models, the DSB induction probability is calculated with radial dose [6], which may not take into account the higher RBE of electron track ends for DSB induction. Therefore, these simulations should help improve models of DSB induction and our understanding of heavy ions biophysics.

  7. A global model simulation for 3-D radiative transfer impact on surface hydrology over Sierra Nevada and Rocky Mountains

    DOE PAGESBeta

    Lee, W. -L.; Gu, Y.; Liou, K. N.; Leung, L. R.; Hsu, H. -H.

    2014-12-15

    We investigate 3-D mountain effects on solar flux distributions and their impact on surface hydrology over the Western United States, specifically the Rocky Mountains and Sierra Nevada using CCSM4 (CAM4/CLM4) global model with a 0.23° × 0.31° resolution for simulations over 6 years. In 3-D radiative transfer parameterization, we have updated surface topography data from a resolution of 1 km to 90 m to improve parameterization accuracy. In addition, we have also modified the upward-flux deviation [3-D - PP (plane-parallel)] adjustment to ensure that energy balance at the surface is conserved in global climate simulations based on 3-D radiation parameterization.more » We show that deviations of the net surface fluxes are not only affected by 3-D mountains, but also influenced by feedbacks of cloud and snow in association with the long-term simulations. Deviations in sensible heat and surface temperature generally follow the patterns of net surface solar flux. The monthly snow water equivalent (SWE) deviations show an increase in lower elevations due to reduced snowmelt, leading to a reduction in cumulative runoff. Over higher elevation areas, negative SWE deviations are found because of increased solar radiation available at the surface. Simulated precipitation increases for lower elevations, while decreases for higher elevations with a minimum in April. Liquid runoff significantly decreases in higher elevations after April due to reduced SWE and precipitation.« less

  8. A global model simulation for 3-D radiative transfer impact on surface hydrology over Sierra Nevada and Rocky Mountains

    NASA Astrophysics Data System (ADS)

    Lee, W.-L.; Gu, Y.; Liou, K. N.; Leung, L. R.; Hsu, H.-H.

    2014-12-01

    We investigate 3-D mountain effects on solar flux distributions and their impact on surface hydrology over the Western United States, specifically the Rocky Mountains and Sierra Nevada using CCSM4 (CAM4/CLM4) global model with a 0.23° × 0.31° resolution for simulations over 6 years. In 3-D radiative transfer parameterization, we have updated surface topography data from a resolution of 1 km to 90 m to improve parameterization accuracy. In addition, we have also modified the upward-flux deviation [3-D - PP (plane-parallel)] adjustment to ensure that energy balance at the surface is conserved in global climate simulations based on 3-D radiation parameterization. We show that deviations of the net surface fluxes are not only affected by 3-D mountains, but also influenced by feedbacks of cloud and snow in association with the long-term simulations. Deviations in sensible heat and surface temperature generally follow the patterns of net surface solar flux. The monthly snow water equivalent (SWE) deviations show an increase in lower elevations due to reduced snowmelt, leading to a reduction in cumulative runoff. Over higher elevation areas, negative SWE deviations are found because of increased solar radiation available at the surface. Simulated precipitation increases for lower elevations, while decreases for higher elevations with a minimum in April. Liquid runoff significantly decreases in higher elevations after April due to reduced SWE and precipitation.

  9. Applications of detailed 3D P-wave velocity crustal model in Poland for local, regional and global seismic tomography

    NASA Astrophysics Data System (ADS)

    Polkowski, Marcin; Grad, Marek

    2015-04-01

    The 3D P-wave seismic velocity model was obtained by combining data from multiple studies during past 50 years. Data sources included refraction seismology, reflection seismology, geological boreholes, vertical seismic profiling, magnetotellurics and gravimetry. Use of many data sources allowed creation of detailed 3D P-wave velocity model that reaches to depth of 60 km and includes 6-layers of sediments and 3-layers of the crust. Purpose of this study is to analyze how 3D model influences local (accuracy of location and source time estimation for local events), regional (identification of wide-angle seismic phases) and global (teleseismic tomography) seismic travel times. Additionally we compare results of forward seismic wave propagation with signals observed on short period and broadband stations. National Science Centre Poland provided financial support for this work by NCN grant DEC-2011/02/A/ST10/00284.

  10. Microfabrication of 3D neural probes with combined electrical and chemical interfaces

    NASA Astrophysics Data System (ADS)

    John, Jessin; Li, Yuefa; Zhang, Jinsheng; Loeb, Jeffrey A.; Xu, Yong

    2011-10-01

    This paper reports a novel neural probe technology for the manufacture of 3D arrays of electrodes with integrated microchannels. This new technology is based on a silicon island structure and a simple folding procedure. This method simplifies the assembly or packaging process of 3D neural probes, leading to higher yield and lower cost. Prototypes with 3D arrays of electrodes have been successfully developed. Microchannels have been successfully integrated into the 3D neural probes via isotropic XeF2 gas phase etching and a parylene resealing process. The probes have been characterized by scanning electron microscopy imaging, optical imaging, impedance analysis, and atomic force microscopy characterization of the electrode surface. Preliminary animal tests have been carried out to demonstrate the recording functionality of the probes. Flow characteristics of the microchannels were also preliminarily measured.

  11. On the Global Regularity of a Helical-Decimated Version of the 3D Navier-Stokes Equations

    NASA Astrophysics Data System (ADS)

    Biferale, Luca; Titi, Edriss S.

    2013-06-01

    We study the global regularity, for all time and all initial data in H 1/2, of a recently introduced decimated version of the incompressible 3D Navier-Stokes (dNS) equations. The model is based on a projection of the dynamical evolution of Navier-Stokes (NS) equations into the subspace where helicity (the L 2-scalar product of velocity and vorticity) is sign-definite. The presence of a second (beside energy) sign-definite inviscid conserved quadratic quantity, which is equivalent to the H 1/2-Sobolev norm, allows us to demonstrate global existence and uniqueness, of space-periodic solutions, together with continuity with respect to the initial conditions, for this decimated 3D model. This is achieved thanks to the establishment of two new estimates, for this 3D model, which show that the H 1/2 and the time average of the square of the H 3/2 norms of the velocity field remain finite. Such two additional bounds are known, in the spirit of the work of H. Fujita and T. Kato (Arch. Ration. Mech. Anal. 16:269-315, 1964; Rend. Semin. Mat. Univ. Padova 32:243-260, 1962), to be sufficient for showing well-posedness for the 3D NS equations. Furthermore, they are directly linked to the helicity evolution for the dNS model, and therefore with a clear physical meaning and consequences.

  12. A global model simulation for 3-D radiative transfer impact on surface hydrology over the Sierra Nevada and Rocky Mountains

    NASA Astrophysics Data System (ADS)

    Lee, W.-L.; Gu, Y.; Liou, K. N.; Leung, L. R.; Hsu, H.-H.

    2015-05-01

    We investigate 3-D mountain effects on solar flux distributions and their impact on surface hydrology over the western United States, specifically the Rocky Mountains and the Sierra Nevada, using the global CCSM4 (Community Climate System Model version 4; Community Atmosphere Model/Community Land Model - CAM4/CLM4) with a 0.23° x 0.31° resolution for simulations over 6 years. In a 3-D radiative transfer parameterization, we have updated surface topography data from a resolution of 1 km to 90 m to improve parameterization accuracy. In addition, we have also modified the upward-flux deviation (3-D-PP (plane-parallel)) adjustment to ensure that the energy balance at the surface is conserved in global climate simulations based on 3-D radiation parameterization. We show that deviations in the net surface fluxes are not only affected by 3-D mountains but also influenced by feedbacks of cloud and snow in association with the long-term simulations. Deviations in sensible heat and surface temperature generally follow the patterns of net surface solar flux. The monthly snow water equivalent (SWE) deviations show an increase in lower elevations due to reduced snowmelt, leading to a reduction in cumulative runoff. Over higher-elevation areas, negative SWE deviations are found because of increased solar radiation available at the surface. Simulated precipitation increases for lower elevations, while it decreases for higher elevations, with a minimum in April. Liquid runoff significantly decreases at higher elevations after April due to reduced SWE and precipitation.

  13. Atmospheric Nitrogen Trifluoride: Optimized emission estimates using 2-D and 3-D Chemical Transport Models from 1973-2008

    NASA Astrophysics Data System (ADS)

    Ivy, D. J.; Rigby, M. L.; Prinn, R. G.; Muhle, J.; Weiss, R. F.

    2009-12-01

    We present optimized annual global emissions from 1973-2008 of nitrogen trifluoride (NF3), a powerful greenhouse gas which is not currently regulated by the Kyoto Protocol. In the past few decades, NF3 production has dramatically increased due to its usage in the semiconductor industry. Emissions were estimated through the 'pulse-method' discrete Kalman filter using both a simple, flexible 2-D 12-box model used in the Advanced Global Atmospheric Gases Experiment (AGAGE) network and the Model for Ozone and Related Tracers (MOZART v4.5), a full 3-D atmospheric chemistry model. No official audited reports of industrial NF3 emissions are available, and with limited information on production, a priori emissions were estimated using both a bottom-up and top-down approach with two different spatial patterns based on semiconductor perfluorocarbon (PFC) emissions from the Emission Database for Global Atmospheric Research (EDGAR v3.2) and Semiconductor Industry Association sales information. Both spatial patterns used in the models gave consistent results, showing the robustness of the estimated global emissions. Differences between estimates using the 2-D and 3-D models can be attributed to transport rates and resolution differences. Additionally, new NF3 industry production and market information is presented. Emission estimates from both the 2-D and 3-D models suggest that either the assumed industry release rate of NF3 or industry production information is still underestimated.

  14. Global Distribution of Tropospheric Aerosols: A 3-D Model Analysis of Satellite Data

    NASA Technical Reports Server (NTRS)

    Chin, Mian

    2002-01-01

    This report describes objectives completed for the GACP (Global Climatology Aerosol Project). The objectives included the analysis of satellite aerosol data, including the optical properties and global distributions of major aerosol types, and human contributions to major aerosol types. The researchers have conducted simulations and field work.

  15. A 3D Model of Double-Helical DNA Showing Variable Chemical Details

    ERIC Educational Resources Information Center

    Cady, Susan G.

    2005-01-01

    Since the first DNA model was created approximately 50 years ago using molecular models, students and teachers have been building simplified DNA models from various practical materials. A 3D double-helical DNA model, made by placing beads on a wire and stringing beads through holes in plastic canvas, is described. Suggestions are given to enhance…

  16. Selective synthesis of rhodium-based nanoframe catalysts by chemical etching of 3d metals.

    PubMed

    Zhang, Zhi-Ping; Zhu, Wei; Yan, Chun-Hua; Zhang, Ya-Wen

    2015-03-01

    We demonstrate a general strategy for the highly selective synthesis of Rh-based multi-metallic nanoframes through preferential etching of 3d metals, including Cu and Ni. Compared with Rh-Cu nanooctahedrons/C, Rh-Cu nanooctahedral frames/C show greatly enhanced activity toward hydrazine decomposition at room temperature. PMID:25665751

  17. Changes in dissolved iron deposition to the oceans driven by human activity: a 3-D global modelling study

    NASA Astrophysics Data System (ADS)

    Myriokefalitakis, S.; Daskalakis, N.; Mihalopoulos, N.; Baker, A. R.; Nenes, A.; Kanakidou, M.

    2015-03-01

    The global atmospheric iron (Fe) cycle is parameterized in the global 3-D chemical transport model TM4-ECPL to simulate the proton- and the organic ligand-promoted mineral Fe dissolution as well as the aqueous-phase photochemical reactions between the oxidative states of Fe(III/II). Primary emissions of total (TFe) and dissolved (DFe) Fe associated with dust and combustion processes are also taken into account. TFe emissions are calculated to amount to ~35 Tg Fe yr-1. The model reasonably simulates the available Fe observations, supporting the reliability of the results of this study. Accounting for proton- and organic ligand-promoted Fe-dissolution in present-day TM4-ECPL simulations, the total Fe-dissolution is calculated to be ~0.163 Tg Fe yr-1 that accounts for up to ~50% of the calculated total DFe emissions. The atmospheric burden of DFe is calculated to be ~0.012 Tg Fe. DFe deposition presents strong spatial and temporal variability with an annual deposition flux ~0.489 Tg Fe yr-1 from which about 25% (~0.124 Tg Fe yr-1) are deposited over the ocean. The impact of air-quality on Fe deposition is studied by performing sensitivity simulations using preindustrial (year 1850), present (year 2008) and future (year 2100) emission scenarios. These simulations indicate that an increase (~2 times) in Fe-dissolution may have occurred in the past 150 years due to increasing anthropogenic emissions and thus atmospheric acidity. On the opposite, a decrease (~2 times) of Fe-dissolution is projected for near future, since atmospheric acidity is expected to be lower than present-day due to air-quality regulations of anthropogenic emissions. The organic ligand contribution to Fe dissolution shows inverse relationship to the atmospheric acidity thus its importance has decreased since the preindustrial period but is projected to increase in the future. The calculated changes also show that the atmospheric DFe supply to High-Nutrient-Low-Chlorophyll oceanic areas (HNLC

  18. Vessels as 4-D curves: global minimal 4-D paths to extract 3-D tubular surfaces and centerlines.

    PubMed

    Li, Hua; Yezzi, Anthony

    2007-09-01

    In this paper, we propose an innovative approach to the segmentation of tubular structures. This approach combines all of the benefits of minimal path techniques such as global minimizers, fast computation, and powerful incorporation of user input, while also having the capability to represent and detect vessel surfaces directly which so far has been a feature restricted to active contour and surface techniques. The key is to represent the trajectory of a tubular structure not as a 3-D curve but to go up a dimension and represent the entire structure as a 4-D curve. Then we are able to fully exploit minimal path techniques to obtain global minimizing trajectories between two user supplied endpoints in order to reconstruct tubular structures from noisy or low contrast 3-D data without the sensitivity to local minima inherent in most active surface techniques. In contrast to standard purely spatial 3-D minimal path techniques, however, we are able to represent a full tubular surface rather than just a curve which runs through its interior. Our representation also yields a natural notion of a tube's "central curve." We demonstrate and validate the utility of this approach on magnetic resonance (MR) angiography and computed tomography (CT) images of coronary arteries. PMID:17896594

  19. The chemical, mechanical, and physical properties of 3D printed materials composed of TiO2-ABS nanocomposites

    PubMed Central

    Skorski, Matthew; Esenther, Jake; Ahmed, Zeeshan; Miller, Abigail E.

    2016-01-01

    To expand the chemical capabilities of 3D printed structures generated from commercial thermoplastic printers, we have produced and printed polymer filaments that contain inorganic nanoparticles. TiO2 was dispersed into acrylonitrile butadiene styrene (ABS) and extruded into filaments with 1.75 mm diameters. We produced filaments with TiO2 compositions of 1%, 5%, and 10% (kg/kg) and printed structures using a commercial 3D printer. Our experiments suggest that ABS undergoes minor degradation in the presence of TiO2 during the different processing steps. The measured mechanical properties (strain and Young’s modulus) for all of the composites are similar to those of structures printed from the pure polymer. TiO2 incorporation at 1% negatively affects the stress at breaking point and the flexural stress. Structures produced from the 5 and 10% nanocomposites display a higher breaking point stress than those printed from the pure polymer. TiO2 within the printed matrix was able to quench the intrinsic fluorescence of the polymer. TiO2 was also able to photocatalyze the degradation of a rhodamine 6G in solution. These experiments display chemical reactivity in nanocomposites that are printed using commercial 3D printers, and we expect that our methodology will help to inform others who seek to incorporate catalytic nanoparticles in 3D printed structures. PMID:27375367

  20. Nondestructive volumetric 3-D chemical mapping of nickel-sulfur compounds at the nanoscale

    SciTech Connect

    Harris W. M.; Chu Y.; Nelson, G.J.; Kiss, A.M.; Izzo Jr, J.R.; Liu, Y.; Liu, M.; Wang, S.; Chiu W.K.S.

    2012-04-04

    Nano-structures of nickel (Ni) and nickel subsulfide (Ni{sub 3}S{sub 2}) materials were studied and mapped in 3D with high-resolution x-ray nanotomography combined with full field XANES spectroscopy. This method for characterizing these phases in complex microstructures is an important new analytical imaging technique, applicable to a wide range of nanoscale and mesoscale electrochemical systems.

  1. Solar Chemical Abundances Determined with a CO5BOLD 3D Model Atmosphere

    NASA Astrophysics Data System (ADS)

    Caffau, E.; Ludwig, H.-G.; Steffen, M.; Freytag, B.; Bonifacio, P.

    2011-02-01

    In the last decade, the photospheric solar metallicity as determined from spectroscopy experienced a remarkable downward revision. Part of this effect can be attributed to an improvement of atomic data and the inclusion of NLTE computations, but also the use of hydrodynamical model atmospheres seemed to play a role. This "decrease" with time of the metallicity of the solar photosphere increased the disagreement with the results from helioseismology. With a CO 5 BOLD 3D model of the solar atmosphere, the CIFIST team at the Paris Observatory re-determined the photospheric solar abundances of several elements, among them C, N, and O. The spectroscopic abundances are obtained by fitting the equivalent width and/or the profile of observed spectral lines with synthetic spectra computed from the 3D model atmosphere. We conclude that the effects of granular fluctuations depend on the characteristics of the individual lines, but are found to be relevant only in a few particular cases. 3D effects are not responsible for the systematic lowering of the solar abundances in recent years. The solar metallicity resulting from this analysis is Z=0.0153, Z/ X=0.0209.

  2. A global model simulation for 3-D radiative transfer impact on surface hydrology over the Sierra Nevada and Rocky Mountains

    DOE PAGESBeta

    Lee, W.-L.; Gu, Y.; Liou, K. N.; Leung, L. R.; Hsu, H.-H.

    2015-05-19

    We investigate 3-D mountain effects on solar flux distributions and their impact on surface hydrology over the western United States, specifically the Rocky Mountains and the Sierra Nevada, using the global CCSM4 (Community Climate System Model version 4; Community Atmosphere Model/Community Land Model – CAM4/CLM4) with a 0.23° × 0.31° resolution for simulations over 6 years. In a 3-D radiative transfer parameterization, we have updated surface topography data from a resolution of 1 km to 90 m to improve parameterization accuracy. In addition, we have also modified the upward-flux deviation (3-D–PP (plane-parallel)) adjustment to ensure that the energy balance atmore » the surface is conserved in global climate simulations based on 3-D radiation parameterization. We show that deviations in the net surface fluxes are not only affected by 3-D mountains but also influenced by feedbacks of cloud and snow in association with the long-term simulations. Deviations in sensible heat and surface temperature generally follow the patterns of net surface solar flux. The monthly snow water equivalent (SWE) deviations show an increase in lower elevations due to reduced snowmelt, leading to a reduction in cumulative runoff. Over higher-elevation areas, negative SWE deviations are found because of increased solar radiation available at the surface. Simulated precipitation increases for lower elevations, while it decreases for higher elevations, with a minimum in April. Liquid runoff significantly decreases at higher elevations after April due to reduced SWE and precipitation.« less

  3. Validation of "AW3D" Global Dsm Generated from Alos Prism

    NASA Astrophysics Data System (ADS)

    Takaku, Junichi; Tadono, Takeo; Tsutsui, Ken; Ichikawa, Mayumi

    2016-06-01

    Panchromatic Remote-sensing Instrument for Stereo Mapping (PRISM), one of onboard sensors carried by Advanced Land Observing Satellite (ALOS), was designed to generate worldwide topographic data with its optical stereoscopic observation. It has an exclusive ability to perform a triplet stereo observation which views forward, nadir, and backward along the satellite track in 2.5 m ground resolution, and collected its derived images all over the world during the mission life of the satellite from 2006 through 2011. A new project, which generates global elevation datasets with the image archives, was started in 2014. The data is processed in unprecedented 5 m grid spacing utilizing the original triplet stereo images in 2.5 m resolution. As the number of processed data is growing steadily so that the global land areas are almost covered, a trend of global data qualities became apparent. This paper reports on up-to-date results of the validations for the accuracy of data products as well as the status of data coverage in global areas. The accuracies and error characteristics of datasets are analyzed by the comparison with existing global datasets such as Ice, Cloud, and land Elevation Satellite (ICESat) data, as well as ground control points (GCPs) and the reference Digital Elevation Model (DEM) derived from the airborne Light Detection and Ranging (LiDAR).

  4. Global 3D-Grids Based on Great Circle Arc QTM Sphere Octree and Its Application

    NASA Astrophysics Data System (ADS)

    Wang, J. X.; Li, Y. H.; Zheng, Y. S.; Liu, J. N.

    2013-10-01

    With the development of computers, network communications, scientific computing, mapping remote sensing and geographic information technologies, Discrete Global Grids (DGGs) and Earth System Spatial Grid(ESSG)have become the integrated spatial data model facing the large-scale and global-scale problems and the complex geo-computation. This paper discusses the property and character of the global spatial data at first. Then it introduces the grid division system based on large arc QTM octree and compares this scheme with degradation octree scheme. At last, it introduces the application of the scheme in land surface, underground and aerial geographic entity modeling. The study suggests that: the grid division system based on large arc QTM octree has the potential to integrate the whole spatial data of different layers of the geospatial. And it will have a broad application prospect in complex large-scale geographic computing.

  5. Modeling Recent Large Earthquakes Using the 3-D Global Wave Field

    NASA Astrophysics Data System (ADS)

    Hjörleifsdóttir, V.; Kanamori, H.; Tromp, J.

    2003-04-01

    We use the spectral-element method (SEM) to accurately compute waveforms at periods of 40 s and longer for three recent large earthquakes using 3D Earth models and finite source models. The M_w~7.6, Jan~26, 2001, Bhuj, India event had a small rupture area and is well modeled at long periods with a point source. We use this event as a calibration event to investigate the effects of 3-D Earth models on the waveforms. The M_w~7.9, Nov~11, 2001, Kunlun, China, event exhibits a large directivity (an asymmetry in the radiation pattern) even at periods longer than 200~s. We used the source time function determined by Kikuchi and Yamanaka (2001) and the overall pattern of slip distribution determined by Lin et al. to guide the wave-form modeling. The large directivity is consistent with a long fault, at least 300 km, and an average rupture speed of 3±0.3~km/s. The directivity at long periods is not sensitive to variations in the rupture speed along strike as long as the average rupture speed is constant. Thus, local variations in rupture speed cannot be ruled out. The rupture speed is a key parameter for estimating the fracture energy of earthquakes. The M_w~8.1, March~25, 1998, event near the Balleny Islands on the Antarctic Plate exhibits large directivity in long period surface waves, similar to the Kunlun event. Many slip models have been obtained from body waves for this earthquake (Kuge et al. (1999), Nettles et al. (1999), Antolik et al. (2000), Henry et al. (2000) and Tsuboi et al. (2000)). We used the slip model from Henry et al. to compute SEM waveforms for this event. The synthetic waveforms show a good fit to the data at periods from 40-200~s, but the amplitude and directivity at longer periods are significantly smaller than observed. Henry et al. suggest that this event comprised two subevents with one triggering the other at a distance of 100 km. To explain the observed directivity however, a significant amount of slip is required between the two subevents

  6. A roadmap to global illumination in 3D scenes: solutions for GPU object recognition applications

    NASA Astrophysics Data System (ADS)

    Picos, Kenia; Díaz-Ramírez, Victor H.; Tapia, Juan J.

    2014-09-01

    Light interactions with matter is of remarkable complexity. An adequate modeling of global illumination is a vastly studied topic since the beginning of computer graphics, and still is an unsolved problem. The rendering equation for global illumination is based of refraction and reflection of light in interaction with matter within an environment. This physical process possesses a high computational complexity when implemented in a digital computer. The appearance of an object depends on light interactions with the surface of the material, such as emission, scattering, and absorption. Several image-synthesis methods have been used to realistically render the appearance of light incidence on an object. Recent global illumination algorithms employ mathematical models and computational strategies that improve the efficiency of the simulation solution. This work presents a review the state of the art of global illumination algorithms and focuses on the efficiency of the solution in a computational implementation in a graphics processing unit. A reliable system is developed to simulate realistics scenes in the context of real-time object recognition under different lighting conditions. Computer simulations results are presented and discussed in terms of discrimination capability, and robustness to additive noise, when considering several lighting model reflections and multiple light sources.

  7. Connecting Global Measures of 3D Magnetic Reconnection to Local Kinetic Physics

    SciTech Connect

    Daughton, William Scott

    2015-07-16

    After giving the motivation for the work, slides present the topic under the following headings: Description of LAPD experiment; Actual simulation setup; Simple kinetic theory of ined-tied tearing; Diagnostics to characterizing 3D reconnection; Example #1 - short-tied system; and Example #2 - long line-tied system. Colorful simulations are shown for quasipotential vs field line exponentiation, field line integrated Ohms Law, and correlation with agyrotopy & energy conversion for example #1; and evolution of current density for largest case, field exponentiation vs quasi-potential, and time evolution of magnetic field lines for example #2. To satisfy line-tied boundary conditions, there is need for superposition of oblique modes--the simple two-mode approximation works surprisingly well. For force-free layers with bg >1, the fastest growing periodic modes are oblique with kxλ ~0.5. This implies a minimum length of Ly > 2πλbg. There are strong correlations between σ → Ξ → A0e (observable with spacecraft). Electron pressure tensor is the dominant non-ideal term.

  8. Bayesian Segmentation of Atrium Wall Using Globally-Optimal Graph Cuts on 3D Meshes

    PubMed Central

    Veni, Gopalkrishna; Fu, Zhisong; Awate, Suyash P.; Whitaker, Ross T.

    2014-01-01

    Efficient segmentation of the left atrium (LA) wall from delayed enhancement MRI is challenging due to inconsistent contrast, combined with noise, and high variation in atrial shape and size. We present a surface-detection method that is capable of extracting the atrial wall by computing an optimal a-posteriori estimate. This estimation is done on a set of nested meshes, constructed from an ensemble of segmented training images, and graph cuts on an associated multi-column, proper-ordered graph. The graph/mesh is a part of a template/model that has an associated set of learned intensity features. When this mesh is overlaid onto a test image, it produces a set of costs which lead to an optimal segmentation. The 3D mesh has an associated weighted, directed multi-column graph with edges that encode smoothness and inter-surface penalties. Unlike previous graph-cut methods that impose hard constraints on the surface properties, the proposed method follows from a Bayesian formulation resulting in soft penalties on spatial variation of the cuts through the mesh. The novelty of this method also lies in the construction of proper-ordered graphs on complex shapes for choosing among distinct classes of base shapes for automatic LA segmentation. We evaluate the proposed segmentation framework on simulated and clinical cardiac MRI. PMID:24684007

  9. A 3-D RBF-FD elliptic solver for irregular boundaries: modeling the atmospheric global electric circuit with topography

    NASA Astrophysics Data System (ADS)

    Bayona, V.; Flyer, N.; Lucas, G. M.; Baumgaertner, A. J. G.

    2015-04-01

    A numerical model based on Radial Basis Function-generated Finite Differences (RBF-FD) is developed for simulating the Global Electric Circuit (GEC) within the Earth's atmosphere, represented by a 3-D variable coefficient linear elliptic PDE in a spherically-shaped volume with the lower boundary being the Earth's topography and the upper boundary a sphere at 60 km. To our knowledge, this is (1) the first numerical model of the GEC to combine the Earth's topography with directly approximating the differential operators in 3-D space, and related to this (2) the first RBF-FD method to use irregular 3-D stencils for discretization to handle the topography. It benefits from the mesh-free nature of RBF-FD, which is especially suitable for modeling high-dimensional problems with irregular boundaries. The RBF-FD elliptic solver proposed here makes no limiting assumptions on the spatial variability of the coefficients in the PDE (i.e. the conductivity profile), the right hand side forcing term of the PDE (i.e. distribution of current sources) or the geometry of the lower boundary.

  10. New 3D parallel GILD electromagnetic modeling and nonlinear inversion using global magnetic integral and local differential equation

    SciTech Connect

    Xie, G.; Li, J.; Majer, E.; Zuo, D.

    1998-07-01

    This paper describes a new 3D parallel GILD electromagnetic (EM) modeling and nonlinear inversion algorithm. The algorithm consists of: (a) a new magnetic integral equation instead of the electric integral equation to solve the electromagnetic forward modeling and inverse problem; (b) a collocation finite element method for solving the magnetic integral and a Galerkin finite element method for the magnetic differential equations; (c) a nonlinear regularizing optimization method to make the inversion stable and of high resolution; and (d) a new parallel 3D modeling and inversion using a global integral and local differential domain decomposition technique (GILD). The new 3D nonlinear electromagnetic inversion has been tested with synthetic data and field data. The authors obtained very good imaging for the synthetic data and reasonable subsurface EM imaging for the field data. The parallel algorithm has high parallel efficiency over 90% and can be a parallel solver for elliptic, parabolic, and hyperbolic modeling and inversion. The parallel GILD algorithm can be extended to develop a high resolution and large scale seismic and hydrology modeling and inversion in the massively parallel computer.

  11. Changes in dissolved iron deposition to the oceans driven by human activity: a 3-D global modelling study

    NASA Astrophysics Data System (ADS)

    Myriokefalitakis, S.; Daskalakis, N.; Mihalopoulos, N.; Baker, A. R.; Nenes, A.; Kanakidou, M.

    2015-07-01

    The global atmospheric iron (Fe) cycle is parameterized in the global 3-D chemical transport model TM4-ECPL to simulate the proton- and the organic ligand-promoted mineral-Fe dissolution as well as the aqueous-phase photochemical reactions between the oxidative states of Fe (III/II). Primary emissions of total (TFe) and dissolved (DFe) Fe associated with dust and combustion processes are also taken into account, with TFe mineral emissions calculated to amount to ~ 35 Tg-Fe yr-1 and TFe emissions from combustion sources of ~ 2 Tg-Fe yr-1. The model reasonably simulates the available Fe observations, supporting the reliability of the results of this study. Proton- and organic ligand-promoted Fe dissolution in present-day TM4-ECPL simulations is calculated to be ~ 0.175 Tg-Fe yr-1, approximately half of the calculated total primary DFe emissions from mineral and combustion sources in the model (~ 0.322 Tg-Fe yr-1). The atmospheric burden of DFe is calculated to be ~ 0.024 Tg-Fe. DFe deposition presents strong spatial and temporal variability with an annual flux of ~ 0.496 Tg-Fe yr-1, from which about 40 % (~ 0.191 Tg-Fe yr-1) is deposited over the ocean. The impact of air quality on Fe deposition is studied by performing sensitivity simulations using preindustrial (year 1850), present (year 2008) and future (year 2100) emission scenarios. These simulations indicate that about a 3 times increase in Fe dissolution may have occurred in the past 150 years due to increasing anthropogenic emissions and thus atmospheric acidity. Air-quality regulations of anthropogenic emissions are projected to decrease atmospheric acidity in the near future, reducing to about half the dust-Fe dissolution relative to the present day. The organic ligand contribution to Fe dissolution shows an inverse relationship to the atmospheric acidity, thus its importance has decreased since the preindustrial period but is projected to increase in the future. The calculated changes also show that the

  12. A hybrid framework of multiple active appearance models and global registration for 3D prostate segmentation in MRI

    NASA Astrophysics Data System (ADS)

    Ghose, Soumya; Oliver, Arnau; Martí, Robert; Lladó, Xavier; Freixenet, Jordi; Mitra, Jhimli; Vilanova, Joan C.; Meriaudeau, Fabrice

    2012-02-01

    Real-time fusion of Magnetic Resonance (MR) and Trans Rectal Ultra Sound (TRUS) images aid in the localization of malignant tissues in TRUS guided prostate biopsy. Registration performed on segmented contours of the prostate reduces computational complexity and improves the multimodal registration accuracy. However, accurate and computationally efficient 3D segmentation of the prostate in MR images could be a challenging task due to inter-patient shape and intensity variability of the prostate gland. In this work, we propose to use multiple statistical shape and appearance models to segment the prostate in 2D and a global registration framework to impose shape restriction in 3D. Multiple mean parametric models of the shape and appearance corresponding to the apex, central and base regions of the prostate gland are derived from principal component analysis (PCA) of prior shape and intensity information of the prostate from the training data. The estimated parameters are then modified with the prior knowledge of the optimization space to achieve segmentation in 2D. The 2D segmented slices are then rigidly registered with the average 3D model produced by affine registration of the ground truth of the training datasets to minimize pose variations and impose 3D shape restriction. The proposed method achieves a mean Dice similarity coefficient (DSC) value of 0.88+/-0.11, and mean Hausdorff distance (HD) of 3.38+/-2.81 mm when validated with 15 prostate volumes of a public dataset in leave-one-out validation framework. The results achieved are better compared to some of the works in the literature.

  13. 3D Dynamics of Magnetopause Reconnection Using Hall-MHD Global Simulations

    NASA Astrophysics Data System (ADS)

    Maynard, K.; Germaschewski, K.; Raeder, J.; Bhattacharjee, A.

    2011-12-01

    Magnetic reconnection at Earth's magnetopause and in the magnetotail is of crucial importance for the dynamics of the global magnetosphere and space weather. Even though the plasma conditions in the magnetosphere are largely in the collisionless regime, most of the existing research using global computational models employ single-fluid magnetohydrodynamics (MHD) with artificial resistivity. Studies of reconnection in simplified, two-dimensional geometries have established that two-fluid and kinetic effects can dramatically alter dynamics and reconnection rates when compared with single-fluid models. These enhanced models also introduce particular signatures, for example a quadrupolar out-of-plane magnetic field component that has already been observed in space by satellite measurements. However, results from simplified geometries cannot be translated directly to the dynamics of three-dimensional magnetospheric reconnection. For instance, magnetic flux originating from the solar wind and arriving at the magnetopause can either reconnect or be advected around the magnetosphere. In this study, we use a new version of the OpenGGCM code that incorporates the Hall term in a Generalized Ohm's Law to study magnetopause reconnection under synthetic solar wind conditions and investigate how reconnection rates and dynamics of flux transfer events depend on the strength of the Hall term. The OpenGGCM, a global model of Earth's magnetosphere, has recently been ported to exploit modern computing architectures like the Cell processor and SIMD capabilities of conventional processors using an automatic code generator. These enhancements provide us with the performance needed to include the computationally expensive Hall physics.

  14. A New Global Model for 3-D variations in P Wave Speed in Earth's Mantle

    NASA Astrophysics Data System (ADS)

    Karason, H.; van der Hilst, R. D.; Li, C.

    2003-12-01

    In an effort to improve the resolution of mantle structure we have combined complementary data sets of short- and long period (absolute and differential) travel time residuals. Our new model is based on short period P (N\\~7.7x10**6), pP (N\\~2.3x10**5), and PKP (N\\~16x10**4) data from the catalog by Engdahl et al (BSSA, 1998), short-period PKP differential times (N\\~1600) measured by McSweeney & Creager, and long-period differential PP-P times - N\\~20,000 measured by Bolton & Masters and N\\~18,000 by Ritsema - and Pdiff-PKP (N\\~560) measured by Wysession. Inversion tests, spectral analysis, and comparison with geology indicate that the large-scale upper mantle structure is better constrained with the addition of PP-P, whereas the Pdiff and PKP data help constrain deep mantle structure (Karason & Van der Hilst, JGR, 2001). The long period data were measured by cross-correlation. We solved the system of equations using 400 iterations of the iterative algorithm LSQR For the short period (1 Hz) data we use a high frequency approximation and trace rays through a fine grid of constant slowness cells to invert for mantle structure. For low frequency Pdiff and PP data we account for sensitivity to structure away from the optical ray path with 3-D Frechet derivatives (sensitivity kernels) estimated from single forward scattering and projected onto basis functions (constant slowness blocks) used for model parameterization. With such kernels the low frequency data can constrain long wavelength heterogeneity without keeping the short period data from mapping details in densely sampled regions. In addition to finite frequency sensitivity kernels we optimized the localization by using a parameterization that adapts to spatial resolution, with small cells in regions of dense sampling and larger cells in regions where sampling is more sparse (the total number of cells was \\~ 350,000). Finally, we corrected all travel times and surface reflections for lateral variations in

  15. New Insights about Meridional Circulation Dynamics from 3D MHD Global Simulations of Solar Convection and Dynamo Action

    NASA Astrophysics Data System (ADS)

    Passos, D.; Charbonneau, P.; Miesch, M. S.

    2016-04-01

    The solar meridional circulation is a "slow", large scale flow that transports magnetic field and plasma throughout the convection zone in the (r,θ) plane and plays a crucial role in controlling the magnetic cycle solutions presented by flux transport dynamo models. Observations indicate that this flow speed varies in anti-phase with the solar cycle at the solar surface. A possible explanation for the source of this variation is based on the fact that inflows into active regions alter the global surface pattern of the meridional circulation. In this work we examine the meridional circulation profile that emerges from a 3D global simulation of the solar convection zone, and its associated dynamics. We find that at the bottom of the convection zone, in the region where the toroidal magnetic field accumulates, the meridional circulation is highly modulated through the action of a magnetic torques and thus provides evidence for a new mechanism to explain the observed cyclic variations.

  16. Particle entry through "Sash" groove simulated by Global 3D Electromagnetic Particle code with duskward IMF By

    NASA Astrophysics Data System (ADS)

    Yan, X.; Cai, D.; Nishikawa, K.; Lembege, B.

    2004-12-01

    We made our efforts to parallelize the global 3D HPF Electromagnetic particle model (EMPM) for several years and have also reported our meaningful simulation results that revealed the essential physics involved in interaction of the solar wind with the Earth's magnetosphere using this EMPM (Nishikawa et al., 1995; Nishikawa, 1997, 1998a, b, 2001, 2002) in our PC cluster and supercomputer(D.S. Cai et al., 2001, 2003). Sash patterns and related phenomena have been observed and reported in some satellite observations (Fujumoto et al. 1997; Maynard, 2001), and have motivated 3D MHD simulations (White and al., 1998). We also investigated it with our global 3D parallelized HPF EMPM with dawnward IMF By (K.-I. Nishikawa, 1998) and recently new simulation with dusk-ward IMF By was accomplished in the new VPP5000 supercomputer. In the new simulations performed on the new VPP5000 supercomputer of Tsukuba University, we used larger domain size, 305×205×205, smaller grid size (Δ ), 0.5R E(the radium of the Earth), more total particle number, 220,000,000 (about 8 pairs per cell). At first, we run this code until we get the so-called quasi-stationary status; After the quasi-stationary status was established, we applied a northward IMF (B z=0.2), and then wait until the IMF arrives around the magnetopuase. After the arrival of IMF, we begin to change the IMF from northward to duskward (IMF B y=-0.2). The results revealed that the groove structure at the day-side magnetopause, that causes particle entry into inner magnetosphere and the cross structure or S-structure at near magneto-tail are formed. Moreover, in contrast with MHD simulations, kinetic characteristic of this event is also analyzed self-consistently with this simulation. The new simulation provides new and more detailed insights for the observed sash event.

  17. Fast and accurate global multiphase arrival tracking: the irregular shortest-path method in a 3-D spherical earth model

    NASA Astrophysics Data System (ADS)

    Huang, Guo-Jiao; Bai, Chao-Ying; Greenhalgh, Stewart

    2013-09-01

    The traditional grid/cell-based wavefront expansion algorithms, such as the shortest path algorithm, can only find the first arrivals or multiply reflected (or mode converted) waves transmitted from subsurface interfaces, but cannot calculate the other later reflections/conversions having a minimax time path. In order to overcome the above limitations, we introduce the concept of a stationary minimax time path of Fermat's Principle into the multistage irregular shortest path method. Here we extend it from Cartesian coordinates for a flat earth model to global ray tracing of multiple phases in a 3-D complex spherical earth model. The ray tracing results for 49 different kinds of crustal, mantle and core phases show that the maximum absolute traveltime error is less than 0.12 s and the average absolute traveltime error is within 0.09 s when compared with the AK135 theoretical traveltime tables for a 1-D reference model. Numerical tests in terms of computational accuracy and CPU time consumption indicate that the new scheme is an accurate, efficient and a practical way to perform 3-D multiphase arrival tracking in regional or global traveltime tomography.

  18. Direct fabrication of 3D graphene on nanoporous anodic alumina by plasma-enhanced chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Zhan, Hualin; Garrett, David J.; Apollo, Nicholas V.; Ganesan, Kumaravelu; Lau, Desmond; Prawer, Steven; Cervenka, Jiri

    2016-01-01

    High surface area electrode materials are of interest for a wide range of potential applications such as super-capacitors and electrochemical cells. This paper describes a fabrication method of three-dimensional (3D) graphene conformally coated on nanoporous insulating substrate with uniform nanopore size. 3D graphene films were formed by controlled graphitization of diamond-like amorphous carbon precursor films, deposited by plasma-enhanced chemical vapour deposition (PECVD). Plasma-assisted graphitization was found to produce better quality graphene than a simple thermal graphitization process. The resulting 3D graphene/amorphous carbon/alumina structure has a very high surface area, good electrical conductivity and exhibits excellent chemically stability, providing a good material platform for electrochemical applications. Consequently very large electrochemical capacitance values, as high as 2.1 mF for a sample of 10 mm3, were achieved. The electrochemical capacitance of the material exhibits a dependence on bias voltage, a phenomenon observed by other groups when studying graphene quantum capacitance. The plasma-assisted graphitization, which dominates the graphitization process, is analyzed and discussed in detail.

  19. Direct fabrication of 3D graphene on nanoporous anodic alumina by plasma-enhanced chemical vapor deposition.

    PubMed

    Zhan, Hualin; Garrett, David J; Apollo, Nicholas V; Ganesan, Kumaravelu; Lau, Desmond; Prawer, Steven; Cervenka, Jiri

    2016-01-01

    High surface area electrode materials are of interest for a wide range of potential applications such as super-capacitors and electrochemical cells. This paper describes a fabrication method of three-dimensional (3D) graphene conformally coated on nanoporous insulating substrate with uniform nanopore size. 3D graphene films were formed by controlled graphitization of diamond-like amorphous carbon precursor films, deposited by plasma-enhanced chemical vapour deposition (PECVD). Plasma-assisted graphitization was found to produce better quality graphene than a simple thermal graphitization process. The resulting 3D graphene/amorphous carbon/alumina structure has a very high surface area, good electrical conductivity and exhibits excellent chemically stability, providing a good material platform for electrochemical applications. Consequently very large electrochemical capacitance values, as high as 2.1 mF for a sample of 10 mm(3), were achieved. The electrochemical capacitance of the material exhibits a dependence on bias voltage, a phenomenon observed by other groups when studying graphene quantum capacitance. The plasma-assisted graphitization, which dominates the graphitization process, is analyzed and discussed in detail. PMID:26805546

  20. Direct fabrication of 3D graphene on nanoporous anodic alumina by plasma-enhanced chemical vapor deposition

    PubMed Central

    Zhan, Hualin; Garrett, David J.; Apollo, Nicholas V.; Ganesan, Kumaravelu; Lau, Desmond; Prawer, Steven; Cervenka, Jiri

    2016-01-01

    High surface area electrode materials are of interest for a wide range of potential applications such as super-capacitors and electrochemical cells. This paper describes a fabrication method of three-dimensional (3D) graphene conformally coated on nanoporous insulating substrate with uniform nanopore size. 3D graphene films were formed by controlled graphitization of diamond-like amorphous carbon precursor films, deposited by plasma-enhanced chemical vapour deposition (PECVD). Plasma-assisted graphitization was found to produce better quality graphene than a simple thermal graphitization process. The resulting 3D graphene/amorphous carbon/alumina structure has a very high surface area, good electrical conductivity and exhibits excellent chemically stability, providing a good material platform for electrochemical applications. Consequently very large electrochemical capacitance values, as high as 2.1 mF for a sample of 10 mm3, were achieved. The electrochemical capacitance of the material exhibits a dependence on bias voltage, a phenomenon observed by other groups when studying graphene quantum capacitance. The plasma-assisted graphitization, which dominates the graphitization process, is analyzed and discussed in detail. PMID:26805546

  1. Global localization of 3D anatomical structures by pre-filtered Hough forests and discrete optimization.

    PubMed

    Donner, René; Menze, Bjoern H; Bischof, Horst; Langs, Georg

    2013-12-01

    The accurate localization of anatomical landmarks is a challenging task, often solved by domain specific approaches. We propose a method for the automatic localization of landmarks in complex, repetitive anatomical structures. The key idea is to combine three steps: (1) a classifier for pre-filtering anatomical landmark positions that (2) are refined through a Hough regression model, together with (3) a parts-based model of the global landmark topology to select the final landmark positions. During training landmarks are annotated in a set of example volumes. A classifier learns local landmark appearance, and Hough regressors are trained to aggregate neighborhood information to a precise landmark coordinate position. A non-parametric geometric model encodes the spatial relationships between the landmarks and derives a topology which connects mutually predictive landmarks. During the global search we classify all voxels in the query volume, and perform regression-based agglomeration of landmark probabilities to highly accurate and specific candidate points at potential landmark locations. We encode the candidates' weights together with the conformity of the connecting edges to the learnt geometric model in a Markov Random Field (MRF). By solving the corresponding discrete optimization problem, the most probable location for each model landmark is found in the query volume. We show that this approach is able to consistently localize the model landmarks despite the complex and repetitive character of the anatomical structures on three challenging data sets (hand radiographs, hand CTs, and whole body CTs), with a median localization error of 0.80 mm, 1.19 mm and 2.71 mm, respectively. PMID:23664450

  2. Influence of Chemical Piles on Convective Structure and the Geoid from 3D Spherical Mantle Convection Models

    NASA Astrophysics Data System (ADS)

    Liu, X.; Zhong, S.

    2013-12-01

    Classic mantle dynamic models for the Earth's geoid are mostly based on whole mantle convection and constrain that the upper mantle is significantly weaker than the lower mantle. Whole mantle convection models with such mantle viscosity structure have successfully explained the long-wavelength structure in the mantle. However, with increasing consensus on the existence of chemically distinct piles above the core mantle boundary (CMB) (also known as large low shear velocity provinces or LLSVPs), questions arise as to what extent the chemical piles influence the Earth's geoid and long-wavelength mantle convection. Some recent studies suggested that the chemical piles have a controlling effect on the Earth's degree two mantle structure, geoid, and true polar wander, although the chemical piles are estimated to be of small volume (~2% of the whole mantle) by seismic studies. We have formulated dynamically consistent 3D mantle convection models using CitcomS and studied how the chemical piles above CMB influence the long-wavelength convective structure and geoid. The models have free slip boundary conditions and temperature dependent viscosity. By comparing with purely thermal convection models, we found that the long wavelength convective structure is not sensitive to the presence of the chemical piles. By determining the geoid from the buoyance of a certain layer of the mantle, we found that for both purely thermal and thermochemical convection, the geoid is mostly contributed by the upper part of the mantle, with ~80% geoid explained by the buoyancy in the upper half of the mantle. In purely thermal convection, the contribution to the geoid from the bottom layer of the mantle always has the same sign with the total geoid (a bottom ~ 600 km thick layer gives ~3.5% of the total geoid). However, in the thermochemical convection, the bottom layer with overall negatively buoyant chemical piles gives rise to the geoid that has opposite sign with the total geoid and has a

  3. Effects of Kinetic Processes in Shaping Io's Global Plasma Environment: A 3D Hybrid Model

    NASA Technical Reports Server (NTRS)

    Lipatov, Alexander S.; Combi, Michael R.

    2004-01-01

    The global dynamics of the ionized and neutral components in the environment of Io plays an important role in the interaction of Jupiter's corotating magnetospheric plasma with Io. The stationary simulation of this problem was done in the MHD and the electrodynamics approaches. One of the main significant results from the simplified two-fluid model simulations was a production of the structure of the double-peak in the magnetic field signature of the I0 flyby that could not be explained by standard MHD models. In this paper, we develop a method of kinetic ion simulation. This method employs the fluid description for electrons and neutrals whereas for ions multilevel, drift-kinetic and particle, approaches are used. We also take into account charge-exchange and photoionization processes. Our model provides much more accurate description for ion dynamics and allows us to take into account the realistic anisotropic ion distribution that cannot be done in fluid simulations. The first results of such simulation of the dynamics of ions in the Io's environment are discussed in this paper.

  4. MERIDIONAL CIRCULATION DYNAMICS FROM 3D MAGNETOHYDRODYNAMIC GLOBAL SIMULATIONS OF SOLAR CONVECTION

    SciTech Connect

    Passos, Dário; Charbonneau, Paul; Miesch, Mark

    2015-02-10

    The form of solar meridional circulation is a very important ingredient for mean field flux transport dynamo models. However, a shroud of mystery still surrounds this large-scale flow, given that its measurement using current helioseismic techniques is challenging. In this work, we use results from three-dimensional global simulations of solar convection to infer the dynamical behavior of the established meridional circulation. We make a direct comparison between the meridional circulation that arises in these simulations and the latest observations. Based on our results, we argue that there should be an equatorward flow at the base of the convection zone at mid-latitudes, below the current maximum depth helioseismic measures can probe (0.75 R{sub ⊙}). We also provide physical arguments to justify this behavior. The simulations indicate that the meridional circulation undergoes substantial changes in morphology as the magnetic cycle unfolds. We close by discussing the importance of these dynamical changes for current methods of observation which involve long averaging periods of helioseismic data. Also noteworthy is the fact that these topological changes indicate a rich interaction between magnetic fields and plasma flows, which challenges the ubiquitous kinematic approach used in the vast majority of mean field dynamo simulations.

  5. Evaluation of Stratospheric Transport in New 3D Models Using the Global Modeling Initiative Grading Criteria

    NASA Technical Reports Server (NTRS)

    Strahan, Susan E.; Douglass, Anne R.; Einaudi, Franco (Technical Monitor)

    2001-01-01

    The Global Modeling Initiative (GMI) Team developed objective criteria for model evaluation in order to identify the best representation of the stratosphere. This work created a method to quantitatively and objectively discriminate between different models. In the original GMI study, 3 different meteorological data sets were used to run an offline chemistry and transport model (CTM). Observationally-based grading criteria were derived and applied to these simulations and various aspects of stratospheric transport were evaluated; grades were assigned. Here we report on the application of the GMI evaluation criteria to CTM simulations integrated with a new assimilated wind data set and a new general circulation model (GCM) wind data set. The Finite Volume Community Climate Model (FV-CCM) is a new GCM developed at Goddard which uses the NCAR CCM physics and the Lin and Rood advection scheme. The FV-Data Assimilation System (FV-DAS) is a new data assimilation system which uses the FV-CCM as its core model. One year CTM simulations of 2.5 degrees longitude by 2 degrees latitude resolution were run for each wind data set. We present the evaluation of temperature and annual transport cycles in the lower and middle stratosphere in the two new CTM simulations. We include an evaluation of high latitude transport which was not part of the original GMI criteria. Grades for the new simulations will be compared with those assigned during the original GMT evaluations and areas of improvement will be identified.

  6. Effects of kinetic processes in shaping Io's global plasma environment: A 3D hybrid model

    NASA Astrophysics Data System (ADS)

    Lipatov, Alexander S.; Combi, Michael R.

    2006-02-01

    The global dynamics of the ionized and neutral gases in the environment of Io plays an important role in the interaction of Jupiter's corotating magnetospheric plasma with Io. Stationary simulations of this problem have already been done using the magnetohydrodynamics (MHD) and the electrodynamics approaches. One of the major results of recent simplified two-fluid model simulations [Saur, J., Neubauer, F.M., Strobel, D.F., Summers, M.E., 2002. J. Geophys. Res. 107 (SMP5), 1-18] was the production of the structure of the double-peak in the magnetic field signature of the I0 flyby. These could not be explained before by standard MHD models. In this paper, we present a hybrid simulation for Io with kinetic ions and fluid electrons. This method employs a fluid description for electrons and neutrals, whereas for ions a particle approach is used. We also take into account charge-exchange and photoionization processes and solve self-consistently for electric and magnetic fields. Our model may provide a much more accurate description for the ion dynamics than previous approaches and allows us to account for the realistic anisotropic ion velocity distribution that cannot be done in fluid simulations with isotropic temperatures. The first results of such a simulation of the dynamics of ions in Io's environment are discussed in this paper. Comparison with the Galileo I0 flyby results shows that this approach provides an accurate physical basis for the interaction and can therefore naturally reproduce all the observed salient features.

  7. Effects of Kinetic Processes in Shaping Io's Global Plasma Environment: A 3D Hybrid Model

    NASA Technical Reports Server (NTRS)

    Lipatov, Alexander S.; Combi, Michael R.

    2006-01-01

    The global dynamics of the ionized and neutral gases in the environment of Io plays an important role in the interaction of Jupiter s corotating magnetospheric plasma with Io. Stationary simulations of this problem have already been done using the magnetohydrodynamics (MHD) and the electrodynamics approaches. One of the major results of recent simplified two-fluid model simulations [Saur, J., Neubauer, F.M., Strobel, D.F., Summers, M.E., 2002. J. Geophys. Res. 107 (SMP5), 1-18] was the production of the structure of the double-peak in the magnetic field signature of the Io flyby. These could not be explained before by standard MHD models. In this paper, we present a hybrid simulation for Io with kinetic ions and fluid electrons. This method employs a fluid description for electrons and neutrals, whereas for ions a particle approach is used. We also take into account charge-exchange and photoionization processes and solve self-consistently for electric and magnetic fields. Our model may provide a much more accurate description for the ion dynamics than previous approaches and allows us to account for the realistic anisotropic ion velocity distribution that cannot be done in fluid simulations with isotropic temperatures. The first results of such a simulation of the dynamics of ions in Io s environment are discussed in this paper. Comparison with the Galileo IO flyby results shows that this approach provides an accurate physical basis for the interaction and can therefore naturally reproduce all the observed salient features.

  8. Global Warming and the Arctic in 3D: A Virtual Globe for Outreach

    NASA Astrophysics Data System (ADS)

    Manley, W. F.

