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Sample records for 3-d electron density

  1. 3D Distribution of the Coronal Electron Density and its Evolution with Solar Cycle

    NASA Astrophysics Data System (ADS)

    Wang, Tongjiang; Reginald, Nelson Leslie; Davila, Joseph M.; St. Cyr, Orville Chris

    2016-05-01

    The variability of the solar white-light corona and its connection to the solar activity has been studied for more than a half century. It is widely accepted that the temporal variation of the total radiance of the K-corona follows the solar cycle pattern (e.g., correlated with sunspot number). However, the origin of this variation and its relationships with regard to coronal mass ejections and the solar wind are yet to be clearly understood. We know that the COR1-A and –B instruments onboard the STEREO spacecraft have continued to perform high-cadence (5 min) polarized brightness measurements from two different vantage points over a long period of time that encompasses the solar minimum of Solar Cycle 23 to the solar maximum of Solar Cycle 24. This extended period of polarized brightness measurements can now be used to reconstruct 3D electron density distributions of the corona between the heliocentric heights of 1.5-4.0 solar radii. In this study we have constructed the 3D coronal density models for 100 Carrington rotations (CRs) from 2007 to 2014 using the spherically symmetric inversion (SSI) method. The validity of these 3D density models is verified by comparing with similar 3D density models created by other means such as tomography, MHD modeling, and 2D density distributions inverted from the polarized brightness images from LASCO/C2 instrument onboard the SOHO spacecraft. When examining the causes for the temporal variation of the global electron content we find that its increase from the solar minimum to maximum depends on changes to both the total area and mean density of coronal streamers. We also find that the global and hemispheric electron contents show quasi-periodic variations with a period of 8-9 CRs during the ascending and maximum phases of Solar Cycle 24 through wavelet analysis. In addition, we also explore any obvious relationships between temporal variation of the global electron content with the photospheric magnetic flux, total mass of

  2. BioMEA: a versatile high-density 3D microelectrode array system using integrated electronics.

    PubMed

    Charvet, Guillaume; Rousseau, Lionel; Billoint, Olivier; Gharbi, Sadok; Rostaing, Jean-Pierre; Joucla, Sébastien; Trevisiol, Michel; Bourgerette, Alain; Chauvet, Philippe; Moulin, Céline; Goy, François; Mercier, Bruno; Colin, Mikael; Spirkovitch, Serge; Fanet, Hervé; Meyrand, Pierre; Guillemaud, Régis; Yvert, Blaise

    2010-04-15

    Microelectrode arrays (MEAs) offer a powerful tool to both record activity and deliver electrical microstimulations to neural networks either in vitro or in vivo. Microelectronics microfabrication technologies now allow building high-density MEAs containing several hundreds of microelectrodes. However, dense arrays of 3D micro-needle electrodes, providing closer contact with the neural tissue than planar electrodes, are not achievable using conventional isotropic etching processes. Moreover, increasing the number of electrodes using conventional electronics is difficult to achieve into compact devices addressing all channels independently for simultaneous recording and stimulation. Here, we present a full modular and versatile 256-channel MEA system based on integrated electronics. First, transparent high-density arrays of 3D-shaped microelectrodes were realized by deep reactive ion etching techniques of a silicon substrate reported on glass. This approach allowed achieving high electrode aspect ratios, and different shapes of tip electrodes. Next, we developed a dedicated analog 64-channel Application Specific Integrated Circuit (ASIC) including one amplification stage and one current generator per channel, and analog output multiplexing. A full modular system, called BIOMEA, has been designed, allowing connecting different types of MEAs (64, 128, or 256 electrodes) to different numbers of ASICs for simultaneous recording and/or stimulation on all channels. Finally, this system has been validated experimentally by recording and electrically eliciting low-amplitude spontaneous rhythmic activity (both LFPs and spikes) in the developing mouse CNS. The availability of high-density MEA systems with integrated electronics will offer new possibilities for both in vitro and in vivo studies of large neural networks.

  3. [The reconstruction of welding arc 3D electron density distribution based on Stark broadening].

    PubMed

    Zhang, Wang; Hua, Xue-Ming; Pan, Cheng-Gang; Li, Fang; Wang, Min

    2012-10-01

    The three-dimensional electron density is very important for welding arc quality control. In the present paper, Side-on characteristic line profile was collected by a spectrometer, and the lateral experimental data were approximated by a polynomial fitting. By applying an Abel inversion technique, the authors obtained the radial intensity distribution at each wavelength and thus constructed a profile for the radial positions. The Fourier transform was used to separate the Lorentz linear from the spectrum reconstructed, thus got the accurate Stark width. And we calculated the electronic density three-dimensional distribution of the TIG welding are plasma. PMID:23285847

  4. Electron-density comparisons between radar observations and 3-D ionospheric model calculations. Master's thesis

    SciTech Connect

    Johnson, M.W.

    1990-01-01

    A comparison of electron densities calculated from the Utah State University First-Principals Ionospheric Model with simultaneous observations taken at Sondrestrom, Millstone, and Arecibo incoherent-scatter radars was undertaken to better understanding the response of the ionosphere at these longitudinally similar yet latitudinally separated locations. The comparison included over 50 days distributed over 3 1/2 years roughly symmetrical about the last solar-minimum in 1986. The overall trend of the comparison was that to first-order the model reproduces electron densities responding to diurnal, seasonal, geomagnetic, and solar-cycle variations for all three radars. However, some model-observation discrepancies were found. These include, failure of the model to correctly produce an evening peak at Millstone, fall-spring equinox differences at Sondrestrom, tidal structure at Arecibo, and daytime NmF2 values at Arecibo.

  5. Kondo effect at low electron density and high particle-hole asymmetry in 1D, 2D, and 3D

    NASA Astrophysics Data System (ADS)

    Žitko, Rok; Horvat, Alen

    2016-09-01

    Using the perturbative scaling equations and the numerical renormalization group, we study the characteristic energy scales in the Kondo impurity problem as a function of the exchange coupling constant J and the conduction-band electron density. We discuss the relation between the energy gain (impurity binding energy) Δ E and the Kondo temperature TK. We find that the two are proportional only for large values of J , whereas in the weak-coupling limit the energy gain is quadratic in J , while the Kondo temperature is exponentially small. The exact relation between the two quantities depends on the detailed form of the density of states of the band. In the limit of low electron density the Kondo screening is affected by the strong particle-hole asymmetry due to the presence of the band-edge van Hove singularities. We consider the cases of one- (1D), two- (2D), and three-dimensional (3D) tight-binding lattices (linear chain, square lattice, cubic lattice) with inverse-square-root, step-function, and square-root onsets of the density of states that are characteristic of the respective dimensionalities. We always find two different regimes depending on whether TK is higher or lower than μ , the chemical potential measured from the bottom of the band. For 2D and 3D, we find a sigmoidal crossover between the large-J and small-J asymptotics in Δ E and a clear separation between Δ E and TK for TK<μ . For 1D, there is, in addition, a sizable intermediate-J regime where the Kondo temperature is quadratic in J due to the diverging density of states at the band edge. Furthermore, we find that in 1D the particle-hole asymmetry leads to a large decrease of TK compared to the standard result obtained by approximating the density of states to be constant (flat-band approximation), while in 3D the opposite is the case; this is due to the nontrivial interplay of the exchange and potential scattering renormalization in the presence of particle-hole asymmetry. The 2D square

  6. An LS-MARS method for modeling regional 3D ionospheric electron density based on GPS data and IRI

    NASA Astrophysics Data System (ADS)

    Kao, Szu-Pyng; Chen, Yao-Chung; Ning, Fang-Shii; Tu, Yuh-Min

    2015-05-01

    The methods of developing an accurate and effective ionospheric electron density (IED) model have greatly interested ionosphere researchers. Numerous scholars have proposed many effective and reliable models and methods of global positioning system (GPS)-based computerized ionospheric tomography (CIT) in the past decades. This study introduced a new function-based CIT method, namely the LS-MARS (Least Squares method-Multivariate Adaptive Regression Splines), combining MARS with IEDs calculated by International Reference Ionosphere (IRI) to automatically choose the best representing basis functions for the three-dimensional (3D) electron density inside that modeling area. This selected basis functions was substituted into the observation equation of the GPS total electron content (TEC) to calculate the design matrix. Finally, the weighted damped least squares (WDLS) were adopted to reestimate the IED model coefficients. In contrast to common function-based CIT methods, the LS-MARS can be used to attain optimal 3D model automatically, flexibly, adaptively based on the IRI without a priori knowledge of the IED distribution mathematical function. The findings indicated that the LS-MARS model had a smaller recovery TEC error than did the MARS_IRI2012 model, and the VTEC calculated using the LS-MARS model was closer to the VTEC obtained from International GNSS Service (IGS) final IONEX files than was the VTEC calculated using the MARS_IRI2012 and IRI2012. Therefore, this method exhibits strong modeling effectiveness and reliability, and can be an efficient alternative method for estimating regional 3D IED models.

  7. Correlation Energy of 3D Spin-Polarized Electron Gas: A Single Interpolation Between High- and Low-Density Limits

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei; Perdew, John; Seidl, Michael

    2008-03-01

    We present an analytic model for the correlation energy per electron ec(rs,ζ) in the three-dimensional (3D) uniform electron gas, covering the full range 0<=rs<∞ and 0<=ζ<=1 of the density parameter rs and the relative spin polarization ζ. An interpolation is made between the exactly known high-density (rs->0) and low-density (rs->∞) limits, using a formula which (unlike previous ones) has the right analytic structures in both limits. We find that there is almost enough information available from these limits to determine the correlation energy over the full range. By minimal fitting to numerical quantum Monte Carlo data, we predict the value of b1(ζ) at ζ=0 close to the theoretical value [1], where b1(ζ) is the coefficient of the rsterm in the high-density expansion. The model finds correlation energies for the unpolarized (ζ=0) and fully polarized (ζ=1) cases in excellent agreement with Monte Carlo data. [1] T. Endo, M. Horiuchi, Y. Takada and H. Yasuhara, Phys. Rev. B 59, 7367 (1999)

  8. A study of 3D structure of nighttime electron density enhancement in the mid-latitude ionosphere by GPS tomography

    NASA Astrophysics Data System (ADS)

    Chen, C.; Saito, A.

    2011-12-01

    The mid-latitude summer nighttime anomaly (MSNA) is a feature that the nighttime electron density larger than that in the daytime mid-latitude ionosphere. This anomaly was first detected in the southern hemisphere five decades ago and observed in the northern hemisphere recently by ionosondes and satellites. Previous studies presented the electron density structure of MSNA by using COSMIC occultation data and found that MSNA is clearly seen around 300 km altitude during local summer. However, due to lack of observation, the day-to-day variation of MSNA was not investigated. A GPS tomography method by SPEL of Kyoto University using the total electron content (TEC) data measured by the ground-based GPS receiver network is employed in this study. The wide coverage and continuous observation of GPS receivers are suitable for investigating the spatial and day-to-day variations of ionospheric electron densities. The algorithm of the GPS tomography developed by SPEL of Kyoto University use a constraint condition that the gradient of election density tends to be smooth in the horizontal direction and steep in the vicinity of the F2 peak, instead of inputting the initial conditions. Therefore, the algorithm is independent of any ionospheric and plasmaspheric electron density distribution models. The dense ground-based GPS receiver network around European region is used to study the three dimensional (3D) structure of MSNA with GPS tomography. Results show that the MSNA usually appear around the geomagnetic mid-latitude region during local summer nighttime. The feature of MSNA is most obvious at the ionospheric F2-peak altitudes. The result also shows a day-to-day variation in the formation of MSNA, in terms of the occurrence time, intensity, and spatial extent. The tomographic results are compared with the ionosondes, satellites, and radar measurements. A theoretical model simulation, SAMI2, is also used to further discuss the mechanism of MSNA. The comparison with other

  9. Polyhedral 3D structure of human plasma very low density lipoproteins by individual particle cryo-electron tomography1[S

    PubMed Central

    Yu, Yadong; Kuang, Yu-Lin; Lei, Dongsheng; Zhai, Xiaobo; Zhang, Meng; Krauss, Ronald M.; Ren, Gang

    2016-01-01

    Human VLDLs assembled in the liver and secreted into the circulation supply energy to peripheral tissues. VLDL lipolysis yields atherogenic LDLs and VLDL remnants that strongly correlate with CVD. Although the composition of VLDL particles has been well-characterized, their 3D structure is elusive because of their variations in size, heterogeneity in composition, structural flexibility, and mobility in solution. Here, we employed cryo-electron microscopy and individual-particle electron tomography to study the 3D structure of individual VLDL particles (without averaging) at both below and above their lipid phase transition temperatures. The 3D reconstructions of VLDL and VLDL bound to antibodies revealed an unexpected polyhedral shape, in contrast to the generally accepted model of a spherical emulsion-like particle. The smaller curvature of surface lipids compared with HDL may also reduce surface hydrophobicity, resulting in lower binding affinity to the hydrophobic distal end of the N-terminal β-barrel domain of cholesteryl ester transfer protein (CETP) compared with HDL. The directional binding of CETP to HDL and VLDL may explain the function of CETP in transferring TGs and cholesteryl esters between these particles. This first visualization of the 3D structure of VLDL could improve our understanding of the role of VLDL in atherogenesis. PMID:27538822

  10. Electronic structure of oxide, peroxide, and superoxide clusters of the 3d elements: A comparative density functional study

    NASA Astrophysics Data System (ADS)

    Uzunova, Ellie L.; Mikosch, Hans; Nikolov, Georgi St.

    2008-03-01

    The 3d-element transition metal dioxide MO2, peroxide M(O2), and superoxide MOO clusters (M=Sc-Zn), are studied by density functional theory with the B1LYP functional. The reliability of the methods and basis sets employed was tested by a reinvestigation of the monoxides, for which a database of experimental data is available. The global minima on the M+O2 potential energy surfaces correspond to dioxide structure, the only exception being CuOO, with a superoxide structure. All Zn dioxygen clusters are thermodynamically unstable-their ground states lie higher than the dissociation limit to Zn+O2. Our calculations are in favor of the high-spin configurations for the FeO2, CoO2, and NiO2 ground states, which are still a subject of extensive theoretical and experimental studies. These assignments are confirmed by the coupled-cluster method, CCSD(T), except for NiO2. Based on the existence of a stable NiO2 monoanion in a 4B1 state, however, it can be concluded that NiO2 in its 5A1 state should also be stable. The vibrational frequencies are calculated for clusters entrapped in the cubic cell of solid Ar matrix and compared with those obtained for gas-phase clusters. The matrix has no influence on the vibrations of the monoxides and most of the dioxides; however, Co and Ni-dioxoclusters interact strongly with the atoms from the noble gas matrix. The most intense frequencies in the IR spectra are shifted to lower energies and the ordering of the low-lying electronic states by stability is also reversed. According to the electrostatic potential maps, the oxygen atoms in the peroxides are more nucleophilic than those in the dioxides and superoxides. The terminal oxygen atom in superoxides is more nucleophilic than its M-bonded oxygen atom, though charge distribution analysis predicts a smaller negative charge on the terminal oxygen. TiO2 is the only dioxide in which nucleophilic character in the vicinity of the metal cation is induced.

  11. 3D electron density distributions in the solar corona during solar minima: assessment for more realistic solar wind modeling

    NASA Astrophysics Data System (ADS)

    de Patoul, J.; Foullon, C.; Riley, P.

    2015-12-01

    Knowledge of the electron density distribution in the solar corona put constraints on the magnetic field configurations for coronal modeling, and on initial conditions for solar wind modeling. We work with polarized SOHO/LASCO-C2 images from the last two recent minima of solar activity (1996-1997 and 2008-2010), devoid of coronal mass ejections. We derive the 4D electron density distributions in the corona by applying a newly developed time-dependent tomographic reconstruction method. First we compare the density distributions obtained from tomography with magnetohydrodynamic (MHD) solutions. The tomography provides more accurate distributions of electron densities in the polar regions, and we find that the observed density varies with the solar cycle in both polar and equatorial regions. Second, we find that the highest-density structures do not always correspond to the predicted large-scale heliospheric current sheet or its helmet streamer but can follow the locations of pseudo-streamers. We conclude that tomography offers reliable density distribution in the corona, reproducing the slow time evolution of coronal structures, without prior knowledge of the coronal magnetic field over a full rotation. Finally, we suggest that the highest-density structures show a differential rotation well above the surface depending on how it is magnetically connected to the surface. Such valuable information on the rotation of large-scale structures could help to connect the sources of the solar wind to their in-situ counterparts in future missions such as Solar Orbiter and Solar Probe Plus. This research combined with the MHD coronal modeling efforts has the potential to increase the reliability for future space weather forecasting.

  12. 3D ELECTRON DENSITY DISTRIBUTIONS IN THE SOLAR CORONA DURING SOLAR MINIMA: ASSESSMENT FOR MORE REALISTIC SOLAR WIND MODELING

    SciTech Connect

    Patoul, Judith de; Foullon, Claire; Riley, Pete E-mail: c.foullon@exeter.ac.uk

    2015-11-20

    Knowledge of the electron density distribution in the solar corona put constraints on the magnetic field configurations for coronal modeling and on initial conditions for solar wind modeling. We work with polarized SOHO/LASCO-C2 images from the last two recent minima of solar activity (1996–1997 and 2008–2010), devoid of coronal mass ejections. The goals are to derive the 4D electron density distributions in the corona by applying a newly developed time-dependent tomographic reconstruction method and to compare the results between the two solar minima and with two magnetohydrodynamic models. First, we confirm that the values of the density distribution in thermodynamic models are more realistic than in polytropic ones. The tomography provides more accurate distributions in the polar regions, and we find that the density in tomographic and thermodynamic solutions varies with the solar cycle in both polar and equatorial regions. Second, we find that the highest-density structures do not always correspond to the predicted large-scale heliospheric current sheet or its helmet streamer but can follow the locations of pseudo-streamers. We deduce that tomography offers reliable density distributions in the corona, reproducing the slow time evolution of coronal structures, without prior knowledge of the coronal magnetic field over a full rotation. Finally, we suggest that the highest-density structures show a differential rotation well above the surface depending on how they are magnetically connected to the surface. Such valuable information on the rotation of large-scale structures could help to connect the sources of the solar wind to their in situ counterparts in future missions such as Solar Orbiter and Solar Probe Plus.

  13. Electronic structure of trioxide, oxoperoxide, oxosuperoxide, and ozonide clusters of the 3d elements: density functional theory study.

    PubMed

    Uzunova, Ellie L

    2011-03-01

    The trioxide clusters with stoichiometry MO3, and the structural isomers with side-on and end-on bonded oxygen atoms, are studied by DFT with the B1LYP functional. For the first half of the 3d elements row (Sc to Cr), pyramidal or distorted pyramidal structures dominate among the trioxide and oxoperoxide ground states, while the remaining elements form planar trioxides, oxoperoxides, oxosuperoxides, and ozonides. Low-lying trioxide clusters are formed by Ti, V, Cr, and Mn, among which the distorted pyramidal VO3 in the (2)A'' state, the pyramidal CrO3 in the (1)A1 state, and the planar MnO3 in the (2)A1' state are global minima. With the exception of the middle-row elements Mn, Fe, and Co, the magnetic moment of the ground-state clusters is formed with a major contribution from unpaired electrons located at the oxygen atoms. The stability of trioxides and oxoperoxides toward release of molecular oxygen is significantly higher for Sc, Ti, and V than for the remaining elements of the row. A trend of increasing the capability to dissociate one oxygen molecule is observed from Cr to Cu, with the exception of OFe(O2) being more reactive than OCo(O2). A gradual increase of reactivity from Ti to Cu is observed for the complete fragmentation reaction M + O + O2.

  14. Comparison of radiotherapy dosimetry for 3D-CRT, IMRT, and SBRT based on electron density calibration

    NASA Astrophysics Data System (ADS)

    Kartutik, K.; Wibowo, W. E.; Pawiro, S. A.

    2016-03-01

    Accurate calculation of dose distribution affected by inhomogeneity tissue is required in radiotherapy planning. This study was performed to determine the ratio between radiotherapy planning using 3D-CRT, IMRT, and SBRT based on a calibrated curve of CT-number in the lung for different target's shape in 3D-CRT, IMRT, and spinal cord for SBRT. Calibration curves of CT-number were generated under measurement basis and introduced into TPS, then planning was performed for 3D-CRT, IMRT, and SBRT with 7, and 15 radiation fields. Afterwards, planning evaluation was performed by comparing the DVH curve, HI, and CI. 3D-CRT and IMRT produced the lowest HI at calibration curve of CIRS 002LFC with the value 0.24 and 10. Whereas SBRT produced the lowest HI on a linear calibration curve with a value of 0.361. The highest CI in IMRT and SBRT technique achieved using a linear calibration curve was 0.97 and 1.77 respectively. For 3D-CRT, the highest CI was obtained by using calibration curve of CIRS 062M with the value of 0.45. From the results of CI and HI, it is concluded that the calibration curve of CT-number does not significantly differ with Schneider's calibrated curve, and inverse planning gives a better result than forward planning.

  15. 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.

  16. Space Electron Density Gradient Studies using a 3D Embedded Reconfigurable Sounder and ESA/NASA CLUSTER Mission

    NASA Astrophysics Data System (ADS)

    Dekoulis, George

    2016-07-01

    This paper provides a direct comparison between data captured by a new embedded reconfigurable digital sounder, different ground-based ionospheric sounders spread around Europe and the ESA/NASA CLUSTER mission. The CLUSTER mission consists of four identical space probes flying in a formation that allows measurements of the electron density gradient in the local magnetic field. Both the ground-based and the spacecraft instrumentations assist in studying the motion, geometry and boundaries of the plasmasphere. The comparison results are in accordance to each other. Some slight deviations among the captured data were expected from the beginning of this investigation. These small discrepancies are reasonable and seriatim analyzed. The results of this research are significant, since the level of the plasma's ionization, which is related to the solar activity, dominates the propagation of electromagnetic waves through it. Similarly, unusually high solar activity presents serious hazards to orbiting satellites, spaceborne instrumentation, satellite communications and infrastructure located on the Earth's surface. Long-term collaborative study of the data is required to continue, in order to identify and determine the enhanced risk in advance. This would allow scientists to propose an immediate cure.

  17. Dust density measurements in 3D dust clouds by tomography

    NASA Astrophysics Data System (ADS)

    Melzer, Andre

    2014-10-01

    Dusty plasmas usually consist of (micron-sized) dust particles trapped in a gaseous discharge plasma. Volume-filling dust clouds can be generated in the laboratory by thermophoretic levitation of the particles against gravity or under the microgravity conditions of parabolic flights. In these discharges, the dust density is typically so high that together with the high charge on the particles, the dust charge density can compete with the ion and electron (charge) density indicating a regime of charge depletion. Here, we present a technique that allows to measure the spatially resolved 3D dust density in such dusty discharges. For that purpose, the dust cloud is transilluminated by a homogeneous light source and the transilluminated cloud is measured under different angles in a tomographic-like manner. This allows to reconstruct the full 3D dust density within the discharge volume and further to deduce the force balance for the dust component. Supported by DLR 50 WM 1138.

  18. Propagation in 3D of microwaves through density perturbations

    NASA Astrophysics Data System (ADS)

    Williams, T. R. N.; Köhn, A.; O'Brien, M. R.; Vann, R. G. L.

    2014-07-01

    Simulations using 3D and 2D full-wave codes have shown that edge filaments in tokamak plasmas can significantly affect the propagation of microwaves across a broad frequency spectrum, resulting in scattering angles of up to 46°. Parameter scans were carried out for density perturbations comparable in width and amplitude to MAST filaments and the effect on the measured emission was calculated. 3D effects were discovered in the case of an obliquely incident beam. In general, the problem of electromagnetic propagation past wavelength-sized 3D inhomogeneities is not well understood, yet is of importance for both heating and diagnostic applications in the electron cyclotron frequency range for tokamaks, as well as atmospheric physics. To improve this understanding, a new cold-plasma code, EMIT-3D, was written to extend full-wave microwave simulations in magnetized plasmas to 3D, and make comparisons to the existing 2D code IPF-FDMC. This work supports MAST experiments using the SAMI diagnostic to image microwave emission from the plasma edge due to mode conversion from electron Bernstein waves. Significant fluctuations in the SAMI data mean that detailed modelling is required to improve its interpretation.

  19. Numerical Solution of 3D Poisson-Nernst-Planck Equations Coupled with Classical Density Functional Theory for Modeling Ion and Electron Transport in a Confined Environment

    SciTech Connect

    Meng, Da; Zheng, Bin; Lin, Guang; Sushko, Maria L.

    2014-08-29

    We have developed efficient numerical algorithms for the solution of 3D steady-state Poisson-Nernst-Planck equations (PNP) with excess chemical potentials described by the classical density functional theory (cDFT). The coupled PNP equations are discretized by finite difference scheme and solved iteratively by Gummel method with relaxation. The Nernst-Planck equations are transformed into Laplace equations through the Slotboom transformation. Algebraic multigrid method is then applied to efficiently solve the Poisson equation and the transformed Nernst-Planck equations. A novel strategy for calculating excess chemical potentials through fast Fourier transforms is proposed which reduces computational complexity from O(N2) to O(NlogN) where N is the number of grid points. Integrals involving Dirac delta function are evaluated directly by coordinate transformation which yields more accurate result compared to applying numerical quadrature to an approximated delta function. Numerical results for ion and electron transport in solid electrolyte for Li ion batteries are shown to be in good agreement with the experimental data and the results from previous studies.

  20. 3-D capacitance density imaging system

    DOEpatents

    Fasching, G.E.

    1988-03-18

    A three-dimensional capacitance density imaging of a gasified bed or the like in a containment vessel is achieved using a plurality of electrodes provided circumferentially about the bed in levels and along the bed in channels. The electrodes are individually and selectively excited electrically at each level to produce a plurality of current flux field patterns generated in the bed at each level. The current flux field patterns are suitably sensed and a density pattern of the bed at each level determined. By combining the determined density patterns at each level, a three-dimensional density image of the bed is achieved. 7 figs.

  1. Visualization of electronic density

    DOE PAGES

    Grosso, Bastien; Cooper, Valentino R.; Pine, Polina; Hashibon, Adham; Yaish, Yuval; Adler, Joan

    2015-04-22

    An atom’s volume depends on its electronic density. Although this density can only be evaluated exactly for hydrogen-like atoms, there are many excellent numerical algorithms and packages to calculate it for other materials. 3D visualization of charge density is challenging, especially when several molecular/atomic levels are intertwined in space. We explore several approaches to 3D charge density visualization, including the extension of an anaglyphic stereo visualization application based on the AViz package to larger structures such as nanotubes. We will describe motivations and potential applications of these tools for answering interesting questions about nanotube properties.

  2. Estimating Density Gradients and Drivers from 3D Ionospheric Imaging

    NASA Astrophysics Data System (ADS)

    Datta-Barua, S.; Bust, G. S.; Curtis, N.; Reynolds, A.; Crowley, G.

    2009-12-01

    The transition regions at the edges of the ionospheric storm-enhanced density (SED) are important for a detailed understanding of the mid-latitude physical processes occurring during major magnetic storms. At the boundary, the density gradients are evidence of the drivers that link the larger processes of the SED, with its connection to the plasmasphere and prompt-penetration electric fields, to the smaller irregularities that result in scintillations. For this reason, we present our estimates of both the plasma variation with horizontal and vertical spatial scale of 10 - 100 km and the plasma motion within and along the edges of the SED. To estimate the density gradients, we use Ionospheric Data Assimilation Four-Dimensional (IDA4D), a mature data assimilation algorithm that has been developed over several years and applied to investigations of polar cap patches and space weather storms [Bust and Crowley, 2007; Bust et al., 2007]. We use the density specification produced by IDA4D with a new tool for deducing ionospheric drivers from 3D time-evolving electron density maps, called Estimating Model Parameters from Ionospheric Reverse Engineering (EMPIRE). The EMPIRE technique has been tested on simulated data from TIMEGCM-ASPEN and on IDA4D-based density estimates with ongoing validation from Arecibo ISR measurements [Datta-Barua et al., 2009a; 2009b]. We investigate the SED that formed during the geomagnetic super storm of November 20, 2003. We run IDA4D at low-resolution continent-wide, and then re-run it at high (~10 km horizontal and ~5-20 km vertical) resolution locally along the boundary of the SED, where density gradients are expected to be highest. We input the high-resolution estimates of electron density to EMPIRE to estimate the ExB drifts and field-aligned plasma velocities along the boundaries of the SED. We expect that these drivers contribute to the density structuring observed along the SED during the storm. Bust, G. S. and G. Crowley (2007

  3. 3D Freeze-Casting of Cellular Graphene Films for Ultrahigh-Power-Density Supercapacitors.

    PubMed

    Shao, Yuanlong; El-Kady, Maher F; Lin, Cheng-Wei; Zhu, Guanzhou; Marsh, Kristofer L; Hwang, Jee Youn; Zhang, Qinghong; Li, Yaogang; Wang, Hongzhi; Kaner, Richard B

    2016-08-01

    3D cellular graphene films with open porosity, high electrical conductivity, and good tensile strength, can be synthesized by a method combining freeze-casting and filtration. The resulting supercapacitors based on 3D porous reduced graphene oxide (RGO) film exhibit extremely high specific power densities and high energy densities. The fabrication process provides an effective means for controlling the pore size, electronic conductivity, and loading mass of the electrode materials, toward devices with high energy-storage performance. PMID:27214752

  4. High density 3D printed microfluidic valves, pumps, and multiplexers.

    PubMed

    Gong, Hua; Woolley, Adam T; Nordin, Gregory P

    2016-07-01

    In this paper we demonstrate that 3D printing with a digital light processor stereolithographic (DLP-SLA) 3D printer can be used to create high density microfluidic devices with active components such as valves and pumps. Leveraging our previous work on optical formulation of inexpensive resins (RSC Adv., 2015, 5, 106621), we demonstrate valves with only 10% of the volume of our original 3D printed valves (Biomicrofluidics, 2015, 9, 016501), which were already the smallest that have been reported. Moreover, we show that incorporation of a thermal initiator in the resin formulation along with a post-print bake can dramatically improve the durability of 3D printed valves up to 1 million actuations. Using two valves and a valve-like displacement chamber (DC), we also create compact 3D printed pumps. With 5-phase actuation and a 15 ms phase interval, we obtain pump flow rates as high as 40 μL min(-1). We also characterize maximum pump back pressure (i.e., maximum pressure the pump can work against), maximum flow rate (flow rate when there is zero back pressure), and flow rate as a function of the height of the pump outlet. We further demonstrate combining 5 valves and one DC to create a 3-to-2 multiplexer with integrated pump. In addition to serial multiplexing, we also show that the device can operate as a mixer. Importantly, we illustrate the rapid fabrication and test cycles that 3D printing makes possible by implementing a new multiplexer design to improve mixing, and fabricate and test it within one day.

  5. High density 3D printed microfluidic valves, pumps, and multiplexers.

    PubMed

    Gong, Hua; Woolley, Adam T; Nordin, Gregory P

    2016-07-01

    In this paper we demonstrate that 3D printing with a digital light processor stereolithographic (DLP-SLA) 3D printer can be used to create high density microfluidic devices with active components such as valves and pumps. Leveraging our previous work on optical formulation of inexpensive resins (RSC Adv., 2015, 5, 106621), we demonstrate valves with only 10% of the volume of our original 3D printed valves (Biomicrofluidics, 2015, 9, 016501), which were already the smallest that have been reported. Moreover, we show that incorporation of a thermal initiator in the resin formulation along with a post-print bake can dramatically improve the durability of 3D printed valves up to 1 million actuations. Using two valves and a valve-like displacement chamber (DC), we also create compact 3D printed pumps. With 5-phase actuation and a 15 ms phase interval, we obtain pump flow rates as high as 40 μL min(-1). We also characterize maximum pump back pressure (i.e., maximum pressure the pump can work against), maximum flow rate (flow rate when there is zero back pressure), and flow rate as a function of the height of the pump outlet. We further demonstrate combining 5 valves and one DC to create a 3-to-2 multiplexer with integrated pump. In addition to serial multiplexing, we also show that the device can operate as a mixer. Importantly, we illustrate the rapid fabrication and test cycles that 3D printing makes possible by implementing a new multiplexer design to improve mixing, and fabricate and test it within one day. PMID:27242064

  6. 3D electron microscopy of biological nanomachines: principles and applications.

    PubMed

    Sorzano, C O S; Jonic, S; Cottevieille, M; Larquet, E; Boisset, N; Marco, S

    2007-11-01

    Transmission electron microscopy is a powerful technique for studying the three-dimensional (3D) structure of a wide range of biological specimens. Knowledge of this structure is crucial for fully understanding complex relationships among macromolecular complexes and organelles in living cells. In this paper, we present the principles and main application domains of 3D transmission electron microscopy in structural biology. Moreover, we survey current developments needed in this field, and discuss the close relationship of 3D transmission electron microscopy with other experimental techniques aimed at obtaining structural and dynamical information from the scale of whole living cells to atomic structure of macromolecular complexes.

  7. Density-tapered spiral arrays for ultrasound 3-D imaging.

    PubMed

    Ramalli, Alessandro; Boni, Enrico; Savoia, Alessandro Stuart; Tortoli, Piero

    2015-08-01

    The current high interest in 3-D ultrasound imaging is pushing the development of 2-D probes with a challenging number of active elements. The most popular approach to limit this number is the sparse array technique, which designs the array layout by means of complex optimization algorithms. These algorithms are typically constrained by a few steering conditions, and, as such, cannot guarantee uniform side-lobe performance at all angles. The performance may be improved by the ungridded extensions of the sparse array technique, but this result is achieved at the expense of a further complication of the optimization process. In this paper, a method to design the layout of large circular arrays with a limited number of elements according to Fermat's spiral seeds and spatial density modulation is proposed and shown to be suitable for application to 3-D ultrasound imaging. This deterministic, aperiodic, and balanced positioning procedure attempts to guarantee uniform performance over a wide range of steering angles. The capabilities of the method are demonstrated by simulating and comparing the performance of spiral and dense arrays. A good trade-off for small vessel imaging is found, e.g., in the 60λ spiral array with 1.0λ elements and Blackman density tapering window. Here, the grating lobe level is -16 dB, the lateral resolution is lower than 6λ the depth of field is 120λ and, the average contrast is 10.3 dB, while the sensitivity remains in a 5 dB range for a wide selection of steering angles. The simulation results may represent a reference guide to the design of spiral sparse array probes for different application fields. PMID:26285181

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

    NASA Astrophysics Data System (ADS)

    Kramar, Maxim; Airapetian, Vladimir; Lin, Haosheng

    2016-08-01

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

  9. Correlated electron pseudopotentials for 3d-transition metals

    SciTech Connect

    Trail, J. R. Needs, R. J.

    2015-02-14

    A recently published correlated electron pseudopotentials (CEPPs) method has been adapted for application to the 3d-transition metals, and to include relativistic effects. New CEPPs are reported for the atoms Sc − Fe, constructed from atomic quantum chemical calculations that include an accurate description of correlated electrons. Dissociation energies, molecular geometries, and zero-point vibrational energies of small molecules are compared with all electron results, with all quantities evaluated using coupled cluster singles doubles and triples calculations. The CEPPs give better results in the correlated-electron calculations than Hartree-Fock-based pseudopotentials available in the literature.

  10. 3D magnetic inversion by planting anomalous densities

    NASA Astrophysics Data System (ADS)

    Uieda, L.; Barbosa, V. C.

    2013-05-01

    We present a new 3D magnetic inversion algorithm based on the computationally efficient method of planting anomalous densities. The algorithm consists of an iterative growth of the anomalous bodies around prismatic elements called "seeds". These seeds are user-specified and have known magnetizations. Thus, the seeds provide a way for the interpreter to specify the desired skeleton of the anomalous bodies. The inversion algorithm is computationally efficient due to various optimizations made possible by the iterative nature of the growth process. The control provided by the use of seeds allows one to test different hypothesis about the geometry and magnetization of targeted anomalous bodies. To demonstrate this capability, we applied our inversion method to the Morro do Engenho (ME) and A2 magnetic anomalies, central Brazil (Figure 1a). ME is an outcropping alkaline intrusion formed by dunites, peridotites and pyroxenites with known magnetization. A2 is a magnetic anomaly to the Northeast of ME and is thought to be a similar intrusion that is not outcropping. Therefore, a plausible hypothesis is that A2 has the same magnetization as ME. We tested this hypothesis by performing an inversion using a single seed for each body. Both seeds had the same magnetization. Figure 1b shows that the inversion produced residuals up to 2000 nT over A2 (i.e., a poor fit) and less than 400 nT over ME (i.e., an acceptable fit). Figure 1c shows that ME is a compact outcropping body with bottom at approximately 5 km, which is in agreement with previous interpretations. However, the estimate produced by the inversion for A2 is outcropping and is not compact. In summary, the estimate for A2 provides a poor fit to the observations and is not in accordance with the geologic information. This leads to the conclusion that A2 does not have the same magnetization as ME. These results indicate the usefulness and capabilities of the inversion method here proposed.; a) total field magnetic anomaly

  11. Boosting Power Density of Microbial Fuel Cells with 3D Nitrogen‐Doped Graphene Aerogel Electrode

    PubMed Central

    Yang, Yang; Liu, Tianyu; Zhang, Feng; Ye, Dingding; Liao, Qiang

    2016-01-01

    A 3D nitrogen‐doped graphene aerogel (N‐GA) as an anode material for microbial fuel cells (MFCs) is reported. Electron microscopy images reveal that the N‐GA possesses hierarchical porous structure that allows efficient diffusion of both bacterial cells and electron mediators in the interior space of 3D electrode, and thus, the colonization of bacterial communities. Electrochemical impedance spectroscopic measurements further show that nitrogen doping considerably reduces the charge transfer resistance and internal resistance of GA, which helps to enhance the MFC power density. Importantly, the dual‐chamber milliliter‐scale MFC with N‐GA anode yields an outstanding volumetric power density of 225 ± 12 W m−3 normalized to the total volume of the anodic chamber (750 ± 40 W m−3 normalized to the volume of the anode). These power densities are the highest values report for milliliter‐scale MFCs with similar chamber size (25 mL) under the similar measurement conditions. The 3D N‐GA electrode shows great promise for improving the power generation of MFC devices.

  12. Recent progress in printed 2/3D electronic devices

    NASA Astrophysics Data System (ADS)

    Klug, Andreas; Patter, Paul; Popovic, Karl; Blümel, Alexander; Sax, Stefan; Lenz, Martin; Glushko, Oleksandr; Cordill, Megan J.; List-Kratochvil, Emil J. W.

    2015-09-01

    New, energy-saving, efficient and cost-effective processing technologies such as 2D and 3D inkjet printing (IJP) for the production and integration of intelligent components will be opening up very interesting possibilities for industrial applications of molecular materials in the near future. Beyond the use of home and office based printers, "inkjet printing technology" allows for the additive structured deposition of photonic and electronic materials on a wide variety of substrates such as textiles, plastics, wood, stone, tiles or cardboard. Great interest also exists in applying IJP in industrial manufacturing such as the manufacturing of PCBs, of solar cells, printed organic electronics and medical products. In all these cases inkjet printing is a flexible (digital), additive, selective and cost-efficient material deposition method. Due to these advantages, there is the prospect that currently used standard patterning processes can be replaced through this innovative material deposition technique. A main issue in this research area is the formulation of novel functional inks or the adaptation of commercially available inks for specific industrial applications and/or processes. In this contribution we report on the design, realization and characterization of novel active and passive inkjet printed electronic devices including circuitry and sensors based on metal nanoparticle ink formulations and the heterogeneous integration into 2/3D printed demonstrators. The main emphasis of this paper will be on how to convert scientific inkjet knowledge into industrially relevant processes and applications.

  13. 3-D capacitance density imaging of fluidized bed

    DOEpatents

    Fasching, George E.

    1990-01-01

    A three-dimensional capacitance density imaging of a gasified bed or the like in a containment vessel is achieved using a plurality of electrodes provided circumferentially about the bed in levels and along the bed in channels. The electrodes are individually and selectively excited electrically at each level to produce a plurality of current flux field patterns generated in the bed at each level. The current flux field patterns are suitably sensed and a density pattern of the bed at each level determined. By combining the determined density patterns at each level, a three-dimensional density image of the bed is achieved.

  14. Hybrid additive manufacturing of 3D electronic systems

    NASA Astrophysics Data System (ADS)

    Li, J.; Wasley, T.; Nguyen, T. T.; Ta, V. D.; Shephard, J. D.; Stringer, J.; Smith, P.; Esenturk, E.; Connaughton, C.; Kay, R.

    2016-10-01

    A novel hybrid additive manufacturing (AM) technology combining digital light projection (DLP) stereolithography (SL) with 3D micro-dispensing alongside conventional surface mount packaging is presented in this work. This technology overcomes the inherent limitations of individual AM processes and integrates seamlessly with conventional packaging processes to enable the deposition of multiple materials. This facilitates the creation of bespoke end-use products with complex 3D geometry and multi-layer embedded electronic systems. Through a combination of four-point probe measurement and non-contact focus variation microscopy, it was identified that there was no obvious adverse effect of DLP SL embedding process on the electrical conductivity of printed conductors. The resistivity maintained to be less than 4  ×  10-4 Ω · cm before and after DLP SL embedding when cured at 100 °C for 1 h. The mechanical strength of SL specimens with thick polymerized layers was also identified through tensile testing. It was found that the polymerization thickness should be minimised (less than 2 mm) to maximise the bonding strength. As a demonstrator a polymer pyramid with embedded triple-layer 555 LED blinking circuitry was successfully fabricated to prove the technical viability.

  15. 3-D numerical evaluation of density effects on tracer tests.

    PubMed

    Beinhorn, M; Dietrich, P; Kolditz, O

    2005-12-01

    In this paper we present numerical simulations carried out to assess the importance of density-dependent flow on tracer plume development. The scenario considered in the study is characterized by a short-term tracer injection phase into a fully penetrating well and a natural hydraulic gradient. The scenario is thought to be typical for tracer tests conducted in the field. Using a reference case as a starting point, different model parameters were changed in order to determine their importance to density effects. The study is based on a three-dimensional model domain. Results were interpreted using concentration contours and a first moment analysis. Tracer injections of 0.036 kg per meter of saturated aquifer thickness do not cause significant density effects assuming hydraulic gradients of at least 0.1%. Higher tracer input masses, as used for geoelectrical investigations, may lead to buoyancy-induced flow in the early phase of a tracer test which in turn impacts further plume development. This also holds true for shallow aquifers. Results of simulations with different tracer injection rates and durations imply that the tracer input scenario has a negligible effect on density flow. Employing model cases with different realizations of a log conductivity random field, it could be shown that small variations of hydraulic conductivity in the vicinity of the tracer injection well have a major control on the local tracer distribution but do not mask effects of buoyancy-induced flow. PMID:16183165

  16. A generalized operational formula based on total electronic densities to obtain 3D pictures of the dual descriptor to reveal nucleophilic and electrophilic sites accurately on closed-shell molecules.

    PubMed

    Martínez-Araya, Jorge I

    2016-09-30

    By means of the conceptual density functional theory, the so-called dual descriptor (DD) has been adapted to be used in any closed-shell molecule that presents degeneracy in its frontier molecular orbitals. The latter is of paramount importance because a correct description of local reactivity will allow to predict the most favorable sites on a molecule to undergo nucleophilic or electrophilic attacks; on the contrary, an incomplete description of local reactivity might have serio us consequences, particularly for those experimental chemists that have the need of getting an insight about reactivity of chemical reagents before using them in synthesis to obtain a new compound. In the present work, the old approach based only on electronic densities of frontier molecular orbitals is replaced by the most accurate procedure that implies the use of total electronic densities thus keeping consistency with the essential principle of the DFT in which the electronic density is the fundamental variable and not the molecular orbitals. As a result of the present work, the DD will be able to properly describe local reactivities only in terms of total electronic densities. To test the proposed operational formula, 12 very common molecules were selected as the original definition of the DD was not able to describe their local reactivities properly. The ethylene molecule was additionally used to test the capability of the proposed operational formula to reveal a correct local reactivity even in absence of degeneracy in frontier molecular orbitals. © 2016 Wiley Periodicals, Inc. PMID:27443264

  17. Towards High Density 3-D Memory in Diamond

    NASA Astrophysics Data System (ADS)

    Henshaw, Jacob; Dhomkar, Siddharth; Meriles, Carlos; Jayakumar, Harishankar

    The nitrogen-vacancy (NV) center in diamond is presently the focus of widespread attention for applications ranging from quantum information processing to nanoscale metrology. Of great utility is the ability to optically initialize the NV charge state, which has an immediate impact on the center's light emission properties. Here, we use two-color microscopy in NV-rich, type-1b diamond to demonstrate fluorescence-encoded long-term storage of classical information. As a proof of principle, we write, reset, and rewrite various patterns with 2-D binary bit density comparable to present DVD-ROM technology. The strong fluorescence signal originating from the diffraction-limited bit volume allows us to transition from binary to multi-valued encoding, which translates into a significant storage capacity boost. Finally, we show that our technique preserves information written on different planes of the diamond crystal and thus serves as a platform for three-dimensional storage. Substantial enhancement in the bit density could be achieved with the aid of super resolution microscopy techniques already employed to discriminate between NVs with sub-diffraction, nanometer accuracy, a regime where the storage capacity could exceed 1017 bytes/cm3 We acknowledge support from the National Science Foundation through Grant NSF-1314205.

  18. Advanced prior modeling for 3D bright field electron tomography

    NASA Astrophysics Data System (ADS)

    Sreehari, Suhas; Venkatakrishnan, S. V.; Drummy, Lawrence F.; Simmons, Jeffrey P.; Bouman, Charles A.

    2015-03-01

    Many important imaging problems in material science involve reconstruction of images containing repetitive non-local structures. Model-based iterative reconstruction (MBIR) could in principle exploit such redundancies through the selection of a log prior probability term. However, in practice, determining such a log prior term that accounts for the similarity between distant structures in the image is quite challenging. Much progress has been made in the development of denoising algorithms like non-local means and BM3D, and these are known to successfully capture non-local redundancies in images. But the fact that these denoising operations are not explicitly formulated as cost functions makes it unclear as to how to incorporate them in the MBIR framework. In this paper, we formulate a solution to bright field electron tomography by augmenting the existing bright field MBIR method to incorporate any non-local denoising operator as a prior model. We accomplish this using a framework we call plug-and-play priors that decouples the log likelihood and the log prior probability terms in the MBIR cost function. We specifically use 3D non-local means (NLM) as the prior model in the plug-and-play framework, and showcase high quality tomographic reconstructions of a simulated aluminum spheres dataset, and two real datasets of aluminum spheres and ferritin structures. We observe that streak and smear artifacts are visibly suppressed, and that edges are preserved. Also, we report lower RMSE values compared to the conventional MBIR reconstruction using qGGMRF as the prior model.

  19. Calculation of the 3D density model of the Earth

    NASA Astrophysics Data System (ADS)

    Piskarev, A.; Butsenko, V.; Poselov, V.; Savin, V.

    2009-04-01

    The study of the Earth's crust is a part of investigation aimed at extension of the Russian Federation continental shelf in the Sea of Okhotsk Gathered data allow to consider the Sea of Okhotsk' area located outside the exclusive economic zone of the Russian Federation as the natural continuation of Russian territory. The Sea of Okhotsk is an Epi-Mesozoic platform with Pre-Cenozoic heterogeneous folded basement of polycyclic development and sediment cover mainly composed of Paleocene - Neocene - Quaternary deposits. Results of processing and complex interpretation of seismic, gravity, and aeromagnetic data along profile 2-DV-M, as well as analysis of available geological and geophysical information on the Sea of Okhotsk region, allowed to calculate of the Earth crust model. 4 layers stand out (bottom-up) in structure of the Earth crust: granulite-basic (density 2.90 g/cm3), granite-gneiss (limits of density 2.60-2.76 g/cm3), volcanogenic-sedimentary (2.45 g/cm3) and sedimentary (density 2.10 g/cm3). The last one is absent on the continent; it is observed only on the water area. Density of the upper mantle is taken as 3.30 g/cm3. The observed gravity anomalies are mostly related to the surface relief of the above mentioned layers or to the density variations of the granite-metamorphic basement. So outlining of the basement blocks of different constitution preceded to the modeling. This operation is executed after Double Fourier Spectrum analysis of the gravity and magnetic anomalies and following compilation of the synthetic anomaly maps, related to the basement density and magnetic heterogeneity. According to bathymetry data, the Sea of Okhotsk can be subdivided at three mega-blocks. Taking in consideration that central Sea of Okhotsk area is aseismatic, i.e. isostatic compensated, it is obvious that Earth crust structure of these three blocks is different. The South-Okhotsk depression is characteristics by 3200-3300 m of sea depths. Moho surface in this area is at

  20. Impact of Building Heights on 3d Urban Density Estimation from Spaceborne Stereo Imagery

    NASA Astrophysics Data System (ADS)

    Peng, Feifei; Gong, Jianya; Wang, Le; Wu, Huayi; Yang, Jiansi

    2016-06-01

    In urban planning and design applications, visualization of built up areas in three dimensions (3D) is critical for understanding building density, but the accurate building heights required for 3D density calculation are not always available. To solve this problem, spaceborne stereo imagery is often used to estimate building heights; however estimated building heights might include errors. These errors vary between local areas within a study area and related to the heights of the building themselves, distorting 3D density estimation. The impact of building height accuracy on 3D density estimation must be determined across and within a study area. In our research, accurate planar information from city authorities is used during 3D density estimation as reference data, to avoid the errors inherent to planar information extracted from remotely sensed imagery. Our experimental results show that underestimation of building heights is correlated to underestimation of the Floor Area Ratio (FAR). In local areas, experimental results show that land use blocks with low FAR values often have small errors due to small building height errors for low buildings in the blocks; and blocks with high FAR values often have large errors due to large building height errors for high buildings in the blocks. Our study reveals that the accuracy of 3D density estimated from spaceborne stereo imagery is correlated to heights of buildings in a scene; therefore building heights must be considered when spaceborne stereo imagery is used to estimate 3D density to improve precision.

  1. 3D Observation of GEMS by Electron Tomography

    NASA Technical Reports Server (NTRS)

    Matsuno, Junya; Miyake, Akira; Tsuchiyama, Akira; Nakamura-Messenger, Keiko; Messenger, Scott

    2014-01-01

    Amorphous silicates in chondritic porous interplanetary dust particles (CP-IDPs) coming from comets are dominated by glass with embedded metal and sulfides (GEMS). GEMS grains are submicron-sized rounded objects (typically 100-500) nm in diameter) with anaometer-sized (10-50 nm) Fe-Ni metal and sulfide grains embedded in an amorphous silicate matrix. Several formation processes for GEMS grains have been proposed so far, but these models are still being debated [2-5]. Bradley et al. proposed that GEMS grains are interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk and that they are amorphiation products of crystalline silicates in the interstellar medium by sputter-deposition of cosmic ray irradiation, similar to space weathering [2,4]. This consideration is based on the observation of nano-sized crystals (approximately 10 nm) called relict grains in GEMS grains and their shapes are pseudomorphs to the host GEMS grains. On the other hand, Keller and Messenger proposed that most GEMS formed in the protoplanetary disk as condensates from high temperature gas [3,5]. This model is based on the fact that most GEMS grains have solar isotopic compositions and have extremely heterogeneous and non-solar elemental compositions. Keller and Messenger (2011) also reported that amorphous silicates in GEMS grains are surrounded by sulfide grains, which formed as sulfidization of metallic iron grains located on the GEMS surface. The previous studies were performed with 2D observation by using transmission electron microscopy (TEM) or scanning TEM (STEM). In order to understand the structure of GEMS grains described above more clearly, we observed 3D structure of GEMS grains by electron tomography using a TEM/STEM (JEM-2100F, JEOL) at Kyoto University. Electron tomography gives not only 3D structures but also gives higher spatial resolution (approximately a few nm) than that in conventional 2D image, which is restricted by

  2. High power density microbial fuel cell with flexible 3D graphene-nickel foam as anode

    NASA Astrophysics Data System (ADS)

    Wang, Hanyu; Wang, Gongming; Ling, Yichuan; Qian, Fang; Song, Yang; Lu, Xihong; Chen, Shaowei; Tong, Yexiang; Li, Yat

    2013-10-01

    The structure and electrical conductivity of anode play a significant role in the power generation of microbial fuel cells (MFCs). In this study, we developed a three-dimensional (3D) reduced graphene oxide-nickel (denoted as rGO-Ni) foam as an anode for MFC through controlled deposition of rGO sheets onto the nickel foam substrate. The loading amount of rGO sheets and electrode surface area can be controlled by the number of rGO loading cycles. 3D rGO-Ni foam anode provides not only a large accessible surface area for microbial colonization and electron mediators, but also a uniform macro-porous scaffold for effective mass diffusion of the culture medium. Significantly, at a steady state of the power generation, the MFC device with flexible rGO-Ni electrodes produced an optimal volumetric power density of 661 W m-3 calculated based on the volume of anode material, or 27 W m-3 based on the volume of the anode chamber. These values are substantially higher than that of plain nickel foam, and other conventional carbon based electrodes (e.g., carbon cloth, carbon felt, and carbon paper) measured in the same conditions. To our knowledge, this is the highest volumetric power density reported for mL-scale MFC device with a pure strain of Shewanella oneidensis MR-1. We also demonstrated that the MFC device can be operated effectively in a batch-mode at least for a week. These new 3D rGO-Ni electrodes show great promise for improving the power generation of MFC devices.The structure and electrical conductivity of anode play a significant role in the power generation of microbial fuel cells (MFCs). In this study, we developed a three-dimensional (3D) reduced graphene oxide-nickel (denoted as rGO-Ni) foam as an anode for MFC through controlled deposition of rGO sheets onto the nickel foam substrate. The loading amount of rGO sheets and electrode surface area can be controlled by the number of rGO loading cycles. 3D rGO-Ni foam anode provides not only a large accessible

  3. 3D Printing: 3D Printing of Shape Memory Polymers for Flexible Electronic Devices (Adv. Mater. 22/2016).

    PubMed

    Zarek, Matt; Layani, Michael; Cooperstein, Ido; Sachyani, Ela; Cohn, Daniel; Magdassi, Shlomo

    2016-06-01

    On page 4449, D. Cohn, S. Magdassi, and co-workers describe a general and facile method based on 3D printing of methacrylated macromonomers to fabricate shape-memory objects that can be used in flexible and responsive electrical circuits. Such responsive objects can be used in the fabrication of soft robotics, minimal invasive medical devices, sensors, and wearable electronics. The use of 3D printing overcomes the poor processing characteristics of thermosets and enables complex geometries that are not easily accessible by other techniques. PMID:27273436

  4. 3D Printing: 3D Printing of Shape Memory Polymers for Flexible Electronic Devices (Adv. Mater. 22/2016).

    PubMed

    Zarek, Matt; Layani, Michael; Cooperstein, Ido; Sachyani, Ela; Cohn, Daniel; Magdassi, Shlomo

    2016-06-01

    On page 4449, D. Cohn, S. Magdassi, and co-workers describe a general and facile method based on 3D printing of methacrylated macromonomers to fabricate shape-memory objects that can be used in flexible and responsive electrical circuits. Such responsive objects can be used in the fabrication of soft robotics, minimal invasive medical devices, sensors, and wearable electronics. The use of 3D printing overcomes the poor processing characteristics of thermosets and enables complex geometries that are not easily accessible by other techniques.

  5. Robust evaluation of 3D electron cryomicroscopy data using tilt-pairs

    PubMed Central

    Russo, Christopher J.; Passmore, Lori A.

    2014-01-01

    Determining the structure of a protein complex using electron microscopy requires the calculation of a 3D density map from 2D images of single particles. Since the individual images are taken at low electron dose to avoid radiation damage, they are noisy and difficult to align with each other. This can result in incorrect maps, making validation essential. Pairs of electron micrographs taken at known angles to each other (tilt-pairs) can be used to measure the accuracy of assigned projection orientations and verify the soundness of calculated maps. Here we establish a statistical framework for evaluating images and density maps using tilt-pairs. The directional distribution of such angular data is modelled using a Fisher distribution on the unit sphere. This provides a simple, quantitative and easily comparable metric, the concentration parameter κ, for evaluating the quality of datasets and density maps that is independent of the data collection and analysis methods. A large κ is indicative of good agreement between the particle images and the 3D density map. For structure validation, we recommend κ>10 and a p-value <0.01. The statistical framework herein allows one to objectively answer the question: Is a reconstructed density map correct within a particular confidence interval? PMID:25016098

  6. High power density microbial fuel cell with flexible 3D graphene-nickel foam as anode.

    PubMed

    Wang, Hanyu; Wang, Gongming; Ling, Yichuan; Qian, Fang; Song, Yang; Lu, Xihong; Chen, Shaowei; Tong, Yexiang; Li, Yat

    2013-11-01

    The structure and electrical conductivity of anode play a significant role in the power generation of microbial fuel cells (MFCs). In this study, we developed a three-dimensional (3D) reduced graphene oxide-nickel (denoted as rGO-Ni) foam as an anode for MFC through controlled deposition of rGO sheets onto the nickel foam substrate. The loading amount of rGO sheets and electrode surface area can be controlled by the number of rGO loading cycles. 3D rGO-Ni foam anode provides not only a large accessible surface area for microbial colonization and electron mediators, but also a uniform macro-porous scaffold for effective mass diffusion of the culture medium. Significantly, at a steady state of the power generation, the MFC device with flexible rGO-Ni electrodes produced an optimal volumetric power density of 661 W m(-3) calculated based on the volume of anode material, or 27 W m(-3) based on the volume of the anode chamber. These values are substantially higher than that of plain nickel foam, and other conventional carbon based electrodes (e.g., carbon cloth, carbon felt, and carbon paper) measured in the same conditions. To our knowledge, this is the highest volumetric power density reported for mL-scale MFC device with a pure strain of Shewanella oneidensis MR-1. We also demonstrated that the MFC device can be operated effectively in a batch-mode at least for a week. These new 3D rGO-Ni electrodes show great promise for improving the power generation of MFC devices.

  7. Virtual rough samples to test 3D nanometer-scale scanning electron microscopy stereo photogrammetry

    NASA Astrophysics Data System (ADS)

    Villarrubia, J. S.; Tondare, V. N.; Vladár, A. E.

    2016-03-01

    The combination of scanning electron microscopy for high spatial resolution, images from multiple angles to provide 3D information, and commercially available stereo photogrammetry software for 3D reconstruction offers promise for nanometer-scale dimensional metrology in 3D. A method is described to test 3D photogrammetry software by the use of virtual samples—mathematical samples from which simulated images are made for use as inputs to the software under test. The virtual sample is constructed by wrapping a rough skin with any desired power spectral density around a smooth near-trapezoidal line with rounded top corners. Reconstruction is performed with images simulated from different angular viewpoints. The software's reconstructed 3D model is then compared to the known geometry of the virtual sample. Three commercial photogrammetry software packages were tested. Two of them produced results for line height and width that were within close to 1 nm of the correct values. All of the packages exhibited some difficulty in reconstructing details of the surface roughness.

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

    SciTech Connect

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

    2009-09-01

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

  9. Note: An improved 3D imaging system for electron-electron coincidence measurements

    SciTech Connect

    Lin, Yun Fei; Lee, Suk Kyoung; Adhikari, Pradip; Herath, Thushani; Lingenfelter, Steven; Winney, Alexander H.; Li, Wen

    2015-09-15

    We demonstrate an improved imaging system that can achieve highly efficient 3D detection of two electrons in coincidence. The imaging system is based on a fast frame complementary metal-oxide semiconductor camera and a high-speed waveform digitizer. We have shown previously that this detection system is capable of 3D detection of ions and electrons with good temporal and spatial resolution. Here, we show that with a new timing analysis algorithm, this system can achieve an unprecedented dead-time (<0.7 ns) and dead-space (<1 mm) when detecting two electrons. A true zero dead-time detection is also demonstrated.

  10. Note: An improved 3D imaging system for electron-electron coincidence measurements

    NASA Astrophysics Data System (ADS)

    Lin, Yun Fei; Lee, Suk Kyoung; Adhikari, Pradip; Herath, Thushani; Lingenfelter, Steven; Winney, Alexander H.; Li, Wen

    2015-09-01

    We demonstrate an improved imaging system that can achieve highly efficient 3D detection of two electrons in coincidence. The imaging system is based on a fast frame complementary metal-oxide semiconductor camera and a high-speed waveform digitizer. We have shown previously that this detection system is capable of 3D detection of ions and electrons with good temporal and spatial resolution. Here, we show that with a new timing analysis algorithm, this system can achieve an unprecedented dead-time (<0.7 ns) and dead-space (<1 mm) when detecting two electrons. A true zero dead-time detection is also demonstrated.

  11. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGES

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

  12. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.

  13. SU-C-213-06: Dosimetric Verification of 3D Printed Electron Bolus

    SciTech Connect

    Rasmussen, K; Corbett, M; Pelletier, C; Huang, Z; Feng, Y; Jung, J

    2015-06-15

    Purpose: To determine the dosimetric effect of 3D printed bolus in an anthropomorphic phantom. Methods: Conformable bolus material was generated for an anthropomorphic phantom from a DICOM volume. The bolus generated was a uniform expansion of 5mm applied to the nose region of the phantom, as this is a difficult area to uniformly apply bolus clinically. A Printrbot metal 3D Printer using PLA plastic generated the bolus. A 9MeV anterior beam with a 5cm cone was used to deliver dose to the nose of the phantom. TLD measurements were compared to predicted values at the phantom surface. Film planes were analyzed for the printed bolus, a standard 5mm bolus sheet placed on the phantom, and the phantom with no bolus applied to determine depth and dose distributions. Results: TLDs measured within 2.5% of predicted value for the 3D bolus. Film demonstrated a more uniform dose distribution in the nostril region for the 3d printed bolus than the standard bolus. This difference is caused by the air gap created around the nostrils by the standard bolus, creating a secondary build-up region. Both demonstrated a 50% central axis dose shift of 5mm relative to the no bolus film. HU for the bolus calculated the PLA electron density to be ∼1.1g/cc. Physical density was measured to be 1.3g/cc overall. Conclusion: 3D printed PLA bolus demonstrates improved dosimetric performance to standard bolus for electron beams with complex phantom geometry.

  14. Exploring the surface reactivity of 3d metal endofullerenes: a density-functional theory study.

    PubMed

    Estrada-Salas, Rubén E; Valladares, Ariel A

    2009-09-24

    Changes in the preferential sites of electrophilic, nucleophilic, and radical attacks on the pristine C60 surface with endohedral doping using 3d transition metal atoms were studied via two useful reactivity indices, namely the Fukui functions and the molecular electrostatic potential. Both of these were calculated at the density functional BPW91 level of theory with the DNP basis set. Our results clearly show changes in the preferential reactivity sites on the fullerene surface when it is doped with Mn, Fe, Co, or Ni atoms, whereas there are no significant changes in the preferential reactivity sites on the C60 surface upon endohedral doping with Cu and Zn atoms. Electron affinities (EA), ionization potentials (IP), and HOMO-LUMO gaps (Eg) were also calculated to complete the study of the endofullerene's surface reactivity. These findings provide insight into endofullerene functionalization, an important issue in their application.

  15. 3-D simulations of magnetic reconnection in high-energy-density laser-produced plasmas

    NASA Astrophysics Data System (ADS)

    Fox, W.; Bhattacharjee, A.; Germaschewski, K.

    2012-10-01

    Magnetic reconnection has recently been observed and studied in high-energy-density, laser-produced plasmas, in a regime characterized by extremely high magnetic fields, high plasma beta and strong, supersonic plasma inflow. These experiments are interesting both for obtaining fundamental data on reconnection, and may also be relevant for inertial fusion, as this magnetic reconnection geometry, with multiple, colliding, magnetized plasma bubbles occurs naturally inside ICF hohlraums. Previous 2-d particle-in-cell reconnection simulations, with parameters and geometry relevant to the experiments, identified key ingredients for obtaining the very fast reconnection rates, namely two-fluid reconnection mediated by collisionless effects (the Hall current and electron pressure tensor), and strong flux pile-up of the inflowing magnetic field [1]. We present results from extending the previous simulations to 3-d, and discuss 3-d effects in the experiments, including instabilities in the reconnection layer, the topological skeleton of null-null lines, and field-generation from the Biermann battery effect. [4pt] [1] W. Fox, A. Bhattacharjee, and K. Germaschewski, PRL 106, 215003 (2011).

  16. 3D high-density localization microscopy using hybrid astigmatic/ biplane imaging and sparse image reconstruction.

    PubMed

    Min, Junhong; Holden, Seamus J; Carlini, Lina; Unser, Michael; Manley, Suliana; Ye, Jong Chul

    2014-11-01

    Localization microscopy achieves nanoscale spatial resolution by iterative localization of sparsely activated molecules, which generally leads to a long acquisition time. By implementing advanced algorithms to treat overlapping point spread functions (PSFs), imaging of densely activated molecules can improve the limited temporal resolution, as has been well demonstrated in two-dimensional imaging. However, three-dimensional (3D) localization of high-density data remains challenging since PSFs are far more similar along the axial dimension than the lateral dimensions. Here, we present a new, high-density 3D imaging system and algorithm. The hybrid system is implemented by combining astigmatic and biplane imaging. The proposed 3D reconstruction algorithm is extended from our state-of-the art 2D high-density localization algorithm. Using mutual coherence analysis of model PSFs, we validated that the hybrid system is more suitable than astigmatic or biplane imaging alone for 3D localization of high-density data. The efficacy of the proposed method was confirmed via simulation and real data of microtubules. Furthermore, we also successfully demonstrated fluorescent-protein-based live cell 3D localization microscopy with a temporal resolution of just 3 seconds, capturing fast dynamics of the endoplasmic recticulum.

