Science.gov

Sample records for 3d electronic states

  1. 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

  2. Electron collisions with Fe-peak elements: Forbidden transitions between the low lying valence states 3d{sup 6}, 3d{sup 5}4s, and 3d{sup 5}4p of Fe III

    SciTech Connect

    McLaughlin, B.M. . E-mail: b.mclaughlin@qub.ac.uk; Scott, M.P.; Sunderland, A.G.; Noble, C.J.; Burke, V.M.; Ramsbottom, C.A.; Reid, R.H.G.; Hibbert, A.; Bell, K.L.; Burke, P.G.

    2007-01-15

    Effective collision strengths are presented for the Fe-peak element Fe III at electron temperatures (T {sub e} in degrees Kelvin) in the range 2 x 10{sup 3} to 1 x 10{sup 6}. Forbidden transitions results are given between the 3d{sup 6}, 3d{sup 5}4s, and the 3d{sup 5}4p manifolds applicable to the modeling of laboratory and astrophysical plasmas.

  3. Positron annihilation study of the influence of doping on the 3 d electron states in the Ni3Al intermetallic compound

    NASA Astrophysics Data System (ADS)

    Druzhkov, A. P.; Perminov, D. A.; Stepanova, N. N.

    2010-10-01

    The 3 d electron states in Ni3Al single crystals doped with Fe, Co, and Nb have been investigated using angular correlation of annihilation radiation (ACAR). The ACAR spectra contain information on the momentum distribution of valence electrons and strongly bound 3 d electrons of the intermetallic compound. It has been established that the positrons in the Ni3Al crystals predominantly annihilate in the nickel sublattice from delocalized states. The doping of the compound by the third element leads to a variation in the momentum distribution of Ni 3 d electrons due to the change in the character of interatomic bonds. An analysis of the momentum distribution has demonstrated that the niobium atoms increase the covalent component of the chemical bond as compared to the binary compound due to the d Nb- d Ni hybridization. The doping with cobalt atoms also enhances the tendency toward the formation of the covalent bond. At the same time, iron atoms have a weak effect on the electronic structure of the intermetallic compound.

  4. 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%.

  5. Doubly-excited {sup 1,3}D{sup e} resonance states of two-electron positive ions Li{sup +} and Be{sup 2+} in Debye plasmas

    SciTech Connect

    Kar, Sabyasachi; Wang, Yang; Jiang, Zishi; Li, Shuxia; Ratnavelu, K.

    2014-01-15

    We investigate the bound {sup 1,3}D states and the doubly-excited {sup 1,3}D{sup e} resonance states of two-electron positive ions Li{sup +} and Be{sup 2+} by employing correlated exponential wave functions. In the framework of the stabilization method, we are able to extract three series (2pnp, 2snd, 2pnf) of {sup 1}D{sup e} resonances and two series (2pnp, 2snd) of {sup 3}D{sup e} resonances below the N = 2 threshold. The {sup 1,3}D{sup e} resonance parameters (resonance energies and widths) for Li{sup +} and Be{sup 2+} along with the bound-excited 1s3d {sup 1,3}D state energies are reported for the first time as functions of the screening parameter. Accurate resonance energies and widths are also reported for Li{sup +} and Be{sup 2+} in vacuum. For free-atomic cases, comparisons are made with the reported results and few resonance states are reported for the first time.

  6. Mediated resonance effect of the vanadium 3d states on phase stability in the Al8V5 γ -brass studied by first-principles FLAPW and LMTO-ASA electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Mizutani, U.; Asahi, R.; Sato, H.; Takeuchi, T.

    2006-12-01

    The mechanism for the stability of the Al8V5γ -brass containing 52 atoms in its cubic unit cell has been investigated by means of first-principles full-potential linearized augmented plane wave (FLAPW) and linearized muffin-tin orbital-atomic sphere approximation (LMTO-ASA) electronic structure calculations. The LMTO-ASA identified a deep valley at 0.5eV above the Fermi level in its density of states (DOS) as arising from orbital hybridizations between V 3d and Al 3p states. On the other hand, the FLAPW revealed the V 3d states mediated resonance of electrons with different sets of lattice planes. The resonance involved is found to be substantial not only at ∣G∣2=18 or {330} and {411} zones but also at those in the range 14⩽∣G∣2⩽30 . A comparison with the electronic structure of the CsCl-type AlV compound proved that the V 3d states mediated resonance occurs only in Al8V5 but not in AlV compound. The V 3d states mediated resonance is proved to result in a significant suppression of the sp -partial DOS over the energy range from the Fermi level up to +2.2eV . A gain in the electronic energy has been attributed to the formation of highly condensed bonding states below the Fermi level, again caused by the V 3d states mediated resonance. It is also proposed that the Al8V5 is stabilized at e/a=1.94 rather than 21/13 as is expected from the Hume-Rothery electron concentration rule.

  7. Singlet-triplet energy splitting between 1D and 3D (1s2 2s nd), n = 3, 4, 5, and 6, Rydberg states of the beryllium atom (9Be) calculated with all-electron explicitly correlated Gaussian functions

    NASA Astrophysics Data System (ADS)

    Sharkey, Keeper L.; Bubin, Sergiy; Adamowicz, Ludwik

    2014-11-01

    Accurate variational nonrelativistic quantum-mechanical calculations are performed for the five lowest 1D and four lowest 3D states of the 9Be isotope of the beryllium atom. All-electron explicitly correlated Gaussian (ECG) functions are used in the calculations and their nonlinear parameters are optimized with the aid of the analytical energy gradient determined with respect to these parameters. The effect of the finite nuclear mass is directly included in the Hamiltonian used in the calculations. The singlet-triplet energy gaps between the corresponding 1D and 3D states, are reported.

  8. Stability and electronic properties of 3D covalent organic frameworks.

    PubMed

    Lukose, Binit; Kuc, Agnieszka; Heine, Thomas

    2013-05-01

    Covalent organic frameworks (COFs) are a class of covalently linked crystalline nanoporous materials, versatile for nanoelectronic and storage applications. 3D COFs, in particular, have very large pores and low mass densities. Extensive theoretical studies of their energetic and mechanical stability, as well as their electronic properties, have been carried out for all known 3D COFs. COFs are energetically stable and their bulk modulus ranges from 3 to 20 GPa. Electronically, all COFs are semiconductors with band gaps corresponding to the HOMO-LUMO gaps of the building units. PMID:23212235

  9. Decay pathways after Xe 3d inner shell ionization using a multi-electron coincidence technique

    NASA Astrophysics Data System (ADS)

    Suzuki, I. H.; Hikosaka, Y.; Shigemasa, E.; Lablanquie, P.; Penent, F.; Soejima, K.; Nakano, M.; Kouchi, N.; Ito, K.

    2011-04-01

    Cascade Auger electron emission following Xe 3d photoionization has been investigated using a multi-electron coincidence technique, which utilizes an electron spectrometer of magnetic bottle type. It has been found that the Xe2+ states of the 4p-14d-1 configuration, formed by the Auger decay of the Xe+ 3d3/2, 5/2-1 states, dominantly turn into triply charged states of the 4d-25p-1/4d-25s-1 configurations. The Xe2+ 4s-14d-1 states, formed by the 3d Auger decay, yield the 4p-14d-15p-1 states as well as the 4d-3 states. From the coincidence spectrum among three Auger electrons, it is suggested that the Xe2+ 4p-14d-1 states give rise to the following cascade processes: 4p-14d-1 → 4d-25p-1 → 4d-15p-3.

  10. 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.

  11. Correlated electron pseudopotentials for 3d-transition metals

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

    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.

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

    PubMed

    McLeod, J A; Buling, A; Green, R J; Boyko, T D; Skorikov, N A; Kurmaev, E Z; Neumann, M; Finkelstein, L D; Ni, N; Thaler, A; Bud'ko, S L; Canfield, P C; Moewes, A

    2012-05-30

    The electronic structure of BaFe(2)As(2) 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 3d(10) shell. These findings help shed light on why superconductivity can occur in BaFe(2)As(2) doped with Co and Ni but not Cu. PMID:22534111

  13. 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.

  14. 3D Visualization of the Iron Oxidation State in FeO/Fe3O4 Core-Shell Nanocubes from Electron Energy Loss Tomography.

    PubMed

    Torruella, Pau; Arenal, Raúl; de la Peña, Francisco; Saghi, Zineb; Yedra, Lluís; Eljarrat, Alberto; López-Conesa, Lluís; Estrader, Marta; López-Ortega, Alberto; Salazar-Alvarez, Germán; Nogués, Josep; Ducati, Caterina; Midgley, Paul A; Peiró, Francesca; Estradé, Sonia

    2016-08-10

    The physicochemical properties used in numerous advanced nanostructured devices are directly controlled by the oxidation states of their constituents. In this work we combine electron energy-loss spectroscopy, blind source separation, and computed tomography to reconstruct in three dimensions the distribution of Fe(2+) and Fe(3+) ions in a FeO/Fe3O4 core/shell cube-shaped nanoparticle with nanometric resolution. The results highlight the sharpness of the interface between both oxides and provide an average shell thickness, core volume, and average cube edge length measurements in agreement with the magnetic characterization of the sample. PMID:27383904

  15. 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.

  16. 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.