    2006-12-01

    Virtual Globes provide a new way to capture and inform the public's interest in environmental change. As an example, a recent Google Earth presentation conveyed 'key findings' from the Arctic Climate Impact Assessment (ACIA, 2004) to middle school students during the 2006 INSTAAR/NSIDC Open House at the University of Colorado. The 20-minute demonstration to 180 eighth graders began with an introduction and a view of the Arctic from space, zooming into the North American Arctic, then to a placemark for the first key finding, 'Arctic climate is now warming rapidly and much larger changes are projected'. An embedded link then opened a custom web page, with brief explanatory text, along with an ACIA graphic illustrating the rise in Arctic temperature, global CO2 concentrations, and carbon emissions for the last millennium. The demo continued with an interactive tour of other key findings (Reduced Sea Ice, Changes for Animals, Melting Glaciers, Coastal Erosion, Changes in Vegetation, Melting Permafrost, and others). Each placemark was located somewhat arbitrarily (which may be a concern for some audiences), but the points represented the messages in a geographic sense and enabled a smooth visual tour of the northern latitudes. Each placemark was linked to custom web pages with photos and concise take-home messages. The demo ended with navigation to Colorado, then Boulder, then the middle school that the students attended, all the while speaking to implications as they live their lives locally. The demo piqued the students' curiosity, and in this way better conveyed important messages about the Arctic and climate change. The use of geospatial visualizations for outreach and education appears to be in its infancy, with much potential.

  9. Materials ``alchemy'': Shape-preserving chemical transformation of micro-to-macroscopic 3-D structures

    NASA Astrophysics Data System (ADS)

    Sandhage, Kenneth H.

    2010-06-01

    The scalable fabrication of nano-structured materials with complex morphologies and tailorable chemistries remains a significant challenge. One strategy for such synthesis consists of the generation of a solid structure with a desired morphology (a “preform”), followed by reactive conversion of the preform into a new chemistry. Several gas/solid and liquid/solid reaction processes that are capable of such chemical conversion into new micro-to-nano-structured materials, while preserving the macroscopic-to-microscopic preform morphologies, are described in this overview. Such shape-preserving chemical transformation of one material into another could be considered a modern type of materials “alchemy.”

  10. Extracting chemical information from plane wave calculations by a 3D 'fuzzy atoms' analysis

    NASA Astrophysics Data System (ADS)

    Bakó, I.; Stirling, A.; Seitsonen, A. P.; Mayer, I.

    2013-03-01

    Bond order and valence indices have been calculated by the method of the three-dimensional 'fuzzy atoms' analysis, using the numerical molecular orbitals obtained from plane wave DFT calculations, i.e., without introducing any external atom-centered functions. Weight functions of both Hirshfeld and Becke types have been applied. The results are rather close to the similar 'fuzzy atoms' ones obtained by using atom-centered basis sets and agree well with the chemical expectations, stressing the power of the genuine chemical concepts.

  11. Facile and rapid generation of 3D chemical gradients within hydrogels for high-throughput drug screening applications.

    PubMed

    Ahadian, Samad; Ramón-Azcón, Javier; Estili, Mehdi; Obregón, Raquel; Shiku, Hitoshi; Matsue, Tomokazu

    2014-09-15

    We propose a novel application of dielectrophoresis (DEP) to make three-dimensional (3D) methacrylated gelatin (GelMA) hydrogels with gradients of micro- and nanoparticles. DEP forces were able to manipulate micro- and nanoparticles of different sizes and materials (i.e., C2C12 myoblasts, polystyrene beads, gold microparticles, and carbon nanotubes) within GelMA hydrogels in a rapid and facile way and create 3D gradients of these particles in a microchamber. Immobilization of drugs, such as fluorescein isothiocyanate-dextran (FITC-dextran) and 6-hydroxydopamine (6-OHDA), on gold microparticles allowed us to investigate the high-throughput release of these drugs from GelMA-gold microparticle gradient systems. The latter gradient constructs were incubated with C2C12 myoblasts for 24h to examine the cell viability through the release of 6-OHDA. The drug was released from the microparticles in a gradient manner, inducing a cell viability gradient. This novel approach to create 3D chemical gradients within hydrogels is scalable to any arbitrary length scale. It is useful for making anisotropic biomimetic materials and high-throughput platforms to investigate cell-microenvironment interactions in a rapid, simple, cost-effective, and reproducible manner. PMID:24727602

  12. The Galactic chemical evolution of oxygen inferred from 3D non-LTE spectral-line-formation calculations

    NASA Astrophysics Data System (ADS)

    Amarsi, A. M.; Asplund, M.; Collet, R.; Leenaarts, J.

    2015-11-01

    We revisit the Galactic chemical evolution of oxygen, addressing the systematic errors inherent in classical determinations of the oxygen abundance that arise from the use of one-dimensional (1D) hydrostatic model atmospheres and from the assumption of local thermodynamic equilibrium (LTE). We perform detailed 3D non-LTE radiative-transfer calculations for atomic oxygen lines across a grid of 3D hydrodynamic STAGGER model atmospheres for dwarfs and subgiants. We apply our grid of predicted line strengths of the [O I] 630 nm and O I 777 nm lines using accurate stellar parameters from the literature. We infer a steep decay in [O/Fe] for [Fe/H] ≳ -1.0, a plateau [O/Fe] ≈ 0.5 down to [Fe/H] ≈ -2.5, and an increasing trend for [Fe/H] ≲ -2.5. Our 3D non-LTE calculations yield overall concordant results from the two oxygen abundance diagnostics.

  13. A comparison study of atlas-based 3D cardiac MRI segmentation: global versus global and local transformations

    NASA Astrophysics Data System (ADS)

    Daryanani, Aditya; Dangi, Shusil; Ben-Zikri, Yehuda Kfir; Linte, Cristian A.

    2016-03-01

    Magnetic Resonance Imaging (MRI) is a standard-of-care imaging modality for cardiac function assessment and guidance of cardiac interventions thanks to its high image quality and lack of exposure to ionizing radiation. Cardiac health parameters such as left ventricular volume, ejection fraction, myocardial mass, thickness, and strain can be assessed by segmenting the heart from cardiac MRI images. Furthermore, the segmented pre-operative anatomical heart models can be used to precisely identify regions of interest to be treated during minimally invasive therapy. Hence, the use of accurate and computationally efficient segmentation techniques is critical, especially for intra-procedural guidance applications that rely on the peri-operative segmentation of subject-specific datasets without delaying the procedure workflow. Atlas-based segmentation incorporates prior knowledge of the anatomy of interest from expertly annotated image datasets. Typically, the ground truth atlas label is propagated to a test image using a combination of global and local registration. The high computational cost of non-rigid registration motivated us to obtain an initial segmentation using global transformations based on an atlas of the left ventricle from a population of patient MRI images and refine it using well developed technique based on graph cuts. Here we quantitatively compare the segmentations obtained from the global and global plus local atlases and refined using graph cut-based techniques with the expert segmentations according to several similarity metrics, including Dice correlation coefficient, Jaccard coefficient, Hausdorff distance, and Mean absolute distance error.

  14. Spontaneous development of arcuate single-sided subduction in global 3-D mantle convection models with a free surface

    NASA Astrophysics Data System (ADS)

    Crameri, Fabio; Tackley, Paul J.

    2014-07-01

    We present temporally evolving 3-D global mantle convection models with single-sided subduction and a free surface in both 3-D Cartesian and fully spherical geometry. Special focus is given to the spontaneous development of three-dimensional structures at the surface and in the upper mantle. We find that an arcuate shape is the natural form for trenches and slabs. Cartesian models are used first to study the dynamic evolution of subduction zones, spreading ridges, and interconnected transform features. These experiments highlight the strong variation of spontaneously developing, arcuate slab curvature and subduction polarity along the trench strike. The spontaneous development of spreading ridges leads to lateral offsets between separated segments that are characterized by normal transform motion. Spherical models then allow insights into the evolution of plate tectonics on a sphere. Investigated are the spontaneous evolution of slab geometry, trench motion, and subduction-induced mantle flow. Two new dynamical features are discovered: "back-slab spiral flow" and "slab tunneling." 2014. American Geophysical Union. All Rights Reserved.

  15. Global well-posedness and zero diffusion limit of classical solutions to 3D conservation laws arising in chemotaxis

    NASA Astrophysics Data System (ADS)

    Peng, Hongyun; Wen, Huanyao; Zhu, Changjiang

    2014-12-01

    In this paper, we study the existence of global classical solutions and the vanishing diffusion limit of a 3D conservation laws derived from the well-known Keller-Segel model. First, we establish the global well-posedness of classical solutions to the Cauchy problem for the model with smooth initial data which is of small L 2 norm, together with some a priori estimates uniform for t and . Then, we investigate the zero diffusion limit and get the global well-posedness of classical solutions to the Cauchy problem for the non-diffusive model. Finally, we derive the convergence rate of the model toward the non-diffusive model. It is shown that the convergence rate in L ∞ norm is of the order . It should be noted that the initial data are small in L 2-norm but can be of large oscillations with constant state at far field. As a byproduct, we improve the corresponding result on the well-posedness of the non-diffusive model which requires small oscillations.

  16. MHD-Epic: Embedded Particle-in-Cell Simulations of Reconnection in Global 3D Extended MHD Simulations

    NASA Astrophysics Data System (ADS)

    Daldorff, L. K. S.; Toth, G.; Borovikov, D.; Gombosi, T. I.; Lapenta, G.

    2014-12-01

    With the new modeling capability in the Space Weather Modeling Framework (SWMF) of embedding an implicit Particle-in-Cell (PIC) model iPIC3D into the BATS-R-US magnetohydrodynamics model (Daldorff et al. 2014, JCP, 268, 236) we are ready to locally handle the full physics of the reconnection and its implications on the full system where globally, away from the reconnection region, a magnetohydrodynamic description is satisfactory. As magnetic reconnection is one of the main drivers in magnetospheric and heliospheric plasma dynamics, the self-consistent description of the electron dynamics in the coupled MHD-EPIC model is well suited for investigating the nature of these systems. We will compare the new embedded MHD-EPIC model with pure MHD and Hall MHD simulations of the Earth's magnetosphere.

  17. Massively parallel computation of 3D flow and reactions in chemical vapor deposition reactors

    SciTech Connect

    Salinger, A.G.; Shadid, J.N.; Hutchinson, S.A.; Hennigan, G.L.; Devine, K.D.; Moffat, H.K.

    1997-12-01

    Computer modeling of Chemical Vapor Deposition (CVD) reactors can greatly aid in the understanding, design, and optimization of these complex systems. Modeling is particularly attractive in these systems since the costs of experimentally evaluating many design alternatives can be prohibitively expensive, time consuming, and even dangerous, when working with toxic chemicals like Arsine (AsH{sub 3}): until now, predictive modeling has not been possible for most systems since the behavior is three-dimensional and governed by complex reaction mechanisms. In addition, CVD reactors often exhibit large thermal gradients, large changes in physical properties over regions of the domain, and significant thermal diffusion for gas mixtures with widely varying molecular weights. As a result, significant simplifications in the models have been made which erode the accuracy of the models` predictions. In this paper, the authors will demonstrate how the vast computational resources of massively parallel computers can be exploited to make possible the analysis of models that include coupled fluid flow and detailed chemistry in three-dimensional domains. For the most part, models have either simplified the reaction mechanisms and concentrated on the fluid flow, or have simplified the fluid flow and concentrated on rigorous reactions. An important CVD research thrust has been in detailed modeling of fluid flow and heat transfer in the reactor vessel, treating transport and reaction of chemical species either very simply or as a totally decoupled problem. Using the analogy between heat transfer and mass transfer, and the fact that deposition is often diffusion limited, much can be learned from these calculations; however, the effects of thermal diffusion, the change in physical properties with composition, and the incorporation of surface reaction mechanisms are not included in this model, nor can transitions to three-dimensional flows be detected.

  18. Development of a 3-D upwind PNS code for chemically reacting hypersonic flowfields

    NASA Technical Reports Server (NTRS)

    Tannehill, J. C.; Wadawadigi, G.

    1992-01-01

    Two new parabolized Navier-Stokes (PNS) codes were developed to compute the three-dimensional, viscous, chemically reacting flow of air around hypersonic vehicles such as the National Aero-Space Plane (NASP). The first code (TONIC) solves the gas dynamic and species conservation equations in a fully coupled manner using an implicit, approximately-factored, central-difference algorithm. This code was upgraded to include shock fitting and the capability of computing the flow around complex body shapes. The revised TONIC code was validated by computing the chemically-reacting (M(sub infinity) = 25.3) flow around a 10 deg half-angle cone at various angles of attack and the Ames All-Body model at 0 deg angle of attack. The results of these calculations were in good agreement with the results from the UPS code. One of the major drawbacks of the TONIC code is that the central-differencing of fluxes across interior flowfield discontinuities tends to introduce errors into the solution in the form of local flow property oscillations. The second code (UPS), originally developed for a perfect gas, has been extended to permit either perfect gas, equilibrium air, or nonequilibrium air computations. The code solves the PNS equations using a finite-volume, upwind TVD method based on Roe's approximate Riemann solver that was modified to account for real gas effects. The dissipation term associated with this algorithm is sufficiently adaptive to flow conditions that, even when attempting to capture very strong shock waves, no additional smoothing is required. For nonequilibrium calculations, the code solves the fluid dynamic and species continuity equations in a loosely-coupled manner. This code was used to calculate the hypersonic, laminar flow of chemically reacting air over cones at various angles of attack. In addition, the flow around the McDonnel Douglas generic option blended-wing-body was computed and comparisons were made between the perfect gas, equilibrium air, and the

  19. C2SM: a mobile system for detecting and 3D mapping of chemical, radiological, and nuclear contamination

    NASA Astrophysics Data System (ADS)

    Jasiobedzki, Piotr; Ng, Ho-Kong; Bondy, Michel; McDiarmid, C. H.

    2009-05-01

    CBRN Crime Scene Modeler (C2SM) is a prototype mobile CBRN mapping system for First Responders in events where Chemical, Biological, Radiological and Nuclear agents where used. The prototype operates on board a small robotic platform, increases situational awareness of the robot operator by providing geo-located images and data, and current robot location. The sensor suite includes stereo and high resolution cameras, a long wave infra red (thermal) camera and gamma and chemical detectors. The system collects and sends geo-located data to a remote command post in near real-time and automatically creates 3D photorealistic model augmented with CBRN measurements. Two prototypes have been successfully tested in field trials and a fully ruggedised commercial version is expected in 2010.

  20. 3D chemical imaging in the laboratory by hyperspectral X-ray computed tomography

    PubMed Central

    Egan, C. K.; Jacques, S. D. M.; Wilson, M. D.; Veale, M. C.; Seller, P.; Beale, A. M.; Pattrick, R. A. D.; Withers, P. J.; Cernik, R. J.

    2015-01-01

    We report the development of laboratory based hyperspectral X-ray computed tomography which allows the internal elemental chemistry of an object to be reconstructed and visualised in three dimensions. The method employs a spectroscopic X-ray imaging detector with sufficient energy resolution to distinguish individual elemental absorption edges. Elemental distributions can then be made by K-edge subtraction, or alternatively by voxel-wise spectral fitting to give relative atomic concentrations. We demonstrate its application to two material systems: studying the distribution of catalyst material on porous substrates for industrial scale chemical processing; and mapping of minerals and inclusion phases inside a mineralised ore sample. The method makes use of a standard laboratory X-ray source with measurement times similar to that required for conventional computed tomography. PMID:26514938

  1. 3D chemical imaging in the laboratory by hyperspectral X-ray computed tomography.

    PubMed

    Egan, C K; Jacques, S D M; Wilson, M D; Veale, M C; Seller, P; Beale, A M; Pattrick, R A D; Withers, P J; Cernik, R J

    2015-01-01

    We report the development of laboratory based hyperspectral X-ray computed tomography which allows the internal elemental chemistry of an object to be reconstructed and visualised in three dimensions. The method employs a spectroscopic X-ray imaging detector with sufficient energy resolution to distinguish individual elemental absorption edges. Elemental distributions can then be made by K-edge subtraction, or alternatively by voxel-wise spectral fitting to give relative atomic concentrations. We demonstrate its application to two material systems: studying the distribution of catalyst material on porous substrates for industrial scale chemical processing; and mapping of minerals and inclusion phases inside a mineralised ore sample. The method makes use of a standard laboratory X-ray source with measurement times similar to that required for conventional computed tomography. PMID:26514938

  2. Chemical synthesis, 3D structure, and ASIC binding site of the toxin mambalgin-2.

    PubMed

    Schroeder, Christina I; Rash, Lachlan D; Vila-Farrés, Xavier; Rosengren, K Johan; Mobli, Mehdi; King, Glenn F; Alewood, Paul F; Craik, David J; Durek, Thomas

    2014-01-20

    Mambalgins are a novel class of snake venom components that exert potent analgesic effects mediated through the inhibition of acid-sensing ion channels (ASICs). The 57-residue polypeptide mambalgin-2 (Ma-2) was synthesized by using a combination of solid-phase peptide synthesis and native chemical ligation. The structure of the synthetic toxin, determined using homonuclear NMR, revealed an unusual three-finger toxin fold reminiscent of functionally unrelated snake toxins. Electrophysiological analysis of Ma-2 on wild-type and mutant ASIC1a receptors allowed us to identify α-helix 5, which borders on the functionally critical acidic pocket of the channel, as a major part of the Ma-2 binding site. This region is also crucial for the interaction of ASIC1a with the spider toxin PcTx1, thus suggesting that the binding sites for these toxins substantially overlap. This work lays the foundation for structure-activity relationship (SAR) studies and further development of this promising analgesic peptide. PMID:24323786

  3. Global well-posedness to the 3-D incompressible inhomogeneous Navier-Stokes equations with a class of large velocity

    NASA Astrophysics Data System (ADS)

    Zhai, Cuili; Zhang, Ting

    2015-09-01

    In this article, we consider the global well-posedness to the 3-D incompressible inhomogeneous Navier-Stokes equations with a class of large velocity. More precisely, assuming a 0 ∈ B˙ q , 1 /3 q ( R 3 ) and u 0 = ( u0 h , u0 3 ) ∈ B˙ p , 1 - 1 + /3 p ( R 3 ) for p, q ∈ (1, 6) with sup ( /1 p , /1 q ) ≤ /1 3 + inf ( /1 p , /1 q ) , we prove that if C a↑0↑ B˙q1/3 q α (↑u0 3↑ B˙ p , 1 - 1 + /3 p/μ + 1 ) ≤ 1 , /C μ (↑u0 h↑ B˙ p , 1 - 1 + /3 p + ↑u03↑ B˙ p , 1 - 1 + /3 p 1 - α ↑u0h↑ B˙ p , 1 - 1 + /3 p α) ≤ 1 , then the system has a unique global solution a ∈ C ˜ ( [ 0 , ∞ ) ; B˙ q , 1 /3 q ( R 3 ) ) , u ∈ C ˜ ( [ 0 , ∞ ) ; B˙ p , 1 - 1 + /3 p ( R 3 ) ) ∩ L 1 ( R + ; B˙ p , 1 1 + /3 p ( R 3 ) ) . It improves the recent result of M. Paicu and P. Zhang [J. Funct. Anal. 262, 3556-3584 (2012)], where the exponent form of the initial smallness condition is replaced by a polynomial form.

  4. Global 3-D FDTD Maxwell's-Equations Modeling of Ionospheric Disturbances Associated with Earthquakes Using an Optimized Geodesic Grid

    NASA Astrophysics Data System (ADS)

    Simpson, J. J.; Taflove, A.

    2005-12-01

    We report a finite-difference time-domain (FDTD) computational solution of Maxwell's equations [1] that models the possibility of detecting and characterizing ionospheric disturbances above seismic regions. Specifically, we study anomalies in Schumann resonance spectra in the extremely low frequency (ELF) range below 30 Hz as observed in Japan caused by a hypothetical cylindrical ionospheric disturbance above Taiwan. We consider excitation of the global Earth-ionosphere waveguide by lightning in three major thunderstorm regions of the world: Southeast Asia, South America (Amazon region), and Africa. Furthermore, we investigate varying geometries and characteristics of the ionospheric disturbance above Taiwan. The FDTD technique used in this study enables a direct, full-vector, three-dimensional (3-D) time-domain Maxwell's equations calculation of round-the-world ELF propagation accounting for arbitrary horizontal as well as vertical geometrical and electrical inhomogeneities and anisotropies of the excitation, ionosphere, lithosphere, and oceans. Our entire-Earth model grids the annular lithosphere-atmosphere volume within 100 km of sea level, and contains over 6,500,000 grid-points (63 km laterally between adjacent grid points, 5 km radial resolution). We use our recently developed spherical geodesic gridding technique having a spatial discretization best described as resembling the surface of a soccer ball [2]. The grid is comprised entirely of hexagonal cells except for a small fixed number of pentagonal cells needed for completion. Grid-cell areas and locations are optimized to yield a smoothly varying area difference between adjacent cells, thereby maximizing numerical convergence. We compare our calculated results with measured data prior to the Chi-Chi earthquake in Taiwan as reported by Hayakawa et. al. [3]. Acknowledgement This work was suggested by Dr. Masashi Hayakawa, University of Electro-Communications, Chofugaoka, Chofu Tokyo. References [1] A

  5. Structure of the antiviral stavudine using quantum chemical methods: Complete conformational space analysis, 3D potential energy surfaces and solid state simulations

    NASA Astrophysics Data System (ADS)

    Alcolea Palafox, M.; Iza, N.

    2012-11-01

    The molecular structure and energy of the anti-HIV, 2',3'-didehydro-3'-deoxythymidine (D4T, stavudine or Zerit) nucleoside analogue was determined by using MP2, B3LYP and B971 quantum chemical methods. The global minimum was determined through 3D potential energy surfaces (PES). These surfaces were built by rotation of the exocyclic χ, γ and β torsional angles, in steps of 20°, and full optimization of the remaining parameters. As consequence 5832 geometries were final optimized. The search located 25 local minimum, 4 of which are by MP2 within a 2 kcal/mol electronic energy range of the global minimum. The whole conformational parameters as well as P, νmax were analyzed in all the stable conformers. The global minimum by MP2 corresponds to the calculated values of the exocyclic torsional angles: χ = -103.6°, β = 63.8° and γ = 60.6°. The results obtained are in accordance to those found in thymidine and in related anti-HIV nucleoside analogues. The effect of hydration on the two most stable conformers is analyzed by continuous and discrete models up to 20 water molecules. The solid state was also simulated. The dimer forms found in the crystal unit cell were accurately determined and they are in accordance to the X-ray data.

  6. Modelling of Criegee Intermediates using the 3-D global model, STOCHEM-CRI and investigating their global impacts on Secondary Organic Aerosol formation

    NASA Astrophysics Data System (ADS)

    Khan, M. Anwar H.; Cooke, Michael; Utembe, Steve; Archibald, Alexander; Derwent, Richard; Jenkin, Mike; Lyons, Kyle; Kent, Adam; Percival, Carl; Shallcross, Dudley E.

    2016-04-01

    Gas phase reactions of ozone with unsaturated compounds form stabilized Criegee intermediates (sCI) which play an important role in controlling the budgets of many tropospheric species including OH, organic acids and secondary organic aerosols (SOA). Recently sCI has been proposed to play a significant role in atmospheric sulfate and nitrate chemistry by forming sulfuric acid (promoter of aerosol formation) and nitrate radical (a powerful oxidizing agent). sCI can also undergo association reactions with water, alcohols, and carboxylic acids to form hydroperoxides and with aldehydes and ketones to form secondary ozonides. The products from these reactions are low volatility compounds which can contribute to the formation of SOA. The importance of plant emitted alkenes (isoprene, monoterpenes, sesquiterpenes) in the production of SOA through sCI formation have already been investigated in laboratory studies. However, the SOA formation from these reactions are absent in current global models. Thus, the formation of SOA has been incorporated in the global model, STOCHEM-CRI, a 3-D global chemistry transport model and the role of CI chemistry in controlling atmospheric composition and climate, and the influence of water vapor has been discussed in the study.

  7. Issues involved in the quantitative 3D imaging of proton doses using optical CT and chemical dosimeters

    NASA Astrophysics Data System (ADS)

    Doran, Simon; Gorjiara, Tina; Kacperek, Andrzej; Adamovics, John; Kuncic, Zdenka; Baldock, Clive

    2015-01-01

    Dosimetry of proton beams using 3D imaging of chemical dosimeters is complicated by a variation with proton linear energy transfer (LET) of the dose-response (the so-called ‘quenching effect’). Simple theoretical arguments lead to the conclusion that the total absorbed dose from multiple irradiations with different LETs cannot be uniquely determined from post-irradiation imaging measurements on the dosimeter. Thus, a direct inversion of the imaging data is not possible and the proposition is made to use a forward model based on appropriate output from a planning system to predict the 3D response of the dosimeter. In addition to the quenching effect, it is well known that chemical dosimeters have a non-linear response at high doses. To the best of our knowledge it has not yet been determined how this phenomenon is affected by LET. The implications for dosimetry of a number of potential scenarios are examined. Dosimeter response as a function of depth (and hence LET) was measured for four samples of the radiochromic plastic PRESAGE®, using an optical computed tomography readout and entrance doses of 2.0 Gy, 4.0 Gy, 7.8 Gy and 14.7 Gy, respectively. The dosimeter response was separated into two components, a single-exponential low-LET response and a LET-dependent quenching. For the particular formulation of PRESAGE® used, deviations from linearity of the dosimeter response became significant for doses above approximately 16 Gy. In a second experiment, three samples were each irradiated with two separate beams of 4 Gy in various different configurations. On the basis of the previous characterizations, two different models were tested for the calculation of the combined quenching effect from two contributions with different LETs. It was concluded that a linear superposition model with separate calculation of the quenching for each irradiation did not match the measured result where two beams overlapped. A second model, which used the concept of an

  8. Issues involved in the quantitative 3D imaging of proton doses using optical CT and chemical dosimeters.

    PubMed

    Doran, Simon; Gorjiara, Tina; Kacperek, Andrzej; Adamovics, John; Kuncic, Zdenka; Baldock, Clive

    2015-01-21

    Dosimetry of proton beams using 3D imaging of chemical dosimeters is complicated by a variation with proton linear energy transfer (LET) of the dose-response (the so-called 'quenching effect'). Simple theoretical arguments lead to the conclusion that the total absorbed dose from multiple irradiations with different LETs cannot be uniquely determined from post-irradiation imaging measurements on the dosimeter. Thus, a direct inversion of the imaging data is not possible and the proposition is made to use a forward model based on appropriate output from a planning system to predict the 3D response of the dosimeter. In addition to the quenching effect, it is well known that chemical dosimeters have a non-linear response at high doses. To the best of our knowledge it has not yet been determined how this phenomenon is affected by LET. The implications for dosimetry of a number of potential scenarios are examined.Dosimeter response as a function of depth (and hence LET) was measured for four samples of the radiochromic plastic PRESAGE(®), using an optical computed tomography readout and entrance doses of 2.0 Gy, 4.0 Gy, 7.8 Gy and 14.7 Gy, respectively. The dosimeter response was separated into two components, a single-exponential low-LET response and a LET-dependent quenching. For the particular formulation of PRESAGE(®) used, deviations from linearity of the dosimeter response became significant for doses above approximately 16 Gy. In a second experiment, three samples were each irradiated with two separate beams of 4 Gy in various different configurations. On the basis of the previous characterizations, two different models were tested for the calculation of the combined quenching effect from two contributions with different LETs. It was concluded that a linear superposition model with separate calculation of the quenching for each irradiation did not match the measured result where two beams overlapped. A second model, which used the concept of an

  9. Exploring the diversity of climates on terrestrial exoplanets using a generic 3D Global Climate Model (Invited)

    NASA Astrophysics Data System (ADS)

    Forget, F.; Leconte, J.; Wordsworth, R.; Millour, E.; Charnay, B.

    2013-12-01

    What kind of environment may exist on terrestrial planets around other stars? In spite of the lack of direct observations, it may not be premature to speculate on the possible exoplanetary climates, for instance to optimize future telescopic observations, or to assess the probability of habitable worlds in the galaxy. A first major question is to imagine the possible atmospheric composition surface volatile inventory. This depends on complex processes which are difficult to model: origins of volatile, atmospheric escape, geochemistry, long-term photochemistry. However, assuming that the atmosphere is known, the possible climates on a given planet around a given star can be explored using 3D Global Climate Models (GCMs) analogous to the ones developed to simulate the Earth climate as well as the other telluric atmospheres in the solar system. Our experience with the Earth, Mars, Titan and Venus suggests that relatively complete and realistic climate simulators can be developed by combining a few components like a dynamical core, a radiative transfer solver, a parametrisation of subgrid- scale turbulence and convection, a thermal ground model, and a volatile phase change code. Solar system GCMs successes and failure also teach us that when modeling climate systems which are poorly observed, it is necessary to carefully explore the sensitivity of the modeled system to key parameters, in order to 'bracket' the reality We will present several examples of studies recently performed using a 'generic' Global Climate Model that we have developed in the past few years, in particular to better understand the processes which controls the stability of liquid water on a planetary surface and its habitability. Climate models confirm that planetary climates primarily depends on 1) The atmospheric composition and mass and the surface volatile inventory 2) The incident stellar flux 3) The tidal evolution of the planetary spin, which can notably lock a planet with a permanent night

  10. A Global 3D P-Velocity Model of the Earth's Crust and Mantle for Improved Event Location

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

    further refinement takes place around adjusted nodes to form a new model, and the process is repeated until no more improvement can be obtained. We thus produce a smooth, multi-resolution model with node density appropriate to both ray coverage and the velocity gradients required by the data. This scheme is computationally expensive, so we use a Java-based distributed computing framework developed by Sandia National Laboratories (SNL), providing us with 300+ processors having an efficiency of better than 90% for the calculations. We evaluate our model both in terms of travel time residual variance reduction and in location improvement for GT events. For the latter, we use a new multi-threaded version of the SNL-developed LocOO code modified to use 3D velocity models.

  11. Global 3-D model of oceanic mercury coupled to carbon biogeochemistry and particle dynamics: application to the transport and fate or riverine mercury

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Jacob, D. J.; Dutkiewicz, S.; Amos, H. M.; Long, M. S.; Sunderland, E. M.

    2014-12-01

    Rivers are estimated to deliver 27 Mmol a-1 of mercury (Hg) to ocean margins, which is comparable to the global atmospheric deposition flux of Hg to the ocean. Previous studies presumed that most of this riverine Hg is sequestered by settling to the coastal regions. However, there has been little investigation of the mechanism and efficiency with which this sequestration takes place, and the implications for riverine influence in different ocean regions. Here we develop a global 3-D chemical transport model for Hg in the ocean (MITgcm-Hg) with ecology (DARWIN model). We track offshore export of the discharged Hg from heterogeneous river systems over different ocean regions, and how it is influenced by the interaction of Hg in a variety of geochemical forms with carbon and suspended particles. We constrain our model assumptions with available offshore observations that bear strong riverine signals. Modeling results suggest that some of the riverine Hg is highly refractory, sorbs strongly to particles and does not follow equilibrium partitioning with the dissolved phase. Simulated global Hg evasion from riverine sources is 50 times larger without this refractory particulate pool, which results in a total evasion flux two times larger than our current best estimate. Based on a typology system of global rivers, we calculate that 10% to 60% of the particulate Hg from different rivers settles in ocean margin sediments because of subgrid sedimentation processes. The remaining 7.5 Mmol a-1 (28% of total river discharge) is available for offshore transport, where it undergoes further sedimentation to the shelf (5.3 Mmol a-1) as well as evasion to the atmosphere (0.44 Mmol a-1). Only 1.7 Mmol a-1 (6.4% of the global riverine Hg) reaches the open ocean, although that fraction varies from 2.6% in East Asia because of the blockage of Korean Peninsula to 25% in east North America facilitated by the Gulf Stream. We find large riverine influences over coastal oceans off East Asia

  12. Three-Dimensional Mapping of Soil Chemical Characteristics at Micrometric Scale by Combining 2D SEM-EDX Data and 3D X-Ray CT Images

    PubMed Central

    Hapca, Simona; Baveye, Philippe C.; Wilson, Clare; Lark, Richard Murray; Otten, Wilfred

    2015-01-01

    There is currently a significant need to improve our understanding of the factors that control a number of critical soil processes by integrating physical, chemical and biological measurements on soils at microscopic scales to help produce 3D maps of the related properties. Because of technological limitations, most chemical and biological measurements can be carried out only on exposed soil surfaces or 2-dimensional cuts through soil samples. Methods need to be developed to produce 3D maps of soil properties based on spatial sequences of 2D maps. In this general context, the objective of the research described here was to develop a method to generate 3D maps of soil chemical properties at the microscale by combining 2D SEM-EDX data with 3D X-ray computed tomography images. A statistical approach using the regression tree method and ordinary kriging applied to the residuals was developed and applied to predict the 3D spatial distribution of carbon, silicon, iron, and oxygen at the microscale. The spatial correlation between the X-ray grayscale intensities and the chemical maps made it possible to use a regression-tree model as an initial step to predict the 3D chemical composition. For chemical elements, e.g., iron, that are sparsely distributed in a soil sample, the regression-tree model provides a good prediction, explaining as much as 90% of the variability in some of the data. However, for chemical elements that are more homogenously distributed, such as carbon, silicon, or oxygen, the additional kriging of the regression tree residuals improved significantly the prediction with an increase in the R2 value from 0.221 to 0.324 for carbon, 0.312 to 0.423 for silicon, and 0.218 to 0.374 for oxygen, respectively. The present research develops for the first time an integrated experimental and theoretical framework, which combines geostatistical methods with imaging techniques to unveil the 3-D chemical structure of soil at very fine scales. The methodology presented

  13. Computer simulated screening of dentin bonding primer monomers through analysis of their chemical functions and their spatial 3D alignment.

    PubMed

    Vaidyanathan, J; Vaidyanathan, T K; Ravichandran, S

    2009-02-01

    Binding interactions between dentin bonding primer monomers and dentinal collagen were studied by an analysis of their chemical functions and their spatial 3D alignment. A trial set of 12 monomers used as primers in dentin adhesives was characterized to assess them for binding to a complementary target. HipHop utility in the Catalyst software from Accelrys was used for the study. Ten hypotheses were generated by HipHop procedures involving (a) conformational generation using a poling technique to promote conformational variation, (b) extraction of functions to remodel ligands as function-based structures, and (c) identification of common patterns of functional alignment displayed by low energy conformations. The hypotheses, designated as pharmacaphores, were also scored and ranked. Analysis of pharmacaphore models through mapping of ligands revealed important differences between ligands. Top-ranked poses from direct docking simulations using type 1 collagen target were mapped in a rigid manner to the highest ranked pharmacophore model. The visual match observed in mapping and associated fit values suggest a strong correspondence between direct and indirect docking simulations. The results elegantly demonstrate that an indirect approach used to identify pharmacaphore models from adhesive ligands without a target may be a simple and viable approach to assess their intermolecular interactions with an intended target. Inexpensive indirect/direct virtual screening of hydrophilic monomer candidates may be a practical way to assess their initial promise for dentin primer use well before additional experimental evaluation of their priming/bonding efficacy. This is also of value in the search/design of new compounds for priming dentin. PMID:18546179

  14. Evaluating the Credibility of Transport Processes in the Global Modeling Initiative 3D Model Simulations of Ozone Recovery

    NASA Technical Reports Server (NTRS)

    Strahan, Susan E.; Douglass, Anne R.

    2003-01-01

    The Global Modeling Initiative has integrated two 35-year simulations of an ozone recovery scenario with an offline chemistry and transport model using two different meteorological inputs. Physically based diagnostics, derived from satellite and aircraft data sets, are described and then used to evaluate the realism of temperature and transport processes in the simulations. Processes evaluated include barrier formation in the subtropics and polar regions, and extratropical wave-driven transport. Some diagnostics are especially relevant to simulation of lower stratospheric ozone, but most are applicable to any stratospheric simulation. The temperature evaluation, which is relevant to gas phase chemical reactions, showed that both sets of meteorological fields have near climatological values at all latitudes and seasons at 30 hPa and below. Both simulations showed weakness in upper stratospheric wave driving. The simulation using input from a general circulation model (GMI(sub GCM)) showed a very good residual circulation in the tropics and northern hemisphere. The simulation with input from a data assimilation system (GMI(sub DAS)) performed better in the midlatitudes than at high latitudes. Neither simulation forms a realistic barrier at the vortex edge, leading to uncertainty in the fate of ozone-depleted vortex air. Overall, tracer transport in the offline GMI(sub GCM) has greater fidelity throughout the stratosphere than the GMI(sub DAS).

  15. Effects of Type of Exploratory Strategy and Prior Knowledge on Middle School Students' Learning of Chemical Formulas from a 3D Role-Playing Game

    ERIC Educational Resources Information Center

    Chen, Ming-Puu; Wong, Yu-Ting; Wang, Li-Chun

    2014-01-01

    The purpose of this study was to examine the effects of the type of exploratory strategy and level of prior knowledge on middle school students' performance and motivation in learning chemical formulas via a 3D role-playing game (RPG). Two types of exploratory strategies-RPG exploratory with worked-example and RPG exploratory without…

  16. Three Dimensional (3D) Printing: A Straightforward, User-Friendly Protocol to Convert Virtual Chemical Models to Real-Life Objects

    ERIC Educational Resources Information Center

    Rossi, Sergio; Benaglia, Maurizio; Brenna, Davide; Porta, Riccardo; Orlandi, Manuel

    2015-01-01

    A simple procedure to convert protein data bank files (.pdb) into a stereolithography file (.stl) using VMD software (Virtual Molecular Dynamic) is reported. This tutorial allows generating, with a very simple protocol, three-dimensional customized structures that can be printed by a low-cost 3D-printer, and used for teaching chemical education…

  17. Alkynes as a versatile platform for construction of chemical molecular complexity and realization of molecular 3D printing

    NASA Astrophysics Data System (ADS)

    Galkin, K. I.; Ananikov, V. P.

    2016-03-01

    The current level of scientific and technological development requires the formation of general tools and techniques. One of the most versatile technologies is 3D printing, which allows fast and efficient creation of materials and biological objects of desired shape and composition. Today, methods have been developed for 3D printing of macro- and nano-sized objects and for production of films and deposited materials with molecular precision but the most promising technology is printing at the molecular level (molecular 3D printing) for the purpose of direct construction of molecular complexity. This process is currently at the initial stage concerning selection of simple molecules to be used as building blocks possessing flexibility, availability and ease of modification. In this review, we examine the possible versatile synthons suitable for preparation of the main types of organic compounds using molecular 3D printing. The surveyed data strongly indicate that alkyne molecules may be used as a building material in a molecular 3D printer working on hydrocarbons. The bibliography includes 428 references.

  18. a Multiple Data Set Joint Inversion Global 3d P-Velocity Model of the Earth's Crust and Mantle for Improved Seismic Event Location

    NASA Astrophysics Data System (ADS)

    Ballard, S.; Begnaud, M. L.; Hipp, J. R.; Chael, E. P.; Encarnacao, A.; Maceira, M.; Yang, X.; Young, C. J.; Phillips, W.

    2013-12-01

    SALSA3D is a global 3D P wave velocity model of the Earth's crust and mantle developed specifically to provide seismic event locations that are more accurate and more precise than are locations from 1D and 2.5D models. In this paper, we present the most recent version of our model, for the first time jointly derived from multiple types of data: body wave travel times, surface wave group velocities, and gravity. The latter two are added to provide information in areas with poor body wave coverage, and are down-weighted in areas where body wave coverage is good. To constrain the inversions, we invoked empirical relations among the density, S velocity, and P velocity. We demonstrate the ability of the new SALSA3D model to reduce mislocations and generate statistically robust uncertainty estimates for a large set of realizations derived from a carefully chosen set of globally-distributed ground truth events. We obtain path-dependent travel time prediction uncertainties for our model by computing the full 3D model covariance matrix of our tomographic system and integrating the model slowness variance and covariance along paths of interest. This approach yields very low travel time prediction uncertainties for well-sampled paths through the Earth and higher uncertainties for paths that are poorly represented in the data set used to develop the model. While the calculation of path-dependent prediction uncertainties with this approach is computationally expensive, uncertainties can be pre-computed for a network of stations and stored in 3D lookup tables that can be quickly and efficiently interrogated using GeoTess software.

  19. Extra high speed modified Lundell alternator parameters and open/short-circuit characteristics from global 3D-FE magnetic field solutions

    NASA Technical Reports Server (NTRS)

    Wang, R.; Demerdash, N. A.

    1992-01-01

    The combined magnetic vector potential - magnetic scalar potential method of computation of 3D magnetic fields by finite elements, introduced in a companion paper, is used for global 3D field analysis and machine performance computations under open-circuit and short-circuit conditions for an example 14.3 kVA modified Lundell alternator, whose magnetic field is of intrinsic 3D nature. The computed voltages and currents under these machine test conditions were verified and found to be in very good agreement with corresponding test data. Results of use of this modelling and computation method in the study of a design alteration example, in which the stator stack length of the example alternator is stretched in order to increase voltage and volt-ampere rating, are given here. These results demonstrate the inadequacy of conventional 2D-based design concepts and the imperative of use of this type of 3D magnetic field modelling in the design and investigation of such machines.

  20. The LLNL-G3D global P-wave velocity model and the significance of the BayesLoc multiple-event location procedure

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    LLNL-G3D is a global-scale model of P-wave velocity designed to accurately predict seismic travel times at regional and teleseismic distances simultaneously. The underlying goal of the model is to provide enhanced seismic event location capabilities. Previous versions of LLNL-G3D (versions 1 and 2) provide substantial improvements in event location accuracy via 3-D ray tracing. The latest models are based on ~2.7 million P and Pn arrivals that are re-processed using our global multi-event locator known as BayesLoc. Bayesloc is a formulation of the joint probability distribution across multiple-event location parameters, including hypocenters, travel time corrections, pick precision, and phase labels. Modeling the whole multiple-event system results in accurate locations and an internally consistent data set that is ideal for tomography. Our recently developed inversion approach (called Progressive Multi-level Tessellation Inversion or PMTI) captures regional trends and fine details where data warrant. Using PMTI, we model multiple heterogeneity scale lengths without defining parameter grids with variable densities based on some ad hoc criteria. LLNL-G3Dv3 (version 3) is produced with data generated with the BayesLoc procedure, recently modified to account for localized travel time trends via a multiple event clustering technique. We demonstrate the significance of BayesLoc processing, the impact on the resulting tomographic images, and the application of LLNL-G3D to seismic event location. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-491805.

  1. Radiochromic 3D Detectors

    NASA Astrophysics Data System (ADS)

    Oldham, Mark

    2015-01-01

    Radiochromic materials exhibit a colour change when exposed to ionising radiation. Radiochromic film has been used for clinical dosimetry for many years and increasingly so recently, as films of higher sensitivities have become available. The two principle advantages of radiochromic dosimetry include greater tissue equivalence (radiologically) and the lack of requirement for development of the colour change. In a radiochromic material, the colour change arises direct from ionising interactions affecting dye molecules, without requiring any latent chemical, optical or thermal development, with important implications for increased accuracy and convenience. It is only relatively recently however, that 3D radiochromic dosimetry has become possible. In this article we review recent developments and the current state-of-the-art of 3D radiochromic dosimetry, and the potential for a more comprehensive solution for the verification of complex radiation therapy treatments, and 3D dose measurement in general.

  2. Three-Dimensional (3-D) Printing: A Cost-Effective Solution for Improving Global Accessibility to Prostheses.

    PubMed

    Silva, Kyle; Rand, Stephanie; Cancel, David; Chen, Yuxi; Kathirithamby, Rani; Stern, Michelle

    2015-12-01

    The lack of access to prostheses is a global problem, partially caused by the high cost associated with the current manufacturing process. Three-dimensional printing is gaining use in the medical field, and one such area is prosthetics. In addition to using cost-effective materials, this technology allows for rapid prototyping, making it an efficient solution for the development of affordable prostheses. If the rehabilitation medicine community embraces this novel technology, we can help alleviate the global disparity of access to prostheses. PMID:26709247

  3. Towards global scale coastal flood hazard in Delta Cities with 30-meter SRTM and 3D_i

    NASA Astrophysics Data System (ADS)

    Winsemius, Hessel; Verhoeven, Govert; Van Leeuwen, Elgard; Van der Klis, Hanneke; Van Wesenbeeck, Bregje; Cumiskey, Lydia; Verlaan, Martin; Muis, Sanne; Ward, Philip; Kwadijk, Jaap

    2015-04-01

    Most attempts to globally simulate inundation at the land-coast interface rely on maximum flood level GIS-based flood spreading models. These are generally not mass conservative, do not account for the genesis of tidal and surges in time, and do not include channel geometry and surface roughness. Furthermore, these methods cannot be used to study the impact of hazard reducing intervention measures that increase roughness at the land-coast interface. These measures include breakwaters and coastal ecosystems, such as mangrove forests and shell fish and coral reefs. Recently, new datasets and models are becoming available that allow us to greatly improve simulation of inundation in global deltas in a rapid and computationally feasible way. In this poster we demonstrate the feasibility of modelling all global deltas with strongly urbanised areas explicitly using these datasets and models. This will allow initiatives such as the 100 resilient cities (Rockefeller foundation) and the 'making cities resilient' campaign (UNISDR) to tackle the issue of coastal flood risk efficiently. We propose to use the following materials: A subgrid enabling 1D-2D model code Outputs from a global tidal and storm surge model Open topographical data We demonstrate the feasibility of this approach by modelling the Mississippi delta with: a) a lidar derived topography dataset (www.gis.ms.gov/); and b) the recently released 30 meter elevation dataset from the Shuttle Radar Topography Mission. We use the new 3Di subgrid code to rapidly schematise the vast delta area with a quadtree mesh. We force the model at the boundaries with water level estimates during the Katrina cyclone. We invite scientists working on global scale inundation modelling to visit our poster in order to discuss possibilities and limitations of the proposed methods related to model codes, data quality and calibration.

  4. A new 3D parallel high resolution electromagnetic nonlinear inversion based on new global magnetic integral and local differential decomposition (GILD)

    SciTech Connect

    Xie, G.; Li, J.

    1997-05-01

    A new 3D electromagnetic modeling and nonlinear inversion algorithm is presented based on global integral and local differential equations decomposition (GILD). The GILD parallel nonlinear inversion algorithm consists of five parts: (1) the domain is decomposed into subdomain SI and subdomain SII; (2) a new global magnetic integral equation in SI and the local magnetic differential equations IN SII will be used together to obtain the magnetic field in the modeling step; (3) the new global magnetic integral Jacobian equation in SI and the local magnetic differential Jacobian equations in SII will be used together to update the electric conductivity and permittivity from the magnetic field data in the inversion step; (4) the subdomain SII can naturally and uniformly be decomposed into 2{sup n} smaller sub-cubic-domains; the sparse matrix in each sub-cubic-domain can be eliminated separately, in parallel; (5) a new parallel multiple hierarchy substructure algorithm will be used to solve the smaller full matrices in SI, in parallel. The applications of the new 3D parallel GILD EM modeling and nonlinear inversion algorithm and software are: (1) to create high resolution controlled-source electric conductivity and permittivity imaging for interpreting electromagnetic field data acquired from cross hole, surface to borehole, surface to surface, single hole, and multiple holes; (2) to create the magnetotelluric high resolution imaging from the surface impedance and field data. The new GILD parallel nonlinear inversion will be a 3D/2.5D powerful imaging tool for the oil geophysical exploration and environmental remediation and monitoring.

  5. Self-consistent Synthetic Mantle Discontinuities From Joint Modeling of Geodynamics and Mineral Physics and Their Effects on the 3D Global Wave Field

    NASA Astrophysics Data System (ADS)

    Schuberth, B.; Piazzoni, A.; Bunge, H.; Igel, H.; Steinle-Neumann, G.; Moder, C.; Oeser, J.

    2007-12-01

    Our current understanding of mantle structure and dynamics is to a large part based on inversion of seismic data resulting in tomographic images and on direct analysis of a wide range of seismic phases such as Pdiff, PcP, ScS SdS etc. For solving inverse problems, forward modeling is needed to obtain a synthetic dataset for a given set of model parameters. In this respect, great progress has been made over the last years in the developement of sophisticated numerical full waveform modeling tools. However, the main limitation in the application of this new class of techniques for the forward problem of seismology is the lack of accurate predictions of mantle heterogeneity that allow us to test hypotheses about Earth's mantle. Such predictive models should be based on geodynamic and mineralogical considerations and derived independently of seismological observations. Here, we demonstrate the feasibility of joining forward simulations from geodynamics, mineral physics and seismology to obtain earth-like seismograms. 3D global wave propagation is simulated for dynamically consistent thermal structures derived from 3D mantle circulation modeling (e.g. Bunge et al. 2002), for which the temperatures are converted to seismic velocities using a recently published, thermodynamically self-consistent mineral physics approach (Piazzoni et al. 2007). Assuming a certain, fixed mantle composition (e.g. pyrolite) our mineralogic modeling algorithm computes the stable phases at mantle pressures for a wide range of temperatures by system Gibbs free energy minimization. Through the same equations of state that model the Gibbs free energy, we compute elastic moduli and density for each stable phase assemblage at the same P-T conditions. One straightforward application of this approach is the study of the seismic signature of synthetic mantle discontinuities arising in such models, as the temperature dependent phase transformations occuring at around 410 Km and 660 Km depth are

  6. The GPlates Portal: Cloud-Based Interactive 3D Visualization of Global Geophysical and Geological Data in a Web Browser

    PubMed Central

    Müller, R. Dietmar; Qin, Xiaodong; Sandwell, David T.; Dutkiewicz, Adriana; Williams, Simon E.; Flament, Nicolas; Maus, Stefan; Seton, Maria

    2016-01-01

    The pace of scientific discovery is being transformed by the availability of ‘big data’ and open access, open source software tools. These innovations open up new avenues for how scientists communicate and share data and ideas with each other and with the general public. Here, we describe our efforts to bring to life our studies of the Earth system, both at present day and through deep geological time. The GPlates Portal (portal.gplates.org) is a gateway to a series of virtual globes based on the Cesium Javascript library. The portal allows fast interactive visualization of global geophysical and geological data sets, draped over digital terrain models. The globes use WebGL for hardware-accelerated graphics and are cross-platform and cross-browser compatible with complete camera control. The globes include a visualization of a high-resolution global digital elevation model and the vertical gradient of the global gravity field, highlighting small-scale seafloor fabric such as abyssal hills, fracture zones and seamounts in unprecedented detail. The portal also features globes portraying seafloor geology and a global data set of marine magnetic anomaly identifications. The portal is specifically designed to visualize models of the Earth through geological time. These space-time globes include tectonic reconstructions of the Earth’s gravity and magnetic fields, and several models of long-wavelength surface dynamic topography through time, including the interactive plotting of vertical motion histories at selected locations. The globes put the on-the-fly visualization of massive data sets at the fingertips of end-users to stimulate teaching and learning and novel avenues of inquiry. PMID:26960151

  7. The GPlates Portal: Cloud-Based Interactive 3D Visualization of Global Geophysical and Geological Data in a Web Browser.

    PubMed

    Müller, R Dietmar; Qin, Xiaodong; Sandwell, David T; Dutkiewicz, Adriana; Williams, Simon E; Flament, Nicolas; Maus, Stefan; Seton, Maria

    2016-01-01

    The pace of scientific discovery is being transformed by the availability of 'big data' and open access, open source software tools. These innovations open up new avenues for how scientists communicate and share data and ideas with each other and with the general public. Here, we describe our efforts to bring to life our studies of the Earth system, both at present day and through deep geological time. The GPlates Portal (portal.gplates.org) is a gateway to a series of virtual globes based on the Cesium Javascript library. The portal allows fast interactive visualization of global geophysical and geological data sets, draped over digital terrain models. The globes use WebGL for hardware-accelerated graphics and are cross-platform and cross-browser compatible with complete camera control. The globes include a visualization of a high-resolution global digital elevation model and the vertical gradient of the global gravity field, highlighting small-scale seafloor fabric such as abyssal hills, fracture zones and seamounts in unprecedented detail. The portal also features globes portraying seafloor geology and a global data set of marine magnetic anomaly identifications. The portal is specifically designed to visualize models of the Earth through geological time. These space-time globes include tectonic reconstructions of the Earth's gravity and magnetic fields, and several models of long-wavelength surface dynamic topography through time, including the interactive plotting of vertical motion histories at selected locations. The globes put the on-the-fly visualization of massive data sets at the fingertips of end-users to stimulate teaching and learning and novel avenues of inquiry. PMID:26960151

  8. A 3-D RBF-FD solver for modeling the atmospheric global electric circuit with topography (GEC-RBFFD v1.0)

    NASA Astrophysics Data System (ADS)

    Bayona, V.; Flyer, N.; Lucas, G. M.; Baumgaertner, A. J. G.

    2015-10-01

    A numerical model based on radial basis function-generated finite differences (RBF-FD) is developed for simulating the global electric circuit (GEC) within the Earth's atmosphere, represented by a 3-D variable coefficient linear elliptic partial differential equation (PDE) in a spherically shaped volume with the lower boundary being the Earth's topography and the upper boundary a sphere at 60 km. To our knowledge, this is (1) the first numerical model of the GEC to combine the Earth's topography with directly approximating the differential operators in 3-D space and, related to this, (2) the first RBF-FD method to use irregular 3-D stencils for discretization to handle the topography. It benefits from the mesh-free nature of RBF-FD, which is especially suitable for modeling high-dimensional problems with irregular boundaries. The RBF-FD elliptic solver proposed here makes no limiting assumptions on the spatial variability of the coefficients in the PDE (i.e., the conductivity profile), the right hand side forcing term of the PDE (i.e., distribution of current sources) or the geometry of the lower boundary.

  9. LLNL-Earth3D

    2013-10-01

    Earth3D is a computer code designed to allow fast calculation of seismic rays and travel times through a 3D model of the Earth. LLNL is using this for earthquake location and global tomography efforts and such codes are of great interest to the Earth Science community.

  10. Coupled simulation of chemical lasers based on intracavity partially coherent light model and 3D CFD model.

    PubMed

    Wu, Kenan; Huai, Ying; Jia, Shuqin; Jin, Yuqi

    2011-12-19

    Coupled simulation based on intracavity partially coherent light model and 3D CFD model is firstly achieved in this paper. The dynamic equation of partially coherent intracavity field is derived based on partially coherent light theory. A numerical scheme for the coupled simulation as well as a method for computing the intracavity partially coherent field is given. The presented model explains the formation of the sugar scooping phenomenon, and enables studies on the dependence of the spatial mode spectrum on physical parameters of laser cavity and gain medium. Computational results show that as the flow rate of iodine increases, higher order mode components dominate in the partially coherent field. Results obtained by the proposed model are in good agreement with experimental results. PMID:22274214

  11. Model Simulations of the Diurnal and Seasonal Variations of the Global Electric Circuit Using a Consistent 3D Model Framework

    NASA Astrophysics Data System (ADS)

    Lucas, G.; Bayona, V.; Flyer, N.; Baumgaertner, A. J. G.; Thayer, J. P.