  17. Electron enrichment in 3d transition metal oxide hetero-nanostructures.

    PubMed

    Kronawitter, Coleman X; Bakke, Jonathan R; Wheeler, Damon A; Wang, Wei-Cheng; Chang, Chinglin; Antoun, Bonnie R; Zhang, Jin Z; Guo, Jinghua; Bent, Stacey F; Mao, Samuel S; Vayssieres, Lionel

    2011-09-14

    Direct experimental observation of spontaneous electron enrichment of metal d orbitals in a new transition metal oxide heterostructure with nanoscale dimensionality is reported. Aqueous chemical synthesis and vapor phase deposition are combined to fabricate oriented arrays of high-interfacial-area hetero-nanostructures comprised of titanium oxide and iron oxide nanomaterials. Synchrotron-based soft X-ray spectroscopy techniques with high spectral resolution are utilized to directly probe the titanium and oxygen orbital character of the interfacial region's occupied and unoccupied densities of states. These data demonstrate the interface to possess electrons in Ti 3d bands and an emergent degree of orbital hybridization that is absent in parent oxide reference crystals. The carrier dynamics of the hetero-nanostructures are studied by ultrafast transient absorption spectroscopy, which reveals the presence of a dense manifold of states, the relaxations from which exhibit multiple exponential decays whose magnitudes depend on their energetic positions within the electronic structure.

  18. Hot deformation characterization of duplex low-density steel through 3D processing map development

    SciTech Connect

    Mohamadizadeh, A.; Zarei-Hanzaki, A.; Abedi, H.R.; Mehtonen, S.; Porter, D.

    2015-09-15

    The high temperature deformation behavior of duplex low-density Fe–18Mn–8Al–0.8C steel was investigated at temperatures in the range of 600–1000 °C. The primary constitutive analysis indicated that the Zener–Hollomon parameter, which represents the coupled effects of temperature and strain rate, significantly varies with the amount of deformation. Accordingly, the 3D processing maps were developed considering the effect of strain and were used to determine the safe and unsafe deformation conditions in association with the microstructural evolution. The deformation at efficiency domain I (900–1100 °C\\10{sup −} {sup 2}–10{sup −} {sup 3} s{sup −} {sup 1}) was found to be safe at different strains due to the occurrence of dynamic recrystallization in austenite. The safe efficiency domain II (700–900 °C\\1–10{sup −} {sup 1} s{sup −} {sup 1}), which appeared at logarithmic strain of 0.4, was characterized by deformation induced ferrite formation. Scanning electron microscopy revealed that the microband formation and crack initiation at ferrite\\austenite interphases were the main causes of deformation instability at 600–800 °C\\10{sup −} {sup 2}–10{sup −} {sup 3} s{sup −} {sup 1}. The degree of instability was found to decrease by increasing the strain due to the uniformity of microbanded structure obtained at higher strains. The shear band formation at 900–1100 °C\\1–10{sup −} {sup 1} s{sup −} {sup 1} was verified by electron backscattered diffraction. The local dynamic recrystallization of austenite and the deformation induced ferrite formation were observed within shear-banded regions as the results of flow localization. - Graphical abstract: Display Omitted - Highlights: • The 3D processing map is developed for duplex low-density Fe–Mn–Al–C steel. • The efficiency domains shrink, expand or appear with increasing strain. • The occurrence of DRX and DIFF increases the power efficiency. • Crack initiation

  19. The 3d International Workshop on Computational Electronics

    NASA Astrophysics Data System (ADS)

    Goodnick, Stephen M.

    1994-09-01

    The Third International Workshop on Computational Electronics (IWCE) was held at the Benson Hotel in downtown Portland, Oregon, on May 18, 19, and 20, 1994. The workshop was devoted to a broad range of topics in computational electronics related to the simulation of electronic transport in semiconductors and semiconductor devices, particularly those which use large computational resources. The workshop was supported by the National Science Foundation (NSF), the Office of Naval Research and the Army Research Office, as well as local support from the Oregon Joint Graduate Schools of Engineering and the Oregon Center for Advanced Technology Education. There were over 100 participants in the Portland workshop, of which more than one quarter represented research groups outside of the United States from Austria, Canada, France, Germany, Italy, Japan, Switzerland, and the United Kingdom. There were a total 81 papers presented at the workshop, 9 invited talks, 26 oral presentations and 46 poster presentations. The emphasis of the contributions reflected the interdisciplinary nature of computational electronics with researchers from the Chemistry, Computer Science, Mathematics, Engineering, and Physics communities participating in the workshop.

  20. Effect of density gradients in confined supersonic shear layers. Part 2: 3-D modes

    NASA Technical Reports Server (NTRS)

    Peroomian, Oshin; Kelly, R. E.

    1994-01-01

    The effect of basic flow density gradients on the supersonic wall modes were investigated in Part 1 of this analysis. In that investigation only the 2-D modes were studied. Tam and Hu investigated the 3-D modes in a confined vortex sheet and reported that the first 2-D Class A mode (A01) had the highest growth rate compared to all other 2-D and 3-D modes present in the vortex sheet for that particular set of flow patterns. They also showed that this result also held true for finite thickness shear layers with delta(sub w) less than 0.125. For free shear layers, Sandham and Reynolds showed that the 3-D K-H mode became the dominant mode for M(sub c) greater than 0.6. Jackson and Grosch investigated the effect of crossflow and obliqueness on the slow and fast odes present in a M(sub c) greater than 1 environment and showed that for certain combination of crossflow and wave angles the growth rates could be increased by up to a factor of 2 with respect to the 2-D case. The case studied here is a confined shear layer shown in Part 1. All solution procedures and basic low profiles are the same as in Part 1. The effect of density gradients on the 3-D modes present in the density ratios considered in Part 1 are investigated.

  1. 3D imaging of sea quarks and gluons at an electron-ion collider

    SciTech Connect

    Vadim Guzey

    2011-11-01

    We outline key objectives and capabilities of an Electron-Ion Collider (EIC) — a high-energy and high-luminosity electron-proton/nucleus collider with polarized electron and proton beams. One of goals of a future EIC is to map the 3D (in configuration and momentum spaces) structure of sea quarks and gluons in the nucleon and nuclei. We briefly present and discuss key observables and measurements pertaining to the program of 3D imaging at an EIC.

  2. 3D printed elastic honeycombs with graded density for tailorable energy absorption

    NASA Astrophysics Data System (ADS)

    Bates, Simon R. G.; Farrow, Ian R.; Trask, Richard S.

    2016-04-01

    This work describes the development and experimental analysis of hyperelastic honeycombs with graded densities, for the purpose of energy absorption. Hexagonal arrays are manufactured from thermoplastic polyurethane (TPU) via fused filament fabrication (FFF) 3D printing and the density graded by varying cell wall thickness though the structures. Manufactured samples are subject to static compression tests and their energy absorbing potential analysed via the formation of energy absorption diagrams. It is shown that by grading the density through the structure, the energy absorption profile of these structures can be manipulated such that a wide range of compression energies can be efficiently absorbed.

  3. Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.

    PubMed

    Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

    2015-03-17

    Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.

  4. Electron crystallography of ultrathin 3D protein crystals: Atomic model with charges

    PubMed Central

    Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

    2015-01-01

    Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca2+-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca2+-binding sites of Ca2+-ATPase and that of the iron atom in the heme in catalase. PMID:25730881

  5. Breast density measurement: 3D cone beam computed tomography (CBCT) images versus 2D digital mammograms

    NASA Astrophysics Data System (ADS)

    Han, Tao; Lai, Chao-Jen; Chen, Lingyun; Liu, Xinming; Shen, Youtao; Zhong, Yuncheng; Ge, Shuaiping; Yi, Ying; Wang, Tianpeng; Yang, Wei T.; Shaw, Chris C.

    2009-02-01

    Breast density has been recognized as one of the major risk factors for breast cancer. However, breast density is currently estimated using mammograms which are intrinsically 2D in nature and cannot accurately represent the real breast anatomy. In this study, a novel technique for measuring breast density based on the segmentation of 3D cone beam CT (CBCT) images was developed and the results were compared to those obtained from 2D digital mammograms. 16 mastectomy breast specimens were imaged with a bench top flat-panel based CBCT system. The reconstructed 3D CT images were corrected for the cupping artifacts and then filtered to reduce the noise level, followed by using threshold-based segmentation to separate the dense tissue from the adipose tissue. For each breast specimen, volumes of the dense tissue structures and the entire breast were computed and used to calculate the volumetric breast density. BI-RADS categories were derived from the measured breast densities and compared with those estimated from conventional digital mammograms. The results show that in 10 of 16 cases the BI-RADS categories derived from the CBCT images were lower than those derived from the mammograms by one category. Thus, breasts considered as dense in mammographic examinations may not be considered as dense with the CBCT images. This result indicates that the relation between breast cancer risk and true (volumetric) breast density needs to be further investigated.

  6. RESEARCH NOTE: Empirical 3-D basis for the internal density of a planet

    NASA Astrophysics Data System (ADS)

    Chambat, Frédéric; Ricard, Yanick

    2005-07-01

    Various papers have discussed the forward relationships between internal density anomalies of a planet and its external gravity field. The inverse modelling, i.e. finding the internal density anomalies from the external potential is known to be highly non-unique. In this research note, we explain how a 3-D basis can be built to represent the internal density variations that includes a subset that explicitly spans the kernel of the forward gravity operator. This representation clarifies the origin of the non-uniqueness of the gravity sources and implies the existence of a natural minimal norm inverse for the internal density. We illustrate these ideas by comparing a tomographic model of the mantle to the minimal norm density.

  7. Dynamic analysis of radial force density in brushless DC motor using 3-D equivalent magnetic circuit network method

    SciTech Connect

    Hur, J.; Chun, Y.D.; Lee, J.; Hyun, D.S.

    1998-09-01

    The distribution of radial force density in brushless permanent magnet DC motor is not uniform in axial direction. The analysis of radial force density has to consider the 3-D shape of teeth and overhand, because the radial force density causes vibration and acts on the surface of teeth inconstantly. For the analysis, a new 3-D equivalent magnetic circuit network method is used to account the rotor movement without remesh. The radial force density is calculated and analyzed by Maxwell stress tensor and discrete Fourier transform (DFT) respectively. The results of 3-D equivalent magnetic circuit method have been compared with the results of 3-D FEM.

  8. 3D hybrid simulations with gyrokinetic particle ions and fluid electrons

    SciTech Connect

    Belova, E.V.; Park, W.; Fu, G.Y.; Strauss, H.R.; Sugiyama, L.E.

    1998-12-31

    The previous hybrid MHD/particle model (MH3D-K code) represented energetic ions as gyrokinetic (or drift-kinetic) particles coupled to MHD equations using the pressure or current coupling scheme. A small energetic to bulk ion density ratio was assumed, n{sub h}/n{sub b} {much_lt} 1, allowing the neglect of the energetic ion perpendicular inertia in the momentum equation and the use of MHD Ohm`s law E = {minus}v{sub b} {times} B. A generalization of this model in which all ions are treated as gyrokinetic/drift-kinetic particles and fluid description is used for the electron dynamics is considered in this paper.

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

    NASA Astrophysics Data System (ADS)

    Lin, He; Duan, Haiming

    2008-05-01

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

  10. 3D model of small-scale density cavities in the auroral magnetosphere with field-aligned current

    NASA Astrophysics Data System (ADS)

    Bespalov, P. A.; Misonova, V. G.; Savina, O. N.

    2016-09-01

    We propose a 3D model of small-scale density cavities stimulated by an auroral field-aligned current and an oscillating field-aligned current of kinetic Alfvén waves. It is shown that when the field-aligned current increases so that the electron drift velocity exceeds a value of the order of the electron thermal velocity, the plasma becomes unstable to the formation of cavities with low density and strong electric field. The condition of instability is associated with the value of the background magnetic field. In the case of a relatively weak magnetic field (where the electron gyro-radius is greater than the ion acoustic wavelength), the current instability can lead to the formation of one-dimensional cavities along the magnetic field. In the case of a stronger magnetic field (where the ion acoustic wavelength is greater than the electron gyro-radius, but still is less than the ion gyro-radius), the instability can lead to the formation of 3D density cavities. In this case, the spatial scales of the cavity, both along and across the background magnetic field, can be comparable, and at the earlier stage of the cavity formation they are of the order of the ion acoustic wavelength. Rarefactions of the cavity density are accompanied by an increase in the electric field and are limited by the pressure of bipolar electric fields that occur within them. The estimates of typical density cavity characteristics and the results of numerical solutions agree with known experimental data: small-scale structures with a sufficiently strong electric field are observed in the auroral regions with strong field-aligned current.

  11. 3D electromagnetic simulation of spatial autoresonance acceleration of electron beams

    NASA Astrophysics Data System (ADS)

    Dugar-Zhabon, V. D.; González, J. D.; Orozco, E. A.

    2016-02-01

    The results of full electromagnetic simulations of the electron beam acceleration by a TE 112 linear polarized electromagnetic field through Space Autoresonance Acceleration mechanism are presented. In the simulations, both the self-sustaned electric field and selfsustained magnetic field produced by the beam electrons are included into the elaborated 3D Particle in Cell code. In this system, the space profile of the magnetostatic field maintains the electron beams in the acceleration regime along their trajectories. The beam current density evolution is calculated applying the charge conservation method. The full magnetic field in the superparticle positions is found by employing the trilinear interpolation of the mesh node data. The relativistic Newton-Lorentz equation presented in the centered finite difference form is solved using the Boris algorithm that provides visualization of the beam electrons pathway and energy evolution. A comparison between the data obtained from the full electromagnetic simulations and the results derived from the motion equation depicted in an electrostatic approximation is carried out. It is found that the self-sustained magnetic field is a factor which improves the resonance phase conditions and reduces the beam energy spread.

  12. FERM3D: A finite element R-matrix electron molecule scattering code

    NASA Astrophysics Data System (ADS)

    Tonzani, Stefano

    2007-01-01

    FERM3D is a three-dimensional finite element program, for the elastic scattering of a low energy electron from a general polyatomic molecule, which is converted to a potential scattering problem. The code is based on tricubic polynomials in spherical coordinates. The electron-molecule interaction is treated as a sum of three terms: electrostatic, exchange, and polarization. The electrostatic term can be extracted directly from ab initio codes ( GAUSSIAN 98 in the work described here), while the exchange term is approximated using a local density functional. A local polarization potential based on density functional theory [C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37 (1988) 785] describes the long range attraction to the molecular target induced by the scattering electron. Photoionization calculations are also possible and illustrated in the present work. The generality and simplicity of the approach is important in extending electron-scattering calculations to more complex targets than it is possible with other methods. Program summaryTitle of program:FERM3D Catalogue identifier:ADYL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYL_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested:Intel Xeon, AMD Opteron 64 bit, Compaq Alpha Operating systems or monitors under which the program has been tested:HP Tru64 Unix v5.1, Red Hat Linux Enterprise 3 Programming language used:Fortran 90 Memory required to execute with typical data:900 MB (neutral CO 2), 2.3 GB (ionic CO 2), 1.4 GB (benzene) No. of bits in a word:32 No. of processors used:1 Has the code been vectorized?:No No. of lines in distributed program, including test data, etc.:58 383 No. of bytes in distributed program, including test data, etc.:561 653 Distribution format:tar.gzip file CPC Program library subprograms used:ADDA, ACDP Nature of physical problem:Scattering of an

  13. Angular distribution of Auger electrons due to 3d-shell impact ionization of krypton

    NASA Technical Reports Server (NTRS)

    Omidvar, K.

    1977-01-01

    Cross sections for electron impact ionization of krypton due to ejection of a 3d-shell electron have been calculated using screened hydrogenic and Hartree-Slater wavefunctions for the target atom. While the total ionization cross sections in the two approximations are within 10% of each other, the Auger electron angular distribution, related to cross sections for specific magnetic quantum numbers of the 3d electrons, are widely different in the two approximations. The angular distribution due to the Hartree-Slater approximation is in excellent agreement with measurement. The physical reason for the discrepancies in the two approximations is explained.

  14. 3D density imaging with muons flux measurements from underground galleries

    NASA Astrophysics Data System (ADS)

    Lesparre, Nolwenn; Cabrera, Justo; Marteau, Jacques

    2016-04-01

    Atmospheric muons flux measurements provide information on sub-surface density distribution, giving insights on the medium structure. We measured the muons flux from the underground galleries of the Tournemire experimental platform to image the medium between the galleries and the surface. The experiment aimed at evaluating the capacity of the method to detect the presence of discontinuities produced either by secondary strike-slip faults that present small vertical displacements or by a karstic network may be present at the level of an upper aquifer. Measurements were performed from three different sites so the trajectories of detected muons paths intersect in the medium. Such a configuration provided complementary information on the density distribution, offering the possibility to seek density variations at different depths. A specific calibration method was applied in order to interpolate the data acquired at different times with the same muons sensor. Muons flux measurements variations were then processed through a non-linear inversion, producing a 3D image of the density together with an evaluation of the different distinguished targets reliability. The density distribution showed the presence of a very low density region at the level of the upper aquifer, suggesting the presence of a karstic network hosting locally cavities. The trace of secondary strike-slip faults did not appear clearly on the image as the density contrast they produce might be too low compared to the signal to noise ratio present in the muons flux data. We propose different strategies to improve the density image accuracy.

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

    SciTech Connect

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

    2012-04-25

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

  16. High Efficiency, Low Distortion 3D Diffusion Tensor Imaging with Variable Density Spiral Fast Spin Echoes (3D DW VDS RARE)

    PubMed Central

    Frank, Lawrence R.; Jung, Youngkyoo; Inati, Souheil; Tyszka, J. Michael; Wong, Eric C.

    2009-01-01

    We present an acquisition and reconstruction method designed to acquire high resolution 3D fast spin echo diffusion tensor images while mitigating the major sources of artifacts in DTI - field distortions, eddy currents and motion. The resulting images, being 3D, are of high SNR, and being fast spin echoes, exhibit greatly reduced field distortions. This sequence utilizes variable density spiral acquisition gradients, which allow for the implementation of a self-navigation scheme by which both eddy current and motion artifacts are removed. The result is that high resolution 3D DTI images are produced without the need for eddy current compensating gradients or B0 field correction. In addition, a novel method for fast and accurate reconstruction of the non-Cartesian data is employed. Results are demonstrated in the brains of normal human volunteers. PMID:19778618

  17. Three-dimensional electronic unpacking of packed bags using 3-D CT images

    NASA Astrophysics Data System (ADS)

    Song, Samuel M.; Crawford, Carl R.; Boyd, Douglas P.

    2009-02-01

    We present a 3-D electronic unpacking technique for airport security images based on volume rendering techniques developed for medical applications. Two electronic unpacking techniques are presented: (1) object-based unpacking and (2) unpacking by bag-slicing. Both techniques provide photo-realistic 3-D views of contents inside a packed bag with clearly marked threats. For the object-based unpacking, the 3-D objects within packed bags are unpacked (or isolated) though object selection tools that cut away undesired regions to isolates the 3-D object from the background clutter. With this selection tool, the operator is able to electronically unpack various 3-D objects and manipulate (rotate and zoom) the 3-D photo-realistic views for the immediate classification of the suspect object. The unpacking by bag-slicing technique places arbitrary cut planes to show the content beyond the cut plane that can be stepped forward or backward electronically. The methods may be used to reduce the need for manual unpacking of suitcases.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

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

    2015-07-17

    Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale. PMID:26185247

  20. 3D structure of individual nanocrystals in solution by electron microscopy

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  1. 3D Modeling Activity for Novel High Power Electron Guns at SLAC

    SciTech Connect

    Krasnykh, Anatoly

    2003-07-29

    The next generation of powerful electronic devices requires new approaches to overcome the known limitations of existing tube technology. Multi-beam and sheet beam approaches are novel concepts for the high power microwave devices. Direct and indirect modeling methods are being developed at SLAC to meet the new requirements in the 3D modeling. The direct method of solving of Poisson's equations for the multi-beam and sheet beam guns is employed in the TOPAZ 3D tool. The combination of TOPAZ 2D and EGUN (in the beginning) with MAFIA 3D and MAGIC 3D (at the end) is used in an indirect method to model the high power electron guns. Both methods complement each other to get reliable representation of the beam trajectories. Several gun ideas are under consideration at the present time. The collected results of these simulations are discussed.

  2. Analysis of the 3D distribution of stacked self-assembled quantum dots by electron tomography

    PubMed Central

    2012-01-01

    The 3D distribution of self-assembled stacked quantum dots (QDs) is a key parameter to obtain the highest performance in a variety of optoelectronic devices. In this work, we have measured this distribution in 3D using a combined procedure of needle-shaped specimen preparation and electron tomography. We show that conventional 2D measurements of the distribution of QDs are not reliable, and only 3D analysis allows an accurate correlation between the growth design and the structural characteristics. PMID:23249477

  3. High-Resolution Variable-Density 3D Cones Coronary MRA

    PubMed Central

    Addy, Nii Okai; Ingle, R. Reeve; Wu, Holden H.; Hu, Bob S.; Nishimura, Dwight G.

    2015-01-01

    Purpose To improve the spatial/temporal resolution of whole-heart coronary MR angiography (CMRA) by developing a variable-density (VD) 3D cones acquisition suitable for image reconstruction with parallel imaging and compressed sensing techniques. Methods A VD 3D cones trajectory design incorporates both radial and spiral trajectory undersampling techniques to achieve higher resolution. This design is used to generate a VD cones trajectory with 0.8 mm/66 ms isotropic spatial/temporal resolution, using a similar number of readouts as our previous fully sampled cones trajectory (1.2 mm/100 ms). Scans of volunteers and patients are performed to evaluate the performance of the VD trajectory, using non-Cartesian L1-ESPIRiT for high-resolution image reconstruction. Results With gridding reconstruction, the high-resolution scans experience an expected drop in signal-to-noise and contrast-to-noise ratios, but with L1-ESPIRiT, the apparent noise is substantially reduced. Compared to 1.2 mm images, in each volunteer, the L1-ESPIRiT 0.8 mm images exhibit higher vessel sharpness values in the right and left anterior descending arteries. Conclusion CMRA with isotropic sub-millimeter spatial resolution and high temporal resolution can be performed with VD 3D cones to improve the depiction of coronary arteries. PMID:26172829

  4. Efficient 3D movement-based kernel density estimator and application to wildlife ecology

    USGS Publications Warehouse

    Tracey-PR, Jeff; Sheppard, James K.; Lockwood, Glenn K.; Chourasia, Amit; Tatineni, Mahidhar; Fisher, Robert N.; Sinkovits, Robert S.

    2014-01-01

    We describe an efficient implementation of a 3D movement-based kernel density estimator for determining animal space use from discrete GPS measurements. This new method provides more accurate results, particularly for species that make large excursions in the vertical dimension. The downside of this approach is that it is much more computationally expensive than simpler, lower-dimensional models. Through a combination of code restructuring, parallelization and performance optimization, we were able to reduce the time to solution by up to a factor of 1000x, thereby greatly improving the applicability of the method.

  5. A simple, low-cost conductive composite material for 3D printing of electronic sensors.

    PubMed

    Leigh, Simon J; Bradley, Robert J; Purssell, Christopher P; Billson, Duncan R; Hutchins, David A

    2012-01-01

    3D printing technology can produce complex objects directly from computer aided digital designs. The technology has traditionally been used by large companies to produce fit and form concept prototypes ('rapid prototyping') before production. In recent years however there has been a move to adopt the technology as full-scale manufacturing solution. The advent of low-cost, desktop 3D printers such as the RepRap and Fab@Home has meant a wider user base are now able to have access to desktop manufacturing platforms enabling them to produce highly customised products for personal use and sale. This uptake in usage has been coupled with a demand for printing technology and materials able to print functional elements such as electronic sensors. Here we present formulation of a simple conductive thermoplastic composite we term 'carbomorph' and demonstrate how it can be used in an unmodified low-cost 3D printer to print electronic sensors able to sense mechanical flexing and capacitance changes. We show how this capability can be used to produce custom sensing devices and user interface devices along with printed objects with embedded sensing capability. This advance in low-cost 3D printing with offer a new paradigm in the 3D printing field with printed sensors and electronics embedded inside 3D printed objects in a single build process without requiring complex or expensive materials incorporating additives such as carbon nanotubes. PMID:23185319

  6. A simple, low-cost conductive composite material for 3D printing of electronic sensors.

    PubMed

    Leigh, Simon J; Bradley, Robert J; Purssell, Christopher P; Billson, Duncan R; Hutchins, David A

    2012-01-01

    3D printing technology can produce complex objects directly from computer aided digital designs. The technology has traditionally been used by large companies to produce fit and form concept prototypes ('rapid prototyping') before production. In recent years however there has been a move to adopt the technology as full-scale manufacturing solution. The advent of low-cost, desktop 3D printers such as the RepRap and Fab@Home has meant a wider user base are now able to have access to desktop manufacturing platforms enabling them to produce highly customised products for personal use and sale. This uptake in usage has been coupled with a demand for printing technology and materials able to print functional elements such as electronic sensors. Here we present formulation of a simple conductive thermoplastic composite we term 'carbomorph' and demonstrate how it can be used in an unmodified low-cost 3D printer to print electronic sensors able to sense mechanical flexing and capacitance changes. We show how this capability can be used to produce custom sensing devices and user interface devices along with printed objects with embedded sensing capability. This advance in low-cost 3D printing with offer a new paradigm in the 3D printing field with printed sensors and electronics embedded inside 3D printed objects in a single build process without requiring complex or expensive materials incorporating additives such as carbon nanotubes.

  7. A Simple, Low-Cost Conductive Composite Material for 3D Printing of Electronic Sensors

    PubMed Central

    Leigh, Simon J.; Bradley, Robert J.; Purssell, Christopher P.; Billson, Duncan R.; Hutchins, David A.

    2012-01-01

    3D printing technology can produce complex objects directly from computer aided digital designs. The technology has traditionally been used by large companies to produce fit and form concept prototypes (‘rapid prototyping’) before production. In recent years however there has been a move to adopt the technology as full-scale manufacturing solution. The advent of low-cost, desktop 3D printers such as the RepRap and Fab@Home has meant a wider user base are now able to have access to desktop manufacturing platforms enabling them to produce highly customised products for personal use and sale. This uptake in usage has been coupled with a demand for printing technology and materials able to print functional elements such as electronic sensors. Here we present formulation of a simple conductive thermoplastic composite we term ‘carbomorph’ and demonstrate how it can be used in an unmodified low-cost 3D printer to print electronic sensors able to sense mechanical flexing and capacitance changes. We show how this capability can be used to produce custom sensing devices and user interface devices along with printed objects with embedded sensing capability. This advance in low-cost 3D printing with offer a new paradigm in the 3D printing field with printed sensors and electronics embedded inside 3D printed objects in a single build process without requiring complex or expensive materials incorporating additives such as carbon nanotubes. PMID:23185319

  8. High-purity 3D nano-objects grown by focused-electron-beam induced deposition

    NASA Astrophysics Data System (ADS)

    Córdoba, Rosa; Sharma, Nidhi; Kölling, Sebastian; Koenraad, Paul M.; Koopmans, Bert

    2016-09-01

    To increase the efficiency of current electronics, a specific challenge for the next generation of memory, sensing and logic devices is to find suitable strategies to move from two- to three-dimensional (3D) architectures. However, the creation of real 3D nano-objects is not trivial. Emerging non-conventional nanofabrication tools are required for this purpose. One attractive method is focused-electron-beam induced deposition (FEBID), a direct-write process of 3D nano-objects. Here, we grow 3D iron and cobalt nanopillars by FEBID using diiron nonacarbonyl Fe2(CO)9, and dicobalt octacarbonyl Co2(CO)8, respectively, as starting materials. In addition, we systematically study the composition of these nanopillars at the sub-nanometer scale by atom probe tomography, explicitly mapping the homogeneity of the radial and longitudinal composition distributions. We show a way of fabricating high-purity 3D vertical nanostructures of ∼50 nm in diameter and a few micrometers in length. Our results suggest that the purity of such 3D nanoelements (above 90 at% Fe and above 95 at% Co) is directly linked to their growth regime, in which the selected deposition conditions are crucial for the final quality of the nanostructure. Moreover, we demonstrate that FEBID and the proposed characterization technique not only allow for growth and chemical analysis of single-element structures, but also offers a new way to directly study 3D core–shell architectures. This straightforward concept could establish a promising route to the design of 3D elements for future nano-electronic devices.

  9. High-purity 3D nano-objects grown by focused-electron-beam induced deposition

    NASA Astrophysics Data System (ADS)

    Córdoba, Rosa; Sharma, Nidhi; Kölling, Sebastian; Koenraad, Paul M.; Koopmans, Bert

    2016-09-01

    To increase the efficiency of current electronics, a specific challenge for the next generation of memory, sensing and logic devices is to find suitable strategies to move from two- to three-dimensional (3D) architectures. However, the creation of real 3D nano-objects is not trivial. Emerging non-conventional nanofabrication tools are required for this purpose. One attractive method is focused-electron-beam induced deposition (FEBID), a direct-write process of 3D nano-objects. Here, we grow 3D iron and cobalt nanopillars by FEBID using diiron nonacarbonyl Fe2(CO)9, and dicobalt octacarbonyl Co2(CO)8, respectively, as starting materials. In addition, we systematically study the composition of these nanopillars at the sub-nanometer scale by atom probe tomography, explicitly mapping the homogeneity of the radial and longitudinal composition distributions. We show a way of fabricating high-purity 3D vertical nanostructures of ˜50 nm in diameter and a few micrometers in length. Our results suggest that the purity of such 3D nanoelements (above 90 at% Fe and above 95 at% Co) is directly linked to their growth regime, in which the selected deposition conditions are crucial for the final quality of the nanostructure. Moreover, we demonstrate that FEBID and the proposed characterization technique not only allow for growth and chemical analysis of single-element structures, but also offers a new way to directly study 3D core-shell architectures. This straightforward concept could establish a promising route to the design of 3D elements for future nano-electronic devices.

  10. Amoeboid migration mode adaption in quasi-3D spatial density gradients of varying lattice geometry

    NASA Astrophysics Data System (ADS)

    Gorelashvili, Mari; Emmert, Martin; Hodeck, Kai F.; Heinrich, Doris

    2014-07-01

    Cell migration processes are controlled by sensitive interaction with external cues such as topographic structures of the cell’s environment. Here, we present systematically controlled assays to investigate the specific effects of spatial density and local geometry of topographic structure on amoeboid migration of Dictyostelium discoideum cells. This is realized by well-controlled fabrication of quasi-3D pillar fields exhibiting a systematic variation of inter-pillar distance and pillar lattice geometry. By time-resolved local mean-squared displacement analysis of amoeboid migration, we can extract motility parameters in order to elucidate the details of amoeboid migration mechanisms and consolidate them in a two-state contact-controlled motility model, distinguishing directed and random phases. Specifically, we find that directed pillar-to-pillar runs are found preferably in high pillar density regions, and cells in directed motion states sense pillars as attractive topographic stimuli. In contrast, cell motion in random probing states is inhibited by high pillar density, where pillars act as obstacles for cell motion. In a gradient spatial density, these mechanisms lead to topographic guidance of cells, with a general trend towards a regime of inter-pillar spacing close to the cell diameter. In locally anisotropic pillar environments, cell migration is often found to be damped due to competing attraction by different pillars in close proximity and due to lack of other potential stimuli in the vicinity of the cell. Further, we demonstrate topographic cell guidance reflecting the lattice geometry of the quasi-3D environment by distinct preferences in migration direction. Our findings allow to specifically control amoeboid cell migration by purely topographic effects and thus, to induce active cell guidance. These tools hold prospects for medical applications like improved wound treatment, or invasion assays for immune cells.

  11. Breast Density Analysis with Automated Whole-Breast Ultrasound: Comparison with 3-D Magnetic Resonance Imaging.

    PubMed

    Chen, Jeon-Hor; Lee, Yan-Wei; Chan, Si-Wa; Yeh, Dah-Cherng; Chang, Ruey-Feng

    2016-05-01

    In this study, a semi-automatic breast segmentation method was proposed on the basis of the rib shadow to extract breast regions from 3-D automated whole-breast ultrasound (ABUS) images. The density results were correlated with breast density values acquired with 3-D magnetic resonance imaging (MRI). MRI images of 46 breasts were collected from 23 women without a history of breast disease. Each subject also underwent ABUS. We used Otsu's thresholding method on ABUS images to obtain local rib shadow information, which was combined with the global rib shadow information (extracted from all slice projections) and integrated with the anatomy's breast tissue structure to determine the chest wall line. The fuzzy C-means classifier was used to extract the fibroglandular tissues from the acquired images. Whole-breast volume (WBV) and breast percentage density (BPD) were calculated in both modalities. Linear regression was used to compute the correlation of density results between the two modalities. The consistency of density measurement was also analyzed on the basis of intra- and inter-operator variation. There was a high correlation of density results between MRI and ABUS (R(2) = 0.798 for WBV, R(2) = 0.825 for PBD). The mean WBV from ABUS images was slightly smaller than the mean WBV from MR images (MRI: 342.24 ± 128.08 cm(3), ABUS: 325.47 ± 136.16 cm(3), p < 0.05). In addition, the BPD calculated from MR images was smaller than the BPD from ABUS images (MRI: 24.71 ± 15.16%, ABUS: 28.90 ± 17.73%, p < 0.05). The intra-operator and inter-operator variant analysis results indicated that there was no statistically significant difference in breast density measurement variation between the two modalities. Our results revealed a high correlation in WBV and BPD between MRI and ABUS. Our study suggests that ABUS provides breast density information useful in the assessment of breast health. PMID:26831342

  12. Breast Density Analysis with Automated Whole-Breast Ultrasound: Comparison with 3-D Magnetic Resonance Imaging.

    PubMed

    Chen, Jeon-Hor; Lee, Yan-Wei; Chan, Si-Wa; Yeh, Dah-Cherng; Chang, Ruey-Feng

    2016-05-01

    In this study, a semi-automatic breast segmentation method was proposed on the basis of the rib shadow to extract breast regions from 3-D automated whole-breast ultrasound (ABUS) images. The density results were correlated with breast density values acquired with 3-D magnetic resonance imaging (MRI). MRI images of 46 breasts were collected from 23 women without a history of breast disease. Each subject also underwent ABUS. We used Otsu's thresholding method on ABUS images to obtain local rib shadow information, which was combined with the global rib shadow information (extracted from all slice projections) and integrated with the anatomy's breast tissue structure to determine the chest wall line. The fuzzy C-means classifier was used to extract the fibroglandular tissues from the acquired images. Whole-breast volume (WBV) and breast percentage density (BPD) were calculated in both modalities. Linear regression was used to compute the correlation of density results between the two modalities. The consistency of density measurement was also analyzed on the basis of intra- and inter-operator variation. There was a high correlation of density results between MRI and ABUS (R(2) = 0.798 for WBV, R(2) = 0.825 for PBD). The mean WBV from ABUS images was slightly smaller than the mean WBV from MR images (MRI: 342.24 ± 128.08 cm(3), ABUS: 325.47 ± 136.16 cm(3), p < 0.05). In addition, the BPD calculated from MR images was smaller than the BPD from ABUS images (MRI: 24.71 ± 15.16%, ABUS: 28.90 ± 17.73%, p < 0.05). The intra-operator and inter-operator variant analysis results indicated that there was no statistically significant difference in breast density measurement variation between the two modalities. Our results revealed a high correlation in WBV and BPD between MRI and ABUS. Our study suggests that ABUS provides breast density information useful in the assessment of breast health.

  13. Dual array 3D electron cyclotron emission imaging at ASDEX Upgrade

    SciTech Connect

    Classen, I. G. J. Bogomolov, A. V.; Domier, C. W.; Luhmann, N. C.; Suttrop, W.; Boom, J. E.; Tobias, B. J.; Donné, A. J. H.

    2014-11-15

    In a major upgrade, the (2D) electron cyclotron emission imaging diagnostic (ECEI) at ASDEX Upgrade has been equipped with a second detector array, observing a different toroidal position in the plasma, to enable quasi-3D measurements of the electron temperature. The new system will measure a total of 288 channels, in two 2D arrays, toroidally separated by 40 cm. The two detector arrays observe the plasma through the same vacuum window, both under a slight toroidal angle. The majority of the field lines are observed by both arrays simultaneously, thereby enabling a direct measurement of the 3D properties of plasma instabilities like edge localized mode filaments.

  14. Dual array 3D electron cyclotron emission imaging at ASDEX Upgrade.

    PubMed

    Classen, I G J; Domier, C W; Luhmann, N C; Bogomolov, A V; Suttrop, W; Boom, J E; Tobias, B J; Donné, A J H

    2014-11-01

    In a major upgrade, the (2D) electron cyclotron emission imaging diagnostic (ECEI) at ASDEX Upgrade has been equipped with a second detector array, observing a different toroidal position in the plasma, to enable quasi-3D measurements of the electron temperature. The new system will measure a total of 288 channels, in two 2D arrays, toroidally separated by 40 cm. The two detector arrays observe the plasma through the same vacuum window, both under a slight toroidal angle. The majority of the field lines are observed by both arrays simultaneously, thereby enabling a direct measurement of the 3D properties of plasma instabilities like edge localized mode filaments. PMID:25430246

  15. Quasi-3D gold nanoring cavity arrays with high-density hot-spots for SERS applications via nanosphere lithography

    NASA Astrophysics Data System (ADS)

    Ho, Chi-Chih; Zhao, Ke; Lee, Tze-Yang

    2014-07-01

    (nanohole + nanoring + nanopillar) were successfully fabricated and compared. The SERS performance of the three-layered nanostructures is about two orders of magnitude higher than the others. Finite-difference time-domain (FDTD) simulations show that incorporating nanopillars and nanorings into a nanohole array not only significantly increases the density of the hot spots but also achieves stronger electromagnetic field enhancements compared to a nanohole array. The simple fabrication of multilayered quasi-3D nanostructures provides a large-area and highly efficient SERS substrates for biological and chemical applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr00902a

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

    PubMed

    Wang, Xiang; Wang, Qiang; Yuan, Caixia; Zhao, Xue-Feng; Li, Jia-Jia; Li, Debao; Wu, Yan-Bo; Wang, Xiaotai

    2016-04-28

    DFT B3LYP/6-31G(d) calculations were performed to examine the feasibility of graphene-like C42H18 and starbenzene C6(BeH)6 (SBz) polymers as ligands of 3D-extensible sandwich compounds (3D-ESCs) with uninterrupted sandwich arrays. The results revealed that sandwich compounds with three or more C42H18 ligands were not feasible. The possible reason may be the localization of π electrons on certain C6 hexagons due to π-metal interactions, which makes the whole ligand lose its electronic structure basis (higher degree of π electron delocalization) to maintain the planar structure. For comparison, with the aid of benzene (Bz) molecules, the SBz polymers can be feasible ligands for designing 3D-ESCs because the C-Be interactions in individual SBz are largely ionic, which will deter the π electrons on one C6 ring from connecting to those on neighbouring C6 rings. This means that high degree of π electron delocalization is not necessary for maintaining the planarity of SBz polymers. Such a locally delocalized π electron structure is desirable for the ligands of 3D-ESCs. Remarkably, the formation of a sandwich compound with SBz is thermodynamically more favourable than that found for bis(Bz)chromium. The assembly of 3D-ESCs is largely exothermic, which will facilitate future experimental synthesis. The different variation trends on the HOMO-LUMO gaps in different directions (relative to the sandwich axes) suggest that they can be developed to form directional conductors or semiconductors, which may be useful in the production of electronic devices. PMID:27004750

  17. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

    Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex. PMID:27493552

  18. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

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

  19. 3D Lithospheric Density Structure of the Central American Subduction Zone from Gravity Data

    NASA Astrophysics Data System (ADS)

    Lücke, O. H.; Arroyo, I. G.; Linkimer, L.

    2013-12-01

    Data from the EGM2008 Combined Geopotential Model has been interpreted to construct a comprehensive three-dimensional model of the lithospheric density structure along the Central American Isthmus. This is the first time that integration of all geophysical information available for the isthmus has been undertaken. The density model is constrained by seismic velocity models, magnetotelluric cross-sections, receiver functions,and hypocenter data from local seismic networks acquired along the Middle American Subduction Zone by different institutes and projects during the last three decades. The segmentation of the crustal basement of the Caribbean Plate was modeled with separate units for the Chortis Block (2.77 Mg/m^3), the Mesquito Composite Oceanic Terrane / SiunaTerrane (3 Mg/m^3), and the Caribbean Large Igneous Province (2.90 Mg/m^3). Furthermore, first order boundary layers such as the Moho and the Cocos-Caribbean plate interface were modeled and extracted for correlation with tectonic features and dynamic processes. The Costa Rican segment has been the most widely studied along the Central American margin. Here, it is possible to review the slab geometry based on the three-dimensional density model against seismological information from local networks in greater detail. By integrating probabilistic relocated hypocenters with the density model by means of 3D visualization, a joint interpretation of the distribution of seismicity with the density units in the subducted slab was carried out.A change in the depth of intra-plate seismicity is observed reaching 220 km for the northwestern part and becoming shallower toward the southeast where it reaches a maximum depth of 75 km. The changes in the maximum depth registered for the seismicity, correlate with changes in the density structure of the subducted slab which were modeled based on the gravity response of the model. The crust of the oceanic plate was assigned an initial density of 2.80 Mg/m3, deeper than this

  20. Electrochemical fields within 3D reconstructed microstructures of mixed ionic and electronic conducting devices

    NASA Astrophysics Data System (ADS)

    Zhang, Yanxiang; Chen, Yu; Lin, Ye; Yan, Mufu; Harris, William M.; Chiu, Wilson K. S.; Ni, Meng; Chen, Fanglin

    2016-11-01

    The performance and stability of the mixed ionic and electronic conducting (MIEC) membrane devices, such as solid oxide cells (SOCs) and oxygen separation membranes (OSMs) interplay tightly with the transport properties and the three-dimensional (3D) microstructure of the membrane. However, development of the MIEC devices is hindered by the limited knowledge about the distribution of electrochemical fields within the 3D local microstructures, especially at surface and interface. In this work, a generic model conforming to local thermodynamic equilibrium is developed to calculate the electrochemical fields, such as electric potential and oxygen chemical potential, within the 3D microstructure of the MIEC membrane. Stability of the MIEC membrane is evaluated by the distribution of oxygen partial pressure. The cell-level performance such as polarization resistance and voltage vs. current curve can be further calculated. Case studies are performed to demonstrate the capability of the framework by using X-ray computed tomography reconstructed 3D microstructures of a SOC and an OSM. The calculation method demonstrates high computational efficiency for large size 3D tomographic microstructures, and permits parallel calculation. The framework can serve as a powerful tool for correlating the transport properties and the 3D microstructure to the performance and the stability of MIEC devices.

  1. Potential energy curves and electronic structure of 3d transition metal hydrides and their cations

    NASA Astrophysics Data System (ADS)

    Goel, Satyender; Masunov, Artëm E.

    2008-12-01

    We investigate gas-phase neutral and cationic hydrides formed by 3d transition metals from Sc to Cu with density functional theory (DFT) methods. The performance of two exchange-correlation functionals, Boese-Martin for kinetics (BMK) and Tao-Perdew-Staroverov-Scuseria (TPSS), in predicting bond lengths and energetics, electronic structures, dipole moments, and ionization potentials is evaluated in comparison with available experimental data. To ensure a unique self-consistent field (SCF) solution, we use stability analysis, Fermi smearing, and continuity analysis of the potential energy curves. Broken-symmetry approach was adapted in order to get the qualitatively correct description of the bond dissociation. We found that on average BMK predicted values of dissociation energies and ionization potentials are closer to experiment than those obtained with high level wave function theory methods. This agreement deteriorates quickly when the fraction of the Hartree-Fock exchange in DFT functional is decreased. Natural bond orbital (NBO) population analysis was used to describe the details of chemical bonding in the systems studied. The multireference character in the wave function description of the hydrides is reproduced in broken-symmetry DFT description, as evidenced by NBO analysis. We also propose a new scheme to correct for spin contamination arising in broken-symmetry DFT approach. Unlike conventional schemes, our spin correction is introduced for each spin-polarized electron pair individually and therefore is expected to yield more accurate energy values. We derive an expression to extract the energy of the pure singlet state from the energy of the broken-symmetry DFT description of the low spin state and the energies of the high spin states (pentuplet and two spin-contaminated triplets in the case of two spin-polarized electron pairs). The high spin states are build with canonical natural orbitals and do not require SCF convergence.

  2. The 3D heat flux density distribution on a novel parabolic trough wavy absorber

    NASA Astrophysics Data System (ADS)

    Demagh, Yassine; Kabar, Yassine; Bordja, Lyes; Noui, Samira

    2016-05-01

    The non-uniform concentrated solar flux distribution on the outer surface of the absorber pipe can lead to large circumferential gradient temperature and high concentrated temperature of the absorber pipe wall, which is one of the primary causes of parabolic trough solar receiver breakdown. In this study, a novel shape of the parabolic trough absorber pipe is proposed as a solution to well homogenize the solar flux distribution, as well as, the temperature in the absorber wall. The conventional straight absorber located along the focal line of the parabola is replaced by wavy one (invention patent by Y. Demagh [1]) for which the heat flux density distribution on the outer surface varies in both axial and azimuthal directions (3D) while it varies only in the azimuthal direction on the former (2D). As far as we know, there is not previous study which has used a longitudinally wavy pipe as an absorber into the parabolic trough collector unit.

  3. 3D image reconstruction algorithms for cryo-electron-microscopy images of virus particles

    NASA Astrophysics Data System (ADS)

    Doerschuk, Peter C.; Johnson, John E.

    2000-11-01

    A statistical model for the object and the complete image formation process in cryo electron microscopy of viruses is presented. Using this model, maximum likelihood reconstructions of the 3D structure of viruses are computed using the expectation maximization algorithm and an example based on Cowpea mosaic virus is provided.

  4. A Review on Energy Harvesting Using 3D Printed Fabrics for Wearable Electronics

    NASA Astrophysics Data System (ADS)

    Gowthaman, Swaminathan; Chidambaram, Gowri Shankar; Rao, Dilli Babu Govardhana; Subramya, Hemakumar Vyudhayagiri; Chandrasekhar, Udhayagiri

    2016-06-01

    Embedding of energy harvesting systems into wearable health and environment monitoring systems, like integration of smart piezoelectric fibers into soldier fabric structures opens up avenues in generating electricity from natural mechanical movements for self-powering of wearable electronics. Emergence of multitudinous of materials and manufacturing technologies has enabled realization of various energy harvesting systems from mechanical movements. The materials and manufacturing related to 3D printing of energy harvesting fabrics are reviewed in this paper. State-of-the-art energy harvesting sources are briefly described following which an in-depth analysis on the materials and 3D printing techniques for energy harvesting fabrics are presented. While tremendous motivation and opportunity exists for wider-scale adoption of 3D printing for this niche area, the success depends on efficient design of three critical factors namely materials, process and structure. The present review discusses on the complex issues of materials selection, modelling and processing of 3D printed fabrics. The paper culminates by presenting a discussion on how future advancements in 3D printing technology might be useful for development of wearable electronics.

  5. Computer-aided microtomography with true 3-D display in electron microscopy.

    PubMed

    Nelson, A C

    1986-01-01

    A novel research system has been designed to permit three-dimensional (3-D) viewing of high resolution image data from transmission electron microscopy (TEM) and scanning electron microscopy (SEM). The system consists of front-end primary data acquisition devices, such as TEM and SEM machines, which are equipped with computer-controlled specimen tilt stages. The output from these machines is in analogue form, where a video camera attached to the TEM provides the sequential analogue image output while the SEM direct video output is utilized. A 10 MHz digitizer transforms the video image to a digital array of 512 X 512 pixel units of 8 bits deep-stored in a frame buffer. Digital images from multiple projections are reconstructed into 3-D image boxes in a dedicated computer. Attached to the computer is a powerful true 3-D display device which has hardware for graphic manipulations including tilt and rotate on any axis and for probing the image with a 3-D cursor. Data editing and automatic contouring functions are used to enhance areas of interest, and specialized software is available for measurement of numbers, distances, areas, and volumes. With proper archiving of reconstructed image sequences, a dynamic 3-D presentation is possible. The microtomography system is highly versatile and can process image data on-line or from remote sites from which data records would typically be transported on computer tape, video tape, or floppy disk. PMID:3753610

  6. Integrated 3D density modelling and segmentation of the Dead Sea Transform

    NASA Astrophysics Data System (ADS)

    Götze, H.-J.; El-Kelani, R.; Schmidt, S.; Rybakov, M.; Hassouneh, M.; Förster, H.-J.; Ebbing, J.

    2007-04-01

    A 3D interpretation of the newly compiled Bouguer anomaly in the area of the “Dead Sea Rift” is presented. A high-resolution 3D model constrained with the seismic results reveals the crustal thickness and density distribution beneath the Arava/Araba Valley (AV), the region between the Dead Sea and the Gulf of Aqaba/Elat. The Bouguer anomalies along the axial portion of the AV, as deduced from the modelling results, are mainly caused by deep-seated sedimentary basins ( D > 10 km). An inferred zone of intrusion coincides with the maximum gravity anomaly on the eastern flank of the AV. The intrusion is displaced at different sectors along the NNW-SSE direction. The zone of maximum crustal thinning (depth 30 km) is attained in the western sector at the Mediterranean. The southeastern plateau, on the other hand, shows by far the largest crustal thickness of the region (38-42 km). Linked to the left lateral movement of approx. 105 km at the boundary between the African and Arabian plate, and constrained with recent seismic data, a small asymmetric topography of the Moho beneath the Dead Sea Transform (DST) was modelled. The thickness and density of the crust suggest that the AV is underlain by continental crust. The deep basins, the relatively large intrusion and the asymmetric topography of the Moho lead to the conclusion that a small-scale asthenospheric upwelling could be responsible for the thinning of the crust and subsequent creation of the Dead Sea basin during the left lateral movement. A clear segmentation along the strike of the DST was obtained by curvature analysis: the northern part in the neighbourhood of the Dead Sea is characterised by high curvature of the residual gravity field. Flexural rigidity calculations result in very low values of effective elastic lithospheric thickness ( t e < 5 km). This points to decoupling of crust in the Dead Sea area. In the central, AV the curvature is less pronounced and t e increases to approximately 10 km

  7. Electronic structure of the chiral helimagnet and 3 d -intercalated transition metal dichalcogenide C r1 /3Nb S2

    NASA Astrophysics Data System (ADS)

    Sirica, N.; Mo, S.-K.; Bondino, F.; Pis, I.; Nappini, S.; Vilmercati, P.; Yi, J.; Gai, Z.; Snijders, P. C.; Das, P. K.; Vobornik, I.; Ghimire, N.; Koehler, M. R.; Li, L.; Sapkota, D.; Parker, D. S.; Mandrus, D. G.; Mannella, N.

    2016-08-01

    The electronic structure of the chiral helimagnet C r1 /3Nb S2 has been studied with core level and angle-resolved photoemission spectroscopy (ARPES). Intercalated Cr atoms are found to be effective in donating electrons to the Nb S2 layers but also cause significant modifications of the electronic structure of the host Nb S2 material. In particular, the data provide evidence that a description of the electronic structure of C r1 /3Nb S2 on the basis of a simple rigid band picture is untenable. The data also reveal substantial inconsistencies with the predictions of standard density functional theory. The relevance of these results to the attainment of a correct description of the electronic structure of chiral helimagnets, magnetic thin films/multilayers, and transition metal dichalcogenides intercalated with 3 d magnetic elements is discussed.

  8. On 3D world perception: towards a definition of a cognitive map based electronic travel aid.

    PubMed

    Pissaloux, E E; Velazquez, R; Maingreaud, F

    2004-01-01

    This paper addresses a 3D world perception principle and their usage for cognitive map building by visually impaired people. These bases are applied to define a new electronic travel aid named intelligent glasses system (IGS), a wearable system. IGS provides to blind people an information on their nearest 3D environment structure, and especially a tactile stimulating cognitive map of the obstacles located in user's peri-personal space. This paper outlines briefly the IG system, and presents first results on the validation of the proposed representation via psycho-physiological experiments.

  9. Prediction of spin-dependent electronic structure in 3d-transition-metal doped antimonene

    NASA Astrophysics Data System (ADS)

    Yang, L. F.; Song, Y.; Mi, W. B.; Wang, X. C.

    2016-07-01

    We investigate the geometric structure and electronic and magnetic properties of 3d-transition-metal atom doped antimonene using spin-polarized first-principles calculations. Strong orbital hybridization exhibits between 3d-transition-metal and Sb atoms, where covalent bonds form in antimonene. A spin-polarized semiconducting state appears in Cr-doped antimonene, while half-metallic states appear by doping Ti, V, and Mn. These findings indicate that once combined with doping states, the bands of antimonene systems offer a variety of features. Specific dopants lead to half-metallic characters with high spin polarization that has potential application in spintronics.

  10. Liquid-type cathode enabled by 3D sponge-like carbon nanotubes for high energy density and long cycling life of Li-S batteries.

    PubMed

    Pu, Xiong; Yang, Gang; Yu, Choongho

    2014-11-26

    High energy density and long-term stability of Li-S batteries are achieved by employing a 3D sponge-like carbon nanotube cathode and a liquid-type polysulfide catholyte. Carbon nanotubes not only provide excellent electron pathways and polysulfide reservoirs, but they can also be used as a standalone cathode without current collectors, which greatly alleviates problems arising from insulating sulfur and polysulfide shuttles as well as remarkably increasing the energy density.

  11. 3D imaging of the early embryonic chicken heart with focused ion beam scanning electron microscopy.

    PubMed

    Rennie, Monique Y; Gahan, Curran G; López, Claudia S; Thornburg, Kent L; Rugonyi, Sandra

    2014-08-01

    Early embryonic heart development is a period of dynamic growth and remodeling, with rapid changes occurring at the tissue, cell, and subcellular levels. A detailed understanding of the events that establish the components of the heart wall has been hampered by a lack of methodologies for three-dimensional (3D), high-resolution imaging. Focused ion beam scanning electron microscopy (FIB-SEM) is a novel technology for imaging 3D tissue volumes at the subcellular level. FIB-SEM alternates between imaging the block face with a scanning electron beam and milling away thin sections of tissue with a FIB, allowing for collection and analysis of 3D data. FIB-SEM was used to image the three layers of the day 4 chicken embryo heart: myocardium, cardiac jelly, and endocardium. Individual images obtained with FIB-SEM were comparable in quality and resolution to those obtained with transmission electron microscopy. Up to 1,100 serial images were obtained in 4 nm increments at 4.88 nm resolution, and image stacks were aligned to create volumes 800-1,500 μm3 in size. Segmentation of organelles revealed their organization and distinct volume fractions between cardiac wall layers. We conclude that FIB-SEM is a powerful modality for 3D subcellular imaging of the embryonic heart wall.

  12. Dynamics of electron emission in double photoionization processes near the krypton 3d threshold

    NASA Astrophysics Data System (ADS)

    Penent, F.; Sheinerman, S.; Andric, L.; Lablanquie, P.; Palaudoux, J.; Becker, U.; Braune, M.; Viefhaus, J.; Eland, J. H. D.

    2008-02-01

    Two-electron emission following photoabsorption near the Kr 3d threshold is investigated both experimentally and theoretically. On the experimental side, electron/electron coincidences using a magnetic bottle time-of-flight spectrometer allow us to observe the complete double photo ionization (DPI) continua of selected Kr2+ final states, and to see how these continua are affected by resonant processes in the vicinity of the Kr 3d threshold. The analysis is based on a quantum mechanical approach that takes into account the contribution of three different processes: (A) Auger decay of the inner 3d vacancy with the associated post-collision interaction (PCI) effects, (B) capture of slow photoelectrons into discrete states followed by valence multiplet decay (VMD) of the excited ionic states and (C) valence shell DPI. The dominant process for each Kr2+(4p-2) final state is the photoionization of the inner shell followed by Auger decay of the 3d vacancies. Moreover, for the 4p-2(3P) and 4p-2(1D) final ionic states an important contribution comes from the processes of slow photoelectron capture followed by VMD as well as from double ionization of the outer shell involving also VMD.

  13. A 3D reconstruction solution to ultrasound Joule heat density tomography based on acousto-electric effect: a simulation study

    NASA Astrophysics Data System (ADS)

    Yang, R.; Song, A.; Li, X. D.; Lu, Y.; Yan, R.; Xu, B.; Li, X.

    2014-10-01

    A 3D reconstruction solution to ultrasound Joule heat density tomography based on acousto-electric effect by deconvolution is proposed for noninvasive imaging of biological tissue. Compared with ultrasound current source density imaging, ultrasound Joule heat density tomography doesn't require any priori knowledge of conductivity distribution and lead fields, so it can gain better imaging result, more adaptive to environment and with wider application scope. For a general 3D volume conductor with broadly distributed current density field, in the AE equation the ultrasound pressure can't simply be separated from the 3D integration, so it is not a common modulation and basebanding (heterodyning) method is no longer suitable to separate Joule heat density from the AE signals. In the proposed method the measurement signal is viewed as the output of Joule heat density convolving with ultrasound wave. As a result, the internal 3D Joule heat density can be reconstructed by means of Wiener deconvolution. A series of computer simulations set for breast cancer imaging applications, with consideration of ultrasound beam diameter, noise level, conductivity contrast, position dependency and size of simulated tumors, have been conducted to evaluate the feasibility and performance of the proposed reconstruction method. The computer simulation results demonstrate that high spatial resolution 3D ultrasound Joule heat density imaging is feasible using the proposed method, and it has potential applications to breast cancer detection and imaging of other organs.

  14. Novel multiresolution mammographic density segmentation using pseudo 3D features and adaptive cluster merging

    NASA Astrophysics Data System (ADS)

    He, Wenda; Juette, Arne; Denton, Erica R. E.; Zwiggelaar, Reyer

    2015-03-01

    Breast cancer is the most frequently diagnosed cancer in women. Early detection, precise identification of women at risk, and application of appropriate disease prevention measures are by far the most effective ways to overcome the disease. Successful mammographic density segmentation is a key aspect in deriving correct tissue composition, ensuring an accurate mammographic risk assessment. However, mammographic densities have not yet been fully incorporated with non-image based risk prediction models, (e.g. the Gail and the Tyrer-Cuzick model), because of unreliable segmentation consistency and accuracy. This paper presents a novel multiresolution mammographic density segmentation, a concept of stack representation is proposed, and 3D texture features were extracted by adapting techniques based on classic 2D first-order statistics. An unsupervised clustering technique was employed to achieve mammographic segmentation, in which two improvements were made; 1) consistent segmentation by incorporating an optimal centroids initialisation step, and 2) significantly reduced the number of missegmentation by using an adaptive cluster merging technique. A set of full field digital mammograms was used in the evaluation. Visual assessment indicated substantial improvement on segmented anatomical structures and tissue specific areas, especially in low mammographic density categories. The developed method demonstrated an ability to improve the quality of mammographic segmentation via clustering, and results indicated an improvement of 26% in segmented image with good quality when compared with the standard clustering approach. This in turn can be found useful in early breast cancer detection, risk-stratified screening, and aiding radiologists in the process of decision making prior to surgery and/or treatment.

  15. 3D-Laser-Scanning Technique Applied to Bulk Density Measurements of Apollo Lunar Samples

    NASA Technical Reports Server (NTRS)

    Macke, R. J.; Kent, J. J.; Kiefer, W. S.; Britt, D. T.

    2015-01-01

    In order to better interpret gravimetric data from orbiters such as GRAIL and LRO to understand the subsurface composition and structure of the lunar crust, it is import to have a reliable database of the density and porosity of lunar materials. To this end, we have been surveying these physical properties in both lunar meteorites and Apollo lunar samples. To measure porosity, both grain density and bulk density are required. For bulk density, our group has historically utilized sub-mm bead immersion techniques extensively, though several factors have made this technique problematic for our work with Apollo samples. Samples allocated for measurement are often smaller than optimal for the technique, leading to large error bars. Also, for some samples we were required to use pure alumina beads instead of our usual glass beads. The alumina beads were subject to undesirable static effects, producing unreliable results. Other investigators have tested the use of 3d laser scanners on meteorites for measuring bulk volumes. Early work, though promising, was plagued with difficulties including poor response on dark or reflective surfaces, difficulty reproducing sharp edges, and large processing time for producing shape models. Due to progress in technology, however, laser scanners have improved considerably in recent years. We tested this technique on 27 lunar samples in the Apollo collection using a scanner at NASA Johnson Space Center. We found it to be reliable and more precise than beads, with the added benefit that it involves no direct contact with the sample, enabling the study of particularly friable samples for which bead immersion is not possible

  16. Resonant structure of the 3d electron`s angular distribution in a free Mn{sup +}Ion

    SciTech Connect

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

    1995-08-01

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

  17. Study of materials and machines for 3D printed large-scale, flexible electronic structures using fused deposition modeling

    NASA Astrophysics Data System (ADS)

    Hwang, Seyeon

    the FDM printer modified in Chapter 5. The mechanical properties are sensitively affected by the morphology of additive materials such as concentration, size, type, and shape. The printing parameters such as fill density, temperature, nozzle diameter, and layer thickness are also influential factors resulting in changes in final properties of 3D printed objects. Thus, mechanical properties of the thermoplastic polymers, e.g. acrylonitrile butadiene styrene (ABS) and polylactic acid (PLA), as a function of fill density and printing temperature are studied in Chapter 4. Chapter 5 describes a way to modify the FDM printer for multi-material printing of flexible composite filaments in order to make single-structured 3D electronics via FDM process. To achieve the goals, the dual-nozzle filament extrusion system is installed to the FDM printer and the part for filament feeding is modified in this chapter.

  18. Interstellar Electron Density Spectra

    NASA Astrophysics Data System (ADS)

    Lambert, Hendrick Clark

    This study concerns the investigation of the form of the wavenumber spectrum of the Galactic electron density fluctuations through an examination of the scattering of the radio pulses emitted by pulsars as they propagate through the diffuse ionized interstellar gas. A widely used model for the electron density spectrum is based on the simple power-law: Pne(q)∝ q-β, where β = 11/3 is usually assumed, corresponding to Kolmogorov's turbulence spectrum. The simple Kolmogorov model provides satisfactory agreement for observations along many lines of sight; however, major inconsistencies remain. The inconsistencies suggest that an increase in the ratio of the power between the high (10-8[ m]-1≤ q<=10-7[ m]-1) and low (10-13[ m]-1≤ q<=10-12[ m]-1) wavenumbers is needed. This enhancement in the ratio can in turn be achieved by either including an inner scale, corresponding to a dissipation scale for the turbulent cascade, in the Kolmogorov spectrum or by considering steeper spectra. Spectra with spectral exponents β > 4 have been in general rejected based on observations of pulsar refractive scintillations. The special case of β = 4 has been given little attention and is analyzed in detail. Physically, this 'β = 4' model corresponds to the random distribution, both in location and orientation, of discrete objects with relatively sharp boundaries across the line of sight. An outer scale is included in the model to account for the average size of such objects. We compare the predictions of the inner-scale and β = 4 models both with published observations and observations we made as part of this investigation. We conclude that the form of the wavenumber spectrum is dependent on the line of sight. We propose a composite spectrum featuring a uniform background turbulence in presence of randomly distributed discrete objects, as modeled by the β = model.

  19. Fast Semantic Segmentation of 3d Point Clouds with Strongly Varying Density

    NASA Astrophysics Data System (ADS)

    Hackel, Timo; Wegner, Jan D.; Schindler, Konrad

    2016-06-01

    We describe an effective and efficient method for point-wise semantic classification of 3D point clouds. The method can handle unstructured and inhomogeneous point clouds such as those derived from static terrestrial LiDAR or photogammetric reconstruction; and it is computationally efficient, making it possible to process point clouds with many millions of points in a matter of minutes. The key issue, both to cope with strong variations in point density and to bring down computation time, turns out to be careful handling of neighborhood relations. By choosing appropriate definitions of a point's (multi-scale) neighborhood, we obtain a feature set that is both expressive and fast to compute. We evaluate our classification method both on benchmark data from a mobile mapping platform and on a variety of large, terrestrial laser scans with greatly varying point density. The proposed feature set outperforms the state of the art with respect to per-point classification accuracy, while at the same time being much faster to compute.

  20. Velocity and Density Models Incorporating the Cascadia Subduction Zone for 3D Earthquake Ground Motion Simulations

    USGS Publications Warehouse

    Stephenson, William J.

    2007-01-01

    INTRODUCTION In support of earthquake hazards and ground motion studies in the Pacific Northwest, three-dimensional P- and S-wave velocity (3D Vp and Vs) and density (3D rho) models incorporating the Cascadia subduction zone have been developed for the region encompassed from about 40.2?N to 50?N latitude, and from about -122?W to -129?W longitude. The model volume includes elevations from 0 km to 60 km (elevation is opposite of depth in model coordinates). Stephenson and Frankel (2003) presented preliminary ground motion simulations valid up to 0.1 Hz using an earlier version of these models. The version of the model volume described here includes more structural and geophysical detail, particularly in the Puget Lowland as required for scenario earthquake simulations in the development of the Seattle Urban Hazards Maps (Frankel and others, 2007). Olsen and others (in press) used the model volume discussed here to perform a Cascadia simulation up to 0.5 Hz using a Sumatra-Andaman Islands rupture history. As research from the EarthScope Program (http://www.earthscope.org) is published, a wealth of important detail can be added to these model volumes, particularly to depths of the upper-mantle. However, at the time of development for this model version, no EarthScope-specific results were incorporated. This report is intended to be a reference for colleagues and associates who have used or are planning to use this preliminary model in their research. To this end, it is intended that these models will be considered a beginning template for a community velocity model of the Cascadia region as more data and results become available.