  17. Atomic-Resolution 3D Electron Microscopy with Dynamic Diffraction

    SciTech Connect

    O'Keefe, Michael A.; Downing, Kenneth H.; Wenk, Hans-Rudolf; Meisheng, Hu

    2005-02-15

    Achievement of atomic-resolution electron-beam tomography will allow determination of the three-dimensional structure of nanoparticles (and other suitable specimens) at atomic resolution. Three-dimensional reconstructions will yield ''section'' images that resolve atoms overlapped in normal electron microscope images (projections), resolving lighter atoms such as oxygen in the presence of heavier atoms, and atoms that lie on non-lattice sites such as those in non-periodic defect structures. Lower-resolution electron microscope tomography has been used to produce reconstructed 3D images of nanoparticles [1] but extension to atomic resolution is considered not to be straightforward. Accurate three-dimensional reconstruction from two-dimensional projections generally requires that intensity in the series of 2-D images be a monotonic function of the specimen structure (often specimen density, but in our case atomic potential). This condition is not satisfied in electron microscopy when specimens with strong periodicity are tilted close to zone-axis orientation and produce ''anomalous'' image contrast because of strong dynamic diffraction components. Atomic-resolution reconstructions from tilt series containing zone-axis images (with their contrast enhanced by strong dynamical scattering) can be distorted when the stronger zone-axis images overwhelm images obtained in other ''random'' orientations in which atoms do not line up in neat columns. The first demonstrations of 3-D reconstruction to atomic resolution used five zone-axis images from test specimens of staurolite consisting of a mix of light and heavy atoms [2,3]. Initial resolution was to the 1.6{angstrom} Scherzer limit of a JEOL-ARM1000. Later experiments used focal-series reconstruction from 5 to 10 images to produce staurolite images from the ARM1000 with resolution extended beyond the Scherzer limit to 1.38{angstrom} [4,5]. To obtain a representation of the three-dimensional structure, images were obtained

  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. 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

  20. 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

  1. Ground-state rotational constants of 12CH 3D

    NASA Astrophysics Data System (ADS)

    Chackerian, C.; Guelachvili, G.

    1980-12-01

    An analysis of ground-state combination differences in the ν2( A1) fundamental band of 12CH 3D ( ν0 = 2200.03896 cm -1) has been made to yield values for the rotational constants B0, D0J, D0JK, H0JJJ, H0JJK, H0JKK, LJJJJ, L0JJJK, and order of magnitude values for L0JJKK and L0JKKK. These constants should be useful in assisting radio searches for this molecule in astrophysical sources. In addition, splittings of A1A2 levels ( J ≥ 17, K = 3) have been measured in both the ground and excited vibrational states of this band.

  2. 3D imaging by serial block face scanning electron microscopy for materials science using ultramicrotomy.

    PubMed

    Hashimoto, Teruo; Thompson, George E; Zhou, Xiaorong; Withers, Philip J

    2016-04-01

    Mechanical serial block face scanning electron microscopy (SBFSEM) has emerged as a means of obtaining three dimensional (3D) electron images over volumes much larger than possible by focused ion beam (FIB) serial sectioning and at higher spatial resolution than achievable with conventional X-ray computed tomography (CT). Such high resolution 3D electron images can be employed for precisely determining the shape, volume fraction, distribution and connectivity of important microstructural features. While soft (fixed or frozen) biological samples are particularly well suited for nanoscale sectioning using an ultramicrotome, the technique can also produce excellent 3D images at electron microscope resolution in a time and resource-efficient manner for engineering materials. Currently, a lack of appreciation of the capabilities of ultramicrotomy and the operational challenges associated with minimising artefacts for different materials is limiting its wider application to engineering materials. Consequently, this paper outlines the current state of the art for SBFSEM examining in detail how damage is introduced during slicing and highlighting strategies for minimising such damage. A particular focus of the study is the acquisition of 3D images for a variety of metallic and coated systems. PMID:26855205

  3. 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.

  4. Contiguous 3 d and 4 f Magnetism: Strongly Correlated 3 d Electrons in YbFe2Al10

    NASA Astrophysics Data System (ADS)

    Khuntia, P.; Peratheepan, P.; Strydom, A. M.; Utsumi, Y.; Ko, K.-T.; Tsuei, K.-D.; Tjeng, L. H.; Steglich, F.; Baenitz, M.

    2014-11-01

    We present magnetization, specific heat, and Al 27 NMR investigations on YbFe2Al10 over a wide range in temperature and magnetic field. The magnetic susceptibility at low temperatures is strongly enhanced at weak magnetic fields, accompanied by a ln (T0/T ) divergence of the low-T specific heat coefficient in zero field, which indicates a ground state of correlated electrons. From our hard-x-ray photoemission spectroscopy study, the Yb valence at 50 K is evaluated to be 2.38. The system displays valence fluctuating behavior in the low to intermediate temperature range, whereas above 400 K, Yb3 + carries a full and stable moment, and Fe carries a moment of about 3.1 μB. The enhanced value of the Sommerfeld-Wilson ratio and the dynamic scaling of the spin-lattice relaxation rate divided by T [(1 /T1T ) 27 ] with static susceptibility suggests admixed ferromagnetic correlations. (1 /T1T ) 27 simultaneously tracks the valence fluctuations from the 4 f Yb ions in the high temperature range and field dependent antiferromagnetic correlations among partially Kondo screened Fe 3 d moments at low temperature; the latter evolve out of an Yb 4 f admixed conduction band.

  5. State-Of of 3d National Mapping in 2016

    NASA Astrophysics Data System (ADS)

    Stoter, Jantien; Vallet, Bruno; Lithen, Thomas; Pla, Maria; Wozniak, Piotr; Kellenberger, Tobias; Streilein, Andre; Ilves, Risto; Ledoux, Hugo

    2016-06-01

    Techniques for 3D mapping are maturing. At the same time the need for 3D data is increasing. This has pushed national (and regional) mapping agencies (NMAs) to consider extending their traditional task of providing topographic data into the third dimension. To show how research results in 3D mapping obtained over the past twenty years have been adopted by practice, this paper presents the ongoing work on 3D mapping within seven NMAs, all member of the 3D Special Interest Group of European Spatial Data Research (EuroSDR). The paper shows that some NMAs are still in the initial (experimental) phase of 3D mapping, while others have already built solid databases to maintain 2.5D and 3D topographic data covering their whole country.

  6. Methods For Electronic 3-D Moving Pictures Without Glasses

    NASA Astrophysics Data System (ADS)

    Collender, Robert B.

    1987-06-01

    This paper describes implementation approaches in image acquisition and playback for 3-D computer graphics, 3-D television and 3-D theatre movies without special glasses. Projection lamps, spatial light modulators, CRT's and dynamic scanning are all eliminated by the application of an active image array, all static components and a semi-specular screen. The resulting picture shows horizontal parallax with a wide horizontal view field (up to 360 de-grees) giving a holographic appearance in full color with smooth continuous viewing without speckle. Static component systems are compared with dynamic component systems using both linear and circular arrays. Implementation of computer graphic systems are shown that allow complex shaded color images to extend from the viewer's eyes to infinity. Large screen systems visible by hundreds of people are feasible by the use of low f-stops and high gain screens in projection. Screen geometries and special screen properties are shown. Viewing characteristics offer no restrictions in view-position over the entire view-field and have a "look-around" feature for all the categories of computer graphics, television and movies. Standard video cassettes and optical discs can also interface the system to generate a 3-D window viewable without glasses. A prognosis is given for technology application to 3-D pictures without glasses that replicate the daily viewing experience. Super-position of computer graphics on real-world pictures is shown feasible.

  7. 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.

  8. 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.

  9. Solid state light source for wavelength multiplex 3D

    NASA Astrophysics Data System (ADS)

    Huang, Junejei

    2012-10-01

    A solid state light source provided for wavelength multiplex 3D Display is proposed. The system of solid state light source includes blue laser arrays of two wavelengths, a 2-ring phosphor wheel, a multi-band filter and a TIR prism. Green and red phosphors excited by blue lasers provide the original green and red lights of wide bandwidth. By passing through or reflected by a multi-band filter, two groups of green and red lights of narrow bandwidth for left or right eyes are selected. Blue lasers of two wavelengths also provide two blue lights for left and right eyes. Instead of using a second rotated narrow band filters that synchronized with the first phosphor wheel, a wheel having two rings coated with mirrors and phosphors is used to replace the synchronization existing in the conventional two wheels method. After passing the 2-ring wheel, the light source switches between two light paths that lead to be reflected or transmitting through the multiband filter. The multi-band filter can be disposed in a telecentric optical path to secure a high efficiency for the filter. A compact spectral multiplex light source is realized and can be directly attached to any existing optical engine.

  10. Research on steady-state visual evoked potentials in 3D displays

    NASA Astrophysics Data System (ADS)

    Chien, Yu-Yi; Lee, Chia-Ying; Lin, Fang-Cheng; Huang, Yi-Pai; Ko, Li-Wei; Shieh, Han-Ping D.

    2015-05-01

    Brain-computer interfaces (BCIs) are intuitive systems for users to communicate with outer electronic devices. Steady state visual evoked potential (SSVEP) is one of the common inputs for BCI systems due to its easy detection and high information transfer rates. An advanced interactive platform integrated with liquid crystal displays is leading a trend to provide an alternative option not only for the handicapped but also for the public to make our lives more convenient. Many SSVEP-based BCI systems have been studied in a 2D environment; however there is only little literature about SSVEP-based BCI systems using 3D stimuli. 3D displays have potentials in SSVEP-based BCI systems because they can offer vivid images, good quality in presentation, various stimuli and more entertainment. The purpose of this study was to investigate the effect of two important 3D factors (disparity and crosstalk) on SSVEPs. Twelve participants participated in the experiment with a patterned retarder 3D display. The results show that there is a significant difference (p-value<0.05) between large and small disparity angle, and the signal-to-noise ratios (SNRs) of small disparity angles is higher than those of large disparity angles. The 3D stimuli with smaller disparity and lower crosstalk are more suitable for applications based on the results of 3D perception and SSVEP responses (SNR). Furthermore, we can infer the 3D perception of users by SSVEP responses, and modify the proper disparity of 3D images automatically in the future.