    2014-12-01

    We introduce a new numeric solver for the partial differential equations of the Global Electric Circuit (GEC). The model is applied to derive the ionospheric potential with respect to the Earth, as well as the current distribution and electric fields throughout the atmosphere. We will discuss its advantages to previously published approaches, and introduce the model's application within a larger model framework that consistently describes the thunderstorm/electrified cloud current source distribution and conductivity. The new source and conductivity distributions will be utilized in the new numeric GEC solver to demonstrate the effect that temporal and spatial variability of these inputs have on electric fields and currents throughout the domain.

  12. Mapping tropical biodiversity using spectroscopic imagery : characterization of structural and chemical diversity with 3-D radiative transfer modeling

    NASA Astrophysics Data System (ADS)

    Feret, J. B.; Gastellu-Etchegorry, J. P.; Lefèvre-Fonollosa, M. J.; Proisy, C.; Asner, G. P.

    2014-12-01

    The accelerating loss of biodiversity is a major environmental trend. Tropical ecosystems are particularly threatened due to climate change, invasive species, farming and natural resources exploitation. Recent advances in remote sensing of biodiversity confirmed the potential of high spatial resolution spectroscopic imagery for species identification and biodiversity mapping. Such information bridges the scale-gap between small-scale, highly detailed field studies and large-scale, low-resolution satellite observations. In order to produce fine-scale resolution maps of canopy alpha-diversity and beta-diversity of the Peruvian Amazonian forest, we designed, applied and validated a method based on spectral variation hypothesis to CAO AToMS (Carnegie Airborne Observatory Airborne Taxonomic Mapping System) images, acquired from 2011 to 2013. There is a need to understand on a quantitative basis the physical processes leading to this spectral variability. This spectral variability mainly depends on canopy chemistry, structure, and sensor's characteristics. 3D radiative transfer modeling provides a powerful framework for the study of the relative influence of each of these factors in dense and complex canopies. We simulated series of spectroscopic images with the 3D radiative model DART, with variability gradients in terms of leaf chemistry, individual tree structure, spatial and spectral resolution, and applied methods for biodiversity mapping. This sensitivity study allowed us to determine the relative influence of these factors on the radiometric signal acquired by different types of sensors. Such study is particularly important to define the domain of validity of our approach, to refine requirements for the instrumental specifications, and to help preparing hyperspectral spatial missions to be launched at the horizon 2015-2025 (EnMAP, PRISMA, HISUI, SHALOM, HYSPIRI, HYPXIM). Simulations in preparation include topographic variations in order to estimate the robustness

  13. 3D chemical mapping: application of scanning transmission (soft) X-ray microscopy (STXM) in combination with angle-scan tomography in bio-, geo-, and environmental sciences.

    PubMed

    Obst, Martin; Schmid, Gregor

    2014-01-01

    The identification of environmental processes and mechanisms often requires information on the organochemical and inorganic composition of specimens at high spatial resolution. X-ray spectroscopy (XAS) performed in the soft X-ray range (100-2,200 eV) provides chemical speciation information for elements that are of high biogeochemical relevance such as carbon, nitrogen, and oxygen but also includes transition metals such as iron, manganese, or nickel. Synchrotron-based scanning transmission X-ray microscopy (STXM) combines XAS with high resolution mapping on the 20-nm scale. This provides two-dimensional (2D) quantitative information about the distribution of chemical species such as organic macromolecules, metals, or mineral phases within environmental samples. Furthermore, the combination of STXM with angle-scan tomography allows for three-dimensional (3D) spectromicroscopic analysis of bio-, geo-, or environmental samples. For the acquisition of STXM tomography data, the sample is rotated around an axis perpendicular to the X-ray beam. Various sample preparation approaches such as stripes cut from TEM grids or the preparation of wet cells allow for preparing environmentally relevant specimens in a dry or in a fully hydrated state for 2D and 3D STXM measurements. In this chapter we give a short overview about the principles of STXM, its application to environmental sciences, different preparation techniques, and the analysis and 3D reconstruction of STXM tomography data. PMID:24357389

  14. Normal-mode function representation of global 3-D data sets: open-access software for the atmospheric research community

    NASA Astrophysics Data System (ADS)

    Žagar, N.; Kasahara, A.; Terasaki, K.; Tribbia, J.; Tanaka, H.

    2015-04-01

    This article presents new software for the analysis of global dynamical fields in (re)analyses, weather forecasts and climate models. A new diagnostic tool, developed within the MODES project, allows one to diagnose properties of balanced and inertio-gravity (IG) circulations across many scales. In particular, the IG spectrum, which has only recently become observable, can be studied simultaneously in the mass and wind fields while considering the whole model depth in contrast to the majority of studies. The paper includes the theory of normal-mode function (NMF) expansion, technical details of the Fortran 90 code, examples of namelists which control the software execution and outputs of the software application on the ERA Interim reanalysis data set. The applied libraries and default compiler are from the open-source domain. A limited understanding of Fortran suffices for the successful implementation of the software. The presented application of the software to the ERA Interim data set reveals several aspects of the large-scale circulation after it has been partitioned into the linearly balanced and IG components. The global energy distribution is dominated by the balanced energy while the IG modes contribute around 10% of the total wave energy. However, on sub-synoptic scales, IG energy dominates and it is associated with the main features of tropical variability on all scales. The presented energy distribution and features of the zonally averaged and equatorial circulation provide a reference for the validation of climate models.

  15. Normal-mode function representation of global 3-D datasets: an open-access software for atmospheric research community

    NASA Astrophysics Data System (ADS)

    Žagar, N.; Kasahara, A.; Terasaki, K.; Tribbia, J.; Tanaka, H.

    2014-12-01

    The paper presents new software for the analysis of global dynamical fields in (re)analyses, weather forecasts and climate models. A new diagnostic tool, developed within the MODES project, allows one to diagnose properties of balanced and inertio-gravity (IG) circulation across many scales. In particular, the IG spectrum, which has only recently become observable, can be studied simultaneously in the mass field and wind field and considering the whole model depth in contrary to majority of studies. The paper presentation includes the theory of normal-mode function expansion, technical details of the Fortran 90 code, examples of namelists which control the software execution and outputs of the software application on the reanalysis dataset ERA Interim. The applied libraries and default compiler are from the open-source domain. A limited understanding of Fortran suffices for the successful implementation of the software. The presented application of the software to the ERA Interim dataset show some features of the large-scale circulation after it has been split into the balanced and IG components. The global energy distribution is dominated by the balanced energy with IG modes making less than 10% of the total wave energy. However, on subsynoptic scales IG energy dominates and it is associated with the main features of tropical variability on all scales. The presented energy distribution and features of the zonally-averaged and equatorial circulation provide a reference for the validation of climate models.

  16. Realistic primary and new productions in a 3D global biogeochemical model: biological complexity or physical forcing?

    NASA Astrophysics Data System (ADS)

    Popova, E. E.; Coward, A. C.

    2003-04-01

    A nitrogen-based, five compartment biological model has been coupled to a one degree OCCAM (Ocean Circulation and Climate Advanced Modelling Project) model with a KPP ("K profile parameterisation") of the vertical mixing. The biological model state variables are Phytoplankton, Zooplankton, Detritus, Nitrate, and Ammonium. A comparison of the solution with global satellite ocean colour shows that the model is capable of a realistic description of the main seasonal and regional patterns of the surface chlorophyll. Agreement is also good for satellite derived estimates of primary production. In situ data available from local study sites (such as BATS, NABE, India, Papa) are used for the detailed comparison of the model output with the observed ecosystem dynamics in different biological provinces. We discuss performance of the physical and biological model in contrasting areas of the World Ocean. In spite of the biological model being a very simple one, we are able to reproduce the major differences between ecosystem dynamics of these areas. We believe that the success of any global biogeochemical model is dependent first of all on the correct representation of the upper mixed layer (UML) dynamics. Without being able to reproduce contrasting UML regimes in different areas of the World Ocean (such as difference between the North Atlantic and Southern Ocean, or North Atlantic and North Pacific), increased complexity biological models are in danger of producing the right results by the wrong reason.

  17. Global effects of transmitted shock wave propagation through the Earth's inner magnetosphere: First results from 3-D hybrid kinetic modeling

    NASA Astrophysics Data System (ADS)

    Lipatov, A. S.; Sibeck, D. G.

    2016-09-01

    We use a new hybrid kinetic model to simulate the response of ring current, outer radiation belt, and plasmaspheric particle populations to impulsive interplanetary shocks. Since particle distributions attending the interplanetary shock waves and in the ring current and radiation belts are non-Maxwellian, wave-particle interactions play a crucial role in energy transport within the inner magnetosphere. Finite gyroradius effects become important in mass loading the shock waves with the background plasma in the presence of higher energy ring current and radiation belt ions and electrons. Initial results show that shocks cause strong deformations in the global structure of the ring current, radiation belt, and plasmasphere. The ion velocity distribution functions at the shock front, in the ring current, and in the radiation belt help us determine energy transport through the Earth's inner magnetosphere.

  18. Chemical Synthesis of Sea-Urchin Shaped 3D-MnO2 Nano Structures and Their Application in Supercapacitors.

    PubMed

    Singu, Bal Sydulu; Hong, Sang Eun; Yoon, Kuk Ro

    2016-06-01

    Sea-urchin shaped α-MnO2 hierarchical nano structures have been synthesized by facile thermal method without using any hard or soft template under the mild conditions. The structural and morphology of the 3D-MnO2 was characterized by X-ray diffraction (XRD) and field emission scanning electron microscopy (FE-SEM). From the XRD analysis indicates that MnO2 present in the α form. Morphology analysis shows that α-MnO2 sea-urchins are made by stacked nanorods, the diameter and length of the stacked nanorods present in the range of 50-120 nm and 200-400 nm respectively. The electrochemical behaviour of α-MnO2 has been investigated by cyclic voltammetry (CV) and charge-discharge (CD). The specific capacitance, energy density and power density are 212.0 F g(-1), 21.2 Wh kg(-1) and 1200 W kg(-1) respectively at the current density of 2 A g(-1). The retention of the specific capacitance after completion of 1000 charge-discharge cycles is around 97%. The results reveal that the prepared Sea-urchin shaped α-MnO2 has high specific capacitance and exhibit excellent cycle life. PMID:27427676

  19. Impact of the IMF rotation on the cusp dynamics on the dayside: Global 3D PIC simulations

    NASA Astrophysics Data System (ADS)

    Huang, Z.; Cai, D.; Lembege, B.; Nishikawa, K.-I.

    The dynamics of the cusp region is analyzed with a new version of a global three-dimensional full particle simulation with changing the interplanetary magnetic field IMF direction progressively from northward to duskward then duskward to southward With the initial northward IMF bands of weak magnetic field sash form poleward of the cusp at high latitudes in each hemisphere and at high altitudes these sashes are located approximately around the pole axis As the IMF rotates duskward these sashes move toward the equator within opposite quadrants Then as the duskward-oriented IMF continue to rotate toward southward these sashes move further and reach the dayside magnetopause at the equator During the progressive rotation of the IMF from northward to duskward i the sash region widens towards lower latitudes banana-shape and with the duskward IMF ii the size of the banana-shape region becomes minimum and its location stops around a maximum deviation of 45degree from the polar axis It should be noted that the sashes are extended from the dayside to the nightside tailward The motion of the sashes is also analyzed during the IMF rotation form duskward to southward

  20. Impact of the IMF rotation on the cusp dynamics on the dayside: Global 3D PIC simulations

    NASA Astrophysics Data System (ADS)

    Tao, W.; Cai, D.; Lembege, B.; Nishikawa, K.

    2005-12-01

    The dynamics of the cusp region as the interplanetary magnetic field (IMF) progressively changes its direction from northward to duskward is analysed with a new version of a global three-dimensional full particle simulation. For northward IMF, bands of weak magnetic field (sash) form poleward of the cusp at high latitudes in each hemisphere (and at high altitudes); these sashs are centered approximately around the pole axis. However, as the newly duskward-oriented IMF approaches and interacts with the magnetosphere, these sashs move to the equator (within opposite quadrants). During the progressive rotation of the IMF, this motion is decomposed in the plane perpendicular to the solar wind as follows: (i) the "sash" region widens towards lower latitudes ("banana-shape"), and (ii) the size of the "banana-shape" region strongly shrinks and its location stabilizes around a maximum deviation of 45?. In addition, this motion is observed both on the day and the night sides where sashs are simultaneously observed. Characteristic time and space scales of the cusp motion are indicated, in order to be compare with results deduced from previous MHD simulations. Changes of local reconnection in the cusp region are analysed.

  1. Spontaneous development of arcuate single-sided subduction in global 3-D mantle convection models with a free surface

    NASA Astrophysics Data System (ADS)

    Crameri, Fabio; Tackley, Paul

    2014-05-01

    The work presented aims at a better understanding of plate tectonics, a crucial dynamical feature within the global framework of mantle convection. Special focus is given to the interaction of subduction-related mantle flow and surface topography. Thereby, the application of a numerical model with two key functional requirements is essential: an evolution over a long time period to naturally model mantle flow and a physically correct topography calculation. The global mantle convection model presented in Crameri et al. (2012a) satisfies both of these requirements. First, it is efficiently calculated by the finite-volume code Stag-YY (e.g., Tackley 2008) using a multi-grid method on a fully staggered grid. Second, it applies the sticky-air method (Matsumoto and Tomoda 1983; Schmeling et al, 2008) and thus approximates a free surface when the sticky-air parameters are chosen carefully (Crameri et al., 2012b). This leads to dynamically self-consistent mantle convection with realistic, single-sided subduction. New insights are thus gained into the interplay of obliquely sinking plates, toroidal mantle flow and the arcuate shape of slabs and trenches. Numerous two-dimensional experiments provide optimal parameter setups that are applied to three-dimensional models in Cartesian and fully spherical geometries. Features observed and characterised in the latter experiments give important insight into the strongly variable behaviour of subduction zones along their strike. This includes (i) the spontaneous development of arcuate trench geometry, (ii) regional subduction polarity reversals and slab tearing, and the newly discovered features (iii) 'slab tunnelling' and (iv) 'back-slab spiral flow'. Overall, this study demonstrates the strong interaction between surface topography and mantle currents and highlights the variability of subduction zones and their individual segments. REFERENCES Crameri, F., P. J. Tackley, I. Meilick, T. V. Gerya, and B. J. P. Kaus (2012a), A free

  2. MRI-driven accretion on to magnetized stars: global 3D MHD simulations of magnetospheric and boundary layer regimes

    NASA Astrophysics Data System (ADS)

    Romanova, M. M.; Ustyugova, G. V.; Koldoba, A. V.; Lovelace, R. V. E.

    2012-03-01

    We discuss results of global three-dimensional magnetohydrodynamic simulations of accretion on to a rotating magnetized star with a tilted dipole magnetic field, where the accretion is driven by the magnetorotational instability (MRI). The simulations show that MRI-driven turbulence develops in the disc, and angular momentum is transported outwards primarily due to the magnetic stress. The turbulent flow is strongly inhomogeneous and the densest matter is in azimuthally stretched turbulent cells. We investigate two regimes of accretion: a magnetospheric regime and a boundary layer (BL) regime. In the magnetospheric regime, the magnetic field of the star is dynamically important: the accretion disc is truncated by the star's magnetic field within a few stellar radii from the star's surface, and matter flows to the star in funnel streams. The funnel streams flow towards the south and north magnetic poles but are not equal due to the inhomogeneity of the flow. The hotspots on the stellar surface are not symmetric as well. In the BL regime, the magnetic field of the star is dynamically unimportant, and matter accretes on to the surface of the star through the BL. The magnetic field in the inner disc is strongly amplified by the shear of the accretion flow, and the matter and magnetic stresses become comparable. Accreting matter forms a belt-shaped hot region on the surface of the star. The belt has inhomogeneous density distribution which varies in time due to variable accretion rate. The peaks in the variability curve are associated with accretion of individual turbulent cells. They show 20-50 per cent density amplifications at periods of ˜5-10 dynamical time-scales at the surface of the star. Spiral waves in the disc are excited in both magnetospheric and BL regimes of accretion. Results of simulations can be applied to classical T Tauri stars, accreting brown dwarfs, millisecond pulsars, dwarf novae cataclysmic variables and other stars with magnetospheres smaller

  3. Global sensitivity analysis of a 3D street canyon model—Part II: Application and physical insight using sensitivity analysis

    NASA Astrophysics Data System (ADS)

    Benson, James; Ziehn, Tilo; Dixon, Nick S.; Tomlin, Alison S.

    In this work global sensitivity studies using Monte Carlo sampling and high dimensional model representations (HDMR) have been carried out on the k- ɛ closure computational fluid dynamic (CFD) model MISKAM, allowing detailed representation of the effects of changing input parameters on the model outputs. The scenario studied is that of a complex street canyon in the city of York, UK. The sensitivity of the turbulence and mean flow fields to the input parameters is detailed both at specific measurement points and in the associated canyon cross-section to aid comparison with field data. This analysis gives insight into how model parameters can influence the predicted outputs. It also shows the relative strength of each parameter in its influence. Four main input parameters are addressed. Three parameters are surface roughness lengths, determining the flow over a surface, and the fourth is the background wind direction. In order to determine the relative importance of each parameter, sensitivity indices are calculated for the canyon cross-section. The sensitivity of the flow structures in and above the canyon to each parameter is found to be very location dependant. In general, at a particular measurement point, it is the closest wall surface that is most influential on the model output. However, due to the complexity of the flow at different wind angles this is not always the case, for example when a re-circulating canyon flow pattern is present. The background wind direction is shown to be an important parameter as it determines the surface features encountered by the flow. The accuracy with which this is specified when modelling a full-scale situation is therefore an important consideration when considering model uncertainty. Overall, the uncertainty due to roughness lengths is small in comparison to the mean outputs, indicating that the model is well defined even with large ranges of input parameter uncertainty.

  4. Radionuclide Incorporation in Secondary Crystalline Minerals Resulting from Chemical Weathering of Selected Waste Glasses: Progress Report for Subtask 3d

    SciTech Connect

    SV Mattigod; DI Kaplan; VL LeGore; RD Orr; HT Schaef; JS Young

    1998-10-23

    Experiments were conducted in fiscal year 1998 by Pacific Northwest National Laboratory to evaluate potential incorporation of radionuclides in secondary mineral phases that form from weathering vitrified nuclear waste glasses. These experiments were conducted as part of the Immobilized Low- Activity Waste-Petiormance Assessment (ILAW-PA) to generate data on radionuclide mobilization and transport in a near-field enviromnent of disposed vitrified wastes. An initial experiment was conducted to identify the types of secondary minerals that form from two glass samples of differing compositions, LD6 and SRL202. Chemical weathering of LD6 glass at 90oC in contact with an aliquot of uncontaminated Hanford Site groundwater resulted in the formation of a Crystalline zeolitic mineral, phillipsite. In contrast similar chemical weathering of SRL202 glass at 90"C resulted in the formation of a microcrystalline smectitic mineral, nontronite. A second experiment was conducted at 90"C to assess the degree to which key radionuclides would be sequestered in the structure of secondary crystalline minerals; namely, phillipsite and nontronite. Chemical weathering of LD6 in contact with radionuclide-spiked Hanford Site groundwater indicated that substantial ilactions of the total activities were retained in the phillipsite structure. Similar chemical weathering of SRL202 at 90"C, also in contact with radionuclide-spiked Hanford Site groundwater, showed that significant fractions of the total activities were retained in the nontronite structure. These results have important implications regarding the radionuclide mobilization aspects of the ILAW-PA. Additional studies are required to confkm the results and to develop an improved under- standing of mechanisms of sequestration and attenuated release of radionuclides to help refine certain aspects of their mobilization.

  5. Studies of Trace Gas Chemical Cycles Using Inverse Methods and Global Chemical Transport Models

    NASA Technical Reports Server (NTRS)

    Prinn, Ronald G.

    2003-01-01

    We report progress in the first year, and summarize proposed work for the second year of the three-year dynamical-chemical modeling project devoted to: (a) development, testing, and refining of inverse methods for determining regional and global transient source and sink strengths for long lived gases important in ozone depletion and climate forcing, (b) utilization of inverse methods to determine these source/sink strengths using either MATCH (Model for Atmospheric Transport and Chemistry) which is based on analyzed observed wind fields or back-trajectories computed from these wind fields, (c) determination of global (and perhaps regional) average hydroxyl radical concentrations using inverse methods with multiple titrating gases, and (d) computation of the lifetimes and spatially resolved destruction rates of trace gases using 3D models. Important goals include determination of regional source strengths of methane, nitrous oxide, methyl bromide, and other climatically and chemically important biogenic/anthropogenic trace gases and also of halocarbons restricted by the Montreal protocol and its follow-on agreements and hydrohalocarbons now used as alternatives to the restricted halocarbons.

  6. 3D mapping of chemical distribution from melting at lower mantle conditions in the laser-heated diamond anvil cell

    NASA Astrophysics Data System (ADS)

    Dorfman, S. M.; Nabiei, F.; Cantoni, M.; Badro, J.; Gaal, R.; Gillet, P.

    2014-12-01

    The laser-heated diamond anvil cell is a unique tool for subjecting materials to pressures over few hundreds of GPa and temperatures of thousands of Kelvins which enables us to experimentally simulate the inaccessible interiors of planets. However, small sample size, laser profile and thermally conductive diamonds cause temperature gradients of 1000s K over a few microns which also affects chemical and structural distribution of phases in the sample. We have examined samples of San Carlos olivine (Mg,Fe)2SiO3 powder melted in the diamond anvil cell by double-sided and single-sided laser heating for 3-6 minutes to ~3000 K at 35-37 GPa. Moreover, MgO is used as an insulating media in one of the sample. Recovered samples were analyzed by a combination of focused ion beam (FIB) and scanning electron microscope (SEM) equipped with energy dispersive x-ray (EDX) detector. Images and chemical maps were acquired for ~300 slices with ~70 nm depth from each sample, comprising about half of the heated zone. Detailed chemical and structural analysis by transmission electron microscopy (TEM) of lamellas prepared from the remaining section of the samples will also be presented. In all samples the heated zone included (Mg,Fe)SiO3 perovskite-structured bridgmanite (PV) phase and two (Mg, Fe)O phases, one of which, magnesiowüstite (MW), is richer in iron than the other one, ferropericlase (FP). In double-side heated samples we observe a Fe-rich quenched melt core surrounded by MW phase. Our results show that with increasing heating time, Fe migrates to the molten center of the sample. In the single-side heated sample, the Fe-rich MW phase is concentrated in the center of heated zone. In all samples a FP crust was observed around the heated zone. This crust, however, is broken in the upper part (colder part) of the single-side heated sample due the high asymmetrical temperature gradient within the sample. The results confirm the importance of double-side heating and insulating media

  7. High-order Godunov schemes for global 3D MHD simulations of accretion disks. I. Testing the linear growth of the magneto-rotational instability

    NASA Astrophysics Data System (ADS)

    Flock, M.; Dzyurkevich, N.; Klahr, H.; Mignone, A.

    2010-06-01

    We assess the suitability of various numerical MHD algorithms for astrophysical accretion disk simulations with the PLUTO code. The well-studied linear growth of the magneto-rotational instability is used as the benchmark test for a comparison between the implementations within PLUTO and against the ZeusMP code. The results demonstrate the importance of using an upwind reconstruction of the electro-motive force (EMF) in the context of a constrained transport scheme, which is consistent with plane-parallel, grid-aligned flows. In contrast, constructing the EMF from the simple average of the Godunov fluxes leads to a numerical instability and the unphysical growth of the magnetic energy. We compare the results from 3D global calculations using different MHD methods against the analytical solution for the linear growth of the MRI, and discuss the effect of numerical dissipation. The comparison identifies a robust and accurate code configuration that is vital for realistic modeling of accretion disk processes.

  8. Evolution of chemical bonding and electron density rearrangements during D(3h) → D(3d) reaction in monolayered TiS2: a QTAIM and ELF study.

    PubMed

    Ryzhikov, Maxim R; Slepkov, Vladimir A; Kozlova, Svetlana G; Gabuda, Svyatoslav P

    2014-08-15

    Monolayered titanium disulfide TiS2, a prospective nanoelectronic material, was previously shown to be subject to an exothermic solid-state D3h -D3d reaction that proceeds via a newly discovered transition state. Here, we study the reaction in detail using topological methods of quantum chemistry (quantum theory of atoms in molecules and electron localization function analysis) and show how electron density and chemical bonding between the atoms change in the course of the reaction. The reaction is shown to undergo a series of topological catastrophes, associated with elementary chemical events such as break and formation of bonds (including the unexpected formation of S-S bonding between sulfur layers), and rearrangement of electron density of outer valence and core shells. PMID:24943852

  9. Global 3-d modeling of atmospheric ozone in the free troposphere and the stratosphere with emphasis on midlatitude regions. Final report, July 1, 1994--June 30, 1997

    SciTech Connect

    Brasseur, G.; Erickson, D.; Tie, X.; Walter, S.

    1997-12-01

    The objective of this research is to use global chemical-transport models to study the chemical and dynamical processes that affect midlatitude stratospheric ozone and to quantify the budget of tropospheric ozone. Four models will be improved and used: (1) a new version of the two-dimensional chemical-radiative-dynamical model with microphysical process of sulfate aerosols and polar stratospheric clouds (PSCs), and heterogeneous conversions on the surfaces of sulfate aerosols and PSCs; (2) the stratospheric version of three-dimensional off-line chemical-transport model (STARS) with a relatively high horizontal resolution (2.8 degree in latitudes) with a microphysical formation of PSCs; (3) the tropospheric version of three-dimensional off-line chemical-transport model (MOZART) with details in the surface emissions and hydrocarbon reactions to estimate the tropospheric ozone budget and perturbations; (4) the intermediate model of the global and annual evolution of species (IMAGES) with a detailed chemical reactions but relatively lower resolutions. Model results will be compared with available data.

  10. Alginate based 3D hydrogels as an in vitro co-culture model platform for the toxicity screening of new chemical entities

    SciTech Connect

    Lan, Shih-Feng; Starly, Binil

    2011-10-01

    Prediction of human response to potential therapeutic drugs is through conventional methods of in vitro cell culture assays and expensive in vivo animal testing. Alternatives to animal testing require sophisticated in vitro model systems that must replicate in vivo like function for reliable testing applications. Advancements in biomaterials have enabled the development of three-dimensional (3D) cell encapsulated hydrogels as in vitro drug screening tissue model systems. In this study, we have developed an in vitro platform to enable high density 3D culture of liver cells combined with a monolayer growth of target breast cancer cell line (MCF-7) in a static environment as a representative example of screening drug compounds for hepatotoxicity and drug efficacy. Alginate hydrogels encapsulated with serial cell densities of HepG2 cells (10{sup 5}-10{sup 8} cells/ml) are supported by a porous poly-carbonate disc platform and co-cultured with MCF-7 cells within standard cell culture plates during a 3 day study period. The clearance rates of drug transformation by HepG2 cells are measured using a coumarin based pro-drug. The platform was used to test for HepG2 cytotoxicity 50% (CT{sub 50}) using commercially available drugs which further correlated well with published in vivo LD{sub 50} values. The developed test platform allowed us to evaluate drug dose concentrations to predict hepatotoxicity and its effect on the target cells. The in vitro 3D co-culture platform provides a scalable and flexible approach to test multiple-cell types in a hybrid setting within standard cell culture plates which may open up novel 3D in vitro culture techniques to screen new chemical entity compounds. - Graphical abstract: Display Omitted Highlights: > A porous support disc design to support the culture of desired cells in 3D hydrogels. > Demonstrated the co-culture of two cell types within standard cell-culture plates. > A scalable, low cost approach to toxicity screening involving

  11. One concept, three implementations of 3D pharmacophore-based virtual screening: distinct coverage of chemical search space.

    PubMed

    Spitzer, Gudrun M; Heiss, Mathias; Mangold, Martina; Markt, Patrick; Kirchmair, Johannes; Wolber, Gerhard; Liedl, Klaus R

    2010-07-26

    Feature-based pharmacophore modeling is a well-established concept to support early stage drug discovery, where large virtual databases are filtered for potential drug candidates. The concept is implemented in popular molecular modeling software, including Catalyst, Phase, and MOE. With these software tools we performed a comparative virtual screening campaign on HSP90 and FXIa, taken from the 'maximum unbiased validation' data set. Despite the straightforward concept that pharmacophores are based on, we observed an unexpectedly high degree of variation among the hit lists obtained. By harmonizing the pharmacophore feature definitions of the investigated approaches, the exclusion volume sphere settings, and the screening parameters, we have derived a rationale for the observed differences, providing insight on the strengths and weaknesses of these algorithms. Application of more than one of these software tools in parallel will result in a widened coverage of chemical space. This is not only rooted in the dissimilarity of feature definitions but also in different algorithmic search strategies. PMID:20583761

  12. Using the Low Freeze-in Height of Heavy Elements to Validate a Global 3D Solar Model with an Upper Chromospheric Boundary

    NASA Astrophysics Data System (ADS)

    Oran, R.; van der Holst, B.; Landi, E.; Gruesbeck, J. R.; Sokolov, I.; Manchester, W. B.; Gombosi, T. I.

    2012-12-01

    We present results from a global 3D magnetohydrodynamic (MHD) model extending from the top of the chromosphere to the inner heliosphere, combined with an ionic charge state evolution model for Carbon, Oxygen, Silicon and Iron ions. The MHD model is driven by Alfvenic turbulence, which is the sole source of heating. The inner boundary of the model is set at the top of the chromosphere with a temperature of 20,000K. Non ideal-MHD processes such as radiative cooling and electron heat conduction are included, as well as separate electron and proton temperatures. The speed, electron temperature and density distribution along magnetic field lines are extracted from the MHD solution and used as input to a charge state evolution model (Michigan Ionization Code, Landi et al. [2012]). Compared to similar analysis based on MHD models starting at the coronal base, where the electron temperature is already in the 1MK range, setting the inner boundary at 20,000K will allow us to fully characterize the evolution of the charge state distribution of the heavy elements accelerated into the slow and fast solar wind. In fact, the transition region is critical to the evolution of elements like Carbon and Oxygen, which are the most abundant heavy species observed by in-situ mass spectrometers. The predicted charge state distribution will be used to validate the global model in two ways. First, the predicted frozen-in charge state distribution can be directly compared to in-situ measurements in the heliosphere made by the SWICS instrument on board ACE and Ulysses. Second, the charge state values predicted in the inner corona (below 1.5 solar radii) can be combined with the CHIANTI database and the global model's 3D temperature and density distributions to calculate spectral line intensities and narrow-band images along any line of sight, to be compared with observations from the SOHO/EIT, STEREO/EUVI, Hinode/EIS and SDO/AIA instruments. We analyze both the solar minimum and maximum cases

  13. Low-cost photodynamic therapy devices for global health settings: Characterization of battery-powered LED performance and smartphone imaging in 3D tumor models.

    PubMed

    Hempstead, Joshua; Jones, Dustin P; Ziouche, Abdelali; Cramer, Gwendolyn M; Rizvi, Imran; Arnason, Stephen; Hasan, Tayyaba; Celli, Jonathan P

    2015-01-01

    A lack of access to effective cancer therapeutics in resource-limited settings is implicated in global cancer health disparities between developed and developing countries. Photodynamic therapy (PDT) is a light-based treatment modality that has exhibited safety and efficacy in the clinic using wavelengths and irradiances achievable with light-emitting diodes (LEDs) operated on battery power. Here we assess low-cost enabling technology to extend the clinical benefit of PDT to regions with little or no access to electricity or medical infrastructure. We demonstrate the efficacy of a device based on a 635 nm high-output LED powered by three AA disposable alkaline batteries, to achieve strong cytotoxic response in monolayer and 3D cultures of A431 squamous carcinoma cells following photosensitization by administering aminolevulinic acid (ALA) to induce the accumulation of protoporphyrin IX (PpIX). Here we characterize challenges of battery-operated device performance, including battery drain and voltage stability specifically over relevant PDT dose parameters. Further motivated by the well-established capacity of PDT photosensitizers to serve as tumour-selective fluorescence contrast agents, we demonstrate the capability of a consumer smartphone with low-cost add-ons to measure concentration-dependent PpIX fluorescence. This study lays the groundwork for the on-going development of image-guided ALA-PDT treatment technologies for global health applications. PMID:25965295

  14. Low-cost photodynamic therapy devices for global health settings: Characterization of battery-powered LED performance and smartphone imaging in 3D tumor models

    NASA Astrophysics Data System (ADS)

    Hempstead, Joshua; Jones, Dustin P.; Ziouche, Abdelali; Cramer, Gwendolyn M.; Rizvi, Imran; Arnason, Stephen; Hasan, Tayyaba; Celli, Jonathan P.

    2015-05-01

    A lack of access to effective cancer therapeutics in resource-limited settings is implicated in global cancer health disparities between developed and developing countries. Photodynamic therapy (PDT) is a light-based treatment modality that has exhibited safety and efficacy in the clinic using wavelengths and irradiances achievable with light-emitting diodes (LEDs) operated on battery power. Here we assess low-cost enabling technology to extend the clinical benefit of PDT to regions with little or no access to electricity or medical infrastructure. We demonstrate the efficacy of a device based on a 635 nm high-output LED powered by three AA disposable alkaline batteries, to achieve strong cytotoxic response in monolayer and 3D cultures of A431 squamous carcinoma cells following photosensitization by administering aminolevulinic acid (ALA) to induce the accumulation of protoporphyrin IX (PpIX). Here we characterize challenges of battery-operated device performance, including battery drain and voltage stability specifically over relevant PDT dose parameters. Further motivated by the well-established capacity of PDT photosensitizers to serve as tumour-selective fluorescence contrast agents, we demonstrate the capability of a consumer smartphone with low-cost add-ons to measure concentration-dependent PpIX fluorescence. This study lays the groundwork for the on-going development of image-guided ALA-PDT treatment technologies for global health applications.

  15. Low-cost photodynamic therapy devices for global health settings: Characterization of battery-powered LED performance and smartphone imaging in 3D tumor models

    PubMed Central

    Hempstead, Joshua; Jones, Dustin P.; Ziouche, Abdelali; Cramer, Gwendolyn M.; Rizvi, Imran; Arnason, Stephen; Hasan, Tayyaba; Celli, Jonathan P.

    2015-01-01

    A lack of access to effective cancer therapeutics in resource-limited settings is implicated in global cancer health disparities between developed and developing countries. Photodynamic therapy (PDT) is a light-based treatment modality that has exhibited safety and efficacy in the clinic using wavelengths and irradiances achievable with light-emitting diodes (LEDs) operated on battery power. Here we assess low-cost enabling technology to extend the clinical benefit of PDT to regions with little or no access to electricity or medical infrastructure. We demonstrate the efficacy of a device based on a 635 nm high-output LED powered by three AA disposable alkaline batteries, to achieve strong cytotoxic response in monolayer and 3D cultures of A431 squamous carcinoma cells following photosensitization by administering aminolevulinic acid (ALA) to induce the accumulation of protoporphyrin IX (PpIX). Here we characterize challenges of battery-operated device performance, including battery drain and voltage stability specifically over relevant PDT dose parameters. Further motivated by the well-established capacity of PDT photosensitizers to serve as tumour-selective fluorescence contrast agents, we demonstrate the capability of a consumer smartphone with low-cost add-ons to measure concentration-dependent PpIX fluorescence. This study lays the groundwork for the on-going development of image-guided ALA-PDT treatment technologies for global health applications. PMID:25965295

  16. Using Global Plate Velocity Boundary Conditions for Embedded Regional Geodynamic Models: Application to 3-D Modeling of the Early Rifting of the South Atlantic

    NASA Astrophysics Data System (ADS)

    Taramón, Jorge M.; Morgan, Jason P.; Pérez-Gussinyé, Marta

    2016-04-01

    The treatment of far-field boundary conditions is one of the most poorly resolved issues for regional modeling of geodynamic processes. In viscous flow, the choice of far-field boundary conditions often strongly shapes the large-scale structure of a geosimulation. The mantle velocity field along the sidewalls and base of a modeling region is typically much more poorly known than the geometry of past global motions of the surface plates as constrained by global plate motion reconstructions. For regional rifting models it has become routine to apply highly simplified 'plate spreading' or 'uniform rifting' boundary conditions to a 3-D model that limits its ability to simulate the geodynamic evolution of a specific rifted margin. One way researchers are exploring the sensitivity of regional models to uncertain boundary conditions is to use a nested modeling approach in which a global model is used to determine a large-scale flow pattern that is imposed as a constraint along the boundaries of the region to be modeled. Here we explore the utility of a different approach that takes advantage of the ability of finite element models to use unstructured meshes than can embed much higher resolution sub-regions. Here we demonstrate the workflow and code tools that we created to generate this unstructured mesh: solver based on springs, guide-mesh and routines to improve the quality, e.g., closeness to a regular tetrahedron, of the tetrahedral elements of the mesh. Note that the same routines are used to generate a new mesh in the remeshing of a distorted Lagrangian mesh. In our initial project to validate this approach, we create a global spherical shell mesh in which a higher resolution sub-region is created around the nascent South Atlantic Rifting Margin. Global Plate motion BCs and plate boundaries are applied for the time of the onset of rifting, continuing through several 10s of Ma of rifting. Thermal, compositional, and melt-related buoyancy forces are only non

  17. Production of Lightning NO(x) and its Vertical Distribution Calculated from 3-D Cloud-scale Chemical Transport Model Simulations

    NASA Technical Reports Server (NTRS)

    Ott, Lesley; Pickering, Kenneth; Stenchikov, Georgiy; Allen, Dale; DeCaria, Alex; Ridley, Brian; Lin, Ruei-Fong; Lang, Steve; Tao, Wei-Kuo

    2009-01-01

    A 3-D cloud scale chemical transport model that includes a parameterized source of lightning NO(x), based on observed flash rates has been used to simulate six midlatitude and subtropical thunderstorms observed during four field projects. Production per intracloud (P(sub IC) and cloud-to-ground (P(sub CG)) flash is estimated by assuming various values of P(sub IC) and P(sub CG) for each storm and determining which production scenario yields NO(x) mixing ratios that compare most favorably with in-cloud aircraft observations. We obtain a mean P(sub CG) value of 500 moles NO (7 kg N) per flash. The results of this analysis also suggest that on average, P(sub IC) may be nearly equal to P(sub CG), which is contrary to the common assumption that intracloud flashes are significantly less productive of NO than are cloud-to-ground flashes. This study also presents vertical profiles of the mass of lightning NO(x), after convection based on 3-D cloud-scale model simulations. The results suggest that following convection, a large percentage of lightning NO(x), remains in the middle and upper troposphere where it originated, while only a small percentage is found near the surface. The results of this work differ from profiles calculated from 2-D cloud-scale model simulations with a simpler lightning parameterization that were peaked near the surface and in the upper troposphere (referred to as a "C-shaped" profile). The new model results (a backward C-shaped profile) suggest that chemical transport models that assume a C-shaped vertical profile of lightning NO(x) mass may place too much mass neat the surface and too little in the middle troposphere.

  18. Europeana and 3D

    NASA Astrophysics Data System (ADS)

    Pletinckx, D.

    2011-09-01

    The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.

  19. Interpretation of Trace Gas Data Using Inverse Methods and Global Chemical Transport Models

    NASA Technical Reports Server (NTRS)

    Prinn, Ronald G.

    1997-01-01

    This is a theoretical research project aimed at: (1) development, testing, and refining of inverse methods for determining regional and global transient source and sink strengths for long lived gases important in ozone depletion and climate forcing, (2) utilization of inverse methods to determine these source/sink strengths which use the NCAR/Boulder CCM2-T42 3-D model and a global 3-D Model for Atmospheric Transport and Chemistry (MATCH) which is based on analyzed observed wind fields (developed in collaboration by MIT and NCAR/Boulder), (3) determination of global (and perhaps regional) average hydroxyl radical concentrations using inverse methods with multiple titrating gases, and, (4) computation of the lifetimes and spatially resolved destruction rates of trace gases using 3-D models. Important goals include determination of regional source strengths of methane, nitrous oxide, and other climatically and chemically important biogenic trace gases and also of halocarbons restricted by the Montreal Protocol and its follow-on agreements and hydrohalocarbons used as alternatives to the restricted halocarbons.

  20. Global 3-D modeling of atmospheric ozone in the free troposphere and the stratosphere with emphasis on midlatitude regions. Final report

    SciTech Connect

    Brasseur, G.; Tie, X.; Walters, S.

    1999-03-01

    The authors have used several global chemical/transport models (1) to study the contribution of various physical, chemical, and dynamical processes to the budget of mid-latitude ozone in the stratosphere and troposphere; (2) to analyze the potential mechanisms which are responsible for the observed ozone perturbations at mid-latitudes of the lower stratosphere and in the upper troposphere; (3) to calculate potential changes in atmospheric ozone response to anthropogenic changes (e.g., emission of industrially manufactured CFCs, CO, and NO{sub x}) and to natural perturbations (e.g., volcanic eruptions and biomass burning); and (4) to estimate the impact of these changes on the radiative forcing to the climate system and on the level of UV-B radiation at the surface.

  1. 3D Global PIC simulation of Alfvenic transition layers at the cusp outer boundary during IMF rotations from north to south

    NASA Astrophysics Data System (ADS)

    Cai, D. S.; Lembege, B.; Esmaeili, A.; Nishikawa, K.

    2013-12-01

    Statistical experimental observations of the cusp boundaries from CLUSTER mission made by Lavraud et al. (2005) have clearly evidenced the presence of a transition layer inside the magnetosheath near the outer boundary of the cusp. This layer characterized by Log(MA)~ 1 allows a transition from super-Alfvenic to sub-Alfvenic bulk flow from the exterior to the interior side of the outer cusp and has been mainly observed experimentally under northward interplanetary magnetic field (IMF). The role of this layer is important in order to understand the flow variations (and later the entry and precipitation of particles) when penetrating the outer boundary of the cusp. In order to analyze this layer, a large 3D PIC simulation of the global solar wind-terrestrial magnetosphere interaction have been performed, and the attention has been focused on the cusp region and its nearby surrounding during IMF rotation from north to south. Present results retrieve quite well the presence of this layer within the meridian plane for exactly northward IMF, but its location differs in the sense that it is located slightly below the X reconnection region associated to the nearby magnetopause (above the outer boundary of the cusp). In order to clarify this question, an extensive study has been performed as follows: (i) a 3D mapping of this transition layer in order to analyze more precisely the thickness, the location and the spatial extension of this layer on the magnetosphere flanks for a fixed Northward IMF configuration; (ii) a parametric study in order to analyze the impact of the IMF rotation from north to south on the persistence and the main features of this transition layer. The locations of this transition layer slightly radially expand and shrink during the IMF rotation and the thickness of the layer increases during the rotation. We show how these transition layers render the flow from super to sub Alfvenic and allow the particles enter into the magnetic cusp region. Alfven

  2. 3d-3d correspondence revisited

    NASA Astrophysics Data System (ADS)

    Chung, Hee-Joong; Dimofte, Tudor; Gukov, Sergei; Sułkowski, Piotr

    2016-04-01

    In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d {N}=2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. We also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  3. Arena3D: visualization of biological networks in 3D

    PubMed Central

    Pavlopoulos, Georgios A; O'Donoghue, Seán I; Satagopam, Venkata P; Soldatos, Theodoros G; Pafilis, Evangelos; Schneider, Reinhard

    2008-01-01

    Background Complexity is a key problem when visualizing biological networks; as the number of entities increases, most graphical views become incomprehensible. Our goal is to enable many thousands of entities to be visualized meaningfully and with high performance. Results We present a new visualization tool, Arena3D, which introduces a new concept of staggered layers in 3D space. Related data – such as proteins, chemicals, or pathways – can be grouped onto separate layers and arranged via layout algorithms, such as Fruchterman-Reingold, distance geometry, and a novel hierarchical layout. Data on a layer can be clustered via k-means, affinity propagation, Markov clustering, neighbor joining, tree clustering, or UPGMA ('unweighted pair-group method with arithmetic mean'). A simple input format defines the name and URL for each node, and defines connections or similarity scores between pairs of nodes. The use of Arena3D is illustrated with datasets related to Huntington's disease. Conclusion Arena3D is a user friendly visualization tool that is able to visualize biological or any other network in 3D space. It is free for academic use and runs on any platform. It can be downloaded or lunched directly from . Java3D library and Java 1.5 need to be pre-installed for the software to run. PMID:19040715

  4. Self consistent particles dynamics in/out of the cusp region by using back tracking technics; a global 3D PIC simulation approach

    NASA Astrophysics Data System (ADS)

    Esmaeili, A.; Cai, D.; Lembege, B.; Nishikawa, K.

    2013-12-01

    Large scale three dimensionbal PIC (particle in cell) simulations are presently used in order to analyze the global solar wind-terrestrial magnetosphere intreraction within a full self-consistent approach, and where both electrons and ions are treated as an assembly of individual particles. This 3D kinetic approach allows us to analyze in particular the dynamics and the fine structures of the cusp region when including self consistently not only its whole neighborhood (in the terrestrial magnetosphere) but also the impact of the solar wind and the interplanetary field (IMF) features. Herein, we focuss our attention on the cusp region and in particular on the acceleration and precipitation of particles (both ions and electrons) within the cusp. In present simulations, the IMF is chosen northward, (i.e. where the X -reconnection region is just above the cusp, in the meridian plane). Back-trackings of self-consistent particles are analyzed in details in order to determine (i) which particles (just above the cusp) are precipitated deeply into the cusp, (ii) which populations are injected from the cusp into the nearby tail, (iii) where the particles suffer the largest energisation along their self-consistent trajectories, (iv) where these populations accumulate, and (v) where the most energetic particles are originally coming from. This approach allows to make a traking of particles within the scenario "solar wind-magnetosheath- cusp -nearbytail"; moreover it strongly differs from the standard test particles technics and allows to provide informations not accessible when using full MHD approach. Keywords: Tracing Particles, Particle In Cell (PIC) simulation, double cusp, test particles method, IMF, Solar wind, Magnetosphere

  5. Accurate electronic and chemical properties of 3d transition metal oxides using a calculated linear response U and a DFT + U(V) method

    NASA Astrophysics Data System (ADS)

    Xu, Zhongnan; Joshi, Yogesh V.; Raman, Sumathy; Kitchin, John R.

    2015-04-01

    We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V ) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.

  6. Accurate electronic and chemical properties of 3d transition metal oxides using a calculated linear response U and a DFT + U(V) method

    SciTech Connect

    Xu, Zhongnan; Kitchin, John R.; Joshi, Yogesh V.; Raman, Sumathy

    2015-04-14

    We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V ) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.

  7. 3D and Education

    NASA Astrophysics Data System (ADS)

    Meulien Ohlmann, Odile

    2013-02-01

    Today the industry offers a chain of 3D products. Learning to "read" and to "create in 3D" becomes an issue of education of primary importance. 25 years professional experience in France, the United States and Germany, Odile Meulien set up a personal method of initiation to 3D creation that entails the spatial/temporal experience of the holographic visual. She will present some different tools and techniques used for this learning, their advantages and disadvantages, programs and issues of educational policies, constraints and expectations related to the development of new techniques for 3D imaging. Although the creation of display holograms is very much reduced compared to the creation of the 90ies, the holographic concept is spreading in all scientific, social, and artistic activities of our present time. She will also raise many questions: What means 3D? Is it communication? Is it perception? How the seeing and none seeing is interferes? What else has to be taken in consideration to communicate in 3D? How to handle the non visible relations of moving objects with subjects? Does this transform our model of exchange with others? What kind of interaction this has with our everyday life? Then come more practical questions: How to learn creating 3D visualization, to learn 3D grammar, 3D language, 3D thinking? What for? At what level? In which matter? for whom?

  8. Study of energy transfer from the solar wind to Earth's magnetosphere using the 3D- MHD BATS-R-US global model

    NASA Astrophysics Data System (ADS)

    Jauer, P. R.; Gonzalez, W. D.; de Souza Costa, C. L.; Souza, V. M.

    2013-12-01

    The interaction, transport and conversion of energy between the solar wind and Earth's magnetosphere have been studied for decades through in situ measurements and Magnetohydrodynamics simulation, (MHD). Nevertheless, due to the vast regions of space and nonlinearities of the physical processes there are many questions that still remain without conclusive answers. Currently, the MHD simulation is a powerful tool that helps other means of already existing research, even within its theoretical limitation; it provides information of the space regions where in situ measurements are rare or nonexistent. The aim of this work is the study of energy transfer from the solar wind through the calculation of the divergence of the Poynting vector for the inner regions of the Earth's magnetosphere, especially the magneto tail using 3D global MHD numerical code Space Weather Modelling Framework (SWMF) / (Block Adaptive Tree Solar wind Roe Upwind Scheme) (BATS-R-US), developed by the University of Michigan. We conducted a simulation study for the event that occurred on September 21-27, 1999, for which the peak value of the interplanetary magnetic field was -22 nT, and gave rise to an intense magnetic storm with peak Dst of -160 nT. Furthermore, we compare the results of the power estimated by the model - through the integration of the Poynting vector in rectangular region of the tail, with a domain -130

  9. Three-dimensional mapping of soil chemical characteristics at micrometric scale: Statistical prediction by combining 2D SEM-EDX data and 3D X-ray computed micro-tomographic images

    NASA Astrophysics Data System (ADS)

    Hapca, Simona

    2015-04-01

    Many soil properties and functions emerge from interactions of physical, chemical and biological processes at microscopic scales, which can be understood only by integrating techniques that traditionally are developed within separate disciplines. While recent advances in imaging techniques, such as X-ray computed tomography (X-ray CT), offer the possibility to reconstruct the 3D physical structure at fine resolutions, for the distribution of chemicals in soil, existing methods, based on scanning electron microscope (SEM) and energy dispersive X-ray detection (EDX), allow for characterization of the chemical composition only on 2D surfaces. At present, direct 3D measurement techniques are still lacking, sequential sectioning of soils, followed by 2D mapping of chemical elements and interpolation to 3D, being an alternative which is explored in this study. Specifically, we develop an integrated experimental and theoretical framework which combines 3D X-ray CT imaging technique with 2D SEM-EDX and use spatial statistics methods to map the chemical composition of soil in 3D. The procedure involves three stages 1) scanning a resin impregnated soil cube by X-ray CT, followed by precision cutting to produce parallel thin slices, the surfaces of which are scanned by SEM-EDX, 2) alignment of the 2D chemical maps within the internal 3D structure of the soil cube, and 3) development, of spatial statistics methods to predict the chemical composition of 3D soil based on the observed 2D chemical and 3D physical data. Specifically, three statistical models consisting of a regression tree, a regression tree kriging and cokriging model were used to predict the 3D spatial distribution of carbon, silicon, iron and oxygen in soil, these chemical elements showing a good spatial agreement between the X-ray grayscale intensities and the corresponding 2D SEM-EDX data. Due to the spatial correlation between the physical and chemical data, the regression-tree model showed a great potential

  10. Global chemical weathering and associated P-release

    NASA Astrophysics Data System (ADS)

    Hartmann, Jens; Moosdorf, Nils; Lauerwald, Ronny; Hinderer, Matthias; West, A. Joshua

    2014-05-01

    Chemical weathering releases phosphorus to soils and ecosystems. To improve understanding of the spatial distribution of the global P-release characteristics, a model framework for estimating global chemical weathering rates was coupled with geochemical information. Results suggest that the global soil shielding reduces chemical weathering fluxes by about 44%, compared to an Earth surface with no deeply weathered soils but relatively young rock surfaces (e.g. as in volcanic arc and other tectonically active areas). About 70% of the weathering fluxes globally derive from 10% of the land area, with Southeast Asia being a primary "hot spot" of chemical weathering and for P-release. In contrast, only 50% of runoff is attributed to 10% of the land area; thus the global chemical weathering rating curve is to some extent disconnected from the global runoff curve due to the spatially heterogeneous climate as well as differences in rock and soil properties. In addition to total chemical weathering fluxes, the release of P, a nutrient that controls biological productivity at large spatial scales, is affected by the spatial correlation between runoff, lithology, temperature and soil properties. The areal abundance of deeply weathered soils in Earth's past may have influenced weathering fluxes and P-fuelled biological productivity significantly, specifically in the case of larger climate shifts when high runoff fields shift to areas with thinner soils or areas with more weatherable rocks and relatively increased P-content. This observation may be particularly important for spatially resolved Earth system models targeting geological time scales. The full research text can be found in: Hartmann, J., N. Moosdorf, R. Lauerwald, M. Hinderer, A.J. West (2014) Global chemical weathering and associated P-release - the role of lithology, temperature and soil properties. Chemical Geology 363, 145-163. doi: 10.1016/j.chemgeo.2013.10.025 (open access)

  11. 3D Imaging.

    ERIC Educational Resources Information Center

    Hastings, S. K.

    2002-01-01

    Discusses 3 D imaging as it relates to digital representations in virtual library collections. Highlights include X-ray computed tomography (X-ray CT); the National Science Foundation (NSF) Digital Library Initiatives; output peripherals; image retrieval systems, including metadata; and applications of 3 D imaging for libraries and museums. (LRW)

  12. The Effects of Lightning NO(x) Production during the July 21 EULINOX Storm studied with a 3-D Cloud-scale Chemical Transport Model

    NASA Technical Reports Server (NTRS)

    Ott, Lesley E.; Pickering, Kenneth E.; Stenchikov, Georgiy L.; Huntrieser, Heidi; Schumann, Ulrich

    2006-01-01

    The July 21,1998 thunderstonn observed during the European Lightning Nitrogen Oxides Project (EULINOX) project was simulated using the three-dimensional Goddard Cumulus Ensemble (GCE) model. The simulation successfully reproduced a number of observed storm features including the splitting of the original cell into a southern cell which developed supercell characteristics, and a northern cell which became multicellular. Output from the GCE simulation was used to drive an offline cloud-scale chemical transport model which calculates tracer transport and includes a parameterization of lightning NO(x) production which uses observed flash rates as input. Estimates of lightning NO(x) production were deduced by assuming various values of production per intracloud and production per cloud-to-ground flash and comparing the results with in-cloud aircraft observations. The assumption that both types of flashes produce 360 moles of NO per flash on average compared most favorably with column mass and probability distribution functions calculated from observations. This assumed production per flash corresponds to a global annual lightning NOx source of 7 Tg N per yr. Chemical reactions were included in the model to evaluate the impact of lightning NO(x), on ozone. During the storm, the inclusion of lightning NOx in the model results in a small loss of ozone (on average less than 4 ppbv) at all model levels. Simulations of the chemical environment in the 24 hours following the storm show on average a small increase in the net production of ozone at most levels resulting from lightning NO(x), maximizing at approximately 5 ppbv per day at 5.5 km. Between 8 and 10.5 km, lightning NO(x) causes decreased net ozone production.