  1. Injectable 3-D Fabrication of Medical Electronics at the Target Biological Tissues

    PubMed Central

    Jin, Chao; Zhang, Jie; Li, Xiaokang; Yang, Xueyao; Li, Jingjing; Liu, Jing

    2013-01-01

    Conventional transplantable biomedical devices generally request sophisticated surgery which however often causes big trauma and serious pain to the patients. Here, we show an alternative way of directly making three-dimensional (3-D) medical electronics inside the biological body through sequential injections of biocompatible packaging material and liquid metal ink. As the most typical electronics, a variety of medical electrodes with different embedded structures were demonstrated to be easily formed at the target tissues. Conceptual in vitro experiments provide strong evidences for the excellent performances of the injectable electrodes. Further in vivo animal experiments disclosed that the formed electrode could serve as both highly efficient ECG (Electrocardiograph) electrode and stimulator electrode. These findings clarified the unique features and practicability of the liquid metal based injectable 3-D fabrication of medical electronics. The present strategy opens the way for directly manufacturing electrophysiological sensors or therapeutic devices in situ via a truly minimally invasive approach. PMID:24309385

  2. Hollow Cone Electron Imaging for Single Particle 3D Reconstruction of Proteins.

    PubMed

    Tsai, Chun-Ying; Chang, Yuan-Chih; Lobato, Ivan; Van Dyck, Dirk; Chen, Fu-Rong

    2016-01-01

    The main bottlenecks for high-resolution biological imaging in electron microscopy are radiation sensitivity and low contrast. The phase contrast at low spatial frequencies can be enhanced by using a large defocus but this strongly reduces the resolution. Recently, phase plates have been developed to enhance the contrast at small defocus but electrical charging remains a problem. Single particle cryo-electron microscopy is mostly used to minimize the radiation damage and to enhance the resolution of the 3D reconstructions but it requires averaging images of a massive number of individual particles. Here we present a new route to achieve the same goals by hollow cone dark field imaging using thermal diffuse scattered electrons giving about a 4 times contrast increase as compared to bright field imaging. We demonstrate the 3D reconstruction of a stained GroEL particle can yield about 13.5 Å resolution but using a strongly reduced number of images. PMID:27292544

  3. Hollow Cone Electron Imaging for Single Particle 3D Reconstruction of Proteins

    PubMed Central

    Tsai, Chun-Ying; Chang, Yuan-Chih; Lobato, Ivan; Van Dyck, Dirk; Chen, Fu-Rong

    2016-01-01

    The main bottlenecks for high-resolution biological imaging in electron microscopy are radiation sensitivity and low contrast. The phase contrast at low spatial frequencies can be enhanced by using a large defocus but this strongly reduces the resolution. Recently, phase plates have been developed to enhance the contrast at small defocus but electrical charging remains a problem. Single particle cryo-electron microscopy is mostly used to minimize the radiation damage and to enhance the resolution of the 3D reconstructions but it requires averaging images of a massive number of individual particles. Here we present a new route to achieve the same goals by hollow cone dark field imaging using thermal diffuse scattered electrons giving about a 4 times contrast increase as compared to bright field imaging. We demonstrate the 3D reconstruction of a stained GroEL particle can yield about 13.5 Å resolution but using a strongly reduced number of images. PMID:27292544

  4. Injectable 3-D Fabrication of Medical Electronics at the Target Biological Tissues

    NASA Astrophysics Data System (ADS)

    Jin, Chao; Zhang, Jie; Li, Xiaokang; Yang, Xueyao; Li, Jingjing; Liu, Jing

    2013-12-01

    Conventional transplantable biomedical devices generally request sophisticated surgery which however often causes big trauma and serious pain to the patients. Here, we show an alternative way of directly making three-dimensional (3-D) medical electronics inside the biological body through sequential injections of biocompatible packaging material and liquid metal ink. As the most typical electronics, a variety of medical electrodes with different embedded structures were demonstrated to be easily formed at the target tissues. Conceptual in vitro experiments provide strong evidences for the excellent performances of the injectable electrodes. Further in vivo animal experiments disclosed that the formed electrode could serve as both highly efficient ECG (Electrocardiograph) electrode and stimulator electrode. These findings clarified the unique features and practicability of the liquid metal based injectable 3-D fabrication of medical electronics. The present strategy opens the way for directly manufacturing electrophysiological sensors or therapeutic devices in situ via a truly minimally invasive approach.

  5. Hollow Cone Electron Imaging for Single Particle 3D Reconstruction of Proteins

    NASA Astrophysics Data System (ADS)

    Tsai, Chun-Ying; Chang, Yuan-Chih; Lobato, Ivan; van Dyck, Dirk; Chen, Fu-Rong

    2016-06-01

    The main bottlenecks for high-resolution biological imaging in electron microscopy are radiation sensitivity and low contrast. The phase contrast at low spatial frequencies can be enhanced by using a large defocus but this strongly reduces the resolution. Recently, phase plates have been developed to enhance the contrast at small defocus but electrical charging remains a problem. Single particle cryo-electron microscopy is mostly used to minimize the radiation damage and to enhance the resolution of the 3D reconstructions but it requires averaging images of a massive number of individual particles. Here we present a new route to achieve the same goals by hollow cone dark field imaging using thermal diffuse scattered electrons giving about a 4 times contrast increase as compared to bright field imaging. We demonstrate the 3D reconstruction of a stained GroEL particle can yield about 13.5 Å resolution but using a strongly reduced number of images.

  6. Electronic spectroscopy and electronic structure of the smallest metal clusters: the diatomic 3D transition metal aluminides

    NASA Astrophysics Data System (ADS)

    Behm, Jane M.; Morse, Michael D.

    1994-06-01

    A systematic study of the electronic spectroscopy, electronic structure, and chemical bonding has been initiated for the 3d series of diatomic transition metal aluminides. This report provides a review of the progress to date, with specific emphasis on AlCa, AlV, AlCr, AlMn, AlCo, AlNi, AlCu, and AlZn.

  7. Correlative Confocal and 3D Electron Microscopy of a Specific Sensory Cell

    PubMed Central

    Bohórquez, Diego; Haque, Fariha; Medicetty, Satish; Liddle, Rodger A.

    2015-01-01

    Delineation of a cell’s ultrastructure is important for understanding its function. This can be a daunting project for rare cell types diffused throughout tissues made of diverse cell types, such as enteroendocrine cells of the intestinal epithelium. These gastrointestinal sensors of food and bacteria have been difficult to study because they are dispersed among other epithelial cells at a ratio of 1:1,000. Recently, transgenic reporter mice have been generated to identify enteroendocrine cells by means of fluorescence. One of those is the peptide YY-GFP mouse. Using this mouse, we developed a method to correlate confocal and serial block-face scanning electron microscopy. We named the method cocem3D and applied it to identify a specific enteroendocrine cell in tissue and unveil the cell’s ultrastructure in 3D. The resolution of cocem3D is sufficient to identify organelles as small as secretory vesicles and to distinguish cell membranes for volume rendering. Cocem3D can be easily adapted to study the 3D ultrastructure of other specific cell types in their native tissue. PMID:26273796

  8. 3D Magnetic Induction Maps of Nanoscale Materials Revealed by Electron Holographic Tomography

    PubMed Central

    2015-01-01

    The investigation of three-dimensional (3D) ferromagnetic nanoscale materials constitutes one of the key research areas of the current magnetism roadmap and carries great potential to impact areas such as data storage, sensing, and biomagnetism. The properties of such nanostructures are closely connected with their 3D magnetic nanostructure, making their determination highly valuable. Up to now, quantitative 3D maps providing both the internal magnetic and electric configuration of the same specimen with high spatial resolution are missing. Here, we demonstrate the quantitative 3D reconstruction of the dominant axial component of the magnetic induction and electrostatic potential within a cobalt nanowire (NW) of 100 nm in diameter with spatial resolution below 10 nm by applying electron holographic tomography. The tomogram was obtained using a dedicated TEM sample holder for acquisition, in combination with advanced alignment and tomographic reconstruction routines. The powerful approach presented here is widely applicable to a broad range of 3D magnetic nanostructures and may trigger the progress of novel spintronic nonplanar nanodevices. PMID:27182110

  9. Simulation-Guided 3D Nanomanufacturing via Focused Electron Beam Induced Deposition

    DOE PAGES

    Fowlkes, Jason D.; Winkler, Robert; Lewis, Brett B.; Stanford, Michael G.; Plank, Harald; Rack, Philip D.

    2016-06-10

    Focused electron beam induced deposition (FEBID) is one of the few techniques that enables direct-write synthesis of free-standing 3D nanostructures. While the fabrication of simple architectures such as vertical or curving nanowires has been achieved by simple trial and error, processing complex 3D structures is not tractable with this approach. This is due, inpart, to the dynamic interplay between electron–solid interactions and the transient spatial distribution of absorbed precursor molecules on the solid surface. Here, we demonstrate the ability to controllably deposit 3D lattice structures at the micro/nanoscale, which have received recent interest owing to superior mechanical and optical properties.more » Moreover, a hybrid Monte Carlo–continuum simulation is briefly overviewed, and subsequently FEBID experiments and simulations are directly compared. Finally, a 3D computer-aided design (CAD) program is introduced, which generates the beam parameters necessary for FEBID by both simulation and experiment. In using this approach, we demonstrate the fabrication of various 3D lattice structures using Pt-, Au-, and W-based precursors.« less

  10. Simulation of 3-D Magnetic Reconnection by Gyrokinetic Electron and Fully Kinetic Ion Particle Model

    NASA Astrophysics Data System (ADS)

    Wang, X.; Lin, Y.; Chen, L.

    2015-12-01

    3-D collisionless magnetic reconnection is investigated using the gyrokinetic electron and fully-kinetic ion (GeFi) particle simulation model. The simulation is carried out for cases with various finite guide field BG in a current sheet as occurring in space and laboratory plasmas. Turbulence power spectrum of magenetic field is found in the reconnection current sheet, with a clear k-5/3 dependence. The wave properties are analyzed. The anomalous resistivity in the electron diffusion region is estimated. The Dependence of the reconnection physics on the ion-to-electron mass ratio mi/me, beta values, and the half-width of the current sheet are also investigated.

  11. Potential of 3D printing technologies for fabrication of electron bolus and proton compensators.

    PubMed

    Zou, Wei; Fisher, Ted; Zhang, Miao; Kim, Leonard; Chen, Ting; Narra, Venkat; Swann, Beth; Singh, Rachana; Siderit, Richard; Yin, Lingshu; Teo, Boon-Keng Kevin; McKenna, Michael; McDonough, James; Ning, Yue J

    2015-05-08

    In electron and proton radiotherapy, applications of patient-specific electron bolus or proton compensators during radiation treatments are often necessary to accommodate patient body surface irregularities, tissue inhomogeneity, and variations in PTV depths to achieve desired dose distributions. Emerging 3D printing technologies provide alternative fabrication methods for these bolus and compensators. This study investigated the potential of utilizing 3D printing technologies for the fabrication of the electron bolus and proton compensators. Two printing technologies, fused deposition modeling (FDM) and selective laser sintering (SLS), and two printing materials, PLA and polyamide, were investigated. Samples were printed and characterized with CT scan and under electron and proton beams. In addition, a software package was developed to convert electron bolus and proton compensator designs to printable Standard Tessellation Language file format. A phantom scalp electron bolus was printed with FDM technology with PLA material. The HU of the printed electron bolus was 106.5 ± 15.2. A prostate patient proton compensator was printed with SLS technology and polyamide material with -70.1 ± 8.1 HU. The profiles of the electron bolus and proton compensator were compared with the original designs. The average over all the CT slices of the largest Euclidean distance between the design and the fabricated bolus on each CT slice was found to be 0.84 ± 0.45 mm and for the compensator to be 0.40 ± 0.42 mm. It is recommended that the properties of specific 3D printed objects are understood before being applied to radiotherapy treatments.

  12. Beyond optical molasses: 3D raman sideband cooling of atomic cesium to high phase-space density

    PubMed

    Kerman; Vuletic; Chin; Chu

    2000-01-17

    We demonstrate a simple, general purpose method to cool neutral atoms. A sample containing 3x10(8) cesium atoms prepared in a magneto-optical trap is cooled and simultaneously spin polarized in 10 ms at a density of 1.1x10(11) cm (-3) to a phase space density nlambda(3)(dB) = 1/500, which is almost 3 orders of magnitude higher than attainable in free space with optical molasses. The technique is based on 3D degenerate Raman sideband cooling in optical lattices and remains efficient even at densities where the mean lattice site occupation is close to unity.

  13. 3D scanning electron microscopy applied to surface characterization of fluorosed dental enamel.

    PubMed

    Limandri, Silvina; Galván Josa, Víctor; Valentinuzzi, María Cecilia; Chena, María Emilia; Castellano, Gustavo

    2016-05-01

    The enamel surfaces of fluorotic teeth were studied by scanning electron stereomicroscopy. Different whitening treatments were applied to 25 pieces to remove stains caused by fluorosis and their surfaces were characterized by stereomicroscopy in order to obtain functional and amplitude parameters. The topographic features resulting for each treatment were determined through these parameters. The results obtained show that the 3D reconstruction achieved from the SEM stereo pairs is a valuable potential alternative for the surface characterization of this kind of samples.

  14. Identifying Components in 3D Density Maps of Protein Nanomachines by Multi-scale Segmentation.

    PubMed

    Pintilie, Grigore; Zhang, Junjie; Chiu, Wah; Gossard, David

    2009-04-01

    Segmentation of density maps obtained using cryo-electron microscopy (cryo-EM) is a challenging task, and is typically accomplished by time-intensive interactive methods. The goal of segmentation is to identify the regions inside the density map that correspond to individual components. We present a multi-scale segmentation method for accomplishing this task that requires very little user interaction. The method uses the concept of scale space, which is created by convolution of the input density map with a Gaussian filter. The latter process smoothes the density map. The standard deviation of the Gaussian filter is varied, with smaller values corresponding to finer scales and larger values to coarser scales. Each of the maps at different scales is segmented using the watershed method, which is very efficient, completely automatic, and does not require the specification of seed points. Some detail is lost in the smoothing process. A sharpening process reintroduces detail into the segmentation at the coarsest scale by using the segmentations at the finer scales. We apply the method to simulated density maps, where the exact segmentation (or ground truth) is known, and rigorously evaluate the accuracy of the resulting segmentations.

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

    NASA Technical Reports Server (NTRS)

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

    2016-01-01

    Surface gravity surveys can detect subsurface density variations that can reveal subsurface geologic features. In 1972, the Apollo 17 (A17) mission conducted the Traverse Gravimeter Experiment (TGE) using a gravimeter that measured the local gravity field near Taurus Littrow Valley (TLV), located on the south-eastern rim of the Serenitatis basin. TLV is hypothesized to be a basaltfilled radial graben resulting from the impact that formed Mare Serenitatis. It is bounded by both the North and South Massifs (NM and SM) as well as other smaller mountains to the East that are thought to be mainly composed of brecciated highland material. The TGE is the first and only successful gravity survey on the surface of the Moon. Other more recent satellite surveys, such as NASA's Gravity Recovery and Interior Laboratory (GRAIL) mission (2011- 2012), have produced the best global gravity field to date (approx. 13km resolution). However, these satellite surveys are not sensitive enough to detect fine-scale (<1km) lunar subsurface structures. This underscores the value of the data collected at the surface by A17. In the original analysis of the data a 2D forward-modelling approach was used to derive a thickness of the subsurface basalt layer of 1.0 km by assuming a simple flat-faced rectangular geometry and using densities derived from Apollo lunar samples. We are investigating whether modern 3D modelling techniques in combination with high-resolution topographical and image datasets can reveal additional fine-scale subsurface structure in TLV.

  16. Bridging microscopes: 3D correlative light and scanning electron microscopy of complex biological structures.

    PubMed

    Lucas, Miriam S; Günthert, Maja; Gasser, Philippe; Lucas, Falk; Wepf, Roger

    2012-01-01

    The rationale of correlative light and electron microscopy (CLEM) is to collect data on different information levels--ideally from an identical area on the same sample--with the aim of combining datasets at different levels of resolution to achieve a more holistic view of the hierarchical structural organization of cells and tissues. Modern three-dimensional (3D) imaging techniques in light and electron microscopy opened up new possibilities to expand morphological studies into the third dimension at the nanometer scale and over various volume dimensions. Here, we present two alternative approaches to correlate 3D light microscopy (LM) data with scanning electron microscopy (SEM) volume data. An adapted sample preparation method based on high-pressure freezing for structure preservation, followed by freeze-substitution for multimodal en-bloc imaging or serial-section imaging is described. The advantages and potential applications are exemplarily shown on various biological samples, such as cells, individual organisms, human tissue, as well as plant tissue. The two CLEM approaches presented here are per se not mutually exclusive, but have their distinct advantages. Confocal laser scanning microscopy (CLSM) and focused ion beam-SEM (FIB-SEM) is most suitable for targeted 3D correlation of small volumes, whereas serial-section LM and SEM imaging has its strength in large-area or -volume screening and correlation. The second method can be combined with immunocytochemical methods. Both methods, however, have the potential to extract statistically relevant data of structural details for systems biology.

  17. Comparisons of Runaway Electron Production in DIII--D with the CQL3D Model

    NASA Astrophysics Data System (ADS)

    Harvey, R. W.; Chan, V. S.; Chiu, S. C.; Evans, T. E.; Whyte, D. G.; Rosenbluth, M. N.

    1997-11-01

    The time-dependent CQL3D relativistic, bounce-averaged Fokker-Planck code is well suited to modeling the electron runaway generation by ``tail slideaway'' and ``knockon'' processes associated with rapid plasma temperature drop as occurs during plasma disruption and pellet injection. ``Rapid temperure drop'' means in a time short compared to the resistive time thus leading to large inductive electric field; and also short compared to tail electron slowing down time thereby providing a significant number of high velocity electrons. The tail electrons find themselves beyond the critical velocity for runaway. During DIII--D pellet injection experiments, in the plasma interior we calculate nearly 100 percent of the plasma current is transferred to runaway electrons by tail slideaway. This effect diminishes towards the plasma edge, where the knockon process can become dominant on a longer time scale. These computational results will be benchmarked against the experimental results.

  18. Front-end receiver electronics for a matrix transducer for 3-D transesophageal echocardiography.

    PubMed

    Yu, Zili; Blaak, Sandra; Chang, Zu-yao; Yao, Jiajian; Bosch, Johan G; Prins, Christian; Lancée, Charles T; de Jong, Nico; Pertijs, Michiel A P; Meijer, Gerard C M

    2012-07-01

    There is a clear clinical need for creating 3-D images of the heart. One promising technique is the use of transesophageal echocardiography (TEE). To enable 3-D TEE, we are developing a miniature ultrasound probe containing a matrix piezoelectric transducer with more than 2000 elements. Because a gastroscopic tube cannot accommodate the cables needed to connect all transducer elements directly to an imaging system, a major challenge is to locally reduce the number of channels, while maintaining a sufficient signal-to-noise ratio. This can be achieved by using front-end receiver electronics bonded to the transducers to provide appropriate signal conditioning in the tip of the probe. This paper presents the design of such electronics, realizing time-gain compensation (TGC) and micro-beamforming using simple, low-power circuits. Prototypes of TGC amplifiers and micro-beamforming cells have been fabricated in 0.35-μm CMOS technology. These prototype chips have been combined on a printed circuit board (PCB) to form an ultrasound-receiver system capable of reading and combining the signals of three transducer elements. Experimental results show that this design is a suitable candidate for 3-D TEE.

  19. Effect of Single-Electron Interface Trapping in Decanano MOSFETs: A 3D Atomistic Simulation Study

    NASA Technical Reports Server (NTRS)

    Asenov, Asen; Balasubramaniam, R.; Brown, A. R.; Davies, J. H.

    2000-01-01

    We study the effect of trapping/detrapping of a single-electron in interface states in the channel of n-type MOSFETs with decanano dimensions using 3D atomistic simulation techniques. In order to highlight the basic dependencies, the simulations are carried out initially assuming continuous doping charge, and discrete localized charge only for the trapped electron. The dependence of the random telegraph signal (RTS) amplitudes on the device dimensions and on the position of the trapped charge in the channel are studied in detail. Later, in full-scale, atomistic simulations assuming discrete charge for both randomly placed dopants and the trapped electron, we highlight the importance of current percolation and of traps with strategic position where the trapped electron blocks a dominant current path.

  20. Synthesizing a 3D auditory scene for use in an electronic travel aid for the blind

    NASA Astrophysics Data System (ADS)

    Bujacz, Michał; Strumiłło, Paweł

    2008-01-01

    A system for auditory presentation of 3D scenes to the blind is presented, with the focus of the paper on the synthesis of sound codes suitable to carry important scene information. First, a short review of existing electronic travel aids for the blind (ETAs) is provided. Second, the project of the wearable ETA device, currently under development at the Technical University of Lodz, is outlined, along with the system modules: 3D scene reconstruction, object (obstacle) selection, synthesis of the sound code and the application of head related transfer functions (HRTFs) for generating spatialized sound. The importance of psychoacoustics, especially Bregman's theory of sound streams, is analyzed and proposed methods of sound code synthesis are presented, along with the software used for their verification.

  1. 3D motion of DNA-Au nanoconjugates in graphene liquid cell electron microscopy.

    PubMed

    Chen, Qian; Smith, Jessica M; Park, Jungwon; Kim, Kwanpyo; Ho, Davy; Rasool, Haider I; Zettl, Alex; Alivisatos, A Paul

    2013-09-11

    Liquid-phase transmission electron microscopy (TEM) can probe and visualize dynamic events with structural or functional details at the nanoscale in a liquid medium. Earlier efforts have focused on the growth and transformation kinetics of hard material systems, relying on their stability under electron beam. Our recently developed graphene liquid cell technique pushed the spatial resolution of such imaging to the atomic scale but still focused on growth trajectories of metallic nanocrystals. Here, we adopt this technique to imaging three-dimensional (3D) dynamics of soft materials instead, double strand (dsDNA) connecting Au nanocrystals as one example, at nanometer resolution. We demonstrate first that a graphene liquid cell can seal an aqueous sample solution of a lower vapor pressure than previously investigated well against the high vacuum in TEM. Then, from quantitative analysis of real time nanocrystal trajectories, we show that the status and configuration of dsDNA dictate the motions of linked nanocrystals throughout the imaging time of minutes. This sustained connecting ability of dsDNA enables this unprecedented continuous imaging of its dynamics via TEM. Furthermore, the inert graphene surface minimizes sample-substrate interaction and allows the whole nanostructure to rotate freely in the liquid environment; we thus develop and implement the reconstruction of 3D configuration and motions of the nanostructure from the series of 2D projected TEM images captured while it rotates. In addition to further proving the nanoconjugate structural stability, this reconstruction demonstrates 3D dynamic imaging by TEM beyond its conventional use in seeing a flattened and dry sample. Altogether, we foresee the new and exciting use of graphene liquid cell TEM in imaging 3D biomolecular transformations or interaction dynamics at nanometer resolution. PMID:23944844

  2. Determination of a new uniform thorax density representative of the living population from 3D external body shape modeling.

    PubMed

    Amabile, Celia; Choisne, Julie; Nérot, Agathe; Pillet, Hélène; Skalli, Wafa

    2016-05-01

    Body segment parameters (BSP) for each body׳s segment are needed for biomechanical analysis. To provide population-specific BSP, precise estimation of body׳s segments volume and density are needed. Widely used uniform densities, provided by cadavers׳ studies, did not consider the air present in the lungs when determining the thorax density. The purpose of this study was to propose a new uniform thorax density representative of the living population from 3D external body shape modeling. Bi-planar X-ray radiographies were acquired on 58 participants allowing 3D reconstructions of the spine, rib cage and human body shape. Three methods of computing the thorax mass were compared for 48 subjects: (1) the Dempster Uniform Density Method, currently in use for BSPs calculation, using Dempster density data, (2) the Personalized Method using full-description of the thorax based on 3D reconstruction of the rib cage and spine and (3) the Improved Uniform Density Method using a uniform thorax density resulting from the Personalized Method. For 10 participants, comparison was made between the body mass obtained from a force-plate and the body mass computed with each of the three methods. The Dempster Uniform Density Method presented a mean error of 4.8% in the total body mass compared to the force-plate vs 0.2% for the Personalized Method and 0.4% for the Improved Uniform Density Method. The adjusted thorax density found from the 3D reconstruction was 0.74g/cm(3) for men and 0.73g/cm(3) for women instead of the one provided by Dempster (0.92g/cm(3)), leading to a better estimate of the thorax mass and body mass.

  3. A nanofiber based artificial electronic skin with high pressure sensitivity and 3D conformability.

    PubMed

    Zhong, Weibin; Liu, Qiongzhen; Wu, Yongzhi; Wang, Yuedan; Qing, Xing; Li, Mufang; Liu, Ke; Wang, Wenwen; Wang, Dong

    2016-06-16

    Pressure sensors with 3D conformability are highly desirable components for artificial electronic skin or e-textiles that can mimic natural skin, especially for application in real-time monitoring of human physiological signals. Here, a nanofiber based electronic skin with ultra-high pressure sensitivity and 3D conformability is designed and built by interlocking two elastic patterned nanofibrous membranes. The patterned membrane is facilely prepared by casting conductive nanofiber ink into a silicon mould to form an array of semi-spheroid-like protuberances. The protuberances composed of intertwined elastic POE nanofibers and PPy@PVA-co-PE nanofibers afford a tunable effective elastic modulus that is capable of capturing varied strains and stresses, thereby contributing to a high sensitivity for pressure sensing. This electronic skin-like sensor demonstrates an ultra-high sensitivity (1.24 kPa(-1)) below 150 Pa with a detection limit as low as about 1.3 Pa. The pixelated sensor array and a RGB-LED light are then assembled into a circuit and show a feasibility for visual detection of spatial pressure. Furthermore, a nanofiber based proof-of-concept wireless pressure sensor with a bluetooth module as a signal transmitter is proposed and has demonstrated great promise for wireless monitoring of human physiological signals, indicating a potential for large scale wearable electronic devices or e-skin. PMID:27250529

  4. Characterization of 3D interconnected microstructural network in mixed ionic and electronic conducting ceramic composites

    NASA Astrophysics Data System (ADS)

    Harris, William M.; Brinkman, Kyle S.; Lin, Ye; Su, Dong; Cocco, Alex P.; Nakajo, Arata; Degostin, Matthew B.; Chen-Wiegart, Yu-Chen Karen; Wang, Jun; Chen, Fanglin; Chu, Yong S.; Chiu, Wilson K. S.

    2014-04-01

    The microstructure and connectivity of the ionic and electronic conductive phases in composite ceramic membranes are directly related to device performance. Transmission electron microscopy (TEM) including chemical mapping combined with X-ray nanotomography (XNT) have been used to characterize the composition and 3-D microstructure of a MIEC composite model system consisting of a Ce0.8Gd0.2O2 (GDC) oxygen ion conductive phase and a CoFe2O4 (CFO) electronic conductive phase. The microstructural data is discussed, including the composition and distribution of an emergent phase which takes the form of isolated and distinct regions. Performance implications are considered with regards to the design of new material systems which evolve under non-equilibrium operating conditions.The microstructure and connectivity of the ionic and electronic conductive phases in composite ceramic membranes are directly related to device performance. Transmission electron microscopy (TEM) including chemical mapping combined with X-ray nanotomography (XNT) have been used to characterize the composition and 3-D microstructure of a MIEC composite model system consisting of a Ce0.8Gd0.2O2 (GDC) oxygen ion conductive phase and a CoFe2O4 (CFO) electronic conductive phase. The microstructural data is discussed, including the composition and distribution of an emergent phase which takes the form of isolated and distinct regions. Performance implications are considered with regards to the design of new material systems which evolve under non-equilibrium operating conditions. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr06684c

  5. Dipole approximation in the L2,3 electron excited spectra in 3d transition metals

    NASA Astrophysics Data System (ADS)

    Nuroh, K.

    2008-12-01

    A theoretical model based on the autoionization and characteristic decay processes following electron impact ionization of a core electron in solids that has previously been used in calculating electron-energy-loss spectra of transition metals near the 3p -excitation edge has been extended to the 2p -excitation edge for S21c through N27i as well. In the first set of calculations, magnetic effects were ignored and the relative scattering intensity was formulated in terms of the electrostatic interaction U(p,d) between the 3p and 3d electrons of the intermediate resonant configuration state p5dn+1 , using many-body perturbation theory that led to a generalized Fano-type formula for the intensity profiles. In the second set of calculations in which magnetic effects were included as well, an analysis based on the Bethe-Born formalism of inelastic scattering of electrons on atoms was used. The nature of the relative magnitudes of U(p,d) and the spin-orbit parameters ς3p and ς3d and the localized nature of the 3p state necessitated the diagonalization of the intermediate configuration state p5dn+1 to determine the multiplet splitting and their corresponding intensities in the LS -coupling limit using fractional parentage scheme. The nonrelativistic multiconfiguration Hartree-Fock (MCHF) code was used in determining the ground and continuum state wave functions, and the itinerant 3d states in the solid were approximated with an atomic MCHF-wave function. The outline above is applied to the 2p -excitation edge, except that because of the relative magnitudes of U(p,d) , ς2p , and ς3d , it is found that LK coupling is suitable for Sc, Ti, and V, while jK coupling is appropriate for Cr to Ni when it comes to the diagonalization of the configuration p5dn+1 to determine the multiplet splitting and their associated scattering intensities. In the dipole approximation, the scattering intensities separate into two distinct manifolds that arise from the p3/2 and p1/2 states. The

  6. Electron Microscopy: From 2D to 3D Images with Special Reference to Muscle

    PubMed Central

    2015-01-01

    This is a brief and necessarily very sketchy presentation of the evolution in electron microscopy (EM) imaging that was driven by the necessity of extracting 3-D views from the essentially 2-D images produced by the electron beam. The lens design of standard transmission electron microscope has not been greatly altered since its inception. However, technical advances in specimen preparation, image collection and analysis gradually induced an astounding progression over a period of about 50 years. From the early images that redefined tissues, cell and cell organelles at the sub-micron level, to the current nano-resolution reconstructions of organelles and proteins the step is very large. The review is written by an investigator who has followed the field for many years, but often from the sidelines, and with great wonder. Her interest in muscle ultrastructure colors the writing. More specific detailed reviews are presented in this issue. PMID:26913146

  7. Electron Microscopy: From 2D to 3D Images with Special Reference to Muscle.

    PubMed

    Franzini-Armstrong, Clara

    2015-01-01

    This is a brief and necessarily very sketchy presentation of the evolution in electron microscopy (EM) imaging that was driven by the necessity of extracting 3-D views from the essentially 2-D images produced by the electron beam. The lens design of standard transmission electron microscope has not been greatly altered since its inception. However, technical advances in specimen preparation, image collection and analysis gradually induced an astounding progression over a period of about 50 years. From the early images that redefined tissues, cell and cell organelles at the sub-micron level, to the current nano-resolution reconstructions of organelles and proteins the step is very large. The review is written by an investigator who has followed the field for many years, but often from the sidelines, and with great wonder. Her interest in muscle ultrastructure colors the writing. More specific detailed reviews are presented in this issue. PMID:26913146

  8. 3-D readout-electronics packaging for high-bandwidth massively paralleled imager

    DOEpatents

    Kwiatkowski, Kris; Lyke, James

    2007-12-18

    Dense, massively parallel signal processing electronics are co-packaged behind associated sensor pixels. Microchips containing a linear or bilinear arrangement of photo-sensors, together with associated complex electronics, are integrated into a simple 3-D structure (a "mirror cube"). An array of photo-sensitive cells are disposed on a stacked CMOS chip's surface at a 45.degree. angle from light reflecting mirror surfaces formed on a neighboring CMOS chip surface. Image processing electronics are held within the stacked CMOS chip layers. Electrical connections couple each of said stacked CMOS chip layers and a distribution grid, the connections for distributing power and signals to components associated with each stacked CSMO chip layer.

  9. Self-Consistent 3D Modeling of Electron Cloud Dynamics and Beam Response

    SciTech Connect

    Furman, Miguel; Furman, M.A.; Celata, C.M.; Kireeff-Covo, M.; Sonnad, K.G.; Vay, J.-L.; Venturini, M.; Cohen, R.; Friedman, A.; Grote, D.; Molvik, A.; Stoltz, P.

    2007-04-02

    We present recent advances in the modeling of beam electron-cloud dynamics, including surface effects such as secondary electron emission, gas desorption, etc, and volumetric effects such as ionization of residual gas and charge-exchange reactions. Simulations for the HCX facility with the code WARP/POSINST will be described and their validity demonstrated by benchmarks against measurements. The code models a wide range of physical processes and uses a number of novel techniques, including a large-timestep electron mover that smoothly interpolates between direct orbit calculation and guiding-center drift equations, and a new computational technique, based on a Lorentz transformation to a moving frame, that allows the cost of a fully 3D simulation to be reduced to that of a quasi-static approximation.

  10. 3D Imaging of Diatoms with Ion-abrasion Scanning Electron Microscopy

    PubMed Central

    Hildebrand, Mark; Kim, Sang; Shi, Dan; Scott, Keana; Subramaniam, Sriram

    2009-01-01

    Ion-abrasion scanning electron microscopy (IASEM) takes advantage of focused ion beams to abrade thin sections from the surface of bulk specimens, coupled with SEM to image the surface of each section, enabling 3D reconstructions of subcellular architecture at ~ 30 nm resolution. Here, we report the first application of IASEM for imaging a biomineralizing organism, the marine diatom Thalassiosira pseudonana. Diatoms have highly patterned silica-based cell wall structures that are unique models for the study and application of directed nanomaterials synthesis by biological systems. Our study provides new insights into the architecture and assembly principles of both the “hard” (siliceous) and “soft” (organic) components of the cell. From 3D reconstructions of developmentally synchronized diatoms captured at different stages, we show that both micro- and nanoscale siliceous structures can be visualized at specific stages in their formation. We show that not only are structures visualized in a whole-cell context, but demonstrate that fragile, early-stage structures are visible, and that this can be combined with elemental mapping in the exposed slice. We demonstrate that the 3D architectures of silica structures, and the cellular components that mediate their creation and positioning can be visualized simultaneously, providing new opportunities to study and manipulate mineral nanostructures in a genetically tractable system. PMID:19269330

  11. Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.

    PubMed

    de la Rosa-Trevín, J M; Quintana, A; Del Cano, L; Zaldívar, A; Foche, I; Gutiérrez, J; Gómez-Blanco, J; Burguet-Castell, J; Cuenca-Alba, J; Abrishami, V; Vargas, J; Otón, J; Sharov, G; Vilas, J L; Navas, J; Conesa, P; Kazemi, M; Marabini, R; Sorzano, C O S; Carazo, J M

    2016-07-01

    In the past few years, 3D electron microscopy (3DEM) has undergone a revolution in instrumentation and methodology. One of the central players in this wide-reaching change is the continuous development of image processing software. Here we present Scipion, a software framework for integrating several 3DEM software packages through a workflow-based approach. Scipion allows the execution of reusable, standardized, traceable and reproducible image-processing protocols. These protocols incorporate tools from different programs while providing full interoperability among them. Scipion is an open-source project that can be downloaded from http://scipion.cnb.csic.es. PMID:27108186

  12. Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.

    PubMed

    de la Rosa-Trevín, J M; Quintana, A; Del Cano, L; Zaldívar, A; Foche, I; Gutiérrez, J; Gómez-Blanco, J; Burguet-Castell, J; Cuenca-Alba, J; Abrishami, V; Vargas, J; Otón, J; Sharov, G; Vilas, J L; Navas, J; Conesa, P; Kazemi, M; Marabini, R; Sorzano, C O S; Carazo, J M

    2016-07-01

    In the past few years, 3D electron microscopy (3DEM) has undergone a revolution in instrumentation and methodology. One of the central players in this wide-reaching change is the continuous development of image processing software. Here we present Scipion, a software framework for integrating several 3DEM software packages through a workflow-based approach. Scipion allows the execution of reusable, standardized, traceable and reproducible image-processing protocols. These protocols incorporate tools from different programs while providing full interoperability among them. Scipion is an open-source project that can be downloaded from http://scipion.cnb.csic.es.

  13. 3-D wave propagation solution of a stable resonator, free-electron laser

    NASA Astrophysics Data System (ADS)

    Bhowmik, A.; Cover, R. A.; Labbe, R. H.

    1983-11-01

    Rigorous numerical solutions of a stable resonator, free-electron laser are obtained using 3-D wave propagation algorithms in the presence of a radially and azimuthally varying gain. Assumptions of this time-independent formulation of the loaded-resonator cavity are discussed. Wave propagation in the cavity is performed by computing numerically the Fresnel-Kirchoff diffraction integral by the Gardner-Fresnel-Kirchoff algorithm. Results of steady-state numerical iterative solutions, in which both the gain and the optical fields achieve self-consistency throughout the resonator, are presented. These consist of: (1) mode pattern and (2) variations in gain with variations in the resonator parameters.

  14. 3D scanning electron microscopy applied to surface characterization of fluorosed dental enamel.

    PubMed

    Limandri, Silvina; Galván Josa, Víctor; Valentinuzzi, María Cecilia; Chena, María Emilia; Castellano, Gustavo

    2016-05-01

    The enamel surfaces of fluorotic teeth were studied by scanning electron stereomicroscopy. Different whitening treatments were applied to 25 pieces to remove stains caused by fluorosis and their surfaces were characterized by stereomicroscopy in order to obtain functional and amplitude parameters. The topographic features resulting for each treatment were determined through these parameters. The results obtained show that the 3D reconstruction achieved from the SEM stereo pairs is a valuable potential alternative for the surface characterization of this kind of samples. PMID:26930005

  15. Scanning transmission and computer-aided volumic electron microscopy: 3-D modeling of entire cells by electronic imaging

    NASA Astrophysics Data System (ADS)

    Bron, Christophe; Gremillet, Philip; Launay, D.; Jourlin, Michel; Gautschi, H. P.; Baechi, Thomas; Schuepbach, Joerg

    1990-05-01

    The digital processing of electron microscopic images from serial sections containing laser-induced topographical references allows a 3-D reconstruction at a depth resolution of 30 to 40 nm of entire cells by the use of image analysis methods, as already demonstrated for Transmission Electron Microscopy (TEM) coupled with a video camera. We decided to use a Scanning Transmission Electron Microscope (STEM) to get higher contrast and better resolution at medium magnification. The scanning of our specimens at video frequencies is an attractive and easy way to link a STEM with an image processing system but the hysteresis of the electronic spools responsible for the magnetic deviation of the scanning electron beam induces deformations of images which have to be modelized and corrected before registration. Computer algorithms developed for image analysis and treatment correct the artifacts caused by the use of STEM and by serial sectioning to automatically reconstruct the third dimension of the cells. They permit the normalization of the images through logarithmic processing of the original grey level infonnation. The automatic extraction of cell limits allows to link the image analysis and treatments with image synthesis methods by minimal human intervention. The surface representation and the registered images provide an ultrastructural data base from which quantitative 3-D morphological parameters, as well as otherwise impossible visualizations, can be computed. This 3-D image processing named C.A.V.U.M. for Computer Aided Volumic Ultra-Microscopy offers a new tool for the documentation and analysis of cell ultrastructure and for 3-D morphometric studies at EM magnifications. Further, a virtual observer can be computed in such a way as to simulate a visit of the reconstructed object.

  16. A nanofiber based artificial electronic skin with high pressure sensitivity and 3D conformability

    NASA Astrophysics Data System (ADS)

    Zhong, Weibin; Liu, Qiongzhen; Wu, Yongzhi; Wang, Yuedan; Qing, Xing; Li, Mufang; Liu, Ke; Wang, Wenwen; Wang, Dong

    2016-06-01

    Pressure sensors with 3D conformability are highly desirable components for artificial electronic skin or e-textiles that can mimic natural skin, especially for application in real-time monitoring of human physiological signals. Here, a nanofiber based electronic skin with ultra-high pressure sensitivity and 3D conformability is designed and built by interlocking two elastic patterned nanofibrous membranes. The patterned membrane is facilely prepared by casting conductive nanofiber ink into a silicon mould to form an array of semi-spheroid-like protuberances. The protuberances composed of intertwined elastic POE nanofibers and PPy@PVA-co-PE nanofibers afford a tunable effective elastic modulus that is capable of capturing varied strains and stresses, thereby contributing to a high sensitivity for pressure sensing. This electronic skin-like sensor demonstrates an ultra-high sensitivity (1.24 kPa-1) below 150 Pa with a detection limit as low as about 1.3 Pa. The pixelated sensor array and a RGB-LED light are then assembled into a circuit and show a feasibility for visual detection of spatial pressure. Furthermore, a nanofiber based proof-of-concept wireless pressure sensor with a bluetooth module as a signal transmitter is proposed and has demonstrated great promise for wireless monitoring of human physiological signals, indicating a potential for large scale wearable electronic devices or e-skin.Pressure sensors with 3D conformability are highly desirable components for artificial electronic skin or e-textiles that can mimic natural skin, especially for application in real-time monitoring of human physiological signals. Here, a nanofiber based electronic skin with ultra-high pressure sensitivity and 3D conformability is designed and built by interlocking two elastic patterned nanofibrous membranes. The patterned membrane is facilely prepared by casting conductive nanofiber ink into a silicon mould to form an array of semi-spheroid-like protuberances. The

  17. Runaway electron production in DIII-D killer pellet experiments, calculated with the CQL3D/KPRAD model

    SciTech Connect

    Harvey, R. W.; Chan, V. S.; Chiu, S. C.; Evans, T. E.; Rosenbluth, M. N.; Whyte, D. G.

    2000-11-01

    Runaway electrons are calculated to be produced during the rapid plasma cooling resulting from ''killer pellet'' injection experiments, in general agreement with observations in the DIII-D [J. L. Luxon , Plasma Physics and Controlled Nuclear Fusion Research 1986 (International Atomic Energy Agency, Vienna, 1987), Vol. I, p. 159] tokamak. The time-dependent dynamics of the kinetic runaway distributions are obtained with the CQL3D [R. W. Harvey and M. G. McCoy, ''The CQL3D Code,'' in Proceedings of the IAEA Technical Committee Meeting on Numerical Modeling, Montreal, 1992 (International Atomic Energy Agency, Vienna, 1992), p. 489] collisional Fokker--Planck code, including the effect of small and large angle collisions and stochastic magnetic field transport losses. The background density, temperature, and Z{sub eff} are evolved according to the KPRAD [D. G. Whyte and T. E. Evans , in Proceedings of the 24th European Conference on Controlled Fusion and Plasma Physics, Berchtesgaden, Germany (European Physical Society, Petit-Lancy, 1997), Vol. 21A, p. 1137] deposition and radiation model of pellet--plasma interactions. Three distinct runway mechanisms are apparent: (1) prompt ''hot-tail runaways'' due to the residual hot electron tail remaining from the pre-cooling phase, (2) ''knock-on'' runaways produced by large-angle Coulomb collisions on existing high energy electrons, and (3) Dreicer ''drizzle'' runaway electrons due to diffusion of electrons up to the critical velocity for electron runaway. For electron densities below {approx}1x10{sup 15}cm{sup -3}, the hot-tail runaways dominate the early time evolution, and provide the seed population for late time knock-on runaway avalanche. For small enough stochastic magnetic field transport losses, the knock-on production of electrons balances the losses at late times. For losses due to radial magnetic field perturbations in excess of {approx}0.1% of the background field, i.e., {delta}B{sub r}/B{>=}0.001, the losses

  18. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography

    PubMed Central

    Nicastro, Daniela; McIntosh, J. Richard; Baumeister, Wolfgang

    2005-01-01

    We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozen-hydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ. PMID:16246999

  19. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography.

    PubMed

    Nicastro, Daniela; McIntosh, J Richard; Baumeister, Wolfgang

    2005-11-01

    We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozen-hydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ. PMID:16246999

  20. 3D mapping of nanoscale electric potentials in semiconductor structures using electron-holographic tomography

    NASA Astrophysics Data System (ADS)

    Wolf, Daniel; Lubk, Axel; Prete, Paola; Lovergine, Nico; Lichte, Hannes

    2016-09-01

    Off-axis electron holography (EH) is a powerful method for mapping projected electric potentials, such as built-in potentials in semiconductor devices, in two dimensions (2D) at nanometer resolution. However, not well-defined thickness profiles, surface effects, and composition changes of the sample under investigation complicate the interpretation of the projected potentials. Here, we demonstrate how these problems can be overcome by combining EH with tomographic techniques, that is, electron holographic tomography (EHT), reconstructing electric potentials in 3D. We present EHT reconstructions of an n-type MOSFET including its dopant-related built-in potentials inside the device, as well as of a GaAs/AlGaAs core-multishell nanowire containing a 5 nm thick quantum well tube.

  1. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography.

    PubMed

    Nicastro, Daniela; McIntosh, J Richard; Baumeister, Wolfgang

    2005-11-01

    We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozen-hydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ.

  2. Cellulose Nanocrystals as Chiral Inducers: Enantioselective Catalysis and Transmission Electron Microscopy 3D Characterization.

    PubMed

    Kaushik, Madhu; Basu, Kaustuv; Benoit, Charles; Cirtiu, Ciprian M; Vali, Hojatollah; Moores, Audrey

    2015-05-20

    Cellulose nanocrystals (CNCs), derived from cellulose, provide us with an opportunity to devise more sustainable solutions to current technological challenges. Enantioselective catalysis, especially heterogeneous, is the preferred method for the synthesis of pure chiral molecules in the fine chemical industries. Cellulose has been long sought as a chiral inducer in enantioselective catalysis. We report herein an unprecedentedly high enantiomeric excess (ee) for Pd patches deposited onto CNCs used as catalysts for the hydrogenation of prochiral ketones in water at room temperature and 4 bar H2. Our system, where CNCs acted as support and sole chiral source, achieved an ee of 65% with 100% conversions. Cryo-electron microscopy, high-resolution transmission electron microscopy, and tomography were used for the first time to study the 3D structure of a metal functionalized CNC hybrid. It established the presence of sub-nanometer-thick Pd patches at the surface of CNCs and provided insight into the chiral induction mechanism.

  3. Inductively Driven, 3D Liner Compression of a Magnetized Plasma to Megabar Energy Densities

    SciTech Connect

    Slough, John

    2015-02-01

    modules. The additional energy and switching capability proposed will thus provide for optimal utilization of the liner energy. The following tasks were outlined for the three year effort: (1) Design and assemble the foil liner compression test structure and chamber including the compression bank and test foils [Year 1]. (2) Perform foil liner compression experiments and obtain performance data over a range on liner dimensions and bank parameters [Year 2]. (3) Carry out compression experiments of the FRC plasma to Megagauss fields and measure key fusion parameters [Year 3]. (4) Develop numerical codes and analyze experimental results, and determine the physics and scaling for future work [Year 1-3]. The principle task of the project was to design and assemble the foil liner FRC formation chamber, the full compression test structure and chamber including the compression bank. This task was completed successfully. The second task was to test foils in the test facility constructed in year one and characterize the performance obtained from liner compression. These experimental measurements were then compared with analytical predictions, and numerical code results. The liner testing was completed and compared with both the analytical results as well as the code work performed with the 3D structural dynamics package of ANSYS Metaphysics®. This code is capable of modeling the dynamic behavior of materials well into the non-linear regime (e.g. a bullet hit plate glass). The liner dynamic behavior was found to be remarkably close to that predicted by the 3D structural dynamics results. Incorporating a code that can also include the magnetics and plasma physics has also made significant progress at the UW. The remaining test bed construction and assembly task is was completed, and the FRC formation and merging experiments were carried out as planned. The liner compression of the FRC to Megagauss fields was not performed due to not obtaining a sufficiently long lived FRC during the

  4. Predicting the Electronic Properties of 3D, Million-atom Semiconductor nanostructure Architectures

    SciTech Connect

    Jack Dongarra; Stanimire Tomov

    2012-03-15

    This final report describes the work done by Jack Dongarra (University Distinguished Professor) and Stanimire Tomov (Research Scientist) related to the DOE project entitled Predicting the Electronic Properties of 3D, Million-Atom Semiconductor Nanostructure Architectures. In this project we addressed the mathematical methodology required to calculate the electronic and transport properties of large nanostructures with comparable accuracy and reliability to that of current ab initio methods. This capability is critical for further developing the field, yet it is missing in all the existing computational methods. Additionally, quantitative comparisons with experiments are often needed for a qualitative understanding of the physics, and for guiding the design of new nanostructures. We focused on the mathematical challenges of the project, in particular on solvers and preconditioners for large scale eigenvalue problems that occur in the computation of electronic states of large nanosystems. Usually, the states of interest lie in the interior of the spectrum and their computation poses great difficulties for existing algorithms. The electronic properties of a semiconductor nanostructure architecture can be predicted/determined by computing its band structure. Of particular importance are the 'band edge states' (electronic states near the energy gap) which can be computed from a properly defined interior eigenvalue problem. Our primary mathematics and computational challenge here has been to develop an efficient solution methodology for finding these interior states for very large systems. Our work has produced excellent results in terms of developing both new and extending current state-of-the-art techniques.

  5. Computational 3D reconstructions by optimization for cryo-electron microscopy

    NASA Astrophysics Data System (ADS)

    Yin, Zhye; Zheng, Yili; Doerschuk, Peter C.; Johnson, John E.

    2003-06-01

    An algorithm for the simultaneous 3-D reconstruction of several types of object, where each type of object may possibly have a rotational symmetry, from 2-D projection images, where for each image the type of object imaged, the projection orientation used to create the image, and the location of the object in the image are unknown, is described. The motivating application is the determination of the 3-D structure of small spherical viruses from cryo electron microscopy images. The algorithm is a maximum likelihood estimator which is computed by expectation maximization (EM). Due to the structure of the statistical model, the maximization step of EM can be easily computed but the expectation step requires 5-D numerical quadrature. The computational burden of the quadratures necessitates parallel computation and three different implementations of two different types of parallelism have been developed using pthreads (for shared memory processors) and MPI (for distributed memory processors). An example applying one of the MPI implementations, running on a 32 node PC cluster, to experimental images of Flock House Virus with comparison to the x-ray crystal diffraction structure of the virus is described.

  6. Microdefects and 3 d electrons in ordered B2-FeAl alloys investigated by positron annihilation techniques

    NASA Astrophysics Data System (ADS)

    Yuyang, Huang; Yanqiong, Lu; Yanyan, Zhu; Yuxia, Li; Wen, Deng

    2009-09-01

    Microdefects and 3d electrons in B2-FeAl alloys with different chemical composition, single crystal of Fe and cold-rolled Fe has been studied by positron lifetime and coincidence Doppler broadening spectroscopy. The coincidence Doppler broadening spectrum of the single crystal of Fe shows the highest 3d electron signal in the spectra of all tested samples. The 3d electron signal in the spectrum of Fe50Al50 alloy is much lower than that of the cold-rolled Fe. This indicates that some of the 3d electrons of Fe atoms and 3p electrons of Al atoms in B2-FeAl alloy are localized to form strong covalent bonds, thus decreasing the probability of positron annihilation with 3d electrons of Fe atoms. With the increase of Al content in B2-FeAl alloys, the 3d electron signal in the spectrum of the alloy decreases, while the open volume of defect increases.

  7. Investigation of resins suitable for the preparation of biological sample for 3-D electron microscopy.

    PubMed

    Kizilyaprak, Caroline; Longo, Giovanni; Daraspe, Jean; Humbel, Bruno M

    2015-02-01

    In the last two decades, the third-dimension has become a focus of attention in electron microscopy to better understand the interactions within subcellular compartments. Initially, transmission electron tomography (TEM tomography) was introduced to image the cell volume in semi-thin sections (∼ 500 nm). With the introduction of the focused ion beam scanning electron microscope, a new tool, FIB-SEM tomography, became available to image much larger volumes. During TEM tomography and FIB-SEM tomography, the resin section is exposed to a high electron/ion dose such that the stability of the resin embedded biological sample becomes an important issue. The shrinkage of a resin section in each dimension, especially in depth, is a well-known phenomenon. To ensure the dimensional integrity of the final volume of the cell, it is important to assess the properties of the different resins and determine the formulation which has the best stability in the electron/ion beam. Here, eight different resin formulations were examined. The effects of radiation damage were evaluated after different times of TEM irradiation. To get additional information on mass-loss and the physical properties of the resins (stiffness and adhesion), the topography of the irradiated areas was analysed with atomic force microscopy (AFM). Further, the behaviour of the resins was analysed after ion milling of the surface of the sample with different ion currents. In conclusion, two resin formulations, Hard Plus and the mixture of Durcupan/Epon, emerged that were considerably less affected and reasonably stable in the electron/ion beam and thus suitable for the 3-D investigation of biological samples. PMID:25433274

  8. Mapping electronic ordering in chromium in 3D with x-ray microdiffraction

    NASA Astrophysics Data System (ADS)

    Xu, Ruqing

    2015-03-01

    In the antiferromagnetic state of chromium, electrons form spin-density waves and charge-density waves with wave vector along one of the lattice cubic axes; the spontaneous ordering of the electrons breaks the lattice symmetry and creates domains within a single crystal. We report the first 3-dimentional mapping of charge-density wave domains in bulk polycrystalline chromium samples using differential-aperture x-ray microdiffraction at the Advanced Photon Source. This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357

  9. Single-Particle Cryo-EM and 3D Reconstruction of Hybrid Nanoparticles with Electron-Dense Components.

    PubMed

    Yu, Guimei; Yan, Rui; Zhang, Chuan; Mao, Chengde; Jiang, Wen

    2015-10-01

    Single-particle cryo-electron microscopy (cryo-EM), accompanied with 3D reconstruction, is a broadly applicable tool for the structural characterization of macromolecules and nanoparticles. Recently, the cryo-EM field has pushed the limits of this technique to higher resolutions and samples of smaller molecular mass, however, some samples still present hurdles to this technique. Hybrid particles with electron-dense components, which have been studied using single-particle cryo-EM yet with limited success in 3D reconstruction due to the interference caused by electron-dense elements, constitute one group of such challenging samples. To process such hybrid particles, a masking method is developed in this work to adaptively remove pixels arising from electron-dense portions in individual projection images while maintaining maximal biomass signals for subsequent 2D alignment, 3D reconstruction, and iterative refinements. As demonstrated by the success in 3D reconstruction of an octahedron DNA/gold hybrid particle, which has been previously published without a 3D reconstruction, the devised strategy that combines adaptive masking and standard single-particle 3D reconstruction approach has overcome the hurdle of electron-dense elements interference, and is generally applicable to cryo-EM structural characterization of most, if not all, hybrid nanomaterials with electron-dense components.

  10. 3D Reconstruction of the Glycocalyx Structure in Mammalian Capillaries using Electron Tomography

    PubMed Central

    Arkill, KP; Neal, CR; Mantell, JM; Michel, CC; Qvortrup, K; Bates, DO; Knupp, C; Squire, JM

    2013-01-01

    Visualising the molecular strands making up the glycocalyx in the lumen of small blood vessels has proved to be difficult using conventional transmission electron microscopy techniques. Images obtained from tissue stained in a variety of ways have revealed a regularity in the organisation of the proteoglycan components of the glycocalyx layer (fundamental spacing about 20 nm), but require a large sample number. Attempts to visualise the glycocalyx face-on (i.e. in a direction perpendicular to the endothelial cell layer in the lumen and directly applicable for permeability modelling) has had limited success (e.g. freeze fracture). A new approach is therefore needed. Here we demonstrate the effectiveness of using the relatively novel electron microscopy technique of 3D electron tomography on two differently stained preparations to reveal details of the architecture of the glycocalyx just above the endothelial cell layer. One preparation uses the novel staining technique using Lanthanum Dysprosium Glycosamino Glycan adhesion (the LaDy GAGa method). PMID:22324320

  11. Interaction of 3d transition metal atoms with charged ion projectiles from Electron Nuclear Dynamics computation

    NASA Astrophysics Data System (ADS)

    Hagelberg, Frank

    2003-03-01

    Computational results on atomic scattering between charged projectiles and transition metal target atoms are presented. This work aims at obtaining detailed information about charge, spin and energy transfer processes that occur between the interacting particles. An in-depth understanding of these phenomena is expected to provide a theoretical basis for the interpretation of various types of ion beam experiments, ranging from gas phase chromatography to spectroscopic observations of fast ions in ferromagnetic media. This contribution focuses on the scattering of light projectiles ranging from He to O, that are prepared in various initial charge states, by 3d transition metal atoms. The presented computations are performed in the framework of Electron Nuclear Dynamics (END)^1 theory which incorporates the coupling between electronic and nuclear degrees of freedom without reliance on the computationally cumbersome and frequently intractable determination of potential energy surfaces. In the present application of END theory to ion - transition metal atom scattering, a supermolecule approach is utilized in conjunction with a spin-unrestricted single determinantal wave function describing the electronic system. Integral scattering, charge and spin exchange cross sections are discussed as functions of the elementary parameters of the problem, such as projectile and target atomic numbers as well as projectile charge and initial kinetic energy. ^1 E.Deumens, A.Diz, R.Longo, Y.Oehrn, Rev.Mod.Phys. 66, 917 (1994)

  12. All oxide semiconductor-based bidirectional vertical p-n-p selectors for 3D stackable crossbar-array electronics

    PubMed Central

    Bae, Yoon Cheol; Lee, Ah Rahm; Baek, Gwang Ho; Chung, Je Bock; Kim, Tae Yoon; Park, Jea Gun; Hong, Jin Pyo

    2015-01-01

    Three-dimensional (3D) stackable memory devices including nano-scaled crossbar array are central for the realization of high-density non-volatile memory electronics. However, an essential sneak path issue affecting device performance in crossbar array remains a bottleneck and a grand challenge. Therefore, a suitable bidirectional selector as a two-way switch is required to facilitate a major breakthrough in the 3D crossbar array memory devices. Here, we show the excellent selectivity of all oxide p-/n-type semiconductor-based p-n-p open-based bipolar junction transistors as selectors in crossbar memory array. We report that bidirectional nonlinear characteristics of oxide p-n-p junctions can be highly enhanced by manipulating p-/n-type oxide semiconductor characteristics. We also propose an associated Zener tunneling mechanism that explains the unique features of our p-n-p selector. Our experimental findings are further extended to confirm the profound functionality of oxide p-n-p selectors integrated with several bipolar resistive switching memory elements working as storage nodes. PMID:26289565

  13. Synthesis of ultralow density 3D graphene-CNT foams using a two-step method.

    PubMed

    Vinod, Soumya; Tiwary, Chandra Sekhar; Machado, Leonardo D; Ozden, Sehmus; Vajtai, Robert; Galvao, Douglas S; Ajayan, Pulickel M

    2016-09-21

    Here, we report a highly scalable two-step method to produce graphene foams with ordered carbon nanotube reinforcements. In our approach, we first used solution assembly methods to obtain graphene oxide foam. Next, we employed chemical vapor deposition to simultaneously grow carbon nanotubes and thermally reduce the 3D graphene oxide scaffold. The resulting structure presented increased stiffness, good mechanical stability and oil absorption properties. Molecular dynamics simulations were carried out to further elucidate failure mechanisms and to understand the enhancement of the mechanical properties. The simulations showed that mechanical failure is directly associated with bending of vertical reinforcements, and that, for similar length and contact area, much more stress is required to bend the corresponding reinforcements of carbon nanotubes, thus explaining the experimentally observed enhanced mechanical properties. PMID:27546001

  14. Synthesis of ultralow density 3D graphene-CNT foams using a two-step method.

    PubMed

    Vinod, Soumya; Tiwary, Chandra Sekhar; Machado, Leonardo D; Ozden, Sehmus; Vajtai, Robert; Galvao, Douglas S; Ajayan, Pulickel M

    2016-09-21

    Here, we report a highly scalable two-step method to produce graphene foams with ordered carbon nanotube reinforcements. In our approach, we first used solution assembly methods to obtain graphene oxide foam. Next, we employed chemical vapor deposition to simultaneously grow carbon nanotubes and thermally reduce the 3D graphene oxide scaffold. The resulting structure presented increased stiffness, good mechanical stability and oil absorption properties. Molecular dynamics simulations were carried out to further elucidate failure mechanisms and to understand the enhancement of the mechanical properties. The simulations showed that mechanical failure is directly associated with bending of vertical reinforcements, and that, for similar length and contact area, much more stress is required to bend the corresponding reinforcements of carbon nanotubes, thus explaining the experimentally observed enhanced mechanical properties.

  15. Low-Amplitude Craniofacial EMG Power Spectral Density and 3D Muscle Reconstruction from MRI.

    PubMed

    Wiedemann, Lukas; Chaberova, Jana; Edmunds, Kyle; Einarsdóttir, Guðrún; Ramon, Ceon; Gargiulo, Paolo

    2015-03-11

    Improving EEG signal interpretation, specificity, and sensitivity is a primary focus of many current investigations, and the successful application of EEG signal processing methods requires a detailed knowledge of both the topography and frequency spectra of low-amplitude, high-frequency craniofacial EMG. This information remains limited in clinical research, and as such, there is no known reliable technique for the removal of these artifacts from EEG data. The results presented herein outline a preliminary investigation of craniofacial EMG high-frequency spectra and 3D MRI segmentation that offers insight into the development of an anatomically-realistic model for characterizing these effects. The data presented highlights the potential for confounding signal contribution from around 60 to 200 Hz, when observed in frequency space, from both low and high-amplitude EMG signals. This range directly overlaps that of both low γ (30-50 Hz) and high γ (50-80 Hz) waves, as defined traditionally in standatrd EEG measurements, and mainly with waves presented in dense-array EEG recordings. Likewise, average EMG amplitude comparisons from each condition highlights the similarities in signal contribution of low-activity muscular movements and resting, control conditions. In addition to the FFT analysis performed, 3D segmentation and reconstruction of the craniofacial muscles whose EMG signals were measured was successful. This recapitulation of the relevant EMG morphology is a crucial first step in developing an anatomical model for the isolation and removal of confounding low-amplitude craniofacial EMG signals from EEG data. Such a model may be eventually applied in a clinical setting to ultimately help to extend the use of EEG in various clinical roles. PMID:26913150

  16. Low-Amplitude Craniofacial EMG Power Spectral Density and 3D Muscle Reconstruction from MRI

    PubMed Central

    Wiedemann, Lukas; Chaberova, Jana; Edmunds, Kyle; Einarsdóttir, Guðrún; Ramon, Ceon

    2015-01-01

    Improving EEG signal interpretation, specificity, and sensitivity is a primary focus of many current investigations, and the successful application of EEG signal processing methods requires a detailed knowledge of both the topography and frequency spectra of low-amplitude, high-frequency craniofacial EMG. This information remains limited in clinical research, and as such, there is no known reliable technique for the removal of these artifacts from EEG data. The results presented herein outline a preliminary investigation of craniofacial EMG high-frequency spectra and 3D MRI segmentation that offers insight into the development of an anatomically-realistic model for characterizing these effects. The data presented highlights the potential for confounding signal contribution from around 60 to 200 Hz, when observed in frequency space, from both low and high-amplitude EMG signals. This range directly overlaps that of both low γ (30-50 Hz) and high γ (50-80 Hz) waves, as defined traditionally in standatrd EEG measurements, and mainly with waves presented in dense-array EEG recordings. Likewise, average EMG amplitude comparisons from each condition highlights the similarities in signal contribution of low-activity muscular movements and resting, control conditions. In addition to the FFT analysis performed, 3D segmentation and reconstruction of the craniofacial muscles whose EMG signals were measured was successful. This recapitulation of the relevant EMG morphology is a crucial first step in developing an anatomical model for the isolation and removal of confounding low-amplitude craniofacial EMG signals from EEG data. Such a model may be eventually applied in a clinical setting to ultimately help to extend the use of EEG in various clinical roles. PMID:26913150

  17. Low-Amplitude Craniofacial EMG Power Spectral Density and 3D Muscle Reconstruction from MRI.

    PubMed

    Wiedemann, Lukas; Chaberova, Jana; Edmunds, Kyle; Einarsdóttir, Guðrún; Ramon, Ceon; Gargiulo, Paolo

    2015-03-11

    Improving EEG signal interpretation, specificity, and sensitivity is a primary focus of many current investigations, and the successful application of EEG signal processing methods requires a detailed knowledge of both the topography and frequency spectra of low-amplitude, high-frequency craniofacial EMG. This information remains limited in clinical research, and as such, there is no known reliable technique for the removal of these artifacts from EEG data. The results presented herein outline a preliminary investigation of craniofacial EMG high-frequency spectra and 3D MRI segmentation that offers insight into the development of an anatomically-realistic model for characterizing these effects. The data presented highlights the potential for confounding signal contribution from around 60 to 200 Hz, when observed in frequency space, from both low and high-amplitude EMG signals. This range directly overlaps that of both low γ (30-50 Hz) and high γ (50-80 Hz) waves, as defined traditionally in standatrd EEG measurements, and mainly with waves presented in dense-array EEG recordings. Likewise, average EMG amplitude comparisons from each condition highlights the similarities in signal contribution of low-activity muscular movements and resting, control conditions. In addition to the FFT analysis performed, 3D segmentation and reconstruction of the craniofacial muscles whose EMG signals were measured was successful. This recapitulation of the relevant EMG morphology is a crucial first step in developing an anatomical model for the isolation and removal of confounding low-amplitude craniofacial EMG signals from EEG data. Such a model may be eventually applied in a clinical setting to ultimately help to extend the use of EEG in various clinical roles.

  18. 3D Mapping of Polymer Crosslink Density with Magnetic Resonance Imaging

    SciTech Connect

    Herberg, J L; Gjersing, E L; Chinn, S C; Maxwell, R S

    2005-03-11

    Magnetic Resonance Imaging (MRI) techniques have been used to detect areas of low crosslink density in damaged silicone parts in an effort to develop a QA/QC protocol to be used in the development of new parts. Model materials of varying crosslink density first demonstrated the applicability of the method. Analysis of damaged pads has been shown to be clearly distinguishable by MRI. It is our belief that both the T{sub 2} weighted SPI NMR and the T{sub 2} weighted water/fat suppression MRI experiments can be used to map out the location of different cross-linking densities, ultimately determining the quality or homogeneity in polymers.

  19. Dynamical electron compressibility in the 3D topological insulator Bi2Se3

    NASA Astrophysics Data System (ADS)

    Inhofer, Andreas; Assaf, Badih; Wilmart, Quentin; Veyrat, Louis; Nowka, Christian; Dufouleur, Joseph; Giraud, Romain; Hampel, Silke; Buechner, Bernd; Fève, Gwendal; Berroir, Jean-Marc; Placais, Bernard

    Measurements of the quantum capacitance cq, related to the electron compressibility χ =cq /e2 is a sensitive tool to probe the density of states. In a topological insulator (TI) the situation is enriched by the coexistence and the interplay of topologically protected surface states and massive bulk carriers. We investigate top-gate metal-oxyde-TI capacitors using Bi2Se3 thin crystals at GHz frequencies. These measurements provide insight into the compressibillity of such a two electron-fluid system. Furthermore, the dynamical response yields information about electron scattering properties in TIs. More specifically, in our measurements we track simultaneously the conductivity σ and the compressibility as a function of a DC-gate voltage. Using the Einstein relation σ =cq D , we have access to the gate dependence of the electron diffusion constant D (Vg) , a signature of the peculiar scattering mechanisms in TIs.