  11. Magnetocentrifugal Winds in 3D: Nonaxisymmetric Steady State

    SciTech Connect

    Anderson, Jeffrey M.; Li, Zhi-Yun; Krasnopolsky, Ruben; Blandford, Roger D.; /SLAC

    2006-11-28

    Outflows can be loaded and accelerated to high speeds along rapidly rotating, open magnetic field lines by centrifugal forces. Whether such magnetocentrifugally driven winds are stable is a longstanding theoretical problem. As a step towards addressing this problem, we perform the first large-scale 3D MHD simulations that extend to a distance {approx} 10{sup 2} times beyond the launching region, starting from steady 2D (axisymmetric) solutions. In an attempt to drive the wind unstable, we increase the mass loading on one half of the launching surface by a factor of {radical}10, and reduce it by the same factor on the other half. The evolution of the perturbed wind is followed numerically. We find no evidence for any rapidly growing instability that could disrupt the wind during the launching and initial phase of propagation, even when the magnetic field of the magnetocentrifugal wind is toroidally dominated all the way to the launching surface. The strongly perturbed wind settles into a new steady state, with a highly asymmetric mass distribution. The distribution of magnetic field strength is, in contrast, much more symmetric. We discuss possible reasons for the apparent stability, including stabilization by an axial poloidal magnetic field, which is required to bend field lines away from the vertical direction and produce a magnetocentrifugal wind in the first place.

  12. 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.

  13. 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.

  14. Dynamics of electronically inelastic collisions from 3D Doppler measurements

    SciTech Connect

    Suits, A.G.; de Pujo, P.; Sublemontier, O.; Visticot, J.; Berlande, J.; Cuvellier, J.; Gustavsson, T.; Mestdagh, J.; Meynadier, P. ); Lee, Y.T. )

    1991-11-25

    Flux-velocity contour maps were obtained for the inelastic collision process Ba({sup 1}{ital P}{sub 1})+O{sub 2}N{sub 2}{r arrow}Ba({sup 3}{ital P}{sub 2})+O{sub 2}N{sub 2} from Doppler scans of scattered Ba({sup 3}{ital P}{sub 2}) taken over a range of probe laser directions in a crossed-beam experiment. Collision with O{sub 2} resulted in sharply forward scattered Ba({sup 3}{ital P}{sub 2}), with efficient conversion of inital electronic energy into O{sub 2} internal energy and little momentum transfer. Collision with N{sub 2} was dominated by wide-angle scattering with most of the available electronic energy appearing in product translation. The results suggest the importance of large-impact-parameter collisions and a near-resonant energy transfer in the case of O{sub 2}, while for N{sub 2} close collisions dominate despite the presence of an analogous near-resonant channel. The results represent the first direct experimental demonstration of a near-resonant quenching process.

  15. Surface states in a 3D topological insulator: The role of hexagonal warping and curvature

    SciTech Connect

    Repin, E. V.; Burmistrov, I. S.

    2015-09-15

    We explore a combined effect of hexagonal warping and a finite effective mass on both the tunneling density of electronic surface states and the structure of Landau levels of 3D topological insulators. We find the increasing warping to transform the square-root van Hove singularity into a logarithmic one. For moderate warping, an additional logarithmic singularity and a jump in the tunneling density of surface states appear. By combining the perturbation theory and the WKB approximation, we calculate the Landau levels in the presence of hexagonal warping. We predict that due to the degeneracy removal, the evolution of Landau levels in the magnetic field is drastically modified.

  16. 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.

  17. Tracking 3D Picometer-Scale Motions of Single Nanoparticles with High-Energy Electron Probes

    PubMed Central

    Ogawa, Naoki; Hoshisashi, Kentaro; Sekiguchi, Hiroshi; Ichiyanagi, Kouhei; Matsushita, Yufuku; Hirohata, Yasuhisa; Suzuki, Seiichi; Ishikawa, Akira; Sasaki, Yuji C.

    2013-01-01

    We observed the high-speed anisotropic motion of an individual gold nanoparticle in 3D at the picometer scale using a high-energy electron probe. Diffracted electron tracking (DET) using the electron back-scattered diffraction (EBSD) patterns of labeled nanoparticles under wet-SEM allowed us to super-accurately measure the time-resolved 3D motion of individual nanoparticles in aqueous conditions. The highly precise DET data corresponded to the 3D anisotropic log-normal Gaussian distributions over time at the millisecond scale. PMID:23868465

  18. 3D Printing of Shape Memory Polymers for Flexible Electronic Devices.

    PubMed

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

    2016-06-01

    The formation of 3D objects composed of shape memory polymers for flexible electronics is described. Layer-by-layer photopolymerization of methacrylated semicrystalline molten macromonomers by a 3D digital light processing printer enables rapid fabrication of complex objects and imparts shape memory functionality for electrical circuits. PMID:26402320

  19. 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. PMID:25730881

  20. 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

  1. 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.

  2. 3D strain measurement in electronic devices using through-focal annular dark-field imaging.

    PubMed

    Kim, Suhyun; Jung, Younheum; Lee, Sungho; Jung Kim, Joong; Byun, Gwangseon; Lee, Sunyoung; Lee, Haebum

    2014-11-01

    Spherical aberration correction in high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) allows us to form an electron probe with reduced depth of field. Using through-focal HAADF imaging, we experimentally demonstrated 3D strain measurement in a strained-channel transistor. The strain field distribution in the channel region was obtained by scanning an electron beam over a plan-view specimen. Furthermore, the decrease in the strain fields toward the silicon substrate was revealed at different focal planes with a 5-nm focal step. These results demonstrate that it is possible to reconstruct the 3D strain field in electronic devices. PMID:24859824

  3. State of the art of 3D scanning systems and inspection of textile surfaces

    NASA Astrophysics Data System (ADS)

    Montilla, M.; Orjuela-Vargas, S. A.; Philips, W.

    2014-02-01

    The rapid development of hardware and software in the digital image processing field has boosted research in computer vision for applications in industry. The development of new electronic devices and the tendency to decrease their prices makes possible new developments that few decades ago were possible only in the imagination. This is the case of 3D imaging technology which permits to detect failures in industrial products by inspecting aspects on their 3D surface. In search of an optimal solution for scanning textiles we present in this paper a review of existing techniques for digitizing 3D surfaces. Topographic details of textiles can be obtained by digitizing surfaces using laser line triangulation, phase shifting optical triangulation, projected-light, stereo-vision systems and silhouette analysis. Although we are focused on methods that have been used in the textile industry, we also consider potential mechanisms used for other applications. We discuss the advantages and disadvantages of the evaluated methods and state a summary of potential implementations for the textile industry.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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

  9. Skyrmion-induced bound states on the surface of 3D Topological Insulators

    NASA Astrophysics Data System (ADS)

    Andrikopoulos, Dimitrios; Soree, Bart

    In this work, we study the interaction between the surface state of a 3D Topological Insulator and a skyrmion magnetic texture. The skyrmion texture couples to the spin of the surface state electron with strength ΔS. Vortex and hedgehog skyrmion and anti-skyrmion structures are considered and their interaction is compared. Due to the vortex structure, the interaction of the in-plane components can be neglected and a step function is used to describe the skyrmion magnetization profile. In the hedgehog case, it is shown that the in-plane components cannot be disregarded and thus a realistic description for the skyrmion is required. Working in the micromagnetic framework, we derive a macrospin description for the skyrmion using the variational principle and then numerically solve for the bound states. It is shown that the existense and properties of these states as a function of skyrmion size, strongly depend on the skyrmion type. Both vortex and hedgehog skyrmions or anti-skyrmions can induce bound states with energies | E | < ΔS . For the hedgehog skyrmion case however, bound state appearance depends on the chirality. Finally, the probability densities in these states are computed and it is demonstrated that the electrons are localized throughout the skyrmion region. Also affiliated with imec, Belgium.

  10. 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.

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

    PubMed

    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. PMID:27454835

  12. Magnetism and superconductivity at LAO/STO-interfaces: the role of Ti 3d interface electrons

    NASA Astrophysics Data System (ADS)

    Pavlenko, Natalia; Kopp, Thilo; Tsymbal, E. Y.; Sawatzky, G. A.; Mannhart, Jochen

    2012-02-01

    Ferromagnetism and superconductivity are in most cases adverse. However, recent experiments reveal that they coexist at interfaces of LaAlO3 and SrTiO3 [1]. We analyze the ferromagnetic state within density functional theory and provide evidence that it is also generated by Ti 3d interface electrons, as is the two-dimensional electron liquid at the interface which gives rise to superconductivity [2]. We demonstrate that oxygen vacancies in the TiO2 interface layer enhance the tendency for ferromagnetism considerably. This allows for the notion that areas with increased density of oxygen vacancies produce ferromagnetic puddles and account for the previous observation of a superparamagnetic behavior in the superconducting state [3].[4pt] [1] Lu Li, C.Richter, J.Mannhart, and R.C.Ashoori, Nature Physics 7, 762 (2011).[0pt] [2] N. Reyren et al., Science 317, 1196 (2007).[0pt] [3] N.Pavlenko, T.Kopp, E.Y.Tsymbal, G.A.Sawatzky, and J.Mannhart, cond-mat/arXiv:1105.1163 (2011)

  13. State-of-The-Art and Applications of 3D Imaging Sensors in Industry, Cultural Heritage, Medicine, and Criminal Investigation

    PubMed Central

    Sansoni, Giovanna; Trebeschi, Marco; Docchio, Franco

    2009-01-01

    3D imaging sensors for the acquisition of three dimensional (3D) shapes have created, in recent years, a considerable degree of interest for a number of applications. The miniaturization and integration of the optical and electronic components used to build them have played a crucial role in the achievement of compactness, robustness and flexibility of the sensors. Today, several 3D sensors are available on the market, even in combination with other sensors in a “sensor fusion” approach. An importance equal to that of physical miniaturization has the portability of the measurements, via suitable interfaces, into software environments designed for their elaboration, e.g., CAD-CAM systems, virtual renders, and rapid prototyping tools. In this paper, following an overview of the state-of-art of 3D imaging sensors, a number of significant examples of their use are presented, with particular reference to industry, heritage, medicine, and criminal investigation applications. PMID:22389618

  14. State-of-The-Art and Applications of 3D Imaging Sensors in Industry, Cultural Heritage, Medicine, and Criminal Investigation.