  13. Effects of Chemical Aging on Global Secondary Organic Aerosol using the Volatility Basis Set Approach

    NASA Astrophysics Data System (ADS)

    Park, R.; Jo, D.; Kim, M.; Spracklen, D. V.; Hodzic, A.

    2014-12-01

    Organic aerosol (OA) constitutes significant mass fractions (20-90%) of total dry fine aerosols in the atmosphere. However, global models of OA have shown large discrepancies when compared to the observations because of the limited capability to simulate secondary OA (SOA). For reducing the discrepancies between observations and models, recent studies have shown that chemical aging reactions in the atmosphere are important because they can lead to decreases in organic volatility, resulting in increase of SOA mass yields. To efficiently simulate chemical aging of SOA in the atmosphere, we implemented the volatility basis set approach in a global 3-D chemical transport model (GEOS-Chem). We present full-year simulations and their comparisons with multiple observations - global aerosol mass spectrometer dataset, the Interagency Monitoring of Protected Visual Environments from the United States, the European Monitoring and Evaluation Programme dataset and water-soluble organic carbon observation data collected over East Asia. Using different input parameters in the model, we also explore the uncertainty of the SOA simulation for which we use an observational constraint to find the optimized values with which the model reduces the discrepancy from the observations. Finally, we estimate the effect of OA on climate using our best simulation results.

  14. TRACE 3-D documentation

    SciTech Connect

    Crandall, K.R.

    1987-08-01

    TRACE 3-D is an interactive beam-dynamics program that calculates the envelopes of a bunched beam, including linear space-charge forces, through a user-defined transport system. TRACE 3-D provides an immediate graphics display of the envelopes and the phase-space ellipses and allows nine types of beam-matching options. This report describes the beam-dynamics calculations and gives detailed instruction for using the code. Several examples are described in detail.

  15. Bootstrapping 3D fermions

    NASA Astrophysics Data System (ADS)

    Iliesiu, Luca; Kos, Filip; Poland, David; Pufu, Silviu S.; Simmons-Duffin, David; Yacoby, Ran

    2016-03-01

    We study the conformal bootstrap for a 4-point function of fermions < ψψψψ> in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge C T . We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N . We also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

  16. Global magnetosphere-like 3D structure formation in kinetics by hot magnetized plasma flow characterized by shape of the particle distribution function

    NASA Astrophysics Data System (ADS)

    Gubchenko, Vladimir

    The task was to provide an analytical elementary magnetosphere-like model in kinetics for verification of the 3D EM PIC codes created for space/aerospace and HED plasmas applications. Kinetic approach versus cold MHD approach takes into account different behavior in the EM fields of resonant and non resonant particles in the velocity phase space, which appears via shape characteristics of the particle velocity distribution function (PVDF) and via the spatial dispersion effect forming the collisionless dissipation in the EM fields. The external flow is a hot collisionless plasma characterized by the particle velocity distribution function (PVDF) with different shapes: Maxwellian, kappa, etc. The flow is in a “hot regime”: it can be supersonic but its velocity remains less the thermal velocity of the electrons. The “internal” part of the magnetosphere formed by trapped particles is the prescribed 3D stationary magnetization considered as a spherical “quasiparticle” with internal magnetodipole and toroidal moments represented as a broadband EM driver. We obtain after the linearization of Vlasov/Maxwell equations a self-consistent 3D large scale kinetic solution of the classic problem. Namely, we: model the “outer” part of the magnetosphere formed by external hot plasma flow of the flyby particles. Solution of the Vlasov equation expressed via a tensor of dielectric permittivity of nonmagnetized and magnetized flowing plasma. Here, we obtain the direct kinetic dissipative effect of the magnetotail formation and the opposite diamagnetic effect of the magnetosphere “dipolization”. We get MHD wave cone in flow magnetized by external guiding magnetic (GM) field. Magnetosphere in our consideration is a 3D dissipative “wave” package structure of the skinned EM fields formed by the “waves” excited at frequency bands where we obtain negative values and singularities (resonances) of squared EM refractive index of the cold plasma. The hot regime

  17. Global surveillance for chemical incidents of international public health concern.

    PubMed Central

    Olowokure, B.; Pooransingh, S.; Tempowski, J.; Palmer, S.; Meredith, T.

    2005-01-01

    OBJECTIVE: In December 2001, an expert consultation convened by WHO identified strengthening national and global chemical incident preparedness and response as a priority. WHO is working towards this objective by developing a surveillance and response system for chemical incidents. This report describes the frequency, nature and geographical location of acute chemical incidents of potential international concern from August 2002 to December 2003. METHODS: Acute chemical incidents were actively identified through several informal (e.g. Internet-based resources) and formal (e.g. various networks of organizations) sources and assessed against criteria for public health emergencies of international concern using the then proposed revised International Health Regulations (IHR). WHO regional and country offices were contacted to obtain additional information regarding identified incidents. FINDINGS: Altogether, 35 chemical incidents from 26 countries met one or more of the IHR criteria. The WHO European Region accounted for 43% (15/35) of reports. The WHO Regions for Africa, Eastern Mediterranean and Western Pacific each accounted for 14% (5/35); South-East Asia and the Americas accounted for 9% (3/35) and 6% (2/35), respectively. Twenty-three (66%) events were identified within 24 hours of their occurrence. CONCLUSION: To our knowledge this is the first global surveillance system for chemical incidents of potential international concern. Limitations such as geographical and language bias associated with the current system are being addressed. Nevertheless, the system has shown that it can provide early detection of important events, as well as information on the magnitude and geographical distribution of such incidents. It can therefore contribute to improving global public health preparedness. PMID:16462985

  18. 3D microscope

    NASA Astrophysics Data System (ADS)

    Iizuka, Keigo

    2008-02-01

    In order to circumvent the fact that only one observer can view the image from a stereoscopic microscope, an attachment was devised for displaying the 3D microscopic image on a large LCD monitor for viewing by multiple observers in real time. The principle of operation, design, fabrication, and performance are presented, along with tolerance measurements relating to the properties of the cellophane half-wave plate used in the design.

  19. Global Materials Structure Search with Chemically Motivated Coordinates.

    PubMed

    Panosetti, Chiara; Krautgasser, Konstantin; Palagin, Dennis; Reuter, Karsten; Maurer, Reinhard J

    2015-12-01

    Identification of relevant reaction pathways in ever more complex composite materials and nanostructures poses a central challenge to computational materials discovery. Efficient global structure search, tailored to identify chemically relevant intermediates, could provide the necessary first-principles atomistic insight to enable a rational process design. In this work we modify a common feature of global geometry optimization schemes by employing automatically generated collective curvilinear coordinates. The similarity of these coordinates to molecular vibrations enhances the generation of chemically meaningful trial structures for covalently bound systems. In the application to hydrogenated Si clusters, we concomitantly observe a significantly increased efficiency in identifying low-energy structures and exploit it for an extensive sampling of potential products of silicon-cluster soft landing on Si(001) surfaces. PMID:26444084

  20. Assessment of Anthropogenic and Climatic Impacts on the Global Carbon Cycle Using a 3-D Model Constrained by Isotopic Carbon Measurements and Remote Sensing of Vegetation

    NASA Technical Reports Server (NTRS)

    Keeling, Charles D.; Piper, S. C.

    1998-01-01

    Our original proposal called for improved modeling of the terrestrial biospheric carbon cycle, specifically using biome-specific process models to account for both the energy and water budgets of plant growth, to facilitate investigations into recent changes in global atmospheric CO2 abundance and regional distribution. The carbon fluxes predicted by these models were to be incorporated into a global model of CO2 transport to establish large-scale regional fluxes of CO2 to and from the terrestrial biosphere subject to constraints imposed by direct measurements of atmospheric CO2 and its 13C/12C isotopic ratio. Our work was coordinated with a NASA project (NASA NAGW-3151) at the University of Montana under the direction of Steven Running, and was partially funded by the Electric Power Research Institute. The primary objective of this project was to develop and test the Biome-BGC model, a global biological process model with a daily time step which simulates the water, energy and carbon budgets of plant growth. The primary product, the unique global gridded daily land temperature, and the precipitation data set which was used to drive the process model is described. The Biome-BGC model was tested by comparison with a simpler biological model driven by satellite-derived (NDVI) Normalized Difference Vegetation Index and (PAR) Photosynthetically Active Radiation data and by comparison with atmospheric CO2 observations. The simple NDVI model is also described. To facilitate the comparison with atmospheric CO2 observations, a three-dimensional atmospheric transport model was used to produce predictions of atmospheric CO2 variations given CO2 fluxes owing to (NPP) Net Primary Productivity and heterotrophic respiration that were produced by the Biome-BGC model and by the NDVI model. The transport model that we used in this project, and errors associated with transport simulations, were characterized by a comparison of 12 transport models.

  1. Tidal energy conversion in a global hot spot: On the 3-D dynamics of baroclinic tides at the Celtic Sea shelf break

    NASA Astrophysics Data System (ADS)

    Vlasenko, Vasiliy; Stashchuk, Nataliya; Inall, Mark E.; Hopkins, Joanne E.

    2014-06-01

    Globally, the Celtic Sea shelf break is ranked highest as an energetic "hot spot" of tidal energy conversion, therefore making it the most significant contributor to global internal tidal energy flux. In this paper, the three-dimensional dynamics of baroclinic tides in the shelf-slope area of the Celtic Sea was investigated numerically and using observational data collected on the 376th cruise of the RV "RRS Discovery" in June 2012. The time series recorded at a shelf break mooring showed that semidiurnal internal waves were accompanied by packets of internal solitary waves with maximum amplitudes up to 105 m, the largest internal waves ever recorded in the Celtic Sea, and ranking among the largest observed in the global ocean. The observed baroclinic wavefields were replicated numerically using the Massachusetts Institute of Technology general circulation model. A fine-resolution grid with 115 m horizontal and 10 m vertical steps allowed the identification of two classes of short-scale internal waves. The first classification was generated over headlands and resembles spiral-type internal waves that are typical for isolated underwater banks. The second classification, generated within an area of several canyons, revealed properties of quasi-planar internal wave packets. The observed in situ intensification of tidal bottom currents at the shelf break mooring is explained in terms of a tidal beam that was formed over supercritical bottom topography at the mooring location.

  2. Analytical finite element matrix elements and global matrix assembly for hierarchical 3-D vector basis functions within the hybrid finite element boundary integral method

    NASA Astrophysics Data System (ADS)

    Li, L.; Wang, K.; Li, H.; Eibert, T. F.

    2014-11-01

    A hybrid higher-order finite element boundary integral (FE-BI) technique is discussed where the higher-order FE matrix elements are computed by a fully analytical procedure and where the gobal matrix assembly is organized by a self-identifying procedure of the local to global transformation. This assembly procedure applys to both, the FE part as well as the BI part of the algorithm. The geometry is meshed into three-dimensional tetrahedra as finite elements and nearly orthogonal hierarchical basis functions are employed. The boundary conditions are implemented in a strong sense such that the boundary values of the volume basis functions are directly utilized within the BI, either for the tangential electric and magnetic fields or for the asssociated equivalent surface current densities by applying a cross product with the unit surface normals. The self-identified method for the global matrix assembly automatically discerns the global order of the basis functions for generating the matrix elements. Higher order basis functions do need more unknowns for each single FE, however, fewer FEs are needed to achieve the same satisfiable accuracy. This improvement provides a lot more flexibility for meshing and allows the mesh size to raise up to λ/3. The performance of the implemented system is evaluated in terms of computation time, accuracy and memory occupation, where excellent results with respect to precision and computation times of large scale simulations are found.

  3. Chemical oxygen-iodine laser (COIL) beam quality predictions using 3D Navier-Stokes (MINT) and wave optics (OCELOT) codes

    NASA Astrophysics Data System (ADS)

    Lampson, Alan I.; Plummer, David N.; Erkkila, John H.; Crowell, Peter G.; Helms, Charles A.

    1998-05-01

    This paper describes a series of analyses using the 3-d MINT Navier-Stokes and OCELOT wave optics codes to calculate beam quality in a COIL laser cavity. To make this analysis tractable, the problem was broken into two contributions to the medium quality; that associated with microscale disturbances primarily from the transverse iodine injectors, and that associated with the macroscale including boundary layers and shock-like effects. Results for both microscale and macroscale medium quality are presented for the baseline layer operating point in terms of single pass wavefront error. These results show that the microscale optical path difference effects are 1D in nature and of low spatial order. The COIL medium quality is shown to be dominated by macroscale effects; primarily pressure waves generated from flow/boundary layer interactions on the cavity shrouds.

  4. 3D Tomography of Accretionary Lapilli From The Island of Stromboli (Aeolian Archipelago, Italy): Spatial Arrangement, Internal Structure, Grain Size Distribution and Chemical Characterization

    NASA Astrophysics Data System (ADS)

    Morgavi, D.; Ielpo, M.; Valentini, L.; Laeger, K.; Paredes, J.; Petrelli, M.; Costa, A.; Perugini, D.

    2015-12-01

    The Secche di Lazzaro formation (7 Ka) is a phreatomagmatic deposit in the south-western part of the island of Stromboli (Aeolian Archipelago, Italy). The volcanic sequence is constituted by three main sub-units. In two of them abundant accretionary lapilli are present. We performed granulometric analysis to describe the spatial arrangement and the grain-size distribution of the lapilli inside the deposit. Lapilli were characterized by SEM investigations (BSE images). EMPA and LA-ICP-MS analyses of major and trace elements on glasses and minerals were performed. Although BSE images provide accurate morphological information, they do not allow the real 3D microstructure to be accessed. Therefore, non-invasive 3D imaging of the lapilli was performed by X-ray micro-tomography (X-mCT). The results of the X-mCT measurements provided a set of 2D cross-sectional slices stacked along the vertical axis, with a voxel size varying between 2.7 and 4.1 mm, depending on the size of the sample. The X-mCT images represent a mapping of X-ray attenuation, which in turn depends on the density of the phases distributed within the sample. This technique helped us to better constrain the particle and crystal distribution inside the accretionary lapilli. The recognized phases are: glass, clinopyroxene, plagioclase and Ti-Fe minerals. We discover also a high concentration of Na, Cl and SO3 in the ash matrix. This evidence is ubiquitous in all the accretionary lapilli. The work presented here could define a new route for future studies in the field of physical volcanology as X-ray micro-tomography could be a useful, non destructive technique to better characterize the internal structure of accretionary lapilli helping us to describe grain-size distribution of component particles and their spatial distribution within aggregates.

  5. Multiviewer 3D monitor

    NASA Astrophysics Data System (ADS)

    Kostrzewski, Andrew A.; Aye, Tin M.; Kim, Dai Hyun; Esterkin, Vladimir; Savant, Gajendra D.

    1998-09-01

    Physical Optics Corporation has developed an advanced 3-D virtual reality system for use with simulation tools for training technical and military personnel. This system avoids such drawbacks of other virtual reality (VR) systems as eye fatigue, headaches, and alignment for each viewer, all of which are due to the need to wear special VR goggles. The new system is based on direct viewing of an interactive environment. This innovative holographic multiplexed screen technology makes it unnecessary for the viewer to wear special goggles.

  6. 3D Audio System

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Ames Research Center research into virtual reality led to the development of the Convolvotron, a high speed digital audio processing system that delivers three-dimensional sound over headphones. It consists of a two-card set designed for use with a personal computer. The Convolvotron's primary application is presentation of 3D audio signals over headphones. Four independent sound sources are filtered with large time-varying filters that compensate for motion. The perceived location of the sound remains constant. Possible applications are in air traffic control towers or airplane cockpits, hearing and perception research and virtual reality development.

  7. 3D Surgical Simulation

    PubMed Central

    Cevidanes, Lucia; Tucker, Scott; Styner, Martin; Kim, Hyungmin; Chapuis, Jonas; Reyes, Mauricio; Proffit, William; Turvey, Timothy; Jaskolka, Michael

    2009-01-01

    This paper discusses the development of methods for computer-aided jaw surgery. Computer-aided jaw surgery allows us to incorporate the high level of precision necessary for transferring virtual plans into the operating room. We also present a complete computer-aided surgery (CAS) system developed in close collaboration with surgeons. Surgery planning and simulation include construction of 3D surface models from Cone-beam CT (CBCT), dynamic cephalometry, semi-automatic mirroring, interactive cutting of bone and bony segment repositioning. A virtual setup can be used to manufacture positioning splints for intra-operative guidance. The system provides further intra-operative assistance with the help of a computer display showing jaw positions and 3D positioning guides updated in real-time during the surgical procedure. The CAS system aids in dealing with complex cases with benefits for the patient, with surgical practice, and for orthodontic finishing. Advanced software tools for diagnosis and treatment planning allow preparation of detailed operative plans, osteotomy repositioning, bone reconstructions, surgical resident training and assessing the difficulties of the surgical procedures prior to the surgery. CAS has the potential to make the elaboration of the surgical plan a more flexible process, increase the level of detail and accuracy of the plan, yield higher operative precision and control, and enhance documentation of cases. Supported by NIDCR DE017727, and DE018962 PMID:20816308

  8. Positional Awareness Map 3D (PAM3D)

    NASA Technical Reports Server (NTRS)

    Hoffman, Monica; Allen, Earl L.; Yount, John W.; Norcross, April Louise

    2012-01-01

    The Western Aeronautical Test Range of the National Aeronautics and Space Administration s Dryden Flight Research Center needed to address the aging software and hardware of its current situational awareness display application, the Global Real-Time Interactive Map (GRIM). GRIM was initially developed in the late 1980s and executes on older PC architectures using a Linux operating system that is no longer supported. Additionally, the software is difficult to maintain due to its complexity and loss of developer knowledge. It was decided that a replacement application must be developed or acquired in the near future. The replacement must provide the functionality of the original system, the ability to monitor test flight vehicles in real-time, and add improvements such as high resolution imagery and true 3-dimensional capability. This paper will discuss the process of determining the best approach to replace GRIM, and the functionality and capabilities of the first release of the Positional Awareness Map 3D.

  9. Did life originate from a global chemical reactor?

    PubMed

    Stüeken, E E; Anderson, R E; Bowman, J S; Brazelton, W J; Colangelo-Lillis, J; Goldman, A D; Som, S M; Baross, J A

    2013-03-01

    Many decades of experimental and theoretical research on the origin of life have yielded important discoveries regarding the chemical and physical conditions under which organic compounds can be synthesized and polymerized. However, such conditions often seem mutually exclusive, because they are rarely encountered in a single environmental setting. As such, no convincing models explain how living cells formed from abiotic constituents. Here, we propose a new approach that considers the origin of life within the global context of the Hadean Earth. We review previous ideas and synthesize them in four central hypotheses: (i) Multiple microenvironments contributed to the building blocks of life, and these niches were not necessarily inhabitable by the first organisms; (ii) Mineral catalysts were the backbone of prebiotic reaction networks that led to modern metabolism; (iii) Multiple local and global transport processes were essential for linking reactions occurring in separate locations; (iv) Global diversity and local selection of reactants and products provided mechanisms for the generation of most of the diverse building blocks necessary for life. We conclude that no single environmental setting can offer enough chemical and physical diversity for life to originate. Instead, any plausible model for the origin of life must acknowledge the geological complexity and diversity of the Hadean Earth. Future research may therefore benefit from identifying further linkages between organic precursors, minerals, and fluids in various environmental contexts. PMID:23331348

  10. 3D polarimetric purity

    NASA Astrophysics Data System (ADS)

    Gil, José J.; San José, Ignacio

    2010-11-01

    From our previous definition of the indices of polarimetric purity for 3D light beams [J.J. Gil, J.M. Correas, P.A. Melero and C. Ferreira, Monogr. Semin. Mat. G. de Galdeano 31, 161 (2004)], an analysis of their geometric and physical interpretation is presented. It is found that, in agreement with previous results, the first parameter is a measure of the degree of polarization, whereas the second parameter (called the degree of directionality) is a measure of the mean angular aperture of the direction of propagation of the corresponding light beam. This pair of invariant, non-dimensional, indices of polarimetric purity contains complete information about the polarimetric purity of a light beam. The overall degree of polarimetric purity is obtained as a weighted quadratic average of the degree of polarization and the degree of directionality.

  11. 3D field harmonics

    SciTech Connect

    Caspi, S.; Helm, M.; Laslett, L.J.

    1991-03-30

    We have developed an harmonic representation for the three dimensional field components within the windings of accelerator magnets. The form by which the field is presented is suitable for interfacing with other codes that make use of the 3D field components (particle tracking and stability). The field components can be calculated with high precision and reduced cup time at any location (r,{theta},z) inside the magnet bore. The same conductor geometry which is used to simulate line currents is also used in CAD with modifications more readily available. It is our hope that the format used here for magnetic fields can be used not only as a means of delivering fields but also as a way by which beam dynamics can suggest correction to the conductor geometry. 5 refs., 70 figs.

  12. 'Bonneville' in 3-D!

    NASA Technical Reports Server (NTRS)

    2004-01-01

    The Mars Exploration Rover Spirit took this 3-D navigation camera mosaic of the crater called 'Bonneville' after driving approximately 13 meters (42.7 feet) to get a better vantage point. Spirit's current position is close enough to the edge to see the interior of the crater, but high enough and far enough back to get a view of all of the walls. Because scientists and rover controllers are so pleased with this location, they will stay here for at least two more martian days, or sols, to take high resolution panoramic camera images of 'Bonneville' in its entirety. Just above the far crater rim, on the left side, is the rover's heatshield, which is visible as a tiny reflective speck.

  13. Influence of Asian outflow on Rishiri Island, northernmost Japan: Application of radon as a tracer for characterizing fetch regions and evaluating a global 3D model

    NASA Astrophysics Data System (ADS)

    Zhu, Chunmao; Yoshikawa-Inoue, Hisayuki; Matsueda, Hidekadzu; Sawa, Yosuke; Niwa, Yosuke; Wada, Akira; Tanimoto, Hiroshi

    2012-04-01

    Atmospheric 222Rn was monitored from December 2008 to November 2010 on Rishiri Island (45°07‧N, 141°12‧E), northernmost Japan. Seasonal 222Rn variation was characterized by high concentrations from November to February and low concentrations from May to July, caused by the alternation of continental and maritime fetch regions. 222Rn tracer and back trajectory cluster analyses indicated that the predominant continental fetch region was southeastern Siberia and northeastern China. 222Rn emitted from China and South Korea, whose economies are growing rapidly, did not significantly affect the Rishiri site. The major maritime fetch region was the Sea of Okhotsk and the Bering Sea. A global three-dimensional model (NICAM-TM) accurately simulated 222Rn concentrations on Rishiri Island and in the seasonal fetch regions. The time series of 222Rn data will make it possible to evaluate the sources and sinks of atmospheric greenhouse gases being monitored at Rishiri Island, which complements other sites in the Asia-Pacific rim region, and to validate model simulations used to examine trans-boundary air pollution.

  14. Investigating Global 3-D Shear-Wave Anisotropy in the Earth's Mantle from Free Oscillations, Body Waves, Surface Waves and Long-period Waveforms

    NASA Astrophysics Data System (ADS)

    Moulik, P.; Ekstrom, G.

    2012-12-01

    We have developed a framework that can be used to investigate anisotropic velocity, density and anelastic heterogeneity in the Earth's mantle using a wide spectrum (0.3-50 mHz) of seismological observables. We start with the extensive dataset of surface-wave phase anomalies, long-period waveforms, and body-wave travel times collected by Kustowski et al. (2008) for the development of the global model S362ANI. The additional data included in our analysis are splitting functions of spheroidal and toroidal modes, which are analogous to phase velocity maps at low frequencies. We include in this set of observations a new dataset containing the splitting functions of 56 spheroidal fundamental modes and overtones, measured by Deuss et al. (2011, 2012) using data from large recent earthquakes. Apart from providing unique constraints on the long-wavelength elastic and density structure in the mantle, the overtone splitting data are especially sensitive to the velocity (and anisotropic) structure in the transition zone and in the deeper mantle. The detection of anisotropy, a marker of flow, in the transition zone has implications for our understanding of mantle convection. Our forward modeling of the splitting functions, like the other types of data, includes the effects of radial anisotropy (Mochizuki, 1986). We show that the upper-mantle shear-wave anisotropy of S362ANI generates a clear contribution to the splitting functions of the modes that are sensitive to the upper-mantle structure. We explore the tradeoffs between fitting the mode splitting functions and the travel-times of body waves that turn in the transition zone or in the lower mantle (e.g. SS), while observing that the waveforms and the surface wave phase-anomalies provide complementary information about the mantle. Our experiments suggest that the splitting data are sufficiently sensitive to the anisotropy in the mantle such that their inclusion may provide a better depth resolution of the anisotropic shear

  15. Xenobiotic metabolism capacities of human skin in comparison with a 3D epidermis model and keratinocyte-based cell culture as in vitro alternatives for chemical testing: activating enzymes (Phase I).

    PubMed

    Götz, Christine; Pfeiffer, Roland; Tigges, Julia; Blatz, Veronika; Jäckh, Christine; Freytag, Eva-Maria; Fabian, Eric; Landsiedel, Robert; Merk, Hans F; Krutmann, Jean; Edwards, Robert J; Pease, Camilla; Goebel, Carsten; Hewitt, Nicola; Fritsche, Ellen

    2012-05-01

    Skin is important for the absorption and metabolism of exposed chemicals such as cosmetics or pharmaceuticals. The Seventh Amendment to the EU Cosmetics Directive prohibits the use of animals for cosmetic testing for certain endpoints, such as genotoxicity; therefore, there is an urgent need to understand the xenobiotic metabolizing capacities of human skin and to compare these activities with reconstructed 3D skin models developed to replace animal testing. We have measured Phase I enzyme activities of cytochrome P450 (CYP) and cyclooxygenase (COX) in ex vivo human skin, the 3D skin model EpiDerm™ (EPI-200), immortalized keratinocyte-based cell lines and primary normal human epidermal keratinocytes. Our data demonstrate that basal CYP enzyme activities are very low in whole human skin and EPI-200 as well as keratinocytes. In addition, activities in monolayer cells differed from organotypic tissues after induction. COX activity was similar in skin, EPI-200 and NHEK cells, but was significantly lower in immortalized keratinocytes. Hence, the 3D model EPI-200 might represent a more suitable model for dermatotoxicological studies. Altogether, these data help to better understand skin metabolism and expand the knowledge of in vitro alternatives used for dermatotoxicity testing. PMID:22509833

  16. Global harmonisation of classification and labelling of hazardous chemicals.

    PubMed

    Pratt, Iona S

    2002-03-10

    The Globally Harmonised System (GHS) for classification and labelling will provide an internationally agreed system for hazard classification of chemical products and for communication of those hazards. Under the system, chemicals will be classified according to their physical (e.g. flammability), health/toxicological and environmental hazards. The toxicological endpoints used in the system are acute toxicity, irritation or corrosivity, sensitisation, carcinogenicity, mutagenicity, reproductive toxicity and chronic or repeat dose toxicity. The intended target audiences are those concerned with transport of dangerous goods, consumers, workers and emergency responders. Labels and safety data sheets (SDS) are the core tools of the GHS hazard communication system, and the harmonised labelling elements are symbols (within a pictogram), signal words and hazard statements. The GHS will use a building block approach in which application may vary according to the circumstances, type of product, and stage of life cycle, allowing selection of the elements appropriate to the needs of the various end users. PMID:11869813

  17. Trophic magnification of organic chemicals: A global synthesis

    USGS Publications Warehouse

    Walters, David; Jardine, T.D.; Cade, Brian S.; Kidd, K.A.; Muir, D.C.G.; Leipzig-Scott, Peter C.

    2016-01-01

    Production of organic chemicals (OCs) is increasing exponentially, and some OCs biomagnify through food webs to potentially toxic levels. Biomagnification under field conditions is best described by trophic magnification factors (TMFs; per trophic level change in log-concentration of a chemical) which have been measured for more than two decades. Syntheses of TMF behavior relative to chemical traits and ecosystem properties are lacking. We analyzed >1500 TMFs to identify OCs predisposed to biomagnify and to assess ecosystem vulnerability. The highest TMFs were for OCs that are slowly metabolized by animals (metabolic rate kM < 0.01 day–1) and are moderately hydrophobic (log KOW 6–8). TMFs were more variable in marine than freshwaters, unrelated to latitude, and highest in food webs containing endotherms. We modeled the probability that any OC would biomagnify as a combined function of KOW and kM. Probability is greatest (∼100%) for slowly metabolized compounds, regardless of KOW, and lowest for chemicals with rapid transformation rates (kM > 0.2 day–1). This probabilistic model provides a new global tool for screening existing and new OCs for their biomagnification potential.

  18. Trophic Magnification of Organic Chemicals: A Global Synthesis.

    PubMed

    Walters, D M; Jardine, T D; Cade, B S; Kidd, K A; Muir, D C G; Leipzig-Scott, P

    2016-05-01

    Production of organic chemicals (OCs) is increasing exponentially, and some OCs biomagnify through food webs to potentially toxic levels. Biomagnification under field conditions is best described by trophic magnification factors (TMFs; per trophic level change in log-concentration of a chemical) which have been measured for more than two decades. Syntheses of TMF behavior relative to chemical traits and ecosystem properties are lacking. We analyzed >1500 TMFs to identify OCs predisposed to biomagnify and to assess ecosystem vulnerability. The highest TMFs were for OCs that are slowly metabolized by animals (metabolic rate kM < 0.01 day(-1)) and are moderately hydrophobic (log KOW 6-8). TMFs were more variable in marine than freshwaters, unrelated to latitude, and highest in food webs containing endotherms. We modeled the probability that any OC would biomagnify as a combined function of KOW and kM. Probability is greatest (∼100%) for slowly metabolized compounds, regardless of KOW, and lowest for chemicals with rapid transformation rates (kM > 0.2 day(-1)). This probabilistic model provides a new global tool for screening existing and new OCs for their biomagnification potential. PMID:27014905

  19. Modeling Cellular Processes in 3-D

    PubMed Central

    Mogilner, Alex; Odde, David

    2011-01-01

    Summary Recent advances in photonic imaging and fluorescent protein technology offer unprecedented views of molecular space-time dynamics in living cells. At the same time, advances in computing hardware and software enable modeling of ever more complex systems, from global climate to cell division. As modeling and experiment become more closely integrated, we must address the issue of modeling cellular processes in 3-D. Here, we highlight recent advances related to 3-D modeling in cell biology. While some processes require full 3-D analysis, we suggest that others are more naturally described in 2-D or 1-D. Keeping the dimensionality as low as possible reduces computational time and makes models more intuitively comprehensible; however, the ability to test full 3-D models will build greater confidence in models generally and remains an important emerging area of cell biological modeling. PMID:22036197

  20. [EVALUATION OF CHANGES OF GEOMETRICAL PARAMETERS OF ALGINATE DENTAL IMPRESSIONS DUE TO THE INFLUENCE OF CHEMICAL AND MICROWAVE DISINFECTION METHOD USING 3D TECHNOLOGIES].

    PubMed

    Nespraydko, V P; Shevchuk, V A; Michaylov, A A; Lyseyko, N V

    2015-01-01

    This clinical and laboratory study evaluated the effect of two methods of disinfection in different modes at the volume changes of alginate dental impressions and plaster models poured from them, as compared to the same parameters of plastic master models (PMM), using three-dimensional non-contact laser scanner and software. Immersion chemical disinfection for 15 min, microwave disinfection at 354 W for 10 minutes and combined disinfection with the power of 319 W for 4 minutes did not significantly affect the volumetric dimensional accuracy of the alginate impressions (P > 0.05). PMID:27491163

  1. Prominent rocks - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Many prominent rocks near the Sagan Memorial Station are featured in this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. Wedge is at lower left; Shark, Half-Dome, and Pumpkin are at center. Flat Top, about four inches high, is at lower right. The horizon in the distance is one to two kilometers away.

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  2. 'Diamond' in 3-D

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 3-D, microscopic imager mosaic of a target area on a rock called 'Diamond Jenness' was taken after NASA's Mars Exploration Rover Opportunity ground into the surface with its rock abrasion tool for a second time.

    Opportunity has bored nearly a dozen holes into the inner walls of 'Endurance Crater.' On sols 177 and 178 (July 23 and July 24, 2004), the rover worked double-duty on Diamond Jenness. Surface debris and the bumpy shape of the rock resulted in a shallow and irregular hole, only about 2 millimeters (0.08 inch) deep. The final depth was not enough to remove all the bumps and leave a neat hole with a smooth floor. This extremely shallow depression was then examined by the rover's alpha particle X-ray spectrometer.

    On Sol 178, Opportunity's 'robotic rodent' dined on Diamond Jenness once again, grinding almost an additional 5 millimeters (about 0.2 inch). The rover then applied its Moessbauer spectrometer to the deepened hole. This double dose of Diamond Jenness enabled the science team to examine the rock at varying layers. Results from those grindings are currently being analyzed.

    The image mosaic is about 6 centimeters (2.4 inches) across.

  3. Radiative Effect of Clouds on Tropospheric Chemistry in a Global Three-Dimensional Chemical Transport Model

    NASA Technical Reports Server (NTRS)

    Liu, Hongyu; Crawford, James H.; Pierce, Robert B.; Norris, Peter; Platnick, Steven E.; Chen, Gao; Logan, Jennifer A.; Yantosca, Robert M.; Evans, Mat J.; Kittaka, Chieko; Feng, Yan; Tie, Xuexi

    2006-01-01

    Clouds exert an important influence on tropospheric photochemistry through modification of solar radiation that determines photolysis frequencies (J-values). We assess the radiative effect of clouds on photolysis frequencies and key oxidants in the troposphere with a global three-dimensional (3-D) chemical transport model (GEOS-CHEM) driven by assimilated meteorological observations from the Goddard Earth Observing System data assimilation system (GEOS DAS) at the NASA Global Modeling and Assimilation Office (GMAO). We focus on the year of 2001 with the GEOS-3 meteorological observations. Photolysis frequencies are calculated using the Fast-J radiative transfer algorithm. The GEOS-3 global cloud optical depth and cloud fraction are evaluated and generally consistent with the satellite retrieval products from the Moderate Resolution Imaging Spectroradiometer (MODIS) and the International Satellite Cloud Climatology Project (ISCCP). Results using the linear assumption, which assumes linear scaling of cloud optical depth with cloud fraction in a grid box, show global mean OH concentrations generally increase by less than 6% because of the radiative effect of clouds. The OH distribution shows much larger changes (with maximum decrease of approx.20% near the surface), reflecting the opposite effects of enhanced (weakened) photochemistry above (below) clouds. The global mean photolysis frequencies for J[O1D] and J[NO2] in the troposphere change by less than 5% because of clouds; global mean O3 concentrations in the troposphere increase by less than 5%. This study shows tropical upper tropospheric O3 to be less sensitive to the radiative effect of clouds than previously reported (approx.5% versus approx.20-30%). These results emphasize that the dominant effect of clouds is to influence the vertical redistribution of the intensity of photochemical activity while global average effects remain modest, again contrasting with previous studies. Differing vertical distributions

  4. Highly-Sensitive Surface-Enhanced Raman Spectroscopy (SERS)-based Chemical Sensor using 3D Graphene Foam Decorated with Silver Nanoparticles as SERS substrate

    PubMed Central

    Srichan, Chavis; Ekpanyapong, Mongkol; Horprathum, Mati; Eiamchai, Pitak; Nuntawong, Noppadon; Phokharatkul, Ditsayut; Danvirutai, Pobporn; Bohez, Erik; Wisitsoraat, Anurat; Tuantranont, Adisorn

    2016-01-01

    In this work, a novel platform for surface-enhanced Raman spectroscopy (SERS)-based chemical sensors utilizing three-dimensional microporous graphene foam (GF) decorated with silver nanoparticles (AgNPs) is developed and applied for methylene blue (MB) detection. The results demonstrate that silver nanoparticles significantly enhance cascaded amplification of SERS effect on multilayer graphene foam (GF). The enhancement factor of AgNPs/GF sensor is found to be four orders of magnitude larger than that of AgNPs/Si substrate. In addition, the sensitivity of the sensor could be tuned by controlling the size of silver nanoparticles. The highest SERS enhancement factor of ∼5 × 104 is achieved at the optimal nanoparticle size of 50 nm. Moreover, the sensor is capable of detecting MB over broad concentration ranges from 1 nM to 100 μM. Therefore, AgNPs/GF is a highly promising SERS substrate for detection of chemical substances with ultra-low concentrations. PMID:27020705

  5. Highly-Sensitive Surface-Enhanced Raman Spectroscopy (SERS)-based Chemical Sensor using 3D Graphene Foam Decorated with Silver Nanoparticles as SERS substrate

    NASA Astrophysics Data System (ADS)

    Srichan, Chavis; Ekpanyapong, Mongkol; Horprathum, Mati; Eiamchai, Pitak; Nuntawong, Noppadon; Phokharatkul, Ditsayut; Danvirutai, Pobporn; Bohez, Erik; Wisitsoraat, Anurat; Tuantranont, Adisorn

    2016-03-01

    In this work, a novel platform for surface-enhanced Raman spectroscopy (SERS)-based chemical sensors utilizing three-dimensional microporous graphene foam (GF) decorated with silver nanoparticles (AgNPs) is developed and applied for methylene blue (MB) detection. The results demonstrate that silver nanoparticles significantly enhance cascaded amplification of SERS effect on multilayer graphene foam (GF). The enhancement factor of AgNPs/GF sensor is found to be four orders of magnitude larger than that of AgNPs/Si substrate. In addition, the sensitivity of the sensor could be tuned by controlling the size of silver nanoparticles. The highest SERS enhancement factor of ∼5 × 104 is achieved at the optimal nanoparticle size of 50 nm. Moreover, the sensor is capable of detecting MB over broad concentration ranges from 1 nM to 100 μM. Therefore, AgNPs/GF is a highly promising SERS substrate for detection of chemical substances with ultra-low concentrations.

  6. Interfacial micropore defect formation in PEDOT:PSS-Si hybrid solar cells probed by TOF-SIMS 3D chemical imaging.

    PubMed

    Thomas, Joseph P; Zhao, Liyan; Abd-Ellah, Marwa; Heinig, Nina F; Leung, K T

    2013-07-16

    Conducting p-type polymer layers on n-type Si have been widely studied for the fabrication of cost-effective hybrid solar cells. In this work, time-of-flight secondary ion mass spectrometry (TOF-SIMS) is used to provide three-dimensional chemical imaging of the interface between poly(3,4-ethylene-dioxythiophene):polystyrenesulfonate (PEDOT:PSS) and SiOx/Si in a hybrid solar cell. To minimize structural damage to the polymer layer, an Ar cluster sputtering source is used for depth profiling. The present result shows the formation of micropore defects in the interface region of the PEDOT:PSS layer on the SiOx/Si substrate. This interfacial micropore defect formation becomes more prominent with increasing thickness of the native oxide layer, which is a key device parameter that greatly affects the hybrid solar cell performance. Three-dimensional chemical imaging coupled with Ar cluster ion sputtering has therefore been demonstrated as an emerging technique for probing the interface of this and other polymer-inorganic systems. PMID:23745755

  7. Detailed and global chemical kinetics model for hydrogen

    SciTech Connect

    Marinov, N.M.; Westbrook, C.K.; Pitz, W.J.

    1995-03-01

    Detailed and global chemical kinetic computations for hydrogen-air mixtures have been performed to describe flame propagation, flame structure and ignition phenomena. Simulations of laminar flame speeds, flame compositions and shock tube ignition delay times have been successfully performed. Sensitivity analysis was applied to determine the governing rate-controlling reactions for the experimental data sets examined. In the flame propagation and structure studies, the reactions, OH + H{sub 2} = H{sub 2}0 + H, 0 + H{sub 2} = OH + H and 0 + OH = 0{sub 2} + H were the most important in flames. The shock tube ignition delay time study indicated the H + 0{sub 2} + M = H0{sub 2} + M (M = N{sub 2}, H{sub 2}) and 0 + OH = 0{sub 2} + H reactions controlled ignition. A global rate expression for a one-step overall reaction was developed and validated against experimental hydrogen-air laminar flame speed data. The global reaction expression was determined to be 1.8 {times} 10{sup 13} exp({minus}17614K/T)[H{sub 2}]{sup 1.0}[O{sub 2}]{sup 0.5} for the single step reaction H{sub 2} + 1/2O{sub 2} = H{sub 2}O.

  8. 3D ¹⁵N/¹⁵N/¹H chemical shift correlation experiment utilizing an RFDR-based ¹H/¹H mixing period at 100 kHz MAS.

    PubMed

    Nishiyama, Yusuke; Malon, Michal; Ishii, Yuji; Ramamoorthy, Ayyalusamy

    2014-07-01

    Homonuclear correlation NMR experiments are commonly used in the high-resolution structural studies of proteins. While (13)C/(13)C chemical shift correlation experiments utilizing dipolar recoupling techniques are fully utilized under MAS, correlation of the chemical shifts of (15)N nuclei in proteins has been a challenge. Previous studies have shown that the negligible (15)N-(15)N dipolar coupling in peptides or proteins necessitates the use of a very long mixing time (typically several seconds) for effective spin diffusion to occur and considerably slows down a (15)N/(15)N correlation experiment. In this study, we show that the use of mixing proton magnetization, instead of (15)N, via the recoupled (1)H-(1)H dipolar couplings enable faster (15)N/(15)N correlation. In addition, the use of proton-detection under ultrafast MAS overcomes the sensitivity loss due to multiple magnetization transfer (between (1)H and (15)N nuclei) steps. In fact, less than 300 nL (∼1.1 micromole quantity) sample is sufficient to acquire the 3D spectrum within 5 h. Our results also demonstrate that a 3D (15)N/(15)N/(1)H experiment can render higher resolution spectra that will be useful in the structural studies of proteins at ultrafast MAS frequencies. 3D (15)N/(15)N/(1)H and 2D radio frequency-driven dipolar recoupling (RFDR)-based (1)H/(1)H experimental results obtained from a powder sample of N-acetyla-L-(15)N-valyl-L-(15)N-leucine at 70 and 100kHz MAS frequencies are presented. PMID:24801998

  9. 3D-patterned polymer brush surfaces

    NASA Astrophysics Data System (ADS)

    Zhou, Xuechang; Liu, Xuqing; Xie, Zhuang; Zheng, Zijian

    2011-12-01

    Polymer brush-based three-dimensional (3D) structures are emerging as a powerful platform to engineer a surface by providing abundant spatially distributed chemical and physical properties. In this feature article, we aim to give a summary of the recent progress on the fabrication of 3D structures with polymer brushes, with a particular focus on the micro- and nanoscale. We start with a brief introduction on polymer brushes and the challenges to prepare their 3D structures. Then, we highlight the recent advances of the fabrication approaches on the basis of traditional polymerization time and grafting density strategies, and a recently developed feature density strategy. Finally, we provide some perspective outlooks on the future directions of engineering the 3D structures with polymer brushes.

  10. Xenobiotic metabolism capacities of human skin in comparison with a 3D-epidermis model and keratinocyte-based cell culture as in vitro alternatives for chemical testing: phase II enzymes.

    PubMed

    Götz, Christine; Pfeiffer, Roland; Tigges, Julia; Ruwiedel, Karsten; Hübenthal, Ulrike; Merk, Hans F; Krutmann, Jean; Edwards, Robert J; Abel, Josef; Pease, Camilla; Goebel, Carsten; Hewitt, Nicola; Fritsche, Ellen

    2012-05-01

    The 7th Amendment to the EU Cosmetics Directive prohibits the use of animals in cosmetic testing for certain endpoints, such as genotoxicity. Therefore, skin in vitro models have to replace chemical testing in vivo. However, the metabolic competence neither of human skin nor of alternative in vitro models has so far been fully characterized, although skin is the first-pass organ for accidentally or purposely (cosmetics and pharmaceuticals) applied chemicals. Thus, there is an urgent need to understand the xenobiotic-metabolizing capacities of human skin and to compare these activities to models developed to replace animal testing. We have measured the activity of the phase II enzymes glutathione S-transferase, UDP-glucuronosyltransferase and N-acetyltransferase in ex vivo human skin, the 3D epidermal model EpiDerm 200 (EPI-200), immortalized keratinocyte-based cell lines (HaCaT and NCTC 2544) and primary normal human epidermal keratinocytes. We show that all three phase II enzymes are present and highly active in skin as compared to phase I. Human skin, therefore, represents a more detoxifying than activating organ. This work systematically compares the activities of three important phase II enzymes in four different in vitro models directly to human skin. We conclude from our studies that 3D epidermal models, like the EPI-200 employed here, are superior over monolayer cultures in mimicking human skin xenobiotic metabolism and thus better suited for dermatotoxicity testing. PMID:22509834

  11. Global mechanistic model of SOA formation: effects of different chemical mechanisms

    NASA Astrophysics Data System (ADS)

    Lin, G.; Penner, J. E.; Sillman, S.; Taraborrelli, D.; Lelieveld, J.

    2011-09-01

    Recent experimental findings indicate that Secondary Organic Aerosol (SOA) represents an important and, under many circumstances, the major fraction of the organic aerosol burden. Here, we use a global 3-d model (IMPACT) to test the results of different mechanisms for the production of SOA. The basic mechanism includes SOA formation from organic nitrates and peroxides produced from an explicit chemical formulation, using partition coefficients based on thermodynamic principles. We also include the formation of non-evaporative SOA from the reaction of glyoxal and methylglyoxal on aqueous aerosols and cloud droplets as well as from the reaction of epoxides on aqueous aerosols. A model simulation including these SOA formation mechanisms gives an annual global SOA production of 113.5 Tg. The global production of SOA is substantially decreased to 85.0 Tg yr-1 if the HOx regeneration mechanism proposed by Peeters et al. (2009) is used. Model predictions with and without this HOx regeneration scheme are compared with multiple surface observation datasets, namely: the Interagency Monitoring of Protected Visual Environments (IMPROVE) for the United States, the European Monitoring and Evaluation Programme (EMEP) as well as Aerosol Mass Spectrometry (AMS) data measured in both Northern Hemisphere and tropical forest regions. All model simulations realistically predict the organic carbon mass observed in the Northern Hemisphere, although they tend to overestimate the concentrations in tropical forest regions. This overestimate may result from an unrealistically high uptake rate of glyoxal and methylglyoxal on aqueous aerosols and in cloud drops. The modeled OC in the free troposphere is in agreement with measurements in the ITCT-2K4 aircraft campaign over the North America and in pollution layers in Asia during the INTEX-B campaign, although the model underestimates OC in the free troposphere during the ACE-Asia campaign off the coast of Japan.

  12. Chemical cycling and deposition of atmospheric mercury: Global constraints from observations

    NASA Astrophysics Data System (ADS)

    Selin, Noelle E.; Jacob, Daniel J.; Park, Rokjin J.; Yantosca, Robert M.; Strode, Sarah; Jaeglé, Lyatt; Jaffe, Daniel

    2007-01-01

    We use a global 3-D model of atmospheric mercury (GEOS-Chem) to interpret worldwide observations of total gaseous mercury (TGM) and reactive gaseous mercury (RGM) in terms of the constraints they provide on the chemical cycling and deposition of mercury. Our simulation including a global mercury source of 7000 Mg yr-1 and a TGM lifetime of 0.8 years reproduces the magnitude and large-scale variability of TGM observations at land sites. However, it cannot capture observations of high TGM from ship cruises, implying a problem either in the measurements or in our fundamental understanding of mercury sources. Observed TGM seasonal variation at northern midlatitudes is consistent with a photochemical oxidation for Hg(0) partly balanced by photochemical reduction of Hg(II). Observations of increasing RGM with altitude imply a long lifetime of Hg(II) in the free troposphere. We find in the model that Hg(II) dominates over Hg(0) in the upper troposphere and stratosphere and that subsidence is the principal source of Hg(II) at remote surface sites. RGM observations at Okinawa Island (Japan) show large diurnal variability implying fast deposition, which we propose is due to RGM uptake by sea-salt aerosols. Observed mercury wet deposition fluxes in the United States show a maximum in the southeast, which we attribute to photochemical oxidation of the global Hg(0) pool. They also show a secondary maximum in the industrial Midwest due to regional emissions that is underestimated in the model, possibly because of excessive dry deposition relative to wet (dry deposition accounts for 68% of total mercury deposition in the United States in the model, but this is sensitive to the assumed phase of Hg(II)). We estimate that North American anthropogenic emissions contribute on average 20% to U.S. mercury deposition.

  13. OVOC (Oxygenated Volatile Organic Chemicals) in the Global Atmosphere: Atmospheric Budgets, Oceanic Concentrations, and Uncertainties

    NASA Technical Reports Server (NTRS)

    Singh, Hanwant B.

    2004-01-01

    Airborne measurements of oxygenated volatile organic chemicals (OVOC), OH free radicals, and tracers of pollution were performed over the Pacific during Winter/Spring of 2001. Large concentrations of OVOC are present in the global troposphere and are expected to play an important role in atmospheric chemistry. Their total abundance (SIGMAOVOC) was nearly twice that of non-methane hydrocarbons (SIGMAC2-C8 NMHC). Throughout the troposphere, the OH reactivity of OVOC is comparable to that of methane and far exceeds that of NHMC. A comparison of these data with western Pacific observations collected some seven years earlier (Feb.-March, 1994) did not reveal significant differences. Analysis of the relative enhancement of selected OVOC with respect to CH3Cl and CO in twelve plumes originating from fires and sampled in the free troposphere (3-11 km) is used to assess their primary and secondary emissions from biomass combustion. The composition of these plumes also indicates a large shift of reactive nitrogen into the PAN reservoir thereby limiting ozone formation. These data are combined with other observations and interpreted with the help of a global 3-D model to assess OVOC global sources and sinks. We further interpret atmospheric observations with the help of an air-sea exchange model io show that oceans can be both net sorces and sinks. An extremely large oceanic reservoir of OVOC, that exceeds the atmospheric reservoir by more than an order of magnitude, can be inferred to be present. We conclude that OVOC sources are extremely large (150-500 TgC y-1) but remain poorly quantified. In many cases, measured concentrations are uncertain and incompatible with our present knowledge of atmospheric chemistry. Results based on observations from several field studies and critical gaps will be discussed.

  14. A 3D Global climate model of the Pluto atmosphere to interpret New Horizons observations, including the N2, CH4 and CO cycles and the formation of organic hazes

    NASA Astrophysics Data System (ADS)

    Forget, Francois; Bertrand, Tanguy; Vangvichith, Melanie; Leconte, Jeremy

    2015-11-01

    To interpret New Horizons observations and simulate the Pluto climate system, we have developed a Global Climate Model (GCM) of Pluto's atmosphere. In addition to a 3D "dynamical core" which solves the equations of meteorology, the model takes into account the N2 condensation and sublimation and its thermal and dynamical effects, the vertical turbulent mixing, the radiative transfer through methane and carbon monoxide, molecular thermal conduction, and a detailed surface thermal model with different thermal inertia for various timescales (diurnal, seasonal).The GCM also includes a detailed model of the CH4 and CO cycles, taking into account their transport by the atmospheric circulation and turbulence, as well as their condensation and sublimation on the surface and in the atmosphere, possibly forming methane ice clouds. The GCM consistently predicts the 3D methane abundance in the atmosphere, which is used as an input for our radiative transfer calculation.Because of the radiative timescales, the surface thermal inertia and the slow evolution of the methane cycle, the model takes more than 20 years to become insensitive to the assumed atmospheric initial states. We typically start our simulations in 1975 to simulate 2015, but remain sensitive to the assumed initial ices distribution and seasonal thermal inertia map. The simulated thermal structure and waves can be compared to the New Horizons occultations measurements. As observed, the longitudinal variability is very limited, for fundamental reasons.In addition, we have developed a 3D model of the formation of organic hazes within the GCM. It includes the different steps of aerosols formation as understood on Titan: photolysis of CH4 in the upper atmosphere by the Lyman-alpha radiation, production of various gaseous precursor species, conversion into solid particles through chemistry and aggregation processes, and gravitational sedimentation. Significant amount of haze particles are found to be present at all

  15. 3D Spectroscopy in Astronomy

    NASA Astrophysics Data System (ADS)

    Mediavilla, Evencio; Arribas, Santiago; Roth, Martin; Cepa-Nogué, Jordi; Sánchez, Francisco

    2011-09-01

    Preface; Acknowledgements; 1. Introductory review and technical approaches Martin M. Roth; 2. Observational procedures and data reduction James E. H. Turner; 3. 3D Spectroscopy instrumentation M. A. Bershady; 4. Analysis of 3D data Pierre Ferruit; 5. Science motivation for IFS and galactic studies F. Eisenhauer; 6. Extragalactic studies and future IFS science Luis Colina; 7. Tutorials: how to handle 3D spectroscopy data Sebastian F. Sánchez, Begona García-Lorenzo and Arlette Pécontal-Rousset.

  16. DYNAMIC 3D QSAR TECHNIQUES: APPLICATIONS IN TOXICOLOGY

    EPA Science Inventory

    Two dynamic techniques recently developed to account for conformational flexibility of chemicals in 3D QSARs are presented. In addition to the impact of conformational flexibility of chemicals in 3D QSAR models, the applicability of various molecular descriptors is discussed. The...

  17. 3D Elevation Program—Virtual USA in 3D

    USGS Publications Warehouse

    Lukas, Vicki; Stoker, J.M.

    2016-01-01

    The U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) uses a laser system called ‘lidar’ (light detection and ranging) to create a virtual reality map of the Nation that is very accurate. 3D maps have many uses with new uses being discovered all the time.  