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

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

  1. Correcting for 3D distortion when using backscattered electron detectors in a scanning electron microscope.

    PubMed

    Proctor, Jacob M

    2009-01-01

    A variable pressure scanning electron microscope (VPSEM) can produce a topographic surface relief of a physical object under examination, in addition to its two-dimensional (2D) image. This topographic surface relief is especially helpful when dealing with porous rock because it may elucidate the pore-space structure as well as grain shape and size. Whether the image accurately reproduces the physical object depends on the management of the hardware, acquisition, and postprocessing. Two problems become apparent during testing: (a) a topographic surface relief of a precision ball bearing is distorted and does not correspond to the physical dimensions of the actual sphere and (b) an image of a topographic surface relief of a Berea sandstone is geometrically tilted and topographically distorted even after standard corrections are applied. The procedure presented here is to ensure the veracity of the image, and includes: (a) adjusting the brightness and contrast levels originally provided by the manufacturer and (b) tuning the amplifiers of the backscatter detector plates to be equal to each other, and producing zero voltage when VPSEM is idle. This procedure is tested and verified on the said two physical samples. SCANNING 31: 59-64, 2009. (c) 2009 Wiley Periodicals, Inc.

  2. Crustal density structure in northwestern South America derived from analysis and 3-D modeling of gravity and seismicity data

    NASA Astrophysics Data System (ADS)

    Sanchez-Rojas, J.; Palma, M.

    2014-11-01

    This paper presents a three-dimensional (3-D) interpretation of new gravity and seismicity datasets for northern South America. A 3-D forward density model was constructed on the basis of deep wide-angle seismic refraction sections, Moho depth from receiver functions, and surface geology. Density values were estimated from published borehole data for sediments by using empirical velocity-density functions and considering mineralogical-chemical composition variations under typical pressure-temperature conditions for upper and lower crustal rocks. The modeled 3-D density structure was kept as simple as possible. The continental and oceanic plates were formed by two sedimentary bodies, one crustal body, and one mantle lithosphere body overlying a sub-lithospheric mantle. The Caribbean plate was modeled with an atypical crustal thickness of ~ 18 km (including sediments). The geometry of the Caribbean plate was modeled using a combination of gravity modeling and analyses of the seismicity and focal-mechanism solutions. Intermediate seismicity and the orientation of the T-axes appeared aligned along the predicted position of the slab. As a result, the estimated slab dip angle under Maracaibo and the Mérida Andes was ~ 15° and increases up to ~ 20° after 100 km depth. The model shows two orientations in the slab strike: ~ N150°E ± 5 in western Colombia and southward underneath the Maracaibo block. The modeling results suggest that the northern South American upper and lower crusts are relatively light and the density of the Caribbean crust is typical for an oceanic crust.

  3. SU-C-213-02: Characterizing 3D Printing in the Fabrication of Variable Density Phantoms

    SciTech Connect

    Madamesila, J; McGeachy, P; Villarreal-Barajas, J; Khan, R

    2015-06-15

    Purpose: In this work, we present characterization, process flow, quality control and application of 3D fabricated low density phantoms for radiotherapy quality assurance. Methods: A Rostock delta 3D printer using polystyrene filament of diameter 1.75 mm was used to print geometric volumes of 2×2×1 cm{sup 3} of varying densities. The variable densities of 0.1 to 0.75 g/cm {sup 3} were created by modulating the infill. A computed tomography (CT) scan was performed to establish an infill-density calibration curve as well as characterize the quality of the print such as uniformity and the infill pattern. The time required to print these volumes was also recorded. Using the calibration, two low density cones (0.19, 0.52 g/cm{sup 3}) were printed and benchmarked against commercially available phantoms. The dosimetric validation of the low density scaling of Anisotropic Analytical Algorithm (AAA) was performed by using a 0.5 g/cm{sup 3} slab of 10×10×2.4 cm{sup 3} with EBT3 GafChromic film. The gamma analysis at 3%/3mm criteria were compared for the measured and computed dose planes. Results: Analysis of the volume of air pockets in the infill resulted in a reasonable uniformity for densities 0.4 to 0.75 g/cm{sup 3}. Printed phantoms with densities below 0.4 g/cm{sup 3} exhibited a higher ratio of air to polystyrene resulting in large non-uniformity. Compared to the commercial inserts, good agreement was observed only for the printed 0.52 g/cm{sup 3} cone. Dosimetric comparison for a printed low density volume placed in-between layers of solid water resulted in >95% gamma agreement between AAA calculated dose planes and measured EBT3 films for a 6MV 5×5 cm{sup 2} clinical beam. The comparison showed disagreement in the penumbra region. Conclusion: In conclusion, 3D printing technology opens the door to desktop fabrication of variable density phantoms at economical prices in an efficient manner for the quality assurance needs of a small clinic.

  4. MO-H-19A-03: Patient Specific Bolus with 3D Printing Technology for Electron Radiotherapy

    SciTech Connect

    Zou, W; Swann, B; Siderits, R; McKenna, M; Khan, A; Yue, N; Zhang, M; Fisher, T

    2014-06-15

    Purpose: Bolus is widely used in electron radiotherapy to achieve desired dose distribution. 3D printing technologies provide clinicians with easy access to fabricate patient specific bolus accommodating patient body surface irregularities and tissue inhomogeneity. This study presents the design and the clinical workflow of 3D printed bolus for patient electron therapy in our clinic. Methods: Patient simulation CT images free of bolus were exported from treatment planning system (TPS) to an in-house developed software package. Bolus with known material properties was designed in the software package and then exported back to the TPS as a structure. Dose calculation was carried out to examine the coverage of the target. After satisfying dose distribution was achieved, the bolus structure was transferred in Standard Tessellation Language (STL) file format for the 3D printer to generate the machine codes for printing. Upon receiving printed bolus, a quick quality assurance was performed with patient resimulated with bolus in place to verify the bolus dosimetric property before treatment started. Results: A patient specific bolus for electron radiotherapy was designed and fabricated in Form 1 3D printer with methacrylate photopolymer resin. Satisfying dose distribution was achieved in patient with bolus setup. Treatment was successfully finished for one patient with the 3D printed bolus. Conclusion: The electron bolus fabrication with 3D printing technology was successfully implemented in clinic practice.

  5. A direct approach for instantaneous 3D density field reconstruction from background-oriented schlieren (BOS) measurements

    NASA Astrophysics Data System (ADS)

    Nicolas, F.; Todoroff, V.; Plyer, A.; Le Besnerais, G.; Donjat, D.; Micheli, F.; Champagnat, F.; Cornic, P.; Le Sant, Y.

    2016-01-01

    We present a new numerical method for reconstruction of instantaneous density volume from 3D background-oriented schlieren (3DBOS) measurements, with a validation on a dedicated flexible experimental BOS bench. In contrast to previous works, we use a direct formulation where density is estimated from measured deviation fields without the intermediate step of density gradient reconstruction. Regularization techniques are implemented to deal with the ill-posed problem encountered. The resulting high-dimensional optimization is conducted by conjugate gradient techniques. A parallel algorithm, implemented on graphics processing unit, helps to speed up the calculation. The resulting software is validated on synthetic BOS images of a 3D density field issued from a numerical simulation. Then, we describe a dedicated 3DBOS experimental facility which has been built to study various BOS settings and to assess the performance of the proposed numerical reconstruction process. Results on various datasets illustrate the potential of the method for flow characterization and measurement in real-world conditions.

  6. Acoustic backing in 3-D integration of CMUT with front-end electronics.

    PubMed

    Berg, Sigrid; Rønnekleiv, Arne

    2012-07-01

    Capacitive micromachined ultrasonic transducers (CMUTs) have shown promising qualities for medical imaging. However, there are still some problems to be investigated, and some challenges to overcome. Acoustic backing is necessary to prevent SAWs excited in the surface of the silicon substrate from affecting the transmit pattern from the array. In addition, echoes resulting from bulk waves in the substrate must be removed. There is growing interest in integrating electronic circuits to do some of the beamforming directly below the transducer array. This may be easier to achieve for CMUTs than for traditional piezoelectric transducers. We will present simulations showing that the thickness of the silicon substrate and thicknesses and acoustic properties of the bonding material must be considered, especially when designing highfrequency transducers. Through simulations, we compare the acoustic properties of 3-D stacks bonded with three different bonding techniques; solid-liquid interdiffusion (SLID) bonding, direct fusion bonding, and anisotropic conductive adhesives (ACA). We look at a CMUT array with a center frequency of 30 MHz and three silicon wafers underneath, having a total silicon thickness of 100 μm. We find that fusion bonding is most beneficial if we want to prevent surface waves from damaging the array response, but SLID and ACA are also promising if bonding layer thicknesses can be reduced.

  7. Single particle cryo-electron microscopy and 3-D reconstruction of viruses.

    PubMed

    Guo, Fei; Jiang, Wen

    2014-01-01

    With fast progresses in instrumentation, image processing algorithms, and computational resources, single particle electron cryo-microscopy (cryo-EM) 3-D reconstruction of icosahedral viruses has now reached near-atomic resolutions (3-4 Å). With comparable resolutions and more predictable outcomes, cryo-EM is now considered a preferred method over X-ray crystallography for determination of atomic structure of icosahedral viruses. At near-atomic resolutions, all-atom models or backbone models can be reliably built that allow residue level understanding of viral assembly and conformational changes among different stages of viral life cycle. With the developments of asymmetric reconstruction, it is now possible to visualize the complete structure of a complex virus with not only its icosahedral shell but also its multiple non-icosahedral structural features. In this chapter, we will describe single particle cryo-EM experimental and computational procedures for both near-atomic resolution reconstruction of icosahedral viruses and asymmetric reconstruction of viruses with both icosahedral and non-icosahedral structure components. Procedures for rigorous validation of the reconstructions and resolution evaluations using truly independent de novo initial models and refinements are also introduced.

  8. A resource from 3D electron microscopy of hippocampal neuropil for user training and tool development

    PubMed Central

    Harris, Kristen M.; Spacek, Josef; Bell, Maria Elizabeth; Parker, Patrick H.; Lindsey, Laurence F.; Baden, Alexander D.; Vogelstein, Joshua T.; Burns, Randal

    2015-01-01

    Resurgent interest in synaptic circuitry and plasticity has emphasized the importance of 3D reconstruction from serial section electron microscopy (3DEM). Three volumes of hippocampal CA1 neuropil from adult rat were imaged at X-Y resolution of ~2 nm on serial sections of ~50–60 nm thickness. These are the first densely reconstructed hippocampal volumes. All axons, dendrites, glia, and synapses were reconstructed in a cube (~10 μm3) surrounding a large dendritic spine, a cylinder (~43 μm3) surrounding an oblique dendritic segment (3.4 μm long), and a parallelepiped (~178 μm3) surrounding an apical dendritic segment (4.9 μm long). The data provide standards for identifying ultrastructural objects in 3DEM, realistic reconstructions for modeling biophysical properties of synaptic transmission, and a test bed for enhancing reconstruction tools. Representative synapses are quantified from varying section planes, and microtubules, polyribosomes, smooth endoplasmic reticulum, and endosomes are identified and reconstructed in a subset of dendrites. The original images, traces, and Reconstruct software and files are freely available and visualized at the Open Connectome Project (Data Citation 1). PMID:26347348

  9. Single Particle Cryo-electron Microscopy and 3-D Reconstruction of Viruses

    PubMed Central

    Guo, Fei; Jiang, Wen

    2014-01-01

    With fast progresses in instrumentation, image processing algorithms, and computational resources, single particle electron cryo-microscopy (cryo-EM) 3-D reconstruction of icosahedral viruses has now reached near-atomic resolutions (3–4 Å). With comparable resolutions and more predictable outcomes, cryo-EM is now considered a preferred method over X-ray crystallography for determination of atomic structure of icosahedral viruses. At near-atomic resolutions, all-atom models or backbone models can be reliably built that allow residue level understanding of viral assembly and conformational changes among different stages of viral life cycle. With the developments of asymmetric reconstruction, it is now possible to visualize the complete structure of a complex virus with not only its icosahedral shell but also its multiple non-icosahedral structural features. In this chapter, we will describe single particle cryo-EM experimental and computational procedures for both near-atomic resolution reconstruction of icosahedral viruses and asymmetric reconstruction of viruses with both icosahedral and non-icosahedral structure components. Procedures for rigorous validation of the reconstructions and resolution evaluations using truly independent de novo initial models and refinements are also introduced. PMID:24357374

  10. Microstructural characterization of the cycling behavior of electrodeposited manganese oxide supercapacitors using 3D electron tomography

    NASA Astrophysics Data System (ADS)

    Dalili, N.; Clark, M. P.; Davari, E.; Ivey, D. G.

    2016-10-01

    Manganese oxide has been investigated extensively as an electrochemical capacitor or supercapacitor electrode material. Manganese oxide is inexpensive to fabricate and exhibits relatively high capacitance values, i.e., in excess of 200 F g-1 in many cases; the actual value depends very much on the fabrication method and test conditions. The cycling behavior of Mn oxide, fabricated using anodic electrodeposition, is investigated using slice and view techniques, via a dual scanning electron microscope (SEM) and focused ion beam (FIB) instrument to generate three-dimensional (3D) images, coupled with electrochemical characterization. The initial as-fabricated electrode has a rod-like appearance, with a fine-scale, sheet-like morphology within the rods. The rod-like structure remains after cycling, but there are significant morphological changes. These include partial dissolution of Mn oxide followed by redeposition of Mn oxide in regions close to the substrate. The redeposited material has a finer morphology than the original as-fabricated Mn oxide. The Mn oxide coverage is also better near the substrate. These effects result in an increase in the specific capacitance.

  11. Portable high-intensity focused ultrasound system with 3D electronic steering, real-time cavitation monitoring, and 3D image reconstruction algorithms: a preclinical study in pigs

    PubMed Central

    2014-01-01

    Purpose: The aim of this study was to evaluate the safety and accuracy of a new portable ultrasonography-guided high-intensity focused ultrasound (USg-HIFU) system with a 3-dimensional (3D) electronic steering transducer, a simultaneous ablation and imaging module, real-time cavitation monitoring, and 3D image reconstruction algorithms. Methods: To address the accuracy of the transducer, hydrophones in a water chamber were used to assess the generation of sonic fields. An animal study was also performed in five pigs by ablating in vivo thighs by single-point sonication (n=10) or volume sonication (n=10) and ex vivo kidneys by single-point sonication (n=10). Histological and statistical analyses were performed. Results: In the hydrophone study, peak voltages were detected within 1.0 mm from the targets on the y- and z-axes and within 2.0-mm intervals along the x-axis (z-axis, direction of ultrasound propagation; y- and x-axes, perpendicular to the direction of ultrasound propagation). Twenty-nine of 30 HIFU sessions successfully created ablations at the target. The in vivo porcine thigh study showed only a small discrepancy (width, 0.5-1.1 mm; length, 3.0 mm) between the planning ultrasonograms and the pathological specimens. Inordinate thermal damage was not observed in the adjacent tissues or sonic pathways in the in vivo thigh and ex vivo kidney studies. Conclusion: Our study suggests that this new USg-HIFU system may be a safe and accurate technique for ablating soft tissues and encapsulated organs. PMID:25038809

  12. From Rice Bran to High Energy Density Supercapacitors: A New Route to Control Porous Structure of 3D Carbon

    PubMed Central

    Hou, Jianhua; Cao, Chuanbao; Ma, Xilan; Idrees, Faryal; Xu, Bin; Hao, Xin; Lin, Wei

    2014-01-01

    Controlled micro/mesopores interconnected structures of three-dimensional (3D) carbon with high specific surface areas (SSA) are successfully prepared by carbonization and activation of biomass (raw rice brans) through KOH. The highest SSA of 2475 m2 g−1 with optimized pore volume of 1.21 cm3 g−1 (40% for mesopores) is achieved for KOH/RBC = 4 mass ratio, than others. The as-prepared 3D porous carbon-based electrode materials for supercapacitors exhibit high specific capacitance specifically at large current densities of 10 A g−1 and 100 A g−1 i.e., 265 F g−1 and 182 F g−1 in 6 M KOH electrolyte, respectively. Moreover, a high power density ca. 1223 W kg−1 (550 W L−1) and energy density 70 W h kg−1 (32 W h L−1) are achieved on the base of active material loading (~10 mg cm2) in the ionic liquid. The findings can open a new avenue to use abundant agricultural by-products as ideal materials with promising applications in high-performance energy-storage devices. PMID:25434348

  13. 3D printed electromagnetic transmission and electronic structures fabricated on a single platform using advanced process integration techniques

    NASA Astrophysics Data System (ADS)

    Deffenbaugh, Paul Issac

    3D printing has garnered immense attention from many fields including in-office rapid prototyping of mechanical parts, outer-space satellite replication, garage functional firearm manufacture, and NASA rocket engine component fabrication. 3D printing allows increased design flexibility in the fabrication of electronics, microwave circuits and wireless antennas and has reached a level of maturity which allows functional parts to be printed. Much more work is necessary in order to perfect the processes of 3D printed electronics especially in the area of automation. Chapter 1 shows several finished prototypes of 3D printed electronics as well as newly developed techniques in fabrication. Little is known about the RF and microwave properties and applications of the standard materials which have been developed for 3D printing. Measurement of a wide variety of materials over a broad spectrum of frequencies up to 10 GHz using a variety of well-established measurement methods is performed throughout chapter 2. Several types of high frequency RF transmission lines are fabricated and valuable model-matched data is gathered and provided in chapter 3 for future designers' use. Of particular note is a fully 3D printed stripline which was automatically fabricated in one process on one machine. Some core advantages of 3D printing RF/microwave components include rapid manufacturing of complex, dimensionally sensitive circuits (such as antennas and filters which are often iteratively tuned) and the ability to create new devices that cannot be made using standard fabrication techniques. Chapter 4 describes an exemplary fully 3D printed curved inverted-F antenna.

  14. Automated voxelization of 3D atom probe data through kernel density estimation.

    PubMed

    Srinivasan, Srikant; Kaluskar, Kaustubh; Dumpala, Santoshrupa; Broderick, Scott; Rajan, Krishna

    2015-12-01

    Identifying nanoscale chemical features from atom probe tomography (APT) data routinely involves adjustment of voxel size as an input parameter, through visual supervision, making the final outcome user dependent, reliant on heuristic knowledge and potentially prone to error. This work utilizes Kernel density estimators to select an optimal voxel size in an unsupervised manner to perform feature selection, in particular targeting resolution of interfacial features and chemistries. The capability of this approach is demonstrated through analysis of the γ / γ' interface in a Ni-Al-Cr superalloy. PMID:25825028

  15. First-principle study of the electronic structure and magnetism of lithium-adsorbed 3d transition-metal phthalocyanines

    NASA Astrophysics Data System (ADS)

    Wang, M.; Hu, Y.; Zhang, Z.; Li, Y.; Zhou, T.; Ren, J.

    2016-02-01

    Based on density functional theory (DFT) calculations, the electronic structures and magnetic properties of 3d transition-metal phthalocyanine (TMPc, TM = Ti, V, Cr, Mn, Fe, Co, Ni and Cu), as well as Li-adsorbed phthalocyanines have been studied. The results show that the pristine TMPcs all have a good D4h symmetry. When there is one Li atom adsorbed on TMPcs directly over (LiTMPc-α) or slantly above (LiTMPc-β) the TM atoms, the geometries and electronic structures will be changed. For LiTMPc-α systems, the central TM atoms will deviate from the molecular plane and the molecules exhibit good C4v symmetry. LiTMPc-β systems are more stable than LiTMPc-α systems but it do not possess D4h and C4v symmetries. The total and local magnetic moments and the charge transfer are also presented. Finally, by using the orbit mixing and splitting theory under D4h and C4v symmetry, we get the ordering of the energy levels of the central TM atoms.

  16. The internal density distribution of comet 67P/C-G based on 3D models

    NASA Astrophysics Data System (ADS)

    Jorda, Laurent; Faurschou Hviid, Stubbe; Capanna, Claire; Gaskell, Robert W.; Gutiérrez, Pedro; Preusker, Frank; Scholten, Frank; Rodionov, Sergey; OSIRIS Team

    2016-10-01

    The OSIRIS camera aboard the Rosetta spacecraft observed the nucleus of comet 67P/C-G from the mapping phase in summer 2014 until now. The images have allowed the reconstruction in three-dimension of nucleus surface with stereophotogrammetry (Preusker et al., Astron. Astrophys.) and stereophotoclinometry (Jorda et al., Icarus) techniques. We use the reconstructed models to constrain the internal density distribution based on: (i) the measurement of the offset between the center of mass and the center of figure of the object, and (ii) the assumption that flat areas observed at the surface of the comet correspond to iso-gravity surfaces. The results of our analysis will be presented, and the consequences for the internal structure and formation of the nucleus of comet 67P/C-G will be discussed.

  17. Calibrating MMS Electron Drift Instrument (EDI) Ambient Electron Flux Measurements and Characterizing 3D Electric Field Signatures of Magnetic Reconnection

    NASA Astrophysics Data System (ADS)

    Shuster, J. R.; Torbert, R. B.; Vaith, H.; Argall, M. R.; Li, G.; Chen, L. J.; Ergun, R. E.; Lindqvist, P. A.; Marklund, G. T.; Khotyaintsev, Y. V.; Russell, C. T.; Magnes, W.; Le Contel, O.; Pollock, C. J.; Giles, B. L.

    2015-12-01

    The electron drift instruments (EDIs) onboard each MMS spacecraft are designed with large geometric factors (~0.01cm2 str) to facilitate detection of weak (~100 nA) electron beams fired and received by the two gun-detector units (GDUs) when EDI is in its "electric field mode" to determine the local electric and magnetic fields. A consequence of the large geometric factor is that "ambient mode" electron flux measurements (500 eV electrons having 0°, 90°, or 180° pitch angle) can vary depending on the orientation of the EDI instrument with respect to the magnetic field, a nonphysical effect that requires a correction. Here, we present determinations of the θ- and ø-dependent correction factors for the eight EDI GDUs, where θ (ø) is the polar (azimuthal) angle between the GDU symmetry axis and the local magnetic field direction, and compare the corrected fluxes with those measured by the fast plasma instrument (FPI). Using these corrected, high time resolution (~1,000 samples per second) ambient electron fluxes, combined with the unprecedentedly high resolution 3D electric field measurements taken by the spin-plane and axial double probes (SDP and ADP), we are equipped to accurately detect electron-scale current layers and electric field waves associated with the non-Maxwellian (anisotropic and agyrotropic) particle distribution functions predicted to exist in the reconnection diffusion region. We compare initial observations of the diffusion region with distributions and wave analysis from PIC simulations of asymmetric reconnection applicable for modeling reconnection at the Earth's magnetopause, where MMS will begin Science Phase 1 as of September 1, 2015.

  18. 3D strain engineered self-rolled thin-film architecture for high-energy density lithium-ion batteries

    NASA Astrophysics Data System (ADS)

    Godbey, Griffin; Gong, Chen; Yu, Cynthia; Blythe, Clayton; Leite, Marina

    Recently, multiple 3D geometries have been implemented into energy storage devices (e . g . nanowire anodes and arrays of interdigitated rods) in order to better accommodate the large volume expansion experienced by the anode during lithiation and to increase the structure energy density. However, most approached structures are difficult to scale up. Here we show how self-rolled thin-films can maintain a high energy density and can potentially accommodate the volume expansion suffered by the anode. The self-rolled tubes are fabricated by physical deposition of the active layers, creating a stress gradient between thin-film stack due to differences in coefficient of thermal expansion. Upon a sacrificial layer removal, the thin-film rolls to relieve this built-in stress. We predict the final dimension of self-rolled battery tubes using known elastic properties of materials commonly used as the active layers of the device. We will discuss an appropriate figure-of-merit that defines how the winding process can ultimately affect the volumetric capacity of 3D self-rolled batteries.

  19. Lab Experiments Probe Interactions Between Dilute Pyroclastic Density Currents and 3D Barriers

    NASA Astrophysics Data System (ADS)

    Fauria, K.; Andrews, B. J.; Manga, M.

    2014-12-01

    We conducted scaled laboratory experiments of unconfined dilute pyroclastic density currents (PDCs) to examine interactions between three - dimensional obstacles and dilute PDCs. While it is known that PDCs can surmount barriers by converting kinetic energy into potential energy, the signature of topography on PDC dynamics is unclear. To examine the interplay between PDCs and topography, we turbulently suspended heated and ambient-temperature 20 μm talc powder in air within an 8.5 x 6.1 x 2.6 m tank. Experimental parameters (Froude number, densimetric and thermal Richardson number, particle Stokes and Settling numbers) were scaled such that the experimental currents were dynamically similar to natural PCS. The Reynolds number, however, is much smaller than in natural currents, but still large enough for the flows to be turbulent. We placed cylindrical and ridge-like objects in the path of the currents, illuminated the currents with orthogonal laser sheets, and recorded each experiment with high definition cameras. We observed currents surmounting ridge-like barriers (barrier height = current height). Slanted ridges redirected the currents upward and parallel to the upstream face of the ridges (~45° from horizontal). Down stream of the slanted ridges, ambient-temperature currents reattached to the floor. By comparison, hot currents reversed buoyancy and lifted off. These observations suggest that obstacles enhance air entrainment, a process key to affecting runout distance and the depletion of fine particles in ignimbrites. Moreover, we observed vortex shedding in the wake of cylinders. Our experiments demonstrate that barriers of various shapes affect PDC dynamics and can shorten PDC runout distances. Understanding the effects of topography on PDCs is required for interpreting many deposits because processes such as vortex shedding and topographically-induced changes in turbulent length scales and entrainment likely leave depositional signatures.

  20. Sizable electron/neutron electric dipole moment in D 3 /D 7 μ -split supersymmetry

    NASA Astrophysics Data System (ADS)

    Dhuria, Mansi; Misra, Aalok

    2014-10-01

    0-32) cm from a one-loop diagram involving a heavy chargino and a light Higgs as propagators in the loop. The neutron EDM gets a dominant contribution of the order dn/e ≡O (1 0-33) cm from the one-loop diagram involving SM-like quarks and Higgs. To justify the possibility of obtaining a large EDM value in the case of a Barr-Zee diagram which involves W± and the Higgs (responsible to generate the nontrivial C P -violating phase) in the two-loop diagrams as discussed by Leigh et al. [Nucl. Phys. B267, 509 (1986)], we provide an analysis of the same in the context of our D 3 /D 7 μ -split SUSY model at the EW scale. By conjecturing that the C P -violating phase can appear from the diagonalization of the Higgs mass matrix obtained in the context of μ -split SUSY, we also get an EDM of the electron/neutron around O (1 0-27) e cm in the case of the two-loop diagram involving W± bosons.

  1. Increased extracellular matrix density decreases MCF10A breast cell acinus formation in 3D culture conditions.

    PubMed

    Lance, Amanda; Yang, Chih-Chao; Swamydas, Muthulekha; Dean, Delphine; Deitch, Sandy; Burg, Karen J L; Dréau, Didier

    2016-01-01

    The extracellular matrix (ECM) contributes to the generation and dynamic of normal breast tissue, in particular to the generation of polarized acinar and ductal structures. In vitro 3D culture conditions, including variations in the composition of the ECM, have been shown to directly influence the formation and organization of acinus-like and duct-like structures. Furthermore, the density of the ECM appears to also play a role in the normal mammary tissue and tumour formation. Here we show that the density of the ECM directly influences the number, organization and function of breast acini. Briefly, non-malignant human breast MCF10A cells were incubated in increasing densities of a Matrigel®-collagen I matrix. Elastic moduli near and distant to the acinus structures were measured by atomic force microscopy, and the number of acinus structures was determined. Immunochemistry was used to investigate the expression levels of E-cadherin, laminin, matrix metalloproteinase-14 and ß-casein in MCF10A cells. The modulus of the ECM was significantly increased near the acinus structures and the number of acinus structures decreased with the increase in Matrigel-collagen I density. As evaluated by the expression of laminin, the organization of the acinus structures present was altered as the density of the ECM increased. Increases in both E-cadherin and MMP14 expression by MCF10A cells as ECM density increased were also observed. In contrast, MCF10A cells expressed lower ß-casein levels as the ECM density increased. Taken together, these observations highlight the key role of ECM density in modulating the number, organization and function of breast acini.

  2. Spectroscopic Evidence for a 3d(10) Ground State Electronic Configuration and Ligand Field Inversion in [Cu(CF3)4](1-).

    PubMed

    Walroth, Richard C; Lukens, James T; MacMillan, Samantha N; Finkelstein, Kenneth D; Lancaster, Kyle M

    2016-02-17

    The contested electronic structure of [Cu(CF3)4](1-) is investigated with UV/visible/near IR spectroscopy, Cu K-edge X-ray absorption spectroscopy, and 1s2p resonant inelastic X-ray scattering. These data, supported by density functional theory, multiplet theory, and multireference calculations, support a ground state electronic configuration in which the lowest unoccupied orbital is of predominantly trifluoromethyl character. The consensus 3d(10) configuration features an inverted ligand field in which all five metal-localized molecular orbitals are located at lower energy relative to the trifluoromethyl-centered σ orbitals.

  3. Gravity data inversion to determine 3D topographycal density contrast of Banten area, Indonesia based on fast Fourier transform

    NASA Astrophysics Data System (ADS)

    Windhari, Ayuty; Handayani, Gunawan

    2015-04-01

    The 3D inversion gravity anomaly to estimate topographical density using a matlab source code from gridded data provided by Parker Oldenburg algorithm based on fast Fourier transform was computed. We extend and improved the source code of 3DINVERT.M invented by Gomez Ortiz and Agarwal (2005) using the relationship between Fourier transform of the gravity anomaly and the sum of the Fourier transform from the topography density. We gave density contrast between the two media to apply the inversion. FFT routine was implemented to construct amplitude spectrum to the given mean depth. The results were presented as new graphics of inverted topography density, the gravity anomaly due to the inverted topography and the difference between the input gravity data and the computed ones. It terminates when the RMS error is lower than pre-assigned value used as convergence criterion or until maximum of iterations is reached. As an example, we used the matlab program on gravity data of Banten region, Indonesia.

  4. 3D Stationary electric current density in a spherical tumor treated with low direct current: an analytical solution.

    PubMed

    Jiménez, Rolando Placeres; Pupo, Ana Elisa Bergues; Cabrales, Jesús Manuel Bergues; Joa, Javier Antonio González; Cabrales, Luis Enrique Bergues; Nava, Juan José Godina; Aguilera, Andrés Ramírez; Mateus, Miguel Angel O'Farril; Jarque, Manuel Verdecia; Brooks, Soraida Candida Acosta

    2011-02-01

    Electrotherapy with direct current delivered through implanted electrodes is used for local control of solid tumors in both preclinical and clinical studies. The aim of this research is to develop a solution method for obtaining a three-dimensional analytical expression for potential and electric current density as functions of direct electric current intensity, differences in conductivities between the tumor and the surrounding healthy tissue, and length, number and polarity of electrodes. The influence of these parameters on electric current density in both media is analyzed. The results show that the electric current density in the tumor is higher than that in the surrounding healthy tissue for any value of these parameters. The conclusion is that the solution method presented in this study is of practical interest because it provides, in a few minutes, a convenient way to visualize in 3D the electric current densities generated by a radial electrode array by means of the adequate selection of direct current intensity, length, number, and polarity of electrodes, and the difference in conductivity between the solid tumor and its surrounding healthy tissue.

  5. First-Principles Study of Electronic Structure and Hydrogen Adsorption of 3d Transition Metal Exposed Paddle Wheel Frameworks

    SciTech Connect

    Bak, J. H.; Le, V. D.; Kang, J.; Wei, S. H.; Kim, Y. H.

    2012-04-05

    Open-site paddle wheels, comprised of two transition metals bridged with four carboxylate ions, have been widely used for constructing metal-organic frameworks with large surface area and high binding energy sites. Using first-principles density functional theory calculations, we have investigated atomic and electronic structures of various 3d transition metal paddle wheels before and after metal exposure and their hydrogen adsorption properties at open metal sites. Notably, the hydrogen adsorption is impeded by covalent metal-metal bonds in early transition metal paddle wheels from Sc to Cr and by the strong ferromagnetic coupling of diatomic Mn and Fe in the paddle wheel configurations. A significantly enhanced H{sub 2} adsorption is predicted in the nonmagnetic Co{sub 2} and Zn{sub 2} paddle wheel with the binding energy of {approx}0.2 eV per H{sub 2}. We also propose the use of two-dimensional Co{sub 2} and Zn{sub 2} paddle wheel frameworks that could have strongly adsorbed dihydrogen up to 1.35 wt % for noncryogenic hydrogen storage applications.

  6. 3-D reconstructions of the early-November 2004 CDAW geomagnetic storms: analysis of Ooty IPS speed and density data

    NASA Astrophysics Data System (ADS)

    Bisi, M. M.; Jackson, B. V.; Clover, J. M.; Manoharan, P. K.; Tokumaru, M.; Hick, P. P.; Buffington, A.

    2009-12-01

    Interplanetary scintillation (IPS) remote-sensing observations provide a view of the solar wind covering a wide range of heliographic latitudes and heliocentric distances from the Sun between ~0.1 AU and 3.0 AU. Such observations are used to study the development of solar coronal transients and the solar wind while propagating out through interplanetary space. They can also be used to measure the inner-heliospheric response to the passage of coronal mass ejections (CMEs) and co-rotating heliospheric structures. IPS observations can, in general, provide a speed estimate of the heliospheric material crossing the observing line of site; some radio antennas/arrays can also provide a radio scintillation level. We use a three-dimensional (3-D) reconstruction technique which obtains perspective views from outward-flowing solar wind and co-rotating structure as observed from Earth by iteratively fitting a kinematic solar wind model to these data. Using this 3-D modelling technique, we are able to reconstruct the velocity and density of CMEs as they travel through interplanetary space. For the time-dependent model used here with IPS data taken from the Ootacamund (Ooty) Radio Telescope (ORT) in India, the digital resolution of the tomography is 10° by 10° in both latitude and longitude with a half-day time cadence. Typically however, the resolutions range from 10° to 20° in latitude and longitude, with a half- to one-day time cadence for IPS data dependant upon how much data are used as input to the tomography. We compare reconstructed structures during early-November 2004 with in-situ measurements from the Wind spacecraft orbiting the Sun-Earth L1-Point to validate the 3-D tomographic reconstruction results and comment on how these improve upon prior reconstructions.

  7. A density-based segmentation for 3D images, an application for X-ray micro-tomography.

    PubMed

    Tran, Thanh N; Nguyen, Thanh T; Willemsz, Tofan A; van Kessel, Gijs; Frijlink, Henderik W; van der Voort Maarschalk, Kees

    2012-05-01

    Density-based spatial clustering of applications with noise (DBSCAN) is an unsupervised classification algorithm which has been widely used in many areas with its simplicity and its ability to deal with hidden clusters of different sizes and shapes and with noise. However, the computational issue of the distance table and the non-stability in detecting the boundaries of adjacent clusters limit the application of the original algorithm to large datasets such as images. In this paper, the DBSCAN algorithm was revised and improved for image clustering and segmentation. The proposed clustering algorithm presents two major advantages over the original one. Firstly, the revised DBSCAN algorithm made it applicable for large 3D image dataset (often with millions of pixels) by using the coordinate system of the image data. Secondly, the revised algorithm solved the non-stability issue of boundary detection in the original DBSCAN. For broader applications, the image dataset can be ordinary 3D images or in general, it can also be a classification result of other type of image data e.g. a multivariate image.

  8. Electronic structure of the chiral helimagnet and 3d-intercalated transition metal dichalcogenide Cr1/3NbS2

    DOE PAGES

    Sirca, N.; Mo, S. -K.; Bondino, F.; Pis, I.; Nappini, S.; Vilmercati, P.; Yi, Jieyu; Gai, Zheng; Snijders, Paul C.; Das, P. K.; et al

    2016-08-18

    The electronic structure of the chiral helimagnet Cr1/3NbS2 has been studied with core level and angle-resolved photoemission spectroscopy (ARPES). Intercalated Cr atoms are found to be effective in donating electrons to the NbS2 layers but also cause significant modifications of the electronic structure of the host NbS2 material. Specifically, the data provide evidence that a description of the electronic structure of Cr1/3NbS2 on the basis of a simple rigid band picture is untenable. The data also reveal substantial inconsistencies with the predictions of standard density functional theory. In conclusion, the relevance of these results to the attainment of a correctmore » description of the electronic structure of chiral helimagnets, magnetic thin films/multilayers, and transition metal dichalcogenides intercalated with 3d magnetic elements is discussed.« less

  9. Electronic and magnetic structure of 3d-transition-metal point defects in silicon calculated from first principles

    NASA Astrophysics Data System (ADS)

    Beeler, F.; Andersen, O. K.; Scheffler, M.

    1990-01-01

    We describe spin-unrestricted self-consistent linear muffin-tin-orbital (LMTO) Green-function calculations for Sc, Ti, V, Cr, Mn, Fe, Co, Ni, and Cu transition-metal impurities in crystalline silicon. Both defect sites of tetrahedral symmetry are considered. All possible charge states with their spin multiplicities, magnetization densities, and energy levels are discussed and explained with a simple physical picture. The early transition-metal interstitial and late transition-metal substitutional 3d ions are found to have low spin. This is in conflict with the generally accepted crystal-field model of Ludwig and Woodbury, but not with available experimental data. For the interstitial 3d ions, the calculated deep donor and acceptor levels reproduce all experimentally observed transitions. For substitutional 3d ions, a large number of predictions is offered to be tested by future experimental studies.

  10. A Bioactive Carbon Nanotube-Based Ink for Printing 2D and 3D Flexible Electronics.

    PubMed

    Shin, Su Ryon; Farzad, Raziyeh; Tamayol, Ali; Manoharan, Vijayan; Mostafalu, Pooria; Zhang, Yu Shrike; Akbari, Mohsen; Jung, Sung Mi; Kim, Duckjin; Comotto, Mattia; Annabi, Nasim; Al-Hazmi, Faten Ebrahim; Dokmeci, Mehmet R; Khademhosseini, Ali

    2016-05-01

    The development of electrically conductive carbon nanotube-based inks is reported. Using these inks, 2D and 3D structures are printed on various flexible substrates such as paper, hydrogels, and elastomers. The printed patterns have mechanical and electrical properties that make them beneficial for various biological applications. PMID:26915715

  11. A Bioactive Carbon Nanotube-Based Ink for Printing 2D and 3D Flexible Electronics.

    PubMed

    Shin, Su Ryon; Farzad, Raziyeh; Tamayol, Ali; Manoharan, Vijayan; Mostafalu, Pooria; Zhang, Yu Shrike; Akbari, Mohsen; Jung, Sung Mi; Kim, Duckjin; Comotto, Mattia; Annabi, Nasim; Al-Hazmi, Faten Ebrahim; Dokmeci, Mehmet R; Khademhosseini, Ali

    2016-05-01

    The development of electrically conductive carbon nanotube-based inks is reported. Using these inks, 2D and 3D structures are printed on various flexible substrates such as paper, hydrogels, and elastomers. The printed patterns have mechanical and electrical properties that make them beneficial for various biological applications.

  12. Deep structure of the crust beneath the Sea of Okhotsk inferred from 3D seismic density modeling

    NASA Astrophysics Data System (ADS)

    Piskarev, A. L.; Butsenko, V. V.; Poselov, V. A.; Savin, V. A.

    2012-05-01

    Potential field anomalies of the Sea of Okhotsk region are analyzed for compiling a map of the basement's tectonic structures. A 3D density model of the Earth's crust is constructed using seismogeological and experimental-petrophysical data, which made it possible to obtain a visual image of main structures of the region reflecting the observable geophysical anomalies. The obtained data allow a domain located in the central part of the Sea of Okhotsk beyond the limits of the exclusive economic zone of the Russian Federation to be considered as a natural continuation of the continental shelf since the latter is structurally similar to western Kamchatka. The deep structural boundaries rise beneath the large sedimentary Deryugin and Tinro basins, which is characteristic of petroliferous basins.

  13. 3D image analysis of plants using electron tomography and micro-CT.

    PubMed

    Mineyuki, Yoshinobu

    2014-11-01

    help to promote MT bundling. Cell plate attachment to the parental wall leads to the fusion of the newly formed middle lamellae in the cell plate to the middle lamella of parental cell wall, and a three-way junction is created. Air space develops from the three-way junction. To determine 3D arrangement of cells and air spaces, we used X-ray micro-CT at the SPring-8 synchrotron radiation facility. Using micro-CT available in BL20XU (8 keV, 0.2 µm/pixel), we were able to elucidate ∼90% of the cortical cell outlines in the hypocotyl-radicle axis of arabidopsis seeds [4] and to analyze cell geometrical properties. As the strength of the system X-ray is too strong for seed survival, we used another beam line BL20B2 (10-15 keV, 2.4-2.7 µm/pixel) to examine air space development during seed imbibition [4,5]. Using this system, we were able to detect air space development at the early imbibition stages of seeds without causing damage during seed germination. AcknowledgmentThe author would like to thank Dr. Ichirou Karahara (Univ. Toyama), Dr. L. Andrew Staehelin (Univ. Colorado), Ms. Naoko Kajimura, Dr. Akio Takaoka (Osaka Univ.), Dr. Kazuyo Misaki, Dr. Shigenobu Yonemura (RIKEN CDB), Dr. Kazuyoshi Murata (NIP), Dr. Kentaro Uesugi, Dr. Akihisa Takeuchi, Dr. Yoshio Suzuki (JASRI), Dr. Miyuki Takeuchi, Dr. Daisuke Tamaoki, Dr. Daisuke Yamauchi, and Ms. Aki Fukuda (Univ. Hyogo) for their collaborations in the work presented here. PMID:25359847

  14. Isolated tree 3D modeling: based on photographing leaf area density(LAD) calculation and L-system method

    NASA Astrophysics Data System (ADS)

    Jin, Shengye; Tamura, Masayuki

    2012-10-01

    In this paper we developed a 3D L-System tree model which expresses the leaf area density (LAD). As a key parameter, which conveys the thickness degree of the canopy and interaction capacity between a tree and the atmosphere, LAD is an important aspect in radiation transfer modeling within the vegetation canopy during the last decades. For modeling a tree, L-System is a good application which explains the internal canopy structure in detail. In the study, we developed the tree model in 3 steps. First we took photographs from eight directions using a commercial digital camera, and then extracted the canopy gap fraction. Secondly, we collected the sample camphor tree's leaf angles in the field for getting the leaf angle density function and computed the G-function from leaf angle density. We calculated the sample tree's LAD by Beer-Lambert's law. LAI-2000 instrument was the standard data source provider for evaluating the photographing method's LAD result. We set the L-System tree parameters in order to coincide with the real tree. The tree model visualization was performed by using POV-Ray v3.60. The eight directions photographing method's LAD result (0.54) was significantly close with the LAI-2000 adjusted data (0.52). Similarly the L-system tree models LAD mean value for 1000 samples was observed to be 0.54 which is close to the validation results.

  15. The 3D study of X-mode reflectometry for density profile measurements on the JET tokamak

    NASA Astrophysics Data System (ADS)

    Hacquin, S.; Fonseca, A.; Meneses, L.; Murari, A.; Walsh, M.; JET EFDA contributors, the

    2007-10-01

    An X-mode swept-frequency reflectometry diagnostic has recently been upgraded for density profile measurement on the JET tokamak. To overcome the extensive computing time required for full-wave simulation, a ray-tracing code has been developed for studying the 3D geometry effects on the JET reflectometry measurement of the density profile. Although such a ray-tracing code is not adequate to examine the role of plasma turbulence, comparisons with full-wave computations have shown that it is still a useful tool for simulation of the density profile measurements in the case of smooth spatial variations of the plasma parameters. The effects of the plasma geometry and the radiation pattern of the reflectometer emitting and receiving antennas on the spatial resolution of these measurements are investigated in this paper. In particular, the results point out the weak role played by the multi-dimensional effects on the reflectometry measurements performed in the equatorial mid-plane of large tokamaks such as JET.

  16. Non-stationary random vibration analysis of a 3D train-bridge system using the probability density evolution method

    NASA Astrophysics Data System (ADS)

    Yu, Zhi-wu; Mao, Jian-feng; Guo, Feng-qi; Guo, Wei

    2016-03-01

    Rail irregularity is one of the main sources causing train-bridge random vibration. A new random vibration theory for the coupled train-bridge systems is proposed in this paper. First, number theory method (NTM) with 2N-dimensional vectors for the stochastic harmonic function (SHF) of rail irregularity power spectrum density was adopted to determine the representative points of spatial frequencies and phases to generate the random rail irregularity samples, and the non-stationary rail irregularity samples were modulated with the slowly varying function. Second, the probability density evolution method (PDEM) was employed to calculate the random dynamic vibration of the three-dimensional (3D) train-bridge system by a program compiled on the MATLAB® software platform. Eventually, the Newmark-β integration method and double edge difference method of total variation diminishing (TVD) format were adopted to obtain the mean value curve, the standard deviation curve and the time-history probability density information of responses. A case study was presented in which the ICE-3 train travels on a three-span simply-supported high-speed railway bridge with excitation of random rail irregularity. The results showed that compared to the Monte Carlo simulation, the PDEM has higher computational efficiency for the same accuracy, i.e., an improvement by 1-2 orders of magnitude. Additionally, the influences of rail irregularity and train speed on the random vibration of the coupled train-bridge system were discussed.

  17. Feasibility study of a single-shot 3D electron bunch shape monitor with an electro-optic sampling technique

    NASA Astrophysics Data System (ADS)

    Okayasu, Yuichi; Tomizawa, Hiromitsu; Matsubara, Shinichi; Kumagai, Noritaka; Maekawa, Akira; Uesaka, Mitsuru; Ishikawa, Tetsuya

    2013-05-01

    We developed a three-dimensional electron bunch charge distribution (3D-BCD) monitor with single-shot detection, and a spectral decoding based electro-optic (EO) sampling technique for a nondestructive monitor enables real-time reconstruction of the three-dimensional distribution of a bunch charge. We realized three goals by simultaneously probing a number of Pockels EO crystals that surround the electron beam axis with hollow and radial polarized laser pulses. First, we performed a feasibility test as a simple case of a 3D-BCD monitor probing two ZnTe crystals as EO detectors installed on the opposite angle to the electron beam axis and confirmed that we simultaneously obtained both EO signals. Since the adopted hollow probe laser pulse is not only radially polarized but also temporally shifted azimuthally, some disorders in the radial polarization distribution of such a laser pulse were numerically analyzed with a plane-wave expansion method. Based on the above investigations, the 3D-BCD monitor is feasible both in experimental and numerical estimations. Furthermore, we previously developed a femtosecond response organic crystal as a Pockels EO detector and a broadband probe laser (≥350nm in FWHM); the 3D-BCD monitor realizes 30- to 40-fs (FWHM) temporal resolution. Eventually, the monitor is expected to be equipped in such advanced accelerators as XFEL to measure and adjust the electron bunch charge distribution in real time. The 3D-BCD measurement works as a critical tool to provide feedback to seeded FELs.

  18. Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations

    SciTech Connect

    Wang, Lin-Wang; Lee, Byounghak; Shan, Hongzhang; Zhao, Zhengji; Meza, Juan; Strohmaier, Erich; Bailey, David H.

    2008-07-01

    We present a new linearly scaling three-dimensional fragment (LS3DF) method for large scale ab initio electronic structure calculations. LS3DF is based on a divide-and-conquer approach, which incorporates a novel patching scheme that effectively cancels out the artificial boundary effects due to the subdivision of the system. As a consequence, the LS3DF program yields essentially the same results as direct density functional theory (DFT) calculations. The fragments of the LS3DF algorithm can be calculated separately with different groups of processors. This leads to almost perfect parallelization on tens of thousands of processors. After code optimization, we were able to achieve 35.1 Tflop/s, which is 39percent of the theoretical speed on 17,280 Cray XT4 processor cores. Our 13,824-atom ZnTeO alloy calculation runs 400 times faster than a direct DFTcalculation, even presuming that the direct DFT calculation can scale well up to 17,280 processor cores. These results demonstrate the applicability of the LS3DF method to material simulations, the advantage of using linearly scaling algorithms over conventional O(N3) methods, and the potential for petascale computation using the LS3DF method.

  19. 3D imaging and quantitative analysis of small solubilized membrane proteins and their complexes by transmission electron microscopy.

    PubMed

    Vahedi-Faridi, Ardeschir; Jastrzebska, Beata; Palczewski, Krzysztof; Engel, Andreas

    2013-02-01

    Inherently unstable, detergent-solubilized membrane protein complexes can often not be crystallized. For complexes that have a mass of >300 kDa, cryo-electron microscopy (EM) allows their three-dimensional (3D) structure to be assessed to a resolution that makes secondary structure elements visible in the best case. However, many interesting complexes exist whose mass is below 300 kDa and thus need alternative approaches. Two methods are reviewed: (i) Mass measurement in a scanning transmission electron microscope, which has provided important information on the stoichiometry of membrane protein complexes. This technique is applicable to particulate, filamentous and sheet-like structures. (ii) 3D-EM of negatively stained samples, which determines the molecular envelope of small membrane protein complexes. Staining and dehydration artifacts may corrupt the quality of the 3D map. Staining conditions thus need to be optimized. 3D maps of plant aquaporin SoPIP2;1 tetramers solubilized in different detergents illustrate that the flattening artifact can be partially prevented and that the detergent itself contributes significantly. Another example discussed is the complex of G protein-coupled receptor rhodopsin with its cognate G protein transducin.

  20. Monitoring and Simulating the 3-D Density Currents at the Confluence of the Snake and Clearwater Rivers

    SciTech Connect

    Cook, Chris B.; Richmond, Marshall C.

    2004-12-01

    Summer temperatures in the Lower Snake River can be altered by releasing cold waters that originate from deep depths within Dworshak Reservoir. These cold releases are used to lower temperatures in the Clearwater River, a major tributary to the Lower Snake River, and to improve hydrodynamic and water quality conditions for migrating aquatic species. This project monitored the complex three-dimensional density currents at the Clearwater and Snake River confluence and the processes that led to stratification of Lower Granite Reservoir (LGR) during the late spring, summer, and fall of 2002. In addition to monitoring the LGR environment, a three-dimensional hydrodynamic and water quality model was also applied. By utilizing both field data and a numerical model, a more holistic view of the 3-D density currents was discovered than by either method alone. During this process, it was discovered that several predictable stratification patterns would develop depending upon the discharge ratio and the thermal gradient between the two rivers. These results illustrate the complex hydrodynamic structure at the confluence of the Clearwater and Snake Rivers, which has previously been shown by fish biologists to be a difficult passage zone for migrating salmonids of various life stages.

  1. Increase in the energy density of the pinch plasma in 3D implosion of quasi-spherical wire arrays

    SciTech Connect

    Aleksandrov, V. V.; Gasilov, V. A.; Grabovski, E. V.; Gritsuk, A. N. Laukhin, Ya. N.; Mitrofanov, K. N.; Oleinik, G. M.; Ol’khovskaya, O. G.; Sasorov, P. V.; Smirnov, V. P.; Frolov, I. N.; Shevel’ko, A. P.

    2014-12-15

    Results are presented from experimental studies of the characteristics of the soft X-ray (SXR) source formed in the implosion of quasi-spherical arrays made of tungsten wires and metalized kapron fibers. The experiments were carried out at the Angara-5-1 facility at currents of up to 3 MA. Analysis of the spatial distribution of hard X-ray emission with photon energies above 20 keV in the pinch images taken during the implosion of quasi-spherical tungsten wire arrays (QTWAs) showed that a compact quasi-spherical plasma object symmetric with respect to the array axis formed in the central region of the array. Using a diffraction grazing incidence spectrograph, spectra of SXR emission with wavelengths of 20–400 Å from the central, axial, and peripheral regions of the emission source were measured with spatial resolutions along the array radius and height in the implosion of QTWAs. It is shown that the emission spectra of the SXR sources formed under the implosion of quasi-spherical and cylindrical tungsten wire arrays at currents of up to 3 MA have a maximum in the wavelength range of 50–150 Å. It is found that, during the implosion of a QTWA with a profiled linear mass, a redistribution of energy in the emission spectrum takes place, which indicates that, during 3D implosion, the energy of longitudinal motion of the array material additionally contributes to the radiation energy. It is also found that, at close masses of the arrays and close values of the current in the range of 2.4{sup −3} MA, the average energy density in the emission source formed during the implosion of a quasi-spherical wire array is larger by a factor of 7 than in the source formed during the implosion of a cylindrical wire array. The experimental data were compared with results of 3D simulations of plasma dynamics and radiation generation during the implosion of quasi-spherical wire arrays with a profiled mass by using the MARPLE-3D radiative magnetohydrodynamic code, developed at the

  2. PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

    PubMed

    Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

    2015-10-01

    There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.

  3. PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps

    PubMed Central

    Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

    2015-01-01

    There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF2 fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF2 fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search. PMID:26469938

  4. PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

    PubMed

    Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

    2015-10-01

    There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search. PMID:26469938

  5. Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB☆

    PubMed Central

    Lagerstedt, Ingvar; Moore, William J.; Patwardhan, Ardan; Sanz-García, Eduardo; Best, Christoph; Swedlow, Jason R.; Kleywegt, Gerard J.

    2013-01-01

    The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed. PMID:24113529

  6. Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.

    PubMed

    Lagerstedt, Ingvar; Moore, William J; Patwardhan, Ardan; Sanz-García, Eduardo; Best, Christoph; Swedlow, Jason R; Kleywegt, Gerard J

    2013-11-01

    The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed.

  7. Density structure and geometry of the Costa Rican subduction zone from 3-D gravity modeling and local earthquake data

    NASA Astrophysics Data System (ADS)

    Lücke, O. H.; Arroyo, I. G.

    2015-10-01

    The eastern part of the oceanic Cocos Plate presents a heterogeneous crustal structure due to diverse origins and ages as well as plate-hot spot interactions which originated the Cocos Ridge, a structure that converges with the Caribbean Plate in southeastern Costa Rica. The complex structure of the oceanic plate directly influences the dynamics and geometry of the subduction zone along the Middle American Trench. In this paper an integrated interpretation of the slab geometry in Costa Rica is presented based on 3-D density modeling of combined satellite and surface gravity data, constrained by available geophysical and geological data and seismological information obtained from local networks. The results show the continuation of steep subduction geometry from the Nicaraguan margin into northwestern Costa Rica, followed by a moderate dipping slab under the Central Cordillera toward the end of the Central American Volcanic Arc. Contrary to commonly assumed, to the southeast end of the volcanic arc, our preferred model shows a steep, coherent slab that extends up to the landward projection of the Panama Fracture Zone. Overall, a gradual change in the depth of the intraplate seismicity is observed, reaching 220 km in the northwestern part, and becoming progressively shallower toward the southeast, where it reaches a maximum depth of 75 km. The changes in the terminal depth of the observed seismicity correlate with the increased density in the modeled slab. The absence of intermediate depth (> 75 km) intraplate seismicity in the southeastern section and the higher densities for the subducted slab in this area, support a model in which dehydration reactions in the subducted slab cease at a shallower depth, originating an anhydrous and thus aseismic slab.

  8. Nanoscale 3D cellular imaging by axial scanning transmission electron tomography

    PubMed Central

    Hohmann-Marriott, Martin F.; Sousa, Alioscka A.; Azari, Afrouz A.; Glushakova, Svetlana; Zhang, Guofeng; Zimmerberg, Joshua; Leapman, Richard D.

    2009-01-01

    Electron tomography provides three-dimensional structural information about supramolecular assemblies and organelles in a cellular context but image degradation, caused by scattering of transmitted electrons, limits applicability in specimens thicker than 300 nm. We show that scanning transmission electron tomography of 1000 nm thick samples using axial detection provides resolution comparable to conventional electron tomography. The method is demonstrated by reconstructing a human erythrocyte infected with the malaria parasite Plasmodium falciparum. PMID:19718033

  9. Simulation of the 3-D Evolution of Electron Scale Magnetic Reconnection - Motivated by Laboratory Experiments Predictions for MMS

    NASA Astrophysics Data System (ADS)

    Buechner, J.; Jain, N.; Sharma, A.

    2013-12-01

    The four s/c of the Magnetospheric Multiscale (MMS) mission, to be launched in 2014, will use the Earth's magnetosphere as a laboratory to study the microphysics of three fundamental plasma processes. One of them is magnetic reconnection, an essentially multi-scale process. While laboratory experiments and past theoretical investigations have shown that important processes necessary to understand magnetic reconnection take place at electron scales the MMS mission for the first time will be able to resolve these scales by in space observations. For the measurement strategy of MMS it is important to make specific predictions of the behavior of current sheets with a thickness of the order of the electron skin depth which play an important role in the evolution of collisionless magnetic reconnection. Since these processes are highly nonlinear and non-local numerical simulation is needed to specify the current sheet evolution. Here we present new results about the nonlinear evolution of electron-scale current sheets starting from the linear stage and using 3-D electron-magnetohydrodynamic (EMHD) simulations. The growth rates of the simulated instabilities compared well with the growth rates obtained from linear theory. Mechanisms and conditions of the formation of flux ropes and of current filamentation will be discussed in comparison with the results of fully kinetic simulations. In 3D the X- and O-point configurations of the magnetic field formed in reconnection planes alternate along the out-of-reconnection-plane direction with the wavelength of the unstable mode. In the presence of multiple reconnection sites, the out-of-plane magnetic field can develop nested structure of quadrupoles in reconnection planes, similar to the 2-D case, but now with variations in the out-of-plane direction. The structures of the electron flow and magnetic field in 3-D simulations will be compared with those in 2-D simulations to discriminate the essentially 3D features. We also discuss

  10. Color 3D electronic imaging of the surface of the human body

    NASA Astrophysics Data System (ADS)

    Rioux, Marc

    1994-10-01

    The NRC laboratories have developed a laser scanning technique to digitize shapes and colors in registration. The technique, known as synchronized scanning, is capable of digitizing topography as small as the relief of a bare finger tip, showing a clear picture of the skin structure (essentially a clean fingerprint without distortion), as well as the shape and size of body components such as hands, face, and feet, and the full body of one or more subjects simultaneously. The laser scanner uses a RGB laser, coupled to an optical fiber, which is projected in the field of view. The 3D color measurements are made by optical triangulation to a resolution of 10 micrometers for finger tip scans and a resolution of 1 mm for whole body scans. Experimental results are presented and discussed. Potential applications of this technology in the field of identification and inspection of humans include face recognition, finger, foot and teeth print identification, and 3D mugshots that can be rapidly broadcast through satellite communication. One of the unique properties of this technology is that absolute measurements, not only appearance and relative position of features, can be used for identification purposes.

  11. Status report on the 'Merging' of the Electron-Cloud Code POSINST with the 3-D Accelerator PIC CODE WARP

    SciTech Connect

    Vay, J.-L.; Furman, M.A.; Azevedo, A.W.; Cohen, R.H.; Friedman, A.; Grote, D.P.; Stoltz, P.H.

    2004-04-19

    We have integrated the electron-cloud code POSINST [1] with WARP [2]--a 3-D parallel Particle-In-Cell accelerator code developed for Heavy Ion Inertial Fusion--so that the two can interoperate. Both codes are run in the same process, communicate through a Python interpreter (already used in WARP), and share certain key arrays (so far, particle positions and velocities). Currently, POSINST provides primary and secondary sources of electrons, beam bunch kicks, a particle mover, and diagnostics. WARP provides the field solvers and diagnostics. Secondary emission routines are provided by the Tech-X package CMEE.

  12. From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

    PubMed Central

    Tsai, Wen-Ting; Hassan, Ahmed; Sarkar, Purbasha; Correa, Joaquin; Metlagel, Zoltan; Jorgens, Danielle M.; Auer, Manfred

    2014-01-01

    Modern 3D electron microscopy approaches have recently allowed unprecedented insight into the 3D ultrastructural organization of cells and tissues, enabling the visualization of large macromolecular machines, such as adhesion complexes, as well as higher-order structures, such as the cytoskeleton and cellular organelles in their respective cell and tissue context. Given the inherent complexity of cellular volumes, it is essential to first extract the features of interest in order to allow visualization, quantification, and therefore comprehension of their 3D organization. Each data set is defined by distinct characteristics, e.g., signal-to-noise ratio, crispness (sharpness) of the data, heterogeneity of its features, crowdedness of features, presence or absence of characteristic shapes that allow for easy identification, and the percentage of the entire volume that a specific region of interest occupies. All these characteristics need to be considered when deciding on which approach to take for segmentation. The six different 3D ultrastructural data sets presented were obtained by three different imaging approaches: resin embedded stained electron tomography, focused ion beam- and serial block face- scanning electron microscopy (FIB-SEM, SBF-SEM) of mildly stained and heavily stained samples, respectively. For these data sets, four different segmentation approaches have been applied: (1) fully manual model building followed solely by visualization of the model, (2) manual tracing segmentation of the data followed by surface rendering, (3) semi-automated approaches followed by surface rendering, or (4) automated custom-designed segmentation algorithms followed by surface rendering and quantitative analysis. Depending on the combination of data set characteristics, it was found that typically one of these four categorical approaches outperforms the others, but depending on the exact sequence of criteria, more than one approach may be successful. Based on these data

  13. Web-based volume slicer for 3D electron-microscopy data from EMDB.

    PubMed

    Salavert-Torres, José; Iudin, Andrii; Lagerstedt, Ingvar; Sanz-García, Eduardo; Kleywegt, Gerard J; Patwardhan, Ardan

    2016-05-01

    We describe the functionality and design of the Volume slicer - a web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. We have employed multiple rounds of user-experience testing with members of the EM community to ensure that the interface is easy and intuitive to use and the information provided is relevant. The impetus to develop the Volume slicer has been calls from the EM community to provide web-based interactive visualisation of 2D slice data. This would be useful for quick initial checks of the quality of a reconstruction. Again in response to calls from the community, we plan to further develop the Volume slicer into a fully-fledged Volume browser that provides integrated visualisation of EMDB and PDB entries from the molecular to the cellular scale.

  14. Web-based volume slicer for 3D electron-microscopy data from EMDB.

    PubMed

    Salavert-Torres, José; Iudin, Andrii; Lagerstedt, Ingvar; Sanz-García, Eduardo; Kleywegt, Gerard J; Patwardhan, Ardan

    2016-05-01

    We describe the functionality and design of the Volume slicer - a web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. We have employed multiple rounds of user-experience testing with members of the EM community to ensure that the interface is easy and intuitive to use and the information provided is relevant. The impetus to develop the Volume slicer has been calls from the EM community to provide web-based interactive visualisation of 2D slice data. This would be useful for quick initial checks of the quality of a reconstruction. Again in response to calls from the community, we plan to further develop the Volume slicer into a fully-fledged Volume browser that provides integrated visualisation of EMDB and PDB entries from the molecular to the cellular scale. PMID:26876163

  15. Parallel 3D Finite Element Numerical Modelling of DC Electron Guns

    SciTech Connect

    Prudencio, E.; Candel, A.; Ge, L.; Kabel, A.; Ko, K.; Lee, L.; Li, Z.; Ng, C.; Schussman, G.; /SLAC

    2008-02-04

    In this paper we present Gun3P, a parallel 3D finite element application that the Advanced Computations Department at the Stanford Linear Accelerator Center is developing for the analysis of beam formation in DC guns and beam transport in klystrons. Gun3P is targeted specially to complex geometries that cannot be described by 2D models and cannot be easily handled by finite difference discretizations. Its parallel capability allows simulations with more accuracy and less processing time than packages currently available. We present simulation results for the L-band Sheet Beam Klystron DC gun, in which case Gun3P is able to reduce simulation time from days to some hours.

  16. Uncertainty studies of topographical measurements on steel surface corrosion by 3D scanning electron microscopy.

    PubMed

    Kang, K W; Pereda, M D; Canafoglia, M E; Bilmes, P; Llorente, C; Bonetto, R

    2012-02-01

    Pitting corrosion is a damage mechanism quite serious and dangerous in both carbon steel boiler tubes for power plants which are vital to most industries and stainless steels for orthopedic human implants whose demand, due to the increase of life expectation and rate of traffic accidents, has sharply increased. Reliable methods to characterize this kind of damage are becoming increasingly necessary, when trying to evaluate the advance of damage and to establish the best procedures for component inspection in order to determine remaining lives and failure mitigation. A study about the uncertainties on the topographies of corrosion pits from 3D SEM images, obtained at low magnifications (where errors are greater) and different stage tilt angles were carried out using an in-house software previously developed. Additionally, measurements of pit depths on biomaterial surfaces, subjected to two different surface treatments on stainless steels, were carried out. The different depth distributions observed were in agreement with electrochemical measurements.

  17. Angular distribution of Auger electrons due to 3d-shell ionization of krypton

    NASA Technical Reports Server (NTRS)

    Omidvar, K.

    1977-01-01

    Cross sections for electron impact ionization of krypton due to ejection of a 3rd shell electron have been calculated using screened hydrogenic and Hartree-Slater wave functions for target atom. While the total ionization cross sections in the two approximations are within 10% of each other, the Auger electron angular distribution, related to cross sections for specific magnetic quantum numbers of the 3rd electrons, is widely different in the two approximations. The angular distribution due to Hartree-Slater approximation is in excellent agreement with measurement. The physical reason for the discrepancies in the two approximations is explained.

  18. Observations of the 3-D distribution of interplanetary electrons and ions from solar wind plasma to low energy cosmic rays

    NASA Technical Reports Server (NTRS)

    Lin, R. P.; Anderson, K. A.; Ashford, S.; Carlson, C.; Curtis, D.; Ergun, R.; Larson, D.; McFadden, J.; McCarthy, M.; Parks, G. K.

    1995-01-01

    The 3-D Plasma and Energetic Particle instrument on the GGS Wind spacecraft (launched November 1, 1994) is designed to make measurements of the full three-dimensional distribution of suprathermal electrons and ions from solar wind plasma to low energy cosmic rays, with high sensitivity, wide dynamic range, good energy and angular resolution, and high time resolution. Three pairs of double-ended telescopes, each with two or three closely sandwiched passivated ion implanted silicon detectors measure electrons and ions from approximately 20 keV to greater than or equal to 300 keV. Four top-hat symmetrical spherical section electrostatic analyzers with microchannel plate detectors, a large and a small geometric factor analyzer for electrons and a similar pair for ions, cover from approximately 3 eV to 30 keV. We present preliminary observations of the electron and ion distributions in the absence of obvious solar impulsive events and upstream particles. The quiet time electron energy spectrum shows a smooth approximately power law fall-off extending from the halo population at a few hundred eV to well above approximately 100 keV The quiet time ion energy spectrum also shows significant fluxes over this energy range. Detailed 3-D distributions and their temporal variations will be presented.