    PubMed

    Sansoni, Giovanna; Trebeschi, Marco; Docchio, Franco

    2009-01-01

    3D imaging sensors for the acquisition of three dimensional (3D) shapes have created, in recent years, a considerable degree of interest for a number of applications. The miniaturization and integration of the optical and electronic components used to build them have played a crucial role in the achievement of compactness, robustness and flexibility of the sensors. Today, several 3D sensors are available on the market, even in combination with other sensors in a "sensor fusion" approach. An importance equal to that of physical miniaturization has the portability of the measurements, via suitable interfaces, into software environments designed for their elaboration, e.g., CAD-CAM systems, virtual renders, and rapid prototyping tools. In this paper, following an overview of the state-of-art of 3D imaging sensors, a number of significant examples of their use are presented, with particular reference to industry, heritage, medicine, and criminal investigation applications. PMID:22389618

  15. 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.

  16. 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

  17. 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

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

    PubMed Central

    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

  19. Poly 3D fault modeling scripts/data for permeability potential of Washington State geothermal prospects

    DOE Data Explorer

    Michael Swyer

    2015-02-05

    Matlab scripts/functions and data used to build Poly3D models and create permeability potential GIS layers for 1) Mount St Helen's, 2) Wind River Valley, and 3) Mount Baker geothermal prospect areas located in Washington state.

  20. Moment coupling in the interaction of atoms and their ions with a 3d-electron shell

    SciTech Connect

    Kosarim, A. V.; Smirnov, B. M.; Capitelli, M.; Laricchiuta, A.

    2011-09-15

    The moment coupling of an interacting ion and an atom with a 3d-electron shell is analyzed for the ground state of identical atoms and ions where resonant charge exchange proceeds with transition of a 4s-electron. The interaction of the ion charge with the atom quadrupole moment is important for this system along with the exchange interactions and spin-orbit interactions inside an isolated atom and an ion. The quadrupole moment for 3d-atoms in the ground states is evaluated. The hierarchy of interactions in a molecular ion is analyzed depending on ion-atom distances and is compared with the standard Hund scheme. The resonant charge exchange proceeds effectively at separations corresponding to an intermediate case between cases 'a' and 'c' of the Hund coupling scheme.

  1. 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.

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

    PubMed

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

    2016-06-28

    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. In part, this is due 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. 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. Using this approach, we demonstrate the fabrication of various 3D lattice structures using Pt-, Au-, and W-based precursors. PMID:27284689

  3. Electronic and spectroscopic properties of early 3d metal atoms on a graphite surface

    NASA Astrophysics Data System (ADS)

    Rakotomahevitra, A.; Garreau, G.; Demangeat, C.; Parlebas, J. C.

    1995-07-01

    High-sensitivity magneto-optic Kerr effect experiments failed to detect manifestations of magnetism in epitaxial films of V on Ag(100) substrates. More recently V 3s XPS of freshly evaporated V clusters on graphite exhibited the appearance of a satellite structure which has then been interpreted by the effect of surface magnetic moments on V. It is the absence of unambiguous results on the electronic properties of early 3d supported metals that prompts us to examine the problem. Our purpose is twofold. In a first part, after a total energy calculation within a tight-binding method which yields the equilibrium position of a given adatom, we use the Hartree-Fock approximation to find out a possible magnetic solution of V (or Cr) upon graphite for a reasonable value of the exchange integral Jdd. In a second part the informations given by the density of states of the graphite surface as well as the additional states of the adsorbed atom are taken into account through a generalised impurity Anderson Hamiltonian which incorporates the various Coulomb and exchange interactions necessary to analyse the 3s XPS results.

  4. Dynamic scattering theory for dark-field electron holography of 3D strain fields.

    PubMed

    Lubk, Axel; Javon, Elsa; Cherkashin, Nikolay; Reboh, Shay; Gatel, Christophe; Hÿtch, Martin

    2014-01-01

    Dark-field electron holography maps strain in crystal lattices into reconstructed phases over large fields of view. Here we investigate the details of the lattice strain-reconstructed phase relationship by applying dynamic scattering theory both analytically and numerically. We develop efficient analytic linear projection rules for 3D strain fields, facilitating a straight-forward calculation of reconstructed phases from 3D strained materials. They are used in the following to quantify the influence of various experimental parameters like strain magnitude, specimen thickness, excitation error and surface relaxation. PMID:24012934

  5. Carbon nanotube based 3-D matrix for enabling three-dimensional nano-magneto-electronics [corrected].

    PubMed

    Hong, Jeongmin; Stefanescu, Eugenia; Liang, Ping; Joshi, Nikhil; Xue, Song; Litvinov, Dmitri; Khizroev, Sakhrat

    2012-01-01

    This letter describes the use of vertically aligned carbon nanotubes (CNT)-based arrays with estimated 2-nm thick cobalt (Co) nanoparticles deposited inside individual tubes to unravel the possibility of using the unique templates for ultra-high-density low-energy 3-D nano-magneto-electronic devices. The presence of oriented 2-nm thick Co layers within individual nanotubes in the CNT-based 3-D matrix is confirmed through VSM measurements as well as an energy-dispersive X-ray spectroscopy (EDS). PMID:22808192

  6. 3D imaging of the early embryonic chicken heart with focused ion beam scanning electron microscopy

    PubMed Central

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

    2015-01-01

    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 focused ion beam, 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 (TEM). Up to 1100 serial images were obtained in 4 nm increments at 4.88 nm resolution, and image stacks were aligned to create volumes 800–1500 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. PMID:24742339

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

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

    DOE PAGESBeta

    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

  14. 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

  15. 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.

  16. 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

  17. Investigation of Charge Gain in Diamond Electron Beam Amplifiers Via 3D Simulations

    SciTech Connect

    Busby,R.; Rao,T.; D.A. Dimitrov, J.R. Cary, I. Ben-Zvi, X. Chang, J. Keister, E. Muller, J. Smedley, Q. Wu

    2009-05-04

    A promising new concept of a diamond amplified photocathode for generation of high-current, high-brightness, and low thermal emittance electron beams was recently proposed and is currently under active development. To better understand the different effects involved in the generation ofelectron beams from diamond, we have been developing models (within the VORPAL computational framework) to simulate secondary electron generation and charge transport. The currently implemented models include inelastic scattering of electrons and holes for generation of electron-hole pairs, elastic, phonon, and charge impurity scattering. We will present results from 3D VORPAL simulations with these capabilities on charge gain as a function of primary electron energy and applied electric field. Moreover, we consider effects of electron and hole cloud expansion (initiated by primary electrons) and separation in a surface domain of diamond.

  18. RKKY interaction in P-N junction based on surface states of 3D topological insulator

    NASA Astrophysics Data System (ADS)

    Zhang, Shuhui; Yang, Wen; Chang, Kai

    The RKKY interaction mediated by conduction electrons supplies a mechanism to realize the long-range coupling of localized spins which is desired for the spin devices. Here, we examine the controllability of RKKY interaction in P-N junction (PNJ) based on surface states of 3D topological insulator (3DTI). In this study, through quantum way but not usual classical analogy to light propagation, the intuitive picture for electron waves across the interface of PNJ is obtained, e.g., Klein tunneling, negative refraction and focusing. Moreover, we perform the numerical calculations for all kinds of RKKY interaction including the Heisenberg, Ising, and Dzyaloshinskii-Moriya terms. We find the focusing of surface states leads to the local augmentation of RKKY interaction. Most importantly, a dimension transition occurs, i.e., the decay rate of RKKY interaction from the deserved 1/R 2 to 1/ R . In addition, the quadratic gate-dependence of RKKY interaction is also beneficial to the application of 3DTI PNJ in the fields of spintronics and quantum computation. This work was supported by the MOST (Grant No. 2015CB921503, and No. 2014CB848700) and NSFC (Grant No. 11434010, No. 11274036, No. 11322542, and No. 11504018).