  18. Chemical Tracking Systems: Not Your Usual Global Positioning System!

    ERIC Educational Resources Information Center

    Roy, Ken

    2007-01-01

    The haphazard storing and tracking of chemicals in the laboratory is a serious safety issue facing science teachers. To get control of your chemicals, try implementing a "chemical tracking system". A chemical tracking system (CTS) is a database of chemicals used in the laboratory. If implemented correctly, a CTS will reduce purchasing costs,…

  19. Thermo-chemical Evolution and Global Contraction of Mercury

    NASA Astrophysics Data System (ADS)

    Grott, M.; Breuer, D.; Laneuville, M.

    2010-12-01

    The surface of Mercury exhibits a global system of tectonic landforms called lobate scarps, which bear witness to periods of global planetary contraction. These scarps have been identified on the basis of Mariner 10 imagery [1], and new estimates based on images acquired during the recent MESSENGER flybys indicate a global radius contraction of 1-2 km since the end of the late heavy bombardment (LHB) [2]. The contraction of Mercury has been attributed to a combination of planetary cooling and the growth of an inner core [3, 4], but the very limited amount of contraction documented on the surface poses severe constraints on admissible models. First of all, secular cooling alone causes radial contraction in excess of 2 km if average mantle temperatures drop by more than 50 K, limiting acceptable models to slowly cooling models with a preferably Th rich, refractory composition. Additionally, mantle rheology should be stiff, demanding the concentration of volatiles inside Mercury to be negligible. Furthermore, core freezing contributes a significant amount of contraction which can easily exceed 10 km if the inner core radius exceeds 50% of the total core radius. This limits admissible models to those with high sulphur content >7 wt%, preventing early core freezing and effectively eliminating inner core freeze-out from the radius balance. Therefore, current thermal evolution models require a refractory rich composition, high sulphur and low volatile content to be compatible with the observed low radial contraction [4]. These requirements are at odds with the evidence for pyroclastic eruptions on Mercury documented in recent MESSENGER images, as the magma volatile content required to emplace pyroclasts to the observed distance is estimated to be >0.4 wt% [5]. Here we reinvestigate the coupled thermal and chemical evolution of Mercury taking the presence of a poorly conducting megaregolith layer [6] and a thermally insulating crust into account. Models incorporating a

  20. 3-D Finite Element Heat Transfer

    1992-02-01

    TOPAZ3D is a three-dimensional implicit finite element computer code for heat transfer analysis. TOPAZ3D can be used to solve for the steady-state or transient temperature field on three-dimensional geometries. Material properties may be temperature-dependent and either isotropic or orthotropic. A variety of time-dependent and temperature-dependent boundary conditions can be specified including temperature, flux, convection, and radiation. By implementing the user subroutine feature, users can model chemical reaction kinetics and allow for any type of functionalmore » representation of boundary conditions and internal heat generation. TOPAZ3D can solve problems of diffuse and specular band radiation in an enclosure coupled with conduction in the material surrounding the enclosure. Additional features include thermal contact resistance across an interface, bulk fluids, phase change, and energy balances.« less

  1. Modular 3-D Transport model

    EPA Science Inventory

    MT3D was first developed by Chunmiao Zheng in 1990 at S.S. Papadopulos & Associates, Inc. with partial support from the U.S. Environmental Protection Agency (USEPA). Starting in 1990, MT3D was released as a pubic domain code from the USEPA. Commercial versions with enhanced capab...

  2. Market study: 3-D eyetracker

    NASA Technical Reports Server (NTRS)

    1977-01-01

    A market study of a proposed version of a 3-D eyetracker for initial use at NASA's Ames Research Center was made. The commercialization potential of a simplified, less expensive 3-D eyetracker was ascertained. Primary focus on present and potential users of eyetrackers, as well as present and potential manufacturers has provided an effective means of analyzing the prospects for commercialization.

  3. [3-D ultrasound in gastroenterology].

    PubMed

    Zoller, W G; Liess, H

    1994-06-01

    Three-dimensional (3D) sonography represents a development of noninvasive diagnostic imaging by real-time two-dimensional (2D) sonography. The use of transparent rotating scans, comparable to a block of glass, generates a 3D effect. The objective of the present study was to optimate 3D presentation of abdominal findings. Additional investigations were made with a new volumetric program to determine the volume of selected findings of the liver. The results were compared with the estimated volumes of 2D sonography and 2D computer tomography (CT). For the processing of 3D images, typical parameter constellations were found for the different findings, which facilitated processing of 3D images. In more than 75% of the cases examined we found an optimal 3D presentation of sonographic findings with respect to the evaluation criteria developed by us for the 3D imaging of processed data. Great differences were found for the estimated volumes of the findings of the liver concerning the three different techniques applied. 3D ultrasound represents a valuable method to judge morphological appearance in abdominal findings. The possibility of volumetric measurements enlarges its potential diagnostic significance. Further clinical investigations are necessary to find out if definite differentiation between benign and malign findings is possible. PMID:7919882

  4. 3D World Building System

    SciTech Connect

    2013-10-30

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  5. 3D World Building System

    ScienceCinema

    None

    2014-02-26

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  6. Euro3D Science Conference

    NASA Astrophysics Data System (ADS)

    Walsh, J. R.

    2004-02-01

    The Euro3D RTN is an EU funded Research Training Network to foster the exploitation of 3D spectroscopy in Europe. 3D spectroscopy is a general term for spectroscopy of an area of the sky and derives its name from its two spatial + one spectral dimensions. There are an increasing number of instruments which use integral field devices to achieve spectroscopy of an area of the sky, either using lens arrays, optical fibres or image slicers, to pack spectra of multiple pixels on the sky (``spaxels'') onto a 2D detector. On account of the large volume of data and the special methods required to reduce and analyse 3D data, there are only a few centres of expertise and these are mostly involved with instrument developments. There is a perceived lack of expertise in 3D spectroscopy spread though the astronomical community and its use in the armoury of the observational astronomer is viewed as being highly specialised. For precisely this reason the Euro3D RTN was proposed to train young researchers in this area and develop user tools to widen the experience with this particular type of data in Europe. The Euro3D RTN is coordinated by Martin M. Roth (Astrophysikalisches Institut Potsdam) and has been running since July 2002. The first Euro3D science conference was held in Cambridge, UK from 22 to 23 May 2003. The main emphasis of the conference was, in keeping with the RTN, to expose the work of the young post-docs who are funded by the RTN. In addition the team members from the eleven European institutes involved in Euro3D also presented instrumental and observational developments. The conference was organized by Andy Bunker and held at the Institute of Astronomy. There were over thirty participants and 26 talks covered the whole range of application of 3D techniques. The science ranged from Galactic planetary nebulae and globular clusters to kinematics of nearby galaxies out to objects at high redshift. Several talks were devoted to reporting recent observations with newly

  7. PLOT3D user's manual

    NASA Technical Reports Server (NTRS)

    Walatka, Pamela P.; Buning, Pieter G.; Pierce, Larry; Elson, Patricia A.

    1990-01-01

    PLOT3D is a computer graphics program designed to visualize the grids and solutions of computational fluid dynamics. Seventy-four functions are available. Versions are available for many systems. PLOT3D can handle multiple grids with a million or more grid points, and can produce varieties of model renderings, such as wireframe or flat shaded. Output from PLOT3D can be used in animation programs. The first part of this manual is a tutorial that takes the reader, keystroke by keystroke, through a PLOT3D session. The second part of the manual contains reference chapters, including the helpfile, data file formats, advice on changing PLOT3D, and sample command files.

  8. 3D printing in dentistry.

    PubMed

    Dawood, A; Marti Marti, B; Sauret-Jackson, V; Darwood, A

    2015-12-01

    3D printing has been hailed as a disruptive technology which will change manufacturing. Used in aerospace, defence, art and design, 3D printing is becoming a subject of great interest in surgery. The technology has a particular resonance with dentistry, and with advances in 3D imaging and modelling technologies such as cone beam computed tomography and intraoral scanning, and with the relatively long history of the use of CAD CAM technologies in dentistry, it will become of increasing importance. Uses of 3D printing include the production of drill guides for dental implants, the production of physical models for prosthodontics, orthodontics and surgery, the manufacture of dental, craniomaxillofacial and orthopaedic implants, and the fabrication of copings and frameworks for implant and dental restorations. This paper reviews the types of 3D printing technologies available and their various applications in dentistry and in maxillofacial surgery. PMID:26657435

  9. Improving Lightning NO(x) Parameterizations for Global Chemical Transport Models

    NASA Technical Reports Server (NTRS)

    Pickering, Kenneth E.; Ott, Lesley E.; DeCaria, Alex J.; Stenchikov, Georgiy L.; Allen, Dale J.; Tao, Wei-Kuo

    2006-01-01

    values of production in the literature that have been deduced from observed NO spikes and from anvil flux calculations. Results show that on a per flash basis, IC flashes are nearly as productive of NO as CG flashes. Estimates of mean NO production per flash vary by a factor of three from one simulated storm to another. Vertical profiles of lightning NOx mass at the end of the 3-D storm simulations have been summarized to yield suggested profiles for use in global models. These profiles show a larger percentage of the total lightning NO(x) mass in the free troposphere than those suggested by Pickering et al. (1998).

  10. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  11. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  12. 3-D Maps and Compasses in the Brain.

    PubMed

    Finkelstein, Arseny; Las, Liora; Ulanovsky, Nachum

    2016-07-01

    The world has a complex, three-dimensional (3-D) spatial structure, but until recently the neural representation of space was studied primarily in planar horizontal environments. Here we review the emerging literature on allocentric spatial representations in 3-D and discuss the relations between 3-D spatial perception and the underlying neural codes. We suggest that the statistics of movements through space determine the topology and the dimensionality of the neural representation, across species and different behavioral modes. We argue that hippocampal place-cell maps are metric in all three dimensions, and might be composed of 2-D and 3-D fragments that are stitched together into a global 3-D metric representation via the 3-D head-direction cells. Finally, we propose that the hippocampal formation might implement a neural analogue of a Kalman filter, a standard engineering algorithm used for 3-D navigation. PMID:27442069

  13. Bioprinting of 3D hydrogels.

    PubMed

    Stanton, M M; Samitier, J; Sánchez, S

    2015-08-01

    Three-dimensional (3D) bioprinting has recently emerged as an extension of 3D material printing, by using biocompatible or cellular components to build structures in an additive, layer-by-layer methodology for encapsulation and culture of cells. These 3D systems allow for cell culture in a suspension for formation of highly organized tissue or controlled spatial orientation of cell environments. The in vitro 3D cellular environments simulate the complexity of an in vivo environment and natural extracellular matrices (ECM). This paper will focus on bioprinting utilizing hydrogels as 3D scaffolds. Hydrogels are advantageous for cell culture as they are highly permeable to cell culture media, nutrients, and waste products generated during metabolic cell processes. They have the ability to be fabricated in customized shapes with various material properties with dimensions at the micron scale. 3D hydrogels are a reliable method for biocompatible 3D printing and have applications in tissue engineering, drug screening, and organ on a chip models. PMID:26066320

  14. Unassisted 3D camera calibration

    NASA Astrophysics Data System (ADS)

    Atanassov, Kalin; Ramachandra, Vikas; Nash, James; Goma, Sergio R.

    2012-03-01

    With the rapid growth of 3D technology, 3D image capture has become a critical part of the 3D feature set on mobile phones. 3D image quality is affected by the scene geometry as well as on-the-device processing. An automatic 3D system usually assumes known camera poses accomplished by factory calibration using a special chart. In real life settings, pose parameters estimated by factory calibration can be negatively impacted by movements of the lens barrel due to shaking, focusing, or camera drop. If any of these factors displaces the optical axes of either or both cameras, vertical disparity might exceed the maximum tolerable margin and the 3D user may experience eye strain or headaches. To make 3D capture more practical, one needs to consider unassisted (on arbitrary scenes) calibration. In this paper, we propose an algorithm that relies on detection and matching of keypoints between left and right images. Frames containing erroneous matches, along with frames with insufficiently rich keypoint constellations, are detected and discarded. Roll, pitch yaw , and scale differences between left and right frames are then estimated. The algorithm performance is evaluated in terms of the remaining vertical disparity as compared to the maximum tolerable vertical disparity.

  15. A microfluidic device for 2D to 3D and 3D to 3D cell navigation

    NASA Astrophysics Data System (ADS)

    Shamloo, Amir; Amirifar, Leyla

    2016-01-01

    Microfluidic devices have received wide attention and shown great potential in the field of tissue engineering and regenerative medicine. Investigating cell response to various stimulations is much more accurate and comprehensive with the aid of microfluidic devices. In this study, we introduced a microfluidic device by which the matrix density as a mechanical property and the concentration profile of a biochemical factor as a chemical property could be altered. Our microfluidic device has a cell tank and a cell culture chamber to mimic both 2D to 3D and 3D to 3D migration of three types of cells. Fluid shear stress is negligible on the cells and a stable concentration gradient can be obtained by diffusion. The device was designed by a numerical simulation so that the uniformity of the concentration gradients throughout the cell culture chamber was obtained. Adult neural cells were cultured within this device and they showed different branching and axonal navigation phenotypes within varying nerve growth factor (NGF) concentration profiles. Neural stem cells were also cultured within varying collagen matrix densities while exposed to NGF concentrations and they experienced 3D to 3D collective migration. By generating vascular endothelial growth factor concentration gradients, adult human dermal microvascular endothelial cells also migrated in a 2D to 3D manner and formed a stable lumen within a specific collagen matrix density. It was observed that a minimum absolute concentration and concentration gradient were required to stimulate migration of all types of the cells. This device has the advantage of changing multiple parameters simultaneously and is expected to have wide applicability in cell studies.

  16. Fdf in US3D

    NASA Astrophysics Data System (ADS)

    Otis, Collin; Ferrero, Pietro; Candler, Graham; Givi, Peyman

    2013-11-01

    The scalar filtered mass density function (SFMDF) methodology is implemented into the computer code US3D. This is an unstructured Eulerian finite volume hydrodynamic solver and has proven very effective for simulation of compressible turbulent flows. The resulting SFMDF-US3D code is employed for large eddy simulation (LES) on unstructured meshes. Simulations are conducted of subsonic and supersonic flows under non-reacting and reacting conditions. The consistency and the accuracy of the simulated results are assessed along with appraisal of the overall performance of the methodology. The SFMDF-US3D is now capable of simulating high speed flows in complex configurations.

  17. A 3D Global Climate Model of the Pluto atmosphere coupled to a volatile transport model to interpret New Horizons observations, including the N2, CH4 and CO cycles and the formation of organic hazes

    NASA Astrophysics Data System (ADS)

    Bertrand, Tanguy; Forget, Francois

    2016-04-01

    To interpret New Horizons observations and simulate the Pluto climate system, we have developed a Global Climate Model (GCM) of Pluto's atmosphere. In addition to a 3D "dynamical core" which solves the equation of meteorology, the model takes into account the N2 condensation and sublimation and its thermal and dynamical effects, the vertical turbulent mixing, the radiative transfer through methane and carbon monoxide, molecular thermal conduction, and a detailed surface thermal model with different thermal inertia for various timescales (diurnal, seasonal). The GCM also includes a detailed model of the CH4 and CO cycles, taking into account their transport by the atmospheric circulation and turbulence, as well as their condensation and sublimation on the surface and in the atmosphere, possibly forming methane ice clouds. The GCM consistently predicts the 3D methane abundance in the atmosphere, which is used as an input for our radiative transfer calculation. In a second phase, we also developed a volatile transport model, derived from the GCM, which can be run over thousands of years in order to reach consistent initial states for the GCM runs and better explore the seasonal processes on Pluto. Results obtained with the volatile transport model show that the distribution of N2, CH4 and CO ices primarily depends on the seasonal thermal inertia used for the different ices, and is affected by the assumed topography as well. As observed, it is possible to form a large and permanent nitrogen glacier with CO and CH4 ice deposits in an equatorial basin corresponding to Sputnik Planum, while having a surface pressure evolution consistent with stellar occultations and New Horizons data. In addition, most of the methane ice is sequestered with N2 ice in the basin but seasonal polar caps of CH4 frosts also form explaining the bright polar caps observed with Hubble in the 1980s and in line with New Horizons observations. Using such balanced combination of surface and

  18. Wavefront construction in 3-D

    SciTech Connect

    Chilcoat, S.R. Hildebrand, S.T.

    1995-12-31

    Travel time computation in inhomogeneous media is essential for pre-stack Kirchhoff imaging in areas such as the sub-salt province in the Gulf of Mexico. The 2D algorithm published by Vinje, et al, has been extended to 3D to compute wavefronts in complicated inhomogeneous media. The 3D wavefront construction algorithm provides many advantages over conventional ray tracing and other methods of computing travel times in 3D. The algorithm dynamically maintains a reasonably consistent ray density without making a priori guesses at the number of rays to shoot. The determination of caustics in 3D is a straight forward geometric procedure. The wavefront algorithm also enables the computation of multi-valued travel time surfaces.

  19. Heterodyne 3D ghost imaging

    NASA Astrophysics Data System (ADS)

    Yang, Xu; Zhang, Yong; Yang, Chenghua; Xu, Lu; Wang, Qiang; Zhao, Yuan

    2016-06-01

    Conventional three dimensional (3D) ghost imaging measures range of target based on pulse fight time measurement method. Due to the limit of data acquisition system sampling rate, range resolution of the conventional 3D ghost imaging is usually low. In order to take off the effect of sampling rate to range resolution of 3D ghost imaging, a heterodyne 3D ghost imaging (HGI) system is presented in this study. The source of HGI is a continuous wave laser instead of pulse laser. Temporal correlation and spatial correlation of light are both utilized to obtain the range image of target. Through theory analysis and numerical simulations, it is demonstrated that HGI can obtain high range resolution image with low sampling rate.

  20. Combinatorial 3D Mechanical Metamaterials

    NASA Astrophysics Data System (ADS)

    Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin

    2015-03-01

    We present a class of elastic structures which exhibit 3D-folding motion. Our structures consist of cubic lattices of anisotropic unit cells that can be tiled in a complex combinatorial fashion. We design and 3d-print this complex ordered mechanism, in which we combine elastic hinges and defects to tailor the mechanics of the material. Finally, we use this large design space to encode smart functionalities such as surface patterning and multistability.

  1. Characterization of Transport Errors in Chemical Forecasts from a Global Tropospheric Chemical Transport Model

    NASA Technical Reports Server (NTRS)

    Bey, I.; Jacob, D. J.; Liu, H.; Yantosca, R. M.; Sachse, G. W.

    2004-01-01

    We propose a new methodology to characterize errors in the representation of transport processes in chemical transport models. We constrain the evaluation of a global three-dimensional chemical transport model (GEOS-CHEM) with an extended dataset of carbon monoxide (CO) concentrations obtained during the Transport and Chemical Evolution over the Pacific (TRACE-P) aircraft campaign. The TRACEP mission took place over the western Pacific, a region frequently impacted by continental outflow associated with different synoptic-scale weather systems (such as cold fronts) and deep convection, and thus provides a valuable dataset. for our analysis. Model simulations using both forecast and assimilated meteorology are examined. Background CO concentrations are computed as a function of latitude and altitude and subsequently subtracted from both the observed and the model datasets to focus on the ability of the model to simulate variability on a synoptic scale. Different sampling strategies (i.e., spatial displacement and smoothing) are applied along the flight tracks to search for systematic model biases. Statistical quantities such as correlation coefficient and centered root-mean-square difference are computed between the simulated and the observed fields and are further inter-compared using Taylor diagrams. We find no systematic bias in the model for the TRACE-P region when we consider the entire dataset (i.e., from the surface to 12 km ). This result indicates that the transport error in our model is globally unbiased, which has important implications for using the model to conduct inverse modeling studies. Using the First-Look assimilated meteorology only provides little improvement of the correlation, in comparison with the forecast meteorology. These general statements can be refined when the entire dataset is divided into different vertical domains, i.e., the lower troposphere (less than 2 km), the middle troposphere (2-6 km), and the upper troposphere (greater than

  2. A 2D driven 3D vessel segmentation algorithm for 3D digital subtraction angiography data.

    PubMed

    Spiegel, M; Redel, T; Struffert, T; Hornegger, J; Doerfler, A

    2011-10-01

    Cerebrovascular disease is among the leading causes of death in western industrial nations. 3D rotational angiography delivers indispensable information on vessel morphology and pathology. Physicians make use of this to analyze vessel geometry in detail, i.e. vessel diameters, location and size of aneurysms, to come up with a clinical decision. 3D segmentation is a crucial step in this pipeline. Although a lot of different methods are available nowadays, all of them lack a method to validate the results for the individual patient. Therefore, we propose a novel 2D digital subtraction angiography (DSA)-driven 3D vessel segmentation and validation framework. 2D DSA projections are clinically considered as gold standard when it comes to measurements of vessel diameter or the neck size of aneurysms. An ellipsoid vessel model is applied to deliver the initial 3D segmentation. To assess the accuracy of the 3D vessel segmentation, its forward projections are iteratively overlaid with the corresponding 2D DSA projections. Local vessel discrepancies are modeled by a global 2D/3D optimization function to adjust the 3D vessel segmentation toward the 2D vessel contours. Our framework has been evaluated on phantom data as well as on ten patient datasets. Three 2D DSA projections from varying viewing angles have been used for each dataset. The novel 2D driven 3D vessel segmentation approach shows superior results against state-of-the-art segmentations like region growing, i.e. an improvement of 7.2% points in precision and 5.8% points for the Dice coefficient. This method opens up future clinical applications requiring the greatest vessel accuracy, e.g. computational fluid dynamic modeling. PMID:21908904

  3. A 2D driven 3D vessel segmentation algorithm for 3D digital subtraction angiography data

    NASA Astrophysics Data System (ADS)

    Spiegel, M.; Redel, T.; Struffert, T.; Hornegger, J.; Doerfler, A.

    2011-10-01

    Cerebrovascular disease is among the leading causes of death in western industrial nations. 3D rotational angiography delivers indispensable information on vessel morphology and pathology. Physicians make use of this to analyze vessel geometry in detail, i.e. vessel diameters, location and size of aneurysms, to come up with a clinical decision. 3D segmentation is a crucial step in this pipeline. Although a lot of different methods are available nowadays, all of them lack a method to validate the results for the individual patient. Therefore, we propose a novel 2D digital subtraction angiography (DSA)-driven 3D vessel segmentation and validation framework. 2D DSA projections are clinically considered as gold standard when it comes to measurements of vessel diameter or the neck size of aneurysms. An ellipsoid vessel model is applied to deliver the initial 3D segmentation. To assess the accuracy of the 3D vessel segmentation, its forward projections are iteratively overlaid with the corresponding 2D DSA projections. Local vessel discrepancies are modeled by a global 2D/3D optimization function to adjust the 3D vessel segmentation toward the 2D vessel contours. Our framework has been evaluated on phantom data as well as on ten patient datasets. Three 2D DSA projections from varying viewing angles have been used for each dataset. The novel 2D driven 3D vessel segmentation approach shows superior results against state-of-the-art segmentations like region growing, i.e. an improvement of 7.2% points in precision and 5.8% points for the Dice coefficient. This method opens up future clinical applications requiring the greatest vessel accuracy, e.g. computational fluid dynamic modeling.

  4. From 3D view to 3D print

    NASA Astrophysics Data System (ADS)

    Dima, M.; Farisato, G.; Bergomi, M.; Viotto, V.; Magrin, D.; Greggio, D.; Farinato, J.; Marafatto, L.; Ragazzoni, R.; Piazza, D.

    2014-08-01

    In the last few years 3D printing is getting more and more popular and used in many fields going from manufacturing to industrial design, architecture, medical support and aerospace. 3D printing is an evolution of bi-dimensional printing, which allows to obtain a solid object from a 3D model, realized with a 3D modelling software. The final product is obtained using an additive process, in which successive layers of material are laid down one over the other. A 3D printer allows to realize, in a simple way, very complex shapes, which would be quite difficult to be produced with dedicated conventional facilities. Thanks to the fact that the 3D printing is obtained superposing one layer to the others, it doesn't need any particular work flow and it is sufficient to simply draw the model and send it to print. Many different kinds of 3D printers exist based on the technology and material used for layer deposition. A common material used by the toner is ABS plastics, which is a light and rigid thermoplastic polymer, whose peculiar mechanical properties make it diffusely used in several fields, like pipes production and cars interiors manufacturing. I used this technology to create a 1:1 scale model of the telescope which is the hardware core of the space small mission CHEOPS (CHaracterising ExOPlanets Satellite) by ESA, which aims to characterize EXOplanets via transits observations. The telescope has a Ritchey-Chrétien configuration with a 30cm aperture and the launch is foreseen in 2017. In this paper, I present the different phases for the realization of such a model, focusing onto pros and cons of this kind of technology. For example, because of the finite printable volume (10×10×12 inches in the x, y and z directions respectively), it has been necessary to split the largest parts of the instrument in smaller components to be then reassembled and post-processed. A further issue is the resolution of the printed material, which is expressed in terms of layers

  5. 3D Cell Culture in Alginate Hydrogels

    PubMed Central

    Andersen, Therese; Auk-Emblem, Pia; Dornish, Michael

    2015-01-01

    This review compiles information regarding the use of alginate, and in particular alginate hydrogels, in culturing cells in 3D. Knowledge of alginate chemical structure and functionality are shown to be important parameters in design of alginate-based matrices for cell culture. Gel elasticity as well as hydrogel stability can be impacted by the type of alginate used, its concentration, the choice of gelation technique (ionic or covalent), and divalent cation chosen as the gel inducing ion. The use of peptide-coupled alginate can control cell–matrix interactions. Gelation of alginate with concomitant immobilization of cells can take various forms. Droplets or beads have been utilized since the 1980s for immobilizing cells. Newer matrices such as macroporous scaffolds are now entering the 3D cell culture product market. Finally, delayed gelling, injectable, alginate systems show utility in the translation of in vitro cell culture to in vivo tissue engineering applications. Alginate has a history and a future in 3D cell culture. Historically, cells were encapsulated in alginate droplets cross-linked with calcium for the development of artificial organs. Now, several commercial products based on alginate are being used as 3D cell culture systems that also demonstrate the possibility of replacing or regenerating tissue. PMID:27600217

  6. YouDash3D: exploring stereoscopic 3D gaming for 3D movie theaters

    NASA Astrophysics Data System (ADS)

    Schild, Jonas; Seele, Sven; Masuch, Maic

    2012-03-01

    Along with the success of the digitally revived stereoscopic cinema, events beyond 3D movies become attractive for movie theater operators, i.e. interactive 3D games. In this paper, we present a case that explores possible challenges and solutions for interactive 3D games to be played by a movie theater audience. We analyze the setting and showcase current issues related to lighting and interaction. Our second focus is to provide gameplay mechanics that make special use of stereoscopy, especially depth-based game design. Based on these results, we present YouDash3D, a game prototype that explores public stereoscopic gameplay in a reduced kiosk setup. It features live 3D HD video stream of a professional stereo camera rig rendered in a real-time game scene. We use the effect to place the stereoscopic effigies of players into the digital game. The game showcases how stereoscopic vision can provide for a novel depth-based game mechanic. Projected trigger zones and distributed clusters of the audience video allow for easy adaptation to larger audiences and 3D movie theater gaming.

  7. 3D visualization of polymer nanostructure

    SciTech Connect

    Werner, James H

    2009-01-01

    Soft materials and structured polymers are extremely useful nanotechnology building blocks. Block copolymers, in particular, have served as 2D masks for nanolithography and 3D scaffolds for photonic crystals, nanoparticle fabrication, and solar cells. F or many of these applications, the precise 3 dimensional structure and the number and type of defects in the polymer is important for ultimate function. However, directly visualizing the 3D structure of a soft material from the nanometer to millimeter length scales is a significant technical challenge. Here, we propose to develop the instrumentation needed for direct 3D structure determination at near nanometer resolution throughout a nearly millimeter-cubed volume of a soft, potentially heterogeneous, material. This new capability will be a valuable research tool for LANL missions in chemistry, materials science, and nanoscience. Our approach to soft materials visualization builds upon exciting developments in super-resolution optical microscopy that have occurred over the past two years. To date, these new, truly revolutionary, imaging methods have been developed and almost exclusively used for biological applications. However, in addition to biological cells, these super-resolution imaging techniques hold extreme promise for direct visualization of many important nanostructured polymers and other heterogeneous chemical systems. Los Alamos has a unique opportunity to lead the development of these super-resolution imaging methods for problems of chemical rather than biological significance. While these optical methods are limited to systems transparent to visible wavelengths, we stress that many important functional chemicals such as polymers, glasses, sol-gels, aerogels, or colloidal assemblies meet this requirement, with specific examples including materials designed for optical communication, manipulation, or light-harvesting Our Research Goals are: (1) Develop the instrumentation necessary for imaging materials

  8. Remote 3D Medical Consultation

    NASA Astrophysics Data System (ADS)

    Welch, Greg; Sonnenwald, Diane H.; Fuchs, Henry; Cairns, Bruce; Mayer-Patel, Ketan; Yang, Ruigang; State, Andrei; Towles, Herman; Ilie, Adrian; Krishnan, Srinivas; Söderholm, Hanna M.

    Two-dimensional (2D) video-based telemedical consultation has been explored widely in the past 15-20 years. Two issues that seem to arise in most relevant case studies are the difficulty associated with obtaining the desired 2D camera views, and poor depth perception. To address these problems we are exploring the use of a small array of cameras to synthesize a spatially continuous range of dynamic three-dimensional (3D) views of a remote environment and events. The 3D views can be sent across wired or wireless networks to remote viewers with fixed displays or mobile devices such as a personal digital assistant (PDA). The viewpoints could be specified manually or automatically via user head or PDA tracking, giving the remote viewer virtual head- or hand-slaved (PDA-based) remote cameras for mono or stereo viewing. We call this idea remote 3D medical consultation (3DMC). In this article we motivate and explain the vision for 3D medical consultation; we describe the relevant computer vision/graphics, display, and networking research; we present a proof-of-concept prototype system; and we present some early experimental results supporting the general hypothesis that 3D remote medical consultation could offer benefits over conventional 2D televideo.

  9. Speaking Volumes About 3-D

    NASA Technical Reports Server (NTRS)

    2002-01-01

    In 1999, Genex submitted a proposal to Stennis Space Center for a volumetric 3-D display technique that would provide multiple users with a 360-degree perspective to simultaneously view and analyze 3-D data. The futuristic capabilities of the VolumeViewer(R) have offered tremendous benefits to commercial users in the fields of medicine and surgery, air traffic control, pilot training and education, computer-aided design/computer-aided manufacturing, and military/battlefield management. The technology has also helped NASA to better analyze and assess the various data collected by its satellite and spacecraft sensors. Genex capitalized on its success with Stennis by introducing two separate products to the commercial market that incorporate key elements of the 3-D display technology designed under an SBIR contract. The company Rainbow 3D(R) imaging camera is a novel, three-dimensional surface profile measurement system that can obtain a full-frame 3-D image in less than 1 second. The third product is the 360-degree OmniEye(R) video system. Ideal for intrusion detection, surveillance, and situation management, this unique camera system offers a continuous, panoramic view of a scene in real time.

  10. Modeling lightning-NOx chemistry at sub-grid scale in a global chemical transport model

    NASA Astrophysics Data System (ADS)

    Gressent, A.; Sauvage, B.; Cariolle, D.; Evans, M.; Leriche, M.; Mari, C.; Thouret, V.

    2015-12-01

    For the first time, a plume-in-grid approach is implemented in a chemical transport model (CTM) to parameterize the effects of the non-linear reactions occurring within high concentrated NOx plumes from lightning NOx emissions (LNOx) in the upper troposphere. It is characterized by a set of parameters including the plume lifetime, the effective reaction rate constant related to NOx-O3 chemical interactions and the fractions of NOx conversion into HNO3 within the plume. Parameter estimates were made using the DSMACC chemical box model, simple plume dispersion simulations and the mesoscale 3-D Meso-NH model. In order to assess the impact of the LNOx plume approach on the NOx and O3 distributions at large scale, simulations for the year 2006 were performed using the GEOS-Chem global model with a horizontal resolution of 2° × 2.5°. The implementation of the LNOx parameterization implies NOx and O3 decrease at large scale over the region characterized by a strong lightning activity (up to 25 and 8 %, respectively, over Central Africa in July) and a relative increase downwind of LNOx emissions (up to 18 and 2 % for NOx and O3, respectively, in July) are derived. The calculated variability of NOx and O3 mixing ratios around the mean value according to the known uncertainties on the parameter estimates is maximum over continental tropical regions with ΔNOx [-33.1; +29.7] ppt and ΔO3 [-1.56; +2.16] ppb, in January, and ΔNOx [-14.3; +21] ppt and ΔO3 [-1.18; +1.93] ppb, in July, mainly depending on the determination of the diffusion properties of the atmosphere and the initial NO mixing ratio injected by lightning. This approach allows (i) to reproduce a more realistic lightning NOx chemistry leading to better NOx and O3 distributions at the large scale and (ii) focus on other improvements to reduce remaining uncertainties from processes related to NOx chemistry in CTM.

  11. The EISCAT_3D Science Case

    NASA Astrophysics Data System (ADS)

    Tjulin, A.; Mann, I.; McCrea, I.; Aikio, A. T.

    2013-05-01

    EISCAT_3D will be a world-leading international research infrastructure using the incoherent scatter technique to study the atmosphere in the Fenno-Scandinavian Arctic and to investigate how the Earth's atmosphere is coupled to space. The EISCAT_3D phased-array multistatic radar system will be operated by EISCAT Scientific Association and thus be an integral part of an organisation that has successfully been running incoherent scatter radars for more than thirty years. The baseline design of the radar system contains a core site with transmitting and receiving capabilities located close to the intersection of the Swedish, Norwegian and Finnish borders and five receiving sites located within 50 to 250 km from the core. The EISCAT_3D project is currently in its Preparatory Phase and can smoothly transit into implementation in 2014, provided sufficient funding. Construction can start 2016 and first operations in 2018. The EISCAT_3D Science Case is prepared as part of the Preparatory Phase. It is regularly updated with annual new releases, and it aims at being a common document for the whole future EISCAT_3D user community. The areas covered by the Science Case are atmospheric physics and global change; space and plasma physics; solar system research; space weather and service applications; and radar techniques, new methods for coding and analysis. Two of the aims for EISCAT_3D are to understand the ways natural variability in the upper atmosphere, imposed by the Sun-Earth system, can influence the middle and lower atmosphere, and to improve the predictivity of atmospheric models by providing higher resolution observations to replace the current parametrised input. Observations by EISCAT_3D will also be used to monitor the direct effects from the Sun on the ionosphere-atmosphere system and those caused by solar wind magnetosphere-ionosphere interaction. In addition, EISCAT_3D will be used for remote sensing the large-scale behaviour of the magnetosphere from its

  12. 3D cartography of the Alpine Arc

    NASA Astrophysics Data System (ADS)

    Vouillamoz, N.; Sue, C.; Champagnac, J. D.; Calcagno, P.

    2012-04-01

    We present a 3D cartography of the alpine arc, a highly non-cylindrical mountain belt, built using the 3D GeoModeller of the BRGM (French geological survey). The model allows to handle the large-scale 3D structure of seventeen major crustal units of the belt (from the lower crust to the sedimentary cover nappes), and two main discontinuities (the Insubric line and the Crustal Penninic Front). It provides a unique document to better understand their structural relationships and to produce new sections. The study area comprises the western alpine arc, from the Jura to the Northwest, up to the Bergell granite intrusion and the Lepontine Dome to the East, and is limited to the South by the Ligurian basin. The model is limited vertically 10 km above sea level at the top, and the moho interface at the bottom. We discarded the structural relationships between the Alps sensus stricto and the surrounding geodynamic systems such as the Rhine graben or the connection with the Apennines. The 3D-model is based on the global integration of various data such as the DEM of the Alps, the moho isobaths, the simplified geological and tectonic maps of the belt, the crustal cross-sections ECORS-CROP and NFP-20, and complementary cross-sections specifically built to precise local complexities. The database has first been integrated in a GIS-project to prepare their implementation in the GeoModeller, by homogenizing the different spatial referencing systems. The global model is finally interpolated from all these data, using the potential field method. The final document is a new tri-dimentional cartography that would be used as input for further alpine studies.

  13. 3D-Printed Microfluidics.

    PubMed

    Au, Anthony K; Huynh, Wilson; Horowitz, Lisa F; Folch, Albert

    2016-03-14

    The advent of soft lithography allowed for an unprecedented expansion in the field of microfluidics. However, the vast majority of PDMS microfluidic devices are still made with extensive manual labor, are tethered to bulky control systems, and have cumbersome user interfaces, which all render commercialization difficult. On the other hand, 3D printing has begun to embrace the range of sizes and materials that appeal to the developers of microfluidic devices. Prior to fabrication, a design is digitally built as a detailed 3D CAD file. The design can be assembled in modules by remotely collaborating teams, and its mechanical and fluidic behavior can be simulated using finite-element modeling. As structures are created by adding materials without the need for etching or dissolution, processing is environmentally friendly and economically efficient. We predict that in the next few years, 3D printing will replace most PDMS and plastic molding techniques in academia. PMID:26854878

  14. 3D Computations and Experiments

    SciTech Connect

    Couch, R; Faux, D; Goto, D; Nikkel, D

    2004-04-05

    This project consists of two activities. Task A, Simulations and Measurements, combines all the material model development and associated numerical work with the materials-oriented experimental activities. The goal of this effort is to provide an improved understanding of dynamic material properties and to provide accurate numerical representations of those properties for use in analysis codes. Task B, ALE3D Development, involves general development activities in the ALE3D code with the focus of improving simulation capabilities for problems of mutual interest to DoD and DOE. Emphasis is on problems involving multi-phase flow, blast loading of structures and system safety/vulnerability studies.

  15. 3D Computations and Experiments

    SciTech Connect

    Couch, R; Faux, D; Goto, D; Nikkel, D

    2003-05-12

    This project is in its first full year after the combining of two previously funded projects: ''3D Code Development'' and ''Dynamic Material Properties''. The motivation behind this move was to emphasize and strengthen the ties between the experimental work and the computational model development in the materials area. The next year's activities will indicate the merging of the two efforts. The current activity is structured in two tasks. Task A, ''Simulations and Measurements'', combines all the material model development and associated numerical work with the materials-oriented experimental activities. Task B, ''ALE3D Development'', is a continuation of the non-materials related activities from the previous project.

  16. 3D Printed Programmable Release Capsules.

    PubMed

    Gupta, Maneesh K; Meng, Fanben; Johnson, Blake N; Kong, Yong Lin; Tian, Limei; Yeh, Yao-Wen; Masters, Nina; Singamaneni, Srikanth; McAlpine, Michael C

    2015-08-12

    The development of methods for achieving precise spatiotemporal control over chemical and biomolecular gradients could enable significant advances in areas such as synthetic tissue engineering, biotic-abiotic interfaces, and bionanotechnology. Living organisms guide tissue development through highly orchestrated gradients of biomolecules that direct cell growth, migration, and differentiation. While numerous methods have been developed to manipulate and implement biomolecular gradients, integrating gradients into multiplexed, three-dimensional (3D) matrices remains a critical challenge. Here we present a method to 3D print stimuli-responsive core/shell capsules for programmable release of multiplexed gradients within hydrogel matrices. These capsules are composed of an aqueous core, which can be formulated to maintain the activity of payload biomolecules, and a poly(lactic-co-glycolic) acid (PLGA, an FDA approved polymer) shell. Importantly, the shell can be loaded with plasmonic gold nanorods (AuNRs), which permits selective rupturing of the capsule when irradiated with a laser wavelength specifically determined by the lengths of the nanorods. This precise control over space, time, and selectivity allows for the ability to pattern 2D and 3D multiplexed arrays of enzyme-loaded capsules along with tunable laser-triggered rupture and release of active enzymes into a hydrogel ambient. The advantages of this 3D printing-based method include (1) highly monodisperse capsules, (2) efficient encapsulation of biomolecular payloads, (3) precise spatial patterning of capsule arrays, (4) "on the fly" programmable reconfiguration of gradients, and (5) versatility for incorporation in hierarchical architectures. Indeed, 3D printing of programmable release capsules may represent a powerful new tool to enable spatiotemporal control over biomolecular gradients. PMID:26042472

  17. 3D Printed Programmable Release Capsules

    PubMed Central

    Gupta, Maneesh K.; Meng, Fanben; Johnson, Blake N.; Kong, Yong Lin; Tian, Limei; Yeh, Yao-Wen; Masters, Nina; Singamaneni, Srikanth; McAlpine, Michael C.

    2015-01-01

    The development of methods for achieving precise spatiotemporal control over chemical and biomolecular gradients could enable significant advances in areas such as synthetic tissue engineering, biotic–abiotic interfaces, and bionanotechnology. Living organisms guide tissue development through highly orchestrated gradients of biomolecules that direct cell growth, migration, and differentiation. While numerous methods have been developed to manipulate and implement biomolecular gradients, integrating gradients into multiplexed, three-dimensional (3D) matrices remains a critical challenge. Here we present a method to 3D print stimuli-responsive core/shell capsules for programmable release of multiplexed gradients within hydrogel matrices. These capsules are composed of an aqueous core, which can be formulated to maintain the activity of payload biomolecules, and a poly(lactic-co-glycolic) acid (PLGA, an FDA approved polymer) shell. Importantly, the shell can be loaded with plasmonic gold nanorods (AuNRs), which permits selective rupturing of the capsule when irradiated with a laser wavelength specifically determined by the lengths of the nanorods. This precise control over space, time, and selectivity allows for the ability to pattern 2D and 3D multiplexed arrays of enzyme-loaded capsules along with tunable laser-triggered rupture and release of active enzymes into a hydrogel ambient. The advantages of this 3D printing-based method include (1) highly monodisperse capsules, (2) efficient encapsulation of biomolecular payloads, (3) precise spatial patterning of capsule arrays, (4) “on the fly” programmable reconfiguration of gradients, and (5) versatility for incorporation in hierarchical architectures. Indeed, 3D printing of programmable release capsules may represent a powerful new tool to enable spatiotemporal control over biomolecular gradients. PMID:26042472

  18. 3D printing in chemistry: past, present and future

    NASA Astrophysics Data System (ADS)

    Shatford, Ryan; Karanassios, Vassili

    2016-05-01

    During the last years, 3d printing for rapid prototyping using additive manufacturing has been receiving increased attention in the technical and scientific literature including some Chemistry-related journals. Furthermore, 3D printing technology (defining size and resolution of 3D objects) and properties of printed materials (e.g., strength, resistance to chemical attack, electrical insulation) proved to be important for chemistry-related applications. In this paper these are discussed in detail. In addition, application of 3D printing for development of Micro Plasma Devices (MPDs) is discussed and 2d-profilometry data of a 3D printed surfaces is reported. And, past and present chemistry and bio-related applications of 3D printing are reviewed and possible future directions are postulated.

  19. SNL3dFace

    2007-07-20

    This software distribution contains MATLAB and C++ code to enable identity verification using 3D images that may or may not contain a texture component. The code is organized to support system performance testing and system capability demonstration through the proper configuration of the available user interface. Using specific algorithm parameters the face recognition system has been demonstrated to achieve a 96.6% verification rate (Pd) at 0.001 false alarm rate. The system computes robust facial featuresmore » of a 3D normalized face using Principal Component Analysis (PCA) and Fisher Linear Discriminant Analysis (FLDA). A 3D normalized face is obtained by alighning each face, represented by a set of XYZ coordinated, to a scaled reference face using the Iterative Closest Point (ICP) algorithm. The scaled reference face is then deformed to the input face using an iterative framework with parameters that control the deformed surface regulation an rate of deformation. A variety of options are available to control the information that is encoded by the PCA. Such options include the XYZ coordinates, the difference of each XYZ coordinates from the reference, the Z coordinate, the intensity/texture values, etc. In addition to PCA/FLDA feature projection this software supports feature matching to obtain similarity matrices for performance analysis. In addition, this software supports visualization of the STL, MRD, 2D normalized, and PCA synthetic representations in a 3D environment.« less

  20. Making Inexpensive 3-D Models

    ERIC Educational Resources Information Center

    Manos, Harry

    2016-01-01

    Visual aids are important to student learning, and they help make the teacher's job easier. Keeping with the "TPT" theme of "The Art, Craft, and Science of Physics Teaching," the purpose of this article is to show how teachers, lacking equipment and funds, can construct a durable 3-D model reference frame and a model gravity…

  1. SNL3dFace

    SciTech Connect

    Russ, Trina; Koch, Mark; Koudelka, Melissa; Peters, Ralph; Little, Charles; Boehnen, Chris; Peters, Tanya

    2007-07-20

    This software distribution contains MATLAB and C++ code to enable identity verification using 3D images that may or may not contain a texture component. The code is organized to support system performance testing and system capability demonstration through the proper configuration of the available user interface. Using specific algorithm parameters the face recognition system has been demonstrated to achieve a 96.6% verification rate (Pd) at 0.001 false alarm rate. The system computes robust facial features of a 3D normalized face using Principal Component Analysis (PCA) and Fisher Linear Discriminant Analysis (FLDA). A 3D normalized face is obtained by alighning each face, represented by a set of XYZ coordinated, to a scaled reference face using the Iterative Closest Point (ICP) algorithm. The scaled reference face is then deformed to the input face using an iterative framework with parameters that control the deformed surface regulation an rate of deformation. A variety of options are available to control the information that is encoded by the PCA. Such options include the XYZ coordinates, the difference of each XYZ coordinates from the reference, the Z coordinate, the intensity/texture values, etc. In addition to PCA/FLDA feature projection this software supports feature matching to obtain similarity matrices for performance analysis. In addition, this software supports visualization of the STL, MRD, 2D normalized, and PCA synthetic representations in a 3D environment.

  2. 3D Printing: Exploring Capabilities

    ERIC Educational Resources Information Center

    Samuels, Kyle; Flowers, Jim

    2015-01-01

    As 3D printers become more affordable, schools are using them in increasing numbers. They fit well with the emphasis on product design in technology and engineering education, allowing students to create high-fidelity physical models to see and test different iterations in their product designs. They may also help students to "think in three…

  3. 3D Printed Molecules and Extended Solid Models for Teaching Symmetry and Point Groups

    ERIC Educational Resources Information Center

    Scalfani, Vincent F.; Vaid, Thomas P.

    2014-01-01

    Tangible models help students and researchers visualize chemical structures in three dimensions (3D). 3D printing offers a unique and straightforward approach to fabricate plastic 3D models of molecules and extended solids. In this article, we prepared a series of digital 3D design files of molecular structures that will be useful for teaching…

  4. TACO3D. 3-D Finite Element Heat Transfer Code

    SciTech Connect

    Mason, W.E.

    1992-03-04

    TACO3D is a three-dimensional, finite-element program for heat transfer analysis. An extension of the two-dimensional TACO program, it can perform linear and nonlinear analyses and can be used to solve either transient or steady-state problems. The program accepts time-dependent or temperature-dependent material properties, and materials may be isotropic or orthotropic. A variety of time-dependent and temperature-dependent boundary conditions and loadings are available including temperature, flux, convection, and radiation boundary conditions and internal heat generation. Additional specialized features treat enclosure radiation, bulk nodes, and master/slave internal surface conditions (e.g., contact resistance). Data input via a free-field format is provided. A user subprogram feature allows for any type of functional representation of any independent variable. A profile (bandwidth) minimization option is available. The code is limited to implicit time integration for transient solutions. TACO3D has no general mesh generation capability. Rows of evenly-spaced nodes and rows of sequential elements may be generated, but the program relies on separate mesh generators for complex zoning. TACO3D does not have the ability to calculate view factors internally. Graphical representation of data in the form of time history and spatial plots is provided through links to the POSTACO and GRAPE postprocessor codes.

  5. 3D modeling of optically challenging objects.

    PubMed

    Park, Johnny; Kak, Avinash

    2008-01-01

    We present a system for constructing 3D models of real-world objects with optically challenging surfaces. The system utilizes a new range imaging concept called multi-peak range imaging, which stores multiple candidates of range measurements for each point on the object surface. The multiple measurements include the erroneous range data caused by various surface properties that are not ideal for structured-light range sensing. False measurements generated by spurious reflections are eliminated by applying a series of constraint tests. The constraint tests based on local surface and local sensor visibility are applied first to individual range images. The constraint tests based on global consistency of coordinates and visibility are then applied to all range images acquired from different viewpoints. We show the effectiveness of our method by constructing 3D models of five different optically challenging objects. To evaluate the performance of the constraint tests and to examine the effects of the parameters used in the constraint tests, we acquired the ground truth data by painting those objects to suppress the surface-related properties that cause difficulties in range sensing. Experimental results indicate that our method significantly improves upon the traditional methods for constructing reliable 3D models of optically challenging objects. PMID:18192707

  6. Optoplasmonics: hybridization in 3D

    NASA Astrophysics Data System (ADS)

    Rosa, L.; Gervinskas, G.; Žukauskas, A.; Malinauskas, M.; Brasselet, E.; Juodkazis, S.

    2013-12-01

    Femtosecond laser fabrication has been used to make hybrid refractive and di ractive micro-optical elements in photo-polymer SZ2080. For applications in micro- uidics, axicon lenses were fabricated (both single and arrays), for generation of light intensity patterns extending through the entire depth of a typically tens-of-micrometers deep channel. Further hybridisation of an axicon with a plasmonic slot is fabricated and demonstrated nu- merically. Spiralling chiral grooves were inscribed into a 100-nm-thick gold coating sputtered over polymerized micro-axicon lenses, using a focused ion beam. This demonstrates possibility of hybridisation between optical and plasmonic 3D micro-optical elements. Numerical modelling of optical performance by 3D-FDTD method is presented.

  7. 3-D Relativistic MHD Simulations

    NASA Astrophysics Data System (ADS)

    Nishikawa, K.-I.; Frank, J.; Koide, S.; Sakai, J.-I.; Christodoulou, D. M.; Sol, H.; Mutel, R. L.

    1998-12-01

    We present 3-D numerical simulations of moderately hot, supersonic jets propagating initially along or obliquely to the field lines of a denser magnetized background medium with Lorentz factors of W = 4.56 and evolving in a four-dimensional spacetime. The new results are understood as follows: Relativistic simulations have consistently shown that these jets are effectively heavy and so they do not suffer substantial momentum losses and are not decelerated as efficiently as their nonrelativistic counterparts. In addition, the ambient magnetic field, however strong, can be pushed aside with relative ease by the beam, provided that the degrees of freedom associated with all three spatial dimensions are followed self-consistently in the simulations. This effect is analogous to pushing Japanese ``noren'' or vertical Venetian blinds out of the way while the slats are allowed to bend in 3-D space rather than as a 2-D slab structure.

  8. Forensic 3D Scene Reconstruction

    SciTech Connect

    LITTLE,CHARLES Q.; PETERS,RALPH R.; RIGDON,J. BRIAN; SMALL,DANIEL E.

    1999-10-12

    Traditionally law enforcement agencies have relied on basic measurement and imaging tools, such as tape measures and cameras, in recording a crime scene. A disadvantage of these methods is that they are slow and cumbersome. The development of a portable system that can rapidly record a crime scene with current camera imaging, 3D geometric surface maps, and contribute quantitative measurements such as accurate relative positioning of crime scene objects, would be an asset to law enforcement agents in collecting and recording significant forensic data. The purpose of this project is to develop a feasible prototype of a fast, accurate, 3D measurement and imaging system that would support law enforcement agents to quickly document and accurately record a crime scene.

  9. Forensic 3D scene reconstruction

    NASA Astrophysics Data System (ADS)

    Little, Charles Q.; Small, Daniel E.; Peters, Ralph R.; Rigdon, J. B.

    2000-05-01

    Traditionally law enforcement agencies have relied on basic measurement and imaging tools, such as tape measures and cameras, in recording a crime scene. A disadvantage of these methods is that they are slow and cumbersome. The development of a portable system that can rapidly record a crime scene with current camera imaging, 3D geometric surface maps, and contribute quantitative measurements such as accurate relative positioning of crime scene objects, would be an asset to law enforcement agents in collecting and recording significant forensic data. The purpose of this project is to develop a fieldable prototype of a fast, accurate, 3D measurement and imaging system that would support law enforcement agents to quickly document and accurately record a crime scene.

  10. 360-degree 3D profilometry

    NASA Astrophysics Data System (ADS)

    Song, Yuanhe; Zhao, Hong; Chen, Wenyi; Tan, Yushan

    1997-12-01

    A new method of 360 degree turning 3D shape measurement in which light sectioning and phase shifting techniques are both used is presented in this paper. A sine light field is applied in the projected light stripe, meanwhile phase shifting technique is used to calculate phases of the light slit. Thereafter wrapped phase distribution of the slit is formed and the unwrapping process is made by means of the height information based on the light sectioning method. Therefore phase measuring results with better precision can be obtained. At last the target 3D shape data can be produced according to geometric relationships between phases and the object heights. The principles of this method are discussed in detail and experimental results are shown in this paper.

  11. 3D Printable Graphene Composite.

    PubMed

    Wei, Xiaojun; Li, Dong; Jiang, Wei; Gu, Zheming; Wang, Xiaojuan; Zhang, Zengxing; Sun, Zhengzong

    2015-01-01

    In human being's history, both the Iron Age and Silicon Age thrived after a matured massive processing technology was developed. Graphene is the most recent superior material which could potentially initialize another new material Age. However, while being exploited to its full extent, conventional processing methods fail to provide a link to today's personalization tide. New technology should be ushered in. Three-dimensional (3D) printing fills the missing linkage between graphene materials and the digital mainstream. Their alliance could generate additional stream to push the graphene revolution into a new phase. Here we demonstrate for the first time, a graphene composite, with a graphene loading up to 5.6 wt%, can be 3D printable into computer-designed models. The composite's linear thermal coefficient is below 75 ppm·°C(-1) from room temperature to its glass transition temperature (Tg), which is crucial to build minute thermal stress during the printing process. PMID:26153673

  12. 3D Printed Robotic Hand

    NASA Technical Reports Server (NTRS)

    Pizarro, Yaritzmar Rosario; Schuler, Jason M.; Lippitt, Thomas C.

    2013-01-01

    Dexterous robotic hands are changing the way robots and humans interact and use common tools. Unfortunately, the complexity of the joints and actuations drive up the manufacturing cost. Some cutting edge and commercially available rapid prototyping machines now have the ability to print multiple materials and even combine these materials in the same job. A 3D model of a robotic hand was designed using Creo Parametric 2.0. Combining "hard" and "soft" materials, the model was printed on the Object Connex350 3D printer with the purpose of resembling as much as possible the human appearance and mobility of a real hand while needing no assembly. After printing the prototype, strings where installed as actuators to test mobility. Based on printing materials, the manufacturing cost of the hand was $167, significantly lower than other robotic hands without the actuators since they have more complex assembly processes.