  19. 3D Plant cell architecture of Arabidopsis thaliana (Brassicaceae) using focused ion beam–scanning electron microscopy1

    PubMed Central

    Bhawana; Miller, Joyce L.; Cahoon, A. Bruce

    2014-01-01

    • Premise of the study: Focused ion beam–scanning electron microscopy (FIB-SEM) combines the ability to sequentially mill the sample surface and obtain SEM images that can be used to create 3D renderings with micron-level resolution. We have applied FIB-SEM to study Arabidopsis cell architecture. The goal was to determine the efficacy of this technique in plant tissue and cellular studies and to demonstrate its usefulness in studying cell and organelle architecture and distribution. • Methods: Seed aleurone, leaf mesophyll, stem cortex, root cortex, and petal lamina from Arabidopsis were fixed and embedded for electron microscopy using protocols developed for animal tissues and modified for use with plant cells. Each sample was sectioned using the FIB and imaged with SEM. These serial images were assembled to produce 3D renderings of each cell type. • Results: Organelles such as nuclei and chloroplasts were easily identifiable, and other structures such as endoplasmic reticula, lipid bodies, and starch grains were distinguishable in each tissue. • Discussion: The application of FIB-SEM produced 3D renderings of five plant cell types and offered unique views of their shapes and internal content. These results demonstrate the usefulness of FIB-SEM for organelle distribution and cell architecture studies. PMID:25202629

  20. New aspects of whistler waves driven by an electron beam studied by a 3-D electromagnetic code

    NASA Technical Reports Server (NTRS)

    Nishikawa, Ken-Ichi; Buneman, Oscar; Neubert, Torsten

    1994-01-01

    We have restudied electron beam driven whistler waves with a 3-D electromagnetic particle code. The simulation results show electromagnetic whistler wave emissions and electrostatic beam modes like those observed in the Spacelab 2 electron beam experiment. It has been suggested in the past that the spatial bunching of beam electrons associated with the beam mode may directly generate whistler waves. However, the simulation results indicate several inconsistencies with this picture: (1) whistler waves continue to be generated even after the beam mode space charge modulation looses its coherence, (2) the parallel (to the background magnetic field) wavelength of the whistler wave is longer than that of the beam instability, and (3) the parallel phase velocity of the whistler wave is smaller than that of the beam mode. The complex structure of the whistler waves in the vicinity of the beam suggest that the transverse motion (gyration) of the beam and background electrons is also involved in the generation of whistler waves.

  1. Viral Infection at High Magnification: 3D Electron Microscopy Methods to Analyze the Architecture of Infected Cells.

    PubMed

    Romero-Brey, Inés; Bartenschlager, Ralf

    2015-12-03

    As obligate intracellular parasites, viruses need to hijack their cellular hosts and reprogram their machineries in order to replicate their genomes and produce new virions. For the direct visualization of the different steps of a viral life cycle (attachment, entry, replication, assembly and egress) electron microscopy (EM) methods are extremely helpful. While conventional EM has given important information about virus-host cell interactions, the development of three-dimensional EM (3D-EM) approaches provides unprecedented insights into how viruses remodel the intracellular architecture of the host cell. During the last years several 3D-EM methods have been developed. Here we will provide a description of the main approaches and examples of innovative applications.

  2. Viral Infection at High Magnification: 3D Electron Microscopy Methods to Analyze the Architecture of Infected Cells

    PubMed Central

    Romero-Brey, Inés; Bartenschlager, Ralf

    2015-01-01

    As obligate intracellular parasites, viruses need to hijack their cellular hosts and reprogram their machineries in order to replicate their genomes and produce new virions. For the direct visualization of the different steps of a viral life cycle (attachment, entry, replication, assembly and egress) electron microscopy (EM) methods are extremely helpful. While conventional EM has given important information about virus-host cell interactions, the development of three-dimensional EM (3D-EM) approaches provides unprecedented insights into how viruses remodel the intracellular architecture of the host cell. During the last years several 3D-EM methods have been developed. Here we will provide a description of the main approaches and examples of innovative applications. PMID:26633469

  3. 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

  4. 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

  5. Improved 3D density modelling of the Central Andes from combining terrestrial datasets with satellite based datasets

    NASA Astrophysics Data System (ADS)

    Schaller, Theresa; Sobiesiak, Monika; Götze, Hans-Jürgen; Ebbing, Jörg

    2015-04-01

    As horizontal gravity gradients are proxies for large stresses, the uniquely high gravity gradients of the South American continental margin seem to be indicative for the frequently occurring large earthquakes at this plate boundary. It has been observed that these earthquakes can break repeatedly the same respective segment but can also combine to form M>9 earthquakes at the end of longer seismic cycles. A large seismic gap left behind by the 1877 M~9 earthquake existed in the northernmost part of Chile. This gap has partially been ruptured in the Mw 7.7 2007 Tocopilla earthquake and the Mw 8.2 2014 Pisagua earthquake. The nature of this seismological segmentation and the distribution of energy release in an earthquake is part of ongoing research. It can be assumed that both features are related to thickness variations of high density bodies located in the continental crust of the coastal area. These batholiths produce a clear maximum in the gravity signal. Those maxima also show a good spatial correlation with seismic asperity structures and seismological segment boundaries. Understanding of the tectonic situation can be improved through 3D forward density modelling of the gravity field. Problems arise in areas with less ground measurements. Especially in the high Andes severe gaps exist due to the inaccessibility of some regions. Also the transition zone between on and offshore date data displays significant problems, particularly since this is the area that is most interesting in terms of seismic hazard. We modelled the continental and oceanic crust and upper mantle using different gravity datasets. The first one includes terrestrial data measured at a station spacing of 5 km or less along all passable roads combined with satellite altimetry data offshore. The second data set is the newly released EIGEN-6C4 which combines the latest satellite data with ground measurements. The spherical harmonics maximum degree of EIGEN-6C4 is 2190 which corresponds to a

  6. Web-based volume slicer for 3D electron-microscopy data from EMDB

    PubMed Central

    Salavert-Torres, José; Iudin, Andrii; Lagerstedt, Ingvar; Sanz-García, Eduardo; Kleywegt, Gerard J.; Patwardhan, Ardan

    2016-01-01

    We describe the functionality and design of the Volume slicer – a web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. We have employed multiple rounds of user-experience testing with members of the EM community to ensure that the interface is easy and intuitive to use and the information provided is relevant. The impetus to develop the Volume slicer has been calls from the EM community to provide web-based interactive visualisation of 2D slice data. This would be useful for quick initial checks of the quality of a reconstruction. Again in response to calls from the community, we plan to further develop the Volume slicer into a fully-fledged Volume browser that provides integrated visualisation of EMDB and PDB entries from the molecular to the cellular scale. PMID:26876163

  7. Electron (charge) density studies of cellulose models

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Introductory material first describes electron density approaches and demonstrates visualization of electron lone pairs and bonding as concentrations of electron density. Then it focuses on the application of Bader’s Quantum Theory of Atoms-in-Molecules (AIM) to cellulose models. The purpose of the ...

  8. Numerical modelling of seawater intrusion in Shenzhen (China) using a 3D density-dependent model including tidal effects

    NASA Astrophysics Data System (ADS)

    Lu, Wei; Yang, Qingchun; Martín, Jordi D.; Juncosa, Ricardo

    2013-04-01

    During the 1990s, groundwater overexploitation has resulted in seawater intrusion in the coastal aquifer of the Shenzhen city, China. Although water supply facilities have been improved and alleviated seawater intrusion in recent years, groundwater overexploitation is still of great concern in some local areas. In this work we present a three-dimensional density-dependent numerical model developed with the FEFLOW code, which is aimed at simulating the extent of seawater intrusion while including tidal effects and different groundwater pumping scenarios. Model calibration, using waterheads and reported chloride concentration, has been performed based on the data from 14 boreholes, which were monitored from May 2008 to December 2009. A fairly good fitness between the observed and computed values was obtained by a manual trial-and-error method. Model prediction has been carried out forward 3 years with the calibrated model taking into account high, medium and low tide levels and different groundwater exploitation schemes. The model results show that tide-induced seawater intrusion significantly affects the groundwater levels and concentrations near the estuarine of the Dasha river, which implies that an important hydraulic connection exists between this river and groundwater, even considering that some anti-seepage measures were taken in the river bed. Two pumping scenarios were considered in the calibrated model in order to predict the future changes in the water levels and chloride concentration. The numerical results reveal a decreased tendency of seawater intrusion if groundwater exploitation does not reach an upper bound of about 1.32 × 104 m3/d. The model results provide also insights for controlling seawater intrusion in such coastal aquifer systems.

  9. Photons, Electrons and Positrons Transport in 3D by Monte Carlo Techniques

    SciTech Connect

    2014-12-01

    Version 04 FOTELP-2014 is a new compact general purpose version of the previous FOTELP-2K6 code designed to simulate the transport of photons, electrons and positrons through three-dimensional material and sources geometry by Monte Carlo techniques, using subroutine package PENGEOM from the PENELOPE code under Linux-based and Windows OS. This new version includes routine ELMAG for electron and positron transport simulation in electric and magnetic fields, RESUME option and routine TIMER for obtaining starting random number and for measuring the time of simulation.

  10. Photons, Electrons and Positrons Transport in 3D by Monte Carlo Techniques

    2014-12-01

    Version 04 FOTELP-2014 is a new compact general purpose version of the previous FOTELP-2K6 code designed to simulate the transport of photons, electrons and positrons through three-dimensional material and sources geometry by Monte Carlo techniques, using subroutine package PENGEOM from the PENELOPE code under Linux-based and Windows OS. This new version includes routine ELMAG for electron and positron transport simulation in electric and magnetic fields, RESUME option and routine TIMER for obtaining starting random numbermore » and for measuring the time of simulation.« less

  11. Efficient Semi-Automatic 3D Segmentation for Neuron Tracing in Electron Microscopy Images

    PubMed Central

    Jones, Cory; Liu, Ting; Cohan, Nathaniel Wood; Ellisman, Mark; Tasdizen, Tolga

    2015-01-01

    0.1. Background In the area of connectomics, there is a significant gap between the time required for data acquisition and dense reconstruction of the neural processes contained in the same dataset. Automatic methods are able to eliminate this timing gap, but the state-of-the-art accuracy so far is insufficient for use without user corrections. If completed naively, this process of correction can be tedious and time consuming. 0.2. New Method We present a new semi-automatic method that can be used to perform 3D segmentation of neurites in EM image stacks. It utilizes an automatic method that creates a hierarchical structure for recommended merges of superpixels. The user is then guided through each predicted region to quickly identify errors and establish correct links. 0.3. Results We tested our method on three datasets with both novice and expert users. Accuracy and timing were compared with published automatic, semi-automatic, and manual results. 0.4. Comparison with Existing Methods Post-automatic correction methods have also been used in [1] and [2]. These methods do not provide navigation or suggestions in the manner we present. Other semi-automatic methods require user input prior to the automatic segmentation such as [3] and [4] and are inherently different than our method. 0.5. Conclusion Using this method on the three datasets, novice users achieved accuracy exceeding state-of-the-art automatic results, and expert users achieved accuracy on par with full manual labeling but with a 70% time improvement when compared with other examples in publication. PMID:25769273

  12. Measuring surface topography with scanning electron microscopy. I. EZEImage: a program to obtain 3D surface data.

    PubMed

    Ponz, Ezequiel; Ladaga, Juan Luis; Bonetto, Rita Dominga

    2006-04-01

    Scanning electron microscopy (SEM) is widely used in the science of materials and different parameters were developed to characterize the surface roughness. In a previous work, we studied the surface topography with fractal dimension at low scale and two parameters at high scale by using the variogram, that is, variance vs. step log-log graph, of a SEM image. Those studies were carried out with the FERImage program, previously developed by us. To verify the previously accepted hypothesis by working with only an image, it is indispensable to have reliable three-dimensional (3D) surface data. In this work, a new program (EZEImage) to characterize 3D surface topography in SEM has been developed. It uses fast cross correlation and dynamic programming to obtain reliable dense height maps in a few seconds which can be displayed as an image where each gray level represents a height value. This image can be used for the FERImage program or any other software to obtain surface topography characteristics. EZEImage also generates anaglyph images as well as characterizes 3D surface topography by means of a parameter set to describe amplitude properties and three functional indices for characterizing bearing and fluid properties. PMID:17481354

  13. Ripple-modulated electronic structure of a 3D topological insulator.

    PubMed

    Okada, Yoshinori; Zhou, Wenwen; Walkup, D; Dhital, Chetan; Wilson, Stephen D; Madhavan, V

    2012-01-01

    Three-dimensional topological insulators host linearly dispersing states with unique properties and a strong potential for applications. An important ingredient in realizing some of the more exotic states in topological insulators is the ability to manipulate local electronic properties. Direct analogy to the Dirac material graphene suggests that a possible avenue for controlling local properties is via a controlled structural deformation such as the formation of ripples. However, the influence of such ripples on topological insulators is yet to be explored. Here we use scanning tunnelling microscopy to determine the effects of one-dimensional buckling on the electronic properties of Bi(2)Te(3.) By tracking spatial variations of the interference patterns generated by the Dirac electrons we show that buckling imposes a periodic potential, which locally modulates the surface-state dispersion. This suggests that forming one- and two-dimensional ripples is a viable method for creating nanoscale potential landscapes that can be used to control the properties of Dirac electrons in topological insulators.

  14. Highly-Ordered 3D Vertical Resistive Switching Memory Arrays with Ultralow Power Consumption and Ultrahigh Density.

    PubMed

    Al-Haddad, Ahmed; Wang, Chengliang; Qi, Haoyuan; Grote, Fabian; Wen, Liaoyong; Bernhard, Jörg; Vellacheri, Ranjith; Tarish, Samar; Nabi, Ghulam; Kaiser, Ute; Lei, Yong

    2016-09-01

    Resistive switching random access memories (RRAM) have attracted great scientific and industrial attention for next generation data storage because of their advantages of nonvolatile properties, high density, low power consumption, fast writing/erasing speed, good endurance, and simple and small operation system. Here, by using a template-assisted technique, we demonstrate a three-dimensional highly ordered vertical RRAM device array with density as high as that of the nanopores of the template (10(8)-10(9) cm(-2)), which can also be fabricated in large area. The high crystallinity of the materials, the large contact area and the intimate semiconductor/electrode interface (3 nm interfacial layer) make the ultralow voltage operation (millivolt magnitude) and ultralow power consumption (picowatt) possible. Our procedure for fabrication of the nanodevice arrays in large area can be used for producing many other different materials and such three-dimensional electronic device arrays with the capability to adjust the device densities can be extended to other applications of the next generation nanodevice technology. PMID:27525738

  15. Isolation, Electron Microscopy and 3D Reconstruction of Invertebrate Muscle Myofilaments

    PubMed Central

    Craig, Roger

    2011-01-01

    Understanding the molecular mechanism of muscle contraction and its regulation has been greatly influenced and aided by studies of myofilament structure in invertebrate muscles. Invertebrates are easily obtained and cover a broad spectrum of species and functional specializations. The thick (myosin-containing) filaments from some invertebrates are especially stable and simple in structure and thus much more amenable to structural analysis than those of vertebrates. Comparative studies of invertebrate filaments by electron microscopy and image processing have provided important generalizations of muscle molecular structure and function. This article reviews methods for preparing thick and thin filaments from invertebrate muscle, for imaging filaments by electron microscopy, and for determining their three dimensional structure by image processing. It also highlights some of the key insights into filament function that have come from these studies. PMID:22155190

  16. Direct observation of multistep energy transfer in LHCII with fifth-order 3D electronic spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Zhengyang; Lambrev, Petar H.; Wells, Kym L.; Garab, Győző; Tan, Howe-Siang

    2015-07-01

    During photosynthesis, sunlight is efficiently captured by light-harvesting complexes, and the excitation energy is then funneled towards the reaction centre. These photosynthetic excitation energy transfer (EET) pathways are complex and proceed in a multistep fashion. Ultrafast two-dimensional electronic spectroscopy (2DES) is an important tool to study EET processes in photosynthetic complexes. However, the multistep EET processes can only be indirectly inferred by correlating different cross peaks from a series of 2DES spectra. Here we directly observe multistep EET processes in LHCII using ultrafast fifth-order three-dimensional electronic spectroscopy (3DES). We measure cross peaks in 3DES spectra of LHCII that directly indicate energy transfer from excitons in the chlorophyll b (Chl b) manifold to the low-energy level chlorophyll a (Chl a) via mid-level Chl a energy states. This new spectroscopic technique allows scientists to move a step towards mapping the complete complex EET processes in photosynthetic systems.

  17. 3D modeling of the electron energy distribution function in negative hydrogen ion sources.

    PubMed

    Terasaki, R; Fujino, I; Hatayama, A; Mizuno, T; Inoue, T

    2010-02-01

    For optimization and accurate prediction of the amount of H-ion production in negative ion sources, analysis of electron energy distribution function (EEDF) is necessary. We are developing a numerical code which analyzes EEDF in the tandem-type arc-discharge source. It is a three-dimensional Monte Carlo simulation code with realistic geometry and magnetic configuration. Coulomb collision between electrons is treated with the "binary collision" model and collisions with hydrogen species are treated with the "null-collision" method. We applied this code to the analysis of the JAEA 10 A negative ion source. The numerical result shows that the obtained EEDF is in good agreement with experimental results.

  18. 3s- and 3p-core level excitations in 3d-transition metal oxides from electron-energy-loss spectroscopy

    NASA Astrophysics Data System (ADS)

    Steiner, P.; Zimmermann, R.; Reinert, F.; Engel, Th.; Hüfner, S.

    1995-03-01

    3s- and 3p-core level excitations for a large number of 3d-transition metal oxides, with a formal 3d occupation from 3d0 to 3d10, have been measured by electron energy loss spectroscopy in reflection geometry (REELS) with primary energies 200 eV≤ E 0≤1600 eV. Their intensities decrease systematically with the formal 3d-count, classifying them as transitions to empty 3d-states. The structure of the 3s excitations is analysed in detail and is compared to the 3s-XPS photoemission spectra of the samples. This 3s-REELS structure and its change with the 3d occupation can be explained by the assumption that the excitation arises mainly from a 3s23dn→3s13dn+1 quadrupole transition.

  19. Teaching Chemistry with Electron Density Models.

    ERIC Educational Resources Information Center

    Shusterman, Gwendolyn P.; Shusterman, Alan J.

    1997-01-01

    Describes a method for teaching electronic structure and its relevance to chemical phenomena that relies on computer-generated three-dimensional models of electron density distributions. Discusses the quantum mechanical background needed and presents ways of using models of electronic ground states to teach electronic structure, bonding concepts,…

  20. Identification of novel histone deacetylase 1 inhibitors by combined pharmacophore modeling, 3D-QSAR analysis, in silico screening and Density Functional Theory (DFT) approaches

    NASA Astrophysics Data System (ADS)

    Choubey, Sanjay K.; Mariadasse, Richard; Rajendran, Santhosh; Jeyaraman, Jeyakanthan

    2016-12-01

    Overexpression of HDAC1, a member of Class I histone deacetylase is reported to be implicated in breast cancer. Epigenetic alteration in carcinogenesis has been the thrust of research for few decades. Increased deacetylation leads to accelerated cell proliferation, cell migration, angiogenesis and invasion. HDAC1 is pronounced as the potential drug target towards the treatment of breast cancer. In this study, the biochemical potential of 6-aminonicotinamide derivatives was rationalized. Five point pharmacophore model with one hydrogen-bond acceptor (A3), two hydrogen-bond donors (D5, D6), one ring (R12) and one hydrophobic group (H8) was developed using 6-aminonicotinamide derivatives. The pharmacophore hypothesis yielded a 3D-QSAR model with correlation-coefficient (r2 = 0.977, q2 = 0.801) and it was externally validated with (r2pred = 0.929, r2cv = 0.850 and r2m = 0.856) which reveals the statistical significance of the model having high predictive power. The model was then employed as 3D search query for virtual screening against compound libraries (Zinc, Maybridge, Enamine, Asinex, Toslab, LifeChem and Specs) in order to identify novel scaffolds which can be experimentally validated to design future drug molecule. Density Functional Theory (DFT) at B3LYP/6-31G* level was employed to explore the electronic features of the ligands involved in charge transfer reaction during receptor ligand interaction. Binding free energy (ΔGbind) calculation was done using MM/GBSA which defines the affinity of ligands towards the receptor.

  1. EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

    DOE PAGES

    Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei; Cheng, Yifan; DiMaio, Frank; Adams, Paul D.; Fraser, James S.

    2015-08-17

    Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report that EMRinger is a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

  2. The linearly scaling 3D fragment method for large scale electronic structure calculations

    SciTech Connect

    Zhao, Zhengji; Meza, Juan; Lee, Byounghak; Shan, Hongzhang; Strohmaier, Erich; Bailey, David; Wang, Lin-Wang

    2009-07-28

    The Linearly Scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method for large-scale nano material simulations. It is a divide-and-conquer approach with a novel patching scheme that effectively cancels out the artificial boundary effects, which exist in all divide-and-conquer schemes. This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while retaining essentially the same accuracy as the direct calculation methods. The LS3DF method won the 2008 ACM Gordon Bell Prize for algorithm innovation. Our code has reached 442 Tflop/s running on 147,456 processors on the Cray XT5 (Jaguar) at OLCF, and has been run on 163,840 processors on the Blue Gene/P (Intrepid) at ALCF, and has been applied to a system containing 36,000 atoms. In this paper, we will present the recent parallel performance results of this code, and will apply the method to asymmetric CdSe/CdS core/shell nanorods, which have potential applications in electronic devices and solar cells.

  3. The Linearly Scaling 3D Fragment Method for Large Scale Electronic Structure Calculations

    SciTech Connect

    Zhao, Zhengji; Meza, Juan; Lee, Byounghak; Shan, Hongzhang; Strohmaier, Erich; Bailey, David; Wang, Lin-Wang

    2009-06-26

    The Linearly Scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method for large-scale nano material simulations. It is a divide-and-conquer approach with a novel patching scheme that effectively cancels out the artificial boundary effects, which exist in all divide-and-conquer schemes. This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while retaining essentially the same accuracy as the direct calculation methods. The LS3DF method won the 2008 ACM Gordon Bell Prize for algorithm innovation. Our code has reached 442 Tflop/s running on 147,456 processors on the Cray XT5 (Jaguar) at OLCF, and has been run on 163,840 processors on the Blue Gene/P (Intrepid) at ALCF, and has been applied to a system containing 36,000 atoms. In this paper, we will present the recent parallel performance results of this code, and will apply the method to asymmetric CdSe/CdS core/shell nanorods, which have potential applications in electronic devices and solar cells.

  4. The linearly scaling 3D fragment method for large scale electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Zhao, Zhengji; Meza, Juan; Lee, Byounghak; Shan, Hongzhang; Strohmaier, Erich; Bailey, David; Wang, Lin-Wang

    2009-07-01

    The linearly scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method for large-scale nano material simulations. It is a divide-and-conquer approach with a novel patching scheme that effectively cancels out the artificial boundary effects, which exist in all divide-and-conquer schemes. This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while retaining essentially the same accuracy as the direct calculation methods. The LS3DF method won the 2008 ACM Gordon Bell Prize for algorithm innovation. Our code has reached 442 Tflop/s running on 147,456 processors on the Cray XT5 (Jaguar) at OLCF, and has been run on 163,840 processors on the Blue Gene/P (Intrepid) at ALCF, and has been applied to a system containing 36,000 atoms. In this paper, we will present the recent parallel performance results of this code, and will apply the method to asymmetric CdSe/CdS core/shell nanorods, which have potential applications in electronic devices and solar cells.

  5. A Detailed Study of FDIRC Prototype with Waveform Digitizing Electronics in Cosmic Ray Telescope Using 3D Tracks.

    SciTech Connect

    Nishimura, K

    2012-07-01

    We present a detailed study of a novel Cherenkov imaging detector called the Focusing DIRC (FDIRC) with waveform digitizing electronics. In this test study, the FDIRC prototype has been instrumented with seven Hamamatsu H-8500 MaPMTs. Waveforms from ~450 pixels are digitized with waveform sampling electronics based on the BLAB2 ASIC, operating at a sampling speed of ~2.5 GSa/s. The FDIRC prototype was tested in a large cosmic ray telescope (CRT) providing 3D muon tracks with ~1.5 mrad angular resolution and muon energy of Emuon greater than 1.6 GeV. In this study we provide a detailed analysis of the tails in the Cherenkov angle distribution as a function of various variables, compare experimental results with simulation, and identify the major contributions to the tails. We demonstrate that to see the full impact of these tails on the Cherenkov angle resolution, it is crucial to use 3D tracks, and have a full understanding of the role of ambiguities. These issues could not be fully explored in previous FDIRC studies where the beam was perpendicular to the quartz radiator bars. This work is relevant for the final FDIRC prototype of the PID detector at SuperB, which will be tested this year in the CRT setup.

  6. A Detailed Study of FDIRC Prototype with Waveform Digitizing Electronics in Cosmic Ray Telescope Using 3D Tracks

    SciTech Connect

    Nishimura, K.; Dey, B.; Aston, D.; Leith, D.W.G.S.; Ratcliff, B.; Roberts, D.; Ruckman, L.; Shtol, D.; Varner, G.S.; Va'vra, J.; Vavra, Jerry; /SLAC

    2012-07-30

    We present a detailed study of a novel Cherenkov imaging detector called the Focusing DIRC (FDIRC) with waveform digitizing electronics. In this test study, the FDIRC prototype has been instrumented with seven Hamamatsu H-8500 MaPMTs. Waveforms from {approx}450 pixels are digitized with waveform sampling electronics based on the BLAB2 ASIC, operating at a sampling speed of {approx}2.5 GSa/s. The FDIRC prototype was tested in a large cosmic ray telescope (CRT) providing 3D muon tracks with {approx}1.5 mrad angular resolution and muon energy of E{sub muon} > 1.6 GeV. In this study we provide a detailed analysis of the tails in the Cherenkov angle distribution as a function of various variables, compare experimental results with simulation, and identify the major contributions to the tails. We demonstrate that to see the full impact of these tails on the Cherenkov angle resolution, it is crucial to use 3D tracks, and have a full understanding of the role of ambiguities. These issues could not be fully explored in previous FDIRC studies where the beam was perpendicular to the quartz radiator bars. This work is relevant for the final FDIRC prototype of the PID detector at SuperB, which will be tested this year in the CRT setup.

  7. Warps, bending and density waves excited by rotating magnetized stars: results of global 3D MHD simulations

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    We report results of the first global three-dimensional (3D) magnetohydrodynamic (MHD) simulations of the waves excited in an accretion disc by a rotating star with a dipole magnetic field misaligned from the star's rotation axis (which is aligned with the disc axis). The main results are the following. (1) If the magnetosphere of the star corotates approximately with the inner disc, then we observe a strong one-armed bending wave (a warp). This warp corotates with the star and has a maximum amplitude between corotation radius and the radius of the vertical resonance. The disc's centre of mass can deviate from the equatorial plane up to the distance of zw ≈ 0.1r. However, the effective height of the warp can be larger, hw ≈ 0.3r, due to the finite thickness of the disc. Stars with a range of misalignment angles excite warps. However, the amplitude of the warps is larger for misalignment angles between 15° and 60°. The location and amplitude of the warp do not depend on viscosity, at least for relatively small values of the standard alpha-parameter, up to 0.08. (2) If the magnetosphere rotates slower than the inner disc, then a bending wave is excited at the disc-magnetosphere boundary, but does not form a large-scale warp. Instead, persistent, high-frequency oscillations become strong at the inner region of the disc. These are (a) trapped density waves which form inside the radius where the disc angular velocity has a maximum, and (b) inner bending waves which appear in the case of accretion through magnetic Rayleigh-Taylor instability. These two types of waves are connected with the inner disc and their frequencies will vary with accretion rate. Bending oscillations at lower frequencies are also excited including global oscillations of the disc. In cases where the simulation region is small, slowly precessing warp forms with the maximum amplitude at the vertical resonance. The present simulations are applicable to young stars, cataclysmic variables and

  8. 3D electron tomography of pretreated biomass informs atomic modeling of cellulose microfibrils.

    PubMed

    Ciesielski, Peter N; Matthews, James F; Tucker, Melvin P; Beckham, Gregg T; Crowley, Michael F; Himmel, Michael E; Donohoe, Bryon S

    2013-09-24

    Fundamental insights into the macromolecular architecture of plant cell walls will elucidate new structure-property relationships and facilitate optimization of catalytic processes that produce fuels and chemicals from biomass. Here we introduce computational methodology to extract nanoscale geometry of cellulose microfibrils within thermochemically treated biomass directly from electron tomographic data sets. We quantitatively compare the cell wall nanostructure in corn stover following two leading pretreatment strategies: dilute acid with iron sulfate co-catalyst and ammonia fiber expansion (AFEX). Computational analysis of the tomographic data is used to extract mathematical descriptions for longitudinal axes of cellulose microfibrils from which we calculate their nanoscale curvature. These nanostructural measurements are used to inform the construction of atomistic models that exhibit features of cellulose within real, process-relevant biomass. By computational evaluation of these atomic models, we propose relationships between the crystal structure of cellulose Iβ and the nanoscale geometry of cellulose microfibrils. PMID:23988022

  9. Electron transfer through ordered metallic chains in LiNbO 3 : (Mg, Zn) : Me(3d)

    NASA Astrophysics Data System (ADS)

    Rakitina, L. G.; Shanina, B. D.; Corradi, G.; Polgar, K.

    1998-04-01

    In crystal and ceramic LiNbO 3 double doped with Mg or Zn above the threshold concentration ( CMg,Zn⩾4-6 mol%) and with transition metals of the 3d group (Cr, Fe, Mn) non-resonant microwave absorption (NRMA) dependent on the magnetic field was studied. Peak-like dependencies of the NRMA signal intensity on the concentration of dopants and stoichiometry of lithium niobate were found. The EPR line of mobile electrons (Δ B=30 mT) with g=2.0023 was detected. The interaction energy between the substitutional impurities of Mg and Cr was calculated. It was concluded, that in LiNbO 3 : (Mg, Zn) : (Cr, Fe, Mn) ordered metallic chains exist with electron conductivity.

  10. Sci—Thur AM: YIS - 07: Design and production of 3D printed bolus for electron radiation therapy

    SciTech Connect

    Su, Shiqin; Moran, Kathryn; Robar, James L.

    2014-08-15

    This is a proof-of-concept study demonstrating the capacity for modulated electron radiation therapy (MERT) using 3D printed bolus. Previous reports have involved bolus design using an electron pencil beam model and fabrication using a milling machine. In this study, an in-house algorithm is presented that optimizes the dose distribution with regard to dose coverage, conformity and homogeneity within planning target volume (PTV). The algorithm uses calculated result of a commercial electron Monte Carlo dose calculation as input. Distances along ray lines from distal side of 90% isodose to distal surface of PTV are used to estimate the bolus thickness. Inhomogeneities within the calculation volume are accounted for using coefficient of equivalent thickness method. Several regional modulation operators are applied to improve dose coverage and uniformity. The process is iterated (usually twice) until an acceptable MERT plan is realized, and the final bolus is printed using solid polylactic acid. The method is evaluated with regular geometric phantoms, anthropomorphic phantoms and a clinical rhabdomyosarcoma pediatric case. In all cases the dose conformity is improved compared to that with uniform bolus. The printed boluses conform well to the surface of complex anthropomorphic phantoms. For the rhabdomyosarcoma patient, the MERT plan yields a reduction of mean dose by 38.2% in left kidney relative to uniform bolus. MERT using 3D printed bolus appears to be a practical, low cost approach to generating optimized bolus for electron therapy. The method is effective in improving conformity of prescription isodose surface and in sparing immediately adjacent normal tissues.

  11. Relativistic radiation belt electron responses to GEM magnetic storms: Comparison of CRRES observations with 3-D VERB simulations

    NASA Astrophysics Data System (ADS)

    Kim, Kyung-Chan; Shprits, Yuri; Subbotin, Dmitriy; Ni, Binbin

    2012-08-01

    Understanding the dynamics of relativistic electron acceleration, loss, and transport in the Earth's radiation belt during magnetic storms is a challenging task. The U.S. National Science Foundation's Geospace Environment Modeling (GEM) has identified five magnetic storms for in-depth study that occurred during the second half of the Combined Release and Radiation Effects Satellite (CRRES) mission in the year 1991. In this study, we show the responses of relativistic radiation belt electrons to the magnetic storms by comparing the time-dependent 3-D Versatile Electron Radiation Belt (VERB) simulations with the CRRES MEA 1 MeV electron observations in order to investigate the relative roles of the competing effects of previously proposed scattering mechanisms at different storm phases, as well as to examine the extent to which the simulations can reproduce observations. The major scattering processes in our model are radial transport due to Ultra Low Frequency (ULF) electromagnetic fluctuations, pitch angle and energy diffusion including mixed diffusion by whistler mode chorus waves outside the plasmasphere, and pitch angle scattering by plasmaspheric hiss inside the plasmasphere. The 3-D VERB simulations show that during the storm main phase and early recovery phase the estimated plasmapause is located deep in the inner region, indicating that pitch angle scattering by chorus waves can be a dominant loss process in the outer belt. We have also confirmed the important role played by mixed energy-pitch angle diffusion by chorus waves, which tends to reduce the fluxes enhanced by local acceleration, resulting in comparable levels of computed and measured fluxes. However, we cannot reproduce the more pronounced flux dropout near the boundary of our simulations during the main phase, which indicates that non-adiabatic losses may extend toL-shells lower than our simulation boundary. We also provide a detailed description of simulations for each of the GEM storm events.

  12. Visualising the 3D Structure of Fine-Grained Estuarine Sediments; Preliminary Interpretations of a Novel Dataset Obtained via Volume Electron Microscopy

    NASA Astrophysics Data System (ADS)

    Wheatland, Jonathan; Bushby, Andy; Spencer, Kate; Carr, Simon

    2014-05-01

    Accurate measurement of the physical characteristics of sediment are critical to determining sediment transport behaviour and the stability of settled deposits. The properties (e.g. particle size, density, and settling velocity) of coarse-grained sediments (> 63 μm φ) can be easily characterised, hence their behaviour is relatively simple to predict and model. However, due to their small size and tendency to interact with their surrounding medium, the characteristics of fine sediments (< 63 μm φ) and their behaviour during transportation, deposition and consolidation is poorly understood. Recent studies have used correlative microscopy, a multi-method technique combining scanning confocal laser microscopy (SCLM), conventional optical microscopy (COM), and transmission electron microscopy (TEM), to characterise fine sediments at both the gross (> 1 μm) and sub-micron scale (Droppo et al., 1996). Whilst this technique has proven insightful, the measurement of geometric properties (e.g. the shape of primary particles and their spatial arrangement) can only be achieved by three-dimensional (3D) analysis and the scale of observation for e.g. TEM does not overlap with those techniques used to characterise sediments at larger scales (100s to 1000s microns) (e.g. video analysis). Volume electron microscopy [or focused ion beam scanning electron microscopy (FIB-SEM)] provides 3D analysis at scales of 10s to 1000s microns and though widely used in cell biology, has not been used to observe sediment. FIB-SEM requires samples that are vacuum stable and a key challenge will be to capture fragile, hydrated sediment samples whilst preserving their structural integrity. The aims of this work are therefore: 1) to modify preparation techniques currently used in cell biology for the stabilization of sedimentary materials; 2) to acquire 3D datasets for both fragile suspended sediments (flocs) and consolidated bed sediments and 3) to interpret the 3D structure of these samples. In

  13. Electron density studies of methyl cellobioside

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Experimental X-ray diffraction crystallography determines the variations in electron density that result from the periodic array of atoms in a crystal. Normally, the positions and type of atom are determined from the electron density based on an approximation that the atoms are spherical. However, t...

  14. An enteroendocrine cell-enteric glia connection revealed by 3D electron microscopy.

    PubMed

    Bohórquez, Diego V; Samsa, Leigh A; Roholt, Andrew; Medicetty, Satish; Chandra, Rashmi; Liddle, Rodger A

    2014-01-01

    The enteroendocrine cell is the cornerstone of gastrointestinal chemosensation. In the intestine and colon, this cell is stimulated by nutrients, tastants that elicit the perception of flavor, and bacterial by-products; and in response, the cell secretes hormones like cholecystokinin and peptide YY--both potent regulators of appetite. The development of transgenic mice with enteroendocrine cells expressing green fluorescent protein has allowed for the elucidation of the apical nutrient sensing mechanisms of the cell. However, the basal secretory aspects of the enteroendocrine cell remain largely unexplored, particularly because a complete account of the enteroendocrine cell ultrastructure does not exist. Today, the fine ultrastructure of a specific cell can be revealed in the third dimension thanks to the invention of serial block face scanning electron microscopy (SBEM). Here, we bridged confocal microscopy with SBEM to identify the enteroendocrine cell of the mouse and study its ultrastructure in the third dimension. The results demonstrated that 73.5% of the peptide-secreting vesicles in the enteroendocrine cell are contained within an axon-like basal process. We called this process a neuropod. This neuropod contains neurofilaments, which are typical structural proteins of axons. Surprisingly, the SBEM data also demonstrated that the enteroendocrine cell neuropod is escorted by enteric glia--the cells that nurture enteric neurons. We extended these structural findings into an in vitro intestinal organoid system, in which the addition of glial derived neurotrophic factors enhanced the development of neuropods in enteroendocrine cells. These findings open a new avenue of exploration in gastrointestinal chemosensation by unveiling an unforeseen physical relationship between enteric glia and enteroendocrine cells. PMID:24587096

  15. An Enteroendocrine Cell – Enteric Glia Connection Revealed by 3D Electron Microscopy

    PubMed Central

    Bohórquez, Diego V.; Samsa, Leigh A.; Roholt, Andrew; Medicetty, Satish; Chandra, Rashmi; Liddle, Rodger A.

    2014-01-01

    The enteroendocrine cell is the cornerstone of gastrointestinal chemosensation. In the intestine and colon, this cell is stimulated by nutrients, tastants that elicit the perception of flavor, and bacterial by-products; and in response, the cell secretes hormones like cholecystokinin and peptide YY – both potent regulators of appetite. The development of transgenic mice with enteroendocrine cells expressing green fluorescent protein has allowed for the elucidation of the apical nutrient sensing mechanisms of the cell. However, the basal secretory aspects of the enteroendocrine cell remain largely unexplored, particularly because a complete account of the enteroendocrine cell ultrastructure does not exist. Today, the fine ultrastructure of a specific cell can be revealed in the third dimension thanks to the invention of serial block face scanning electron microscopy (SBEM). Here, we bridged confocal microscopy with SBEM to identify the enteroendocrine cell of the mouse and study its ultrastructure in the third dimension. The results demonstrated that 73.5% of the peptide-secreting vesicles in the enteroendocrine cell are contained within an axon-like basal process. We called this process a neuropod. This neuropod contains neurofilaments, which are typical structural proteins of axons. Surprisingly, the SBEM data also demonstrated that the enteroendocrine cell neuropod is escorted by enteric glia – the cells that nurture enteric neurons. We extended these structural findings into an in vitro intestinal organoid system, in which the addition of glial derived neurotrophic factors enhanced the development of neuropods in enteroendocrine cells. These findings open a new avenue of exploration in gastrointestinal chemosensation by unveiling an unforeseen physical relationship between enteric glia and enteroendocrine cells. PMID:24587096

  16. The mapping of electronic energy distributions using experimental electron density.

    PubMed

    Tsirelson, Vladimir G

    2002-08-01

    It is demonstrated that the approximate kinetic energy density calculated using the second-order gradient expansion with parameters of the multipole model fitted to experimental structure factors reproduces the main features of this quantity in a molecular or crystal position space. The use of the local virial theorem provides an appropriate derivation of approximate potential energy density and electronic energy density from the experimental (model) electron density and its derivatives. Consideration of these functions is not restricted by the critical points in the electron density and provides a comprehensive characterization of bonding in molecules and crystals.

  17. The mapping of electronic energy distributions using experimental electron density.

    PubMed

    Tsirelson, Vladimir G

    2002-08-01

    It is demonstrated that the approximate kinetic energy density calculated using the second-order gradient expansion with parameters of the multipole model fitted to experimental structure factors reproduces the main features of this quantity in a molecular or crystal position space. The use of the local virial theorem provides an appropriate derivation of approximate potential energy density and electronic energy density from the experimental (model) electron density and its derivatives. Consideration of these functions is not restricted by the critical points in the electron density and provides a comprehensive characterization of bonding in molecules and crystals. PMID:12149553

  18. Basis set limit electronic excitation energies, ionization potentials, and electron affinities for the 3d transition metal atoms: Coupled cluster and multireference methods

    NASA Astrophysics Data System (ADS)

    Balabanov, Nikolai B.; Peterson, Kirk A.

    2006-08-01

    Recently developed correlation consistent basis sets for the first row transition metal elements Sc-Zn have been utilized to determine complete basis set (CBS) scalar relativistic electron affinities, ionization potentials, and 4s23dn -2-4s1dn -1 electronic excitation energies with single reference coupled cluster methods [CCSD(T), CCSDT, and CCSDTQ] and multireference configuration interaction with three reference spaces: 3d4s, 3d4s4p, and 3d4s4p3d'. The theoretical values calculated with the highest order coupled cluster techniques at the CBS limit, including extrapolations to full configuration interaction, are well within 1kcal/mol of the corresponding experimental data. For the early transition metal elements (Sc-Mn) the internally contracted multireference averaged coupled pair functional method yielded excellent agreement with experiment; however, the atomic properties for the late transition metals (Mn-Zn) proved to be much more difficult to describe with this level of theory, even with the largest reference function of the present work.

  19. Dual nature of 3 d electrons in YbT 2 Zn 20 (T = Co; Fe) evidenced by electron spin resonance

    DOE PAGES

    Ivanshin, V. A.; Litvinova, T. O.; Gimranova, K.; Sukhanov, A. A.; Jia, S.; Bud'ko, S. L.; Canfield, P. C.

    2015-03-18

    The electron spin resonance experiments were carried out in the single crystals YbFe2Zn20. The observed spin dynamics is compared with that in YbCo2Zn20 and Yb2Co12P7 as well as with the data of inelastic neutron scattering and electronic band structure calculations. Our results provide direct evidence that 3d electrons are itinerant in YbFe2Zn20 and localized in YbCo2Zn20. Possible connection between spin paramagnetism of dense heavy fermion systems, quantum criticality effects, and ESR spectra is discussed.

  20. 3D bone mineral density distribution and shape reconstruction of the proximal femur from a single simulated DXA image: an in vitro study

    NASA Astrophysics Data System (ADS)

    Whitmarsh, Tristan; Humbert, Ludovic; De Craene, Mathieu; del Río Barquero, Luis M.; Fritscher, Karl; Schubert, Rainer; Eckstein, Felix; Link, Thomas; Frangi, Alejandro F.

    2010-03-01

    Area Bone Mineral Density (aBMD) measured by Dual-energy X-ray Absorptiometry (DXA) is an established criterion in the evaluation of hip fracture risk. The evaluation from these planar images, however, is limited to 2D while it has been shown that proper 3D assessment of both the shape and the Bone Mineral Density (BMD) distribution improves the fracture risk estimation. In this work we present a method to reconstruct both the 3D bone shape and 3D BMD distribution of the proximal femur from a single DXA image. A statistical model of shape and a separate statistical model of the BMD distribution were automatically constructed from a set of Quantitative Computed Tomography (QCT) scans. The reconstruction method incorporates a fully automatic intensity based 3D-2D registration process, maximizing the similarity between the DXA and a digitally reconstructed radiograph of the combined model. For the construction of the models, an in vitro dataset of QCT scans of 60 anatomical specimens was used. To evaluate the reconstruction accuracy, experiments were performed on simulated DXA images from the QCT scans of 30 anatomical specimens. Comparisons between the reconstructions and the same subject QCT scans showed a mean shape accuracy of 1.2mm, and a mean density error of 81mg/cm3. The results show that this method is capable of accurately reconstructing both the 3D shape and 3D BMD distribution of the proximal femur from DXA images used in clinical routine, potentially improving the diagnosis of osteoporosis and fracture risk assessments at a low radiation dose and low cost.

  1. Electron microscopic evidence for nucleation and growth of 3D acetylcholine receptor microcrystals in structured lipid-detergent matrices.

    PubMed

    Paas, Yoav; Cartaud, Jean; Recouvreur, Michel; Grailhe, Regis; Dufresne, Virginie; Pebay-Peyroula, Eva; Landau, Ehud M; Changeux, Jean-Pierre

    2003-09-30

    Nicotinic acetylcholine receptors (AChRs) belong to a superfamily of oligomeric proteins that transduce electric signals across the cell membrane on binding of neurotransmitters. These receptors harbor a large extracellular ligand-binding domain directly linked to an ion-conducting channel-forming domain that spans the cell membrane 20 times and considerably extends into the cytoplasm. Thus far, none of these receptor channels has been crystallized in three dimensions. The crystallization of the AChR from Torpedo marmorata electric organs is challenged here in lipidic-detergent matrices. Detergent-soluble AChR complexed with alpha-bungarotoxin (alphaBTx), a polypeptidic competitive antagonist, was purified. The AChR-alphaBTx complex was reconstituted in a lipidic matrix composed of monoolein bilayers that are structured in three dimensions. The alphaBTx was conjugated to a photo-stable fluorophore, enabling us to monitor the physical behavior of the receptor-toxin complex in the lipidic matrix under light stereomicroscope, and to freeze fracture regions containing the receptor-toxin complex for visualization under a transmission electron microscope. Conditions were established for forming 2D receptor-toxin lattices that are stacked in the third dimension. 3D AChR nanocrystals were thereby grown inside the highly viscous lipidic 3D matrix. Slow emulsification of the lipidic matrix converted these nanocrystals into 3D elongated thin crystal plates of micrometer size. The latter are stable in detergent-containing aqueous solutions and can currently be used for seeding and epitaxial growth, en route to crystals of appropriate dimensions for x-ray diffraction studies.

  2. Carbon Nanofibers Synthesized on Selective Substrates for Nonvolatile Memory and 3D Electronics

    NASA Technical Reports Server (NTRS)

    Kaul, Anupama B.; Khan, Abdur R.

    2011-01-01

    A plasma-enhanced chemical vapor deposition (PECVD) growth technique has been developed where the choice of starting substrate was found to influence the electrical characteristics of the resulting carbon nanofiber (CNF) tubes. It has been determined that, if the tubes are grown on refractory metallic nitride substrates, then the resulting tubes formed with dc PECVD are also electrically conducting. Individual CNFs were formed by first patterning Ni catalyst islands using ebeam evaporation and liftoff. The CNFs were then synthesized using dc PECVD with C2H2:NH3 = [1:4] at 5 Torr and 700 C, and approximately equal to 200-W plasma power. Tubes were grown directly on degenerately doped silicon <100> substrates with resistivity rho approximately equal to 1-5 meterohm-centimeter, as well as NbTiN. The approximately equal to 200-nanometer thick refractory NbTiN deposited using magnetron sputtering had rho approximately equal to 113 microohm-centimeter and was also chemically compatible with CNF synthesis. The sample was then mounted on a 45 beveled Al holder, and placed inside a SEM (scanning electron microscope). A nanomanipulator probe stage was placed inside the SEM equipped with an electrical feed-through, where tungsten probes were used to make two-terminal electrical measurements with an HP 4156C parameter analyzer. The positive terminal nanoprobe was mechanically manipulated to physically contact an individual CNF grown directly on NbTiN as shown by the SEM image in the inset of figure (a), while the negative terminal was grounded to the substrate. This revealed the tube was electrically conductive, although measureable currents could not be detected until approximately equal to 6 V, after which point current increased sharply until compliance (approximately equal to 50 nA) was reached at approximately equal to 9.5 V. A native oxide on the tungsten probe tips may contribute to a tunnel barrier, which could be the reason for the suppressed transport at low biases

  3. Experimental study of the maximum resolution and packing density achievable in sintered and non-sintered binder-jet 3D printed steel microchannels

    SciTech Connect

    Elliott, Amy M; Mehdizadeh Momen, Ayyoub; Benedict, Michael; Kiggans Jr, James O

    2015-01-01

    Developing high resolution 3D printed metallic microchannels is a challenge especially when there is an essential need for high packing density of the primary material. While high packing density could be achieved by heating the structure to the sintering temperature, some heat sensitive applications require other strategies to improve the packing density of primary materials. In this study the goal is to develop high green or pack densities microchannels on the scale of 2-300 microns which have a robust mechanical structure. Binder-jet 3D printing is an additive manufacturing process in which droplets of binder are deposited via inkjet into a bed of powder. By repeatedly spreading thin layers of powder and depositing binder into the appropriate 2D profiles, complex 3D objects can be created one layer at time. Microchannels with features on the order of 500 microns were fabricated via binder jetting of steel powder and then sintered and/or infiltrated with a secondary material. The average particle size of the steel powder was varied along with the droplet volume of the inkjet-deposited binder. The resolution of the process, packing density of the primary material, the subsequent features sizes of the microchannels, and the overall microchannel quality were characterized as a function of particle size distribution, droplet sizes and heat treatment temperatures.

  4. Increase in the Random Dopant Induced Threshold Fluctuations and Lowering in Sub 100 nm MOSFETs Due to Quantum Effects: A 3-D Density-Gradient Simulation Study

    NASA Technical Reports Server (NTRS)

    Asenov, Asen; Slavcheva, G.; Brown, A. R.; Davies, J. H.; Saini, S.

    2000-01-01

    In this paper we present a detailed simulation study of the influence of quantum mechanical effects in the inversion layer on random dopant induced threshold voltage fluctuations and lowering in sub 100 nm MOSFETs. The simulations have been performed using a 3-D implementation of the density gradient (DG) formalism incorporated in our established 3-D atomistic simulation approach. This results in a self-consistent 3-D quantum mechanical picture, which implies not only the vertical inversion layer quantisation but also the lateral confinement effects related to current filamentation in the 'valleys' of the random potential fluctuations. We have shown that the net result of including quantum mechanical effects, while considering statistical dopant fluctuations, is an increase in both threshold voltage fluctuations and lowering. At the same time, the random dopant induced threshold voltage lowering partially compensates for the quantum mechanical threshold voltage shift in aggressively scaled MOSFETs with ultrathin gate oxides.

  5. FT3D: three-dimensional Fourier analysis on small Unix workstations for electron microscopy and tomographic studies.

    PubMed

    Lanzavecchia, S; Bellon, P L; Tosoni, L

    1993-12-01

    FT3D is a self-contained package of tools for three-dimensional Fourier analysis, written in the C language for Unix workstations. It can evaluate direct transforms of three-dimensional real functions, inverse transforms, auto- and cross-correlations and spectra. The library has been developed to support three-dimensional reconstructions of biological structures from projections obtained in the electron microscope. This paper discusses some features of the library, which has been implemented in such a way as to profit from the resources of modern workstations. A table of elapsed times for jobs of different dimensions with different RAM buffers is reported for the particular hardware used in the authors' laboratory.

  6. Structure-function studies of blood and air capillaries in chicken lung using 3D electron microscopy.

    PubMed

    West, John B; Fu, Zhenxing; Deerinck, Thomas J; Mackey, Mason R; Obayashi, James T; Ellisman, Mark H

    2010-02-28

    Avian pulmonary capillaries differ from those of mammals in three important ways. The blood-gas barrier is much thinner, it is more uniform in thickness, and the capillaries are far more rigid when their transmural pressure is altered. The thinness of the barrier is surprising because it predisposes the capillaries to stress failure. A possible mechanism for these differences is that avian pulmonary capillaries, unlike mammalian, are supported from the outside by air capillaries, but the details of the support are poorly understood. To clarify this we studied the blood and air capillaries in chicken lung using transmission electron microscopy (EM) and two relatively new techniques that allow 3D visualization: electron tomography and serial block-face scanning EM. These studies show that the pulmonary capillaries are flanked by epithelial bridges composed of two extremely thin epithelial cells with large surface areas. The junctions of the bridges with the capillary walls show thickening of the epithelial cells and an accumulation of extracellular matrix. Collapse of the pulmonary capillaries when the pressure outside them is increased is apparently prevented by the guy wire-like action of the epithelial bridges. The enlarged junctions between the bridges and the walls could provide a mechanism that limits the hoop stress in the capillary walls when the pressure inside them is increased. The support of the pulmonary capillaries may also be explained by an interdependence mechanism whereby the capillaries are linked to a rigid assemblage of air capillaries. These EM studies show the supporting structures in greater detail than has previously been possible, particularly in 3D, and they allow a more complete analysis of the mechanical forces affecting avian pulmonary capillaries. PMID:20038456

  7. 3D Reconstruction of VZV Infected Cell Nuclei and PML Nuclear Cages by Serial Section Array Scanning Electron Microscopy and Electron Tomography

    PubMed Central

    Reichelt, Mike; Joubert, Lydia; Perrino, John; Koh, Ai Leen; Phanwar, Ibanri; Arvin, Ann M.

    2012-01-01

    Varicella-zoster virus (VZV) is a human alphaherpesvirus that causes varicella (chickenpox) and herpes zoster (shingles). Like all herpesviruses, the VZV DNA genome is replicated in the nucleus and packaged into nucleocapsids that must egress across the nuclear membrane for incorporation into virus particles in the cytoplasm. Our recent work showed that VZV nucleocapsids are sequestered in nuclear cages formed from promyelocytic leukemia protein (PML) in vitro and in human dorsal root ganglia and skin xenografts in vivo. We sought a method to determine the three-dimensional (3D) distribution of nucleocapsids in the nuclei of herpesvirus-infected cells as well as the 3D shape, volume and ultrastructure of these unique PML subnuclear domains. Here we report the development of a novel 3D imaging and reconstruction strategy that we term Serial Section Array-Scanning Electron Microscopy (SSA-SEM) and its application to the analysis of VZV-infected cells and these nuclear PML cages. We show that SSA-SEM permits large volume imaging and 3D reconstruction at a resolution sufficient to localize, count and distinguish different types of VZV nucleocapsids and to visualize complete PML cages. This method allowed a quantitative determination of how many nucleocapsids can be sequestered within individual PML cages (sequestration capacity), what proportion of nucleocapsids are entrapped in single nuclei (sequestration efficiency) and revealed the ultrastructural detail of the PML cages. More than 98% of all nucleocapsids in reconstructed nuclear volumes were contained in PML cages and single PML cages sequestered up to 2,780 nucleocapsids, which were shown by electron tomography to be embedded and cross-linked by an filamentous electron-dense meshwork within these unique subnuclear domains. This SSA-SEM analysis extends our recent characterization of PML cages and provides a proof of concept for this new strategy to investigate events during virion assembly at the single cell

  8. The GaOH-HGaO potential energy hypersurface and the necessity of correlating the 3d electrons

    NASA Astrophysics Data System (ADS)

    Richards, Claude A., Jr.; Yamaguchi, Yukio; Kim, Seung-Joon; Schaefer, Henry F., III

    1996-06-01

    The ground state potential energy hypersurface of the GaOH-HGaO system has been investigated using high level ab initio molecular electronic structure theory. The geometries and physical properties of two equilibrium structures, one isomerization transition state and one inversion transition state were determined at the self-consistent field (SCF), configuration interaction with single and double excitations (CISD), coupled cluster with single and double excitations (CCSD), and CCSD with perturbative triple excitations [CCSD(T)] levels of theory with four sets of basis functions. It has been found that freezing the 3d electrons of the Ga atom in the correlation procedures is not appropriate for this system. For the energy difference ΔE (GaOH-HGaO) the freezing of the 3d electrons results in an error of 25 kcal/mol! The dipole moments, harmonic vibrational frequencies, and infrared (IR) intensities are predicted for the four stationary points. At the highest level of theory employed in this study, CCSD(T) using triple zeta plus double polarization with higher angular momentum and diffuse functions [TZ2P(f,d)+diff] basis set, the bent GaOH was found to be 41.9 kcal/mol more stable than the linear HGaO species; with the zero-point vibrational energy (ZPVE) correction, the energy separation becomes 40.4 kcal/mol. The classical barrier height for the exothermic isomerization (1,2 hydrogen shift) reaction HGaO→GaOH is determined to be 44.5 kcal/mol and the barrier height with the ZPVE correction 42.3 kcal/mol. The classical barrier to linearity for the bent GaOH molecule is determined to be 1.7 kcal/mol and the barrier height with the ZPVE correction to be 1.2 kcal/mol. The predicted dipole moments of GaOH and HGaO are 1.41 and 4.45 Debye, respectively. The effects of electron correlation reduce the dipole moment of HGaO by the sizable amount of 1.2 Debye. The two equilibrium species may be suitable for microwave spectroscopic investigation. Furthermore, they may also

  9. Electron density measurements in highly electronegative plasmas

    NASA Astrophysics Data System (ADS)

    Rafalskyi, D.; Lafleur, T.; Aanesland, A.

    2016-08-01

    In this paper we present experimental measurements of the electron density in very electronegative ‘ion–ion’ Ar–SF6 plasmas where previous investigations using Langmuir probes have observed electronegativities of up to 5000. The electron density is measured using a short matched dipole probe technique that provides a tolerance better than  ±2 · 1013 m‑3. The results demonstrate that the electron density in the low pressure plasma source (which contains a magnetic filter) can be reduced to around 2.7 · 1013 m‑3 with a corresponding plasma electronegativity of about 4000; close to that from fluid simulation predictions. The highest electronegativity, and lowest electron density, is achieved with a pure SF6 plasma, while adding only 6% SF6 to Ar allows the electronegativity to be increased from 0 to a few hundred with a corresponding decrease in the electron density by more than a thousand. The impedance probe based on a short matched dipole appears to be a practical diagnostic that can be used for independent measurements of the electron density in very electronegative plasmas, and opens up the possibility to further investigate and optimize electronegative plasma sources.

  10. Electron density measurements in highly electronegative plasmas

    NASA Astrophysics Data System (ADS)

    Rafalskyi, D.; Lafleur, T.; Aanesland, A.

    2016-08-01

    In this paper we present experimental measurements of the electron density in very electronegative ‘ion-ion’ Ar-SF6 plasmas where previous investigations using Langmuir probes have observed electronegativities of up to 5000. The electron density is measured using a short matched dipole probe technique that provides a tolerance better than  ±2 · 1013 m-3. The results demonstrate that the electron density in the low pressure plasma source (which contains a magnetic filter) can be reduced to around 2.7 · 1013 m-3 with a corresponding plasma electronegativity of about 4000; close to that from fluid simulation predictions. The highest electronegativity, and lowest electron density, is achieved with a pure SF6 plasma, while adding only 6% SF6 to Ar allows the electronegativity to be increased from 0 to a few hundred with a corresponding decrease in the electron density by more than a thousand. The impedance probe based on a short matched dipole appears to be a practical diagnostic that can be used for independent measurements of the electron density in very electronegative plasmas, and opens up the possibility to further investigate and optimize electronegative plasma sources.

  11. Theoretical study of lithium ionic conductors by electronic stress tensor density and electronic kinetic energy density.

    PubMed

    Nozaki, Hiroo; Fujii, Yosuke; Ichikawa, Kazuhide; Watanabe, Taku; Aihara, Yuichi; Tachibana, Akitomo

    2016-07-01

    We analyze the electronic structure of lithium ionic conductors, Li3PO4 and Li3PS4, using the electronic stress tensor density and kinetic energy density with special focus on the ionic bonds among them. We find that, as long as we examine the pattern of the eigenvalues of the electronic stress tensor density, we cannot distinguish between the ionic bonds and bonds among metalloid atoms. We then show that they can be distinguished by looking at the morphology of the electronic interface, the zero surface of the electronic kinetic energy density. © 2016 Wiley Periodicals, Inc.

  12. Electronic structures in coupled two quantum dots by 3D-mesh Hartree-Fock-Kohn-Sham calculation

    NASA Astrophysics Data System (ADS)

    Matsuse, T.; Hama, T.; Kaihatsu, H.; Toyoda, N.; Takizawa, T.

    To study the electronic structures of quantum dots in the framework of self-interaction-free including three dimensional effects, we adopt the theory of nonlocal effective potential introduced by Kohn and Sham [#!ks65!#]. For utilizing the advantageous point of the real space (3D) mesh method to solve the original nonlinear and nonlocal Hartree-Fock-Kohn-Sham (HFKS)-equation, we introduce a linearization of the equation in the local form by introducing the local Coulomb potentials which depend on explicitly the two single particle states. In practice, for solving the local form HFKS-equation, we use the Car-Parrinello-like relaxation method and the Coulomb potentials are obtained by solving the Poisson equation under proper boundary conditions. Firstly the observed energy gap between triplet- and singlet-states of N = 4 in DBS [#!tarucha96!#] is discussed to reproduce the addition energies and chemical potentials depending the magnetic field. Next the coupling between two-quantum dots in TBS [#!aht97!#] is studied by adding the square barrier between two dots. The spin-degeneracy [#!aht97!#] measured in gate-voltage depending on magnetic field is well reproduced in the limit of small mismatch. Finally, the electronic states in the ring structure are calculated and discussed how the ring size and magnetic field affect to the structures.

  13. 3D nanostructured inkjet printed graphene via UV-pulsed laser irradiation enables paper-based electronics and electrochemical devices.

    PubMed

    Das, Suprem R; Nian, Qiong; Cargill, Allison A; Hondred, John A; Ding, Shaowei; Saei, Mojib; Cheng, Gary J; Claussen, Jonathan C

    2016-09-21

    Emerging research on printed and flexible graphene-based electronics is beginning to show tremendous promise for a wide variety of fields including wearable sensors and thin film transistors. However, post-print annealing/reduction processes that are necessary to increase the electrical conductivity of the printed graphene degrade sensitive substrates (e.g., paper) and are whole substrate processes that are unable to selectively anneal/reduce only the printed graphene-leaving sensitive device components exposed to damaging heat or chemicals. Herein a pulsed laser process is introduced that can selectively irradiate inkjet printed reduced graphene oxide (RGO) and subsequently improve the electrical conductivity (Rsheet∼0.7 kΩ□(-1)) of printed graphene above previously published reports. Furthermore, the laser process is capable of developing 3D petal-like graphene nanostructures from 2D planar printed graphene. These visible morphological changes display favorable electrochemical sensing characteristics-ferricyanide cyclic voltammetry with a redox peak separation (ΔEp) ≈ 0.7 V as well as hydrogen peroxide (H2O2) amperometry with a sensitivity of 3.32 μA mM(-1) and a response time of <5 s. Thus this work paves the way for not only paper-based electronics with graphene circuits, it enables the creation of low-cost and disposable graphene-based electrochemical electrodes for myriad applications including sensors, biosensors, fuel cells, and theranostic devices.

  14. 2D/3D electron temperature fluctuations near explosive MHD instabilities accompanied by minor and major disruptions

    NASA Astrophysics Data System (ADS)

    Choi, M. J.; Park, H. K.; Yun, G. S.; Lee, W.; Luhmann, N. C., Jr.; Lee, K. D.; Ko, W.-H.; Park, Y.-S.; Park, B. H.; In, Y.

    2016-06-01

    Minor and major disruptions by explosive MHD instabilities were observed with the novel quasi 3D electron cyclotron emission imaging (ECEI) system in the KSTAR plasma. The fine electron temperature (T e) fluctuation images revealed two types of minor disruptions: a small minor disruption is a q∼ 2 localized fast transport event due to a single m/n  =  2/1 magnetic island growth, while a large minor disruption is partial collapse of the q≤slant 2 region with two successive fast heat transport events by the correlated m/n  =  2/1 and m/n  =  1/1 instabilities. The m/n  =  2/1 magnetic island growth during the minor disruption is normally limited below the saturation width. However, as the additional interchange-like perturbation grows near the inner separatrix of the 2/1 island, the 2/1 island can expand beyond the limit through coupling with the cold bubble formed by the interchange-like perturbation.

  15. 3D nanostructured inkjet printed graphene via UV-pulsed laser irradiation enables paper-based electronics and electrochemical devices.

    PubMed

    Das, Suprem R; Nian, Qiong; Cargill, Allison A; Hondred, John A; Ding, Shaowei; Saei, Mojib; Cheng, Gary J; Claussen, Jonathan C

    2016-09-21

    Emerging research on printed and flexible graphene-based electronics is beginning to show tremendous promise for a wide variety of fields including wearable sensors and thin film transistors. However, post-print annealing/reduction processes that are necessary to increase the electrical conductivity of the printed graphene degrade sensitive substrates (e.g., paper) and are whole substrate processes that are unable to selectively anneal/reduce only the printed graphene-leaving sensitive device components exposed to damaging heat or chemicals. Herein a pulsed laser process is introduced that can selectively irradiate inkjet printed reduced graphene oxide (RGO) and subsequently improve the electrical conductivity (Rsheet∼0.7 kΩ□(-1)) of printed graphene above previously published reports. Furthermore, the laser process is capable of developing 3D petal-like graphene nanostructures from 2D planar printed graphene. These visible morphological changes display favorable electrochemical sensing characteristics-ferricyanide cyclic voltammetry with a redox peak separation (ΔEp) ≈ 0.7 V as well as hydrogen peroxide (H2O2) amperometry with a sensitivity of 3.32 μA mM(-1) and a response time of <5 s. Thus this work paves the way for not only paper-based electronics with graphene circuits, it enables the creation of low-cost and disposable graphene-based electrochemical electrodes for myriad applications including sensors, biosensors, fuel cells, and theranostic devices. PMID:27510913

  16. Electronic and magnetic properties of monolayer SiC sheet doped with 3d-transition metals

    NASA Astrophysics Data System (ADS)

    Bezi Javan, Masoud

    2016-03-01

    We theoretically studied the electronic and magnetic properties of the monolayer SiC sheet doped by 3d transition-metal (TM) atoms. The structural properties, induced strain, electronic and magnetic properties were studied for cases that a carbon or silicon of the SiC sheet replaced with TM atoms. We found that the mount of induced strain to the lattice structure of the SiC sheet with substituting TM atoms is different for Si (TMSi) and C (TMC) sites as the TMSi structures have lower value of the strain. Also the TM atoms can be substituted in the lattice of the SiC sheet with different binding energy values for TMSi and TMC structures as the TMSi structures have higher value of the binding energies. Dependent to the structural properties, the TM doped SiC sheets show magnetic or nonmagnetic properties. We found that some structures such as MnSi, CuSi and CoC configurations have significant total magnetic moment about 3 μB.

  17. SMEI 3D RECONSTRUCTION OF A CORONAL MASS EJECTION INTERACTING WITH A COROTATING SOLAR WIND DENSITY ENHANCEMENT: THE 2008 APRIL 26 CME

    SciTech Connect

    Jackson, B. V.; Buffington, A.; Hick, P. P.; Clover, J. M.; Bisi, M. M.; Webb, D. F.