  19. Study of Electron Acceleration and Multiple Dipolarization Fronts in 3D kinetic models

    NASA Astrophysics Data System (ADS)

    Lapenta, Giovanni; Ashour-Abdalla, Maha; Walker, Raymond; El-Alaoui, Mostafa

    2014-05-01

    The THEMIS mission encountered a depolarization front (DF) during a magnetotail crossing in the interval 035600 - 035900 UT on February 15, 2008 [1]. We present the results of an innovative investigative approach: we combine a global MHD model of the full Earth environment with a local PIC simulation. The global MHD view is provided on the UCLA model applied to the conditions for the interval of interest on Feb 15, 2008. At the specific time of 034800UT, a reconnection site first appear at about x=-15RE, y=4RE. We then use this specific MHD state as the initial setup for a fully kinetic PIC simulation, performed with the iPic3D code [2]. We consider a one way coupling where the MHD state is used as initial state and boundary conditions for the kinetic study [3]. In the present case, the time span of the kinetic simulation is short form the perspective of the global MHD simulation and does not require a full coupling where the MHD then process the information received back from the kinetic run [4]. The fields and particles are advanced self-consistently from the MHD state using a completely kinetic treatment. Many features missed by the MHD model emerge. Most notably a fast reconnection pattern develops and an unsteady reconnection process develops. The typical signatures of fast kinetic reconnection (Hall field) are observed and particle acceleration is obtained self consistently in the fields generated by the PIC simulation. The focus of the presentation will be the mechanisms of unsteady reconnection leading to multiple DFs. We observe intense wave activity propagating off the separatrices. We conduct a spectral analysis to isolate the different wave components in the lower hybrid and whistler regime. The unsteady reconnection and multiple DFs are also analysed in their impact on the energy transfer. We track the conversion of magnetic energy to particle energy and Poynting flux. The processes observed in the simulation are then compared with in situ THEMIS data

  20. 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography

    PubMed Central

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

    2015-01-01

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions. PMID:25940394

  1. 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.

  2. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGESBeta

    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

  3. 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.

  4. 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.

  5. Finite-element 3D simulation tools for high-current relativistic electron beams

    NASA Astrophysics Data System (ADS)

    Humphries, Stanley; Ekdahl, Carl

    2002-08-01

    The DARHT second-axis injector is a challenge for computer simulations. Electrons are subject to strong beam-generated forces. The fields are fully three-dimensional and accurate calculations at surfaces are critical. We describe methods applied in OmniTrak, a 3D finite-element code suite that can address DARHT and the full range of charged-particle devices. The system handles mesh generation, electrostatics, magnetostatics and self-consistent particle orbits. The MetaMesh program generates meshes of conformal hexahedrons to fit any user geometry. The code has the unique ability to create structured conformal meshes with cubic logic. Organized meshes offer advantages in speed and memory utilization in the orbit and field solutions. OmniTrak is a versatile charged-particle code that handles 3D electric and magnetic field solutions on independent meshes. The program can update both 3D field solutions from the calculated beam space-charge and current-density. We shall describe numerical methods for orbit tracking on a hexahedron mesh. Topics include: 1) identification of elements along the particle trajectory, 2) fast searches and adaptive field calculations, 3) interpolation methods to terminate orbits on material surfaces, 4) automatic particle generation on multiple emission surfaces to model space-charge-limited emission and field emission, 5) flexible Child law algorithms, 6) implementation of the dual potential model for 3D magnetostatics, and 7) assignment of charge and current from model particle orbits for self-consistent fields.

  6. Preservation of protein fluorescence in embedded human dendritic cells for targeted 3D light and electron microscopy.

    PubMed

    Höhn, K; Fuchs, J; Fröber, A; Kirmse, R; Glass, B; Anders-Össwein, M; Walther, P; Kräusslich, H-G; Dietrich, C

    2015-08-01

    In this study, we present a correlative microscopy workflow to combine detailed 3D fluorescence light microscopy data with ultrastructural information gained by 3D focused ion beam assisted scanning electron microscopy. The workflow is based on an optimized high pressure freezing/freeze substitution protocol that preserves good ultrastructural detail along with retaining the fluorescence signal in the resin embedded specimens. Consequently, cellular structures of interest can readily be identified and imaged by state of the art 3D confocal fluorescence microscopy and are precisely referenced with respect to an imprinted coordinate system on the surface of the resin block. This allows precise guidance of the focused ion beam assisted scanning electron microscopy and limits the volume to be imaged to the structure of interest. This, in turn, minimizes the total acquisition time necessary to conduct the time consuming ultrastructural scanning electron microscope imaging while eliminating the risk to miss parts of the target structure. We illustrate the value of this workflow for targeting virus compartments, which are formed in HIV-pulsed mature human dendritic cells. PMID:25786567

  7. Preservation of protein fluorescence in embedded human dendritic cells for targeted 3D light and electron microscopy

    PubMed Central

    HÖHN, K.; FUCHS, J.; FRÖBER, A.; KIRMSE, R.; GLASS, B.; ANDERS‐ÖSSWEIN, M.; WALTHER, P.; KRÄUSSLICH, H.‐G.

    2015-01-01

    Summary In this study, we present a correlative microscopy workflow to combine detailed 3D fluorescence light microscopy data with ultrastructural information gained by 3D focused ion beam assisted scanning electron microscopy. The workflow is based on an optimized high pressure freezing/freeze substitution protocol that preserves good ultrastructural detail along with retaining the fluorescence signal in the resin embedded specimens. Consequently, cellular structures of interest can readily be identified and imaged by state of the art 3D confocal fluorescence microscopy and are precisely referenced with respect to an imprinted coordinate system on the surface of the resin block. This allows precise guidance of the focused ion beam assisted scanning electron microscopy and limits the volume to be imaged to the structure of interest. This, in turn, minimizes the total acquisition time necessary to conduct the time consuming ultrastructural scanning electron microscope imaging while eliminating the risk to miss parts of the target structure. We illustrate the value of this workflow for targeting virus compartments, which are formed in HIV‐pulsed mature human dendritic cells. PMID:25786567

  8. Inner-shell excitations of krypton 3d investigated by electron impact with high resolution

    SciTech Connect

    Yuan Zhensheng; Zhu Linfan; Liu Xiaojing; Li Wenbin; Cheng Huadong; Sun Jianmin; Xu Kezun

    2005-06-15

    The inner-shell excitation spectra of krypton 3d electrons were measured at scattering angles of 0 deg. and 4 deg. by a fast-electron energy-loss spectrometer at an incident energy of 2.5 keV with an energy resolution better than 80 meV. Some interesting optically forbidden transitions were observed and the natural widths of the optically allowed and optically forbidden transitions were analyzed. It shows that the natural widths for the resonances having the same core hole are nearly equal, no matter whether they are optically allowed, optically forbidden, or different members of a Rydberg series.

  9. Accurate nonrelativistic ground-state energies of 3d transition metal atoms

    SciTech Connect

    Scemama, A.; Applencourt, T.; Giner, E.; Caffarel, M.

    2014-12-28

    We present accurate nonrelativistic ground-state energies of the transition metal atoms of the 3d series calculated with Fixed-Node Diffusion Monte Carlo (FN-DMC). Selected multi-determinantal expansions obtained with the CIPSI (Configuration Interaction using a Perturbative Selection made Iteratively) method and including the most prominent determinants of the full configuration interaction expansion are used as trial wavefunctions. Using a maximum of a few tens of thousands determinants, fixed-node errors on total DMC energies are found to be greatly reduced for some atoms with respect to those obtained with Hartree-Fock nodes. To the best of our knowledge, the FN-DMC/(CIPSI nodes) ground-state energies presented here are the lowest variational total energies reported so far. They differ from the recently recommended non-variational values of McCarthy and Thakkar [J. Chem. Phys. 136, 054107 (2012)] only by a few percents of the correlation energy. Thanks to the variational property of FN-DMC total energies, our results provide exact lower bounds for the absolute value of all-electron correlation energies, |E{sub c}|.

  10. Study on the electronic structure and Fermi surface of 3d-transition-metal disilisides CoSi2

    NASA Astrophysics Data System (ADS)

    Hamid, A. S.

    2012-09-01

    We have investigated the electronic structure, the momentum density distribution ρ( p), and the Fermi surface FS of single crystals of the Pyrite-type 3d-transition-metal disilisides CoSi2. The band structure calculations, the density of states DOS, and the FS, in vicinity of Fermi level, have been carried out using the full-potential linearized augmented plane wave FP-LAPW method within generalized gradient approximation GGA for exchange and correlation potential. The measurements have been performed via the 2D angular correlation of annihilation radiation ACAR experiments. ρ( p) has been reconstructed by using the Fourier transformation technique. The FS has been reconstructed within the first Brillion zone BZ through the Locks, Crisp, and West LCW folding procedures. The analysis confirmed that Si 3 sp states hybrid with both Co 3 d- t 2 g and Co 3 d- e g states around Γ and X points, respectively. The dimensions of the FS of CoSi2 have been compared to the present calculations as well as to the earlier results.

  11. Equation-of-State Test Suite for the DYNA3D Code

    SciTech Connect

    Benjamin, Russell D.

    2015-11-05

    This document describes the creation and implementation of a test suite for the Equationof- State models in the DYNA3D code. A customized input deck has been created for each model, as well as a script that extracts the relevant data from the high-speed edit file created by DYNA3D. Each equation-of-state model is broken apart and individual elements of the model are tested, as well as testing the entire model. The input deck for each model is described and the results of the tests are discussed. The intent of this work is to add this test suite to the validation suite presently used for DYNA3D.

  12. 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.

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

    PubMed Central

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-01-01

    Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3 Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. PMID:23796504

  14. 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

  15. Tunable interplay between 3d and 4f electrons in Co-doped iron pnictides

    NASA Astrophysics Data System (ADS)

    Shang, T.; Yang, L.; Chen, Y.; Cornell, N.; Ronning, F.; Zhang, J. L.; Jiao, L.; Chen, Y. H.; Chen, J.; Howard, A.; Dai, J.; Thompson, J. D.; Zakhidov, A.; Salamon, M. B.; Yuan, H. Q.