  13. 3D light scanning macrography.

    PubMed

    Huber, D; Keller, M; Robert, D

    2001-08-01

    The technique of 3D light scanning macrography permits the non-invasive surface scanning of small specimens at magnifications up to 200x. Obviating both the problem of limited depth of field inherent to conventional close-up macrophotography and the metallic coating required by scanning electron microscopy, 3D light scanning macrography provides three-dimensional digital images of intact specimens without the loss of colour, texture and transparency information. This newly developed technique offers a versatile, portable and cost-efficient method for the non-invasive digital and photographic documentation of small objects. Computer controlled device operation and digital image acquisition facilitate fast and accurate quantitative morphometric investigations, and the technique offers a broad field of research and educational applications in biological, medical and materials sciences. PMID:11489078

  14. 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.

  15. 3D Models of Symbiotic Binaries

    NASA Astrophysics Data System (ADS)

    Mohamed, S.; Booth, R.; Podsiadlowski, Ph.; Ramstedt, S.; Vlemmings, W.; Maercker, M.

    2015-12-01

    Symbiotic binaries consist of a cool, mass-losing giant and an accreting, compact companion. We present 3D Smoothed Particle Hydrodynamics (SPH) models of two such interacting binaries, RS Oph and Mira AB. RS Oph is also a recurrent nova system, thus we model multiple quiescent mass transfer-nova outburst cycles. The resulting circumstellar structures of both systems are highly complex with the formation of spirals, arcs, shells, equatorial and bipolar outflows. We compare the models to recent observations and discuss the implications of our results for related systems, e.g., bipolar nebulae and jets, chemically peculiar stars, and the progenitors of Type Ia supernovae.

  16. [Real time 3D echocardiography].

    PubMed

    Bauer, F; Shiota, T; Thomas, J D

    2001-07-01

    Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients. PMID:11494630

  17. [Real time 3D echocardiography

    NASA Technical Reports Server (NTRS)

    Bauer, F.; Shiota, T.; Thomas, J. D.

    2001-01-01

    Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients.

  18. GPU-Accelerated Denoising in 3D (GD3D)

    2013-10-01

    The raw computational power GPU Accelerators enables fast denoising of 3D MR images using bilateral filtering, anisotropic diffusion, and non-local means. This software addresses two facets of this promising application: what tuning is necessary to achieve optimal performance on a modern GPU? And what parameters yield the best denoising results in practice? To answer the first question, the software performs an autotuning step to empirically determine optimal memory blocking on the GPU. To answer themore » second, it performs a sweep of algorithm parameters to determine the combination that best reduces the mean squared error relative to a noiseless reference image.« less

  19. 3D scanning modeling method application in ancient city reconstruction

    NASA Astrophysics Data System (ADS)

    Ren, Pu; Zhou, Mingquan; Du, Guoguang; Shui, Wuyang; Zhou, Pengbo

    2015-07-01

    With the development of optical engineering technology, the precision of 3D scanning equipment becomes higher, and its role in 3D modeling is getting more distinctive. This paper proposed a 3D scanning modeling method that has been successfully applied in Chinese ancient city reconstruction. On one hand, for the existing architectures, an improved algorithm based on multiple scanning is adopted. Firstly, two pieces of scanning data were rough rigid registered using spherical displacers and vertex clustering method. Secondly, a global weighted ICP (iterative closest points) method is used to achieve a fine rigid registration. On the other hand, for the buildings which have already disappeared, an exemplar-driven algorithm for rapid modeling was proposed. Based on the 3D scanning technology and the historical data, a system approach was proposed for 3D modeling and virtual display of ancient city.

  20. Global impact of the Antarctic ozone hole: Chemical Propagation

    SciTech Connect

    Prather, M.; Jaffe, A.H. )

    1990-03-20

    A model is presented for the chemical mixing of stratosphere air over spatial scales from tens of kilometers to meters. Photochemistry, molecular diffusion, and strain (the stretching of air parcels due to wind shear) are combined into a single one-dimensional model. The model is applied to the case in which chemically perturbed air parcels from the Antarctic stratosphere are transported to mid-latitudes and strained into thin ribbon-like filaments until they are diffusively mixed with the ambient stratosphere. For this sensitivity study the authors consider four types of Antarctic air: a control case representing unprocessed polar air; heterogeneous processing by polar stratospheric clouds (PSCs) that has repartitioned the Cl{sub x} and NO{sub y} families; processing that also includes denitrification and dehydration; and all processing plus 90% ozone depletion. Large abundances of ClO, resulting initially from heterogeneous processing of stratospheric air on PSCs, are sustained by extensive denitrification. (One exception is the case of Antarctic air with major ozone depletion in which ClO is converted rapidly to HCl upon release of small amounts of NO{sub x} as a result of the extremely nonlinear Cl{sub x}-NO{sub y} chemical system.) ClO concentrations in the mid-latitude stratosphere should be enhanced by as much as a factor of 5 due to the mixing of air processed around the Antarctic vortex and will remain elevated for most of the following season. Chemical propagation of the Antarctic ozone hole occurs in two phases: rapid loss of ozone in the heterogeneously processed parcels as they evolve in isolation, and more slowly, a relative recovery of ozone over the following months. Another important effect is the transport of denitrified Antarctic air reducing NO{sub x} and hence the total catalytic destruction of ozone throughout the southern mid-latitudes.

  1. Magmatic Systems in 3-D

    NASA Astrophysics Data System (ADS)

    Kent, G. M.; Harding, A. J.; Babcock, J. M.; Orcutt, J. A.; Bazin, S.; Singh, S.; Detrick, R. S.; Canales, J. P.; Carbotte, S. M.; Diebold, J.

    2002-12-01

    Multichannel seismic (MCS) images of crustal magma chambers are ideal targets for advanced visualization techniques. In the mid-ocean ridge environment, reflections originating at the melt-lens are well separated from other reflection boundaries, such as the seafloor, layer 2A and Moho, which enables the effective use of transparency filters. 3-D visualization of seismic reflectivity falls into two broad categories: volume and surface rendering. Volumetric-based visualization is an extremely powerful approach for the rapid exploration of very dense 3-D datasets. These 3-D datasets are divided into volume elements or voxels, which are individually color coded depending on the assigned datum value; the user can define an opacity filter to reject plotting certain voxels. This transparency allows the user to peer into the data volume, enabling an easy identification of patterns or relationships that might have geologic merit. Multiple image volumes can be co-registered to look at correlations between two different data types (e.g., amplitude variation with offsets studies), in a manner analogous to draping attributes onto a surface. In contrast, surface visualization of seismic reflectivity usually involves producing "fence" diagrams of 2-D seismic profiles that are complemented with seafloor topography, along with point class data, draped lines and vectors (e.g. fault scarps, earthquake locations and plate-motions). The overlying seafloor can be made partially transparent or see-through, enabling 3-D correlations between seafloor structure and seismic reflectivity. Exploration of 3-D datasets requires additional thought when constructing and manipulating these complex objects. As numbers of visual objects grow in a particular scene, there is a tendency to mask overlapping objects; this clutter can be managed through the effective use of total or partial transparency (i.e., alpha-channel). In this way, the co-variation between different datasets can be investigated

  2. The PRISM3D paleoenvironmental reconstruction

    USGS Publications Warehouse

    Dowsett, H.; Robinson, M.; Haywood, A.M.; Salzmann, U.; Hill, Daniel; Sohl, L.E.; Chandler, M.; Williams, Mark; Foley, K.; Stoll, D.K.

    2010-01-01

    The Pliocene Research, Interpretation and Synoptic Mapping (PRISM) paleoenvironmental reconstruction is an internally consistent and comprehensive global synthesis of a past interval of relatively warm and stable climate. It is regularly used in model studies that aim to better understand Pliocene climate, to improve model performance in future climate scenarios, and to distinguish model-dependent climate effects. The PRISM reconstruction is constantly evolving in order to incorporate additional geographic sites and environmental parameters, and is continuously refined by independent research findings. The new PRISM three dimensional (3D) reconstruction differs from previous PRISM reconstructions in that it includes a subsurface ocean temperature reconstruction, integrates geochemical sea surface temperature proxies to supplement the faunal-based temperature estimates, and uses numerical models for the first time to augment fossil data. Here we describe the components of PRISM3D and describe new findings specific to the new reconstruction. Highlights of the new PRISM3D reconstruction include removal of Hudson Bay and the Great Lakes and creation of open waterways in locations where the current bedrock elevation is less than 25m above modern sea level, due to the removal of the West Antarctic Ice Sheet and the reduction of the East Antarctic Ice Sheet. The mid-Piacenzian oceans were characterized by a reduced east-west temperature gradient in the equatorial Pacific, but PRISM3D data do not imply permanent El Niño conditions. The reduced equator-to-pole temperature gradient that characterized previous PRISM reconstructions is supported by significant displacement of vegetation belts toward the poles, is extended into the Arctic Ocean, and is confirmed by multiple proxies in PRISM3D. Arctic warmth coupled with increased dryness suggests the formation of warm and salty paleo North Atlantic Deep Water (NADW) and a more vigorous thermohaline circulation system that may

  3. Interactive 3D Mars Visualization

    NASA Technical Reports Server (NTRS)

    Powell, Mark W.

    2012-01-01

    The Interactive 3D Mars Visualization system provides high-performance, immersive visualization of satellite and surface vehicle imagery of Mars. The software can be used in mission operations to provide the most accurate position information for the Mars rovers to date. When integrated into the mission data pipeline, this system allows mission planners to view the location of the rover on Mars to 0.01-meter accuracy with respect to satellite imagery, with dynamic updates to incorporate the latest position information. Given this information so early in the planning process, rover drivers are able to plan more accurate drive activities for the rover than ever before, increasing the execution of science activities significantly. Scientifically, this 3D mapping information puts all of the science analyses to date into geologic context on a daily basis instead of weeks or months, as was the norm prior to this contribution. This allows the science planners to judge the efficacy of their previously executed science observations much more efficiently, and achieve greater science return as a result. The Interactive 3D Mars surface view is a Mars terrain browsing software interface that encompasses the entire region of exploration for a Mars surface exploration mission. The view is interactive, allowing the user to pan in any direction by clicking and dragging, or to zoom in or out by scrolling the mouse or touchpad. This set currently includes tools for selecting a point of interest, and a ruler tool for displaying the distance between and positions of two points of interest. The mapping information can be harvested and shared through ubiquitous online mapping tools like Google Mars, NASA WorldWind, and Worldwide Telescope.

  4. A Clean Adirondack (3-D)

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This is a 3-D anaglyph showing a microscopic image taken of an area measuring 3 centimeters (1.2 inches) across on the rock called Adirondack. The image was taken at Gusev Crater on the 33rd day of the Mars Exploration Rover Spirit's journey (Feb. 5, 2004), after the rover used its rock abrasion tool brush to clean the surface of the rock. Dust, which was pushed off to the side during cleaning, can still be seen to the left and in low areas of the rock.

  5. Making Inexpensive 3-D Models

    NASA Astrophysics Data System (ADS)

    Manos, Harry

    2016-03-01

    Visual aids are important to student learning, and they help make the teacher's job easier. Keeping with the TPT theme of "The Art, Craft, and Science of Physics Teaching," the purpose of this article is to show how teachers, lacking equipment and funds, can construct a durable 3-D model reference frame and a model gravity well tailored to specific class lessons. Most of the supplies are readily available in the home or at school: rubbing alcohol, a rag, two colors of spray paint, art brushes, and masking tape. The cost of these supplies, if you don't have them, is less than 20.

  6. What Lies Ahead (3-D)

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 3-D cylindrical-perspective mosaic taken by the navigation camera on the Mars Exploration Rover Spirit on sol 82 shows the view south of the large crater dubbed 'Bonneville.' The rover will travel toward the Columbia Hills, seen here at the upper left. The rock dubbed 'Mazatzal' and the hole the rover drilled in to it can be seen at the lower left. The rover's position is referred to as 'Site 22, Position 32.' This image was geometrically corrected to make the horizon appear flat.

  7. Vacant Lander in 3-D

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 3-D image captured by the Mars Exploration Rover Opportunity's rear hazard-identification camera shows the now-empty lander that carried the rover 283 million miles to Meridiani Planum, Mars. Engineers received confirmation that Opportunity's six wheels successfully rolled off the lander and onto martian soil at 3:01 a.m. PST, January 31, 2004, on the seventh martian day, or sol, of the mission. The rover is approximately 1 meter (3 feet) in front of the lander, facing north.

  8. Hazard Classification of Household Chemical Products in Korea according to the Globally Harmonized System of Classification and labeling of Chemicals

    PubMed Central

    2013-01-01

    Objectives This study was conducted to review the validity of the need for the application of the Globally Harmonized System of Classification and Labeling of Chemicals (GHS) to household chemical products in Korea. The study also aimed to assess the severity of health and environmental hazards of household chemical products using the GHS. Methods 135 products were classified as ‘cleaning agents and polishing agents’ and 98 products were classified as ‘bleaches, disinfectants, and germicides.’ The current status of carcinogenic classification of GHS and carcinogenicity was examined for 272 chemical substances contained in household chemical products by selecting the top 11 products for each of the product categories. In addition, the degree of toxicity was assessed through analysis of whether the standard of the Republic of Korea’s regulations on household chemical products had been exceeded or not. Results According to GHS health and environmental hazards, “acute toxicity (oral)” was found to be the highest for two product groups, ‘cleaning agents and polishing agents’, and ‘bleaches, disinfectants, and germicides’ (result of classification of 233 household chemical products) at 37.8% and 52.0% respectively. In an analysis of carcinogenicity assuming a threshold of IARC 2B for the substances in household chemical products, we found ‘cleaning agents and polishing agents’ to contain 12 chemical substances and ‘bleaches, disinfectants, and germicides’ 11 chemical substances. Conclusion Some of the household chemical products were found to have a high hazard level including acute toxicity and germ cell mutagenicity, carcinogenicity, and reproductive toxicity. Establishing a hazard information delivery system including the application of GHS to household chemical products in Korea is urgent as well. PMID:24472347

  9. 3D Printable Graphene Composite

    NASA Astrophysics Data System (ADS)

    Wei, Xiaojun; Li, Dong; Jiang, Wei; Gu, Zheming; Wang, Xiaojuan; Zhang, Zengxing; Sun, Zhengzong

    2015-07-01

    In human being’s history, both the Iron Age and Silicon Age thrived after a matured massive processing technology was developed. Graphene is the most recent superior material which could potentially initialize another new material Age. However, while being exploited to its full extent, conventional processing methods fail to provide a link to today’s personalization tide. New technology should be ushered in. Three-dimensional (3D) printing fills the missing linkage between graphene materials and the digital mainstream. Their alliance could generate additional stream to push the graphene revolution into a new phase. Here we demonstrate for the first time, a graphene composite, with a graphene loading up to 5.6 wt%, can be 3D printable into computer-designed models. The composite’s linear thermal coefficient is below 75 ppm·°C-1 from room temperature to its glass transition temperature (Tg), which is crucial to build minute thermal stress during the printing process.

  10. 3D acoustic atmospheric tomography

    NASA Astrophysics Data System (ADS)

    Rogers, Kevin; Finn, Anthony

    2014-10-01

    This paper presents a method for tomographically reconstructing spatially varying 3D atmospheric temperature profiles and wind velocity fields based. Measurements of the acoustic signature measured onboard a small Unmanned Aerial Vehicle (UAV) are compared to ground-based observations of the same signals. The frequency-shifted signal variations are then used to estimate the acoustic propagation delay between the UAV and the ground microphones, which are also affected by atmospheric temperature and wind speed vectors along each sound ray path. The wind and temperature profiles are modelled as the weighted sum of Radial Basis Functions (RBFs), which also allow local meteorological measurements made at the UAV and ground receivers to supplement any acoustic observations. Tomography is used to provide a full 3D reconstruction/visualisation of the observed atmosphere. The technique offers observational mobility under direct user control and the capacity to monitor hazardous atmospheric environments, otherwise not justifiable on the basis of cost or risk. This paper summarises the tomographic technique and reports on the results of simulations and initial field trials. The technique has practical applications for atmospheric research, sound propagation studies, boundary layer meteorology, air pollution measurements, analysis of wind shear, and wind farm surveys.

  11. 3D Printed Bionic Ears

    PubMed Central

    Mannoor, Manu S.; Jiang, Ziwen; James, Teena; Kong, Yong Lin; Malatesta, Karen A.; Soboyejo, Winston O.; Verma, Naveen; Gracias, David H.; McAlpine, Michael C.

    2013-01-01

    The ability to three-dimensionally interweave biological tissue with functional electronics could enable the creation of bionic organs possessing enhanced functionalities over their human counterparts. Conventional electronic devices are inherently two-dimensional, preventing seamless multidimensional integration with synthetic biology, as the processes and materials are very different. Here, we present a novel strategy for overcoming these difficulties via additive manufacturing of biological cells with structural and nanoparticle derived electronic elements. As a proof of concept, we generated a bionic ear via 3D printing of a cell-seeded hydrogel matrix in the precise anatomic geometry of a human ear, along with an intertwined conducting polymer consisting of infused silver nanoparticles. This allowed for in vitro culturing of cartilage tissue around an inductive coil antenna in the ear, which subsequently enables readout of inductively-coupled signals from cochlea-shaped electrodes. The printed ear exhibits enhanced auditory sensing for radio frequency reception, and complementary left and right ears can listen to stereo audio music. Overall, our approach suggests a means to intricately merge biologic and nanoelectronic functionalities via 3D printing. PMID:23635097

  12. 3-D Relativistic MHD Simulations

    NASA Astrophysics Data System (ADS)

    Nishikaw, K.-I.; Frank, J.; Christodoulou, D. M.; Koide, S.; Sakai, J.-I.; Sol, H.; Mutel, R. L.

    1998-12-01

    We present 3-D numerical simulations of moderately hot, supersonic jets propagating initially along or obliquely to the field lines of a denser magnetized background medium with Lorentz factors of W=4.56 and evolving in a four-dimensional spacetime. The new results are understood as follows: Relativistic simulations have consistently shown that these jets are effectively heavy and so they do not suffer substantial momentum losses and are not decelerated as efficiently as their nonrelativistic counterparts. In addition, the ambient magnetic field, however strong, can be pushed aside with relative ease by the beam, provided that the degrees of freedom associated with all three spatial dimensions are followed self-consistently in the simulations. This effect is analogous to pushing Japanese ``noren'' or vertical Venetian blinds out of the way while the slats are allowed to bend in 3-D space rather than as a 2-D slab structure. We also simulate jets with the more realistic initial conditions for injecting jets for helical mangetic field, perturbed density, velocity, and internal energy, which are supposed to be caused in the process of jet generation. Three possible explanations for the observed variability are (i) tidal disruption of a star falling into the black hole, (ii) instabilities in the relativistic accretion disk, and (iii) jet-related PRocesses. New results will be reported at the meeting.

  13. 3D printed bionic ears.

    PubMed

    Mannoor, Manu S; Jiang, Ziwen; James, Teena; Kong, Yong Lin; Malatesta, Karen A; Soboyejo, Winston O; Verma, Naveen; Gracias, David H; McAlpine, Michael C

    2013-06-12

    The ability to three-dimensionally interweave biological tissue with functional electronics could enable the creation of bionic organs possessing enhanced functionalities over their human counterparts. Conventional electronic devices are inherently two-dimensional, preventing seamless multidimensional integration with synthetic biology, as the processes and materials are very different. Here, we present a novel strategy for overcoming these difficulties via additive manufacturing of biological cells with structural and nanoparticle derived electronic elements. As a proof of concept, we generated a bionic ear via 3D printing of a cell-seeded hydrogel matrix in the anatomic geometry of a human ear, along with an intertwined conducting polymer consisting of infused silver nanoparticles. This allowed for in vitro culturing of cartilage tissue around an inductive coil antenna in the ear, which subsequently enables readout of inductively-coupled signals from cochlea-shaped electrodes. The printed ear exhibits enhanced auditory sensing for radio frequency reception, and complementary left and right ears can listen to stereo audio music. Overall, our approach suggests a means to intricately merge biologic and nanoelectronic functionalities via 3D printing. PMID:23635097

  14. 3D Printable Graphene Composite

    PubMed Central

    Wei, Xiaojun; Li, Dong; Jiang, Wei; Gu, Zheming; Wang, Xiaojuan; Zhang, Zengxing; Sun, Zhengzong

    2015-01-01

    In human being’s history, both the Iron Age and Silicon Age thrived after a matured massive processing technology was developed. Graphene is the most recent superior material which could potentially initialize another new material Age. However, while being exploited to its full extent, conventional processing methods fail to provide a link to today’s personalization tide. New technology should be ushered in. Three-dimensional (3D) printing fills the missing linkage between graphene materials and the digital mainstream. Their alliance could generate additional stream to push the graphene revolution into a new phase. Here we demonstrate for the first time, a graphene composite, with a graphene loading up to 5.6 wt%, can be 3D printable into computer-designed models. The composite’s linear thermal coefficient is below 75 ppm·°C−1 from room temperature to its glass transition temperature (Tg), which is crucial to build minute thermal stress during the printing process. PMID:26153673

  15. 3D medical thermography device

    NASA Astrophysics Data System (ADS)

    Moghadam, Peyman

    2015-05-01

    In this paper, a novel handheld 3D medical thermography system is introduced. The proposed system consists of a thermal-infrared camera, a color camera and a depth camera rigidly attached in close proximity and mounted on an ergonomic handle. As a practitioner holding the device smoothly moves it around the human body parts, the proposed system generates and builds up a precise 3D thermogram model by incorporating information from each new measurement in real-time. The data is acquired in motion, thus it provides multiple points of view. When processed, these multiple points of view are adaptively combined by taking into account the reliability of each individual measurement which can vary due to a variety of factors such as angle of incidence, distance between the device and the subject and environmental sensor data or other factors influencing a confidence of the thermal-infrared data when captured. Finally, several case studies are presented to support the usability and performance of the proposed system.

  16. 3D Ion Temperature Reconstruction

    NASA Astrophysics Data System (ADS)

    Tanabe, Hiroshi; You, Setthivoine; Balandin, Alexander; Inomoto, Michiaki; Ono, Yasushi

    2009-11-01

    The TS-4 experiment at the University of Tokyo collides two spheromaks to form a single high-beta compact toroid. Magnetic reconnection during the merging process heats and accelerates the plasma in toroidal and poloidal directions. The reconnection region has a complex 3D topology determined by the pitch of the spheromak magnetic fields at the merging plane. A pair of multichord passive spectroscopic diagnostics have been established to measure the ion temperature and velocity in the reconnection volume. One setup measures spectral lines across a poloidal plane, retrieving velocity and temperature from Abel inversion. The other, novel setup records spectral lines across another section of the plasma and reconstructs velocity and temperature from 3D vector and 2D scalar tomography techniques. The magnetic field linking both measurement planes is determined from in situ magnetic probe arrays. The ion temperature is then estimated within the volume between the two measurement planes and at the reconnection region. The measurement is followed over several repeatable discharges to follow the heating and acceleration process during the merging reconnection.

  17. Distributed 3D Information Visualization - Towards Integration of the Dynamic 3D Graphics and Web Services

    NASA Astrophysics Data System (ADS)

    Vucinic, Dean; Deen, Danny; Oanta, Emil; Batarilo, Zvonimir; Lacor, Chris

    This paper focuses on visualization and manipulation of graphical content in distributed network environments. The developed graphical middleware and 3D desktop prototypes were specialized for situational awareness. This research was done in the LArge Scale COllaborative decision support Technology (LASCOT) project, which explored and combined software technologies to support human-centred decision support system for crisis management (earthquake, tsunami, flooding, airplane or oil-tanker incidents, chemical, radio-active or other pollutants spreading, etc.). The performed state-of-the-art review did not identify any publicly available large scale distributed application of this kind. Existing proprietary solutions rely on the conventional technologies and 2D representations. Our challenge was to apply the "latest" available technologies, such Java3D, X3D and SOAP, compatible with average computer graphics hardware. The selected technologies are integrated and we demonstrate: the flow of data, which originates from heterogeneous data sources; interoperability across different operating systems and 3D visual representations to enhance the end-users interactions.

  18. LOTT RANCH 3D PROJECT

    SciTech Connect

    Larry Lawrence; Bruce Miller

    2004-09-01

    The Lott Ranch 3D seismic prospect located in Garza County, Texas is a project initiated in September of 1991 by the J.M. Huber Corp., a petroleum exploration and production company. By today's standards the 126 square mile project does not seem monumental, however at the time it was conceived it was the most intensive land 3D project ever attempted. Acquisition began in September of 1991 utilizing GEO-SEISMIC, INC., a seismic data contractor. The field parameters were selected by J.M. Huber, and were of a radical design. The recording instruments used were GeoCor IV amplifiers designed by Geosystems Inc., which record the data in signed bit format. It would not have been practical, if not impossible, to have processed the entire raw volume with the tools available at that time. The end result was a dataset that was thought to have little utility due to difficulties in processing the field data. In 1997, Yates Energy Corp. located in Roswell, New Mexico, formed a partnership to further develop the project. Through discussions and meetings with Pinnacle Seismic, it was determined that the original Lott Ranch 3D volume could be vastly improved upon reprocessing. Pinnacle Seismic had shown the viability of improving field-summed signed bit data on smaller 2D and 3D projects. Yates contracted Pinnacle Seismic Ltd. to perform the reprocessing. This project was initiated with high resolution being a priority. Much of the potential resolution was lost through the initial summing of the field data. Modern computers that are now being utilized have tremendous speed and storage capacities that were cost prohibitive when this data was initially processed. Software updates and capabilities offer a variety of quality control and statics resolution, which are pertinent to the Lott Ranch project. The reprocessing effort was very successful. The resulting processed data-set was then interpreted using modern PC-based interpretation and mapping software. Production data, log data

  19. 3D Printing of Graphene Aerogels.

    PubMed

    Zhang, Qiangqiang; Zhang, Feng; Medarametla, Sai Pradeep; Li, Hui; Zhou, Chi; Lin, Dong

    2016-04-01

    3D printing of a graphene aerogel with true 3D overhang structures is highlighted. The aerogel is fabricated by combining drop-on-demand 3D printing and freeze casting. The water-based GO ink is ejected and freeze-cast into designed 3D structures. The lightweight (<10 mg cm(-3) ) 3D printed graphene aerogel presents superelastic and high electrical conduction. PMID:26861680

  20. Global CO2-consumption by chemical weathering: What is the contribution of highly active weathering regions?

    NASA Astrophysics Data System (ADS)

    Hartmann, Jens; Jansen, Nils; Dürr, Hans H.; Kempe, Stephan; Köhler, Peter

    2010-05-01

    CO2-consumption by chemical weathering of silicates and resulting silicate/carbonate weathering ratios influences the terrestrial lateral inorganic carbon flux to the ocean and long-term climate changes. However, little is known of the spatial extension of highly active weathering regions and their proportion of global CO2-consumption. As those regions may be of significant importance for global climate change, global CO2-consumption is calculated here at high resolution, to adequately represent them. In previous studies global CO2-consumption is estimated using two different approaches: i) a reverse approach based on hydrochemical fluxes from large rivers and ii) a forward approach applying spatially explicit a function for CO2-consumption. The first approach results in an estimate without providing a spatial resolution for highly active regions and the second approach applied six lithological classes while including three sediment classes (shale, sandstone and carbonate rock) based at a 1° or 2° grid resolution. It remained uncertain, if the applied lithological classification schemes represent adequately CO2-consumption from sediments on a global scale (as well as liberation of other elements like phosphorus or silicon by chemical weatheirng). This is due to the large variability of sediment properties, their diagenetic history and the contribution from carbonates apparent in silicate dominated lithological classes. To address these issues, a CO2-consumption model, trained at high-resolution data, is applied here to a global vector based lithological map with 15 lithological classes. The calibration data were obtained from areas representing a wide range of weathering rates. Resulting global CO2-consumption by chemical weathering is similar to earlier estimates (237 Mt C a-1) but the proportion of silicate weathering is 63%, and thus larger than previous estimates (49 to 60%). The application of the enhanced lithological classification scheme reveals that it

  1. DSI3D-RCS: Theory manual

    SciTech Connect

    Madsen, N.; Steich, D.; Cook, G.; Eme, B.

    1995-03-16

    The DSI3D-RCS code is designed to numerically evaluate radar cross sections on complex objects by solving Maxwell`s curl equations in the time-domain and in three space dimensions. The code has been designed to run on the new parallel processing computers as well as on conventional serial computers. The DSI3D-RCS code is unique for the following reasons: Allows the use of unstructured non-orthogonal grids, allows a variety of cell or element types, reduces to be the Finite Difference Time Domain (FDTD) method when orthogonal grids are used, preserves charge or divergence locally (and globally), is conditionally stable, is non-dissipative, is accurate for non-orthogonal grids. This method is derived using a Discrete Surface Integration (DSI) technique. As formulated, the DSI technique can be used with essentially arbitrary unstructured grids composed of convex polyhedral cells. This implementation of the DSI algorithm allows the use of unstructured grids that are composed of combinations of non-orthogonal hexahedrons, tetrahedrons, triangular prisms and pyramids. This algorithm reduces to the conventional FDTD method when applied on a structured orthogonal hexahedral grid.

  2. DSI3D - RCS user manual

    SciTech Connect

    Madsen, N.; Steich, D.; Cook, G.

    1995-08-23

    The DSI3D-RCS code is designed to numerically evaluate radar cross sections on complex objects by solving Maxwell`s curl equations in the time-domain and in three space dimensions. The code has been designed to run on the new parallel processing computers as well as on conventional serial computers. The DSI3D-RCS code is unique for the following reasons: Allows the use of unstructured non-orthogonal grids, allows a variety of cell or element types, reduces to be the Finite Difference Time Domain (FDTD) method when orthogonal grids are used, preserves charge or divergence locally (and globally), is conditionally stable, is selectively non-dissipative, and is accurate for non-orthogonal grids. This method is derived using a Discrete Surface Integration (DSI) technique. As formulated, the DSI technique can be used with essentially arbitrary unstructured grids composed of convex polyhedral cells. This implementation of the DSI algorithm allows the use of unstructured grids that are composed of combinations of non-orthogonal the use of unstructured grids that are composed of combinations of non-orthogonal hexahedrons, tetrahedrons, triangular prisms and pyramids. This algorithm reduces to the conventional FDTD method when applied on a structured orthogonal hexahedral grid.

  3. 3D Model of Surfactant Replacement Therapy

    NASA Astrophysics Data System (ADS)

    Grotberg, James; Tai, Cheng-Feng; Filoche, Marcel

    2015-11-01

    Surfactant Replacement Therapy (SRT) involves instillation of a liquid-surfactant mixture directly into the lung airway tree. Though successful in neonatal applications, its use in adults had early success followed by failure. We present the first mathematical model of 3D SRT where a liquid plug propagates through the tree from forced inspiration. In two separate modeling steps, the plug first deposits a coating film on the airway wall which subtracts from its volume, a ``coating cost''. Then the plug splits unevenly at the airway bifurcation due to gravity. The steps are repeated until a plug ruptures or reaches the tree endpoint alveoli/acinus. The model generates 3D images of the resulting acinar distribution and calculates two global indexes, efficiency and homogeneity. Simulating published literature, the earlier successful adult SRT studies show comparatively good index values, while the later failed studies do not. Those unsuccessful studies used smaller dose volumes with higher concentration mixtures, apparently assuming a well mixed compartment. The model shows that adult lungs are not well mixed in SRT due to the coating cost and gravity effects. Returning to the higher dose volume protocols could save many thousands of lives annually in the US. Supported by NIH Grants HL85156, HL84370 and Agence Nationale de la Recherche, ANR no. 2010-BLAN-1119-05.

  4. ShowMe3D

    2012-01-05

    ShowMe3D is a data visualization graphical user interface specifically designed for use with hyperspectral image obtained from the Hyperspectral Confocal Microscope. The program allows the user to select and display any single image from a three dimensional hyperspectral image stack. By moving a slider control, the user can easily move between images of the stack. The user can zoom into any region of the image. The user can select any pixel or region from themore » displayed image and display the fluorescence spectrum associated with that pixel or region. The user can define up to 3 spectral filters to apply to the hyperspectral image and view the image as it would appear from a filter-based confocal microscope. The user can also obtain statistics such as intensity average and variance from selected regions.« less

  5. ShowMe3D

    SciTech Connect

    Sinclair, Michael B

    2012-01-05

    ShowMe3D is a data visualization graphical user interface specifically designed for use with hyperspectral image obtained from the Hyperspectral Confocal Microscope. The program allows the user to select and display any single image from a three dimensional hyperspectral image stack. By moving a slider control, the user can easily move between images of the stack. The user can zoom into any region of the image. The user can select any pixel or region from the displayed image and display the fluorescence spectrum associated with that pixel or region. The user can define up to 3 spectral filters to apply to the hyperspectral image and view the image as it would appear from a filter-based confocal microscope. The user can also obtain statistics such as intensity average and variance from selected regions.

  6. 3D Elastic Wavefield Tomography

    NASA Astrophysics Data System (ADS)

    Guasch, L.; Warner, M.; Stekl, I.; Umpleby, A.; Shah, N.

    2010-12-01

    Wavefield tomography, or waveform inversion, aims to extract the maximum information from seismic data by matching trace by trace the response of the solid earth to seismic waves using numerical modelling tools. Its first formulation dates from the early 80's, when Albert Tarantola developed a solid theoretical basis that is still used today with little change. Due to computational limitations, the application of the method to 3D problems has been unaffordable until a few years ago, and then only under the acoustic approximation. Although acoustic wavefield tomography is widely used, a complete solution of the seismic inversion problem requires that we account properly for the physics of wave propagation, and so must include elastic effects. We have developed a 3D tomographic wavefield inversion code that incorporates the full elastic wave equation. The bottle neck of the different implementations is the forward modelling algorithm that generates the synthetic data to be compared with the field seismograms as well as the backpropagation of the residuals needed to form the direction update of the model parameters. Furthermore, one or two extra modelling runs are needed in order to calculate the step-length. Our approach uses a FD scheme explicit time-stepping by finite differences that are 4th order in space and 2nd order in time, which is a 3D version of the one developed by Jean Virieux in 1986. We chose the time domain because an explicit time scheme is much less demanding in terms of memory than its frequency domain analogue, although the discussion of wich domain is more efficient still remains open. We calculate the parameter gradients for Vp and Vs by correlating the normal and shear stress wavefields respectively. A straightforward application would lead to the storage of the wavefield at all grid points at each time-step. We tackled this problem using two different approaches. The first one makes better use of resources for small models of dimension equal

  7. The development of the globally harmonized system (GHS) of classification and labelling of hazardous chemicals.

    PubMed

    Winder, Chris; Azzi, Rola; Wagner, Drew

    2005-10-17

    The hazards of chemicals can be classified using classification criteria that are based on physical, chemical and ecotoxicological endpoints. These criteria may be developed be iteratively, based on scientific or regulatory processes. A number of national and international schemes have been developed over the past 50 years, and some, such as the UN Dangerous Goods system or the EC system for hazardous substances, are in widespread use. However, the unnecessarily complicated multiplicity of existing hazard classifications created much unnecessary confusion at the user level, and a recommendation was made at the 1992 Rio Earth summit to develop a globally harmonized chemical hazard classification and compatible labelling system, including material safety data sheets and easily understandable symbols, that could be used for manufacture, transport, use and disposal of chemical substances. This became the globally harmonized system for the Classification and Labelling of Chemicals (GHS). The developmental phase of the GHS is largely complete. Consistent criteria for categorising chemicals according to their toxic, physical, chemical and ecological hazards are now available. Consistent hazard communication tools such as labelling and material safety data sheets are also close to finalisation. The next phase is implementation of the GHS. The Intergovernmental Forum for Chemical Safety recommends that all countries implement the GHS as soon as possible with a view to have the system fully operational by 2008. When the GHS is in place, the world will finally have one system for classification of chemical hazards. PMID:16039045

  8. Chemical activity induces dynamical force with global structure in a reaction-diffusion-convection system.

    PubMed

    Mahara, Hitoshi; Okada, Koichi; Nomura, Atsushi; Miike, Hidetoshi; Sakurai, Tatsunari

    2009-07-01

    We found a rotating global structure induced by the dynamical force of local chemical activity in a thin solution layer of excitable Belousov-Zhabotinsky reaction coupled with diffusion. The surface flow and deformation associated with chemical spiral waves (wavelength about 1 mm) represents a global unidirectional structure and a global tilt in the entire Petri dish (100 mm in diameter), respectively. For these observations, we scanned the condition of hierarchal pattern selection. From this result, the bromomalonic acid has an important role to induce the rotating global structure. An interaction between a reaction-diffusion process and a surface-tension-driven effect leads to such hierarchal pattern with different scales. PMID:19658764

  9. Supernova Remnant in 3-D

    NASA Technical Reports Server (NTRS)

    2009-01-01

    wavelengths. Since the amount of the wavelength shift is related to the speed of motion, one can determine how fast the debris are moving in either direction. Because Cas A is the result of an explosion, the stellar debris is expanding radially outwards from the explosion center. Using simple geometry, the scientists were able to construct a 3-D model using all of this information. A program called 3-D Slicer modified for astronomical use by the Astronomical Medicine Project at Harvard University in Cambridge, Mass. was used to display and manipulate the 3-D model. Commercial software was then used to create the 3-D fly-through.

    The blue filaments defining the blast wave were not mapped using the Doppler effect because they emit a different kind of light synchrotron radiation that does not emit light at discrete wavelengths, but rather in a broad continuum. The blue filaments are only a representation of the actual filaments observed at the blast wave.

    This visualization shows that there are two main components to this supernova remnant: a spherical component in the outer parts of the remnant and a flattened (disk-like) component in the inner region. The spherical component consists of the outer layer of the star that exploded, probably made of helium and carbon. These layers drove a spherical blast wave into the diffuse gas surrounding the star. The flattened component that astronomers were unable to map into 3-D prior to these Spitzer observations consists of the inner layers of the star. It is made from various heavier elements, not all shown in the visualization, such as oxygen, neon, silicon, sulphur, argon and iron.

    High-velocity plumes, or jets, of this material are shooting out from the explosion in the plane of the disk-like component mentioned above. Plumes of silicon appear in the northeast and southwest, while those of iron are seen in the southeast and north. These jets were already known and Doppler velocity measurements have been made for these

  10. A 3-D microfluidic combinatorial cell array.

    PubMed

    Liu, Mike C; Tai, Yu-Chong

    2011-02-01

    We present the development of a three-dimensional (3-D) combinatorial cell culture array device featured with integrated three-input, eight-output combinatorial mixer and cell culture chambers. The device is designed for cell-based screening of multiple compounds simultaneously on a microfluidic platform. The final assembled device is composed of a porous membrane integrated in between a Parylene 3-D microfluidic chip and a PDMS microfluidic chip. The membrane turned the cell culture chambers into two-level configuration to facilitate cell loading and to maintain cells in a diffusion dominated space during device operation. Experimentally, we first characterized the combined compound concentration profile at each chamber using a fluorescence method. We then successfully demonstrated the functionality of the quantitative cell-based assay by culturing B35 rat neuronal cells on this device and screening the ability of three compounds (1,5-dihydroxyisoquinoline, deferoxamine, and 3-aminobenzoic acid) to attenuate cell death caused by cytotoxic hydrogen peroxide. In another experiment, we assayed for the combinatorial effects of three chemotherapeutic compound exposures (vinorelbine, paclitaxel, and γ-linolenic acid) on human breast cancer cells, MDA-MB-231. The same technology will enable the construction of inexpensive lab-on-a-chip devices with high-input combinatorial mixer for performing high-throughput cell-based assay and highly parallel and combinatorial chemical or biochemical reactions. PMID:21063783

  11. 3D printing of microscopic bacterial communities

    PubMed Central

    Connell, Jodi L.; Ritschdorff, Eric T.; Whiteley, Marvin; Shear, Jason B.

    2013-01-01

    Bacteria communicate via short-range physical and chemical signals, interactions known to mediate quorum sensing, sporulation, and other adaptive phenotypes. Although most in vitro studies examine bacterial properties averaged over large populations, the levels of key molecular determinants of bacterial fitness and pathogenicity (e.g., oxygen, quorum-sensing signals) may vary over micrometer scales within small, dense cellular aggregates believed to play key roles in disease transmission. A detailed understanding of how cell–cell interactions contribute to pathogenicity in natural, complex environments will require a new level of control in constructing more relevant cellular models for assessing bacterial phenotypes. Here, we describe a microscopic three-dimensional (3D) printing strategy that enables multiple populations of bacteria to be organized within essentially any 3D geometry, including adjacent, nested, and free-floating colonies. In this laser-based lithographic technique, microscopic containers are formed around selected bacteria suspended in gelatin via focal cross-linking of polypeptide molecules. After excess reagent is removed, trapped bacteria are localized within sealed cavities formed by the cross-linked gelatin, a highly porous material that supports rapid growth of fully enclosed cellular populations and readily transmits numerous biologically active species, including polypeptides, antibiotics, and quorum-sensing signals. Using this approach, we show that a picoliter-volume aggregate of Staphylococcus aureus can display substantial resistance to β-lactam antibiotics by enclosure within a shell composed of Pseudomonas aeruginosa. PMID:24101503

  12. Supernova Remnant in 3-D

    NASA Technical Reports Server (NTRS)

    2009-01-01

    wavelengths. Since the amount of the wavelength shift is related to the speed of motion, one can determine how fast the debris are moving in either direction. Because Cas A is the result of an explosion, the stellar debris is expanding radially outwards from the explosion center. Using simple geometry, the scientists were able to construct a 3-D model using all of this information. A program called 3-D Slicer modified for astronomical use by the Astronomical Medicine Project at Harvard University in Cambridge, Mass. was used to display and manipulate the 3-D model. Commercial software was then used to create the 3-D fly-through.

    The blue filaments defining the blast wave were not mapped using the Doppler effect because they emit a different kind of light synchrotron radiation that does not emit light at discrete wavelengths, but rather in a broad continuum. The blue filaments are only a representation of the actual filaments observed at the blast wave.

    This visualization shows that there are two main components to this supernova remnant: a spherical component in the outer parts of the remnant and a flattened (disk-like) component in the inner region. The spherical component consists of the outer layer of the star that exploded, probably made of helium and carbon. These layers drove a spherical blast wave into the diffuse gas surrounding the star. The flattened component that astronomers were unable to map into 3-D prior to these Spitzer observations consists of the inner layers of the star. It is made from various heavier elements, not all shown in the visualization, such as oxygen, neon, silicon, sulphur, argon and iron.

    High-velocity plumes, or jets, of this material are shooting out from the explosion in the plane of the disk-like component mentioned above. Plumes of silicon appear in the northeast and southwest, while those of iron are seen in the southeast and north. These jets were already known and Doppler velocity measurements have been made for these

  13. Sperm navigation along helical paths in 3D chemoattractant landscapes

    NASA Astrophysics Data System (ADS)

    Jikeli, Jan F.; Alvarez, Luis; Friedrich, Benjamin M.; Wilson, Laurence G.; Pascal, René; Colin, Remy; Pichlo, Magdalena; Rennhack, Andreas; Brenker, Christoph; Kaupp, U. Benjamin

    2015-08-01

    Sperm require a sense of direction to locate the egg for fertilization. They follow gradients of chemical and physical cues provided by the egg or the oviduct. However, the principles underlying three-dimensional (3D) navigation in chemical landscapes are unknown. Here using holographic microscopy and optochemical techniques, we track sea urchin sperm navigating in 3D chemoattractant gradients. Sperm sense gradients on two timescales, which produces two different steering responses. A periodic component, resulting from the helical swimming, gradually aligns the helix towards the gradient. When incremental path corrections fail and sperm get off course, a sharp turning manoeuvre puts sperm back on track. Turning results from an `off' Ca2+ response signifying a chemoattractant stimulation decrease and, thereby, a drop in cyclic GMP concentration and membrane voltage. These findings highlight the computational sophistication by which sperm sample gradients for deterministic klinotaxis. We provide a conceptual and technical framework for studying microswimmers in 3D chemical landscapes.

  14. Sperm navigation along helical paths in 3D chemoattractant landscapes

    PubMed Central

    Jikeli, Jan F.; Alvarez, Luis; Friedrich, Benjamin M.; Wilson, Laurence G.; Pascal, René; Colin, Remy; Pichlo, Magdalena; Rennhack, Andreas; Brenker, Christoph; Kaupp, U. Benjamin

    2015-01-01

    Sperm require a sense of direction to locate the egg for fertilization. They follow gradients of chemical and physical cues provided by the egg or the oviduct. However, the principles underlying three-dimensional (3D) navigation in chemical landscapes are unknown. Here using holographic microscopy and optochemical techniques, we track sea urchin sperm navigating in 3D chemoattractant gradients. Sperm sense gradients on two timescales, which produces two different steering responses. A periodic component, resulting from the helical swimming, gradually aligns the helix towards the gradient. When incremental path corrections fail and sperm get off course, a sharp turning manoeuvre puts sperm back on track. Turning results from an ‘off' Ca2+ response signifying a chemoattractant stimulation decrease and, thereby, a drop in cyclic GMP concentration and membrane voltage. These findings highlight the computational sophistication by which sperm sample gradients for deterministic klinotaxis. We provide a conceptual and technical framework for studying microswimmers in 3D chemical landscapes. PMID:26278469

  15. Sperm navigation along helical paths in 3D chemoattractant landscapes.

    PubMed

    Jikeli, Jan F; Alvarez, Luis; Friedrich, Benjamin M; Wilson, Laurence G; Pascal, René; Colin, Remy; Pichlo, Magdalena; Rennhack, Andreas; Brenker, Christoph; Kaupp, U Benjamin

    2015-01-01

    Sperm require a sense of direction to locate the egg for fertilization. They follow gradients of chemical and physical cues provided by the egg or the oviduct. However, the principles underlying three-dimensional (3D) navigation in chemical landscapes are unknown. Here using holographic microscopy and optochemical techniques, we track sea urchin sperm navigating in 3D chemoattractant gradients. Sperm sense gradients on two timescales, which produces two different steering responses. A periodic component, resulting from the helical swimming, gradually aligns the helix towards the gradient. When incremental path corrections fail and sperm get off course, a sharp turning manoeuvre puts sperm back on track. Turning results from an 'off' Ca(2+) response signifying a chemoattractant stimulation decrease and, thereby, a drop in cyclic GMP concentration and membrane voltage. These findings highlight the computational sophistication by which sperm sample gradients for deterministic klinotaxis. We provide a conceptual and technical framework for studying microswimmers in 3D chemical landscapes. PMID:26278469

  16. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  17. Embedding objects during 3D printing to add new functionalities.

    PubMed

    Yuen, Po Ki

    2016-07-01

    A novel method for integrating and embedding objects to add new functionalities during 3D printing based on fused deposition modeling (FDM) (also known as fused filament fabrication or molten polymer deposition) is presented. Unlike typical 3D printing, FDM-based 3D printing could allow objects to be integrated and embedded during 3D printing and the FDM-based 3D printed devices do not typically require any post-processing and finishing. Thus, various fluidic devices with integrated glass cover slips or polystyrene films with and without an embedded porous membrane, and optical devices with embedded Corning(®) Fibrance™ Light-Diffusing Fiber were 3D printed to demonstrate the versatility of the FDM-based 3D printing and embedding method. Fluid perfusion flow experiments with a blue colored food dye solution were used to visually confirm fluid flow and/or fluid perfusion through the embedded porous membrane in the 3D printed fluidic devices. Similar to typical 3D printed devices, FDM-based 3D printed devices are translucent at best unless post-polishing is performed and optical transparency is highly desirable in any fluidic devices; integrated glass cover slips or polystyrene films would provide a perfect optical transparent window for observation and visualization. In addition, they also provide a compatible flat smooth surface for biological or biomolecular applications. The 3D printed fluidic devices with an embedded porous membrane are applicable to biological or chemical applications such as continuous perfusion cell culture or biocatalytic synthesis but without the need for any post-device assembly and finishing. The 3D printed devices with embedded Corning(®) Fibrance™ Light-Diffusing Fiber would have applications in display, illumination, or optical applications. Furthermore, the FDM-based 3D printing and embedding method could also be utilized to print casting molds with an integrated glass bottom for polydimethylsiloxane (PDMS) device replication

  18. Response of the global climate to changes in atmospheric chemical composition due to fossil fuel burning

    NASA Astrophysics Data System (ADS)

    Hameed, Sultan; Cess, Robert D.; Hogan, Joseph S.

    1980-12-01

    Recent modeling of atmospheric chemical processes (Logan et al., 1978; Hameed et al., 1979) suggests that tropospheric ozone and methane might significantly increase in the future as the result of increasing anthropogenic emissions of CO, NOx, and CH4 due to fossil fuel burning. Since O3 and CH4 are both greenhouse gases, increases in their concentrations could augment global warming due to larger future amounts of atmospheric CO2. To test the possible climatic impact of changes in tropospheric chemical composition, a zonal energy-balance climate model has been combined with a vertically averaged tropospheric chemical model. The latter model includes all relevant chemical reactions which affect species derived from H2O, O2, CH4, and NOx. The climate model correspondingly incorporates changes in the infrared heating of the surface-troposphere system resulting from chemically induced changes in tropospheric ozone and methane. This coupled climate-chemical model indicates that global climate is sensitive to changes in emissions of CO, NOx, and CH4, and that future increases in these emissions could augment global warming due to increasing atmospheric CO2.

  19. Response of the global climate to changes in atmospheric chemical composition due to fossil fuel burning

    NASA Technical Reports Server (NTRS)

    Hameed, S.; Cess, R. D.; Hogan, J. S.

    1980-01-01

    Recent modeling of atmospheric chemical processes (Logan et al, 1978; Hameed et al, 1979) suggests that tropospheric ozone and methane might significantly increase in the future as the result of increasing anthropogenic emissions of CO, NO(x), and CH4 due to fossil fuel burning. Since O3 and CH4 are both greenhouse gases, increases in their concentrations could augment global warming due to larger future amounts of atmospheric CO2. To test the possible climatic impact of changes in tropospheric chemical composition, a zonal energy-balance climate model has been combined with a vertically averaged tropospheric chemical model. The latter model includes all relevant chemical reactions which affect species derived from H2O, O2, CH4, and NO(x). The climate model correspondingly incorporates changes in the infrared heating of the surface-troposphere system resulting from chemically induced changes in tropospheric ozone and methane. This coupled climate-chemical model indicates that global climate is sensitive to changes in emissions of CO, NO(x) and CH4, and that future increases in these emissions could augment global warming due to increasing atmospheric CO2.

  20. NIF Ignition Target 3D Point Design

    SciTech Connect

    Jones, O; Marinak, M; Milovich, J; Callahan, D

    2008-11-05

    We have developed an input file for running 3D NIF hohlraums that is optimized such that it can be run in 1-2 days on parallel computers. We have incorporated increasing levels of automation into the 3D input file: (1) Configuration controlled input files; (2) Common file for 2D and 3D, different types of capsules (symcap, etc.); and (3) Can obtain target dimensions, laser pulse, and diagnostics settings automatically from NIF Campaign Management Tool. Using 3D Hydra calculations to investigate different problems: (1) Intrinsic 3D asymmetry; (2) Tolerance to nonideal 3D effects (e.g. laser power balance, pointing errors); and (3) Synthetic diagnostics.

  1. 3D multiplexed immunoplasmonics microscopy.

    PubMed

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-21

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K(+) channel subunit KV1.1) on human cancer CD44(+) EGFR(+) KV1.1(+) MDA-MB-231 cells and reference CD44(-) EGFR(-) KV1.1(+) 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third

  2. Filling gaps in cultural heritage documentation by 3D photography

    NASA Astrophysics Data System (ADS)

    Schuhr, W.; Lee, J. D.

    2015-08-01

    geometry" and to multistage concepts of 3D photographs in Cultural Heritage just started. Furthermore a revised list of the 3D visualization principles, claiming completeness, has been carried out. Beside others in an outlook *It is highly recommended, to list every historical and current stereo view with relevance to Cultural Heritage in a global Monument Information System (MIS), like in google earth. *3D photographs seem to be very suited, to complete and/or at least partly to replace manual archaeological sketches. In this concern the still underestimated 3D effect will be demonstrated, which even allows, e.g., the spatial perception of extremely small scratches etc... *A consequent dealing with 3D Technology even seems to indicate, currently we experience the beginning of a new age of "real 3DPC- screens", which at least could add or even partly replace the conventional 2D screens. Here the spatial visualization is verified without glasses in an all-around vitreous body. In this respect nowadays widespread lasered crystals showing monuments are identified as "Early Bird" 3D products, which, due to low resolution and contrast and due to lack of color, currently might even remember to the status of the invention of photography by Niepce (1827), but seem to promise a great future also in 3D Cultural Heritage documentation. *Last not least 3D printers more and more seem to conquer the IT-market, obviously showing an international competition.

  3. Studies of Trace Gas Chemical Cycles Using Observations, Inverse Methods and Global Chemical Transport Models

    NASA Technical Reports Server (NTRS)

    Prinn, Ronald G.

    2001-01-01

    For interpreting observational data, and in particular for use in inverse methods, accurate and realistic chemical transport models are essential. Toward this end we have, in recent years, helped develop and utilize a number of three-dimensional models including the Model for Atmospheric Transport and Chemistry (MATCH).

  4. 3D Kitaev spin liquids

    NASA Astrophysics Data System (ADS)

    Hermanns, Maria

    The Kitaev honeycomb model has become one of the archetypal spin models exhibiting topological phases of matter, where the magnetic moments fractionalize into Majorana fermions interacting with a Z2 gauge field. In this talk, we discuss generalizations of this model to three-dimensional lattice structures. Our main focus is the metallic state that the emergent Majorana fermions form. In particular, we discuss the relation of the nature of this Majorana metal to the details of the underlying lattice structure. Besides (almost) conventional metals with a Majorana Fermi surface, one also finds various realizations of Dirac semi-metals, where the gapless modes form Fermi lines or even Weyl nodes. We introduce a general classification of these gapless quantum spin liquids using projective symmetry analysis. Furthermore, we briefly outline why these Majorana metals in 3D Kitaev systems provide an even richer variety of Dirac and Weyl phases than possible for electronic matter and comment on possible experimental signatures. Work done in collaboration with Kevin O'Brien and Simon Trebst.