    2010-12-01

    The Solar Mass Ejection Imager (SMEI) has recorded the brightness responses of hundreds of interplanetary coronal mass ejections (CMEs) in the interplanetary medium. Using a three-dimensional (3D) reconstruction technique that derives its perspective views from outward-flowing solar wind, analysis of SMEI data has revealed the shapes, extents, and masses of CMEs. Here, for the first time, and using SMEI data, we report on the 3D reconstruction of a CME that intersects a corotating region marked by a curved density enhancement in the ecliptic. Both the CME and the corotating region are reconstructed and demonstrate that the CME disrupts the otherwise regular density pattern of the corotating material. Most of the dense CME material passes north of the ecliptic and east of the Sun-Earth line: thus, in situ measurements in the ecliptic near Earth and at the Solar-TErrestrial RElations Observatory Behind spacecraft show the CME as a minor density increase in the solar wind. The mass of the dense portion of the CME is consistent with that measured by the Large Angle Spectrometric Coronagraph on board the Solar and Heliospheric Observatory spacecraft, and is comparable to the masses of many other three-dimensionally reconstructed solar wind features at 1 AU observed in SMEI 3D reconstructions.

  18. Absolute Measurement of Electron Cloud Density

    SciTech Connect

    Covo, M K; Molvik, A W; Cohen, R H; Friedman, A; Seidl, P A; Logan, G; Bieniosek, F; Baca, D; Vay, J; Orlando, E; Vujic, J L

    2007-06-21

    Beam interaction with background gas and walls produces ubiquitous clouds of stray electrons that frequently limit the performance of particle accelerator and storage rings. Counterintuitively we obtained the electron cloud accumulation by measuring the expelled ions that are originated from the beam-background gas interaction, rather than by measuring electrons that reach the walls. The kinetic ion energy measured with a retarding field analyzer (RFA) maps the depressed beam space-charge potential and provides the dynamic electron cloud density. Clearing electrode current measurements give the static electron cloud background that complements and corroborates with the RFA measurements, providing an absolute measurement of electron cloud density during a 5 {micro}s duration beam pulse in a drift region of the magnetic transport section of the High-Current Experiment (HCX) at LBNL.

  19. A correlative approach for combining microCT, light and transmission electron microscopy in a single 3D scenario

    PubMed Central

    2013-01-01

    Background In biomedical research, a huge variety of different techniques is currently available for the structural examination of small specimens, including conventional light microscopy (LM), transmission electron microscopy (TEM), confocal laser scanning microscopy (CLSM), microscopic X-ray computed tomography (microCT), and many others. Since every imaging method is physically limited by certain parameters, a correlative use of complementary methods often yields a significant broader range of information. Here we demonstrate the advantages of the correlative use of microCT, light microscopy, and transmission electron microscopy for the analysis of small biological samples. Results We used a small juvenile bivalve mollusc (Mytilus galloprovincialis, approximately 0.8 mm length) to demonstrate the workflow of a correlative examination by microCT, LM serial section analysis, and TEM-re-sectioning. Initially these three datasets were analyzed separately, and subsequently they were fused in one 3D scene. This workflow is very straightforward. The specimen was processed as usual for transmission electron microscopy including post-fixation in osmium tetroxide and embedding in epoxy resin. Subsequently it was imaged with microCT. Post-fixation in osmium tetroxide yielded sufficient X-ray contrast for microCT imaging, since the X-ray absorption of epoxy resin is low. Thereafter, the same specimen was serially sectioned for LM investigation. The serial section images were aligned and specific organ systems were reconstructed based on manual segmentation and surface rendering. According to the region of interest (ROI), specific LM sections were detached from the slides, re-mounted on resin blocks and re-sectioned (ultrathin) for TEM. For analysis, image data from the three different modalities was co-registered into a single 3D scene using the software AMIRA®. We were able to register both the LM section series volume and TEM slices neatly to the microCT dataset, with

  20. Major structural features of the northern North Sea and adjacent areas of the continent according to lithosphere-scale 3D density and thermal modelling

    NASA Astrophysics Data System (ADS)

    Maystrenko, Y. P.; Olesen, O.; Ebbing, J.

    2013-12-01

    In order to analyse the regional configuration of the crystalline crust within the northern North Sea and adjacent areas of the continent, a lithosphere-scale 3D structural model has been constructed in the frame of the Crustal Onshore-Offshore Project (COOP project). Construction of the 3D model has been done by use of recently published/released structural data. For upper part of the model, all available data were merged into the following layers: sea water, the Cenozoic, the Upper Cretaceous, the Lower Cretaceous, the Jurassic, the Triassic, the Upper Permian (Zechstein) salt, Upper Permian clastics/carbonates and, finally, the Lower Permian-pre-Permian sedimentary rocks. Configuration of the crystalline crust and the Moho topography have been constrained by the published interpretations of deep seismic lines. The lithosphere-asthenosphere boundary has been compiled from previously published data. To evaluate the deep structure of the crystalline crust, a 3D density modelling has been carried out by use of the software IGMAS+ (the Interactive Gravity and Magnetic Application System). According to the 3D density modeling, the crystalline crust of the study area consists of several layers. Within the upper crystalline crust, gabbro to anorthositic rocks have been included into the 3D model along the western coast of Norway. In addition, a low-density (2627 kg/m3) upper crustal layer is modelled beneath the Horda Platform. The next upper crustal layer is characterized by regional distribution and has a density of 2670 kg/m3. The modelled middle crust of the study area contains four layers with similar densities around 2700 kg/m3. The lower crust consists of three layers. The deepest crustal layer is the high-density lower crustal layer (3060 kg/m3) which corresponds to the high-velocity layer. This layer thickens strongly beneath the Norwegian-Danish Basin and the eastern part of the East-Shetland platform. In addition to this high-density lower crustal layer, the

  1. Application of 3D Scanned Imaging Methodology for Volume, Surface Area, and Envelope Density Evaluation of Densified Biomass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Measurement of surface area, volume, and density is an essential for quantifying, evaluating, and designing the biomass densification, storage, and transport operations. Acquiring accurate and repeated measurements of these parameters for hygroscopic densified biomass are not straightforward and on...

  2. 3D density model of the western US lithosphere: Insights on chemistry, temperature, topography, and intraplate stress

    NASA Astrophysics Data System (ADS)

    Levandowski, W.; Jones, C. H.

    2014-12-01

    Although seismic velocity generally reflects material density, density models drawn solely from seismic interpretations suffer from the fact that temperature, melt-depletion, variations in quartz content, and in-situ melt—as well as myriad other factors—have different effects on the relationship between velocity and density. To wit, such models generally do not accurately recover gravity and/or topography variations. We have developed a probabilistic density modeling method that estimates density from seismic velocity and heat flow and refines these initial estimates in order to reproduce gravity and topography, accounting for lithospheric flexure. Both the input seismic velocity modeling and the refinement are Monte Carlo-type approaches, so the posterior distribution of models provides a direct measure of uncertainty. We leverage the aforementioned difference in sensitivity to separate density variations into thermal and compositional components, providing information on the chemistry and physical state of the crust and upper mantle. Using this approach and Transportable Array seismic data, we present a density model of the western US lithosphere (from central Kansas west) to a depth of 150 km that reveals: 1) remarkably uniform, near- to supra-solidus mantle temperatures beneath regions deformed in the Cenozoic--including the Colorado Plateau--that are ~400 °C higher than those beneath the nominally stable interior of North America; 2) crustal melt (~1%) beneath Miocene-Recent volcanic provinces; 3) depleted mantle lithosphere beneath the Wyoming craton and northern High Plains; 4) likely hydrated lower crust in the Colorado Plateau and Great Plains; and 5) that horizontal differences in lithostatic pressure create deviatoric extensional stress of ~10 MPa in the northern Basin and Range and along the margins of the Colorado Plateau. This density model is a rich source of information, shedding light on the causes and consequences of tectonism, crust

  3. High density resolution synchrotron radiation based x-ray microtomography (SR μCT) for quantitative 3D-morphometrics in zoological sciences

    NASA Astrophysics Data System (ADS)

    Nickel, Michael; Hammel, Jörg U.; Herzen, Julia; Bullinger, Eric; Beckmann, Felix

    2008-08-01

    Zoological sciences widely rely on morphological data to reconstruct and understand body structures of animals. The best suitable methods like tomography allow for a direct representation of 3D-structures. In recent years, synchrotron radiation based x-ray microtomography (SR μCT) placed high resolutions to the disposal of morphologists. With the development of highly brilliant and collimated third generation synchrotron sources, phase contrast SR μCT became widely available. A number of scientific contributions stressed the superiority of phase contrast over absorption contrast. However, here we demonstrate the power of high density resolution methods based on absorption-contrast SRμCT for quantitative 3D-measurements of tissues and other delicate bio-structures in zoological sciences. We used beamline BW2 at DORIS III (DESY, Hamburg, Germany) to perform microtomography on tissue and mineral skeletons of marine sponges (Porifera) which were shock frozen and/or fixed in a glutamate osmium tetroxide solution, followed by critical point drying. High density resolution tomographic reconstructions allowed running quantitative 3D-image analyses in Matlab and ImageJ. By applying contrast and shape rule based algorithms we semi-automatically extracted and measured sponge body structures like mineral spicules, elements of the canal system or tissue structures. This lead to a better understanding of sponge biology: from skeleton functional morphology and internal water flow regimes to body contractility. Our high density resolution based quantitative approach can be applied to a wide variety of biological structures. However, two prerequisites apply: (1) maximum density resolution is necessary; (2) edge effects as seen for example in phase outline contrast SR μCT must not be present. As a consequence, to allow biological sciences to fully exploit the power of SR μCT further increase of density resolution in absorption contrast methods is desirable.

  4. Stiffness of the microenvironment upregulates ERBB2 expression in 3D cultures of MCF10A within the range of mammographic density

    PubMed Central

    Cheng, Qingsu; Bilgin, Cemal Cagatay; Fonteney, Gerald; Chang, Hang; Henderson, Matthew; Han, Ju; Parvin, Bahram

    2016-01-01

    The effects of the stiffness of the microenvironment on the molecular response of 3D colony organization, at the maximum level of mammographic density (MD), are investigated. Phenotypic profiling reveals that 3D colony formation is heterogeneous and increased stiffness of the microenvironment, within the range of the MD, correlates with the increased frequency of aberrant 3D colony formation. Further integrative analysis of the genome-wide transcriptome and phenotypic profiling hypothesizes overexpression of ERBB2 in the premalignant MCF10A cell lines at a stiffness value that corresponds to the collagen component at high mammographic density. Subsequently, ERBB2 overexpression has been validated in the same cell line. Similar experiments with a more genetically stable cell line of 184A1 also revealed an increased frequency of aberrant colony formation with the increased stiffness; however, 184A1 did not demonstrate overexpression of ERBB2 at the same stiffness value of the high MD. These results suggest that stiffness exacerbates premalignant cell line of MCF10A. PMID:27383056

  5. Plasma response measurements of external magnetic perturbations using electron cyclotron emission and comparisons to 3D ideal MHD equilibrium

    NASA Astrophysics Data System (ADS)

    Willensdorfer, M.; Denk, S. S.; Strumberger, E.; Suttrop, W.; Vanovac, B.; Brida, D.; Cavedon, M.; Classen, I.; Dunne, M.; Fietz, S.; Fischer, R.; Kirk, A.; Laggner, F. M.; Liu, Y. Q.; Odstrčil, T.; Ryan, D. A.; Viezzer, E.; Zohm, H.; Luhmann, I. C.; The ASDEX Upgrade Team; The EUROfusion MST1 Team

    2016-11-01

    The plasma response from an external n  =  2 magnetic perturbation field in ASDEX Upgrade has been measured using mainly electron cyclotron emission (ECE) diagnostics and a rigid rotating field. To interpret ECE and ECE-imaging (ECE-I) measurements accurately, forward modeling of the radiation transport has been combined with ray tracing. The measured data is compared to synthetic ECE data generated from a 3D ideal magnetohydrodynamics (MHD) equilibrium calculated by VMEC. The measured amplitudes of the helical displacement around the outboard midplane are in reasonable agreement with the one from the synthetic VMEC diagnostics. Both exceed the predictions from the vacuum field calculations and indicate the presence of a kink response at the edge, which amplifies the perturbation. VMEC and MARS-F have been used to calculate the properties of this kink mode. The poloidal mode structure of the magnetic perturbation of this kink mode at the edge peaks at poloidal mode numbers larger than the resonant components |m|>|nq| , whereas the poloidal mode structure of its displacement is almost resonant |m|≈ |nq| . This is expected from ideal MHD in the proximity of rational surfaces. The displacement measured by ECE-I confirms this resonant response.

  6. Optical sectioning and 3D reconstructions as an alternative to scanning electron microscopy for analysis of cell shape1

    PubMed Central

    Landis, Jacob B.; Ventura, Kayla L.; Soltis, Douglas E.; Soltis, Pamela S.; Oppenheimer, David G.

    2015-01-01

    Premise of the study: Visualizing flower epidermal cells is often desirable for investigating the interaction between flowers and their pollinators, in addition to the broader range of ecological interactions in which flowers are involved. We developed a protocol for visualizing petal epidermal cells without the limitations of the commonly used method of scanning electron microscopy (SEM). Methods: Flower material was collected and fixed in glutaraldehyde, followed by dehydration in an ethanol series. Flowers were dissected to collect petals, and subjected to a Histo-Clear series to remove the cuticle. Material was then stained with aniline blue, mounted on microscope slides, and imaged using a compound fluorescence microscope to obtain optical sections that were reconstructed into a 3D image. Results: This optical sectioning method yielded high-quality images of the petal epidermal cells with virtually no damage to cells. Flowers were processed in larger batches than are possible using common SEM methods. Also, flower size was not a limiting factor as often observed in SEM studies. Flowers up to 5 cm in length were processed and mounted for visualization. Conclusions: This method requires no special equipment for sample preparation prior to imaging and should be seen as an alternative method to SEM. PMID:25909040

  7. Deep structure of the northern North Sea and adjacent areas according to regional-scale 3D density and thermal modelling

    NASA Astrophysics Data System (ADS)

    Maystrenko, Yuriy P.; Olesen, Odleiv; Ebbing, Jörg

    2013-04-01

    To analyse the regional configuration of the crystalline crust within the northern North Sea and adjacent areas of the continent, a lithosphere-scale 3D structural model has been constructed in the frame of the Crustal Onshore-Offshore Project (COOP project). Construction of the 3D model has been carried out using recently published/released data. For upper part of the model, all available data were merged into the following layers: sea water, the Cenozoic, the Upper Cretaceous, the Lower Cretaceous, the Jurassic, the Triassic, the Upper Permian (Zechstein) salt, Upper Permian clastics/carbonates and, finally, the Lower Permian-pre-Permian sedimentary rocks. Configuration of the crystalline crust and the Moho topography have been constrained by the published interpretations of deep seismic lines. The lithosphere-asthenosphere boundary has been compiled from previously published data. To evaluate the internal structure of the crystalline crust, a 3D density modelling has been carried out by use of the software IGMAS+ (the Interactive Gravity and Magnetic Application System). According to the 3D density modeling, the crystalline crust of the study area consists of several layers. Within the upper crystalline crust, gabbro to anorthositic rocks have been included into the 3D model along the western coast of Norway. In addition, a low-density (2627 kg/m3) upper crustal layer is modelled beneath the Horda Platform. The next upper crustal layer is characterized by regional distribution and has a density of 2670 kg/m3. The modelled middle crust of the study area contains four layers with similar densities around 2700 kg/m3. The lower crust consists of three layers. The deepest crustal layer is the high-density lower crustal layer (3060 kg/m3) which corresponds to the high-velocity layer. This layer thickens strongly beneath the Norwegian-Danish Basin and the eastern part of the East-Shetland platform. The obtained Moho is strongly uplifted beneath the Central and Viking

  8. Charge density waves in strongly correlated electron systems.

    PubMed

    Chen, Chih-Wei; Choe, Jesse; Morosan, E

    2016-08-01

    Strong electron correlations are at the heart of many physical phenomena of current interest to the condensed matter community. Here we present a survey of the mechanisms underlying such correlations in charge density wave (CDW) systems, including the current theoretical understanding and experimental evidence for CDW transitions. The focus is on emergent phenomena that result as CDWs interact with other charge or spin states, such as magnetism and superconductivity. In addition to reviewing the CDW mechanisms in 1D, 2D, and 3D systems, we pay particular attention to the prevalence of this state in two particular classes of compounds, the high temperature superconductors (cuprates) and the layered transition metal dichalcogenides. The possibilities for quantum criticality resulting from the competition between magnetic fluctuations and electronic instabilities (CDW, unconventional superconductivity) are also discussed. PMID:27376547

  9. Charge density waves in strongly correlated electron systems

    NASA Astrophysics Data System (ADS)

    Chen, Chih-Wei; Choe, Jesse; Morosan, E.

    2016-08-01

    Strong electron correlations are at the heart of many physical phenomena of current interest to the condensed matter community. Here we present a survey of the mechanisms underlying such correlations in charge density wave (CDW) systems, including the current theoretical understanding and experimental evidence for CDW transitions. The focus is on emergent phenomena that result as CDWs interact with other charge or spin states, such as magnetism and superconductivity. In addition to reviewing the CDW mechanisms in 1D, 2D, and 3D systems, we pay particular attention to the prevalence of this state in two particular classes of compounds, the high temperature superconductors (cuprates) and the layered transition metal dichalcogenides. The possibilities for quantum criticality resulting from the competition between magnetic fluctuations and electronic instabilities (CDW, unconventional superconductivity) are also discussed.

  10. 3D visualization of TiO2 nanocrystals in mesoporous nanocomposite using energy filtered transmission electron microscopy tomography.

    PubMed

    Gondo, Takashi; Kasama, Takeshi; Kaneko, Kenji

    2014-11-01

    IntroductionMesoporous silica, SBA-15, is one of the best candidate for the supporting material of catalytic nanoparticles because of its relative large and controllable pore size and large specific surface area [1]. So far, various nanoparticles, such as Au, Pt and Pd, have been introduced into the pore for catalytic application [2]. The size of nanoparticles supported inside SBA-15 is restricted by that of the pore, and they are usually ranging from 2 nm and 50 nm in space.It is necessary to anchor the nanoparticles within pores to avoid segregation / sintering of them. However, it is difficult to anchor them within pores in the case of use of deposition-precipitation method due to extreme low iso-electric point (IEP) of silica (∼2). Therefore, TiO2 nanocrystals (IEP 6-8) were then introduced to anchor AuNPs [3].In this study, EFTEM tomography was applied to examine the effectiveness of TiO2 for AuNPs. Materials and methodAu/TiO2-SBA-15 was embedded into epoxy resin for electron microscopy and microtomed to about 30 nm thickness. EFTEM-tomography was operated at 120 kV and using Ti-L ionization edge via three-window method. Prior to EFTEM, STEM-HAADF tomography was also carried out for visualizing AuNPs and for comparison. Result and discussionFigure 1 shows 3D-volume of AuNPs and TiO2 nanocrystals from EFTEM-tomography. TiO2 nanocrystals in the porous material were successfully visualized using EFTEM -tomography, and local relationship between AuNPs and TiO2 nanocrystals were revealed. A large number of TiO2 nanocrystals were randomly distributed in the SBA-15. It was found that most AuNPs were directly on the exposed TiO2 nanocrystals. It implies that TiO2 nanocrystals were exposed on the surface of the pore and anchored AuNPs inside the pores.jmicro;63/suppl_1/i27/DFU081F1F1DFU081F1Fig. 1.3D volume of AuNPs and TiO2 nanocrystals.

  11. A New Approach to Sap Flow Measurement Using 3D Printed Gauges and Open-source Electronics

    NASA Astrophysics Data System (ADS)

    Ham, J. M.; Miner, G. L.; Kluitenberg, G. J.

    2015-12-01

    A new type of sap flow gauge was developed to measure transpiration from herbaceous plants using a modified heat pulse technique. Gauges were fabricated using 3D-printing technology and low-cost electronics to keep the materials cost under $20 (U.S.) per sensor. Each gauge consisted of small-diameter needle probes fastened to a 3D-printed frame. One needle contained a resistance heater to provide a 6 to 8 second heat pulse while the other probes measured the resultant temperature increase at two distances from the heat source. The data acquisition system for the gauges was built from a low-cost Arduino microcontroller. The system read the gauges every 10 minutes and stored the results on a SD card. Different numerical techniques were evaluated for estimating sap velocity from the heat pulse data - including analytical solutions and parameter estimation approaches . Prototype gauges were tested in the greenhouse on containerized corn and sunflower. Sap velocities measured by the gauges were compared to independent gravimetric measurements of whole plant transpiration. Results showed the system could measure daily transpiration to within 3% of the gravimetric measurements. Excellent agreement was observed when two gauges were attached the same stem. Accuracy was not affected by rapidly changing transpiration rates observed under partly cloudy conditions. The gauge-based estimates of stem thermal properties suggested the system may also detect the onset of water stress. A field study showed the gauges could run for 1 to 2 weeks on a small battery pack. Sap flow measurements on multiple corn stems were scaled up by population to estimate field-scale transpiration. During full canopy cover, excellent agreement was observed between the scaled-up sap flow measurements and reference crop evapotranspiration calculated from weather data. Data also showed promise as a way to estimate real-time canopy resistance required for model verification and development. Given the low

  12. 3-D density modeling of Mt. Paekdu (N Korea/China) stratovolcano and its evolution by a combination of EGM2008/terrestrial gravity field

    NASA Astrophysics Data System (ADS)

    Götze, Hans-Jürgen; Choi, Sungchan

    2015-04-01

    We combined the global gravity dataset EGM2008 and a local terrestrial gravity data survey to conduct constrained 3-D crustal density modeling of a strato-volcanic complex and the surrounding area located close to the border of North Korea and China. The independent geophysical (seismic, seismology, geochemistry) and petrological constraints will be presented together with the preprocessing of data base by curvature analysis and Euler deconvolution. The multiple data base is used to assist a general interpretation of the investigated area, and the 3D density model (modelled by the in-house IGMAS+ software). Mt. Paekdu is characterized by a low of Bouguer anomaly of some -110 × 10-5 m/s2, which is caused by the combined gravity effects of (1) Moho depth of about 40 km, (2) a zone with both lower P-wave velocity and density than the surrounding, (3) low density volcanic rocks at the surface, and (4) the presence of a magma chamber that has not previously been identified. The terrestrial gravity field measured along the seismic profile shows a remarkable anomaly descending from the southern- to the northern flank of the Mt. Paekdu volcano, which should be a typical anomaly pattern generally observed over the active volcanic area in the world (e.g. the Yellow Stone volcano). The trend is interpreted to be caused by a prominent density difference between a serious of high density mid crustal sill beneath the southern flank and a predicted partial melted zone locating in the northern flank. With the help of several geoscientific observations (seismic, electromagnetic, gravity and geochemistry) and the 3D density model we conclude that a high density sill was formed in Pliocene and early Pleistocene after pre-shield plateau-forming eruption. Since the Pliocene, volcanic activity in the Mt. Paekdu region might be migrated from the southeastern of North Korea to the northwest, following the path of NW-SE-trending faults. Recently observed seismic tremors can be explained

  13. 3-D Density Modeling of the Combined EGM2008/Terrestrial Gravity Field over the Mt. Paekdu (N Korea/China) Stratovolcano and Its Evolution

    NASA Astrophysics Data System (ADS)

    Goetze, H. J.; Choi, S.

    2014-12-01

    In the presentation we get use of the global gravity dataset EGM2008 and a local terrestrial gravity data survey for a constrained 3-D crustal density modeling of a stratovolcano and its surrounding area located close to the border of North Korea and China. The independent geophysical (seismic, seismology, geochemistry) and petrological constraints will be presented together with the preprocessing of data base by curvature analysis and Euler deconvolution. The multiple data base is used to assist a general interpretation of the investigated area in time, and the 3D density model (modelled by the inhouse IGMAS+ software). Mt. Paekdu is characterized by a low of Bouguer anomaly of some -110 ´ 10-5 m/s2, which is caused by the combined gravity effects of (1) Moho depth of about 40 km, (2) a zone with both lower P-wave velocity and density than the surrounding, (3) low density volcanic rocks at the surface, and (4) the presence of a magma chamber that has not previously been identified. The terrestrial gravity field measured along the seismic profile shows a remarkable anomaly descending from the southern- to the northern flank of the Mt. Paekdu volcano, which should be a typical anomaly pattern generally obsered over the active volcanic area in the world (e.g. the Yellow Stone volcano). The trend is interpreted to be caused by a prominent density difference between a serious of high density mid crustal sill beneath the southern flank and a predicted partial melted zone locating in the northern flank. With the help of several geoscientific observations (seismic, electromagnetic, gravity and geochemistry) and the 3D density model we conclude that a high density sill was formed in Pliocene and early Pleistocene after pre-shield plateau-forming eruption. Since the Pliocene, volcanic activity in the Mt. Paekdu region might be migrated from the southeastern of North Korea to the northwest, following the path of NW-SE-trending faults. Recently observed seismic tremors can

  14. Immersed boundary Eulerian-Lagrangian 3D simulation of pyroclastic density currents: numerical scheme and experimental validation

    NASA Astrophysics Data System (ADS)

    Doronzo, Domenico Maria; de Tullio, Marco; Pascazio, Giuseppe; Dellino, Pierfrancesco

    2010-05-01

    Pyroclastic density currents are ground hugging, hot, gas-particle flows representing the most hazardous events of explosive volcanism. Their impact on structures is a function of dynamic pressure, which expresses the lateral load that such currents exert over buildings. In this paper we show how analog experiments can be matched with numerical simulations for capturing the essential physics of the multiphase flow. We used an immersed boundary scheme for the mesh generation, which helped in reconstructing the steep velocity and particle concentration gradients near the ground surface. Results show that the calculated values of dynamic pressure agree reasonably with the experimental measurements. These outcomes encourage future application of our method for the assessment of the impact of pyroclastic density currents at the natural scale.

  15. Visualizing the 3D Architecture of Multiple Erythrocytes Infected with Plasmodium at Nanoscale by Focused Ion Beam-Scanning Electron Microscopy

    PubMed Central

    Soares Medeiros, Lia Carolina; De Souza, Wanderley; Jiao, Chengge; Barrabin, Hector; Miranda, Kildare

    2012-01-01

    Different methods for three-dimensional visualization of biological structures have been developed and extensively applied by different research groups. In the field of electron microscopy, a new technique that has emerged is the use of a focused ion beam and scanning electron microscopy for 3D reconstruction at nanoscale resolution. The higher extent of volume that can be reconstructed with this instrument represent one of the main benefits of this technique, which can provide statistically relevant 3D morphometrical data. As the life cycle of Plasmodium species is a process that involves several structurally complex developmental stages that are responsible for a series of modifications in the erythrocyte surface and cytoplasm, a high number of features within the parasites and the host cells has to be sampled for the correct interpretation of their 3D organization. Here, we used FIB-SEM to visualize the 3D architecture of multiple erythrocytes infected with Plasmodium chabaudi and analyzed their morphometrical parameters in a 3D space. We analyzed and quantified alterations on the host cells, such as the variety of shapes and sizes of their membrane profiles and parasite internal structures such as a polymorphic organization of hemoglobin-filled tubules. The results show the complex 3D organization of Plasmodium and infected erythrocyte, and demonstrate the contribution of FIB-SEM for the obtainment of statistical data for an accurate interpretation of complex biological structures. PMID:22432024

  16. Optimization and analysis of 3D nanostructures for power-density enhancement in ultra-thin photovoltaics under oblique illumination.

    PubMed

    Shen, Bing; Wang, Peng; Menon, Rajesh

    2014-03-10

    Nanostructures have the potential to significantly increase the output power-density of ultra-thin photovoltaic devices by scattering incident sunlight into resonant guided modes. We applied a modified version of the direct-binary-search algorithm to design such nanostructures in order to maximize the output power-density under oblique-illumination conditions. We show that with appropriate design of nanostructured cladding layers, it is possible for a 10nm-thick organic absorber to produce an average peak power-density of 4mW/cm(2) with incident polar angle ranging from −90° to 90° and incident azimuthal angle ranging from −23.5° to 23.5°. Using careful modal and spectral analysis, we further show that an optimal trade-off of absorption at λ~510nm among various angles of incidence is essential to excellent performance under oblique illumination. Finally, we show that the optimized device with no sun tracking can produce on an average 7.23 times more energy per year than that produced by a comparable unpatterned device with an optimal anti-reflection coating.

  17. Optimization and analysis of 3D nanostructures for power-density enhancement in ultra-thin photovoltaics under oblique illumination.

    PubMed

    Shen, Bing; Wang, Peng; Menon, Rajesh

    2014-03-10

    Nanostructures have the potential to significantly increase the output power-density of ultra-thin photovoltaic devices by scattering incident sunlight into resonant guided modes. We applied a modified version of the direct-binary-search algorithm to design such nanostructures in order to maximize the output power-density under oblique-illumination conditions. We show that with appropriate design of nanostructured cladding layers, it is possible for a 10nm-thick organic absorber to produce an average peak power-density of 4 mW/cm² with incident polar angle ranging from -90° to 90° and incident azimuthal angle ranging from -23.5° to 23.5°. Using careful modal and spectral analysis, we further show that an optimal trade-off of absorption at λ~510 nm among various angles of incidence is essential to excellent performance under oblique illumination. Finally, we show that the optimized device with no sun tracking can produce on an average 7.23 times more energy per year than that produced by a comparable unpatterned device with an optimal anti-reflection coating.

  18. Density structure and geometry of the Costa Rican subduction zone from 3-D gravity modeling and local earthquake data

    NASA Astrophysics Data System (ADS)

    Lücke, O. H.; Arroyo, I. G.

    2015-07-01

    The eastern part of the oceanic Cocos Plate presents a heterogeneous crustal structure due to diverse origins and ages as well as plate-hot spot interactions which originated the Cocos Ridge, a structure that converges with the Caribbean Plate in southeastern Costa Rica. The complex structure of the oceanic plate directly influences the dynamics and geometry of the subduction zone along the Middle American Trench. In this paper an integrated interpretation of the slab geometry is presented based on three-dimensional density modeling of combined satellite and surface gravity data, constrained by available geophysical and geological data and seismological information obtained from local networks. The results show the continuation of steep subduction geometry from the Nicaraguan margin into Northwestern Costa Rica, followed by a moderate dipping slab under the Central Cordillera toward the end of the Central American Volcanic Arc. To the southeast end of the volcanic arc, our preferred model shows a steep, coherent slab that extends up to the landward projection of the Panama Fracture Zone. Overall, a gradual change in the depth of the intraplate seismicity is observed, reaching 220 km in the northwestern part, and becoming progressively shallower toward the southeast, where it reaches a terminal depth of 75 km. The changes in the terminal depth of the observed seismicity correlate with the increased density in the modeled slab. The absence of intermediate depth intraplate seismicity in the southeastern section and the higher densities for the subducted slab in this area, support a model in which dehydration reactions in the subducted slab cease at a shallower depth, originating an anhydrous and thus aseismic slab.

  19. A method for 3D-reconstruction of a muscle thick filament using the tilt series images of a single filament electron tomogram.

    PubMed

    Márquez, G; Pinto, A; Alamo, L; Baumann, B; Ye, F; Winkler, H; Taylor, K; Padrón, R

    2014-05-01

    Myosin interacting-heads (MIH) motifs are visualized in 3D-reconstructions of thick filaments from striated muscle. These reconstructions are calculated by averaging methods using images from electron micrographs of grids prepared using numerous filament preparations. Here we propose an alternative method to calculate the 3D-reconstruction of a single thick filament using only a tilt series images recorded by electron tomography. Relaxed thick filaments, prepared from tarantula leg muscle homogenates, were negatively stained. Single-axis tilt series of single isolated thick filaments were obtained with the electron microscope at a low electron dose, and recorded on a CCD camera by electron tomography. An IHRSR 3D-recontruction was calculated from the tilt series images of a single thick filament. The reconstruction was enhanced by including in the search stage dual tilt image segments while only single tilt along the filament axis is usually used, as well as applying a band pass filter just before the back projection. The reconstruction from a single filament has a 40 Å resolution and clearly shows the presence of MIH motifs. In contrast, the electron tomogram 3D-reconstruction of the same thick filament - calculated without any image averaging and/or imposition of helical symmetry - only reveals MIH motifs infrequently. This is - to our knowledge - the first application of the IHRSR method to calculate a 3D reconstruction from tilt series images. This single filament IHRSR reconstruction method (SF-IHRSR) should provide a new tool to assess structural differences between well-ordered thick (or thin) filaments in a grid by recording separately their electron tomograms.

  20. A method for 3D-reconstruction of a muscle thick filament using the tilt series images of a single filament electron tomogram.

    PubMed

    Márquez, G; Pinto, A; Alamo, L; Baumann, B; Ye, F; Winkler, H; Taylor, K; Padrón, R

    2014-05-01

    Myosin interacting-heads (MIH) motifs are visualized in 3D-reconstructions of thick filaments from striated muscle. These reconstructions are calculated by averaging methods using images from electron micrographs of grids prepared using numerous filament preparations. Here we propose an alternative method to calculate the 3D-reconstruction of a single thick filament using only a tilt series images recorded by electron tomography. Relaxed thick filaments, prepared from tarantula leg muscle homogenates, were negatively stained. Single-axis tilt series of single isolated thick filaments were obtained with the electron microscope at a low electron dose, and recorded on a CCD camera by electron tomography. An IHRSR 3D-recontruction was calculated from the tilt series images of a single thick filament. The reconstruction was enhanced by including in the search stage dual tilt image segments while only single tilt along the filament axis is usually used, as well as applying a band pass filter just before the back projection. The reconstruction from a single filament has a 40 Å resolution and clearly shows the presence of MIH motifs. In contrast, the electron tomogram 3D-reconstruction of the same thick filament - calculated without any image averaging and/or imposition of helical symmetry - only reveals MIH motifs infrequently. This is - to our knowledge - the first application of the IHRSR method to calculate a 3D reconstruction from tilt series images. This single filament IHRSR reconstruction method (SF-IHRSR) should provide a new tool to assess structural differences between well-ordered thick (or thin) filaments in a grid by recording separately their electron tomograms. PMID:24727133

  1. Influence of critical current density on magnetic force of HTSC bulk above PMR with 3D-modeling numerical solutions

    NASA Astrophysics Data System (ADS)

    Lu, Yiyun; Qin, Yujie

    2015-09-01

    Numerical simulations of thermo-electromagnetic properties of a high temperature superconducting (HTS) bulk levitating over a permanent magnetic guideway (PMG) are performed by resorting to the quasistatic approximation of the H-method coupling with the classical description of the heat conduction equation. The numerical resolving codes are practiced with the help of the finite element program generation system (FEPG) platform using finite element method (FEM). The E-J power law is used to describe the electric current nonlinear characteristics of HTS bulk. The simulation results show that the heat conduction and the critical current density are tightly relative to the thermal effects of the HTS bulk over the PMG. The heat intensity which responds to the heat loss of the HTS bulk is mainly distributed at the two bottom-corners of the bulk sample.

  2. Teaching Chemistry with Electron Density Models

    NASA Astrophysics Data System (ADS)

    Shusterman, Gwendolyn P.; Shusterman, Alan J.

    1997-07-01

    Linus Pauling once said that a topic must satisfy two criteria before it can be taught to students. First, students must be able to assimilate the topic within a reasonable amount of time. Second, the topic must be relevant to the educational needs and interests of the students. Unfortunately, the standard general chemistry textbook presentation of "electronic structure theory", set as it is in the language of molecular orbitals, has a difficult time satisfying either criterion. Many of the quantum mechanical aspects of molecular orbitals are too difficult for most beginning students to appreciate, much less master, and the few applications that are presented in the typical textbook are too limited in scope to excite much student interest. This article describes a powerful new method for teaching students about electronic structure and its relevance to chemical phenomena. This method, which we have developed and used for several years in general chemistry (G.P.S.) and organic chemistry (A.J.S.) courses, relies on computer-generated three-dimensional models of electron density distributions, and largely satisfies Pauling's two criteria. Students find electron density models easy to understand and use, and because these models are easily applied to a broad range of topics, they successfully convey to students the importance of electronic structure. In addition, when students finally learn about orbital concepts they are better prepared because they already have a well-developed three-dimensional picture of electronic structure to fall back on. We note in this regard that the types of models we use have found widespread, rigorous application in chemical research (1, 2), so students who understand and use electron density models do not need to "unlearn" anything before progressing to more advanced theories.

  3. A new type of 3-D peripheral ultrastructure in Glaucocystis (Glaucocystales, Glaucophyta) as revealed by ultra-high voltage electron microscopy.

    PubMed

    Takahashi, Toshiyuki; Nishida, Tomoki; Saito, Chieko; Yasuda, Hidehiro; Nozaki, Hisayoshi

    2016-06-01

    The coccoid glaucophyte genus Glaucocystis is characterized by having a thick cell wall, which has to date prohibited examination of the native ultrastructural features of the protoplast periphery. Recently, however, the three-dimensional (3-D) ultrastructure of the protoplast periphery was revealed in two divergent Glaucocystis species, with the world's most powerful ultra-high voltage electron microscope (UHVEM). The two species exhibit morphological diversity in terms of their 3-D ultrastructural features. However, these two types do not seem to encompass actual ultrastructural diversity in the genetically diverse genus Glaucocystis. Here, we report a new type of peripheral 3-D ultrastructure resolved in "G. incrassata" SAG 229-2 cells by 3-D modeling based on UHVEM tomography using high-pressure freezing and freeze-substitution fixation. The plasma membrane and underlying flattened vesicles in "G. incrassata" SAG 229-2 exhibited grooves at intervals of 200-600 nm, and the flattened vesicles often overlapped one another at the protoplast periphery. This 3-D ultrastructure differs from those of the two types previously reported in other species of Glaucocystis. The possibility of classification of Glaucocystis species based on the 3-D ultrastructure of the protoplast periphery is discussed. PMID:27273537

  4. A comparison of three SPRITE techniques for the quantitative 3D imaging of the 23Na spin density on a 4T whole-body machine.

    PubMed

    Romanzetti, S; Halse, M; Kaffanke, J; Zilles, K; Balcom, B J; Shah, N J

    2006-03-01

    Sodium density maps acquired with three SPRITE-based methods have been compared in terms of the resulting quantitative information as well as image quality and acquisition times. Consideration of factors relevant for the clinical implementation of SPRITE shows that the Conical-SPRITE variant is preferred because of a 20-fold reduction in acquisition time, slightly improved image quality, and no loss of quantitative information. The acquisition of a 3D data set (32x32x16; FOV=256x256x160 mm) for the quantitative determination of sodium density is demonstrated. In vivo Conical-SPRITE 23Na images of the brain of a healthy volunteer were acquired in 30 min with a resolution of 7.5x7.5x7.5 mm and a signal-to-noise ratio of 23 in cerebrospinal fluid and 17 in brain tissue. PMID:16325438

  5. Interplay between spin-density wave and 3 d local moments with random exchange in a molecular conductor

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Genta; Maesato, Mitsuhiko; Komatsu, Tokutaro; Imakubo, Tatsuro; Kitagawa, Hiroshi

    2016-02-01

    We present the results of high-pressure transport measurements on the anion-mixed molecular conductors (DIETSe)2M Br2Cl2 [DIETSe = diiodo(ethylenedithio)tetraselenafulvalene; M =Fe , Ga]. They undergo a metal-insulator (M-I) transition below 9 K at ambient pressure, which is suppressed by applying pressure, indicating a spin-density-wave (SDW) transition caused by a nesting instability of the quasi-one-dimensional (Q1D) Fermi surface, as observed in the parent compounds (DIETSe)2M Cl4 (M =Fe , Ga). In the metallic state, the existence of the Q1D Fermi surface is confirmed by observing the Lebed resonance. The critical pressures of the SDW, Pc, of the M Br2Cl2 (M =Fe , Ga) salts are significantly lower than those of the the M Cl4 (M = Fe, Ga) salts, suggesting chemical pressure effects. Above Pc, field-induced SDW transitions appear, as evidenced by kink structures in the magnetoresistance (MR) in both salts. The FeBr2Cl2 salt also shows antiferromagnetic (AF) ordering of d spins at 4 K, below which significant spin-charge coupling is observed. A large positive MR change up to 150% appears above the spin-flop field at high pressure. At low pressure, in particular below Pc, a dip or kink structure appears in MR at the spin-flop field, which shows unconventionally large hysteresis at low temperature (T <1 K). The hysteresis region clearly decreases with increasing pressure towards Pc, strongly indicating that the coexisting SDW plays an important role in the enhancement of magnetic hysteresis besides the random exchange interaction.

  6. Method for dose-reduced 3D catheter tracking on a scanning-beam digital x-ray system using dynamic electronic collimation

    NASA Astrophysics Data System (ADS)

    Dunkerley, David A. P.; Funk, Tobias; Speidel, Michael A.

    2016-03-01

    Scanning-beam digital x-ray (SBDX) is an inverse geometry x-ray fluoroscopy system capable of tomosynthesis-based 3D catheter tracking. This work proposes a method of dose-reduced 3D tracking using dynamic electronic collimation (DEC) of the SBDX scanning x-ray tube. Positions in the 2D focal spot array are selectively activated to create a regionof- interest (ROI) x-ray field around the tracked catheter. The ROI position is updated for each frame based on a motion vector calculated from the two most recent 3D tracking results. The technique was evaluated with SBDX data acquired as a catheter tip inside a chest phantom was pulled along a 3D trajectory. DEC scans were retrospectively generated from the detector images stored for each focal spot position. DEC imaging of a catheter tip in a volume measuring 11.4 cm across at isocenter required 340 active focal spots per frame, versus 4473 spots in full-FOV mode. The dose-area-product (DAP) and peak skin dose (PSD) for DEC versus full field-of-view (FOV) scanning were calculated using an SBDX Monte Carlo simulation code. DAP was reduced to 7.4% to 8.4% of the full-FOV value, consistent with the relative number of active focal spots (7.6%). For image sequences with a moving catheter, PSD was 33.6% to 34.8% of the full-FOV value. The root-mean-squared-deviation between DEC-based 3D tracking coordinates and full-FOV 3D tracking coordinates was less than 0.1 mm. The 3D distance between the tracked tip and the sheath centerline averaged 0.75 mm. Dynamic electronic collimation can reduce dose with minimal change in tracking performance.

  7. Integration of 3D scale-based pseudo-enhancement correction and partial volume image segmentation for improving electronic colon cleansing in CT colonograpy.

    PubMed

    Zhang, Hao; Li, Lihong; Zhu, Hongbin; Han, Hao; Song, Bowen; Liang, Zhengrong

    2014-01-01

    Orally administered tagging agents are usually used in CT colonography (CTC) to differentiate residual bowel content from native colonic structures. However, the high-density contrast agents tend to introduce pseudo-enhancement (PE) effect on neighboring soft tissues and elevate their observed CT attenuation value toward that of the tagged materials (TMs), which may result in an excessive electronic colon cleansing (ECC) since the pseudo-enhanced soft tissues are incorrectly identified as TMs. To address this issue, we integrated a 3D scale-based PE correction into our previous ECC pipeline based on the maximum a posteriori expectation-maximization partial volume (PV) segmentation. The newly proposed ECC scheme takes into account both the PE and PV effects that commonly appear in CTC images. We evaluated the new scheme on 40 patient CTC scans, both qualitatively through display of segmentation results, and quantitatively through radiologists' blind scoring (human observer) and computer-aided detection (CAD) of colon polyps (computer observer). Performance of the presented algorithm has shown consistent improvements over our previous ECC pipeline, especially for the detection of small polyps submerged in the contrast agents. The CAD results of polyp detection showed that 4 more submerged polyps were detected for our new ECC scheme over the previous one.

  8. 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.

  9. Enhancing the Contrast of ApoB to Locate the Surface Components in the 3D Density Map of Human LDL

    PubMed Central

    Liu, Yuhang; Atkinson, David

    2010-01-01

    A 26Å resolution map of the structure of human LDL was obtained from cryo-EM and single particle image reconstruction. The structure showed a discoidal shaped LDL particle with high-density regions mainly distributed at the edge of the particle and low-density regions at the flat surface that covers the core region. To determine the chemical components that correspond to these density regions and to delineate the distribution of protein and phospholipid located at the particle surface at the resolution of the map, we used Mono-Sulfo-NHS-Undecagold labeling to increase preferentially the contrast of the apoB protein component on the LDL particle. In the 3D maps from the image reconstruction of the undecagold labeled LDL particles, the high-density region from the undecagold label was distributed mainly at the edge of the particle and lower density regions were found at the flat surfaces that cover the neutral lipid core. This suggests that apoB mainly encircles LDL at the edge of the particle and the phospholipid monolayers are located at the flat surfaces, which are parallel to the cholesterol ester layers in the core and may interact with the core lipid layers through the acyl-chains. PMID:21029740

  10. The Uppsala Electron-Density Server.

    PubMed

    Kleywegt, Gerard J; Harris, Mark R; Zou, Jin Yu; Taylor, Thomas C; Wählby, Anders; Jones, T Alwyn

    2004-12-01

    The Uppsala Electron Density Server (EDS; http://eds.bmc.uu.se/) is a web-based facility that provides access to electron-density maps and statistics concerning the fit of crystal structures and their maps. Maps are available for approximately 87% of the crystallographic Protein Data Bank (PDB) entries for which structure factors have been deposited and for which straightforward map calculations succeed in reproducing the published R value to within five percentage points. Here, an account is provided of the methods that are used to generate the information contained in the server. Some of the problems that are encountered in the map-generation process as well as some spin-offs of the project are also discussed.

  11. Electron Density Profiles of the Topside Ionosphere

    NASA Technical Reports Server (NTRS)

    Huang, Xue-Qin; Reinsch, Bodo W.; Bilitza, Dieter; Benson, Robert F.

    2002-01-01

    The existing uncertainties about the electron density profiles in the topside ionosphere, i.e., in the height region from h,F2 to - 2000 km, require the search for new data sources. The ISIS and Alouette topside sounder satellites from the sixties to the eighties recorded millions of ionograms but most were not analyzed in terms of electron density profiles. In recent years an effort started to digitize the analog recordings to prepare the ionograms for computerized analysis. As of November 2001 about 350000 ionograms have been digitized from the original 7-track analog tapes. These data are available in binary and CDF format from the anonymous ftp site of the National Space Science Data Center. A search site and browse capabilities on CDAWeb assist the scientific usage of these data. All information and access links can be found at http://nssdc.gsfc.nasa.gov/space/isis/isis- status.htm1. This paper describes the ISIS data restoration effort and shows how the digital ionograms are automatically processed into electron density profiles from satellite orbit altitude (1400 km for ISIS-2) down to the F peak. Because of the large volume of data an automated processing algorithm is imperative. The TOPside Ionogram Scaler with True height algorithm TOPIST software developed for this task is successfully scaling - 70% of the ionograms. An <> is available to manually scale the more difficult ionograms. The automated processing of the digitized ISIS ionograms is now underway, producing a much-needed database of topside electron density profiles for ionospheric modeling covering more than one solar cycle.

  12. Multivariate analysis of X-ray, ion and electron spectral images: from surface to 3D materials characterization.

    SciTech Connect

    Kotula, Paul Gabriel; Keenan, Michael Robert

    2005-02-01

    Spectral imaging where a complete spectrum is collected from each of a series of spatial locations (1D lines, 2D images or 3D volumes) is now available on a wide range of analytical tools - from electron and x-ray to ion beam instruments. With this capability to collect extremely large spectral images comes the need for automated data analysis tools that can rapidly and without bias reduce a large number of raw spectra to a compact, chemically relevant, and easily interpreted representation. It is clear that manual interrogation of individual spectra is impractical even for very small spectral images (< 5000 spectra). More typical spectral images can contain tens of thousands to millions of spectra, which given the constraint of acquisition time may contain between 5 and 300 counts per 1000-channel spectrum. Conventional manual approaches to spectral image analysis such as summing spectra from regions or constructing x-ray maps are prone to bias and possibly error. One way to comprehensively analyze spectral image data, which has been automated, is to utilize an unsupervised self-modeling multivariate statistical analysis method such as multivariate curve resolution (MCR). This approach has proven capable of solving a wide range of analytical problems based upon the counting of x-rays (SEM/STEM-EDX, XRF, PIXE), electrons (EELS, XPS) and ions (TOF-SIMS). As an example of the MCR approach, a STEM x-ray spectral image from a ZrB2-SiC composite was acquired and analyzed. The data were generated in a FEI Tecnai F30-ST TEM/STEM operated at 300kV, equipped with an EDAX SUTW x-ray detector. The spectral image was acquired with the TIA software on the STEM at 128 by 128 pixels (12nm/pixel) for 100msec dwell per pixel (total acquisition time was 30 minutes) with a probe of approximately the same size as each pixel. Each spectrum in the image had, on average, 500 counts. The calculation took 5 seconds on a PC workstation with dual 2.4GHz PentiumIV Xeon processors and 2Gbytes

  13. Compositional Density Structure of the Upper Mantle from Constrained 3-D Inversion of Gravity Anomaly: A Case Study of Southeast Asia

    NASA Astrophysics Data System (ADS)

    Liang, Q.; Chen, C.; Kaban, M. K.; Thomas, M.

    2014-12-01

    Mantle density structure is a key for tectonics. The density variations in the upper mantle are affected by temperature and composition. Seismic tomography method has been widely applied to obtain the P- and S-wave velocity structure in the mantle, which is then used to calculate the density perturbation. However, the velocity model is mainly due to the thermal effects but not the compositional effects. A method of 3-D inversion of gravity anomaly developed in spherical coordinates is used to image the large-scale density structure of upper mantle in Southeast Asia. The mantle gravity anomalies used in inversion are calculated by removing the crustal effects from the observed gravity. With constraints of thermal density model from seismic tomography, the integrative density structure is estimated from gravity inversion. Consequently, we obtain the compositional density by subtracting the thermal density from the integrative structure. The result of inversion shows the anisotropic composition of subduction zones, Cratons and plates boundary in Southeast Asia. In the shallow depth, the compositional density anomalies of large scales present uniform features in oceanic and continental mantle. In depth of 75-175 km, there are differences between the thermal and the compositional variations. The density anomalies at these depths are both affected by temperature and composition of the upper mantle. Below 175-km depth, the density anomalies are dominated by the compositional variations. Furthermore, comparing with high seismicity occurred at moderate-depth (50-300 km), we found that the compositional density variations is one of the factor that inducing earthquakes. The constrained inversion of mantle gravity anomaly has possibility to reveal the subduction which is not clearly seen from low-resolution tomography data, and may reveal the relation of seismicity and composition in the upper mantle. This study is supported by the Program of International Science and

  14. Structural, mechanical and electronic properties of 3d transition metal nitrides in cubic zincblende, rocksalt and cesium chloride structures: a first-principles investigation.

    PubMed

    Liu, Z T Y; Zhou, X; Khare, S V; Gall, D

    2014-01-15

    We report systematic results from ab initio calculations with density functional theory on three cubic structures, zincblende (zb), rocksalt (rs) and cesium chloride (cc), of the ten 3d transition metal nitrides. We computed lattice constants, elastic constants, their derived moduli and ratios that characterize mechanical properties. Experimental measurements exist in the literature of lattice constants for rs-ScN, rs-TiN and rs-VN and of elastic constants for rs-TiN and rs-VN, all of which are in good agreement with our computational results. Similarly, computed Vickers hardness (HV) values for rs-TiN and rs-VN are consistent with earlier experimental results. Several trends were observed in our rich data set of 30 compounds. All nitrides, except for zb-CrN, rs-MnN, rs-FeN, cc-ScN, cc-CrN, cc-NiN and cc-ZnN, were found to be mechanically stable. A clear correlation in the atomic density with the bulk modulus (B) was observed with maximum values of B around FeN, MnN and CrN. The shear modulus, Young's modulus, HV and indicators of brittleness showed similar trends and all showed maxima for cc-VN. The calculated value of HV for cc-VN was about 30 GPa, while the next highest values were for rs-ScN and rs-TiN, about 24 GPa. A relation (H(V) is proportional to θ(D)(2)) between HV and Debye temperature (θD) was investigated and verified for each structure type. A tendency for anti-correlation of the elastic constant C44, which strongly influences stability and hardness, with the number of electronic states around the Fermi energy was observed.

  15. Factors contributing to accuracy in the estimation of the woody canopy leaf area density profile using 3D portable lidar imaging.

    PubMed

    Hosoi, Fumiki; Omasa, Kenji

    2007-01-01

    Factors that contribute to the accuracy of estimating woody canopy's leaf area density (LAD) using 3D portable lidar imaging were investigated. The 3D point cloud data for a Japanese zelkova canopy [Zelkova serrata (Thunberg) Makino] were collected using a portable scanning lidar from several points established on the ground and at 10 m above the ground. The LAD profiles were computed using voxel-based canopy profiling (VCP). The best LAD results [a root-mean-square error (RMSE) of 0.21 m(2) m(-3)] for the measurement plot (corresponding to an absolute LAI error of 9.5%) were obtained by compositing the ground-level and 10 m measurements. The factors that most strongly affected estimation accuracy included the presence of non-photosynthetic tissues, distribution of leaf inclination angles, number (N) of incident laser beams in each region within the canopy, and G(theta(m)) (the mean projection of a unit leaf area on a plane perpendicular to the direction of the laser beam at the measurement zenith angle of theta(m)). The influences of non-photosynthetic tissues and leaf inclination angle on the estimates amounted to 4.2-32.7% and 7.2-94.2%, respectively. The RMSE of the LAD estimations was expressed using a function of N and G(theta(m)). PMID:17977852

  16. Depth-varying density and organization of chondrocytes in immature and mature bovine articular cartilage assessed by 3d imaging and analysis

    NASA Technical Reports Server (NTRS)

    Jadin, Kyle D.; Wong, Benjamin L.; Bae, Won C.; Li, Kelvin W.; Williamson, Amanda K.; Schumacher, Barbara L.; Price, Jeffrey H.; Sah, Robert L.

    2005-01-01

    Articular cartilage is a heterogeneous tissue, with cell density and organization varying with depth from the surface. The objectives of the present study were to establish a method for localizing individual cells in three-dimensional (3D) images of cartilage and quantifying depth-associated variation in cellularity and cell organization at different stages of growth. Accuracy of nucleus localization was high, with 99% sensitivity relative to manual localization. Cellularity (million cells per cm3) decreased from 290, 310, and 150 near the articular surface in fetal, calf, and adult samples, respectively, to 120, 110, and 50 at a depth of 1.0 mm. The distance/angle to the nearest neighboring cell was 7.9 microm/31 degrees , 7.1 microm/31 degrees , and 9.1 microm/31 degrees for cells at the articular surface of fetal, calf, and adult samples, respectively, and increased/decreased to 11.6 microm/31 degrees , 12.0 microm/30 degrees , and 19.2 microm/25 degrees at a depth of 0.7 mm. The methodologies described here may be useful for analyzing the 3D cellular organization of cartilage during growth, maturation, aging, degeneration, and regeneration.

  17. Bulk crystal growth and electronic characterization of the 3D Dirac semimetal Na{sub 3}Bi

    SciTech Connect

    Kushwaha, Satya K.; Krizan, Jason W.; Cava, R. J.; Feldman, Benjamin E.; Gyenis, András; Randeria, Mallika T.; Xiong, Jun; Xu, Su-Yang; Alidoust, Nasser; Belopolski, Ilya; Liang, Tian; Zahid Hasan, M.; Ong, N. P.; Yazdani, A.

    2015-04-01

    High quality hexagon plate-like Na{sub 3}Bi crystals with large (001) plane surfaces were grown from a molten Na flux. The freshly cleaved crystals were analyzed by low temperature scanning tunneling microscopy and angle-resolved photoemission spectroscopy, allowing for the characterization of the three-dimensional (3D) Dirac semimetal (TDS) behavior and the observation of the topological surface states. Landau levels were observed, and the energy-momentum relations exhibited a linear dispersion relationship, characteristic of the 3D TDS nature of Na{sub 3}Bi. In transport measurements on Na{sub 3}Bi crystals, the linear magnetoresistance and Shubnikov-de Haas quantum oscillations are observed for the first time.

  18. Enhanced detection of 3D individual trees in forested areas using airborne full-waveform LiDAR data by combining normalized cuts with spatial density clustering

    NASA Astrophysics Data System (ADS)

    Yao, W.; Krzystek, P.; Heurich, M.

    2013-10-01

    A detailed understanding of the spatial distribution of forest understory is important but difficult. LiDAR remote sensing has been developing as a promising additional instrument to the conventional field work towards automated forest inventory. Unfortunately, understory (up to 50% of the top-tree height) in mixed and multilayered forests is often ignored due to a difficult observation scenario and limitation of the tree detection algorithm. Currently, the full-waveform (FWF) LiDAR with high penetration ability against overstory crowns can give us new hope to resolve the forest understory. Former approach based on 3D segmentation confirmed that the tree detection rates in both middle and lower forest layers are still low. Therefore, detecting sub-dominant and suppressed trees cannot be regarded as fully solved. In this work, we aim to improve the performance of the FWF laser scanner for the mapping of forest understory. The paper is to develop an enhanced methodology for detecting 3D individual trees by partitioning point clouds of airborne LiDAR. After extracting 3D coordinates of the laser beam echoes, the pulse intensity and width by waveform decomposition, the newly developed approach resolves 3D single trees are by an integrated approach, which delineates tree crowns by applying normalized cuts segmentation to the graph structure of local dense modes in point clouds constructed by mean shift clustering. In the context of our strategy, the mean shift clusters approximate primitives of (sub) single trees in LiDAR data and allow to define more significant features to reflect geometric and reflectional characteristics towards the single tree level. The developed methodology can be regarded as an object-based point cloud analysis approach for tree detection and is applied to datasets captured with the Riegl LMS-Q560 laser scanner at a point density of 25 points/m2 in the Bavarian Forest National Park, Germany, respectively under leaf-on and leaf-off conditions

  19. Nuclear contribution into single-event upset in 3D on-board electronics at moderate energy cosmic proton impact

    NASA Astrophysics Data System (ADS)

    Chechenin, N. G.; Chuvilskaya, T. V.; Shirokova, A. A.

    2016-05-01

    In continuation and development of our previous works where nuclear reactions of moderate energy (10 - 400 MeV) protons with Si, Al and W have been investigated, the results of reactions with Cu are reported in this paper. Cu is a most important component in composition of materials in contact pads and pathways of modern and perspective ultra large-scale integration circuitry, especially in 3D topology.

  20. Theoretical study of H2/+/ spectroscopic properties. II, III. [2p and 3d excited electronic states

    NASA Technical Reports Server (NTRS)

    Beckel, C. L.; Shafi, M.; Peek, J. M.

    1973-01-01

    Description of the theoretical spectroscopic properties of the 2p pi/sub u/ and 3d sigma/sub g/ excited states of the H2/+/ hydrogen molecular ion. Numerical integration of the Schrodinger equation is used to determine vibration-rotation eigenvalues. Dunham power series expansions are used to determine the equilibrium separation, potential coefficients, and spectroscopic constants. The eigenvalues are used to determine delta-G, Bv, Dv, and Hv.

  1. Estimation of topside electron density profile using on-orbit measured GPS and electron density data.

    NASA Astrophysics Data System (ADS)

    Lee, J.

    2015-12-01

    The topside ionophere have lacks of information about plasma, but it is important for human beings and scientific applicaiton. We establish an estimation method for electron density profile using Langmuir Probe and GPS data of CHAMP satellite and have comparision the method results with other satellites measurements. In order to develop the model, hydrostatic mapping function, vertical scale height, and vertical TEC(Total Electron Contents) are used for calculations. The electron density and GPS data with hydrostatic mapping function give the vertical TEC and after some algebra using exponential model of density profile give the vertical scale height of ionosphere. The scale height have about 10^2~10^3 km order of magnitude so it can be used exponential model again since the altitude of CHAMP. Therefore, apply the scale height to exponoential model we can get the topside electron density profile. The result of the density profile model can be compared with other satellite data as STSAT-1, ROCSAT, DMSP which is measured the electron density in similar Local Time, Latitude, Longitude but above the CHAMP. This comparison shows the method is accecptable and it can be applied to other reseach for topside ionosphere.

  2. Experimental electronic structure and Fermi-surface instability of the correlated 3d sulphide BaVS3 : High-resolution angle-resolved photoemission spectroscopy

    NASA Astrophysics Data System (ADS)

    Mitrovic, S.; Fazekas, P.; Søndergaard, C.; Ariosa, D.; Barišić, N.; Berger, H.; Cloëtta, D.; Forró, L.; Höchst, H.; Kupčić, I.; Pavuna, D.; Margaritondo, G.

    2007-04-01

    The correlated 3d sulphide BaVS3 exhibits an interesting coexistence of one-dimensional and three-dimensional properties. Our experiments determine the electronic band structure and shed light on this puzzle. High-resolution angle-resolved photoemission measurements in a 4-eV -wide range below the Fermi energy level uncover and investigate the coexistence of a1g wide-band and eg narrow-band d electrons, which lead to the complicated electronic properties of this material. We explore the effects of strong correlations and the Fermi surface instability associated with the metal-insulator transition.

  3. High energy density asymmetric supercapacitor based on NiOOH/Ni3S2/3D graphene and Fe3O4/graphene composite electrodes.

    PubMed

    Lin, Tsung-Wu; Dai, Chao-Shuan; Hung, Kuan-Chung

    2014-01-01

    The application of the composite of Ni3S2 nanoparticles and 3D graphene as a novel cathode material for supercapacitors is systematically investigated in this study. It is found that the electrode capacitance increases by up to 111% after the composite electrode is activated by the consecutive cyclic voltammetry scanning in 1 M KOH. Due to the synergistic effect, the capacitance and the diffusion coefficient of electrolyte ions of the activated composite electrode are ca. 3.7 and 6.5 times higher than those of the Ni3S2 electrode, respectively. Furthermore, the activated composite electrode exhibits an ultrahigh specific capacitance of 3296 F/g and great cycling stability at a current density of 16 A/g. To obtain the reasonable matching of cathode/anode electrodes, the composite of Fe(3)O(4) nanoparticles and chemically reduced graphene oxide (Fe(3)O(4)/rGO) is synthesized as the anode material. The Fe(3)O(4)/rGO electrode exhibits the specific capacitance of 661 F/g at 1 A/g and excellent rate capability. More importantly, an asymmetric supercapacitor fabricated by two different composite electrodes can be operated reversibly between 0 and 1.6 V and obtain a high specific capacitance of 233 F/g at 5 mV/s, which delivers a maximum energy density of 82.5 Wh/kg at a power density of 930 W/kg.

  4. The role of 3d electrons in the appearance of ferromagnetism in the antiferromagnetic Ru2MnGe Heusler compound: a magnetic Compton scattering study.

    PubMed

    Mizusaki, S; Ohnishi, T; Douzono, A; Hirose, M; Nagata, Y; Itou, M; Sakurai, Y; Ozawa, T C; Samata, H; Noro, Y

    2012-06-27

    The antiferromagnetism in Ru(2)MnGe can be suppressed by the substitution of V by Mn and ferromagnetism appears. Synchrotron-based magnetic Compton scattering experiments are used in order to investigates the role of 3d electrons in the indirect/direct exchange interactions for the appearance of ferromagnetism. A small spin moment for the itinerant electron part on the magnetic Compton profile indicates that the metallic ferromagnet Ru(2)Mn(0.5)V(0.5)Ge has a weak indirect exchange interaction between the d-like and sp-like (itinerant) electrons. This suggests that the appearance of ferromagnetism is caused by the enhancement of the direct exchange interactions between d-d electrons in the Ru(2)MnGe Heusler compound. These findings indicate that the indirect exchange interaction between itinerant electrons and localized electrons is a significant key point for the appearance of ferromagnetism in this system.

  5. Electron Density Calibration for Radiotherapy Treatment Planning

    SciTech Connect

    Herrera-Martinez, F.; Rodriguez-Villafuerte, M.; Martinez-Davalos, A.; Ruiz-Trejo, C.; Celis-Lopez, M. A.; Larraga-Gutierrez, J. M.; Garcia-Garduno, A.

    2006-09-08

    Computed tomography (CT) images are used as basic input data for most modern radiosurgery treatment planning systems (TPS). CT data not only provide anatomic information to delineate target volumes, but also allow the introduction of corrections for tissue inhomogeneities into dose calculations during the treatment planning procedure. These corrections involve the determination of a relationship between tissue electron density ({rho}e) and their corresponding Hounsfield Units (HU). In this work, an elemental analysis of different commercial tissue equivalent materials using Scanning Electron Microscopy was carried out to characterize their chemical composition. The tissue equivalent materials were chosen to ensure a large range of {rho}e to be included in the CT scanner calibration. A phantom was designed and constructed with these materials to simulate the size of a human head.

  6. Electron density in the equatorial topside

    NASA Technical Reports Server (NTRS)

    Bilitza, D.

    1985-01-01

    Ionospheric electron content studies have revealed severe discrepancies between Faraday measurements and model predictions at low latitudes. In this investigation, satellite data of AE-C and Aeros and incoherent scatter data from Jicamarca, Peru and Arecibo, Puerto Rico are used to examine the latitudinal and diurnal extent of this disagreement. It is found that in the modified dip range -30 deg to +30 deg the present IRI relative layer shape underestimates the thickness of the topside electron density during both, day and night. The Bent model which was used as a source for the IRI description performs somewhat better in this critical dip range, though it does not reach the observed values. Also it does not show the observed diurnal variation. A correction to the IRI formula is proposed that guarantees better agreement with the satellite and incoherent scatter data.

  7. High-Throughput Processes and Structural Characterization of Single-Nanotube Based Devices for 3D Electronics

    NASA Technical Reports Server (NTRS)

    Kaul, A. B.; Megerian, K. G.; Baron, R. L.; Jennings, A. T.; Jang, D.; Greer, J. R.

    2011-01-01

    We have developed manufacturable approaches to form single, vertically aligned carbon nanotubes, where the tubes are centered precisely, and placed within a few hundred nm of 1-1.5 micron deep trenches. These wafer-scale approaches were enabled by chemically amplified resists and inductively coupled Cryo-etchers to form the 3D nanoscale architectures. The tube growth was performed using dc plasmaenhanced chemical vapor deposition (PECVD), and the materials used for the pre-fabricated 3D architectures were chemically and structurally compatible with the high temperature (700 C) PECVD synthesis of our tubes, in an ammonia and acetylene ambient. The TEM analysis of our tubes revealed graphitic basal planes inclined to the central or fiber axis, with cone angles up to 30 deg. for the particular growth conditions used. In addition, bending tests performed using a custom nanoindentor, suggest that the tubes are well adhered to the Si substrate. Tube characteristics were also engineered to some extent, by adjusting growth parameters, such as Ni catalyst thickness, pressure and plasma power during growth.