    2013-02-01

    We study the interplay of 3d and 4f electrons in the iron pnictides CeFe1-xCoxAsO and GdFe1-yCoyAsO, which correspond to two very different cases of 4f-magnetic moment. Both CeFeAsO and GdFeAsO undergo a spin-density-wave (SDW) transition associated with Fe 3d electrons at high temperatures, which is rapidly suppressed by Fe/Co substitution. Superconductivity appears in a narrow doping range: 0.05electrons form an antiferromagnetic (AFM) order at low temperatures over the entire doping range and Co 3d electrons are ferromagnetically ordered on the Co-rich side; the Curie temperature reaches TCCo≈ 75 K at x=1 and y=1. In the Ce compounds, the Néel temperature TNCe increases upon suppressing the SDW transition of Fe and then remains nearly unchanged with further increasing Co concentration up to x≃0.8 (TNCe≈ 4 K). Furthermore, evidence of Co-induced polarization on Ce moments is observed on the Co-rich side. In the Gd compounds, the two magnetic species of Gd and Co are coupled antiferromagnetically to give rise to ferrimagnetic behavior in the magnetic susceptibility on the Co-rich side. For 0.7≤y<1.0, the system undergoes a possible magnetic reorientation below the Néel temperature of Gd (TNGd). Our results suggest that the effects of both electron hybridizations and magnetic exchange coupling between the 3d-4f electrons give rise to a rich phase diagram in the rare-earth iron pnictides.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  17. 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

  18. 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.

  19. Correlated fluorescence and 3D electron microscopy with high sensitivity and spatial precision

    PubMed Central

    Kukulski, Wanda; Schorb, Martin; Welsch, Sonja; Picco, Andrea

    2011-01-01

    Correlative electron and fluorescence microscopy has the potential to elucidate the ultrastructural details of dynamic and rare cellular events, but has been limited by low precision and sensitivity. Here we present a method for direct mapping of signals originating from ∼20 fluorescent protein molecules to 3D electron tomograms with a precision of less than 100 nm. We demonstrate that this method can be used to identify individual HIV particles bound to mammalian cell surfaces. We also apply the method to image microtubule end structures bound to mal3p in fission yeast, and demonstrate that growing microtubule plus-ends are flared in vivo. We localize Rvs167 to endocytic sites in budding yeast, and show that scission takes place halfway through a 10-s time period during which amphiphysins are bound to the vesicle neck. This new technique opens the door for direct correlation of fluorescence and electron microscopy to visualize cellular processes at the ultrastructural scale. PMID:21200030

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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

  5. Catching HIV ‘in the act’ with 3D electron microscopy

    PubMed Central

    Earl, Lesley A.; Lifson, Jeffrey D.; Subramaniam, Sriram

    2013-01-01

    The development of a safe, effective vaccine to prevent human immunodeficiency virus (HIV) infection is a key step for controlling the disease on a global scale. However, many aspects of HIV biology make vaccine design problematic, including the sequence diversity and structural variability of the surface envelope glycoproteins and the poor accessibility of neutralization-sensitive epitopes on the virus. In this review, we discuss recent progress in understanding HIV in a structural context using emerging tools in 3D electron microscopy, and outline how some of these advances could be important for a better understanding of mechanisms of viral entry and for vaccine design. PMID:23850373

  6. Effects of 3d and 4d transition metal substitutional impurities on the electronic properties of CrO2

    NASA Astrophysics Data System (ADS)

    Williams, M. E.; Sims, H.; Mazumdar, D.; Butler, W. H.

    2012-12-01

    We present first-principles-based density functional theory calculations of the electronic and magnetic structure of CrO2 with 3d and 4d substitutional impurities. We find that the half-metallicity of CrO2 remains intact for the ground state of all of the calculated substitutions. We also observe two periodic trends as a function of the number of valence electrons: if the substituted atom has six or fewer valence electrons, the number of down spin electrons associated with the impurity ion is zero, resulting in ferromagnetic alignment of the impurity magnetic moment with the magnetization of the CrO2 host. For substituent atoms with eight to ten valence electrons (with the exception of Ni), the number of down-spin electrons contributed by the impurity ion remains fixed at three as the number contributed to the majority increases from one to three resulting in antiferromagnetic alignment between impurity moment and host magnetization. In impurities with seven valence electrons, the zero down-spin and threse down-spin configurations are very close in energy. At 11 valence electrons, the energy is minimized when the substituent ion contributes five down-spin electrons. The moments on the 4d impurities, particularly Nb and Mo, tend to be delocalized compared with those of the 3ds.

  7. 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

  8. Isolation, electron microscopic imaging, and 3-D visualization of native cardiac thin myofilaments.

    PubMed

    Spiess, M; Steinmetz, M O; Mandinova, A; Wolpensinger, B; Aebi, U; Atar, D

    1999-06-15

    An increasing number of cardiac diseases are currently pinpointed to reside at the level of the thin myofilaments (e.g., cardiomyopathies, reperfusion injury). Hence the aim of our study was to develop a new method for the isolation of mammalian thin myofilaments suitable for subsequent high-resolution electron microscopic imaging. Native cardiac thin myofilaments were extracted from glycerinated porcine myocardial tissue in the presence of protease inhibitors. Separation of thick and thin myofilaments was achieved by addition of ATP and several centrifugation steps. Negative staining and subsequent conventional and scanning transmission electron microscopy (STEM) of thin myofilaments permitted visualization of molecular details; unlike conventional preparations of thin myofilaments, our method reveals the F-actin moiety and allows direct recognition of thin myofilament-associated porcine cardiac troponin complexes. They appear as "bulges" at regular intervals of approximately 36 nm along the actin filaments. Protein analysis using SDS-polyacrylamide gel electrophoresis revealed that only approximately 20% troponin I was lost during the isolation procedure. In a further step, 3-D helical reconstructions were calculated using STEM dark-field images. These 3-D reconstructions will allow further characterization of molecular details, and they will be useful for directly visualizing molecular alterations related to diseased cardiac thin myofilaments (e.g., reperfusion injury, alterations of Ca2+-mediated tropomyosin switch). PMID:10388621

  9. 3D imaging of particle tracks in Solid State Nuclear Track Detectors

    NASA Astrophysics Data System (ADS)

    Wertheim, D.; Gillmore, G.; Brown, L.; Petford, N.

    2009-04-01

    Inhalation of radon gas (222Rn) and associated ionizing decay products is known to cause lung cancer in human. In the U.K., it has been suggested that 3 to 5 % of total lung cancer deaths can be linked to elevated radon concentrations in the home and/or workplace. Radon monitoring in buildings is therefore routinely undertaken in areas of known risk. Indeed, some organisations such as the Radon Council in the UK and the Environmental Protection Agency in the USA, advocate a ‘to test is best' policy. Radon gas occurs naturally, emanating from the decay of 238U in rock and soils. Its concentration can be measured using CR?39 plastic detectors which conventionally are assessed by 2D image analysis of the surface; however there can be some variation in outcomes / readings even in closely spaced detectors. A number of radon measurement methods are currently in use (for examples, activated carbon and electrets) but the most widely used are CR?39 solid state nuclear track?etch detectors (SSNTDs). In this technique, heavily ionizing alpha particles leave tracks in the form of radiation damage (via interaction between alpha particles and the atoms making up the CR?39 polymer). 3D imaging of the tracks has the potential to provide information relating to angle and energy of alpha particles but this could be time consuming. Here we describe a new method for rapid high resolution 3D imaging of SSNTDs. A ‘LEXT' OLS3100 confocal laser scanning microscope was used in confocal mode to successfully obtain 3D image data on four CR?39 plastic detectors. 3D visualisation and image analysis enabled characterisation of track features. This method may provide a means of rapid and detailed 3D analysis of SSNTDs. Keywords: Radon; SSNTDs; confocal laser scanning microscope; 3D imaging; LEXT

  10. 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.

  11. Design and production of 3D printed bolus for electron radiation therapy.

    PubMed

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

    2014-01-01

    This is a proof-of-concept study demonstrating the capacity for modulated electron radiation therapy (MERT) dose distributions 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 the planning target volume (PTV). The algorithm takes advantage of a commercial electron Monte Carlo dose calculation and uses the calculated result as input. Distances along ray lines from the distal side of 90% isodose line to distal surface of the PTV are used to estimate the bolus thickness. Inhomogeneities within the calculation volume are accounted for using the coefficient of equivalent thickness method. Several regional modulation operators are applied to improve the 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 are improved compared to that with uniform bolus. For geometric phantoms with air or bone inhomogeneities, the dose homogeneity is markedly improved. The actual printed boluses conform well to the surface of complex anthropomorphic phantoms. The correspondence of the dose distribution between the calculated synthetic bolus and the actual manufactured bolus is shown. 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 the prescription isodose surface and in sparing immediately adjacent normal

  12. CMOS array of photodiodes with electronic processing for 3D optical reconstruction

    NASA Astrophysics Data System (ADS)

    Hornero, Gemma; Montane, Enric; Chapinal, Genis; Moreno, Mauricio; Herms, Atila

    2001-04-01

    It is well known that laser time-of-flight (TOF) and optical triangulation are the most useful optical techniques for distance measurements. The first one is more suitable for large distances, since for short range of distances high modulation frequencies of laser diodes (©200-500MHz) are needed. For these ranges, optical triangulation is simpler, as it is only necessary to read the projection of the laser point over a linear optical sensor without any laser modulation. Laser triangulation is based on the rotation of the object. This motion shifts the projected point over the linear sensor, resulting on 3D information, by means of the whole readout of the linear sensor in each angle position. On the other hand, a hybrid method of triangulation and TOF can be implemented. In this case, a synchronized scanning of a laser beam over the object results in different arrival times of light to each pixel. The 3D information is carried by these delays. Only a single readout of the linear sensor is needed. In this work we present the design of two different linear arrays of photodiodes in CMOS technology, the first one based on the Optical triangulation measurement and the second one based in this hybrid method (TFO). In contrast to PSD (Position Sensitive Device) and CCDs, CMOS technology can include, on the same chip, photodiodes, control and processing electronics, that in the other cases should be implemented with external microcontrollers.