  5. Yogi the rock - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Yogi, a rock taller than rover Sojourner, is the subject of this image, taken in stereo by the deployed Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. The soil in the foreground has been the location of multiple soil mechanics experiments performed by Sojourner's cleated wheels. Pathfinder scientists were able to control the force inflicted on the soil beneath the rover's wheels, giving them insight into the soil's mechanical properties. The soil mechanics experiments were conducted after this image was taken.

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  6. 3D ultrafast laser scanner

    NASA Astrophysics Data System (ADS)

    Mahjoubfar, A.; Goda, K.; Wang, C.; Fard, A.; Adam, J.; Gossett, D. R.; Ayazi, A.; Sollier, E.; Malik, O.; Chen, E.; Liu, Y.; Brown, R.; Sarkhosh, N.; Di Carlo, D.; Jalali, B.

    2013-03-01

    Laser scanners are essential for scientific research, manufacturing, defense, and medical practice. Unfortunately, often times the speed of conventional laser scanners (e.g., galvanometric mirrors and acousto-optic deflectors) falls short for many applications, resulting in motion blur and failure to capture fast transient information. Here, we present a novel type of laser scanner that offers roughly three orders of magnitude higher scan rates than conventional methods. Our laser scanner, which we refer to as the hybrid dispersion laser scanner, performs inertia-free laser scanning by dispersing a train of broadband pulses both temporally and spatially. More specifically, each broadband pulse is temporally processed by time stretch dispersive Fourier transform and further dispersed into space by one or more diffractive elements such as prisms and gratings. As a proof-of-principle demonstration, we perform 1D line scans at a record high scan rate of 91 MHz and 2D raster scans and 3D volumetric scans at an unprecedented scan rate of 105 kHz. The method holds promise for a broad range of scientific, industrial, and biomedical applications. To show the utility of our method, we demonstrate imaging, nanometer-resolved surface vibrometry, and high-precision flow cytometry with real-time throughput that conventional laser scanners cannot offer due to their low scan rates.

  7. Crowdsourcing Based 3d Modeling

    NASA Astrophysics Data System (ADS)

    Somogyi, A.; Barsi, A.; Molnar, B.; Lovas, T.

    2016-06-01

    Web-based photo albums that support organizing and viewing the users' images are widely used. These services provide a convenient solution for storing, editing and sharing images. In many cases, the users attach geotags to the images in order to enable using them e.g. in location based applications on social networks. Our paper discusses a procedure that collects open access images from a site frequently visited by tourists. Geotagged pictures showing the image of a sight or tourist attraction are selected and processed in photogrammetric processing software that produces the 3D model of the captured object. For the particular investigation we selected three attractions in Budapest. To assess the geometrical accuracy, we used laser scanner and DSLR as well as smart phone photography to derive reference values to enable verifying the spatial model obtained from the web-album images. The investigation shows how detailed and accurate models could be derived applying photogrammetric processing software, simply by using images of the community, without visiting the site.

  8. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  9. a Fast Method for Measuring the Similarity Between 3d Model and 3d Point Cloud

    NASA Astrophysics Data System (ADS)

    Zhang, Zongliang; Li, Jonathan; Li, Xin; Lin, Yangbin; Zhang, Shanxin; Wang, Cheng

    2016-06-01

    This paper proposes a fast method for measuring the partial Similarity between 3D Model and 3D point Cloud (SimMC). It is crucial to measure SimMC for many point cloud-related applications such as 3D object retrieval and inverse procedural modelling. In our proposed method, the surface area of model and the Distance from Model to point Cloud (DistMC) are exploited as measurements to calculate SimMC. Here, DistMC is defined as the weighted distance of the distances between points sampled from model and point cloud. Similarly, Distance from point Cloud to Model (DistCM) is defined as the average distance of the distances between points in point cloud and model. In order to reduce huge computational burdens brought by calculation of DistCM in some traditional methods, we define SimMC as the ratio of weighted surface area of model to DistMC. Compared to those traditional SimMC measuring methods that are only able to measure global similarity, our method is capable of measuring partial similarity by employing distance-weighted strategy. Moreover, our method is able to be faster than other partial similarity assessment methods. We demonstrate the superiority of our method both on synthetic data and laser scanning data.

  10. Photochemical Copper Coating on 3D Printed Thermoplastics

    NASA Astrophysics Data System (ADS)

    Yung, Winco K. C.; Sun, Bo; Huang, Junfeng; Jin, Yingdi; Meng, Zhengong; Choy, Hang Shan; Cai, Zhixiang; Li, Guijun; Ho, Cheuk Lam; Yang, Jinlong; Wong, Wai Yeung

    2016-08-01

    3D printing using thermoplastics has become very popular in recent years, however, it is challenging to provide a metal coating on 3D objects without using specialized and expensive tools. Herein, a novel acrylic paint containing malachite for coating on 3D printed objects is introduced, which can be transformed to copper via one-step laser treatment. The malachite containing pigment can be used as a commercial acrylic paint, which can be brushed onto 3D printed objects. The material properties and photochemical transformation processes have been comprehensively studied. The underlying physics of the photochemical synthesis of copper was characterized using density functional theory calculations. After laser treatment, the surface coating of the 3D printed objects was transformed to copper, which was experimentally characterized by XRD. 3D printed prototypes, including model of the Statue of Liberty covered with a copper surface coating and a robotic hand with copper interconnections, are demonstrated using this painting method. This composite material can provide a novel solution for coating metals on 3D printed objects. The photochemical reduction analysis indicates that the copper rust in malachite form can be remotely and photo-chemically reduced to pure copper with sufficient photon energy.

  11. Photochemical Copper Coating on 3D Printed Thermoplastics

    PubMed Central

    Yung, Winco K. C.; Sun, Bo; Huang, Junfeng; Jin, Yingdi; Meng, Zhengong; Choy, Hang Shan; Cai, Zhixiang; Li, Guijun; Ho, Cheuk Lam; Yang, Jinlong; Wong, Wai Yeung

    2016-01-01

    3D printing using thermoplastics has become very popular in recent years, however, it is challenging to provide a metal coating on 3D objects without using specialized and expensive tools. Herein, a novel acrylic paint containing malachite for coating on 3D printed objects is introduced, which can be transformed to copper via one-step laser treatment. The malachite containing pigment can be used as a commercial acrylic paint, which can be brushed onto 3D printed objects. The material properties and photochemical transformation processes have been comprehensively studied. The underlying physics of the photochemical synthesis of copper was characterized using density functional theory calculations. After laser treatment, the surface coating of the 3D printed objects was transformed to copper, which was experimentally characterized by XRD. 3D printed prototypes, including model of the Statue of Liberty covered with a copper surface coating and a robotic hand with copper interconnections, are demonstrated using this painting method. This composite material can provide a novel solution for coating metals on 3D printed objects. The photochemical reduction analysis indicates that the copper rust in malachite form can be remotely and photo-chemically reduced to pure copper with sufficient photon energy. PMID:27501761

  12. Photochemical Copper Coating on 3D Printed Thermoplastics.

    PubMed

    Yung, Winco K C; Sun, Bo; Huang, Junfeng; Jin, Yingdi; Meng, Zhengong; Choy, Hang Shan; Cai, Zhixiang; Li, Guijun; Ho, Cheuk Lam; Yang, Jinlong; Wong, Wai Yeung

    2016-01-01

    3D printing using thermoplastics has become very popular in recent years, however, it is challenging to provide a metal coating on 3D objects without using specialized and expensive tools. Herein, a novel acrylic paint containing malachite for coating on 3D printed objects is introduced, which can be transformed to copper via one-step laser treatment. The malachite containing pigment can be used as a commercial acrylic paint, which can be brushed onto 3D printed objects. The material properties and photochemical transformation processes have been comprehensively studied. The underlying physics of the photochemical synthesis of copper was characterized using density functional theory calculations. After laser treatment, the surface coating of the 3D printed objects was transformed to copper, which was experimentally characterized by XRD. 3D printed prototypes, including model of the Statue of Liberty covered with a copper surface coating and a robotic hand with copper interconnections, are demonstrated using this painting method. This composite material can provide a novel solution for coating metals on 3D printed objects. The photochemical reduction analysis indicates that the copper rust in malachite form can be remotely and photo-chemically reduced to pure copper with sufficient photon energy. PMID:27501761

  13. 3D affine registration using teaching-learning based optimization

    NASA Astrophysics Data System (ADS)

    Jani, Ashish; Savsani, Vimal; Pandya, Abhijit

    2013-09-01

    3D image registration is an emerging research field in the study of computer vision. In this paper, two effective global optimization methods are considered for the 3D registration of point clouds. Experiments were conducted by applying each algorithm and their performance was evaluated with respect to rigidity, similarity and affine transformations. Comparison of algorithms and its effectiveness was tested for the average performance to find the global solution for minimizing the error in the terms of distance between the model cloud and the data cloud. The parameters for the transformation matrix were considered as the design variables. Further comparisons of the considered methods were done for the computational effort, computational time and the convergence of the algorithm. The results reveal that the use of TLBO was outstanding for image processing application involving 3D registration. [Figure not available: see fulltext.

  14. Global Chemical Composition of Ambient Fine Particulate Matter for Exposure Assessment

    PubMed Central

    2015-01-01

    Epidemiologic and health impact studies are inhibited by the paucity of global, long-term measurements of the chemical composition of fine particulate matter. We inferred PM2.5 chemical composition at 0.1° × 0.1° spatial resolution for 2004–2008 by combining aerosol optical depth retrieved from the MODIS and MISR satellite instruments, with coincident profile and composition information from the GEOS-Chem global chemical transport model. Evaluation of the satellite-model PM2.5 composition data set with North American in situ measurements indicated significant spatial agreement for secondary inorganic aerosol, particulate organic mass, black carbon, mineral dust, and sea salt. We found that global population-weighted PM2.5 concentrations were dominated by particulate organic mass (11.9 ± 7.3 μg/m3), secondary inorganic aerosol (11.1 ± 5.0 μg/m3), and mineral dust (11.1 ± 7.9 μg/m3). Secondary inorganic PM2.5 concentrations exceeded 30 μg/m3 over East China. Sensitivity simulations suggested that population-weighted ambient PM2.5 from biofuel burning (11 μg/m3) could be almost as large as from fossil fuel combustion sources (17 μg/m3). These estimates offer information about global population exposure to the chemical components and sources of PM2.5. PMID:25343705

  15. Global chemical composition of ambient fine particulate matter for exposure assessment.

    PubMed

    Philip, Sajeev; Martin, Randall V; van Donkelaar, Aaron; Lo, Jason Wai-Ho; Wang, Yuxuan; Chen, Dan; Zhang, Lin; Kasibhatla, Prasad S; Wang, Siwen; Zhang, Qiang; Lu, Zifeng; Streets, David G; Bittman, Shabtai; Macdonald, Douglas J

    2014-11-18

    Epidemiologic and health impact studies are inhibited by the paucity of global, long-term measurements of the chemical composition of fine particulate matter. We inferred PM2.5 chemical composition at 0.1° × 0.1° spatial resolution for 2004-2008 by combining aerosol optical depth retrieved from the MODIS and MISR satellite instruments, with coincident profile and composition information from the GEOS-Chem global chemical transport model. Evaluation of the satellite-model PM2.5 composition data set with North American in situ measurements indicated significant spatial agreement for secondary inorganic aerosol, particulate organic mass, black carbon, mineral dust, and sea salt. We found that global population-weighted PM2.5 concentrations were dominated by particulate organic mass (11.9 ± 7.3 μg/m(3)), secondary inorganic aerosol (11.1 ± 5.0 μg/m(3)), and mineral dust (11.1 ± 7.9 μg/m(3)). Secondary inorganic PM2.5 concentrations exceeded 30 μg/m(3) over East China. Sensitivity simulations suggested that population-weighted ambient PM2.5 from biofuel burning (11 μg/m(3)) could be almost as large as from fossil fuel combustion sources (17 μg/m(3)). These estimates offer information about global population exposure to the chemical components and sources of PM2.5. PMID:25343705

  16. Global Chemical Composition of Ambient Fine Particulate Matter for Exposure Assessment

    DOE PAGESBeta

    Philip, Sajeev; Martin, Randall V.; van Donkelaar, Aaron; Lo, Jason Wai-Ho; Wang, Yuxuan; Chen, Dan; Zhang, Lin; Kasibhatla, Prasad S.; Wang, Siwen; Zhang, Qiang; et al

    2014-10-24

    Epidemiologic and health impact studies are inhibited by the paucity of global, long-term measurements of the chemical composition of fine particulate matter. We inferred PM2.5 chemical composition at 0.1° × 0.1° spatial resolution for 2004–2008 by combining aerosol optical depth retrieved from the MODIS and MISR satellite instruments, with coincident profile and composition information from the GEOS-Chem global chemical transport model. Evaluation of the satellite-model PM2.5 composition data set with North American in situ measurements indicated significant spatial agreement for secondary inorganic aerosol, particulate organic mass, black carbon, mineral dust, and sea salt. We found that global population-weighted PM2.5 concentrationsmore » were dominated by particulate organic mass (11.9 ± 7.3 μg/m3), secondary inorganic aerosol (11.1 ± 5.0 μg/m3), and mineral dust (11.1 ± 7.9 μg/m3). Secondary inorganic PM2.5 concentrations exceeded 30 μg/m3 over East China. Sensitivity simulations suggested that population-weighted ambient PM2.5 from biofuel burning (11 μg/m3) could be almost as large as from fossil fuel combustion sources (17 μg/m3). In conclusion, these estimates offer information about global population exposure to the chemical components and sources of PM2.5.« less

  17. Virtual and Printed 3D Models for Teaching Crystal Symmetry and Point Groups

    ERIC Educational Resources Information Center

    Casas, Lluís; Estop, Euge`nia

    2015-01-01

    Both, virtual and printed 3D crystal models can help students and teachers deal with chemical education topics such as symmetry and point groups. In the present paper, two freely downloadable tools (interactive PDF files and a mobile app) are presented as examples of the application of 3D design to study point-symmetry. The use of 3D printing to…

  18. 3-D Cavern Enlargement Analyses

    SciTech Connect

    EHGARTNER, BRIAN L.; SOBOLIK, STEVEN R.

    2002-03-01

    Three-dimensional finite element analyses simulate the mechanical response of enlarging existing caverns at the Strategic Petroleum Reserve (SPR). The caverns are located in Gulf Coast salt domes and are enlarged by leaching during oil drawdowns as fresh water is injected to displace the crude oil from the caverns. The current criteria adopted by the SPR limits cavern usage to 5 drawdowns (leaches). As a base case, 5 leaches were modeled over a 25 year period to roughly double the volume of a 19 cavern field. Thirteen additional leaches where then simulated until caverns approached coalescence. The cavern field approximated the geometries and geologic properties found at the West Hackberry site. This enabled comparisons are data collected over nearly 20 years to analysis predictions. The analyses closely predicted the measured surface subsidence and cavern closure rates as inferred from historic well head pressures. This provided the necessary assurance that the model displacements, strains, and stresses are accurate. However, the cavern field has not yet experienced the large scale drawdowns being simulated. Should they occur in the future, code predictions should be validated with actual field behavior at that time. The simulations were performed using JAS3D, a three dimensional finite element analysis code for nonlinear quasi-static solids. The results examine the impacts of leaching and cavern workovers, where internal cavern pressures are reduced, on surface subsidence, well integrity, and cavern stability. The results suggest that the current limit of 5 oil drawdowns may be extended with some mitigative action required on the wells and later on to surface structure due to subsidence strains. The predicted stress state in the salt shows damage to start occurring after 15 drawdowns with significant failure occurring at the 16th drawdown, well beyond the current limit of 5 drawdowns.

  19. Imaging a Sustainable Future in 3D

    NASA Astrophysics Data System (ADS)

    Schuhr, W.; Lee, J. D.; Kanngieser, E.

    2012-07-01

    It is the intention of this paper, to contribute to a sustainable future by providing objective object information based on 3D photography as well as promoting 3D photography not only for scientists, but also for amateurs. Due to the presentation of this article by CIPA Task Group 3 on "3D Photographs in Cultural Heritage", the presented samples are masterpieces of historic as well as of current 3D photography concentrating on cultural heritage. In addition to a report on exemplarily access to international archives of 3D photographs, samples for new 3D photographs taken with modern 3D cameras, as well as by means of a ground based high resolution XLITE staff camera and also 3D photographs taken from a captive balloon and the use of civil drone platforms are dealt with. To advise on optimum suited 3D methodology, as well as to catch new trends in 3D, an updated synoptic overview of the 3D visualization technology, even claiming completeness, has been carried out as a result of a systematic survey. In this respect, e.g., today's lasered crystals might be "early bird" products in 3D, which, due to lack in resolution, contrast and color, remember to the stage of the invention of photography.

  20. Teaching Geography with 3-D Visualization Technology

    ERIC Educational Resources Information Center

    Anthamatten, Peter; Ziegler, Susy S.

    2006-01-01

    Technology that helps students view images in three dimensions (3-D) can support a broad range of learning styles. "Geo-Wall systems" are visualization tools that allow scientists, teachers, and students to project stereographic images and view them in 3-D. We developed and presented 3-D visualization exercises in several undergraduate courses.…

  1. 3D Printing and Its Urologic Applications

    PubMed Central

    Soliman, Youssef; Feibus, Allison H; Baum, Neil

    2015-01-01

    3D printing is the development of 3D objects via an additive process in which successive layers of material are applied under computer control. This article discusses 3D printing, with an emphasis on its historical context and its potential use in the field of urology. PMID:26028997

  2. 3D Flow Visualization Using Texture Advection

    NASA Technical Reports Server (NTRS)

    Kao, David; Zhang, Bing; Kim, Kwansik; Pang, Alex; Moran, Pat (Technical Monitor)

    2001-01-01

    Texture advection is an effective tool for animating and investigating 2D flows. In this paper, we discuss how this technique can be extended to 3D flows. In particular, we examine the use of 3D and 4D textures on 3D synthetic and computational fluid dynamics flow fields.

  3. 3D Elastic Seismic Wave Propagation Code

    1998-09-23

    E3D is capable of simulating seismic wave propagation in a 3D heterogeneous earth. Seismic waves are initiated by earthquake, explosive, and/or other sources. These waves propagate through a 3D geologic model, and are simulated as synthetic seismograms or other graphical output.

  4. 3D Printing and Its Urologic Applications.

    PubMed

    Soliman, Youssef; Feibus, Allison H; Baum, Neil

    2015-01-01

    3D printing is the development of 3D objects via an additive process in which successive layers of material are applied under computer control. This article discusses 3D printing, with an emphasis on its historical context and its potential use in the field of urology. PMID:26028997

  5. MOSSFRAC: An anisotropic 3D fracture model

    SciTech Connect

    Moss, W C; Levatin, J L

    2006-08-14

    Despite the intense effort for nearly half a century to construct detailed numerical models of plastic flow and plastic damage accumulation, models for describing fracture, an equally important damage mechanism still cannot describe basic fracture phenomena. Typical fracture models set the stress tensor to zero for tensile fracture and set the deviatoric stress tensor to zero for compressive fracture. One consequence is that the simple case of the tensile fracture of a cylinder under combined compressive radial and tensile axial loads is not modeled correctly. The experimental result is a cylinder that can support compressive radial loads, but no axial load, whereas, the typical numerical result is a cylinder with all stresses equal to zero. This incorrect modeling of fracture locally also has a global effect, because material that is fracturing produces stress release waves, which propagate from the fracture and influence the surrounding material. Consequently, it would be useful to have a model that can describe the stress relief and the resulting anisotropy due to fracture. MOSSFRAC is a material model that simulates three-dimensional tensile and shear fracture in initially isotropic elastic-plastic materials, although its framework is also amenable to initially anisotropic materials. It differs from other models by accounting for the effects of cracks on the constitutive response of the material, so that the previously described experiment, as well as complicated fracture scenarios are simulated more accurately. The model is implemented currently in the LLNL hydrocodes DYNA3D, PARADYN, and ALE3D. The purpose of this technical note is to present a complete qualitative description of the model and quantitative descriptions of salient features.

  6. Consistent global structures of complex RNA states through multidimensional chemical mapping

    PubMed Central

    Cheng, Clarence Yu; Chou, Fang-Chieh; Kladwang, Wipapat; Tian, Siqi; Cordero, Pablo; Das, Rhiju

    2015-01-01

    Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states. DOI: http://dx.doi.org/10.7554/eLife.07600.001 PMID:26035425

  7. 3-D Perspective Pasadena, California

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This perspective view shows the western part of the city of Pasadena, California, looking north towards the San Gabriel Mountains. Portions of the cities of Altadena and La Canada, Flintridge are also shown. The image was created from three datasets: the Shuttle Radar Topography Mission (SRTM) supplied the elevation data; Landsat data from November 11, 1986 provided the land surface color (not the sky) and U.S. Geological Survey digital aerial photography provides the image detail. The Rose Bowl, surrounded by a golf course, is the circular feature at the bottom center of the image. The Jet Propulsion Laboratory is the cluster of large buildings north of the Rose Bowl at the base of the mountains. A large landfill, Scholl Canyon, is the smooth area in the lower left corner of the scene. This image shows the power of combining data from different sources to create planning tools to study problems that affect large urban areas. In addition to the well-known earthquake hazards, Southern California is affected by a natural cycle of fire and mudflows. Wildfires strip the mountains of vegetation, increasing the hazards from flooding and mudflows for several years afterwards. Data such as shown on this image can be used to predict both how wildfires will spread over the terrain and also how mudflows will be channeled down the canyons. The Shuttle Radar Topography Mission (SRTM), launched on February 11, 2000, uses the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) that flew twice on the Space Shuttle Endeavour in 1994. The mission was designed to collect three dimensional measurements of the Earth's surface. To collect the 3-D data, engineers added a 60-meter-long (200-foot) mast, an additional C-band imaging antenna and improved tracking and navigation devices. The mission is a cooperative project between the National Aeronautics and Space Administration (NASA), the National Imagery and Mapping Agency

  8. The Esri 3D city information model

    NASA Astrophysics Data System (ADS)

    Reitz, T.; Schubiger-Banz, S.

    2014-02-01

    With residential and commercial space becoming increasingly scarce, cities are going vertical. Managing the urban environments in 3D is an increasingly important and complex undertaking. To help solving this problem, Esri has released the ArcGIS for 3D Cities solution. The ArcGIS for 3D Cities solution provides the information model, tools and apps for creating, analyzing and maintaining a 3D city using the ArcGIS platform. This paper presents an overview of the 3D City Information Model and some sample use cases.

  9. 3D Bioprinting of Tissue/Organ Models.

    PubMed

    Pati, Falguni; Gantelius, Jesper; Svahn, Helene Andersson

    2016-04-01

    In vitro tissue/organ models are useful platforms that can facilitate systematic, repetitive, and quantitative investigations of drugs/chemicals. The primary objective when developing tissue/organ models is to reproduce physiologically relevant functions that typically require complex culture systems. Bioprinting offers exciting prospects for constructing 3D tissue/organ models, as it enables the reproducible, automated production of complex living tissues. Bioprinted tissues/organs may prove useful for screening novel compounds or predicting toxicity, as the spatial and chemical complexity inherent to native tissues/organs can be recreated. In this Review, we highlight the importance of developing 3D in vitro tissue/organ models by 3D bioprinting techniques, characterization of these models for evaluating their resemblance to native tissue, and their application in the prioritization of lead candidates, toxicity testing, and as disease/tumor models. PMID:26895542

  10. The Feasibility of 3d Point Cloud Generation from Smartphones

    NASA Astrophysics Data System (ADS)

    Alsubaie, N.; El-Sheimy, N.

    2016-06-01

    This paper proposes a new technique for increasing the accuracy of direct geo-referenced image-based 3D point cloud generated from low-cost sensors in smartphones. The smartphone's motion sensors are used to directly acquire the Exterior Orientation Parameters (EOPs) of the captured images. These EOPs, along with the Interior Orientation Parameters (IOPs) of the camera/ phone, are used to reconstruct the image-based 3D point cloud. However, because smartphone motion sensors suffer from poor GPS accuracy, accumulated drift and high signal noise, inaccurate 3D mapping solutions often result. Therefore, horizontal and vertical linear features, visible in each image, are extracted and used as constraints in the bundle adjustment procedure. These constraints correct the relative position and orientation of the 3D mapping solution. Once the enhanced EOPs are estimated, the semi-global matching algorithm (SGM) is used to generate the image-based dense 3D point cloud. Statistical analysis and assessment are implemented herein, in order to demonstrate the feasibility of 3D point cloud generation from the consumer-grade sensors in smartphones.

  11. 3D laser imaging for concealed object identification

    NASA Astrophysics Data System (ADS)

    Berechet, Ion; Berginc, Gérard; Berechet, Stefan

    2014-09-01

    This paper deals with new optical non-conventional 3D laser imaging. Optical non-conventional imaging explores the advantages of laser imaging to form a three-dimensional image of the scene. 3D laser imaging can be used for threedimensional medical imaging, topography, surveillance, robotic vision because of ability to detect and recognize objects. In this paper, we present a 3D laser imaging for concealed object identification. The objective of this new 3D laser imaging is to provide the user a complete 3D reconstruction of the concealed object from available 2D data limited in number and with low representativeness. The 2D laser data used in this paper come from simulations that are based on the calculation of the laser interactions with the different interfaces of the scene of interest and from experimental results. We show the global 3D reconstruction procedures capable to separate objects from foliage and reconstruct a threedimensional image of the considered object. In this paper, we present examples of reconstruction and completion of three-dimensional images and we analyse the different parameters of the identification process such as resolution, the scenario of camouflage, noise impact and lacunarity degree.

  12. Case study: Beauty and the Beast 3D: benefits of 3D viewing for 2D to 3D conversion

    NASA Astrophysics Data System (ADS)

    Handy Turner, Tara

    2010-02-01

    From the earliest stages of the Beauty and the Beast 3D conversion project, the advantages of accurate desk-side 3D viewing was evident. While designing and testing the 2D to 3D conversion process, the engineering team at Walt Disney Animation Studios proposed a 3D viewing configuration that not only allowed artists to "compose" stereoscopic 3D but also improved efficiency by allowing artists to instantly detect which image features were essential to the stereoscopic appeal of a shot and which features had minimal or even negative impact. At a time when few commercial 3D monitors were available and few software packages provided 3D desk-side output, the team designed their own prototype devices and collaborated with vendors to create a "3D composing" workstation. This paper outlines the display technologies explored, final choices made for Beauty and the Beast 3D, wish-lists for future development and a few rules of thumb for composing compelling 2D to 3D conversions.

  13. 3D laptop for defense applications

    NASA Astrophysics Data System (ADS)

    Edmondson, Richard; Chenault, David

    2012-06-01

    Polaris Sensor Technologies has developed numerous 3D display systems using a US Army patented approach. These displays have been developed as prototypes for handheld controllers for robotic systems and closed hatch driving, and as part of a TALON robot upgrade for 3D vision, providing depth perception for the operator for improved manipulation and hazard avoidance. In this paper we discuss the prototype rugged 3D laptop computer and its applications to defense missions. The prototype 3D laptop combines full temporal and spatial resolution display with the rugged Amrel laptop computer. The display is viewed through protective passive polarized eyewear, and allows combined 2D and 3D content. Uses include robot tele-operation with live 3D video or synthetically rendered scenery, mission planning and rehearsal, enhanced 3D data interpretation, and simulation.

  14. Response of the global climate to changes in atmospheric chemical composition due to fossil fuel burning

    NASA Technical Reports Server (NTRS)

    Cess, R. D.; Hameed, S.; Hogan, J. S.

    1980-01-01

    Tropospheric ozone and methane might increase in the future as the result of increasing anthropogenic emissions of CO, NOx and CH4 due to fossil fuel burning. Since O3 and CH4 are both greenhouse gases, increases in their concentrations could augment global warming due to larger future amounts of atmospheric CO2. To test this possible climatic impact, a zonal energy-balance climate model has been combined with a vertically-averaged tropospheric chemical model. The latter model includes all relevant chemical reactions which affect species derived from H2O, O2, CH4 and NOx. The climate model correspondingly incorporates changes in the infrared heating of the surface-troposphere system resulting from chemically induced changes in tropospheric ozone and methane. This coupled climate-chemical model indicates that global climate is sensitive to changes in emissions of CO, NOx and CH4, and that future increases in these emissions could enhance global warming due to increasing atmospheric CO2.

  15. Dark matter in 3D

    NASA Astrophysics Data System (ADS)

    Alves, Daniele S. M.; El Hedri, Sonia; Wacker, Jay G.

    2016-03-01

    We discuss the relevance of directional detection experiments in the post-discovery era and propose a method to extract the local dark matter phase space distribution from directional data. The first feature of this method is a parameterization of the dark matter distribution function in terms of integrals of motion, which can be analytically extended to infer properties of the global distribution if certain equilibrium conditions hold. The second feature of our method is a decomposition of the distribution function in moments of a model independent basis, with minimal reliance on the ansatz for its functional form. We illustrate our method using the Via Lactea II N-body simulation as well as an analytical model for the dark matter halo. We conclude that {O}(1000) events are necessary to measure deviations from the Standard Halo Model and constrain or measure the presence of anisotropies.

  16. Dark Matter in 3D

    SciTech Connect

    Alves, Daniele S.M.; Hedri, Sonia El; Wacker, Jay G.

    2012-04-01

    We discuss the relevance of directional detection experiments in the post-discovery era and propose a method to extract the local dark matter phase space distribution from directional data. The first feature of this method is a parameterization of the dark matter distribution function in terms of integrals of motion, which can be analytically extended to infer properties of the global distribution if certain equilibrium conditions hold. The second feature of our method is a decomposition of the distribution function in moments of a model independent basis, with minimal reliance on the ansatz for its functional form. We illustrate our method using the Via Lactea II N-body simulation as well as an analytical model for the dark matter halo. We conclude that O(1000) events are necessary to measure deviations from the Standard Halo Model and constrain or measure the presence of anisotropies.

  17. Dark matter in 3D

    DOE PAGESBeta

    Alves, Daniele S. M.; El Hedri, Sonia; Wacker, Jay G.

    2016-03-21

    We discuss the relevance of directional detection experiments in the post-discovery era and propose a method to extract the local dark matter phase space distribution from directional data. The first feature of this method is a parameterization of the dark matter distribution function in terms of integrals of motion, which can be analytically extended to infer properties of the global distribution if certain equilibrium conditions hold. The second feature of our method is a decomposition of the distribution function in moments of a model independent basis, with minimal reliance on the ansatz for its functional form. We illustrate our methodmore » using the Via Lactea II N-body simulation as well as an analytical model for the dark matter halo. Furthermore, we conclude that O(1000) events are necessary to measure deviations from the Standard Halo Model and constrain or measure the presence of anisotropies.« less

  18. 3D quantitative phase imaging of neural networks using WDT

    NASA Astrophysics Data System (ADS)

    Kim, Taewoo; Liu, S. C.; Iyer, Raj; Gillette, Martha U.; Popescu, Gabriel

    2015-03-01

    White-light diffraction tomography (WDT) is a recently developed 3D imaging technique based on a quantitative phase imaging system called spatial light interference microscopy (SLIM). The technique has achieved a sub-micron resolution in all three directions with high sensitivity granted by the low-coherence of a white-light source. Demonstrations of the technique on single cell imaging have been presented previously; however, imaging on any larger sample, including a cluster of cells, has not been demonstrated using the technique. Neurons in an animal body form a highly complex and spatially organized 3D structure, which can be characterized by neuronal networks or circuits. Currently, the most common method of studying the 3D structure of neuron networks is by using a confocal fluorescence microscope, which requires fluorescence tagging with either transient membrane dyes or after fixation of the cells. Therefore, studies on neurons are often limited to samples that are chemically treated and/or dead. WDT presents a solution for imaging live neuron networks with a high spatial and temporal resolution, because it is a 3D imaging method that is label-free and non-invasive. Using this method, a mouse or rat hippocampal neuron culture and a mouse dorsal root ganglion (DRG) neuron culture have been imaged in order to see the extension of processes between the cells in 3D. Furthermore, the tomogram is compared with a confocal fluorescence image in order to investigate the 3D structure at synapses.

  19. 3-D Technology Approaches for Biological Ecologies

    NASA Astrophysics Data System (ADS)

    Liu, Liyu; Austin, Robert; U. S-China Physical-Oncology Sciences Alliance (PS-OA) Team

    Constructing three dimensional (3-D) landscapes is an inevitable issue in deep study of biological ecologies, because in whatever scales in nature, all of the ecosystems are composed by complex 3-D environments and biological behaviors. Just imagine if a 3-D technology could help complex ecosystems be built easily and mimic in vivo microenvironment realistically with flexible environmental controls, it will be a fantastic and powerful thrust to assist researchers for explorations. For years, we have been utilizing and developing different technologies for constructing 3-D micro landscapes for biophysics studies in in vitro. Here, I will review our past efforts, including probing cancer cell invasiveness with 3-D silicon based Tepuis, constructing 3-D microenvironment for cell invasion and metastasis through polydimethylsiloxane (PDMS) soft lithography, as well as explorations of optimized stenting positions for coronary bifurcation disease with 3-D wax printing and the latest home designed 3-D bio-printer. Although 3-D technologies is currently considered not mature enough for arbitrary 3-D micro-ecological models with easy design and fabrication, I hope through my talk, the audiences will be able to sense its significance and predictable breakthroughs in the near future. This work was supported by the State Key Development Program for Basic Research of China (Grant No. 2013CB837200), the National Natural Science Foundation of China (Grant No. 11474345) and the Beijing Natural Science Foundation (Grant No. 7154221).

  20. Automated building of organometallic complexes from 3D fragments.

    PubMed

    Foscato, Marco; Venkatraman, Vishwesh; Occhipinti, Giovanni; Alsberg, Bjørn K; Jensen, Vidar R

    2014-07-28

    A method for the automated construction of three-dimensional (3D) molecular models of organometallic species in design studies is described. Molecular structure fragments derived from crystallographic structures and accurate molecular-level calculations are used as 3D building blocks in the construction of multiple molecular models of analogous compounds. The method allows for precise control of stereochemistry and geometrical features that may otherwise be very challenging, or even impossible, to achieve with commonly available generators of 3D chemical structures. The new method was tested in the construction of three sets of active or metastable organometallic species of catalytic reactions in the homogeneous phase. The performance of the method was compared with those of commonly available methods for automated generation of 3D models, demonstrating higher accuracy of the prepared 3D models in general, and, in particular, a much wider range with respect to the kind of chemical structures that can be built automatically, with capabilities far beyond standard organic and main-group chemistry. PMID:24998944

  1. RT3D tutorials for GMS users

    SciTech Connect

    Clement, T.P.; Jones, N.L.

    1998-02-01

    RT3D (Reactive Transport in 3-Dimensions) is a computer code that solves coupled partial differential equations that describe reactive-flow and transport of multiple mobile and/or immobile species in a three dimensional saturated porous media. RT3D was developed from the single-species transport code, MT3D (DoD-1.5, 1997 version). As with MT3D, RT3D also uses the USGS groundwater flow model MODFLOW for computing spatial and temporal variations in groundwater head distribution. This report presents a set of tutorial problems that are designed to illustrate how RT3D simulations can be performed within the Department of Defense Groundwater Modeling System (GMS). GMS serves as a pre- and post-processing interface for RT3D. GMS can be used to define all the input files needed by RT3D code, and later the code can be launched from within GMS and run as a separate application. Once the RT3D simulation is completed, the solution can be imported to GMS for graphical post-processing. RT3D v1.0 supports several reaction packages that can be used for simulating different types of reactive contaminants. Each of the tutorials, described below, provides training on a different RT3D reaction package. Each reaction package has different input requirements, and the tutorials are designed to describe these differences. Furthermore, the tutorials illustrate the various options available in GMS for graphical post-processing of RT3D results. Users are strongly encouraged to complete the tutorials before attempting to use RT3D and GMS on a routine basis.

  2. The global chemical systematics of arc front stratovolcanoes: Evaluating the role of crustal processes

    NASA Astrophysics Data System (ADS)

    Turner, Stephen J.; Langmuir, Charles H.

    2015-07-01

    Petrogenetic models for convergent margins should be consistent with the global systematics of convergent margin volcanic compositions. A newly developed tool for compiling and screening data from the GEOROC database was used to generate a global dataset of whole rock chemical analyses from arc front stratovolcano samples. Data from 227 volcanoes within 31 volcanic arc segments were first averaged by volcano and then by arc to explore global systematics. Three different methods of data normalization produce consistent results that persist across a wide range of Mg# [Mg# =Mg / (Mg +Fe) ]. Remarkably coherent systematics are present among major and trace element concentrations and ratios, with the exception of three arcs influenced by mantle plumes and Peru/N. Chile, which is built on exceptionally thick crust. Chemical parameters also correlate with the thickness of the overlying arc crust. In addition to previously established correlations of Na6.0 with Ca6.0 and crustal thickness, correlations are observed among major elements, trace elements, and trace element ratios (e.g. La/Yb, Dy/Yb, Zr/Sm, Zr/Ti). Positive correlations include "fluid mobile," "high field strength," and "large ion lithophile" element groups, with concentrations that vary by a factor of five in all groups. Incompatible element enrichments also correlate well with crustal thickness, with the greatest enrichment found at arcs with the thickest crust. Intra-crustal processes, however, do not reproduce the global variations. High pressure fractionation produces intermediate magmas enriched in aluminum, but such magmas are rare. Furthermore, differences among magma compositions at various volcanic arcs persist from primitive to evolved compositions, which is inconsistent with the possibility that global variations are produced by crystal fractionation at any pressure. Linear relationships among elements appear to be consistent with mixing between depleted primary magma and an enriched contaminant

  3. 3D Dynamic Echocardiography with a Digitizer

    NASA Astrophysics Data System (ADS)

    Oshiro, Osamu; Matani, Ayumu; Chihara, Kunihiro

    1998-05-01

    In this paper,a three-dimensional (3D) dynamic ultrasound (US) imaging system,where a US brightness-mode (B-mode) imagetriggered with an R-wave of electrocardiogram (ECG)was obtained with an ultrasound diagnostic deviceand the location and orientation of the US probewere simultaneously measured with a 3D digitizer, is described.The obtained B-mode imagewas then projected onto a virtual 3D spacewith the proposed interpolation algorithm using a Gaussian operator.Furthermore, a 3D image was presented on a cathode ray tube (CRT)and stored in virtual reality modeling language (VRML).We performed an experimentto reconstruct a 3D heart image in systole using this system.The experimental results indicatethat the system enables the visualization ofthe 3D and internal structure of a heart viewed from any angleand has potential for use in dynamic imaging,intraoperative ultrasonography and tele-medicine.

  4. Global Chemical Composition of Ambient Fine Particulate Matter for Exposure Assessment

    SciTech Connect

    Philip, Sajeev; Martin, Randall V.; van Donkelaar, Aaron; Lo, Jason Wai-Ho; Wang, Yuxuan; Chen, Dan; Zhang, Lin; Kasibhatla, Prasad S.; Wang, Siwen; Zhang, Qiang; Lu, Zifeng; Streets, David G.; Bittman, Shabtai; Macdonald, Douglas J.

    2014-10-24

    Epidemiologic and health impact studies are inhibited by the paucity of global, long-term measurements of the chemical composition of fine particulate matter. We inferred PM2.5 chemical composition at 0.1° × 0.1° spatial resolution for 2004–2008 by combining aerosol optical depth retrieved from the MODIS and MISR satellite instruments, with coincident profile and composition information from the GEOS-Chem global chemical transport model. Evaluation of the satellite-model PM2.5 composition data set with North American in situ measurements indicated significant spatial agreement for secondary inorganic aerosol, particulate organic mass, black carbon, mineral dust, and sea salt. We found that global population-weighted PM2.5 concentrations were dominated by particulate organic mass (11.9 ± 7.3 μg/m3), secondary inorganic aerosol (11.1 ± 5.0 μg/m3), and mineral dust (11.1 ± 7.9 μg/m3). Secondary inorganic PM2.5 concentrations exceeded 30 μg/m3 over East China. Sensitivity simulations suggested that population-weighted ambient PM2.5 from biofuel burning (11 μg/m3) could be almost as large as from fossil fuel combustion sources (17 μg/m3). In conclusion, these estimates offer information about global population exposure to the chemical components and sources of PM2.5.

  5. 3D Buildings Extraction from Aerial Images

    NASA Astrophysics Data System (ADS)

    Melnikova, O.; Prandi, F.

    2011-09-01

    This paper introduces a semi-automatic method for buildings extraction through multiple-view aerial image analysis. The advantage of the used semi-automatic approach is that it allows processing of each building individually finding the parameters of buildings features extraction more precisely for each area. On the early stage the presented technique uses an extraction of line segments that is done only inside of areas specified manually. The rooftop hypothesis is used further to determine a subset of quadrangles, which could form building roofs from a set of extracted lines and corners obtained on the previous stage. After collecting of all potential roof shapes in all images overlaps, the epipolar geometry is applied to find matching between images. This allows to make an accurate selection of building roofs removing false-positive ones and to identify their global 3D coordinates given camera internal parameters and coordinates. The last step of the image matching is based on geometrical constraints in contrast to traditional correlation. The correlation is applied only in some highly restricted areas in order to find coordinates more precisely, in such a way significantly reducing processing time of the algorithm. The algorithm has been tested on a set of Milan's aerial images and shows highly accurate results.

  6. 3D Scientific Visualization with Blender

    NASA Astrophysics Data System (ADS)

    Kent, Brian R.

    2015-03-01

    This is the first book written on using Blender for scientific visualization. It is a practical and interesting introduction to Blender for understanding key parts of 3D rendering and animation that pertain to the sciences via step-by-step guided tutorials. 3D Scientific Visualization with Blender takes you through an understanding of 3D graphics and modelling for different visualization scenarios in the physical sciences.

  7. Software for 3D radiotherapy dosimetry. Validation

    NASA Astrophysics Data System (ADS)

    Kozicki, Marek; Maras, Piotr; Karwowski, Andrzej C.

    2014-08-01

    The subject of this work is polyGeVero® software (GeVero Co., Poland), which has been developed to fill the requirements of fast calculations of 3D dosimetry data with the emphasis on polymer gel dosimetry for radiotherapy. This software comprises four workspaces that have been prepared for: (i) calculating calibration curves and calibration equations, (ii) storing the calibration characteristics of the 3D dosimeters, (iii) calculating 3D dose distributions in irradiated 3D dosimeters, and (iv) comparing 3D dose distributions obtained from measurements with the aid of 3D dosimeters and calculated with the aid of treatment planning systems (TPSs). The main features and functions of the software are described in this work. Moreover, the core algorithms were validated and the results are presented. The validation was performed using the data of the new PABIGnx polymer gel dosimeter. The polyGeVero® software simplifies and greatly accelerates the calculations of raw 3D dosimetry data. It is an effective tool for fast verification of TPS-generated plans for tumor irradiation when combined with a 3D dosimeter. Consequently, the software may facilitate calculations by the 3D dosimetry community. In this work, the calibration characteristics of the PABIGnx obtained through four calibration methods: multi vial, cross beam, depth dose, and brachytherapy, are discussed as well.

  8. Dimensional accuracy of 3D printed vertebra

    NASA Astrophysics Data System (ADS)

    Ogden, Kent; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Aslan, Can

    2014-03-01

    3D printer applications in the biomedical sciences and medical imaging are expanding and will have an increasing impact on the practice of medicine. Orthopedic and reconstructive surgery has been an obvious area for development of 3D printer applications as the segmentation of bony anatomy to generate printable models is relatively straightforward. There are important issues that should be addressed when using 3D printed models for applications that may affect patient care; in particular the dimensional accuracy of the printed parts needs to be high to avoid poor decisions being made prior to surgery or therapeutic procedures. In this work, the dimensional accuracy of 3D printed vertebral bodies derived from CT data for a cadaver spine is compared with direct measurements on the ex-vivo vertebra and with measurements made on the 3D rendered vertebra using commercial 3D image processing software. The vertebra was printed on a consumer grade 3D printer using an additive print process using PLA (polylactic acid) filament. Measurements were made for 15 different anatomic features of the vertebral body, including vertebral body height, endplate width and depth, pedicle height and width, and spinal canal width and depth, among others. It is shown that for the segmentation and printing process used, the results of measurements made on the 3D printed vertebral body are substantially the same as those produced by direct measurement on the vertebra and measurements made on the 3D rendered vertebra.

  9. Stereo 3-D Vision in Teaching Physics

    NASA Astrophysics Data System (ADS)

    Zabunov, Svetoslav

    2012-03-01

    Stereo 3-D vision is a technology used to present images on a flat surface (screen, paper, etc.) and at the same time to create the notion of three-dimensional spatial perception of the viewed scene. A great number of physical processes are much better understood when viewed in stereo 3-D vision compared to standard flat 2-D presentation. The current paper describes the modern stereo 3-D technologies that are applicable to various tasks in teaching physics in schools, colleges, and universities. Examples of stereo 3-D simulations developed by the author can be observed on online.

  10. Accuracy in Quantitative 3D Image Analysis

    PubMed Central

    Bassel, George W.

    2015-01-01

    Quantitative 3D imaging is becoming an increasingly popular and powerful approach to investigate plant growth and development. With the increased use of 3D image analysis, standards to ensure the accuracy and reproducibility of these data are required. This commentary highlights how image acquisition and postprocessing can introduce artifacts into 3D image data and proposes steps to increase both the accuracy and reproducibility of these analyses. It is intended to aid researchers entering the field of 3D image processing of plant cells and tissues and to help general readers in understanding and evaluating such data. PMID:25804539

  11. FastScript3D - A Companion to Java 3D

    NASA Technical Reports Server (NTRS)

    Koenig, Patti

    2005-01-01

    FastScript3D is a computer program, written in the Java 3D(TM) programming language, that establishes an alternative language that helps users who lack expertise in Java 3D to use Java 3D for constructing three-dimensional (3D)-appearing graphics. The FastScript3D language provides a set of simple, intuitive, one-line text-string commands for creating, controlling, and animating 3D models. The first word in a string is the name of a command; the rest of the string contains the data arguments for the command. The commands can also be used as an aid to learning Java 3D. Developers can extend the language by adding custom text-string commands. The commands can define new 3D objects or load representations of 3D objects from files in formats compatible with such other software systems as X3D. The text strings can be easily integrated into other languages. FastScript3D facilitates communication between scripting languages [which enable programming of hyper-text markup language (HTML) documents to interact with users] and Java 3D. The FastScript3D language can be extended and customized on both the scripting side and the Java 3D side.

  12. 3D PDF - a means of public access to geological 3D - objects, using the example of GTA3D

    NASA Astrophysics Data System (ADS)

    Slaby, Mark-Fabian; Reimann, Rüdiger

    2013-04-01

    In geology, 3D modeling has become very important. In the past, two-dimensional data such as isolines, drilling profiles, or cross-sections based on those, were used to illustrate the subsurface geology, whereas now, we can create complex digital 3D models. These models are produced with special software, such as GOCAD ®. The models can be viewed, only through the software used to create them, or through viewers available for free. The platform-independent PDF (Portable Document Format), enforced by Adobe, has found a wide distribution. This format has constantly evolved over time. Meanwhile, it is possible to display CAD data in an Adobe 3D PDF file with the free Adobe Reader (version 7). In a 3D PDF, a 3D model is freely rotatable and can be assembled from a plurality of objects, which can thus be viewed from all directions on their own. In addition, it is possible to create moveable cross-sections (profiles), and to assign transparency to the objects. Based on industry-standard CAD software, 3D PDFs can be generated from a large number of formats, or even be exported directly from this software. In geoinformatics, different approaches to creating 3D PDFs exist. The intent of the Authority for Mining, Energy and Geology to allow free access to the models of the Geotectonic Atlas (GTA3D), could not be realized with standard software solutions. A specially designed code converts the 3D objects to VRML (Virtual Reality Modeling Language). VRML is one of the few formats that allow using image files (maps) as textures, and to represent colors and shapes correctly. The files were merged in Acrobat X Pro, and a 3D PDF was generated subsequently. A topographic map, a display of geographic directions and horizontal and vertical scales help to facilitate the use.

  13. Modeling lightning-NOx chemistry on a sub-grid scale in a global chemical transport model

    NASA Astrophysics Data System (ADS)

    Gressent, Alicia; Sauvage, Bastien; Cariolle, Daniel; Evans, Mathew; Leriche, Maud; Mari, Céline; Thouret, Valérie

    2016-05-01

    For the first time, a plume-in-grid approach is implemented in a chemical transport model (CTM) to parameterize the effects of the nonlinear reactions occurring within high concentrated NOx plumes from lightning NOx emissions (LNOx) in the upper troposphere. It is characterized by a set of parameters including the plume lifetime, the effective reaction rate constant related to NOx-O3 chemical interactions, and the fractions of NOx conversion into HNO3 within the plume. Parameter estimates were made using the Dynamical Simple Model of Atmospheric Chemical Complexity (DSMACC) box model, simple plume dispersion simulations, and the 3-D Meso-NH (non-hydrostatic mesoscale atmospheric model). In order to assess the impact of the LNOx plume approach on the NOx and O3 distributions on a large scale, simulations for the year 2006 were performed using the GEOS-Chem global model with a horizontal resolution of 2° × 2.5°. The implementation of the LNOx parameterization implies an NOx and O3 decrease on a large scale over the region characterized by a strong lightning activity (up to 25 and 8 %, respectively, over central Africa in July) and a relative increase downwind of LNOx emissions (up to 18 and 2 % for NOx and O3, respectively, in July). The calculated variability in NOx and O3 mixing ratios around the mean value according to the known uncertainties in the parameter estimates is at a maximum over continental tropical regions with ΔNOx [-33.1, +29.7] ppt and ΔO3 [-1.56, +2.16] ppb, in January, and ΔNOx [-14.3, +21] ppt and ΔO3 [-1.18, +1.93] ppb, in July, mainly depending on the determination of the diffusion properties of the atmosphere and the initial NO mixing ratio injected by lightning. This approach allows us (i) to reproduce a more realistic lightning NOx chemistry leading to better NOx and O3 distributions on the large scale and (ii) to focus on other improvements to reduce remaining uncertainties from processes related to NOx chemistry in CTM.

  14. Multivariate 3D modelling of Scottish soil properties

    NASA Astrophysics Data System (ADS)

    Poggio, Laura; Gimona, Alessandro

    2015-04-01

    Information regarding soil properties across landscapes at national or continental scales is critical for better soil and environmental management and for climate regulation and adaptation policy. The prediction of soil properties variation in space and time and their uncertainty is an important part of environmental modelling. Soil properties, and in particular the 3 fractions of soil texture, exhibit strong co-variation among themselves and therefore taking into account this correlation leads to spatially more accurate results. In this study the continuous vertical and lateral distributions of relevant soil properties in Scottish soils were modelled with a multivariate 3D-GAM+GS approach. The approach used involves 1) modelling the multivariate trend with full 3D spatial correlation, i.e., exploiting the values of the neighbouring pixels in 3D-space, and 2) 3D kriging to interpolate the residuals. The values at each cell for each of the considered depth layers were defined using a hybrid GAM-geostatistical 3D model, combining the fitting of a GAM (generalised Additive Models) to estimate multivariate trend of the variables, using a 3D smoother with related covariates. Gaussian simulations of the model residuals were used as spatial component to account for local details. A dataset of about 26,000 horizons (7,800 profiles) was used for this study. A validation set was randomly selected as 25% of the full dataset. Numerous covariates derived from globally available data, such as MODIS and SRTM, are considered. The results of the 3D-GAM+kriging showed low RMSE values, good R squared and an accurate reproduction of the spatial structure of the data for a range of soil properties. The results have an out-of-sample RMSE between 10 to 15% of the observed range when taking into account the whole profile. The approach followed allows the assessment of the uncertainty of both the trend and the residuals.

  15. Lessons learned in building a global information network on chemicals (GINC)

    SciTech Connect

    Kaminuma, Tsuguchika . E-mail: kaminuma@cbi.or.jp

    2005-09-01

    The Global Information Network on Chemicals (GINC) was a project to construct a worldwide information network linking international, national, and other organizations working for the safe management of chemicals. Proposed in 1993, the project started the next year and lasted almost 10 years. It was begun as a joint project of World Health Organization (WHO), International Labor Organization (ILO), and United Nations Environment Program (UNEP), and later endorsed by the Intergovernmental Forum on Chemical Safety (IFCS). Asia, particularly East Asia and the Pacific islands, was chosen as the feasibility study region. The author's group then at the National Institute of Health Sciences (NIHS) of Japan led this initiative and hosted numerous meetings. At these meetings, tutorial sessions for communicating chemical safety expertise and emerging new information technologies relevant to the safe management of chemicals were offered. Our experience with this project, particularly the Web-based system and the tutorial sessions, may be of use to others involved with Web-based instruction and the training of chemical safety specialists from both developed and developing countries.

  16. Kinetic isotope effects of 12CH3D + OH and 13CH3D + OH from 278 to 313 K

    NASA Astrophysics Data System (ADS)

    Joelsson, L. M. T.; Schmidt, J. A.; Nilsson, E. J. K.; Blunier, T.; Griffith, D. W. T.; Ono, S.; Johnson, M. S.

    2016-04-01

    Methane is the second most important long-lived greenhouse gas and plays a central role in the chemistry of the Earth's atmosphere. Nonetheless there are significant uncertainties in its source budget. Analysis of the isotopic composition of atmospheric methane, including the doubly substituted species 13CH3D, offers new insight into the methane budget as the sources and sinks have distinct isotopic signatures. The most important sink of atmospheric methane is oxidation by OH in the troposphere, which accounts for around 84 % of all methane removal. Here we present experimentally derived methane + OH kinetic isotope effects and their temperature dependence over the range of 278 to 313 K for CH3D and 13CH3D; the latter is reported here for the first time. We find kCH4/kCH3D = 1.31 ± 0.01 and kCH4/k13CH3D = 1.34 ± 0.03 at room temperature, implying that the methane + OH kinetic isotope effect is multiplicative such that (kCH4/k13CH4)(kCH4/kCH3D) = kCH4/k13CH3D, within the experimental uncertainty, given the literature value of kCH4/k13CH4 = 1.0039 ± 0.0002. In addition, the kinetic isotope effects were characterized using transition state theory with tunneling corrections. Good agreement between the experimental, quantum chemical, and available literature values was obtained. Based on the results we conclude that the OH reaction (the main sink of methane) at steady state can produce an atmospheric clumped isotope signal (Δ(13CH3D) = ln([CH4][13CH3D]/[13CH4][CH3D])) of 0.02 ± 0.02. This implies that the bulk tropospheric Δ(13CH3D) reflects the source signal with relatively small adjustment due to the sink signal (i.e., mainly OH oxidation).