  8. High-throughput processes and structural characterization of single-nanotube based devices for 3D electronics

    NASA Astrophysics Data System (ADS)

    Kaul, A. B.; Megerian, K. G.; Baron, R. L.; Jennings, A. T.; Jang, D.; Greer, J. R.

    2009-05-01

    We have developed manufacturable approaches to form single, vertically aligned carbon nanotubes, where the tubes are centered precisely, and placed within a few hundred nm of 1-1.5 μm deep trenches. These wafer-scale approaches were enabled by chemically amplified resists and inductively coupled Cryo-etchers to form the 3D nanoscale architectures. The tube growth was performed using dc plasmaenhanced chemical vapor deposition (PECVD), and the materials used for the pre-fabricated 3D architectures were chemically and structurally compatible with the high temperature (700 °C) PECVD synthesis of our tubes, in an ammonia and acetylene ambient. The TEM analysis of our tubes revealed graphitic basal planes inclined to the central or fiber axis, with cone angles up to 30° for the particular growth conditions used. In addition, bending tests performed using a custom nanoindentor, suggest that the tubes are well adhered to the Si substrate. Tube characteristics were also engineered to some extent, by adjusting growth parameters, such as Ni catalyst thickness, pressure and plasma power during growth.

  9. SUTRA: A model for 2D or 3D saturated-unsaturated, variable-density ground-water flow with solute or energy transport

    USGS Publications Warehouse

    Voss, Clifford I.; Provost, A.M.

    2002-01-01

    SUTRA (Saturated-Unsaturated Transport) is a computer program that simulates fluid movement and the transport of either energy or dissolved substances in a subsurface environment. This upgraded version of SUTRA adds the capability for three-dimensional simulation to the former code (Voss, 1984), which allowed only two-dimensional simulation. The code employs a two- or three-dimensional finite-element and finite-difference method to approximate the governing equations that describe the two interdependent processes that are simulated: 1) fluid density-dependent saturated or unsaturated ground-water flow; and 2) either (a) transport of a solute in the ground water, in which the solute may be subject to: equilibrium adsorption on the porous matrix, and both first-order and zero-order production or decay; or (b) transport of thermal energy in the ground water and solid matrix of the aquifer. SUTRA may also be used to simulate simpler subsets of the above processes. A flow-direction-dependent dispersion process for anisotropic media is also provided by the code and is introduced in this report. As the primary calculated result, SUTRA provides fluid pressures and either solute concentrations or temperatures, as they vary with time, everywhere in the simulated subsurface system. SUTRA flow simulation may be employed for two-dimensional (2D) areal, cross sectional and three-dimensional (3D) modeling of saturated ground-water flow systems, and for cross sectional and 3D modeling of unsaturated zone flow. Solute-transport simulation using SUTRA may be employed to model natural or man-induced chemical-species transport including processes of solute sorption, production, and decay. For example, it may be applied to analyze ground-water contaminant transport problems and aquifer restoration designs. In addition, solute-transport simulation with SUTRA may be used for modeling of variable-density leachate movement, and for cross sectional modeling of saltwater intrusion in

  10. Electron density measurements for plasma adaptive optics

    NASA Astrophysics Data System (ADS)

    Neiswander, Brian W.

    Over the past 40 years, there has been growing interest in both laser communications and directed energy weapons that operate from moving aircraft. As a laser beam propagates from an aircraft in flight, it passes through boundary layers, turbulence, and shear layers in the near-region of the aircraft. These fluid instabilities cause strong density gradients which adversely affect the transmission of laser energy to a target. Adaptive optics provides corrective measures for this problem but current technology cannot respond quickly enough to be useful for high speed flight conditions. This research investigated the use of plasma as a medium for adaptive optics for aero-optics applications. When a laser beam passes through plasma, its phase is shifted proportionally to the electron density and gas heating within the plasma. As a result, plasma can be utilized as a dynamically controllable optical medium. Experiments were carried out using a cylindrical dielectric barrier discharge plasma chamber which generated a sub-atmospheric pressure, low-temperature plasma. An electrostatic model of this design was developed and revealed an important design constraint relating to the geometry of the chamber. Optical diagnostic techniques were used to characterize the plasma discharge. Single-wavelength interferometric experiments were performed and demonstrated up to 1.5 microns of optical path difference (OPD) in a 633 nm laser beam. Dual-wavelength interferometry was used to obtain time-resolved profiles of the plasma electron density and gas heating inside the plasma chamber. Furthermore, a new multi-wavelength infrared diagnostic technique was developed and proof-of-concept simulations were conducted to demonstrate the system's capabilities.

  11. Cognitive MMN and P300 in mild cognitive impairment and Alzheimer's disease: A high density EEG-3D vector field tomography approach.

    PubMed

    Papadaniil, Chrysa D; Kosmidou, Vasiliki E; Tsolaki, Anthoula; Tsolaki, Magda; Kompatsiaris, Ioannis Yiannis; Hadjileontiadis, Leontios J

    2016-10-01

    Precise preclinical detection of dementia for effective treatment and stage monitoring is of great importance. Miscellaneous types of biomarkers, e.g., biochemical, genetic, neuroimaging, and physiological, have been proposed to diagnose Alzheimer's disease (AD), the usual suspect behind manifested cognitive decline, and mild cognitive impairment (MCI), a neuropathology prior to AD that does not affect cognitive functions. Event related potential (ERP) methods constitute a non-invasive, inexpensive means of analysis and have been proposed as sensitive biomarkers of cognitive impairment; besides, various ERP components are strongly linked with working memory, attention, sensory processing and motor responses. In this study, an auditory oddball task is employed, to acquire high density electroencephalograhy recordings from healthy elderly controls, MCI and AD patients. The mismatch negativity (MMN) and P300 ERP components are then extracted and their relationship with neurodegeneration is examined. Then, the neural activation at these components is reconstructed using the 3D vector field tomography (3D-VFT) inverse solution. The results reveal a decline of both ERPs amplitude, and a statistically significant prolongation of their latency as cognitive impairment advances. For the MMN, higher brain activation is usually localized in the inferior frontal and superior temporal gyri in the controls. However, in AD, parietal sites exhibit strong activity. Stronger P300 generators are mostly found in the frontal lobe for the controls, but in AD they often shift to the temporal lobe. Reduction in inferior frontal source strength and the switch of the maximum intensity area to parietal and superior temporal sites suggest that these areas, especially the former, are of particular significance when neurodegenerative disorders are investigated. The modulation of MMN and P300 can serve to produce biomarkers of dementia and its progression, and brain imaging can further contribute

  12. The hybridizations of cobalt 3 d bands with the electron band structure of the graphene/cobalt interface on a tungsten substrate

    NASA Astrophysics Data System (ADS)

    Hwang, Jinwoong; Hwang, Choongyu; Chung, Nak-Kwan; N'Diaye, A. D.; Schmid, A. K.; Denlinger, Jonathan

    2016-08-01

    The interface between graphene and a ferromagnetic substrate has attracted recent research interests due to its potential for spintronic applications. We report an angle-resolved photoemission spectroscopy study on the interface between graphene and cobalt epitaxially grown on a tungsten substrate. We find that the electron band structure of the interface exhibits clear discontinuities at the crossing points with cobalt 3 d bands. These observations indicate strong hybridizations between the electronic states in the interface and provide an important clue to understand the intriguing electromagnetic properties of the graphene/ferromagnet interface.

  13. Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction

    PubMed Central

    Cabra, Vanessa; Samsó, Montserrat

    2015-01-01

    Cryo-electron microscopy (cryoEM) entails flash-freezing a thin layer of sample on a support, and then visualizing the sample in its frozen hydrated state by transmission electron microscopy (TEM). This can be achieved with very low quantity of protein and in the buffer of choice, without the use of any stain, which is very useful to determine structure-function correlations of macromolecules. When combined with single-particle image processing, the technique has found widespread usefulness for 3D structural determination of purified macromolecules. The protocol presented here explains how to perform cryoEM and examines the causes of most commonly encountered problems for rational troubleshooting; following all these steps should lead to acquisition of high quality cryoEM images. The technique requires access to the electron microscope instrument and to a vitrification device. Knowledge of the 3D reconstruction concepts and software is also needed for computerized image processing. Importantly, high quality results depend on finding the right purification conditions leading to a uniform population of structurally intact macromolecules. The ability of cryoEM to visualize macromolecules combined with the versatility of single particle image processing has proven very successful for structural determination of large proteins and macromolecular machines in their near-native state, identification of their multiple components by 3D difference mapping, and creation of pseudo-atomic structures by docking of x-ray structures. The relentless development of cryoEM instrumentation and image processing techniques for the last 30 years has resulted in the possibility to generate de novo 3D reconstructions at atomic resolution level. PMID:25651412

  14. A 3D computer simulation of negative ion extraction influenced by electron diffusion and weak magnetic field

    SciTech Connect

    Turek, M.; Sielanko, J.

    2008-03-19

    The numerical model of negative ion beam extraction from the RF ion source by different kinds of large extraction grid systems is considered. The model takes into account the influence of the transversal magnetic field and the electron diffusion. The magnetic filter field increases H{sup -} yields significantly. The random-walk electron diffusion model enables electrons to travel through magnetic field. The H{sup -} currents obtained from simulations with or without the diffusion are compared.

  15. Detecting VMAT delivery errors: A study on the sensitivity of the ArcCHECK-3D electronic dosimeter

    NASA Astrophysics Data System (ADS)

    Arumugam, S.; Xing, A.; Goozee, G.; Holloway, L.

    2013-06-01

    The sensitivity of the ArcCHECK 3D dosimeter in detecting VMAT delivery errors has been investigated. Dose and leaf positional errors of different magnitudes were introduced to whole arc and individual control points (CPs) of a simple open arc VMAT plan. The error introduced and error free plans were delivered and measured using the ArcCHECK device. The measured doses were compared against the treatment planning system calculated doses using gamma (γ) criteria with 2%/2mm and 3%/3mm tolerance levels. ArcCHECK effectively detected the dose errors resulting from MLC leaf positioning errors in limited CPs and Whole arc. For errors introduced to MU, ArcCHECK effectively detected the MU delivery errors in whole arc but not the MU errors introduced to CPs in integrated dose comparison.

  16. High Energy Density Asymmetric Supercapacitor Based on NiOOH/Ni3S2/3D Graphene and Fe3O4/Graphene Composite Electrodes

    PubMed Central

    Lin, Tsung-Wu; Dai, Chao-Shuan; Hung, Kuan-Chung

    2014-01-01

    The application of the composite of Ni3S2 nanoparticles and 3D graphene as a novel cathode material for supercapacitors is systematically investigated in this study. It is found that the electrode capacitance increases by up to 111% after the composite electrode is activated by the consecutive cyclic voltammetry scanning in 1 M KOH. Due to the synergistic effect, the capacitance and the diffusion coefficient of electrolyte ions of the activated composite electrode are ca. 3.7 and 6.5 times higher than those of the Ni3S2 electrode, respectively. Furthermore, the activated composite electrode exhibits an ultrahigh specific capacitance of 3296 F/g and great cycling stability at a current density of 16 A/g. To obtain the reasonable matching of cathode/anode electrodes, the composite of Fe3O4 nanoparticles and chemically reduced graphene oxide (Fe3O4/rGO) is synthesized as the anode material. The Fe3O4/rGO electrode exhibits the specific capacitance of 661 F/g at 1 A/g and excellent rate capability. More importantly, an asymmetric supercapacitor fabricated by two different composite electrodes can be operated reversibly between 0 and 1.6 V and obtain a high specific capacitance of 233 F/g at 5 mV/s, which delivers a maximum energy density of 82.5 Wh/kg at a power density of 930 W/kg. PMID:25449978

  17. Extracellular vesicles of calcifying turkey leg tendon characterized by immunocytochemistry and high voltage electron microscopic tomography and 3-D graphic image reconstruction

    NASA Technical Reports Server (NTRS)

    Landis, W. J.; Hodgens, K. J.; McKee, M. D.; Nanci, A.; Song, M. J.; Kiyonaga, S.; Arena, J.; McEwen, B.

    1992-01-01

    To gain insight into the structure and possible function of extracellular vesicles in certain calcifying vertebrate tissues, normally mineralizing leg tendons from the domestic turkey, Meleagris gallopavo, have been studied in two separate investigations, one concerning the electron microscopic immunolocalization of the 66 kDa phosphoprotein, osteopontin, and the other detailing the organization and distribution of mineral crystals associated with the vesicles as determined by high voltage microscopic tomography and 3-D graphic image reconstruction. Immunolabeling shows that osteopontin is related to extracellular vesicles of the tendon in the sense that its initial presence appears coincident with the development of mineral associated with the vesicle loci. By high voltage electron microscopy and 3-D imaging techniques, mineral crystals are found to consist of small irregularly shaped particles somewhat randomly oriented throughout individual vesicles sites. Their appearance is different from that found for the mineral observed within calcifying tendon collagen, and their 3-D disposition is not regularly ordered. Possible spatial and temporal relationships of vesicles, osteopontin, mineral, and collagen are being examined further by these approaches.

  18. Preparation of cultured cells using high-pressure freezing and freeze substitution for subsequent 2D or 3D visualization in the transmission electron microscope.

    PubMed

    Hawes, Philippa C

    2015-01-01

    Transmission electron microscopy (TEM) is an invaluable technique used for imaging the ultrastructure of samples and it is particularly useful when determining virus-host interactions at a cellular level. The environment inside a TEM is not favorable for biological material (high vacuum and high energy electrons). Also biological samples have little or no intrinsic electron contrast, and rarely do they naturally exist in very thin sheets, as is required for optimum resolution in the TEM. To prepare these samples for imaging in the TEM therefore requires extensive processing which can alter the ultrastructure of the material. Here we describe a method which aims to minimize preparation artifacts by freezing the samples at high pressure to instantaneously preserve ultrastructural detail, then rapidly substituting the ice and infiltrating with resin to provide a firm matrix which can be cut into thin sections for imaging. Thicker sections of this material can also be imaged and reconstructed into 3D volumes using electron tomography.

  19. Differential and integrated cross sections for excitation to the 3s, 3p, and 3d states of atomic hydrogen by electron impact below the n=4 threshold

    SciTech Connect

    Bartlett, Philip L.; Bray, Igor; Stelbovics, Andris T.; Williams, J. F.; Mikosza, A. G.

    2006-08-15

    Integrated cross sections for the electron-impact excitation of ground-state hydrogen to the 3s, 3p, and 3d final states have been calculated using propagating exterior complex scaling and convergent close-coupling methods at energies between the n=3 and 4 excitation thresholds. The calculations are in excellent agreement and demonstrate that exterior complex scaling methods can accurately reproduce the resonance structure and magnitude of the excitation cross sections below the ionization threshold. Measurements of the separate 3s, 3p, and 3d differential cross sections were made at 12.24 eV, and are consistent with both calculations within a total experimental uncertainty of about 35%.

  20. DAMQT 2.0: A new version of the DAMQT package for the analysis of electron density in molecules

    NASA Astrophysics Data System (ADS)

    López, Rafael; Rico, Jaime Fernández; Ramírez, Guillermo; Ema, Ignacio; Zorrilla, David

    2015-07-01

    DAMQT 2.0 is a new version of the DAMQT package for the analysis of electron density in molecules and the fast computation of the density, density deformations, electrostatic potential and field, and Hellmann-Feynman forces. Algorithms for the partition of the electron density and the computation of related properties like density deformations, electrostatic potential and field and Hellmann-Feynman forces have been improved and their codes, fully rewritten. MPI versions of the most computational demanding modules are now included in the package for parallel computation. The Graphical User Interface has been also enhanced, with new features including a 2D plotter and significant improvements in the 3D viewer.

  1. The ATLAS3D project - VII. A new look at the morphology of nearby galaxies: the kinematic morphology-density relation

    NASA Astrophysics Data System (ADS)

    Cappellari, Michele; Emsellem, Eric; Krajnović, Davor; McDermid, Richard M.; Serra, Paolo; Alatalo, Katherine; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Bureau, M.; Davies, Roger L.; Davis, Timothy A.; de Zeeuw, P. T.; Khochfar, Sadegh; Kuntschner, Harald; Lablanche, Pierre-Yves; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Scott, Nicholas; Weijmans, Anne-Marie; Young, Lisa M.

    2011-09-01

    In Paper I of this series we introduced a volume-limited parent sample of 871 galaxies from which we extracted the ATLAS3D sample of 260 early-type galaxies (ETGs). In Papers II and III we classified the ETGs using their stellar kinematics, in a way that is nearly insensitive to the projection effects, and we separated them into fast and slow rotators. Here we look at galaxy morphology and note that the edge-on fast rotators generally are lenticular galaxies. They appear like spiral galaxies with the gas and dust removed, and in some cases are flat ellipticals (E5 or flatter) with discy isophotes. Fast rotators are often barred and span the same full range of bulge fractions as spiral galaxies. The slow rotators are rounder (E4 or rounder, except for counter-rotating discs) and are generally consistent with being genuine, namely spheroidal-like, elliptical galaxies. We propose a revision to the tuning-fork diagram by Hubble as it gives a misleading description of ETGs by ignoring the large variation in the bulge sizes of fast rotators. Motivated by the fact that only one third (34 per cent) of the ellipticals in our sample are slow rotators, we study for the first time the kinematic morphology-density T-Σ relation using fast and slow rotators to replace lenticulars and ellipticals. We find that our relation is cleaner than using classic morphology. Slow rotators are nearly absent at the lowest density environments [? per cent] and generally constitute a small fraction [f(SR) ≈ 4 per cent] of the total galaxy population in the relatively low-density environments explored by our survey, with the exception of the densest core of the Virgo cluster [f(SR) ≈ 20 per cent]. This contrasts with the classic studies that invariably find significant fractions of (misclassified) ellipticals down to the lowest environmental densities. We find a clean log-linear relation between the fraction f(Sp) of spiral galaxies and the local galaxy surface density Σ3, within a cylinder

  2. Ag Nanoparticle-Grafted PAN-Nanohump Array Films with 3D High-Density Hot Spots as Flexible and Reliable SERS Substrates.

    PubMed

    Li, Zhongbo; Meng, Guowen; Huang, Qing; Hu, Xiaoye; He, Xuan; Tang, Haibin; Wang, Zhiwei; Li, Fadi

    2015-10-28

    A facile fabrication approach of large-scale flexible films is reported, with one surface side consisting of Ag-nanoparticle (Ag-NP) decorated polyacrylonitrile (PAN) nanohump (denoted as Ag-NPs@PAN-nanohump) arrays. This is achieved via molding PAN films with ordered nanohump arrays on one side and then sputtering much smaller Ag-NPs onto each of the PAN-nanohumps. Surface-enhanced Raman scattering (SERS) activity of the Ag-NPs@PAN-nanohump array films can be improved by curving the flexible PAN film with ordered nanohump arrays during the Ag-sputtering process to increase the density of the Ag-NPs on the sidewalls of the PAN-nanohumps. More 3D hot spots are thus achieved on a large-scale. The Ag-NPs@PAN-nanohump array films show high SERS activity with good Raman signal reproducibility for Rhodamine 6G probe molecules. To trial their practical application, the Ag-NPs@PAN-nanohump array films are employed as SERS substrates for trace detection of trinitrotoluene and a congener of polychlorinated biphenyls. A lower detection limit of 10(-12) m and 10(-5) m can be achieved, respectively. Furthermore, the flexible Ag-NPs@PAN-nanohump array films can also be utilized as swabs to probe traces of methyl parathion on the surface of fruits such as apples. The as-fabricated SERS substrates therefore have promising potential for applications in rapid safety inspection and environmental protection.

  3. A 3D density-dependent model for assessment and optimization of water management policy in a coastal carbonate aquifer exploited for water supply and fish farming

    NASA Astrophysics Data System (ADS)

    Nocchi, M.; Salleolini, M.

    2013-06-01

    The Ansedonia promontory (southern Tuscany, Italy) is characterized by the presence of fish farms that pump thermal saline groundwater. The water is extracted from a carbonate aquifer with high permeability due to fracturing and karstification that is also exploited for irrigation purposes and domestic use. Such exploitation has led to the degradation of groundwater quality, producing conflict among the different users. The conceptualization of the aquifer allowed the development of a 3D finite element density-dependent numerical model using the FEFLOW code. The slightly negative freshwater budget in the very humid hydrologic year of 2004-2005 revealed that the aquifer was overexploited, especially due to the extraction of freshwater (along with seawater) from fish farm wells and pumping from public supply wells. The model was also used to forecast the quantitative and qualitative evolution of resources over time, thus testing the effects of different management hypotheses. Results demonstrate that the sustainable management of the aquifer mostly depends on withdrawals from public supply wells; the quantity extracted by fish farms only significantly affects the freshwater/saltwater interface and, locally, the salinity of groundwater. Actions to counteract seawater intrusion are proposed.

  4. Imaginary time density-density correlations for two-dimensional electron gases at high density

    SciTech Connect

    Motta, M.; Galli, D. E.; Moroni, S.; Vitali, E.

    2015-10-28

    We evaluate imaginary time density-density correlation functions for two-dimensional homogeneous electron gases of up to 42 particles in the continuum using the phaseless auxiliary field quantum Monte Carlo method. We use periodic boundary conditions and up to 300 plane waves as basis set elements. We show that such methodology, once equipped with suitable numerical stabilization techniques necessary to deal with exponentials, products, and inversions of large matrices, gives access to the calculation of imaginary time correlation functions for medium-sized systems. We discuss the numerical stabilization techniques and the computational complexity of the methodology and we present the limitations related to the size of the systems on a quantitative basis. We perform the inverse Laplace transform of the obtained density-density correlation functions, assessing the ability of the phaseless auxiliary field quantum Monte Carlo method to evaluate dynamical properties of medium-sized homogeneous fermion systems.

  5. Electronic structure and 3d-4f exchange interactions in zircon-type RCrO{sub 4} oxides (R=Dy, Ho and Gd)

    SciTech Connect

    Ray, Avijeet Maitra, Tulika

    2015-06-24

    Using first principles density functional theory (DFT) calculations within GGA and GGA+U approximations we studied both ferromagnetic (FM) and antiferromagnetic (AFM) phases of zircon type RCrO{sub 4} (R= Dy, Ho, Gd) oxides. We estimated and compared the 3d-4f exchange interaction strengths J between the nearest neighbor R{sup 3+} and Cr{sup 5+} ions for R=Dy, Gd. Our results predict that DyCrO{sub 4}, GdCrO{sub 4} and HoCrO{sub 4} have ferromagnetic ground state which is consistent with experimental observations.

  6. Initial Self-Consistent 3D Electron-Cloud Simulations of the LHC Beam with the Code WARP+POSINST

    SciTech Connect

    Vay, J; Furman, M A; Cohen, R H; Friedman, A; Grote, D P

    2005-10-11

    We present initial results for the self-consistent beam-cloud dynamics simulations for a sample LHC beam, using a newly developed set of modeling capability based on a merge [1] of the three-dimensional parallel Particle-In-Cell (PIC) accelerator code WARP [2] and the electron-cloud code POSINST [3]. Although the storage ring model we use as a test bed to contain the beam is much simpler and shorter than the LHC, its lattice elements are realistically modeled, as is the beam and the electron cloud dynamics. The simulated mechanisms for generation and absorption of the electrons at the walls are based on previously validated models available in POSINST [3, 4].

  7. Magnetic Properties of 3D Printed Toroids

    NASA Astrophysics Data System (ADS)

    Bollig, Lindsey; Otto, Austin; Hilpisch, Peter; Mowry, Greg; Nelson-Cheeseman, Brittany; Renewable Energy; Alternatives Lab (REAL) Team

    Transformers are ubiquitous in electronics today. Although toroidal geometries perform most efficiently, transformers are traditionally made with rectangular cross-sections due to the lower manufacturing costs. Additive manufacturing techniques (3D printing) can easily achieve toroidal geometries by building up a part through a series of 2D layers. To get strong magnetic properties in a 3D printed transformer, a composite filament is used containing Fe dispersed in a polymer matrix. How the resulting 3D printed toroid responds to a magnetic field depends on two structural factors of the printed 2D layers: fill factor (planar density) and fill pattern. In this work, we investigate how the fill factor and fill pattern affect the magnetic properties of 3D printed toroids. The magnetic properties of the printed toroids are measured by a custom circuit that produces a hysteresis loop for each toroid. Toroids with various fill factors and fill patterns are compared to determine how these two factors can affect the magnetic field the toroid can produce. These 3D printed toroids can be used for numerous applications in order to increase the efficiency of transformers by making it possible for manufacturers to make a toroidal geometry.

  8. Layered nano-gratings by electron beam writing to form 3-level diffractive optical elements for 3D phase-offset holographic lithography.

    PubMed

    Yuan, Liang Leon; Herman, Peter R

    2015-12-21

    A multi-level nanophotonic structure is a major goal in providing advanced optical functionalities as found in photonic crystals and metamaterials. A three-level nano-grating phase mask has been fabricated in an electron-beam resist (ma-N) to meet the requirement of holographic generation of a diamond-like 3D nanostructure in photoresist by a single exposure step. A 2D mask with 600 nm periodicity is presented for generating first order diffracted beams with a preferred π/2 phase shift on the X- and Y-axes and with sufficient 1(st) order diffraction efficiency of 3.5% at 800 nm wavelength for creating a 3D periodic nanostructure in SU-8 photoresist. The resulting 3D structure is anticipated to provide an 8% complete photonic band gap (PBG) upon silicon inversion. A thin SiO2 layer was used to isolate the grating layers and multiple spin-coating steps served to planarize the final resist layer. A reversible soft coating (aquaSAVE) was introduced to enable SEM inspection and verification of each insulating grating layer. This e-beam lithographic method is extensible to assembling multiple layers of a nanophotonic structure.

  9. High-Throughput Top-Down and Bottom-Up Processes for Forming Single-Nanotube Based Architectures for 3D Electronics

    NASA Technical Reports Server (NTRS)

    Kaul, Anupama B.; Megerian, Krikor G.; von Allmen, Paul; Kowalczyk, Robert; Baron, Richard

    2009-01-01

    We have developed manufacturable approaches to form single, vertically aligned carbon nanotubes, where the tubes are centered precisely, and placed within a few hundred nm of 1-1.5 micron deep trenches. These wafer-scale approaches were enabled by chemically amplified resists and inductively coupled Cryo-etchers for forming the 3D nanoscale architectures. The tube growth was performed using dc plasma-enhanced chemical vapor deposition (PECVD), and the materials used for the pre-fabricated 3D architectures were chemically and structurally compatible with the high temperature (700 C) PECVD synthesis of our tubes, in an ammonia and acetylene ambient. Tube characteristics were also engineered to some extent, by adjusting growth parameters, such as Ni catalyst thickness, pressure and plasma power during growth. Such scalable, high throughput top-down fabrication techniques, combined with bottom-up tube synthesis, should accelerate the development of PECVD tubes for applications such as interconnects, nano-electromechanical (NEMS), sensors or 3D electronics in general.

  10. Spectroscopy of jet-cooled AlMn and trends in the electronic structure of the 3d transition metal aluminides

    NASA Astrophysics Data System (ADS)

    Behm, Jane M.; Morse, Michael D.

    1994-10-01

    Jet-cooled diatomic AlMn has been spectroscopically investigated and is shown to possess a 5Πi ground state deriving from the Al (3s23p1,2P0)+Mn (3d54s2,6S) separated atom limit. This implies that the aluminum atom favors a 3pπ approach to the manganese atom, a result that is in agreement with previous studies on the related AlCa and AlZn molecules. The ground state bond length has been measured as 2.6384±0.0010 Å, a value which includes corrections due to spin-uncoupling effects in the X 5Πi state. It is suggested that the 5Πi state emerges as the ground state due to a particularly favorable configuration interaction with a low-lying 5Πi state that derives from the interaction of Al (3s23p1,2P0)+Mn [3d6(5D)4s1,6D]. Combination of the atoms in this excited state leads to a strong σ2 covalent bond via a 3pσAl-4sσMn interaction, which causes this excited electronic state to drop in energy so that it is expected to lie within a few thousand cm-1 of the ground electronic state. Following a discussion of the spectroscopic results on AlMn, an overall summary of the spectroscopic results on the 3d series of transition metal aluminides is presented, along with predictions of the ground electronic states of the as yet unobserved AlSc, AlTi, and AlFe molecules.

  11. Electrons trapped in single crystals of sucrose: Induced spin densities

    SciTech Connect

    Box, H.C.; Budzinski, E.E.; Freund, H.G. )

    1990-07-01

    Electrons are trapped at intermolecular sites in single crystals of sucrose {ital X} irradiated at 4.2 K. The coupling tensors for the hyperfine couplings between the electron and surrounding protons have been deduced from electron-nuclear double resonance (ENDOR) data. Electron spin densities at nearby hydroxy protons are positive, whereas spin densities at the more remote protons of carbon-bound hydrogen atoms are negative. The origin of these negative spin densities is discussed.

  12. Electrons trapped in single crystals of sucrose: Induced spin densities

    NASA Astrophysics Data System (ADS)

    Box, Harold C.; Budzinski, Edwin E.; Freund, Harold G.

    1990-07-01

    Electrons are trapped at intermolecular sites in single crystals of sucrose X irradiated at 4.2 K. The coupling tensors for the hyperfine couplings between the electron and surrounding protons have been deduced from electron-nuclear double resonance (ENDOR) data. Electron spin densities at nearby hydroxy protons are positive, whereas spin densities at the more remote protons of carbon-bound hydrogen atoms are negative. The origin of these negative spin densities is discussed.

  13. Maintenance of a bone collagen phenotype by osteoblast-like cells in 3D periodic porous titanium (Ti-6Al-4 V) structures fabricated by selective electron beam melting.

    PubMed

    Hrabe, Nikolas W; Heinl, Peter; Bordia, Rajendra K; Körner, Carolin; Fernandes, Russell J

    2013-01-01

    Regular 3D periodic porous Ti-6Al-4 V structures were fabricated by the selective electron beam melting method (EBM) over a range of relative densities (0.17-0.40) and pore sizes (500-1500 µm). Structures were seeded with human osteoblast-like cells (SAOS-2) and cultured for four weeks. Cells multiplied within these structures and extracellular matrix collagen content increased. Type I and type V collagens typically synthesized by osteoblasts were deposited in the newly formed matrix with time in culture. High magnification scanning electron microscopy revealed cells attached to surfaces on the interior of the structures with an increasingly fibrous matrix. The in-vitro results demonstrate that the novel EBM-processed porous structures, designed to address the effect of stress-shielding, are conducive to osteoblast attachment, proliferation and deposition of a collagenous matrix characteristic of bone.

  14. Front-end electronics and data acquisition system for a multi-wire 3D gas tracker

    NASA Astrophysics Data System (ADS)

    Łojek, K.; Rozpȩdzik, D.; Bodek, K.; Perkowski, M.; Severijns, N.

    2015-12-01

    This paper presents the design and implementation of the front-end electronics and the data acquisition (DAQ) system for readout of multi-wire drift chambers (MWDC). Apart of the conventional drift time measurement the system delivers the hit position along the wire utilizing the charge division technique. The system consists of preamplifiers, and analog and digital boards sending data to a back-end computer via an Ethernet interface. The data logging software formats the received data and enables an easy access to the data analysis software. The use of specially designed preamplifiers and peak detectors allows the charge-division readout of the low resistance signal wire. The implication of the charge-division circuitry onto the drift time measurement was studied and the overall performance of the electronic system was evaluated in dedicated off-line tests.

  15. Preconditioning techniques for constrained vector potential integral equations, with application to 3-D magnetoquasistatic analysis of electronic packages

    SciTech Connect

    Kamon, M.; Phillips, J.R.

    1994-12-31

    In this paper techniques are presented for preconditioning equations generated by discretizing constrained vector integral equations associated with magnetoquasistatic analysis. Standard preconditioning approaches often fail on these problems. The authors present a specialized preconditioning technique and prove convergence bounds independent of the constraint equations and electromagnetic excitation frequency. Computational results from analyzing several electronic packaging examples are given to demonstrate that the new preconditioning approach can sometimes reduce the number of GMRES iterations by more than an order of magnitude.

  16. 3D electrostatic gyrokinetic electron and fully kinetic ion simulation of lower-hybrid drift instability of Harris current sheet

    DOE PAGES

    Wang, Zhenyu; Lin, Yu; Wang, Xueyi; Tummel, Kurt; Chen, Liu

    2016-07-07

    The eigenmode stability properties of three-dimensional lower-hybrid-drift-instabilities (LHDI) in a Harris current sheet with a small but finite guide magnetic field have been systematically studied by employing the gyrokinetic electron and fully kinetic ion (GeFi) particle-in-cell (PIC) simulation model with a realistic ion-to-electron mass ratio mi/me. In contrast to the fully kinetic PIC simulation scheme, the fast electron cyclotron motion and plasma oscillations are systematically removed in the GeFi model, and hence one can employ the realistic mi/me. The GeFi simulations are benchmarked against and show excellent agreement with both the fully kinetic PIC simulation and the analytical eigenmode theory. Our studies indicate that, for small wavenumbers, ky, along the current direction, the most unstable eigenmodes are peaked at the location wheremore » $$\\vec{k}$$• $$\\vec{B}$$ =0, consistent with previous analytical and simulation studies. Here, $$\\vec{B}$$ is the equilibrium magnetic field and $$\\vec{k}$$ is the wavevector perpendicular to the nonuniformity direction. As ky increases, however, the most unstable eigenmodes are found to be peaked at $$\\vec{k}$$ •$$\\vec{B}$$ ≠0. Additionally, the simulation results indicate that varying mi/me, the current sheet width, and the guide magnetic field can affect the stability of LHDI. Simulations with the varying mass ratio confirm the lower hybrid frequency and wave number scalings.« less

  17. 3D electrostatic gyrokinetic electron and fully kinetic ion simulation of lower-hybrid drift instability of Harris current sheet

    NASA Astrophysics Data System (ADS)

    Wang, Zhenyu; Lin, Yu; Wang, Xueyi; Tummel, Kurt; Chen, Liu

    2016-07-01

    The eigenmode stability properties of three-dimensional lower-hybrid-drift-instabilities (LHDI) in a Harris current sheet with a small but finite guide magnetic field have been systematically studied by employing the gyrokinetic electron and fully kinetic ion (GeFi) particle-in-cell (PIC) simulation model with a realistic ion-to-electron mass ratio mi/me . In contrast to the fully kinetic PIC simulation scheme, the fast electron cyclotron motion and plasma oscillations are systematically removed in the GeFi model, and hence one can employ the realistic mi/me . The GeFi simulations are benchmarked against and show excellent agreement with both the fully kinetic PIC simulation and the analytical eigenmode theory. Our studies indicate that, for small wavenumbers, ky, along the current direction, the most unstable eigenmodes are peaked at the location where k →.B → =0 , consistent with previous analytical and simulation studies. Here, B → is the equilibrium magnetic field and k → is the wavevector perpendicular to the nonuniformity direction. As ky increases, however, the most unstable eigenmodes are found to be peaked at k →.B → ≠0 . In addition, the simulation results indicate that varying mi/me , the current sheet width, and the guide magnetic field can affect the stability of LHDI. Simulations with the varying mass ratio confirm the lower hybrid frequency and wave number scalings.

  18. 3D printing in X-ray and Gamma-Ray Imaging: A novel method for fabricating high-density imaging apertures.

    PubMed

    Miller, Brian W; Moore, Jared W; Barrett, Harrison H; Fryé, Teresa; Adler, Steven; Sery, Joe; Furenlid, Lars R

    2011-12-10

    Advances in 3D rapid-prototyping printers, 3D modeling software, and casting techniques allow for cost-effective fabrication of custom components in gamma-ray and X-ray imaging systems. Applications extend to new fabrication methods for custom collimators, pinholes, calibration and resolution phantoms, mounting and shielding components, and imaging apertures. Details of the fabrication process for these components, specifically the 3D printing process, cold casting with a tungsten epoxy, and lost-wax casting in platinum are presented.

  19. 3D printing in X-ray and Gamma-Ray Imaging: A novel method for fabricating high-density imaging apertures☆

    PubMed Central

    Miller, Brian W.; Moore, Jared W.; Barrett, Harrison H.; Fryé, Teresa; Adler, Steven; Sery, Joe; Furenlid, Lars R.

    2011-01-01

    Advances in 3D rapid-prototyping printers, 3D modeling software, and casting techniques allow for cost-effective fabrication of custom components in gamma-ray and X-ray imaging systems. Applications extend to new fabrication methods for custom collimators, pinholes, calibration and resolution phantoms, mounting and shielding components, and imaging apertures. Details of the fabrication process for these components, specifically the 3D printing process, cold casting with a tungsten epoxy, and lost-wax casting in platinum are presented. PMID:22199414

  20. Metastable atom probe for measuring electron beam density profiles

    NASA Technical Reports Server (NTRS)

    Lockhart, J. M.; Zorn, J. C.

    1972-01-01

    Metastable atom probe was developed for measuring current density in electron beam as function of two arbitrary coordinates, with spatial resolution better than 0.5 mm. Probe shows effects of space charge, magnetic fields, and other factors which influence electron current density, but operates with such low beam densities that introduced perturbation is very small.

  1. Electron density distributions in the high-latitude magnetosphere

    NASA Technical Reports Server (NTRS)

    Persoon, Ann M.

    1988-01-01

    Electron density profiles were constructed to study the plasma density depletions in the nightside auroral zone and the density variations with increasing altitude in the polar cap, using electric field spectrum measurements from the plasma wave instrument on DE-1. Sharply defined regions of depleted plasma densities were commonly observed on nightside auroral field lines, in which electron densities were strongly depleted in relation to the adjacent plasmaspheric and polar densities, forming a low-density cavity at about 70 deg invariant latitude. A correlation was found between low auroral plasma densities, upflowing ion distributions, and an energetic precipitating electron population, indicating that electron density depletions in the nightside auroral zone are directly associated with auroral acceleration processes.

  2. Toroidal mode number estimation of the edge-localized modes using the KSTAR 3-D electron cyclotron emission imaging system

    SciTech Connect

    Lee, J.; Yun, G. S. Lee, J. E.; Kim, M.; Choi, M. J.; Lee, W.; Park, H. K.; Domier, C. W.; Luhmann, N. C.; Sabbagh, S. A.; Park, Y. S.; Lee, S. G.; Bak, J. G.

    2014-06-15

    A new and more accurate technique is presented for determining the toroidal mode number n of edge-localized modes (ELMs) using two independent electron cyclotron emission imaging (ECEI) systems in the Korea Superconducting Tokamak Advanced Research (KSTAR) device. The technique involves the measurement of the poloidal spacing between adjacent ELM filaments, and of the pitch angle α{sub *} of filaments at the plasma outboard midplane. Equilibrium reconstruction verifies that α{sub *} is nearly constant and thus well-defined at the midplane edge. Estimates of n obtained using two ECEI systems agree well with n measured by the conventional technique employing an array of Mirnov coils.

  3. 3D imaging of cells and tissues by focused ion beam/scanning electron microscopy (FIB/SEM).

    PubMed

    Drobne, Damjana

    2013-01-01

    Integration of a scanning electron microscope (SEM) and focused ion beam (FIB) technology into a single FIB/SEM system permits use of the FIB as a nano-scalpel to reveal site-specific subsurface microstructures which can be examined in great detail by SEM. The FIB/SEM technology is widely used in the semiconductor industry and material sciences, and recently its use in the life sciences has been initiated. Samples for FIB/SEM investigation can be either embedded in a plastic matrix, the traditional means of preparation of transmission electron microscopy (TEM) specimens, or simply dried as in samples prepared for SEM imaging. Currently, FIB/SEM is used in the life sciences for (a) preparation by the lift-out technique of lamella for TEM analysis, (b) tomography of samples embedded in a matrix, and (c) in situ site-specific FIB milling and SEM imaging using a wide range of magnifications. Site-specific milling and imaging has attracted wide interest as a technique in structural research of single eukaryotic and prokaryotic cells, small animals, and different animal tissue, but it still remains to be explored more thoroughly. In the past, preparation of samples for site-specific milling and imaging by FIB/SEM has typically adopted the embedding techniques used for TEM samples, and which have been very well described in the literature. Sample preparation protocols for the use of dried samples in FIB/SEM have been less well investigated. The aim of this chapter is to encourage application of FIB/SEM on dried biological samples. A detailed description of conventional dried sample preparation and FIB/SEM investigation of dried biological samples is presented. The important steps are described and illustrated, and direct comparison between embedded and dried samples of same tissues is provided. The ability to discover links between gross morphology of the tissue or organ, surface characteristics of any selected region, and intracellular structural details on the nanometer

  4. Numerical simulations - Some results for the 2- and 3-D Hubbard models and a 2-D electron phonon model

    NASA Technical Reports Server (NTRS)

    Scalapino, D. J.; Sugar, R. L.; White, S. R.; Bickers, N. E.; Scalettar, R. T.

    1989-01-01

    Numerical simulations on the half-filled three-dimensional Hubbard model clearly show the onset of Neel order. Simulations of the two-dimensional electron-phonon Holstein model show the competition between the formation of a Peierls-CDW state and a superconducting state. However, the behavior of the partly filled two-dimensional Hubbard model is more difficult to determine. At half-filling, the antiferromagnetic correlations grow as T is reduced. Doping away from half-filling suppresses these correlations, and it is found that there is a weak attractive pairing interaction in the d-wave channel. However, the strength of the pair field susceptibility is weak at the temperatures and lattice sizes that have been simulated, and the nature of the low-temperature state of the nearly half-filled Hubbard model remains open.

  5. mr-PosEBR: a novel positive tone resist for high resolution electron beam lithography and 3D surface patterning

    NASA Astrophysics Data System (ADS)

    Pfirrmann, Stefan; Kirchner, Robert; Lohse, Olga; Guzenko, Vitaliy A.; Voigt, Anja; Harder, Irina; Kolander, Anett; Schift, Helmut; Grützner, Gabi

    2016-03-01

    In this contribution, we present the results of a systematic material variation for the development of a resist material for high resolution positive tone electron beam lithography (EBL). Several acrylic copolymer materials with different compositions, that is varying mass fractions of the comonomers and different molecular weights, were synthesized and - as resist solutions - evaluated in terms of EBL performance at acceleration voltages of 30 kV and 100 kV. The resist material exhibiting the best combination of the desired properties, named mr-PosEBR, is two times more sensitive than PMMA 495k and performs comparably to the known high resolution resist ZEP520A at 30 kV. For example, a grating pattern with 29 nm wide lines with a period of 100 nm could be lithographically generated in films of mr-PosEBR with an area dose of 100 μC/cm2. In terms of resolution, single lines of only 35 nm width could be fabricated via metal liftoff. Furthermore, the dry etch stability of mr-PosEBR in a CF4/SF6 process is similar to the one of ZEP520A. Consequently, via dry etching nano patterns in mr-PosEBR could be smoothly transferred into the underlying Si substrate with high fidelity. Moreover, mr-PosEBR was evaluated as electron beam grayscale patterning and reflow resist. It was shown that the resist exhibits a good grayscale and reflow performance very similar to PMMA 120k and ZEP520A. Via these well controllable processes the generation of a wide variety of features and applications is possible.

  6. Electronic Flux Density beyond the Born-Oppenheimer Approximation.

    PubMed

    Schild, Axel; Agostini, Federica; Gross, E K U

    2016-05-19

    In the Born-Oppenheimer approximation, the electronic wave function is typically real-valued and hence the electronic flux density (current density) seems to vanish. This is unfortunate for chemistry, because it precludes the possibility to monitor the electronic motion associated with the nuclear motion during chemical rearrangements from a Born-Oppenheimer simulation of the process. We study an electronic flux density obtained from a correction to the electronic wave function. This correction is derived via nuclear velocity perturbation theory applied in the framework of the exact factorization of electrons and nuclei. To compute the correction, only the ground state potential energy surface and the electronic wave function are needed. For a model system, we demonstrate that this electronic flux density approximates the true one very well, for coherent tunneling dynamics as well as for over-the-barrier scattering, and already for mass ratios between electrons and nuclei that are much larger than the true mass ratios.

  7. Electronic structure evolution of single bilayer Bi(1 1 1) film on 3D topological insulator Bi2Se x Te3-x surfaces

    NASA Astrophysics Data System (ADS)

    Lei, Tao; Jin, Kyung-Hwan; Zhang, Nian; Zhao, Jia-Li; Liu, Chen; Li, Wen-Jie; Wang, Jia-Ou; Wu, Rui; Qian, Hai-Jie; Liu, Feng; Ibrahim, Kurash

    2016-06-01

    The electronic state evolution of single bilayer (1BL) Bi(1 1 1) deposited on three-dimensional (3D) Bi2Se x Te3-x topological insulators at x  =  0, 1.26, 2, 2.46, 3 is systematically investigated by angle-resolved photoemission spectroscopy (ARPES). Our results indicate that the electronic structures of epitaxial Bi films are strongly influenced by the substrate especially the topmost sublayer near the Bi films, manifesting in two main aspects. First, the Se atoms cause a stronger charge transfer effect, which induces a giant Rashba-spin splitting, while the low electronegativity of Te atoms induces a strong hybridization at the interface. Second, the lattice strain notably modifies the band dispersion of the surface bands. Furthermore, our experimental results are elucidated by first-principles band structure calculations.

  8. 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.

  9. Dissipation mechanism in 3D magnetic reconnection

    SciTech Connect

    Fujimoto, Keizo

    2011-11-15

    Dissipation processes responsible for fast magnetic reconnection in collisionless plasmas are investigated using 3D electromagnetic particle-in-cell simulations. The present study revisits the two simulation runs performed in the previous study (Fujimoto, Phys. Plasmas 16, 042103 (2009)); one with small system size in the current density direction, and the other with larger system size. In the case with small system size, the reconnection processes are almost the same as those in 2D reconnection, while in the other case a kink mode evolves along the current density and deforms the current sheet structure drastically. Although fast reconnection is achieved in both the cases, the dissipation mechanism is very different between them. In the case without kink mode, the electrons transit the electron diffusion region without thermalization, so that the magnetic dissipation is supported by the inertia resistivity alone. On the other hand, in the kinked current sheet, the electrons are not only accelerated in bulk, but they are also partly scattered and thermalized by the kink mode, which results in the anomalous resistivity in addition to the inertia resistivity. It is demonstrated that in 3D reconnection the thickness of the electron current sheet becomes larger than the local electron inertia length, consistent with the theoretical prediction in Fujimoto and Sydora (Phys. Plasmas 16, 112309 (2009)).

  10. Electron energy-loss near-edge structures of 3d transition metal oxides recorded at high-energy resolution.

    PubMed

    Mitterbauer, C; Kothleitner, G; Grogger, W; Zandbergen, H; Freitag, B; Tiemeijer, P; Hofer, F

    2003-09-01

    Near-edge fine structures of the metal L(2,3) and O K-edges in transition metal-oxides have been studied with a transmission electron microscope equipped with a monochromator and a high-resolution imaging filter. This system enables the recording of EELS spectra with an energy resolution of 0.1eV thus providing new near-edge fine structure details which could not be observed previously by EELS in conventional TEM instruments. EELS-spectra from well-defined oxides like titanium oxide (TiO(2)), vanadium oxide (V(2)O(5)), chromium oxide (Cr(2)O(3)), iron oxide (Fe(2)O(3)), cobalt oxide (CoO) and nickel oxide (NiO) have been measured with the new system. These spectra are compared with EELS data obtained from a conventional microscope and the main spectral features are interpreted. Additionally, the use of monochromised TEMs is discussed in view of the natural line widths of K and L(2,3) edges. PMID:12871809

  11. 3d electron transitions in Co- and Ni-doped MgSO3·6H2O

    NASA Astrophysics Data System (ADS)

    Petkova, P.; Bunzarov, Zh; Iliev, I.; Dimov, T.; Tzoukrovsky, Y.

    2012-05-01

    Absorption spectra of magnesium sulfite hexahydrate (MgSO3·6H2O), doped with Co and Ni, have been studied in the spectral region 1.46-3.1 eV. Investigations have been carried out with linear polarized light E||c, E⊥c (c is the optical axis of MgSO3·6H2O) that propagates in the (1210) direction. The Co structure manifests in the spectral region 2.06-3.1 eV and the Ni structures manifest in the spectral region 1.46-2.26 eV. The peculiarities of the Jahn-Teller effect and spin-orbit interaction with respect to the impurity ions in the crystal lattice of MgSO3·6H2O are analyzed and discussed. The electron transitions in Co2+ and Ni2+ ions are determined for E||c, E⊥c. The crystal field parameter Dq and Racah parameters B and C are also calculated.

  12. Ionospheric E-region electron density and neutral atmosphere variations

    NASA Technical Reports Server (NTRS)

    Stick, T. L.

    1976-01-01

    Electron density deviations from a basic variation with the solar zenith angle were investigated. A model study was conducted in which the effects of changes in neutral and relative densities of atomic and molecular oxygen on calculated electron densities were compared with incoherent scatter measurements in the height range 100-117 km at Arecibo, Puerto Rico. The feasibility of determining tides in the neutral atmosphere from electron density profiles was studied. It was determined that variations in phase between the density and temperature variation and the comparable magnitudes of their components make it appear improbable that the useful information on tidal modes can be obtained in this way.

  13. Probing Electron Dynamics with the Laplacian of the Momentum Density

    SciTech Connect

    Sukumar, N.; MacDougall, Preston J.; Levit, M. Creon

    2012-09-24

    This chapter in the above-titled monograph presents topological analysis of the Laplacian of the electron momentum density in organic molecules. It relates topological features in this distribution to chemical and physical properties, particularly aromaticity and electron transport.

  14. PLOT3D/AMES, DEC VAX VMS VERSION USING DISSPLA (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

  15. PLOT3D/AMES, DEC VAX VMS VERSION USING DISSPLA (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P. G.

    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

  16. Spatially resolved 3D noise

    NASA Astrophysics Data System (ADS)

    Haefner, David P.; Preece, Bradley L.; Doe, Joshua M.; Burks, Stephen D.

    2016-05-01

    When evaluated with a spatially uniform irradiance, an imaging sensor exhibits both spatial and temporal variations, which can be described as a three-dimensional (3D) random process considered as noise. In the 1990s, NVESD engineers developed an approximation to the 3D power spectral density (PSD) for noise in imaging systems known as 3D noise. In this correspondence, we describe how the confidence intervals for the 3D noise measurement allows for determination of the sampling necessary to reach a desired precision. We then apply that knowledge to create a smaller cube that can be evaluated spatially across the 2D image giving the noise as a function of position. The method presented here allows for both defective pixel identification and implements the finite sampling correction matrix. In support of the reproducible research effort, the Matlab functions associated with this work can be found on the Mathworks file exchange [1].

  17. Momentum-space properties from coordinate-space electron density

    SciTech Connect

    Harbola, Manoj K.; Zope, Rajendra R.; Kshirsagar, Anjali; Pathak, Rajeev K.

    2005-05-22

    Electron density and electron momentum density, while independently tractable experimentally, bear no direct connection without going through the many-electron wave function. However, invoking a variant of the constrained-search formulation of density-functional theory, we develop a general scheme (valid for arbitrary external potentials) yielding decent momentum-space properties, starting exclusively from the coordinate-space electron density. A numerical illustration of the scheme is provided for the closed-shell atomic systems He, Be, and Ne in their ground state and for 1s{sup 1} 2s{sup 1} singlet electronic excited state for helium by calculating the Compton profiles and the expectation values derived from given coordinate-space electron densities.

  18. PLOT3D/AMES, GENERIC UNIX VERSION USING DISSPLA (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

  19. PLOT3D/AMES, GENERIC UNIX VERSION USING DISSPLA (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

  20. Relative electron density distribution in a low nd helium dc discharge

    NASA Astrophysics Data System (ADS)

    Ganguly, Biswa N.; Scofield, James D.

    2016-09-01

    The axial and radial variations of the relative electron density distributions have been measured in an obstructed helium dc discharge by a laser collision induced fluorescence (LCIF) from 4 3D to 2 3P state at 447 nm. For this 1.75 Torr, 6.5 mm gap, 1.6 mA helium obstructed gas discharge, the on-axis LCIF intensity is mostly determined by the neutral atom collision. On the basis of this information, we have plotted the LCIF data to obtain a normalized electron density variation in the inter-electrode volume by plotting the ratio, I/-Io n -a x i s Io n -a x i s , where I is the radial variation of the LCIF intensity and Ion-axis is the on-axis LCIF intensity. The normalized LCIF data show an annular current density distribution in this obstructed discharge with the current peaking near the radial boundary of the electrodes.

  1. Electronic and nuclear flux densities in the H2 molecule

    NASA Astrophysics Data System (ADS)

    Hermann, G.; Paulus, B.; Pérez-Torres, J. F.; Pohl, V.

    2014-05-01

    We present a theoretical study of the electronic and nuclear flux densities of a vibrating H2 molecule after an electronic excitation by a short femtosecond laser pulse. The final state, a coherent superposition of the electronic ground state X1Σg+ and the electronic excited state B1Σu+, evolves freely and permits the partition of the electronic flux density into two competing fluxes: the adiabatic and the transition flux density. The nature of the two fluxes allows us to identify two alternating dynamics of the electronic motion, occurring on the attosecond and the femtosecond time scales. In contradistinction to the adiabatic electronic flux density, the transition electronic flux density shows a dependence on the carrier-envelope phase of the laser field, encoding information of the interaction of the electrons with the electric field. Furthermore, the nuclear flux density displays multiple reversals, a quantum effect recently discovered by Manz et al. [J. Manz, J. F. Pérez-Torres, and Y. Yang, Phys. Rev. Lett. 111, 153004 (2013), 10.1103/PhysRevLett.111.153004], calling for investigation of the electronic flux density.

  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. 3d-3d correspondence revisited

    DOE PAGES

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

    2016-04-21

    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. As a result, we also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  4. Dense Helical Electron Bunch Generation in Near-Critical Density Plasmas with Ultrarelativistic Laser Intensities

    PubMed Central

    Hu, Ronghao; Liu, Bin; Lu, Haiyang; Zhou, Meilin; Lin, Chen; Sheng, Zhengming; Chen, Chia-erh; He, Xiantu; Yan, Xueqing

    2015-01-01

    The mechanism for emergence of helical electron bunch(HEB) from an ultrarelativistic circularly polarized laser pulse propagating in near-critical density(NCD) plasma is investigated. Self-consistent three-dimensional(3D) Particle-in-Cell(PIC) simulations are performed to model all aspects of the laser plasma interaction including laser pulse evolution, electron and ion motions. At a laser intensity of 1022 W/cm2, the accelerated electrons have a broadband spectrum ranging from 300 MeV to 1.3 GeV, with the charge of 22 nano-Coulombs(nC) within a solid-angle of 0.14 Sr. Based on the simulation results, a phase-space dynamics model is developed to explain the helical density structure and the broadband energy spectrum. PMID:26503634

  5. Ligand identification using electron-density mapcorrelations

    SciTech Connect

    Terwilliger, Thomas C.; Adams, Paul D.; Moriarty, Nigel W.; Cohn,Judith D.

    2006-12-01

    A procedure for the identification of ligands bound incrystal structuresof macromolecules is described. Two characteristics ofthe density corresponding to a ligand are used in the identificationprocedure. One is the correlation of the ligand density with each of aset of test ligands after optimization of the fit of that ligand to thedensity. The other is the correlation of a fingerprint of the densitywith the fingerprint of model density for each possible ligand. Thefingerprints consist of an ordered list of correlations of each the testligands with the density. The two characteristics are scored using aZ-score approach in which the correlations are normalized to the mean andstandard deviation of correlations found for a variety of mismatchedligand-density pairs, so that the Z scores are related to the probabilityof observing a particular value of the correlation by chance. Theprocedure was tested with a set of 200 of the most commonly found ligandsin the Protein Data Bank, collectively representing 57 percent of allligands in the Protein Data Bank. Using a combination of these twocharacteristics of ligand density, ranked lists of ligand identificationswere made for representative (F-o-F-c) exp(i phi(c)) difference densityfrom entries in the Protein Data Bank. In 48 percent of the 200 cases,the correct ligand was at the top of the ranked list of ligands. Thisapproach may be useful in identification of unknown ligands in newmacromolecular structures as well as in the identification of whichligands in a mixture have bound to a macromolecule.

  6. A Modeling Study of the Ionospheric F Region Electron Densities

    NASA Astrophysics Data System (ADS)

    Wang, W.; Burns, A. G.; Killeen, T. L.

    2002-12-01

    The high-resolution Thermosphere/Ionosphere Nested Grid (TING) model has been used to study the variability of ionospheric F region electron densities under various geophysical conditions. Important space weather phenomena such as the tongue of ionization and mid-latitude electron density trough, which are not well simulated in global models, can be readily studied using high spatial resolution nested grids. In this presentation we will discuss the effects of geomagnetic activity, solar cycle, seasonal and UT variations on the ionospheric F-region electron densities. It is found that geomagnetic activity can greatly enhance the polar cap tongue of ionization and nighttime auroral F region electron densities (blobs). Such enhancements in auroral electron densities have a strong effect not only locally, but also in the mid latitudes as a result of changes in the neutral circulation.

  7. Electron density depletions in the nightside auroral zone

    NASA Technical Reports Server (NTRS)

    Persoon, A. M.; Gurnett, D. A.; Peterson, W. K.; Waite, J. H., Jr.; Burch, J. L.; Green, J. L.

    1988-01-01

    Dynamics Explorer 1 measurements are used to investigate regions of low electron density in the nightside auroral zone. Sharply defined regions of low electron density are found in auroral zone crossings from the predusk hours until the early morning hours at all radial distances up to at least 4.6 earth radii. Densities in the auroral cavity are shown to fall to values below 0.3/cu cm. Within the auroral cavity, electron-density-profile variations of a factor of 2 or more on spatial scales of tens of kilometers are found, and the electron plasma frequency to electron cyclotron frequency ratios are 0.02-0.4. The results suggest associations between the density depletions in the nightside auroral zone and auroral acceleration processes.

  8. Focused ion beam (FIB) combined with high resolution scanning electron microscopy: a promising tool for 3D analysis of chromosome architecture.

    PubMed

    Schroeder-Reiter, Elizabeth; Pérez-Willard, Fabián; Zeile, Ulrike; Wanner, Gerhard

    2009-02-01

    Focused ion beam (FIB) milling in combination with field emission scanning electron microscopy (FESEM) was applied to investigations of metaphase barley chromosomes, providing new insight into the chromatin packaging in the chromosome interior and 3D distribution of histone variants in the centromeric region. Whole mount chromosomes were sectioned with FIB with thicknesses in the range of 7-20nm, resulting in up to 2000 sections, which allow high resolution three-dimensional reconstruction. For the first time, it could be shown that the chromosome interior is characterized by a network of interconnected cavities, with openings to the chromosome surface. In combination with immunogold labeling, the centromere-correlated distribution of histone variants (phosphorylated histone H3, CENH3) could be investigated with FIB in three dimensions. Limitations of classical SEM analysis of whole mount chromosomes with back-scattered electrons requiring higher accelerating voltages, e.g. faint and blurred interior signals, could be overcome with FIB milling: from within the chromosome even very small labels in the range of 10nm could be precisely visualized. This allowed direct quantification of marker molecules in a three-dimensional context. Distribution of DNA in the chromosome interior could be directly analyzed after staining with a DNA-specific platinorganic compound Platinum Blue. Higher resolution visualization of DNA distribution could be performed by preparation of FIB lamellae with the in situ lift-out technique followed by investigation in dark field with a scanning transmission electron detector (STEM) at 30kV. PMID:19059341

  9. PLOT3D/AMES, UNIX SUPERCOMPUTER AND SGI IRIS VERSION (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

  10. PLOT3D/AMES, UNIX SUPERCOMPUTER AND SGI IRIS VERSION (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. 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?

  12. Dynamics of 3D isolated thermal filaments

    NASA Astrophysics Data System (ADS)

    Walkden, N. R.; Easy, L.; Militello, F.; Omotani, J. T.

    2016-11-01

    Simulations have been carried out to establish how electron thermal physics, introduced in the form of a dynamic electron temperature, affects isolated filament motion and dynamics in 3D. It is found that thermal effects impact filament motion in two major ways when the pressure perturbation within the filament is supported primarily through a temperature increase as opposed to density: they lead to a strong increase in filament propagation in the bi-normal direction and a significant decrease in net radial propagation. Both effects arise from the temperature dependence of the sheath current which leads to a non-uniform floating potential, with the latter effect supplemented by faster pressure loss. The reduction in radial velocity can only occur when the filament cross-section loses angular symmetry. The behaviour is observed across different filament sizes and suggests that filaments with much larger temperature perturbations than density perturbations are more strongly confined to the near SOL region.

  13. Gutzwiller density functional theory for correlated electron systems

    SciTech Connect

    Ho, K. M.; Schmalian, J.; Wang, C. Z.

    2008-02-04

    We develop a density functional theory (DFT) and formalism for correlated electron systems by taking as reference an interacting electron system that has a ground state wave function which exactly obeys the Gutzwiller approximation for all one-particle operators. The solution of the many-electron problem is mapped onto the self-consistent solution of a set of single-particle Schroedinger equations, analogously to standard DFT-local density approximation calculations.

  14. PLOT3D/AMES, SGI IRIS VERSION (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

  15. PLOT3D/AMES, SGI IRIS VERSION (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

  16. Modification of ionospheric electron density by dust suspension

    NASA Astrophysics Data System (ADS)

    Srivastava, Sweta; Mishra, Rashmi; Singh Sodha, Mahendra

    2016-05-01

    On the basis of a dynamic analysis the effectiveness of dust suspension for the reduction and enhancement of electron density in the E-layer of the ionosphere has been investigated in this paper. The analysis is based on the modelling of the E-layer as the Chapman α layer (validated earlier); the electron/ion production function, arrived at by Chapman and effective electron temperature-dependent electron-ion recombination coefficients in agreement with observations have been used. The balance of the charge on the particles and the number/energy balance of the constituents have been taken into account. The following is the physics of the change in electron density in the ionosphere by the suspension of dust. First, the dust provides a source (emission) and sink (accretion) of electrons. Second, the dust emits photoelectrons with energies much higher than those of ambient electrons, which enhances the electron temperature, leading to a reduced electron-ion recombination coefficient, and thus to a higher electron density. An interplay of these processes and the natural processes of electron production/annihilation determines the electron density and temperature in the dust suspension in the ionosphere. The numerical results, corresponding to suspension of dust of silicate (high work function) and Cs coated bronze (low work function) in the E-layer at 105 \\text{km} are presented and discussed.

  17. Electron Tomography of Cryo-Immobilized Plant Tissue: A Novel Approach to Studying 3D Macromolecular Architecture of Mature Plant Cell Walls In Situ

    PubMed Central

    Sarkar, Purbasha; Bosneaga, Elena; Yap, Edgar G.; Das, Jyotirmoy; Tsai, Wen-Ting; Cabal, Angelo; Neuhaus, Erica; Maji, Dolonchampa; Kumar, Shailabh; Joo, Michael; Yakovlev, Sergey; Csencsits, Roseann; Yu, Zeyun; Bajaj, Chandrajit; Downing, Kenneth H.; Auer, Manfred

    2014-01-01

    Cost-effective production of lignocellulosic biofuel requires efficient breakdown of cell walls present in plant biomass to retrieve the wall polysaccharides for fermentation. In-depth knowledge of plant cell wall composition is therefore essential for improving the fuel production process. The precise spatial three-dimensional (3D) organization of cellulose, hemicellulose, pectin and lignin within plant cell walls remains unclear to date since the microscopy techniques used so far have been limited to two-dimensional, topographic or low-resolution imaging, or required isolation or chemical extraction of the cell walls. In this paper we demonstrate that by cryo-immobilizing fresh tissue, then either cryo-sectioning or freeze-substituting and resin embedding, followed by cryo- or room temperature (RT) electron tomography, respectively, we can visualize previously unseen details of plant cell wall architecture in 3D, at macromolecular resolution (∼2 nm), and in near-native state. Qualitative and quantitative analyses showed that wall organization of cryo-immobilized samples were preserved remarkably better than conventionally prepared samples that suffer substantial extraction. Lignin-less primary cell walls were well preserved in both self-pressurized rapidly frozen (SPRF), cryo-sectioned samples as well as high-pressure frozen, freeze-substituted and resin embedded (HPF-FS-resin) samples. Lignin-rich secondary cell walls appeared featureless in HPF-FS-resin sections presumably due to poor stain penetration, but their macromolecular features could be visualized in unprecedented details in our cryo-sections. While cryo-tomography of vitreous tissue sections is currently proving to be instrumental in developing 3D models of lignin-rich secondary cell walls, here we confirm that the technically easier method of RT-tomography of HPF-FS-resin sections could be used immediately for routine study of low-lignin cell walls. As a proof of principle, we characterized the

  18. Electron tomography of cryo-immobilized plant tissue: a novel approach to studying 3D macromolecular architecture of mature plant cell walls in situ.

    PubMed

    Sarkar, Purbasha; Bosneaga, Elena; Yap, Edgar G; Das, Jyotirmoy; Tsai, Wen-Ting; Cabal, Angelo; Neuhaus, Erica; Maji, Dolonchampa; Kumar, Shailabh; Joo, Michael; Yakovlev, Sergey; Csencsits, Roseann; Yu, Zeyun; Bajaj, Chandrajit; Downing, Kenneth H; Auer, Manfred

    2014-01-01

    Cost-effective production of lignocellulosic biofuel requires efficient breakdown of cell walls present in plant biomass to retrieve the wall polysaccharides for fermentation. In-depth knowledge of plant cell wall composition is therefore essential for improving the fuel production process. The precise spatial three-dimensional (3D) organization of cellulose, hemicellulose, pectin and lignin within plant cell walls remains unclear to date since the microscopy techniques used so far have been limited to two-dimensional, topographic or low-resolution imaging, or required isolation or chemical extraction of the cell walls. In this paper we demonstrate that by cryo-immobilizing fresh tissue, then either cryo-sectioning or freeze-substituting and resin embedding, followed by cryo- or room temperature (RT) electron tomography, respectively, we can visualize previously unseen details of plant cell wall architecture in 3D, at macromolecular resolution (∼ 2 nm), and in near-native state. Qualitative and quantitative analyses showed that wall organization of cryo-immobilized samples were preserved remarkably better than conventionally prepared samples that suffer substantial extraction. Lignin-less primary cell walls were well preserved in both self-pressurized rapidly frozen (SPRF), cryo-sectioned samples as well as high-pressure frozen, freeze-substituted and resin embedded (HPF-FS-resin) samples. Lignin-rich secondary cell walls appeared featureless in HPF-FS-resin sections presumably due to poor stain penetration, but their macromolecular features could be visualized in unprecedented details in our cryo-sections. While cryo-tomography of vitreous tissue sections is currently proving to be instrumental in developing 3D models of lignin-rich secondary cell walls, here we confirm that the technically easier method of RT-tomography of HPF-FS-resin sections could be used immediately for routine study of low-lignin cell walls. As a proof of principle, we characterized the

  19. Measurement of electron density using reactance cutoff probe

    NASA Astrophysics Data System (ADS)

    You, K. H.; You, S. J.; Kim, D. W.; Na, B. K.; Seo, B. H.; Kim, J. H.; Seong, D. J.; Chang, H. Y.