  13. A novel bottom-up copper filling of blind silicon vias in 3D electronic packaging

    NASA Astrophysics Data System (ADS)

    Du, Li; Shi, Tielin; Su, Lei; Xue, Dongmin; Liao, Guanglan

    2015-04-01

    Through silicon via is a promising technology that has benefits of high density, excellent performance and heterogeneous integration for 3D stacked devices, where blind silicon via plating in via first and via middle approaches is widely used. However, using conventional damascene copper plating technology to achieve high quality copper filling of blind vias is very difficult. In this paper, we demonstrate a novel approach for realizing bottom-up copper filling of blind silicon vias. Electroplating of the blind vias is carried out by using a titanium barrier layer, instead of the traditional copper seed layer, as the conductive medium. A vacuum process is introduced to push photoresist completely into the blind vias. By controlling the exposure and development processes, the photoresist at the top and middle of the vias is removed while that at the bottom it is retained for protecting the seed layer. After etching the exposed seed layer, we obtain a unique metal layer structure in which the copper seed layer is reserved at the via bottom, facilitating spontaneous bottom-up plating. Using this approach, we realize high quality copper filling of blind silicon vias of 30 µm in diameter and 120 µm in depth, which will be of noteworthy benefit in 3D electronic packaging.

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. New spiral state and skyrmion lattice in 3D model of chiral magnets

    NASA Astrophysics Data System (ADS)

    Rybakov, Filipp N.; Borisov, Aleksandr B.; Blügel, Stefan; Kiselev, Nikolai S.

    2016-04-01

    We present the phase diagram of magnetic states for films of isotropic chiral magnets (ChMs) calculated as function of applied magnetic field and thickness of the film. We have found a novel magnetic state driven by the natural confinement of the crystal, localized at the surface and stacked on top of the conical bulk phase. This magnetic surface state has a three-dimensional (3D) chiral spin-texture described by the superposition of helical and cycloidal spin spirals. This surface state exists for a large range of applied magnetic fields and for any film thickness beyond a critical one. We also identified the whole thickness and field range for which the skyrmion lattice becomes the ground state of the system. Below a certain critical thickness the surface state and bulk conical phase are suppressed in favor of the skyrmion lattice. Unraveling of those phases and the construction of the phase diagram became possible using advanced computational techniques for direct energy minimization applied to a basic 3D model for ChMs. Presented results provide a comprehensive theoretical description for those effects already observed in experiments on thin films of ChMs, predict new effects important for applications and open perspectives for experimental studies of such systems.

  19. Real time reconstruction of 3-D electron density distribution over Europe with TaD profiler

    NASA Astrophysics Data System (ADS)

    Kutiev, Ivan; Marinov, Pencho; Belehaki, Anna

    2015-04-01

    TaD (TSM-assisted Digisonde) profiler, developed on the base of Topside Sounder Model (TSM), provides vertical electron density profile (EDP) from the bottom of ionosphere up to the GNSS orbit heights over Digisonde sounding stations. TaD EDP uses the bottomside profile provided by Digisonde software and extends it above the F layer peak by representing O+ distribution by α-Chapman formula and H+ distribution by a single exponent. The profile above F layer peak takes the topside scale height HT and transition height hT from TSM and plasmasphere scale height Hp defined as a function of HT. All these profile parameters are adjusted to the current conditions by comparing the profile integral with measured GNSS TEC. The latter is taken from GNSS TEC maps produced by Royal Observatory of Belgium in the area (35˚, 60˚)N and (-15˚, 25˚)E. Maps of foF2 and hmF2 are produced in the same area on the base of DIAS (European Digital Upper Atmosphere Server) network of Digisonde stations and TaD profiles are calculated at all grid nodes (1˚x1˚) on latitude and longitude. Electron density at any point of the 3-D space is then obtained by simple interpolation between nodes. Possible use of reconstruction technique to GNSS applications is demonstrated by calculating the distribution of electron density along various ray paths of GNSS signals.

  20. Assessment of the isostatic state and the load distribution of the European Molasse basin by means of lithospheric-scale 3D structural and 3D gravity modelling

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    The European Molasse basin is a foreland basin situated at the northern front of the European Alps and has formed as a consequence of the Euro-Adriatic continental collision since the Tertiary. Today, it is underlain by Mesozoic sedimentary successions on top of a Paleozoic crust. To investigate the deep structure, the isostatic state, as well as the load distribution in the basin and the adjacent Alpine area, we constructed a lithospheric-scale 3D structural model by implementing available surface, well and seismic data. Subsequently, the structure of the model was constrained by means of 3D gravity modelling. Complementary, the isostatic state has been assessed based on the calculation of the 3D load distribution. Our results show that the Molasse basin is not in isostatic equilibrium and that the gravity field of the area is strongly controlled by the configuration of the crystalline crust. Furthermore, we show that the area is influenced by significant lateral load variations down to a depth of -150 km, which are considerably larger than commonly assumed for this level. Furthermore, our results allow a first-order assessment of the minimum compensating horizontal stress required to prevent gravitational collapse.

  1. 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

  2. Excited state population of a 3D transmon in thermal equilibrium

    NASA Astrophysics Data System (ADS)

    Jin, X. Y.; Gustavsson, S.; Kamal, A.; Sears, A. P.; Gudmundsen, T.; Hover, D.; Kerman, A. J.; Yan, F.; Yoder, J.; Orlando, T. P.; Oliver, W. D.

    2014-03-01

    We present a systematic study of the excited state population of a 3D transmon qubit at various temperatures. We experimentally demonstrate that the population of the first excited state follows the Maxwell-Boltzmann distribution in the temperature range of 35-150 mK. For bath temperatures below 35 mK, the excited-state population saturates, with an upper-bound estimate of 0.1%. The saturation suggests a qubit effective temperature of approximately 35 mK. The Lincoln Laboratory portion of this work was sponsored by the Assistant Secretary of Defense for Research & Engineering under Air Force Contract number FA8721-05-C-0002. Opinions, interpretations, conclusions and recommendations are those of the author and are not necessarily endorsed by the United States Government.

  3. 3D imaging of mammalian cells with ion-abrasion scanning electron microscopy.

    PubMed

    Heymann, Jurgen A W; Shi, Dan; Kim, Sang; Bliss, Donald; Milne, Jacqueline L S; Subramaniam, Sriram

    2009-04-01

    Understanding the hierarchical organization of molecules and organelles within the interior of large eukaryotic cells is a challenge of fundamental interest in cell biology. We are using ion-abrasion scanning electron microscopy (IA-SEM) to visualize this hierarchical organization in an approach that combines focused ion-beam milling with scanning electron microscopy. Here, we extend our previous studies on imaging yeast cells to image subcellular architecture in human melanoma cells and melanocytes at resolutions as high as approximately 6 and approximately 20 nm in the directions parallel and perpendicular, respectively, to the direction of ion-beam milling. The 3D images demonstrate the striking spatial relationships between specific organelles such as mitochondria and membranes of the endoplasmic reticulum, and the distribution of unique cellular components such as melanosomes. We also show that 10nm-sized gold particles and quantum dot particles with 7 nm-sized cores can be detected in single cross-sectional images. IA-SEM is thus a useful tool for imaging large mammalian cells in their entirety at resolutions in the nanometer range. PMID:19116171

  4. 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. PMID:19204999

  5. 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.

  6. 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.

  7. Using low-contrast negative-tone PMMA at cryogenic temperatures for 3D electron beam lithography.

    PubMed

    Schnauber, Peter; Schmidt, Ronny; Kaganskiy, Arsenty; Heuser, Tobias; Gschrey, Manuel; Rodt, Sven; Reitzenstein, Stephan

    2016-05-13

    We report on a 3D electron beam lithography (EBL) technique using polymethyl methacrylate (PMMA) in the negative-tone regime as a resist. First, we briefly demonstrate 3D EBL at room temperature. Then we concentrate on cryogenic temperatures where PMMA exhibits a low contrast, which allows for straightforward patterning of 3D nano- and microstructures. However, conventional EBL patterning at cryogenic temperatures is found to cause severe damage to the microstructures. Through an extensive study of lithography parameters, exposure techniques, and processing steps we deduce a hypothesis for the cryogenic PMMA's structural evolution under electron beam irradiation that explains the damage. In accordance with this hypothesis, a two step lithography technique involving a wide-area pre-exposure dose slightly smaller than the onset dose is applied. It enables us to demonstrate a >95% process yield for the low-temperature fabrication of 3D microstructures. PMID:27023850

  8. Using low-contrast negative-tone PMMA at cryogenic temperatures for 3D electron beam lithography

    NASA Astrophysics Data System (ADS)

    Schnauber, Peter; Schmidt, Ronny; Kaganskiy, Arsenty; Heuser, Tobias; Gschrey, Manuel; Rodt, Sven; Reitzenstein, Stephan

    2016-05-01

    We report on a 3D electron beam lithography (EBL) technique using polymethyl methacrylate (PMMA) in the negative-tone regime as a resist. First, we briefly demonstrate 3D EBL at room temperature. Then we concentrate on cryogenic temperatures where PMMA exhibits a low contrast, which allows for straightforward patterning of 3D nano- and microstructures. However, conventional EBL patterning at cryogenic temperatures is found to cause severe damage to the microstructures. Through an extensive study of lithography parameters, exposure techniques, and processing steps we deduce a hypothesis for the cryogenic PMMA’s structural evolution under electron beam irradiation that explains the damage. In accordance with this hypothesis, a two step lithography technique involving a wide-area pre-exposure dose slightly smaller than the onset dose is applied. It enables us to demonstrate a >95% process yield for the low-temperature fabrication of 3D microstructures.