  17. PMAS - Faint Object 3D Spectrophotometry

    NASA Astrophysics Data System (ADS)

    Roth, M. M.; Becker, T.; Kelz, A.

    2002-01-01

    will describe PMAS (Potsdam Multiaperture Spectrophotometer) which was commissioned at the Calar Alto Observatory 3.5m Telescope on May 28-31, 2001. PMAS is a dedicated, highly efficient UV-visual integral field spectrograph which is optimized for the spectrophotometry of faint point sources, typically superimposed on a bright background. PMAS is ideally suited for the study of resolved stars in local group galaxies. I will present results of our preliminary work with MPFS at the Russian 6m Telescope in Selentchuk, involving the development of new 3D data reduction software, and observations of faint planetary nebulae in the bulge of M31 for the determination of individual chemical abundances of these objects. Using this data, it will be demonstrated that integral field spectroscopy provides superior techniques for background subtraction, avoiding the otherwise inevitable systematic errors of conventional slit spetroscopy. The results will be put in perspective of the study of resolved stellar populations in nearby galaxies with a new generation of Extremely Large Telescopes.

  18. An aerial 3D printing test mission

    NASA Astrophysics Data System (ADS)

    Hirsch, Michael; McGuire, Thomas; Parsons, Michael; Leake, Skye; Straub, Jeremy

    2016-05-01

    This paper provides an overview of an aerial 3D printing technology, its development and its testing. This technology is potentially useful in its own right. In addition, this work advances the development of a related in-space 3D printing technology. A series of aerial 3D printing test missions, used to test the aerial printing technology, are discussed. Through completing these test missions, the design for an in-space 3D printer may be advanced. The current design for the in-space 3D printer involves focusing thermal energy to heat an extrusion head and allow for the extrusion of molten print material. Plastics can be used as well as composites including metal, allowing for the extrusion of conductive material. A variety of experiments will be used to test this initial 3D printer design. High altitude balloons will be used to test the effects of microgravity on 3D printing, as well as parabolic flight tests. Zero pressure balloons can be used to test the effect of long 3D printing missions subjected to low temperatures. Vacuum chambers will be used to test 3D printing in a vacuum environment. The results will be used to adapt a current prototype of an in-space 3D printer. Then, a small scale prototype can be sent into low-Earth orbit as a 3-U cube satellite. With the ability to 3D print in space demonstrated, future missions can launch production hardware through which the sustainability and durability of structures in space will be greatly improved.

  19. 3D ultrafast ultrasound imaging in vivo

    NASA Astrophysics Data System (ADS)

    Provost, Jean; Papadacci, Clement; Esteban Arango, Juan; Imbault, Marion; Fink, Mathias; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu

    2014-10-01

    Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in 3D based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32  ×  32 matrix-array probe. Its ability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3D Shear-Wave Imaging, 3D Ultrafast Doppler Imaging, and, finally, 3D Ultrafast combined Tissue and Flow Doppler Imaging. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3D Ultrafast Doppler was used to obtain 3D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, at thousands of volumes per second, the complex 3D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, as well as the 3D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3D Ultrafast Ultrasound Imaging for the 3D mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra—and inter-observer variability.

  20. Faceless identification: a model for person identification using the 3D shape and 3D motion as cues

    NASA Astrophysics Data System (ADS)

    Klasen, Lena M.; Li, Haibo

    1999-02-01

    Person identification by using biometric methods based on image sequences, or still images, often requires a controllable and cooperative environment during the image capturing stage. In the forensic case the situation is more likely to be the opposite. In this work we propose a method that makes use of the anthropometry of the human body and human actions as cues for identification. Image sequences from surveillance systems are used, which can be seen as monocular image sequences. A 3D deformable wireframe body model is used as a platform to handle the non-rigid information of the 3D shape and 3D motion of the human body from the image sequence. A recursive method for estimating global motion and local shape variations is presented, using two recursive feedback systems.

  1. Dynamic mechanisms of generation of oscillatory cluster patterns in a globally coupled chemical system

    NASA Astrophysics Data System (ADS)

    Rotstein, Horacio G.; Wu, Hui

    2012-09-01

    We use simulations and dynamical systems tools to investigate the mechanisms of generation of phase-locked and localized oscillatory cluster patterns in a globally coupled Oregonator model where the activator receives global feedback from the inhibitor, mimicking experimental results observed in the photosensitive Belousov-Zhabotinsky reaction. A homogeneous two-cluster system (two clusters with equal cluster size) displays antiphase patterns. Heterogenous two-cluster systems (two clusters with different sizes) display both phase-locked and localized patterns depending on the parameter values. In a localized pattern the oscillation amplitude of the largest cluster is roughly an order of magnitude smaller than the oscillation amplitude of the smaller cluster, reflecting the effect of self-inhibition exerted by the global feedback term. The transition from phase-locked to localized cluster patterns occurs as the intensity of global feedback increases. Three qualitatively different basic mechanisms, described previously for a globally coupled FitzHugh-Nagumo model, are involved in the generation of the observed patterns. The swing-and-release mechanism is related to the canard phenomenon (canard explosion of limit cycles) in relaxation oscillators. The hold-and-release and hold-and-escape mechanisms are related to the release and escape mechanisms in synaptically connected neural models. The methods we use can be extended to the investigation of oscillatory chemical reactions with other types of non-local coupling.

  2. Dynamic mechanisms of generation of oscillatory cluster patterns in a globally coupled chemical system.

    PubMed

    Rotstein, Horacio G; Wu, Hui

    2012-09-14

    We use simulations and dynamical systems tools to investigate the mechanisms of generation of phase-locked and localized oscillatory cluster patterns in a globally coupled Oregonator model where the activator receives global feedback from the inhibitor, mimicking experimental results observed in the photosensitive Belousov-Zhabotinsky reaction. A homogeneous two-cluster system (two clusters with equal cluster size) displays antiphase patterns. Heterogenous two-cluster systems (two clusters with different sizes) display both phase-locked and localized patterns depending on the parameter values. In a localized pattern the oscillation amplitude of the largest cluster is roughly an order of magnitude smaller than the oscillation amplitude of the smaller cluster, reflecting the effect of self-inhibition exerted by the global feedback term. The transition from phase-locked to localized cluster patterns occurs as the intensity of global feedback increases. Three qualitatively different basic mechanisms, described previously for a globally coupled FitzHugh-Nagumo model, are involved in the generation of the observed patterns. The swing-and-release mechanism is related to the canard phenomenon (canard explosion of limit cycles) in relaxation oscillators. The hold-and-release and hold-and-escape mechanisms are related to the release and escape mechanisms in synaptically connected neural models. The methods we use can be extended to the investigation of oscillatory chemical reactions with other types of non-local coupling. PMID:22979891

  3. 3D Microperiodic Hydrogel Scaffolds for Robust Neuronal Cultures

    PubMed Central

    Hanson Shepherd, Jennifer N.; Parker, Sara T.; Shepherd, Robert F.; Gillette, Martha U.; Lewis, Jennifer A.; Nuzzo, Ralph G.

    2011-01-01

    Three-dimensional (3D) microperiodic scaffolds of poly(2-hydroxyethyl methacrylate) (pHEMA) have been fabricated by direct-write assembly of a photopolymerizable hydrogel ink. The ink is initially composed of physically entangled pHEMA chains dissolved in a solution of HEMA monomer, comonomer, photoinitiator and water. Upon printing 3D scaffolds of varying architecture, the ink filaments are exposed to UV light, where they are transformed into an interpenetrating hydrogel network of chemically cross-linked and physically entangled pHEMA chains. These 3D microperiodic scaffolds are rendered growth compliant for primary rat hippocampal neurons by absorption of polylysine. Neuronal cells thrive on these scaffolds, forming differentiated, intricately branched networks. Confocal laser scanning microscopy reveals that both cell distribution and extent of neuronal process alignment depend upon scaffold architecture. This work provides an important step forward in the creation of suitable platforms for in vitro study of sensitive cell types. PMID:21709750

  4. 3D RISM theory with fast reciprocal-space electrostatics

    SciTech Connect

    Heil, Jochen; Kast, Stefan M.

    2015-03-21

    The calculation of electrostatic solute-solvent interactions in 3D RISM (“three-dimensional reference interaction site model”) integral equation theory is recast in a form that allows for a computational treatment analogous to the “particle-mesh Ewald” formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems.

  5. 3D RISM theory with fast reciprocal-space electrostatics.

    PubMed

    Heil, Jochen; Kast, Stefan M

    2015-03-21

    The calculation of electrostatic solute-solvent interactions in 3D RISM ("three-dimensional reference interaction site model") integral equation theory is recast in a form that allows for a computational treatment analogous to the "particle-mesh Ewald" formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems. PMID:25796231

  6. Topology dictionary for 3D video understanding.

    PubMed

    Tung, Tony; Matsuyama, Takashi

    2012-08-01

    This paper presents a novel approach that achieves 3D video understanding. 3D video consists of a stream of 3D models of subjects in motion. The acquisition of long sequences requires large storage space (2 GB for 1 min). Moreover, it is tedious to browse data sets and extract meaningful information. We propose the topology dictionary to encode and describe 3D video content. The model consists of a topology-based shape descriptor dictionary which can be generated from either extracted patterns or training sequences. The model relies on 1) topology description and classification using Reeb graphs, and 2) a Markov motion graph to represent topology change states. We show that the use of Reeb graphs as the high-level topology descriptor is relevant. It allows the dictionary to automatically model complex sequences, whereas other strategies would require prior knowledge on the shape and topology of the captured subjects. Our approach serves to encode 3D video sequences, and can be applied for content-based description and summarization of 3D video sequences. Furthermore, topology class labeling during a learning process enables the system to perform content-based event recognition. Experiments were carried out on various 3D videos. We showcase an application for 3D video progressive summarization using the topology dictionary. PMID:22745004

  7. 3-D seismology in the Arabian Gulf

    SciTech Connect

    Al-Husseini, M.; Chimblo, R.

    1995-08-01

    Since 1977 when Aramco and GSI (Geophysical Services International) pioneered the first 3-D seismic survey in the Arabian Gulf, under the guidance of Aramco`s Chief Geophysicist John Hoke, 3-D seismology has been effectively used to map many complex subsurface geological phenomena. By the mid-1990s extensive 3-D surveys were acquired in Abu Dhabi, Oman, Qatar and Saudi Arabia. Also in the mid-1990`s Bahrain, Kuwait and Dubai were preparing to record surveys over their fields. On the structural side 3-D has refined seismic maps, focused faults and fractures systems, as well as outlined the distribution of facies, porosity and fluid saturation. In field development, 3D has not only reduced drilling costs significantly, but has also improved the understanding of fluid behavior in the reservoir. In Oman, Petroleum Development Oman (PDO) has now acquired the first Gulf 4-D seismic survey (time-lapse 3D survey) over the Yibal Field. The 4-D survey will allow PDO to directly monitor water encroachment in the highly-faulted Cretaceous Shu`aiba reservoir. In exploration, 3-D seismology has resolved complex prospects with structural and stratigraphic complications and reduced the risk in the selection of drilling locations. The many case studies from Saudi Arabia, Oman, Qatar and the United Arab Emirates, which are reviewed in this paper, attest to the effectiveness of 3D seismology in exploration and producing, in clastics and carbonates reservoirs, and in the Mesozoic and Paleozoic.

  8. A 3D Geostatistical Mapping Tool

    1999-02-09

    This software provides accurate 3D reservoir modeling tools and high quality 3D graphics for PC platforms enabling engineers and geologists to better comprehend reservoirs and consequently improve their decisions. The mapping algorithms are fractals, kriging, sequential guassian simulation, and three nearest neighbor methods.

  9. 3D, or Not to Be?

    ERIC Educational Resources Information Center

    Norbury, Keith

    2012-01-01

    It may be too soon for students to be showing up for class with popcorn and gummy bears, but technology similar to that behind the 3D blockbuster movie "Avatar" is slowly finding its way into college classrooms. 3D classroom projectors are taking students on fantastic voyages inside the human body, to the ruins of ancient Greece--even to faraway…

  10. Stereoscopic Investigations of 3D Coulomb Balls

    SciTech Connect

    Kaeding, Sebastian; Melzer, Andre; Arp, Oliver; Block, Dietmar; Piel, Alexander

    2005-10-31

    In dusty plasmas particles are arranged due to the influence of external forces and the Coulomb interaction. Recently Arp et al. were able to generate 3D spherical dust clouds, so-called Coulomb balls. Here, we present measurements that reveal the full 3D particle trajectories from stereoscopic imaging.

  11. 3-D structures of planetary nebulae

    NASA Astrophysics Data System (ADS)

    Steffen, W.

    2016-07-01

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

  12. Wow! 3D Content Awakens the Classroom

    ERIC Educational Resources Information Center

    Gordon, Dan

    2010-01-01

    From her first encounter with stereoscopic 3D technology designed for classroom instruction, Megan Timme, principal at Hamilton Park Pacesetter Magnet School in Dallas, sensed it could be transformative. Last spring, when she began pilot-testing 3D content in her third-, fourth- and fifth-grade classrooms, Timme wasn't disappointed. Students…

  13. 3D Printed Block Copolymer Nanostructures

    ERIC Educational Resources Information Center

    Scalfani, Vincent F.; Turner, C. Heath; Rupar, Paul A.; Jenkins, Alexander H.; Bara, Jason E.

    2015-01-01

    The emergence of 3D printing has dramatically advanced the availability of tangible molecular and extended solid models. Interestingly, there are few nanostructure models available both commercially and through other do-it-yourself approaches such as 3D printing. This is unfortunate given the importance of nanotechnology in science today. In this…

  14. Static & Dynamic Response of 3D Solids

    1996-07-15

    NIKE3D is a large deformations 3D finite element code used to obtain the resulting displacements and stresses from multi-body static and dynamic structural thermo-mechanics problems with sliding interfaces. Many nonlinear and temperature dependent constitutive models are available.

  15. Immersive 3D Geovisualization in Higher Education

    ERIC Educational Resources Information Center

    Philips, Andrea; Walz, Ariane; Bergner, Andreas; Graeff, Thomas; Heistermann, Maik; Kienzler, Sarah; Korup, Oliver; Lipp, Torsten; Schwanghart, Wolfgang; Zeilinger, Gerold

    2015-01-01

    In this study, we investigate how immersive 3D geovisualization can be used in higher education. Based on MacEachren and Kraak's geovisualization cube, we examine the usage of immersive 3D geovisualization and its usefulness in a research-based learning module on flood risk, called GEOSimulator. Results of a survey among participating students…

  16. Stereo 3-D Vision in Teaching Physics

    ERIC Educational Resources Information Center

    Zabunov, Svetoslav

    2012-01-01

    Stereo 3-D vision is a technology used to present images on a flat surface (screen, paper, etc.) and at the same time to create the notion of three-dimensional spatial perception of the viewed scene. A great number of physical processes are much better understood when viewed in stereo 3-D vision compared to standard flat 2-D presentation. The…

  17. Pathways for Learning from 3D Technology

    ERIC Educational Resources Information Center

    Carrier, L. Mark; Rab, Saira S.; Rosen, Larry D.; Vasquez, Ludivina; Cheever, Nancy A.

    2012-01-01

    The purpose of this study was to find out if 3D stereoscopic presentation of information in a movie format changes a viewer's experience of the movie content. Four possible pathways from 3D presentation to memory and learning were considered: a direct connection based on cognitive neuroscience research; a connection through "immersion" in that 3D…

  18. Clinical applications of 3-D dosimeters

    NASA Astrophysics Data System (ADS)

    Wuu, Cheng-Shie

    2015-01-01

    Both 3-D gels and radiochromic plastic dosimeters, in conjunction with dose image readout systems (MRI or optical-CT), have been employed to measure 3-D dose distributions in many clinical applications. The 3-D dose maps obtained from these systems can provide a useful tool for clinical dose verification for complex treatment techniques such as IMRT, SRS/SBRT, brachytherapy, and proton beam therapy. These complex treatments present high dose gradient regions in the boundaries between the target and surrounding critical organs. Dose accuracy in these areas can be critical, and may affect treatment outcome. In this review, applications of 3-D gels and PRESAGE dosimeter are reviewed and evaluated in terms of their performance in providing information on clinical dose verification as well as commissioning of various treatment modalities. Future interests and clinical needs on studies of 3-D dosimetry are also discussed.

  19. Biocompatible 3D Matrix with Antimicrobial Properties.

    PubMed

    Ion, Alberto; Andronescu, Ecaterina; Rădulescu, Dragoș; Rădulescu, Marius; Iordache, Florin; Vasile, Bogdan Ștefan; Surdu, Adrian Vasile; Albu, Madalina Georgiana; Maniu, Horia; Chifiriuc, Mariana Carmen; Grumezescu, Alexandru Mihai; Holban, Alina Maria

    2016-01-01

    The aim of this study was to develop, characterize and assess the biological activity of a new regenerative 3D matrix with antimicrobial properties, based on collagen (COLL), hydroxyapatite (HAp), β-cyclodextrin (β-CD) and usnic acid (UA). The prepared 3D matrix was characterized by Scanning Electron Microscopy (SEM), Fourier Transform Infrared Microscopy (FT-IRM), Transmission Electron Microscopy (TEM), and X-ray Diffraction (XRD). In vitro qualitative and quantitative analyses performed on cultured diploid cells demonstrated that the 3D matrix is biocompatible, allowing the normal development and growth of MG-63 osteoblast-like cells and exhibited an antimicrobial effect, especially on the Staphylococcus aureus strain, explained by the particular higher inhibitory activity of usnic acid (UA) against Gram positive bacterial strains. Our data strongly recommend the obtained 3D matrix to be used as a successful alternative for the fabrication of three dimensional (3D) anti-infective regeneration matrix for bone tissue engineering. PMID:26805790

  20. Fabrication of 3D Silicon Sensors

    SciTech Connect

    Kok, A.; Hansen, T.E.; Hansen, T.A.; Lietaer, N.; Summanwar, A.; Kenney, C.; Hasi, J.; Da Via, C.; Parker, S.I.; /Hawaii U.

    2012-06-06

    Silicon sensors with a three-dimensional (3-D) architecture, in which the n and p electrodes penetrate through the entire substrate, have many advantages over planar silicon sensors including radiation hardness, fast time response, active edge and dual readout capabilities. The fabrication of 3D sensors is however rather complex. In recent years, there have been worldwide activities on 3D fabrication. SINTEF in collaboration with Stanford Nanofabrication Facility have successfully fabricated the original (single sided double column type) 3D detectors in two prototype runs and the third run is now on-going. This paper reports the status of this fabrication work and the resulted yield. The work of other groups such as the development of double sided 3D detectors is also briefly reported.

  1. BEAMS3D Neutral Beam Injection Model

    SciTech Connect

    Lazerson, Samuel

    2014-04-14

    With the advent of applied 3D fi elds in Tokamaks and modern high performance stellarators, a need has arisen to address non-axisymmetric effects on neutral beam heating and fueling. We report on the development of a fully 3D neutral beam injection (NBI) model, BEAMS3D, which addresses this need by coupling 3D equilibria to a guiding center code capable of modeling neutral and charged particle trajectories across the separatrix and into the plasma core. Ionization, neutralization, charge-exchange, viscous velocity reduction, and pitch angle scattering are modeled with the ADAS atomic physics database [1]. Benchmark calculations are presented to validate the collisionless particle orbits, neutral beam injection model, frictional drag, and pitch angle scattering effects. A calculation of neutral beam heating in the NCSX device is performed, highlighting the capability of the code to handle 3D magnetic fields.

  2. Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization

    PubMed Central

    Chaumeil, Julie; Micsinai, Mariann; Skok, Jane A.

    2013-01-01

    Fluorescent in situ hybridization using DNA probes on 3-dimensionally preserved nuclei followed by 3D confocal microscopy (3D DNA FISH) represents the most direct way to visualize the location of gene loci, chromosomal sub-regions or entire territories in individual cells. This type of analysis provides insight into the global architecture of the nucleus as well as the behavior of specific genomic loci and regions within the nuclear space. Immunofluorescence, on the other hand, permits the detection of nuclear proteins (modified histones, histone variants and modifiers, transcription machinery and factors, nuclear sub-compartments, etc). The major challenge in combining immunofluorescence and 3D DNA FISH is, on the one hand to preserve the epitope detected by the antibody as well as the 3D architecture of the nucleus, and on the other hand, to allow the penetration of the DNA probe to detect gene loci or chromosome territories 1-5. Here we provide a protocol that combines visualization of chromatin modifications with genomic loci in 3D preserved nuclei. PMID:23407477

  3. 3D Visualization Development of SIUE Campus

    NASA Astrophysics Data System (ADS)

    Nellutla, Shravya

    Geographic Information Systems (GIS) has progressed from the traditional map-making to the modern technology where the information can be created, edited, managed and analyzed. Like any other models, maps are simplified representations of real world. Hence visualization plays an essential role in the applications of GIS. The use of sophisticated visualization tools and methods, especially three dimensional (3D) modeling, has been rising considerably due to the advancement of technology. There are currently many off-the-shelf technologies available in the market to build 3D GIS models. One of the objectives of this research was to examine the available ArcGIS and its extensions for 3D modeling and visualization and use them to depict a real world scenario. Furthermore, with the advent of the web, a platform for accessing and sharing spatial information on the Internet, it is possible to generate interactive online maps. Integrating Internet capacity with GIS functionality redefines the process of sharing and processing the spatial information. Enabling a 3D map online requires off-the-shelf GIS software, 3D model builders, web server, web applications and client server technologies. Such environments are either complicated or expensive because of the amount of hardware and software involved. Therefore, the second objective of this research was to investigate and develop simpler yet cost-effective 3D modeling approach that uses available ArcGIS suite products and the free 3D computer graphics software for designing 3D world scenes. Both ArcGIS Explorer and ArcGIS Online will be used to demonstrate the way of sharing and distributing 3D geographic information on the Internet. A case study of the development of 3D campus for the Southern Illinois University Edwardsville is demonstrated.

  4. 3D Ultrafast Ultrasound Imaging In Vivo

    PubMed Central

    Provost, Jean; Papadacci, Clement; Arango, Juan Esteban; Imbault, Marion; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu

    2014-01-01

    Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative real-time imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in three dimensions based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32×32 matrix-array probe. Its capability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3-D Shear-Wave Imaging, 3-D Ultrafast Doppler Imaging and finally 3D Ultrafast combined Tissue and Flow Doppler. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3-D Ultrafast Doppler was used to obtain 3-D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, for the first time, the complex 3-D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, and the 3-D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3-D Ultrafast Ultrasound Imaging for the 3-D real-time mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra- and inter-observer variability. PMID:25207828

  5. The psychology of the 3D experience

    NASA Astrophysics Data System (ADS)

    Janicke, Sophie H.; Ellis, Andrew

    2013-03-01

    With 3D televisions expected to reach 50% home saturation as early as 2016, understanding the psychological mechanisms underlying the user response to 3D technology is critical for content providers, educators and academics. Unfortunately, research examining the effects of 3D technology has not kept pace with the technology's rapid adoption, resulting in large-scale use of a technology about which very little is actually known. Recognizing this need for new research, we conducted a series of studies measuring and comparing many of the variables and processes underlying both 2D and 3D media experiences. In our first study, we found narratives within primetime dramas had the power to shift viewer attitudes in both 2D and 3D settings. However, we found no difference in persuasive power between 2D and 3D content. We contend this lack of effect was the result of poor conversion quality and the unique demands of 3D production. In our second study, we found 3D technology significantly increased enjoyment when viewing sports content, yet offered no added enjoyment when viewing a movie trailer. The enhanced enjoyment of the sports content was shown to be the result of heightened emotional arousal and attention in the 3D condition. We believe the lack of effect found for the movie trailer may be genre-related. In our final study, we found 3D technology significantly enhanced enjoyment of two video games from different genres. The added enjoyment was found to be the result of an increased sense of presence.

  6. 3D image of protein visualization in a whole rice grain using an automatic precision microtome system

    NASA Astrophysics Data System (ADS)

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

    2000-05-01

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

  7. Optimizing visual comfort for stereoscopic 3D display based on color-plus-depth signals.

    PubMed

    Shao, Feng; Jiang, Qiuping; Fu, Randi; Yu, Mei; Jiang, Gangyi

    2016-05-30

    Visual comfort is a long-facing problem in stereoscopic 3D (S3D) display. In this paper, targeting to produce S3D content based on color-plus-depth signals, a general framework for depth mapping to optimize visual comfort for S3D display is proposed. The main motivation of this work is to remap the depth range of color-plus-depth signals to a new depth range that is suitable to comfortable S3D display. Towards this end, we first remap the depth range globally based on the adjusted zero disparity plane, and then present a two-stage global and local depth optimization solution to solve the visual comfort problem. The remapped depth map is used to generate the S3D output. We demonstrate the power of our approach on perceptually uncomfortable and comfortable stereoscopic images. PMID:27410090

  8. Polymer-Enriched 3D Graphene Foams for Biomedical Applications.

    PubMed

    Wang, Jun Kit; Xiong, Gordon Minru; Zhu, Minmin; Özyilmaz, Barbaros; Castro Neto, Antonio Helio; Tan, Nguan Soon; Choong, Cleo

    2015-04-22

    Graphene foams (GFs) are versatile nanoplatforms for biomedical applications because of their excellent physical, chemical, and mechanical properties. However, the brittleness and inflexibility of pristine GF (pGF) are some of the important factors restricting their widespread application. Here, a chemical-vapor-deposition-assisted method was used to synthesize 3D GFs, which were subsequently spin-coated with polymer to produce polymer-enriched 3D GFs with high conductivity and flexibility. Compared to pGF, both poly(vinylidene fluoride)-enriched GF (PVDF/GF) and polycaprolactone-enriched GF (PCL/GF) scaffolds showed improved flexibility and handleability. Despite the presence of the polymers, the polymer-enriched 3D GF scaffolds retained high levels of electrical conductivity because of the presence of microcracks that allowed for the flow of electrons through the material. In addition, polymer enrichment of GF led to an enhancement in the formation of calcium phosphate (Ca-P) compounds when the scaffolds were exposed to simulated body fluid. Between the two polymers tested, PCL enrichment of GF resulted in a higher in vitro mineralization nucleation rate because the oxygen-containing functional group of PCL had a higher affinity for Ca-P deposition and formation compared to the polar carbon-fluorine (C-F) bond in PVDF. Taken together, our current findings are a stepping stone toward future applications of polymer-enriched 3D GFs in the treatment of bone defects as well as other biomedical applications. PMID:25822669

  9. 3-D Terahertz Synthetic-Aperture Imaging and Spectroscopy

    NASA Astrophysics Data System (ADS)

    Henry, Samuel C.

    Terahertz (THz) wavelengths have attracted recent interest in multiple disciplines within engineering and science. Situated between the infrared and the microwave region of the electromagnetic spectrum, THz energy can propagate through non-polar materials such as clothing or packaging layers. Moreover, many chemical compounds, including explosives and many drugs, reveal strong absorption signatures in the THz range. For these reasons, THz wavelengths have great potential for non-destructive evaluation and explosive detection. Three-dimensional (3-D) reflection imaging with considerable depth resolution is also possible using pulsed THz systems. While THz imaging (especially 3-D) systems typically operate in transmission mode, reflection offers the most practical configuration for standoff detection, especially for objects with high water content (like human tissue) which are opaque at THz frequencies. In this research, reflection-based THz synthetic-aperture (SA) imaging is investigated as a potential imaging solution. THz SA imaging results presented in this dissertation are unique in that a 2-D planar synthetic array was used to generate a 3-D image without relying on a narrow time-window for depth isolation cite [Shen 2005]. Novel THz chemical detection techniques are developed and combined with broadband THz SA capabilities to provide concurrent 3-D spectral imaging. All algorithms are tested with various objects and pressed pellets using a pulsed THz time-domain system in the Northwest Electromagnetics and Acoustics Research Laboratory (NEAR-Lab).

  10. [Globally harmonized system of classification and labelling of chemicals (GHS) and its implementation in Japan].

    PubMed

    Miyagawa, Muneyuki

    2010-01-01

    The Globally Harmonized System of Classification and Labelling of Chemicals (GHS) is a set of recommendations by the United Nations, first issued in 2003 as a communication tool for the sound management of chemicals, comprising harmonized classification criteria for physical, health and environmental hazards, a unified format for material safety data sheets (MSDS), and labeling elements including pictograms and hazard statements preassigned to each classification category. The GHS has been introduced into Japan and implemented in the regulatory framework for chemical safety. The Japanese Industrial Standards (JIS) adopted the GHS, and the GHS-based JIS rules have become the Japanese standards for labels and MSDS. The use of the JIS format for labels and MSDS is recommended by several competent authorities in Japan although mostly on a voluntary basis. In the workplace, however, GHS-based JIS labels and MSDS have become legal requirements by the Industrial Safety and Health Law since 2006; namely, issuing MSDS in such a format is mandatory for the 640 specified chemicals and also labeling for the 99 targeted chemicals*. Although the GHS provides definitions and classification criteria for 10 classes of health hazards (acute toxicity, skin and eye corrosion/irritation, sensitization, germ cell mutagenicity, carcinogenicity, reproductive toxicity, specific target organ toxicity single/repeated exposures, and aspiration hazard), it does not provide actual classification of chemicals, so that competent authorities and industries need to classify a number of chemicals and/or mixtures. Weight-of-evidence judgment and/or expert judgment would be necessary in many cases. In this paper, the outline of the GHS classification is described and problems of the GHS and its implementation are discussed. PMID:20134103

  11. Regional geothermal 3D modelling in Denmark

    NASA Astrophysics Data System (ADS)

    Poulsen, S. E.; Balling, N.; Bording, T. S.; Nielsen, S. B.

    2012-04-01

    In the pursuit of sustainable and low carbon emission energy sources, increased global attention has been given to the exploration and exploitation of geothermal resources within recent decades. In 2009 a national multi-disciplinary geothermal research project was established. As a significant part of this project, 3D temperature modelling is to be carried out, with special emphasis on temperatures of potential geothermal reservoirs in the Danish area. The Danish subsurface encompasses low enthalpy geothermal reservoirs of mainly Triassic and Jurassic age. Geothermal plants at Amager (Copenhagen) and Thisted (Northern Jutland) have the capacity of supplying the district heating network with up to 14 MW and 7 MW, respectively, by withdrawing warm pore water from the Gassum (Lower Jurassic/Upper Triassic) and Bunter (Lower Triassic) sandstone reservoirs, respectively. Explorative studies of the subsurface temperature regime typically are based on a combination of observations and modelling. In this study, the open-source groundwater modelling code MODFLOW is modified to simulate the subsurface temperature distribution in three dimensions by taking advantage of the mathematical similarity between saturated groundwater flow (Darcy flow) and heat conduction. A numerical model of the subsurface geology in Denmark is built and parameterized from lithological information derived from joint interpretation of seismic surveys and borehole information. Boundary conditions are constructed from knowledge about the heat flow from the Earth's interior and the shallow ground temperature. Matrix thermal conductivities have been estimated from analysis of high-resolution temperature logs measured in deep wells and porosity-depth relations are included using interpreted main lithologies. The model takes into account the dependency of temperature and pressure on thermal conductivity. Moreover, a transient model based correction of the paleoclimatic thermal disturbance caused by the

  12. Medical 3D Printing for the Radiologist.

    PubMed

    Mitsouras, Dimitris; Liacouras, Peter; Imanzadeh, Amir; Giannopoulos, Andreas A; Cai, Tianrun; Kumamaru, Kanako K; George, Elizabeth; Wake, Nicole; Caterson, Edward J; Pomahac, Bohdan; Ho, Vincent B; Grant, Gerald T; Rybicki, Frank J

    2015-01-01

    While use of advanced visualization in radiology is instrumental in diagnosis and communication with referring clinicians, there is an unmet need to render Digital Imaging and Communications in Medicine (DICOM) images as three-dimensional (3D) printed models capable of providing both tactile feedback and tangible depth information about anatomic and pathologic states. Three-dimensional printed models, already entrenched in the nonmedical sciences, are rapidly being embraced in medicine as well as in the lay community. Incorporating 3D printing from images generated and interpreted by radiologists presents particular challenges, including training, materials and equipment, and guidelines. The overall costs of a 3D printing laboratory must be balanced by the clinical benefits. It is expected that the number of 3D-printed models generated from DICOM images for planning interventions and fabricating implants will grow exponentially. Radiologists should at a minimum be familiar with 3D printing as it relates to their field, including types of 3D printing technologies and materials used to create 3D-printed anatomic models, published applications of models to date, and clinical benefits in radiology. Online supplemental material is available for this article. PMID:26562233

  13. 3D bioprinting of tissues and organs.

    PubMed

    Murphy, Sean V; Atala, Anthony

    2014-08-01

    Additive manufacturing, otherwise known as three-dimensional (3D) printing, is driving major innovations in many areas, such as engineering, manufacturing, art, education and medicine. Recent advances have enabled 3D printing of biocompatible materials, cells and supporting components into complex 3D functional living tissues. 3D bioprinting is being applied to regenerative medicine to address the need for tissues and organs suitable for transplantation. Compared with non-biological printing, 3D bioprinting involves additional complexities, such as the choice of materials, cell types, growth and differentiation factors, and technical challenges related to the sensitivities of living cells and the construction of tissues. Addressing these complexities requires the integration of technologies from the fields of engineering, biomaterials science, cell biology, physics and medicine. 3D bioprinting has already been used for the generation and transplantation of several tissues, including multilayered skin, bone, vascular grafts, tracheal splints, heart tissue and cartilaginous structures. Other applications include developing high-throughput 3D-bioprinted tissue models for research, drug discovery and toxicology. PMID:25093879

  14. Optically rewritable 3D liquid crystal displays.

    PubMed

    Sun, J; Srivastava, A K; Zhang, W; Wang, L; Chigrinov, V G; Kwok, H S

    2014-11-01

    Optically rewritable liquid crystal display (ORWLCD) is a concept based on the optically addressed bi-stable display that does not need any power to hold the image after being uploaded. Recently, the demand for the 3D image display has increased enormously. Several attempts have been made to achieve 3D image on the ORWLCD, but all of them involve high complexity for image processing on both hardware and software levels. In this Letter, we disclose a concept for the 3D-ORWLCD by dividing the given image in three parts with different optic axis. A quarter-wave plate is placed on the top of the ORWLCD to modify the emerging light from different domains of the image in different manner. Thereafter, Polaroid glasses can be used to visualize the 3D image. The 3D image can be refreshed, on the 3D-ORWLCD, in one-step with proper ORWLCD printer and image processing, and therefore, with easy image refreshing and good image quality, such displays can be applied for many applications viz. 3D bi-stable display, security elements, etc. PMID:25361316

  15. Extra Dimensions: 3D in PDF Documentation

    NASA Astrophysics Data System (ADS)

    Graf, Norman A.

    2012-12-01

    Experimental science is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universal 3D (U3D) and the ISO PRC file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. Until recently, Adobe's Acrobat software was also capable of incorporating 3D content into PDF files from a variety of 3D file formats, including proprietary CAD formats. However, this functionality is no longer available in Acrobat X, having been spun off to a separate company. Incorporating 3D content now requires the additional purchase of a separate plug-in. In this talk we present alternatives based on open source libraries which allow the programmatic creation of 3D content in PDF format. While not providing the same level of access to CAD files as the commercial software, it does provide physicists with an alternative path to incorporate 3D content into PDF files from such disparate applications as detector geometries from Geant4, 3D data sets, mathematical surfaces or tesselated volumes.

  16. INFLUENCE OF GLOBAL CLIMATE CHANGE ON CHEMICAL FATE AND BIOACCUMULATION: THE ROLE OF MULTIMEDIA MODELS

    PubMed Central

    Gouin, Todd; Armitage, James M; Cousins, Ian T; Muir, Derek CG; Ng, Carla A; Reid, Liisa; Tao, Shu

    2013-01-01

    Multimedia environmental fate models are valuable tools for investigating potential changes associated with global climate change, particularly because thermodynamic forcing on partitioning behavior as well as diffusive and nondiffusive exchange processes are implicitly considered. Similarly, food-web bioaccumulation models are capable of integrating the net effect of changes associated with factors such as temperature, growth rates, feeding preferences, and partitioning behavior on bioaccumulation potential. For the climate change scenarios considered in the present study, such tools indicate that alterations to exposure concentrations are typically within a factor of 2 of the baseline output. Based on an appreciation for the uncertainty in model parameters and baseline output, the authors recommend caution when interpreting or speculating on the relative importance of global climate change with respect to how changes caused by it will influence chemical fate and bioavailability. Environ. Toxicol. Chem. 2013;32:20–31. © 2012 SETAC PMID:23136071

  17. FUN3D Manual: 12.7

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2015-01-01

    This manual describes the installation and execution of FUN3D version 12.7, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  18. FUN3D Manual: 12.9

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2016-01-01

    This manual describes the installation and execution of FUN3D version 12.9, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  19. FUN3D Manual: 13.0

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bill; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2016-01-01

    This manual describes the installation and execution of FUN3D version 13.0, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  20. FUN3D Manual: 12.8

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2015-01-01

    This manual describes the installation and execution of FUN3D version 12.8, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  1. 3D packaging for integrated circuit systems

    SciTech Connect

    Chu, D.; Palmer, D.W.

    1996-11-01

    A goal was set for high density, high performance microelectronics pursued through a dense 3D packing of integrated circuits. A {open_quotes}tool set{close_quotes} of assembly processes have been developed that enable 3D system designs: 3D thermal analysis, silicon electrical through vias, IC thinning, mounting wells in silicon, adhesives for silicon stacking, pretesting of IC chips before commitment to stacks, and bond pad bumping. Validation of these process developments occurred through both Sandia prototypes and subsequent commercial examples.

  2. A high capacity 3D steganography algorithm.

    PubMed

    Chao, Min-Wen; Lin, Chao-hung; Yu, Cheng-Wei; Lee, Tong-Yee

    2009-01-01

    In this paper, we present a very high-capacity and low-distortion 3D steganography scheme. Our steganography approach is based on a novel multilayered embedding scheme to hide secret messages in the vertices of 3D polygon models. Experimental results show that the cover model distortion is very small as the number of hiding layers ranges from 7 to 13 layers. To the best of our knowledge, this novel approach can provide much higher hiding capacity than other state-of-the-art approaches, while obeying the low distortion and security basic requirements for steganography on 3D models. PMID:19147891

  3. New method of 3-D object recognition

    NASA Astrophysics Data System (ADS)

    He, An-Zhi; Li, Qun Z.; Miao, Peng C.

    1991-12-01

    In this paper, a new method of 3-D object recognition using optical techniques and a computer is presented. We perform 3-D object recognition using moire contour to obtain the object's 3- D coordinates, projecting drawings of the object in three coordinate planes to describe it and using a method of inquiring library of judgement to match objects. The recognition of a simple geometrical entity is simulated by computer and studied experimentally. The recognition of an object which is composed of a few simple geometrical entities is discussed.

  4. Explicit 3-D Hydrodynamic FEM Program

    2000-11-07

    DYNA3D is a nonlinear explicit finite element code for analyzing 3-D structures and solid continuum. The code is vectorized and available on several computer platforms. The element library includes continuum, shell, beam, truss and spring/damper elements to allow maximum flexibility in modeling physical problems. Many materials are available to represent a wide range of material behavior, including elasticity, plasticity, composites, thermal effects and rate dependence. In addition, DYNA3D has a sophisticated contact interface capability, includingmore » frictional sliding, single surface contact and automatic contact generation.« less

  5. How We 3D-Print Aerogel

    SciTech Connect

    2015-04-23

    A new type of graphene aerogel will make for better energy storage, sensors, nanoelectronics, catalysis and separations. Lawrence Livermore National Laboratory researchers have made graphene aerogel microlattices with an engineered architecture via a 3D printing technique known as direct ink writing. The research appears in the April 22 edition of the journal, Nature Communications. The 3D printed graphene aerogels have high surface area, excellent electrical conductivity, are lightweight, have mechanical stiffness and exhibit supercompressibility (up to 90 percent compressive strain). In addition, the 3D printed graphene aerogel microlattices show an order of magnitude improvement over bulk graphene materials and much better mass transport.

  6. An Improved Version of TOPAZ 3D

    SciTech Connect

    Krasnykh, Anatoly

    2003-07-29

    An improved version of the TOPAZ 3D gun code is presented as a powerful tool for beam optics simulation. In contrast to the previous version of TOPAZ 3D, the geometry of the device under test is introduced into TOPAZ 3D directly from a CAD program, such as Solid Edge or AutoCAD. In order to have this new feature, an interface was developed, using the GiD software package as a meshing code. The article describes this method with two models to illustrate the results.

  7. FUN3D Manual: 12.4

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2014-01-01

    This manual describes the installation and execution of FUN3D version 12.4, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixedelement unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  8. FUN3D Manual: 12.5

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, William L.; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2014-01-01

    This manual describes the installation and execution of FUN3D version 12.5, including optional dependent packages. FUN3D is a suite of computational uid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables ecient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  9. FUN3D Manual: 12.6

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, William L.; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2015-01-01

    This manual describes the installation and execution of FUN3D version 12.6, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  10. Explicit 3-D Hydrodynamic FEM Program

    SciTech Connect

    2000-11-07

    DYNA3D is a nonlinear explicit finite element code for analyzing 3-D structures and solid continuum. The code is vectorized and available on several computer platforms. The element library includes continuum, shell, beam, truss and spring/damper elements to allow maximum flexibility in modeling physical problems. Many materials are available to represent a wide range of material behavior, including elasticity, plasticity, composites, thermal effects and rate dependence. In addition, DYNA3D has a sophisticated contact interface capability, including frictional sliding, single surface contact and automatic contact generation.

  11. Computations of Emissions Using a 3-D Combustor Program

    NASA Technical Reports Server (NTRS)

    Srivatsa, S. K.

    1983-01-01

    A general 3-D combustor performance program developed by Garrett was extended to predict soot and NOx emissions. The soot formation and oxidation rates were computed by quasi-global models, taking into account the influence of turbulence. Radiation heat transfer was computed by the six-flux radiation mode. The radiation properties include the influence of CO2 and H2O in addition to soot. NOx emissions were computed from a global four-step hydrocarbon oxidation scheme and a set of rate-controlled reactions involving radicals and nitrogen oxides.

  12. Gold@silver bimetal nanoparticles/pyramidal silicon 3D substrate with high reproducibility for high-performance SERS

    NASA Astrophysics Data System (ADS)

    Zhang, Chao; Jiang, Shou Zhen; Yang, Cheng; Li, Chong Hui; Huo, Yan Yan; Liu, Xiao Yun; Liu, Ai Hua; Wei, Qin; Gao, Sai Sai; Gao, Xing Guo; Man, Bao Yuan

    2016-05-01

    A novel and efficient surface enhanced Raman scattering (SERS) substrate has been presented based on Gold@silver/pyramidal silicon 3D substrate (Au@Ag/3D-Si). By combining the SERS activity of Ag, the chemical stability of Au and the large field enhancement of 3D-Si, the Au@Ag/3D-Si substrate possesses perfect sensitivity, homogeneity, reproducibility and chemical stability. Using R6G as probe molecule, the SERS results imply that the Au@Ag/3D-Si substrate is superior to the 3D-Si, Ag/3D-Si and Au/3D-Si substrate. We also confirmed these excellent behaviors in theory via a commercial COMSOL software. The corresponding experimental and theoretical results indicate that our proposed Au@Ag/3D-Si substrate is expected to develop new opportunities for label-free SERS detections in biological sensors, biomedical diagnostics and food safety.

  13. Gold@silver bimetal nanoparticles/pyramidal silicon 3D substrate with high reproducibility for high-performance SERS

    PubMed Central

    Zhang, Chao; Jiang, Shou Zhen; Yang, Cheng; Li, Chong Hui; Huo, Yan Yan; Liu, Xiao Yun; Liu, Ai Hua; Wei, Qin; Gao, Sai Sai; Gao, Xing Guo; Man, Bao Yuan

    2016-01-01

    A novel and efficient surface enhanced Raman scattering (SERS) substrate has been presented based on Gold@silver/pyramidal silicon 3D substrate (Au@Ag/3D-Si). By combining the SERS activity of Ag, the chemical stability of Au and the large field enhancement of 3D-Si, the Au@Ag/3D-Si substrate possesses perfect sensitivity, homogeneity, reproducibility and chemical stability. Using R6G as probe molecule, the SERS results imply that the Au@Ag/3D-Si substrate is superior to the 3D-Si, Ag/3D-Si and Au/3D-Si substrate. We also confirmed these excellent behaviors in theory via a commercial COMSOL software. The corresponding experimental and theoretical results indicate that our proposed Au@Ag/3D-Si substrate is expected to develop new opportunities for label-free SERS detections in biological sensors, biomedical diagnostics and food safety. PMID:27143507

  14. Gold@silver bimetal nanoparticles/pyramidal silicon 3D substrate with high reproducibility for high-performance SERS.

    PubMed

    Zhang, Chao; Jiang, Shou Zhen; Yang, Cheng; Li, Chong Hui; Huo, Yan Yan; Liu, Xiao Yun; Liu, Ai Hua; Wei, Qin; Gao, Sai Sai; Gao, Xing Guo; Man, Bao Yuan

    2016-01-01

    A novel and efficient surface enhanced Raman scattering (SERS) substrate has been presented based on Gold@silver/pyramidal silicon 3D substrate (Au@Ag/3D-Si). By combining the SERS activity of Ag, the chemical stability of Au and the large field enhancement of 3D-Si, the Au@Ag/3D-Si substrate possesses perfect sensitivity, homogeneity, reproducibility and chemical stability. Using R6G as probe molecule, the SERS results imply that the Au@Ag/3D-Si substrate is superior to the 3D-Si, Ag/3D-Si and Au/3D-Si substrate. We also confirmed these excellent behaviors in theory via a commercial COMSOL software. The corresponding experimental and theoretical results indicate that our proposed Au@Ag/3D-Si substrate is expected to develop new opportunities for label-free SERS detections in biological sensors, biomedical diagnostics and food safety. PMID:27143507

  15. XML3D and Xflow: combining declarative 3D for the Web with generic data flows.

    PubMed

    Klein, Felix; Sons, Kristian; Rubinstein, Dmitri; Slusallek, Philipp

    2013-01-01

    Researchers have combined XML3D, which provides declarative, interactive 3D scene descriptions based on HTML5, with Xflow, a language for declarative, high-performance data processing. The result lets Web developers combine a 3D scene graph with data flows for dynamic meshes, animations, image processing, and postprocessing. PMID:24808080

  16. JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.

    PubMed

    Roll, James; Zirbel, Craig L; Sweeney, Blake; Petrov, Anton I; Leontis, Neocles

    2016-07-01

    Many non-coding RNAs have been identified and may function by forming 2D and 3D structures. RNA hairpin and internal loops are often represented as unstructured on secondary structure diagrams, but RNA 3D structures show that most such loops are structured by non-Watson-Crick basepairs and base stacking. Moreover, different RNA sequences can form the same RNA 3D motif. JAR3D finds possible 3D geometries for hairpin and internal loops by matching loop sequences to motif groups from the RNA 3D Motif Atlas, by exact sequence match when possible, and by probabilistic scoring and edit distance for novel sequences. The scoring gauges the ability of the sequences to form the same pattern of interactions observed in 3D structures of the motif. The JAR3D webserver at http://rna.bgsu.edu/jar3d/ takes one or many sequences of a single loop as input, or else one or many sequences of longer RNAs with multiple loops. Each sequence is scored against all current motif groups. The output shows the ten best-matching motif groups. Users can align input sequences to each of the motif groups found by JAR3D. JAR3D will be updated with every release of the RNA 3D Motif Atlas, and so its performance is expected to improve over time. PMID:27235417

  17. A chemical proteomics approach for global analysis of lysine monomethylome profiling.

    PubMed

    Wu, Zhixiang; Cheng, Zhongyi; Sun, Mingwei; Wan, Xuelian; Liu, Ping; He, Tieming; Tan, Minjia; Zhao, Yingming

    2015-02-01

    Methylation of lysine residues on histone proteins is known to play an important role in chromatin structure and function. However, non-histone protein substrates of this modification remain largely unknown. An effective approach for system-wide analysis of protein lysine methylation, particularly lysine monomethylation, is lacking. Here we describe a chemical proteomics approach for global screening for monomethyllysine substrates, involving chemical propionylation of monomethylated lysine, affinity enrichment of the modified monomethylated peptides, and HPLC/MS/MS analysis. Using this approach, we identified with high confidence 446 lysine monomethylation sites in 398 proteins, including three previously unknown histone monomethylation marks, representing the largest data set of protein lysine monomethylation described to date. Our data not only confirms previously discovered lysine methylation substrates in the nucleus and spliceosome, but also reveals new substrates associated with diverse biological processes. This method hence offers a powerful approach for dynamic study of protein lysine monomethylation under diverse cellular conditions and in human diseases. PMID:25505155

  18. 3D-CAD Effects on Creative Design Performance of Different Spatial Abilities Students

    ERIC Educational Resources Information Center

    Chang, Y.

    2014-01-01

    Students' creativity is an important focus globally and is interrelated with students' spatial abilities. Additionally, three-dimensional computer-assisted drawing (3D-CAD) overcomes barriers to spatial expression during the creative design process. Does 3D-CAD affect students' creative abilities? The purpose of this study was to…

  19. 3D-printed bioanalytical devices

    NASA Astrophysics Data System (ADS)

    Bishop, Gregory W.; Satterwhite-Warden, Jennifer E.; Kadimisetty, Karteek; Rusling, James F.

    2016-07-01

    While 3D printing technologies first appeared in the 1980s, prohibitive costs, limited materials, and the relatively small number of commercially available printers confined applications mainly to prototyping for manufacturing purposes. As technologies, printer cost, materials, and accessibility continue to improve, 3D printing has found widespread implementation in research and development in many disciplines due to ease-of-use and relatively fast design-to-object workflow. Several 3D printing techniques have been used to prepare devices such as milli- and microfluidic flow cells for analyses of cells and biomolecules as well as interfaces that enable bioanalytical measurements using cellphones. This review focuses on preparation and applications of 3D-printed bioanalytical devices.

  20. Nonlaser-based 3D surface imaging

    SciTech Connect

    Lu, Shin-yee; Johnson, R.K.; Sherwood, R.J.

    1994-11-15

    3D surface imaging refers to methods that generate a 3D surface representation of objects of a scene under viewing. Laser-based 3D surface imaging systems are commonly used in manufacturing, robotics and biomedical research. Although laser-based systems provide satisfactory solutions for most applications, there are situations where non laser-based approaches are preferred. The issues that make alternative methods sometimes more attractive are: (1) real-time data capturing, (2) eye-safety, (3) portability, and (4) work distance. The focus of this presentation is on generating a 3D surface from multiple 2D projected images using CCD cameras, without a laser light source. Two methods are presented: stereo vision and depth-from-focus. Their applications are described.

  1. Tropical Cyclone Jack in Satellite 3-D

    NASA Video Gallery

    This 3-D flyby from NASA's TRMM satellite of Tropical Cyclone Jack on April 21 shows that some of the thunderstorms were shown by TRMM PR were still reaching height of at least 17 km (10.5 miles). ...

  2. 3D Printing for Tissue Engineering

    PubMed Central

    Jia, Jia; Yao, Hai; Mei, Ying

    2016-01-01

    Tissue engineering aims to fabricate functional tissue for applications in regenerative medicine and drug testing. More recently, 3D printing has shown great promise in tissue fabrication with a structural control from micro- to macro-scale by using a layer-by-layer approach. Whether through scaffold-based or scaffold-free approaches, the standard for 3D printed tissue engineering constructs is to provide a biomimetic structural environment that facilitates tissue formation and promotes host tissue integration (e.g., cellular infiltration, vascularization, and active remodeling). This review will cover several approaches that have advanced the field of 3D printing through novel fabrication methods of tissue engineering constructs. It will also discuss the applications of synthetic and natural materials for 3D printing facilitated tissue fabrication. PMID:26869728

  3. 3D Visualization of Recent Sumatra Earthquake

    NASA Astrophysics Data System (ADS)

    Nayak, Atul; Kilb, Debi

    2005-04-01

    Scientists and visualization experts at the Scripps Institution of Oceanography have created an interactive three-dimensional visualization of the 28 March 2005 magnitude 8.7 earthquake in Sumatra. The visualization shows the earthquake's hypocenter and aftershocks recorded until 29 March 2005, and compares it with the location of the 26 December 2004 magnitude 9 event and the consequent seismicity in that region. The 3D visualization was created using the Fledermaus software developed by Interactive Visualization Systems (http://www.ivs.unb.ca/) and stored as a ``scene'' file. To view this visualization, viewers need to download and install the free viewer program iView3D (http://www.ivs3d.com/products/iview3d).

  4. Future Engineers 3-D Print Timelapse

    NASA Video Gallery

    NASA Challenges K-12 students to create a model of a container for space using 3-D modeling software. Astronauts need containers of all kinds - from advanced containers that can study fruit flies t...

  5. 3-D Flyover Visualization of Veil Nebula

    NASA Video Gallery

    This 3-D visualization flies across a small portion of the Veil Nebula as photographed by the Hubble Space Telescope. This region is a small part of a huge expanding remnant from a star that explod...

  6. Quantifying Modes of 3D Cell Migration.

    PubMed

    Driscoll, Meghan K; Danuser, Gaudenz

    2015-12-01

    Although it is widely appreciated that cells migrate in a variety of diverse environments in vivo, we are only now beginning to use experimental workflows that yield images with sufficient spatiotemporal resolution to study the molecular processes governing cell migration in 3D environments. Since cell migration is a dynamic process, it is usually studied via microscopy, but 3D movies of 3D processes are difficult to interpret by visual inspection. In this review, we discuss the technologies required to study the diversity of 3D cell migration modes with a focus on the visualization and computational analysis tools needed to study cell migration quantitatively at a level comparable to t