    2016-05-01

    This paper proposes a new measurement method of electron density using the reactance spectrum of the plasma in the cutoff probe system instead of the transmission spectrum. The highly accurate reactance spectrum of the plasma-cutoff probe system, as expected from previous circuit simulations [Kim et al., Appl. Phys. Lett. 99, 131502 (2011)], was measured using the full two-port error correction and automatic port extension methods of the network analyzer. The electron density can be obtained from the analysis of the measured reactance spectrum, based on circuit modeling. According to the circuit simulation results, the reactance cutoff probe can measure the electron density more precisely than the previous cutoff probe at low densities or at higher pressure. The obtained results for the electron density are presented and discussed for a wide range of experimental conditions, and this method is compared with previous methods (a cutoff probe using the transmission spectrum and a single Langmuir probe).

  20. Ionospheric Electron Density during Magnetically Active Times over Istanbul

    NASA Astrophysics Data System (ADS)

    Naz Erbaş, Bute; Kaymaz, Zerefsan; Ceren Moral, Aysegul; Emine Ceren Kalafatoglu Eyiguler, R. A..

    2016-07-01

    In this study, we analyze electron density variations over Istanbul using Dynasonde observations during the magnetically active times. In order to perform statistical analyses, we first determined magnetic storms and magnetospheric substorm intervals from October 2012 to October 2015 using Kyoto's magnetic index data. Corresponding ionospheric parameters, such as critical frequency of F2 region (foF2), maximum electron density height (hmF2), total electron density (TEC) etc. were retrieved from Dynasonde data base at Istanbul Technical University's Space Weather Laboratory. To understand the behavior of electron density during the magnetically active times, we remove the background quiet time variations first and then quantify the anomalies. In this presentation, we will report results from our preliminary analyses from the selected cases corresponding to the strong magnetic storms. Initial results show lower electron densities at noon times and higher electron densities in the late afternoon toward sunset times when compared to the electron densities of magnetically quiet times. We also compare the results with IRI and TIEGCM ionospheric models in order to understand the physical and dynamical causes of these variations. During the presentation we will also discuss the role of these changes during the magnetically active times on the GPS communications through ionosphere.

  1. Validation of Ionosonde Electron Density Reconstruction Algorithms with IONOLAB-RAY in Central Europe

    NASA Astrophysics Data System (ADS)

    Gok, Gokhan; Mosna, Zbysek; Arikan, Feza; Arikan, Orhan; Erdem, Esra

    2016-07-01

    Ionospheric observation is essentially accomplished by specialized radar systems called ionosondes. The time delay between the transmitted and received signals versus frequency is measured by the ionosondes and the received signals are processed to generate ionogram plots, which show the time delay or reflection height of signals with respect to transmitted frequency. The critical frequencies of ionospheric layers and virtual heights, that provide useful information about ionospheric structurecan be extracted from ionograms . Ionograms also indicate the amount of variability or disturbances in the ionosphere. With special inversion algorithms and tomographical methods, electron density profiles can also be estimated from the ionograms. Although structural pictures of ionosphere in the vertical direction can be observed from ionosonde measurements, some errors may arise due to inaccuracies that arise from signal propagation, modeling, data processing and tomographic reconstruction algorithms. Recently IONOLAB group (www.ionolab.org) developed a new algorithm for effective and accurate extraction of ionospheric parameters and reconstruction of electron density profile from ionograms. The electron density reconstruction algorithm applies advanced optimization techniques to calculate parameters of any existing analytical function which defines electron density with respect to height using ionogram measurement data. The process of reconstructing electron density with respect to height is known as the ionogram scaling or true height analysis. IONOLAB-RAY algorithm is a tool to investigate the propagation path and parameters of HF wave in the ionosphere. The algorithm models the wave propagation using ray representation under geometrical optics approximation. In the algorithm , the structural ionospheric characteristics arerepresented as realistically as possible including anisotropicity, inhomogenity and time dependence in 3-D voxel structure. The algorithm is also used

  2. Poster 10: Explaining the high electron density observed during T57

    NASA Astrophysics Data System (ADS)

    Snowden, Darci; Smith, Mike; Jimson, Theo

    2016-06-01

    RPWS observed abnormally high electron densities on the solar limb of Titan's atmosphere during T57 and several other flybys. We show that ion precipitation likely provided the additional ionization needed to explain the T57 data. To show this we use a 3D model of Titan's interaction with Saturn's magnetosphere to simulate the magnetic and electric fields near Titan. Then we use a particle tracing code to calculate the global energy flux of ions onto Titan's exobase. Finally, we calculate the energy deposition rates and ionization rates of the ions as they penetrate Titan's atmosphere.

  3. Electronic and structural properties of superionic Cu2Se from density functional theory

    NASA Astrophysics Data System (ADS)

    Råsander, Mikael; Bergqvist, Lars; Delin, Anna

    2013-03-01

    The superionic high temperature phase of Cu2Se has been found to yield high thermoelectric efficiency due to an interesting combination of low thermal conductivity and a rather high power factor. The low thermal conductivity has been found to be due to the quasi-liquid behaviour of the superionic Cu atoms (Liu et al., Nature Materials, 11, 422-425 (2012)). Here we will present results obtained using density functional theory calculations of the electronic and structural properties of the superionic Cu2Se phase. We will especially address how the inclusion of non-local exchange by the use of hybrid density functionals as well as how localization of the Cu 3d-states affect the electronic structure of Cu2Se. This work was financed through the EU project NexTec, VR (the Swedish Research Council) and SSF (Swedish Foundation for Strategic Research)

  4. 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)

  5. Modification of ionospheric electron density by dust suspension

    NASA Astrophysics Data System (ADS)

    Srivastava, Sweta; Mishra, Rashmi; Singh Sodha, Mahendra

    2016-05-01

    On the basis of a dynamic analysis the effectiveness of dust suspension for the reduction and enhancement of electron density in the E-layer of the ionosphere has been investigated in this paper. The analysis is based on the modelling of the E-layer as the Chapman α layer (validated earlier); the electron/ion production function, arrived at by Chapman and effective electron temperature-dependent electron–ion recombination coefficients in agreement with observations have been used. The balance of the charge on the particles and the number/energy balance of the constituents have been taken into account. The following is the physics of the change in electron density in the ionosphere by the suspension of dust. First, the dust provides a source (emission) and sink (accretion) of electrons. Second, the dust emits photoelectrons with energies much higher than those of ambient electrons, which enhances the electron temperature, leading to a reduced electron–ion recombination coefficient, and thus to a higher electron density. An interplay of these processes and the natural processes of electron production/annihilation determines the electron density and temperature in the dust suspension in the ionosphere. The numerical results, corresponding to suspension of dust of silicate (high work function) and Cs coated bronze (low work function) in the E-layer at 105 \\text{km} are presented and discussed.

  6. Electronic and magnetic properties of spiral spin-density-wave states in transition-metal chains

    NASA Astrophysics Data System (ADS)

    Tanveer, M.; Ruiz-Díaz, P.; Pastor, G. M.

    2016-09-01

    The electronic and magnetic properties of one-dimensional (1D) 3 d transition-metal nanowires are investigated in the framework of density functional theory. The relative stability of collinear and noncollinear (NC) ground-state magnetic orders in V, Mn, and Fe monoatomic chains is quantified by computing the frozen-magnon dispersion relation Δ E (q ⃗) as a function of the spin-density-wave vector q ⃗. The dependence on the local environment of the atoms is analyzed by varying systematically the lattice parameter a of the chains. Electron correlation effects are explored by comparing local spin-density and generalized-gradient approximations to the exchange and correlation functional. Results are given for Δ E (q ⃗) , the local magnetic moments μ⃗i at atom i , the magnetization-vector density m ⃗(r ⃗) , and the local electronic density of states ρi σ(ɛ ) . The frozen-magnon dispersion relations are analyzed from a local perspective. Effective exchange interactions Ji j between the local magnetic moments μ⃗i and μ⃗j are derived by fitting the ab initio Δ E (q ⃗) to a classical 1D Heisenberg model. The dominant competing interactions Ji j at the origin of the NC magnetic order are identified. The interplay between the various Ji j is revealed as a function of a in the framework of the corresponding magnetic phase diagrams.

  7. Guide for 3D WARP simulations of hollow electron beam lenses. Practical explanation on basis of Tevatron electron lens test stand

    SciTech Connect

    Moens, Vince

    2014-06-08

    The purpose of this guide is to help successive students handle WARP. It outlines the installation of WARP on personal computers as well as super-computers and clusters. It furthermore teaches the reader how to handle the WARP environment and run basic scripts. Lastly it outlines how to execute the current Hollow Electron Beam Lens scripts.

  8. Determination of Jupiter's electron density profile from plasma wave observations

    NASA Astrophysics Data System (ADS)

    Gurnett, D. A.; Scarf, F. L.; Kurth, W. S.; Shaw, R. R.; Poynter, R. L.

    1981-09-01

    The electron density measurements obtained in the Jovian magnetosphere from the plasma wave instruments on the Voyager 1 and 2 spacecraft are summarized. Three basic techniques for determining the electron density are discussed. They are (1) local measurements from the low-frequency cutoff of continuum radiation, (2) local measurements from the frequency of upper hybrid resonance emissions, and (3) integral measurements from the dispersion of whistlers. The limitations and advantages of each technique are reviewed.

  9. Electron Densities Near Io from Galileo Plasma Wave Observations

    NASA Technical Reports Server (NTRS)

    Gurnett, D. A.; Persoon, A. M.; Kurth, W. S.; Roux, A.; Bolton, S. J.

    2001-01-01

    This paper presents an overview of electron densities obtained near Io from the Galileo plasma wave instrument during the first four flybys of Io. These flybys were Io, which was a downstream wake pass that occurred on December 7, 1995; I24, which was an upstream pass that occurred on October 11, 1999; I25, which was a south polar pass that occurred on November 26, 1999; and I27, which was an upstream pass that occurred on February 22, 2000. Two methods were used to measure the electron density. The first was based on the frequency of upper hybrid resonance emissions, and the second was based on the low-frequency cutoff of electromagnetic radiation at the electron plasma frequency. For three of the flybys, Io, I25, and I27, large density enhancements were observed near the closest approach to Io. The peak electron densities ranged from 2.1 to 6.8 x 10(exp 4) per cubic centimeters. These densities are consistent with previous radio occultation measurements of Io's ionosphere. No density enhancement was observed during the I24 flyby, most likely because the spacecraft trajectory passed too far upstream to penetrate Io's ionosphere. During two of the flybys, I25 and I27, abrupt step-like changes were observed at the outer boundaries of the region of enhanced electron density. Comparisons with magnetic field models and energetic particle measurements show that the abrupt density steps occur as the spacecraft penetrated the boundary of the Io flux tube, with the region of high plasma density on the inside of the flux tube. Most likely the enhanced electron density within the Io flux tube is associated with magnetic field lines that are frozen to Io by the high conductivity of Io's atmosphere, thereby enhancing the escape of plasma along the magnetic field lines that pass through Io's ionosphere.

  10. 3D Data Assimilation using VERB Diffusion Code

    NASA Astrophysics Data System (ADS)

    Shprits, Y.; Kondrashov, D. A.; Kellerman, A. C.; Subbotin, D.

    2012-12-01

    Significant progress has been done in recent years in application of the data assimilation tools to the radiation belt research. Previous studies concentrated on the analysis of radial profiles of phase space density using multi-satellite measurements and radial transport models. In this study we present analysis of the 3D phase space density using the VERB-3D code blended with CRRES observations by means of operator-splitting Kalman filtering. Assimilation electron fluxes at various energies and pitch-angles into the model allows us to utilize a vast amount of data including information on pitch-angle distributions and radial energy spectra. 3D data assimilation of the radiation belts allows us to differentiate between various acceleration and loss mechanisms. We present reanalysis of the radiation belts and find tell-tale signatures of various physical processes.

  11. X-ray fluorescence (conventional and 3D) and scanning electron microscopy for the investigation of Portuguese polychrome glazed ceramics: Advances in the knowledge of the manufacturing techniques

    NASA Astrophysics Data System (ADS)

    Guilherme, A.; Coroado, J.; dos Santos, J. M. F.; Lühl, L.; Wolff, T.; Kanngießer, B.; Carvalho, M. L.

    2011-05-01

    This work shows the first analytical results obtained by X-Ray Fluorescence (XRF) (conventional and 3D) and Scanning Electron Microscopy with Energy Dispersive System (SEM-EDS) on original Portuguese ceramic pieces produced between the 16th and 18th centuries in Coimbra and Lisbon. Experts distinguished these productions based only on the color, texture and brightness, which originates mislabeling in some cases. Thanks to lateral and spatial resolution in the micrometer regime, the results obtained with μ-XRF were essential in determining the glaze and pigment thicknesses by monitoring the profile of the most abundant element in each "layer". Furthermore, the dissemination of these elements throughout the glaze is different depending on the glaze composition, firing temperature and on the pigment itself. Hence, the crucial point of this investigation was to analyze and understand the interfaces color/glaze and glaze/ceramic support. Together with the XRF results, images captured by SEM and the corresponding semi-quantitative EDS data revealed different manufacturing processes used by the two production centers. Different capture modes were suitable to distinguish different crystals from the minerals that confer the color of the pigments used and to enhance the fact that some of them are very well spread through the glassy matrix, sustaining the theory of an evolved and careful procedure in the manufacturing process of the glaze.

  12. Characterization of a sub-assembly of 3D position sensitive cadmium zinc telluride detectors and electronics from a sub-millimeter resolution PET system

    NASA Astrophysics Data System (ADS)

    Abbaszadeh, Shiva; Gu, Yi; Reynolds, Paul D.; Levin, Craig S.

    2016-09-01

    Cadmium zinc telluride (CZT) offers key advantages for small animal positron emission tomography (PET), including high spatial and energy resolution and simple metal deposition for fabrication of very small pixel arrays. Previous studies have investigated the intrinsic spatial, energy, and timing resolution of an individual sub-millimeter resolution CZT detector. In this work we present the first characterization results of a system of these detectors. The 3D position sensitive dual-CZT detector module and readout electronics developed in our lab was scaled up to complete a significant portion of the final PET system. This sub-system was configured as two opposing detection panels containing a total of twelve 40~\\text{mm}× 40~\\text{mm}× 5 mm monolithic CZT crystals for proof of concept. System-level characterization studies, including optimizing the trigger threshold of each channel’s comparators, were performed. 68Ge and 137Cs radioactive isotopes were used to characterize the energy resolution of all 468 anode channels in the sub-system. The mean measured global 511 keV photopeak energy resolution over all anodes was found to be 7.35+/- 1.75 % FWHM after correction for photon interaction depth-dependent signal variation. The measured global time resolution was 37 ns FWHM, a parameter to be further optimized, and the intrinsic spatial resolution was 0.76 mm FWHM.

  13. 3D Micro-topography of Transferred Laboratory and Natural Ice Crystal Surfaces Imaged by Cryo and Environmental Scanning Electron Microscopy

    NASA Astrophysics Data System (ADS)

    Magee, N. B.; Boaggio, K.; Bancroft, L.; Bandamede, M.

    2015-12-01

    Recent work has highlighted micro-scale roughness on the surfaces of ice crystals grown and imaged in-situ within the chambers of environmental scanning electron microscopes (ESEM). These observations appear to align with theoretical and satellite observations that suggest a prevalence of rough ice in cirrus clouds. However, the atmospheric application of the lab observations are indeterminate because the observations have been based only on crystals grown on substrates and in pure-water vapor environments. In this work, we present details and results from the development of a transfer technique which allows natural and lab-grown ice and snow crystals to be captured, preserved, and transferred into the ESEM for 3D imaging. Ice crystals were gathered from 1) natural snow, 2) a balloon-borne cirrus particle capture device, and 3) lab-grown ice crystals from a diffusion chamber. Ice crystals were captured in a pre-conditioned small-volume (~1 cm3) cryo-containment cell. The cell was then sealed closed and transferred to a specially-designed cryogenic dewer (filled with liquid nitrogen or crushed dry ice) for transport to a new Hitachi Field Emission, Variable Pressure SEM (SU-5000). The cryo-cell was then removed from the dewer and quickly placed onto the pre-conditioned cryo transfer stage attached to the ESEM (Quorum 3010T). Quantitative 3D topographical digital elevation models of ice surfaces are reported from SEM for the first time, including a variety of objective measures of statistical surface roughness. The surfaces of the transported crystals clearly exhibit signatures of mesoscopic roughening that are similar to examples of roughness seen in ESEM-grown crystals. For most transported crystals, the habits and crystal edges are more intricate that those observed for ice grown directly on substrates within the ESEM chamber. Portions of some crystals do appear smooth even at magnification greater than 1000x, a rare observation in our ESEM-grown crystals. The

  14. Do-It-Yourself: 3D Models of Hydrogenic Orbitals through 3D Printing

    ERIC Educational Resources Information Center

    Griffith, Kaitlyn M.; de Cataldo, Riccardo; Fogarty, Keir H.

    2016-01-01

    Introductory chemistry students often have difficulty visualizing the 3-dimensional shapes of the hydrogenic electron orbitals without the aid of physical 3D models. Unfortunately, commercially available models can be quite expensive. 3D printing offers a solution for producing models of hydrogenic orbitals. 3D printing technology is widely…

  15. Laser Induced Tunnel Ionization and Electron Density Evolution in Air

    NASA Astrophysics Data System (ADS)

    Tiwari, Pawan K.; Brussaard, G. J. H.; Wiel, M. J. v. d.; Tripathi, V. K.

    2005-08-01

    An indigenously built Ti:sapphire laser system delivering 50 mJ, 100 fs pulses at a repetition rate of 10 Hz, is employed to tunnel ionize air at 1 atm pressure and form a plasma channel. The laser is line focused using a cylindrical lens to a spot size of 20 μm× 1 mm. A folded wave interferometry is used to deduce the radial electron density profile by measuring the phase shift and employing Abel inversion. The maximum value of chord-integrated electron density and radial electron density are estimated to be approximately equal to 3.0× 1016 cm-2 and 4.0× 1018 cm-3 respectively with density scale length of 20 μm. These results have been theoretically interpreted by developing a unified formalism of tunnel ionization. The experimental results are in reasonable agreement with the theory.

  16. Evidence of Electron Density Enhancements at Enceladus' Apoapsis

    NASA Astrophysics Data System (ADS)

    Persoon, A. M.; Gurnett, D. A.; Kurth, W. S.; Hospodarsky, G. B.; Groene, J. B.

    2015-12-01

    Enceladus' plumes are the dominant source of plasma in Saturn's magnetosphere. Icy particles and water vapor are vented into the inner magnetosphere through fissures in Enceladus' southern polar region. These fissures are subjected to tidal stresses that vary as Enceladus moves in a slightly eccentric orbit around Saturn. Plume activity is greatest when tidal stress is minimal. This occurs when Enceladus is farthest away from Saturn in its orbit (the Enceladus apoapsis). This study will show temporal variations in the electron density distribution that correlate with the position of Enceladus in its orbit around Saturn, with strong density enhancements in the vicinity of Enceladus when the moon is near apoapsis. Equatorial electron density measurements derived from the upper hybrid resonance frequency from the Cassini Radio and Plasma Wave Science (RPWS) experiment are used to illustrate these electron density enhancements.

  17. FPGA architectures for electronically scanned wide-band RF beams using 3-D FIR/IIR digital filters for rectangular array aperture receivers

    NASA Astrophysics Data System (ADS)

    Wijayaratna, Sewwandi; Madanayake, Arjuna; Beall, Brandon D.; Bruton, Len T.

    2014-05-01

    Real-time digital implementation of three-dimensional (3-D) infinite impulse response (IIR) beam filters are discussed. The 3-D IIR filter building blocks have filter coefficients, which are defined using algebraic closed-form expressions that are functions of desired beam personalities, such as the look-direction of the aperture, the bandwidth and sampling frequency of interest, inter antenna spacing, and 3dB beam size. Real-time steering of such 3-D beam filters are obtained by proposed calculation of filter coefficients. Application specific computing units for rapidly calculating the 3-D IIR filter coefficients at nanosecond speed potentially allows fast real-time tracking of low radar cross section (RCS) objects at close range. Proposed design consists of 3-D IIR beam filter with 4 4 antenna grid and the filter coefficient generation block in separate FPGAs. The hardware is designed and co-simulated using a Xilinx Virtex-6 XC6VLX240T FPGA. The 3-D filter operates over 90 MHz and filter coefficient computing structure can operate at up to 145 MHz.

  18. Amplification of current density modulation in a FEL with an infinite electron beam

    SciTech Connect

    Wang, G.; Litvinenko, V.N.; Webb, S.D.

    2011-03-28

    We show that the paraxial field equation for a free electron laser (FEL) in an infinitely wide electron beam with {kappa}-2 energy distribution can be reduced to a fourth ordinary differential equation (ODE). Its solution for arbitrary initial phase space density modulation has been derived in the wave-vector domain. For initial current modulation with Gaussian profile, close form solutions are obtained in space-time domain. In developing an analytical model for a FEL-based coherent electron cooling system, an infinite electron beam has been assumed for the modulation and correction processes. While the assumption has its limitation, it allows for an analytical close form solution to be obtained, which is essential for investigating the underlying scaling law, benchmarking the simulation codes and understanding the fundamental physics. 1D theory was previously applied to model a CeC FEL amplifier. However, the theory ignores diffraction effects and does not provide the transverse profile of the amplified electron density modulation. On the other hand, 3D theories developed for a finite electron beam usually have solutions expanded over infinite number of modes determined by the specific transverse boundary conditions. Unless the mode with the largest growth rate substantially dominates other modes, both evaluation and extracting scaling laws can be complicated. Furthermore, it is also preferable to have an analytical FEL model with assumptions consistent with the other two sections of a CeC system. Recently, we developed the FEL theory in an infinitely wide electron beam with {kappa}-1 (Lorentzian) energy distribution. Close form solutions have been obtained for the amplified current modulation initiated by an external electric field with various spatial-profiles. In this work, we extend the theory into {kappa}-2 energy distribution and study the evolution of current density induced by an initial density modulation.

  19. Three-Dimensional Reconstruction of the Electron Density in the Solar Corona

    NASA Astrophysics Data System (ADS)

    Burnett, L. W.; Nychka, D. W.; Gibson, S. E.; Dalmasse, K.

    2015-12-01

    The need to understand the Sun's magnetic field motivates much of present-day solar physics research. Our ultimate goal is to quantitatively validate models of the global coronal magnetic field by comparing forward models of synthetic data to real observations. As a necessary first step, we seek to build a three-dimensional (3D) model of the electron density in the solar corona, based on white-light coronagraph data. Given that these observations are two-dimensional snapshots, we employ a new application of statistical tomography to piece together the full 3D picture. In an initial step, we demonstrate that our method is capable of reconstructing geometrically-simple density formations. We next turn to more realistic coronal density structures as represented by the global magnetohydrodynamic models made available by Predictive Science Inc., and integrated to create synthetic data using the FORWARD SolarSoft codes. Finally, we consider the application of our method to Mauna Loa Solar Observatory K-Coronagraph observations, and discuss the strengths and limitations of our method.

  20. Influence of the Terminal Electron Donor in D-D-π-A Organic Dye-Sensitized Solar Cells: Dithieno[3,2-b:2',3'-d]pyrrole versus Bis(amine).

    PubMed

    Dai, Panpan; Yang, Lin; Liang, Mao; Dong, Huanhuan; Wang, Peng; Zhang, Chunyao; Sun, Zhe; Xue, Song

    2015-10-14

    With respect to the electron-withdrawing acceptors of D-A-π-A organic dyes, reports on the second electron-donating donors for D-D-π-A organic dyes are very limited. Both of the dyes have attracted significant attention in the field of dye-sensitized solar cells (DSCs). In this work, four new D-D-π-A organic dyes with dithieno[3,2-b:2',3'-d]pyrrole (DTP) or bis(amine) donor have been designed and synthesized for a investigation of the influence of the terminal electron donor in D-D-π-A organic dye-sensitized solar cells. It is found that DTP is a promising building block as the terminal electron donor when introduced in the dithiophenepyrrole direction, but not just a good bridge, which exhibits several characteristics: (i) efficiently increasing the maximum molar absorption coefficient and extending the absorption bands; (ii) showing stronger charge transfer interaction as compared with the pyrrole direction; (iii) beneficial to photocurrent generation of DSCs employing cobalt electrolytes. DSCs based on M45 with the Co-phen electrolyte exhibit good light-to-electric energy conversion efficiencies as high as 9.02%, with a short circuit current density (JSC) of 15.3 mA cm(-2), open circuit voltage (VOC) of 867 mV and fill factor (FF) of 0.68 under AM 1.5 illumination (100 mW cm(-2)). The results demonstrate that N,S-heterocycles such as DTP unit could be promising candidates for application in highly efficient DSCs employing cobalt electrolyte.

  1. Influence of the Terminal Electron Donor in D-D-π-A Organic Dye-Sensitized Solar Cells: Dithieno[3,2-b:2',3'-d]pyrrole versus Bis(amine).

    PubMed

    Dai, Panpan; Yang, Lin; Liang, Mao; Dong, Huanhuan; Wang, Peng; Zhang, Chunyao; Sun, Zhe; Xue, Song

    2015-10-14

    With respect to the electron-withdrawing acceptors of D-A-π-A organic dyes, reports on the second electron-donating donors for D-D-π-A organic dyes are very limited. Both of the dyes have attracted significant attention in the field of dye-sensitized solar cells (DSCs). In this work, four new D-D-π-A organic dyes with dithieno[3,2-b:2',3'-d]pyrrole (DTP) or bis(amine) donor have been designed and synthesized for a investigation of the influence of the terminal electron donor in D-D-π-A organic dye-sensitized solar cells. It is found that DTP is a promising building block as the terminal electron donor when introduced in the dithiophenepyrrole direction, but not just a good bridge, which exhibits several characteristics: (i) efficiently increasing the maximum molar absorption coefficient and extending the absorption bands; (ii) showing stronger charge transfer interaction as compared with the pyrrole direction; (iii) beneficial to photocurrent generation of DSCs employing cobalt electrolytes. DSCs based on M45 with the Co-phen electrolyte exhibit good light-to-electric energy conversion efficiencies as high as 9.02%, with a short circuit current density (JSC) of 15.3 mA cm(-2), open circuit voltage (VOC) of 867 mV and fill factor (FF) of 0.68 under AM 1.5 illumination (100 mW cm(-2)). The results demonstrate that N,S-heterocycles such as DTP unit could be promising candidates for application in highly efficient DSCs employing cobalt electrolyte. PMID:26394089

  2. Stabilization of electron-scale turbulence by electron density gradient in national spherical torus experiment

    NASA Astrophysics Data System (ADS)

    Ruiz Ruiz, J.; Ren, Y.; Guttenfelder, W.; White, A. E.; Kaye, S. M.; Leblanc, B. P.; Mazzucato, E.; Lee, K. C.; Domier, C. W.; Smith, D. R.; Yuh, H.

    2015-12-01

    Theory and experiments have shown that electron temperature gradient (ETG) turbulence on the electron gyro-scale, kρe ≲ 1, can be responsible for anomalous electron thermal transport in NSTX. Electron scale (high-k) turbulence is diagnosed in NSTX with a high-k microwave scattering system [D. R. Smith et al., Rev. Sci. Instrum. 79, 123501 (2008)]. Here we report on stabilization effects of the electron density gradient on electron-scale density fluctuations in a set of neutral beam injection heated H-mode plasmas. We found that the absence of high-k density fluctuations from measurements is correlated with large equilibrium density gradient, which is shown to be consistent with linear stabilization of ETG modes due to the density gradient using the analytical ETG linear threshold in F. Jenko et al. [Phys. Plasmas 8, 4096 (2001)] and linear gyrokinetic simulations with GS2 [M. Kotschenreuther et al., Comput. Phys. Commun. 88, 128 (1995)]. We also found that the observed power of electron-scale turbulence (when it exists) is anti-correlated with the equilibrium density gradient, suggesting density gradient as a nonlinear stabilizing mechanism. Higher density gradients give rise to lower values of the plasma frame frequency, calculated based on the Doppler shift of the measured density fluctuations. Linear gyrokinetic simulations show that higher values of the electron density gradient reduce the value of the real frequency, in agreement with experimental observation. Nonlinear electron-scale gyrokinetic simulations show that high electron density gradient reduces electron heat flux and stiffness, and increases the ETG nonlinear threshold, consistent with experimental observations.

  3. Stabilization of electron-scale turbulence by electron density gradient in national spherical torus experiment

    SciTech Connect

    Ruiz Ruiz, J.; White, A. E.; Ren, Y.; Guttenfelder, W.; Kaye, S. M.; Leblanc, B. P.; Mazzucato, E.; Lee, K. C.; Domier, C. W.; Smith, D. R.; Yuh, H.

    2015-12-15

    Theory and experiments have shown that electron temperature gradient (ETG) turbulence on the electron gyro-scale, k{sub ⊥}ρ{sub e} ≲ 1, can be responsible for anomalous electron thermal transport in NSTX. Electron scale (high-k) turbulence is diagnosed in NSTX with a high-k microwave scattering system [D. R. Smith et al., Rev. Sci. Instrum. 79, 123501 (2008)]. Here we report on stabilization effects of the electron density gradient on electron-scale density fluctuations in a set of neutral beam injection heated H-mode plasmas. We found that the absence of high-k density fluctuations from measurements is correlated with large equilibrium density gradient, which is shown to be consistent with linear stabilization of ETG modes due to the density gradient using the analytical ETG linear threshold in F. Jenko et al. [Phys. Plasmas 8, 4096 (2001)] and linear gyrokinetic simulations with GS2 [M. Kotschenreuther et al., Comput. Phys. Commun. 88, 128 (1995)]. We also found that the observed power of electron-scale turbulence (when it exists) is anti-correlated with the equilibrium density gradient, suggesting density gradient as a nonlinear stabilizing mechanism. Higher density gradients give rise to lower values of the plasma frame frequency, calculated based on the Doppler shift of the measured density fluctuations. Linear gyrokinetic simulations show that higher values of the electron density gradient reduce the value of the real frequency, in agreement with experimental observation. Nonlinear electron-scale gyrokinetic simulations show that high electron density gradient reduces electron heat flux and stiffness, and increases the ETG nonlinear threshold, consistent with experimental observations.

  4. Electron density and gas density measurements in a millimeter-wave discharge

    NASA Astrophysics Data System (ADS)

    Schaub, S. C.; Hummelt, J. S.; Guss, W. C.; Shapiro, M. A.; Temkin, R. J.

    2016-08-01

    Electron density and neutral gas density have been measured in a non-equilibrium air breakdown plasma using optical emission spectroscopy and two-dimensional laser interferometry, respectively. A plasma was created with a focused high frequency microwave beam in air. Experiments were run with 110 GHz and 124.5 GHz microwaves at powers up to 1.2 MW. Microwave pulses were 3 μs long at 110 GHz and 2.2 μs long at 124.5 GHz. Electron density was measured over a pressure range of 25 to 700 Torr as the input microwave power was varied. Electron density was found to be close to the critical density, where the collisional plasma frequency is equal to the microwave frequency, over the pressure range studied and to vary weakly with input power. Neutral gas density was measured over a pressure range from 150 to 750 Torr at power levels high above the threshold for initiating breakdown. The two-dimensional structure of the neutral gas density was resolved. Intense, localized heating was found to occur hundreds of nanoseconds after visible plasma formed. This heating led to neutral gas density reductions of greater than 80% where peak plasma densities occurred. Spatial structure and temporal dynamics of gas heating at atmospheric pressure were found to agree well with published numerical simulations.

  5. 3D reconstruction of two-dimensional crystals.

    PubMed

    Stahlberg, Henning; Biyani, Nikhil; Engel, Andreas

    2015-09-01

    Electron crystallography of two-dimensional (2D) crystals determines the structure of membrane proteins in the lipid bilayer by imaging with cryo-electron microscopy and image processing. Membrane proteins can be packed in regular 2D arrays by their reconstitution in the presence of lipids at low lipid to protein weight-to-weight ratio. The crystal quality depends on the protein purity and homogeneity, its stability, and on the crystallization conditions. A 2D crystal presents the membrane protein in a functional and fully lipidated state. Electron crystallography determines the 3D structure even of small membrane proteins up to atomic resolution, but 3D density maps have a better resolution in the membrane plane than in the vertical direction. This problem can be partly eliminated by applying an iterative algorithm that exploits additional known constraints about the 2D crystal. 2D electron crystallography is particularly attractive for the structural analysis of membrane proteins that are too small for single particle analyses and too unstable to form 3D crystals. With the recent introduction of direct electron detector cameras, the routine determination of the atomic 3D structure of membrane-embedded membrane proteins is in reach. PMID:26093179

  6. Validation of Spherically Symmetric Inversion by Use of a Tomographically Reconstructed Three-Dimensional Electron Density of the Solar Corona

    NASA Technical Reports Server (NTRS)

    Wang, Tongjiang; Davila, Joseph M.

    2014-01-01

    Determining the coronal electron density by the inversion of white-light polarized brightness (pB) measurements by coronagraphs is a classic problem in solar physics. An inversion technique based on the spherically symmetric geometry (spherically symmetric inversion, SSI) was developed in the 1950s and has been widely applied to interpret various observations. However, to date there is no study of the uncertainty estimation of this method. We here present the detailed assessment of this method using a three-dimensional (3D) electron density in the corona from 1.5 to 4 solar radius as a model, which is reconstructed by a tomography method from STEREO/COR1 observations during the solar minimum in February 2008 (Carrington Rotation, CR 2066).We first show in theory and observation that the spherically symmetric polynomial approximation (SSPA) method and the Van de Hulst inversion technique are equivalent. Then we assess the SSPA method using synthesized pB images from the 3D density model, and find that the SSPA density values are close to the model inputs for the streamer core near the plane of the sky (POS) with differences generally smaller than about a factor of two; the former has the lower peak but extends more in both longitudinal and latitudinal directions than the latter. We estimate that the SSPA method may resolve the coronal density structure near the POS with angular resolution in longitude of about 50 deg. Our results confirm the suggestion that the SSI method is applicable to the solar minimum streamer (belt), as stated in some previous studies. In addition, we demonstrate that the SSPA method can be used to reconstruct the 3D coronal density, roughly in agreement with the reconstruction by tomography for a period of low solar activity (CR 2066). We suggest that the SSI method is complementary to the 3D tomographic technique in some cases, given that the development of the latter is still an ongoing research effort.

  7. Density-shear instability in electron magneto-hydrodynamics

    SciTech Connect

    Wood, T. S. Hollerbach, R.; Lyutikov, M.

    2014-05-15

    We discuss a novel instability in inertia-less electron magneto-hydrodynamics (EMHD), which arises from a combination of electron velocity shear and electron density gradients. The unstable modes have a lengthscale longer than the transverse density scale, and a growth-rate of the order of the inverse Hall timescale. We suggest that this density-shear instability may be of importance in magnetic reconnection regions on scales smaller than the ion skin depth, and in neutron star crusts. We demonstrate that the so-called Hall drift instability, previously argued to be relevant in neutron star crusts, is a resistive tearing instability rather than an instability of the Hall term itself. We argue that the density-shear instability is of greater significance in neutron stars than the tearing instability, because it generally has a faster growth-rate and is less sensitive to geometry and boundary conditions. We prove that, for uniform electron density, EMHD is “at least as stable” as regular, incompressible MHD, in the sense that any field configuration that is stable in MHD is also stable in EMHD. We present a connection between the density-shear instability in EMHD and the magneto-buoyancy instability in anelastic MHD.

  8. Localized electron heating and density peaking in downstream helicon plasma

    NASA Astrophysics Data System (ADS)

    Ghosh, Soumen; Barada, K. K.; Chattopadhyay, P. K.; Ghosh, J.; Bora, D.

    2015-06-01

    Localized electron temperature and density peaking at different axial locations in the downstream helicon plasma have been observed in a linear helicon device with both geometrical and magnetic expansion. The discharge is produced with an m=+1 right helical antenna powered by a RF source operating at 13.56 MHz. Axial wave field measurement shows the presence of damped helicon waves with standing wave character folded into it even at low densities (˜ {{10}16} m-3 ). The measured helicon wavelength is just about twice the antenna length and the phase velocity ≤ft({{v}p}\\right) is almost the speed required for electron impact ionization. These experimental observations strongly advocate the Landau damping heating and density production by the helicon waves, particularly in low density plasma such as ours. The electron temperature maximizes at 35-45 cm away from the antenna center in our experiments indicating a local source of heating at those locations. Different mechanisms responsible for this additional heating at a particular spatial location have been discussed for their possible roles. Further downstream from the location of the maximum electron temperature, a density peak located 55-65 cm away from the antenna is observed. This downstream density peaking can be explained through pressure balance in the system.

  9. Density-shear instability in electron magneto-hydrodynamics

    NASA Astrophysics Data System (ADS)

    Wood, T. S.; Hollerbach, R.; Lyutikov, M.

    2014-05-01

    We discuss a novel instability in inertia-less electron magneto-hydrodynamics (EMHD), which arises from a combination of electron velocity shear and electron density gradients. The unstable modes have a lengthscale longer than the transverse density scale, and a growth-rate of the order of the inverse Hall timescale. We suggest that this density-shear instability may be of importance in magnetic reconnection regions on scales smaller than the ion skin depth, and in neutron star crusts. We demonstrate that the so-called Hall drift instability, previously argued to be relevant in neutron star crusts, is a resistive tearing instability rather than an instability of the Hall term itself. We argue that the density-shear instability is of greater significance in neutron stars than the tearing instability, because it generally has a faster growth-rate and is less sensitive to geometry and boundary conditions. We prove that, for uniform electron density, EMHD is "at least as stable" as regular, incompressible MHD, in the sense that any field configuration that is stable in MHD is also stable in EMHD. We present a connection between the density-shear instability in EMHD and the magneto-buoyancy instability in anelastic MHD.

  10. Measuring ionospheric electron density using the plasma frequency probe

    SciTech Connect

    Jensen, M.D.; Baker, K.D. )

    1992-02-01

    During the past decade, the plasma frequency probe (PFP) has evolved into an accurate, proven method of measuring electron density in the ionosphere above about 90 km. The instrument uses an electrically short antenna mounted on a sounding rocket that is immersed in the plasma and notes the frequency where the antenna impedance is large and nonreactive. This frequency is closely related to the plasma frequency, which is a direct function of free electron concentration. The probe uses phase-locked loop technology to follow a changing electron density. Several sections of the plasma frequency probe circuitry are unique, especially the voltage-controlled oscillator that uses both an electronically tuned capacitor and inductor to give the wide tuning range needed for electron density measurements. The results from two recent sounding rocket flights (Thunderstorm II and CRIT II) under vastly different plasma conditions demonstrate the capabilities of the PFP and show the importance of in situ electron density measurements of understanding plasma processes. 9 refs.

  11. 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.

  12. 3-D Seismic Interpretation

    NASA Astrophysics Data System (ADS)

    Moore, Gregory F.

    2009-05-01

    This volume is a brief introduction aimed at those who wish to gain a basic and relatively quick understanding of the interpretation of three-dimensional (3-D) seismic reflection data. The book is well written, clearly illustrated, and easy to follow. Enough elementary mathematics are presented for a basic understanding of seismic methods, but more complex mathematical derivations are avoided. References are listed for readers interested in more advanced explanations. After a brief introduction, the book logically begins with a succinct chapter on modern 3-D seismic data acquisition and processing. Standard 3-D acquisition methods are presented, and an appendix expands on more recent acquisition techniques, such as multiple-azimuth and wide-azimuth acquisition. Although this chapter covers the basics of standard time processing quite well, there is only a single sentence about prestack depth imaging, and anisotropic processing is not mentioned at all, even though both techniques are now becoming standard.

  13. Calculation of all-electron wavefunction of hemoprotein cytochrome c by density functional theory

    NASA Astrophysics Data System (ADS)

    Sato, Fumitoshi; Yoshihiro, Tamotsu; Era, Makoto; Kashiwagi, Hiroshi

    2001-06-01

    An all-electron wavefunction of horse heart d 6-low-spin ferrocytochrome c (ferrocyt. c) was calculated by our Gaussian-based density functional theory (DFT) molecular orbital (MO) program, ProteinDF with a workstation cluster. It may be the first full-scale DFT calculation of a metalloprotein, and the numbers of orbitals and auxiliary functions are 9600 and 17 578, respectively. We show that the highest occupied MO (HOMO) derives from 3d orbitals of heme Fe and is unexpectedly delocalized while preserving the essential atomic character, which will give room for consideration of the electron transfer processes between proteins. The potential of MO calculations on larger proteins is also discussed with the computational data of cytochrome c (cyt. c).

  14. Rocket radio measurement of electron density in the nighttime ionosphere

    NASA Technical Reports Server (NTRS)

    Gilchrist, B. E.; Smith, L. G.

    1979-01-01

    One experimental technique based on the Faraday rotation effect of radio waves is presented for measuring electron density in the nighttime ionosphere at midlatitudes. High frequency linearly-polarized radio signals were transmitted to a linearly-polarized receiving system located in a spinning rocket moving through the ionosphere. Faraday rotation was observed in the reference plane of the rocket as a change in frequency of the detected receiver output. The frequency change was measured and the information was used to obtain electron density data. System performance was evaluated and some sources of error were identified. The data obtained was useful in calibrating a Langmuir probe experiment for electron density values of 100/cu cm and greater. Data from two rocket flights are presented to illustrate the experiment.

  15. Ionospheric electron density profile estimation using commercial AM broadcast signals

    NASA Astrophysics Data System (ADS)

    Yu, De; Ma, Hong; Cheng, Li; Li, Yang; Zhang, Yufeng; Chen, Wenjun

    2015-08-01

    A new method for estimating the bottom electron density profile by using commercial AM broadcast signals as non-cooperative signals is presented in this paper. Without requiring any dedicated transmitters, the required input data are the measured elevation angles of signals transmitted from the known locations of broadcast stations. The input data are inverted for the QPS model parameters depicting the electron density profile of the signal's reflection area by using a probabilistic inversion technique. This method has been validated on synthesized data and used with the real data provided by an HF direction-finding system situated near the city of Wuhan. The estimated parameters obtained by the proposed method have been compared with vertical ionosonde data and have been used to locate the Shijiazhuang broadcast station. The simulation and experimental results indicate that the proposed ionospheric sounding method is feasible for obtaining useful electron density profiles.

  16. Rocket measurements of electron density irregularities during MAC/SINE

    NASA Technical Reports Server (NTRS)

    Ulwick, J. C.

    1989-01-01

    Four Super Arcas rockets were launched at the Andoya Rocket Range, Norway, as part of the MAC/SINE campaign to measure electron density irregularities with high spatial resolution in the cold summer polar mesosphere. They were launched as part of two salvos: the turbulent/gravity wave salvo (3 rockets) and the EISCAT/SOUSY radar salvo (one rocket). In both salvos meteorological rockets, measuring temperature and winds, were also launched and the SOUSY radar, located near the launch site, measured mesospheric turbulence. Electron density irregularities and strong gradients were measured by the rocket probes in the region of most intense backscatter observed by the radar. The electron density profiles (8 to 4 on ascent and 4 on descent) show very different characteristics in the peak scattering region and show marked spatial and temporal variability. These data are intercompared and discussed.

  17. Bootstrapping 3D fermions

    DOE PAGES

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

    2016-03-17

    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 CT. We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N. Finally, we also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

  18. Three-Dimensional Electron Realm in VSe2 by Soft-X-Ray Photoelectron Spectroscopy: Origin of Charge-Density Waves

    NASA Astrophysics Data System (ADS)

    Strocov, Vladimir N.; Shi, Ming; Kobayashi, Masaki; Monney, Claude; Wang, Xiaoqiang; Krempasky, Juraj; Schmitt, Thorsten; Patthey, Luc; Berger, Helmuth; Blaha, Peter

    2012-08-01

    The resolution of angle-resolved photoelectron spectroscopy (ARPES) in three-dimensional (3D) momentum k is fundamentally limited by ill defined surface-perpendicular wave vector k⊥ associated with the finite photoelectron mean free path. Pushing ARPES into the soft-x-ray energy region sharpens the k⊥ definition, allowing accurate electronic structure investigations in 3D materials. We apply soft-x-ray ARPES to explore the 3D electron realm in a paradigm transition metal dichalcogenide VSe2. Essential to break through the dramatic loss of the valence band photoexcitation cross section at soft-x-ray energies is the advanced photon flux performance of our synchrotron instrumentation. By virtue of the sharp 3D momentum definition, the soft-x-ray ARPES experimental band structure and Fermi surface of VSe2 show a textbook clarity. We identify pronounced 3D warping of the Fermi surface and show that its concomitant nesting acts as the precursor for the exotic 3D charge-density waves in VSe2. Our results demonstrate the immense potential of soft-x-ray ARPES to explore details of 3D electronic structure.

  19. Electron density and plasma dynamics of a colliding plasma experiment

    NASA Astrophysics Data System (ADS)

    Wiechula, J.; Schönlein, A.; Iberler, M.; Hock, C.; Manegold, T.; Bohlender, B.; Jacoby, J.

    2016-07-01

    We present experimental results of two head-on colliding plasma sheaths accelerated by pulsed-power-driven coaxial plasma accelerators. The measurements have been performed in a small vacuum chamber with a neutral-gas prefill of ArH2 at gas pressures between 17 Pa and 400 Pa and load voltages between 4 kV and 9 kV. As the plasma sheaths collide, the electron density is significantly increased. The electron density reaches maximum values of ≈8 ṡ 1015 cm-3 for a single accelerated plasma and a maximum value of ≈2.6 ṡ 1016 cm-3 for the plasma collision. Overall a raise of the plasma density by a factor of 1.3 to 3.8 has been achieved. A scaling behavior has been derived from the values of the electron density which shows a disproportionately high increase of the electron density of the collisional case for higher applied voltages in comparison to a single accelerated plasma. Sequences of the plasma collision have been taken, using a fast framing camera to study the plasma dynamics. These sequences indicate a maximum collision velocity of 34 km/s.

  20. Shock-wave-based density down ramp for electron injection

    NASA Astrophysics Data System (ADS)

    Wang, Chunmei; Li, Ji; Sun, Jun; Luo, Xisheng

    2012-02-01

    We demonstrate a sharp density transition for electron injection in laser wakefield acceleration through numerical study. This density transition is generated by a detached shock wave induced by a cylinder inserted into a supersonic helium gas flow. In a Mach 1.5 flow, the scale length of the density transition Lgrad can approximately equal to plasma wavelength λp at the shock front, and can be further reduced with an increase of the flow Mach number. A density down ramp with Lgrad≥λp can reduce the phase velocity of the wakefield and lower the energy threshold for the electrons to be trapped. Moreover, the quality of the accelerated beam may be greatly improved by precisely controlling of Lgrad to be one λp. For an even sharper density down ramp with Lgrad≪λp, the oscillating electrons in the plasma wave will up shift their phase when crossing the ramp, therefore a fraction of the electrons are injected into the accelerating field. For this injection mechanism, there is no threshold requirement for the pump laser intensity to reach wave breaking, which is a big advantage as compared with other injection mechanisms.

  1. Features of Electron Density Distribution in Delafossite Cualo2

    NASA Astrophysics Data System (ADS)

    Pogoreltsev, A. I.; Schmidt, S. V.; Gavrilenko, A. N.; Shulgin, D. A.; Korzun, B. V.; Matukhin, V. L.

    2015-07-01

    We have used pulsed 63,65Cu nuclear quadrupole resonance at room temperature to study the semiconductor compound CuAlO2 with a delafossite crystal structure, and we have determined the quadrupole frequency νQ = 28.12 MHz and the asymmetry parameter η ~ 0, which we used to study the features of the electron density distribution in the vicinity of the quadrupolar nucleus. In order to take into account the influence of correlation effects on the electric field gradient, we carried out ab initio calculations within the density functional theory (DFT) approximation using a set of correlation functionals VWN1RPA, VWN5, PW91LDA, CPW91, and B3LYP1. We mapped the electron density distribution in the vicinity of the quadrupolar copper nucleus for the Cu7Al6o{14/- 1} cluster and we calculated the size of the LUMO-HOMO gap, Δ ~ 3.33 eV. We established the anisotropy of the spatial electron density distribution. Based on analysis of the electron density distribution obtained, we suggest that the bond in CuAlO2 is not purely covalent.

  2. Electron temperature and density measurements of laser induced germanium plasma

    NASA Astrophysics Data System (ADS)

    Shakeel, Hira; Arshad, Saboohi; Haq, S. U.; Nadeem, Ali

    2016-05-01

    The germanium plasma produced by the fundamental harmonics (1064 nm) of Nd:YAG laser in single and double pulse configurations have been studied spectroscopically. The plasma is characterized by measuring the electron temperature using the Boltzmann plot method for neutral and ionized species and electron number density as a function of laser irradiance, ambient pressure, and distance from the target surface. It is observed that the plasma parameters have an increasing trend with laser irradiance (9-33 GW/cm2) and with ambient pressure (8-250 mbar). However, a decreasing trend is observed along the plume length up to 4.5 mm. The electron temperature and electron number density are also determined using a double pulse configuration, and their behavior at fixed energy ratio and different interpulse delays is discussed.

  3. Mobility of electrons in supercritical krypton: Role of density fluctuations

    NASA Astrophysics Data System (ADS)

    Nishikawa, Masaru; Holroyd, Richard A.; Preses, Jack M.

    2007-07-01

    Excess electrons were generated in supercritical krypton by means of pulsed x-ray irradiation, and the electron transport phenomena were studied. Electron signals immediately after a 30ps pulse showed a distinctive feature characteristic of the presence of the Ramsauer-Townsend minimum in the momentum transfer cross section. The dependence of the drift velocity vD on field strength was found to be concave upward in the low field region and then to go through a maximum with increasing field strength, which is also typical of the presence of a minimum in the scattering cross section at an intermediate field strength. A minimum in the electron mobility was observed at about one-half the critical density. The acoustical phonon scattering model, which successfully explained the mobility change in this density region in supercritical xenon, was again found to account for the mobility in supercritical krypton.

  4. Neutral wind estimation from 4-D ionospheric electron density images

    NASA Astrophysics Data System (ADS)

    Datta-Barua, S.; Bust, G. S.; Crowley, G.; Curtis, N.

    2009-06-01

    We develop a new inversion algorithm for Estimating Model Parameters from Ionospheric Reverse Engineering (EMPIRE). The EMPIRE method uses four-dimensional images of global electron density to estimate the field-aligned neutral wind ionospheric driver when direct measurement is not available. We begin with a model of the electron continuity equation that includes production and loss rate estimates, as well as E × B drift, gravity, and diffusion effects. We use ion, electron, and neutral species temperatures and neutral densities from the Thermosphere Ionosphere Mesosphere Electrodynamics General Circulation Model (TIMEGCM-ASPEN) for estimating the magnitude of these effects. We then model the neutral wind as a power series at a given longitude for a range of latitudes and altitudes. As a test of our algorithm, we have input TIMEGCM electron densities to our algorithm. The model of the neutral wind is computed at hourly intervals and validated by comparing to the “true” TIMEGCM neutral wind fields. We show results for a storm day: 10 November 2004. The agreement between the winds derived from EMPIRE versus the TIMEGCM “true” winds appears to be time-dependent for the day under consideration. This may indicate that the diurnal variation in certain driving processes impacts the accuracy of our neutral wind model. Despite the potential temporal and spatial limits on accuracy, estimating neutral wind speed from measured electron density fields via our algorithm shows great promise as a complement to the more sparse radar and satellite measurements.

  5. Electron Density Measurement of Argon Containing Plasmas by Saturation Spectroscopy

    NASA Astrophysics Data System (ADS)

    Nishiyama, S.; Wang, H.; Tomioka, S.; Sasaki, K.

    2014-10-01

    Langmuir probes are widely used for electron density measurements in plasmas. However, the use of a conventional probe should be avoided in a plasma which needs high purity because of the possibility of contamination. Optical measurements are suitable for these plasmas. In this work, we applied saturation spectroscopy to the electron density measurement. The peak height of the saturation spectrum is affected by the relaxation frequency of the related energy levels. In the case of the metastable levels of argon, the electron impact quenching rate, which is proportional to the electron density, is the dominant factor. In our experiments, an inductively coupled plasma source and a tunable cw diode laser were used. The frequency of the laser was scanned over the Doppler width of the 4 s[3/ 2 ] 2 o - 4 p[ 3 / 2 ] 2 (763.51 nm) transition. The experimental saturation spectrum was composed of a sharp Lorentzian peak and a broad base component, which was caused by velocity changing collisions. We deduced a new relationship between the saturation parameter and the measured saturated absorption spectrum with considering velocity changing collisions. We confirmed a linear relationship, which was expected theoretically, between the inverse of the saturation parameter and the electron density. Part of this work is supported by JSPS KAKENHI Grant Number 24540529.

  6. Statistical quality indicators for electron-density maps

    SciTech Connect

    Tickle, Ian J.

    2012-04-01

    A likelihood-based metric for scoring the local agreement of a structure model with the observed electron density is described. The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a χ{sup 2} significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.

  7. Electronic structures and optical properties of TiO2: Improved density-functional-theory investigation

    NASA Astrophysics Data System (ADS)

    Gong, Sai; Liu, Bang-Gui

    2012-05-01

    TiO2 has been recently used to realize high-temperature ferromagnetic semiconductors. In fact, it has been widely used for a long time as white pigment and sunscreen because of its whiteness, high refractive index, and excellent optical properties. However, its electronic structures and the related properties have not been satisfactorily understood. Here, we use Tran and Blaha's modified Becke-Johnson (TB-mBJ) exchange potential (plus a local density approximation correlation potential) within the density functional theory to investigate electronic structures and optical properties of rutile and anatase TiO2. Our comparative calculations show that the energy gaps obtained from mBJ method agree better with the experimental results than that obtained from local density approximation (LDA) and generalized gradient approximation (GGA), in contrast with substantially overestimated values from many-body perturbation (GW) calculations. As for optical dielectric functions (both real and imaginary parts), refractive index, and extinction coefficients as functions of photon energy, our mBJ calculated results are in excellent agreement with the experimental curves. Our further analysis reveals that these excellent improvements are achieved because mBJ potential describes accurately the energy levels of Ti 3d states. These results should be helpful to understand the high temperature ferromagnetism in doped TiO2. This approach can be used as a standard to understand electronic structures and the related properties of such materials as TiO2.

  8. Venus in 3D

    NASA Astrophysics Data System (ADS)

    Plaut, J. J.

    1993-08-01

    Stereographic images of the surface of Venus which enable geologists to reconstruct the details of the planet's evolution are discussed. The 120-meter resolution of these 3D images make it possible to construct digital topographic maps from which precise measurements can be made of the heights, depths, slopes, and volumes of geologic structures.

  9. 3D reservoir visualization

    SciTech Connect

    Van, B.T.; Pajon, J.L.; Joseph, P. )

    1991-11-01

    This paper shows how some simple 3D computer graphics tools can be combined to provide efficient software for visualizing and analyzing data obtained from reservoir simulators and geological simulations. The animation and interactive capabilities of the software quickly provide a deep understanding of the fluid-flow behavior and an accurate idea of the internal architecture of a reservoir.

  10. Highly-stretchable 3D-architected Mechanical Metamaterials

    NASA Astrophysics Data System (ADS)

    Jiang, Yanhui; Wang, Qiming

    2016-09-01

    Soft materials featuring both 3D free-form architectures and high stretchability are highly desirable for a number of engineering applications ranging from cushion modulators, soft robots to stretchable electronics; however, both the manufacturing and fundamental mechanics are largely elusive. Here, we overcome the manufacturing difficulties and report a class of mechanical metamaterials that not only features 3D free-form lattice architectures but also poses ultrahigh reversible stretchability (strain > 414%), 4 times higher than that of the existing counterparts with the similar complexity of 3D architectures. The microarchitected metamaterials, made of highly stretchable elastomers, are realized through an additive manufacturing technique, projection microstereolithography, and its postprocessing. With the fabricated metamaterials, we reveal their exotic mechanical behaviors: Under large-strain tension, their moduli follow a linear scaling relationship with their densities regardless of architecture types, in sharp contrast to the architecture-dependent modulus power-law of the existing engineering materials; under large-strain compression, they present tunable negative-stiffness that enables ultrahigh energy absorption efficiencies. To harness their extraordinary stretchability and microstructures, we demonstrate that the metamaterials open a number of application avenues in lightweight and flexible structure connectors, ultraefficient dampers, 3D meshed rehabilitation structures and stretchable electronics with designed 3D anisotropic conductivity.

  11. Highly-stretchable 3D-architected Mechanical Metamaterials

    PubMed Central

    Jiang, Yanhui; Wang, Qiming

    2016-01-01

    Soft materials featuring both 3D free-form architectures and high stretchability are highly desirable for a number of engineering applications ranging from cushion modulators, soft robots to stretchable electronics; however, both the manufacturing and fundamental mechanics are largely elusive. Here, we overcome the manufacturing difficulties and report a class of mechanical metamaterials that not only features 3D free-form lattice architectures but also poses ultrahigh reversible stretchability (strain > 414%), 4 times higher than that of the existing counterparts with the similar complexity of 3D architectures. The microarchitected metamaterials, made of highly stretchable elastomers, are realized through an additive manufacturing technique, projection microstereolithography, and its postprocessing. With the fabricated metamaterials, we reveal their exotic mechanical behaviors: Under large-strain tension, their moduli follow a linear scaling relationship with their densities regardless of architecture types, in sharp contrast to the architecture-dependent modulus power-law of the existing engineering materials; under large-strain compression, they present tunable negative-stiffness that enables ultrahigh energy absorption efficiencies. To harness their extraordinary stretchability and microstructures, we demonstrate that the metamaterials open a number of application avenues in lightweight and flexible structure connectors, ultraefficient dampers, 3D meshed rehabilitation structures and stretchable electronics with designed 3D anisotropic conductivity. PMID:27667638

  12. 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

  13. Modeling Ionosphere Environments: Creating an ISS Electron Density Tool

    NASA Technical Reports Server (NTRS)

    Gurgew, Danielle N.; Minow, Joseph I.

    2011-01-01

    The International Space Station (ISS) maintains an altitude typically between 300 km and 400 km in low Earth orbit (LEO) which itself is situated in the Earth's ionosphere. The ionosphere is a region of partially ionized gas (plasma) formed by the photoionization of neutral atoms and molecules in the upper atmosphere of Earth. It is important to understand what electron density the spacecraft is/will be operating in because the ionized gas along the ISS orbit interacts with the electrical power system resulting in charging of the vehicle. One instrument that is already operational onboard the ISS with a goal of monitoring electron density, electron temperature, and ISS floating potential is the Floating Potential Measurement Unit (FPMU). Although this tool is a valuable addition to the ISS, there are limitations concerning the data collection periods. The FPMU uses the Ku band communication frequency to transmit data from orbit. Use of this band for FPMU data runs is often terminated due to necessary observation of higher priority Extravehicular Activities (EVAs) and other operations on ISS. Thus, large gaps are present in FPMU data. The purpose of this study is to solve the issue of missing environmental data by implementing a secondary electron density data source, derived from the COSMIC satellite constellation, to create a model of ISS orbital environments. Extrapolating data specific to ISS orbital altitudes, we model the ionospheric electron density along the ISS orbit track to supply a set of data when the FPMU is unavailable. This computer model also provides an additional new source of electron density data that is used to confirm FPMU is operating correctly and supplements the original environmental data taken by FPMU.

  14. Analysis of the IMAGE RPI electron density data and CHAMP plasmasphere electron density reconstructions with focus on plasmasphere modelling

    NASA Astrophysics Data System (ADS)

    Gerzen, T.; Feltens, J.; Jakowski, N.; Galkin, I.; Reinisch, B.; Zandbergen, R.

    2016-09-01

    The electron density of the topside ionosphere and the plasmasphere contributes essentially to the overall Total Electron Content (TEC) budget affecting Global Navigation Satellite Systems (GNSS) signals. The plasmasphere can cause half or even more of the GNSS range error budget due to ionospheric propagation errors. This paper presents a comparative study of different plasmasphere and topside ionosphere data aiming at establishing an appropriate database for plasmasphere modelling. We analyze electron density profiles along the geomagnetic field lines derived from the Imager for Magnetopause-to-Aurora Global Exploration (IMAGE) satellite/Radio Plasma Imager (RPI) records of remote plasma sounding with radio waves. We compare these RPI profiles with 2D reconstructions of the topside ionosphere and plasmasphere electron density derived from GNSS based TEC measurements onboard the Challenging Minisatellite Payload (CHAMP) satellite. Most of the coincidences between IMAGE profiles and CHAMP reconstructions are detected in the region with L-shell between 2 and 5. In general the CHAMP reconstructed electron densities are below the IMAGE profile densities, with median of the CHAMP minus IMAGE residuals around -588 cm-3. Additionally, a comparison is made with electron densities derived from passive radio wave RPI measurements onboard the IMAGE satellite. Over the available 2001-2005 period of IMAGE measurements, the considered combined data from the active and passive RPI operations cover the region within a latitude range of ±60°N, all longitudes, and an L-shell ranging from 1.2 to 15. In the coincidence regions (mainly 2 ⩽ L ⩽ 4), we check the agreement between available active and passive RPI data. The comparison shows that the measurements are well correlated, with a median residual of ∼52 cm-3. The RMS and STD values of the relative residuals are around 22% and 21% respectively. In summary, the results encourage the application of IMAGE RPI data for

  15. Assessing the effect of electron density in photon dose calculations

    SciTech Connect

    Seco, J.; Evans, P. M.

    2006-02-15

    Photon dose calculation algorithms (such as the pencil beam and collapsed cone, CC) model the attenuation of a primary photon beam in media other than water, by using pathlength scaling based on the relative mass density of the media to water. In this study, we assess if differences in the electron density between the water and media, with different atomic composition, can influence the accuracy of conventional photon dose calculations algorithms. A comparison is performed between an electron-density scaling method and the standard mass-density scaling method for (i) tissues present in the human body (such as bone, muscle, etc.), and for (ii) water-equivalent plastics, used in radiotherapy dosimetry and quality assurance. We demonstrate that the important material property that should be taken into account by photon dose algorithms is the electron density, and not the mass density. The mass-density scaling method is shown to overestimate, relative to electron-density predictions, the primary photon fluence for tissues in the human body and water-equivalent plastics, where 6%-7% and 10% differences were observed respectively for bone and air. However, in the case of patients, differences are expected to be smaller due to the large complexity of a treatment plan and of the patient anatomy and atomic composition and of the smaller thickness of bone/air that incident photon beams of a treatment plan may have to traverse. Differences have also been observed for conventional dose algorithms, such as CC, where an overestimate of the lung dose occurs, when irradiating lung tumors. The incorrect lung dose can be attributed to the incorrect modeling of the photon beam attenuation through the rib cage (thickness of 2-3 cm in bone upstream of the lung tumor) and through the lung and the oversimplified modeling of electron transport in convolution algorithms. In the present study, the overestimation of the primary photon fluence, using the mass-density scaling method, was shown

  16. Probabilistic Fatigue Life Analysis of High Density Electronics Packaging

    NASA Technical Reports Server (NTRS)

    Moore, N. R.; Kolawa, E. A.; Sutharshana, S.; Newlin, L. E.; Creager, M.

    1996-01-01

    The fatigue of thin film metal interconnections in high density electronics packaging subjected to thermal cycling has been evaluated using a probabilistic fracture mechanics methodology. This probabilistic methodology includes characterization of thin film stress using an experimentally calibrated finite element model and simulation of flaw growth in the thin films using a stochastic crack growth model.

  17. Extreme atmospheric electron densities created by extensive air showers

    NASA Astrophysics Data System (ADS)

    Rutjes, Casper; Camporeale, Enrico; Ebert, Ute; Buitink, Stijn; Scholten, Olaf; Trinh, Gia

    2016-04-01

    A sufficient density of free electrons and strong electric fields are the basic requirements to start any electrical discharge. In the context of thunderstorm discharges it has become clear that in addition droplets and or ice particles are required to enhance the electric field to values above breakdown. In our recent study [1] we have shown that these three ingredients have to interplay to allow for lightning inception, triggered by an extensive air shower event. The extensive air showers are a very stochastic natural phenomenon, creating highly coherent bursts of extreme electron density in our atmosphere. Predicting these electron density bursts accurately one has to take the uncertainty of the input variables into account. To this end we use uncertainty quantification methods, like in [2], to post-process our detailed Monte Carlo extensive air shower simulations, done with the CORSIKA [3] software package, which provides an efficient and elegant way to determine the distribution of the atmospheric electron density enhancements. We will present the latest results. [1] Dubinova, A., Rutjes, C., Ebert, E., Buitink, S., Scholten, O., and Trinh, G. T. N. "Prediction of Lightning Inception by Large Ice Particles and Extensive Air Showers." PRL 115 015002 (2015) [2] G.J.A. Loeven, J.A.S. Witteveen, H. Bijl, Probabilistic collocation: an efficient nonintrusive approach for arbitrarily distributed parametric uncertainties, 45th AIAA Aerospace Sciences Meeting, Reno, Nevada, 2007, AIAA-2007-317 [3] Heck, Dieter, et al. CORSIKA: A Monte Carlo code to simulate extensive air showers. No. FZKA-6019. 1998.

  18. Interferometric measurement of the electron density in a pseudospark switch

    SciTech Connect

    Goertler, A.; Schwandner, A.; Frank, K.; Christians