  9. 3D visualisation and analysis of single and coalescing tracks in Solid state Nuclear Track Detectors

    NASA Astrophysics Data System (ADS)

    Wertheim, David; Gillmore, Gavin; Brown, Louise; Petford, Nick

    2010-05-01

    Exposure to radon gas (222Rn) and associated ionising decay products can cause lung cancer in humans (1). Solid state Nuclear Track Detectors (SSNTDs) can be used to monitor radon concentrations (2). Radon particles form tracks in the detectors and these tracks can be etched in order to enable 2D surface image analysis. We have previously shown that confocal microscopy can be used for 3D visualisation of etched SSNTDs (3). The aim of the study was to further investigate track angles and patterns in SSNTDs. A 'LEXT' confocal laser scanning microscope (Olympus Corporation, Japan) was used to acquire 3D image datasets of five CR-39 plastic SSNTD's. The resultant 3D visualisations were analysed by eye and inclination angles assessed on selected tracks. From visual assessment, single isolated tracks as well as coalescing tracks were observed on the etched detectors. In addition varying track inclination angles were observed. Several different patterns of track formation were seen such as single isolated and double coalescing tracks. The observed track angles of inclination may help to assess the angle at which alpha particles hit the detector. Darby, S et al. Radon in homes and risk of lung cancer : collaborative analysis of individual data from 13 European case-control studies. British Medical Journal 2005; 330, 223-226. Phillips, P.S., Denman, A.R., Crockett, R.G.M., Gillmore, G., Groves-Kirkby, C.J., Woolridge, A., Comparative Analysis of Weekly vs. Three monthly radon measurements in dwellings. DEFRA Report No., DEFRA/RAS/03.006. (2004). Wertheim D, Gillmore G, Brown L, and Petford N. A new method of imaging particle tracks in Solid State Nuclear Track Detectors. Journal of Microscopy 2010; 237: 1-6.

  10. 3D and 4D Seismic Imaging in the Oilfield; the state of the art

    NASA Astrophysics Data System (ADS)

    Strudley, A.

    2005-05-01

    Seismic imaging in the oilfield context has seen enormous changes over the last 20 years driven by a combination of improved subsurface illumination (2D to 3D), increased computational power and improved physical understanding. Today Kirchhoff Pre-stack migration (in time or depth) is the norm with anisotropic parameterisation and finite difference methods being increasingly employed. In the production context Time-Lapse (4D) Seismic is of growing importance as a tool for monitoring reservoir changes to facilitate increased productivity and recovery. In this paper we present an overview of state of the art technology in 3D and 4D seismic and look at future trends. Pre-stack Kirchhoff migration in time or depth is the imaging tool of choice for the majority of contemporary 3D datasets. Recent developments in 3D pre-stack imaging have been focussed around finite difference solutions to the acoustic wave equation, the so-called Wave Equation Migration methods (WEM). Application of finite difference solutions to imaging is certainly not new, however 3D pre-stack migration using these schemes is a relatively recent development driven by the need for imaging complex geologic structures such as sub salt, and facilitated by increased computational resources. Finally there are a class of imaging methods referred to as beam migration. These methods may be based on either the wave equation or rays, but all operate on a localised (in space and direction) part of the wavefield. These methods offer a bridge between the computational efficiency of Kirchhoff schemes and the improved image quality of WEM methods. Just as 3D seismic has had a radical impact on the quality of the static model of the reservoir, 4D seismic is having a dramatic impact on the dynamic model. Repeat shooting of seismic surveys after a period of production (typically one to several years) reveals changes in pressure and saturation through changes in the seismic response. The growth in interest in 4D seismic

  11. 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. PMID:21299242

  12. 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

  13. 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

  14. Quantum Criticality of Topological Phase Transitions in 3D Interacting Electronic Systems

    NASA Astrophysics Data System (ADS)

    Moon, Eun Gook; Yang, Bohm-Jung; Isobe, Hiroki; Nagaosa, Naoto

    2014-03-01

    We investigate the quantum criticality of topological phase transitions in three dimensional (3D) interacting electronic systems lacking either the time-reversal symmetry or the inversion symmetry. The minimal model, Weyl fermions with anisotropic dispersion relation, is suggested as the quantum critical theory based on the zerochirality condition. The interplay between the fermions and the long range Coulomb interaction is investigated by the standard renormalization group (RG) approach. We find that the quantum fluctuations of the anisotropic Weyl fermions induce the anisotropic partial screening of the Coulomb interaction, which eventually makes the Coulomb interaction irrelevant. It is in sharp contrast to the quantum criticality of conventional semi-metallic phases such as graphene where physical quantities receive logarithmic corrections from the marginal Coulomb interaction. Thus, the critical point is described by the non-interacting fermion theory allowing the complete theoretical understanding of the problem. The renormalized Coulomb potential shows the anisotropic power law. Its physical consequence is further illustrated by the screening problem of a charged impurity due to anisotropic Weyl fermions.

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

    PubMed

    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 μm(3)) surrounding a large dendritic spine, a cylinder (~43 μm(3)) surrounding an oblique dendritic segment (3.4 μm long), and a parallelepiped (~178 μm(3)) 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

  16. 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

  17. 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.

  18. Thermal hydraulic analysis for the Oregon State TRIGA reactor using RELAP5-3D

    SciTech Connect

    Marcum, W.R.; Woods, B.G.; Hartman, M.

    2008-07-15

    Thermal hydraulic analyses have being conducted at Oregon State University (OSU) in support of the conversion of the OSU TRIGA reactor (OSTR) core from high-enriched uranium (HEU) to low-enriched uranium (LEU) fuel as part of the Reduced Enrichment for Research and Test Reactors program. The goals of the thermal hydraulic analyses were to calculate natural circulation flow rates, coolant temperatures and fuel temperatures as a function of core power for both the HEU and LEU cores; calculate peak values of fuel temperature, cladding temperature, surface heat flux as well as departure from nuclear boiling ratio (DNBR) for steady state and pulse operation; and perform accident analyses for the accident scenarios identified in the OSTR safety analysis report. RELAP5-3D Version 2.4.2 was implemented to develop a model for the thermal hydraulic study. The OSTR core conversion is planned to take place in late 2008. (author)

  19. DFT-based studies on the Jahn-Teller effect in 3d hexacyanometalates with orbitally degenerate ground states.

    PubMed

    Atanasov, Mihial; Comba, Peter; Daul, Claude A; Hauser, Andreas

    2007-09-20

    The topology of the ground-state potential energy surface of M(CN)(6) with orbitally degenerate (2)T(2g) (M = Ti(III) (t(2g)(1)), Fe(III) and Mn(II) (both low-spin t(2g)(5))) and (3)T(1g) ground states (M = V(III) (t(2g)(2)), Mn(III) and Cr(II) (both low-spin t(2g)(4))) has been studied with linear and quadratic Jahn-Teller coupling models in the five-dimensional space of the epsilon(g) and tau(2g) octahedral vibrations (Tg[symbol: see text](epsilon(g)+tau(2g)) Jahn-Teller coupling problem (T(g) = (2)T(2g), (3)T(1g))). A procedure is proposed to give access to all vibronic coupling parameters from geometry optimization with density functional theory (DFT) and the energies of a restricted number of Slater determinants, derived from electron replacements within the t(2g)(1,5) or t(2g)(2,4) ground-state electronic configurations. The results show that coupling to the tau(2g) bending mode is dominant and leads to a stabilization of D(3d) structures (absolute minima on the ground-state potential energy surface) for all complexes considered, except for [Ti(CN)(6)](3-), where the minimum is of D(4h) symmetry. The Jahn-Teller stabilization energies for the D3d minima are found to increase in the order of increasing CN-M pi back-donation (Ti(III) < V(III) < Mn(III) < Fe(III) < Mn(II) < Cr(II)). With the angular overlap model and bonding parameters derived from angular distortions, which correspond to the stable D(3d) minima, the effect of configuration interaction and spin-orbit coupling on the ground-state potential energy surface is explored. This approach is used to correlate Jahn-Teller distortion parameters with structures from X-ray diffraction data. Jahn-Teller coupling to trigonal modes is also used to reinterpret the anisotropy of magnetic susceptibilities and g tensors of [Fe(CN)(6)](3-), and the (3)T(1g) ground-state splitting of [Mn(CN)(6)](3-), deduced from near-IR spectra. The implications of the pseudo Jahn-Teller coupling due to t(2g)-e(g) orbital mixing via

  20. Intermediate-spin state of a 3d ion in the octahedral environment and generalization of the Tanabe-Sugano diagrams.

    PubMed

    Lamonova, Karina V; Zhitlukhina, Elena S; Babkin, Roman Yu; Orel, Sergei M; Ovchinnikov, Sergei G; Pashkevich, Yurii G

    2011-11-24

    Electronic spectra of 3d(n) transition ions in an octahedral ligand surrounding have been studied using the modified crystal field approach (MCFA), which includes a relativistic spin-orbital interaction. A new variable parameter, the effective nuclear charge Z(eff) of a metal ion that allows accounting implicitly the covalence degree of a metal-ligand bond, has been introduced. Energy diagrams similar to the Tanabe-Sugano ones have been calculated. To study the spin state evolution of the metal ion in an arbitrary distorted octahedral complex, a spin state diagram approach has been proposed. The intermediate-spin (IS) state problem for 3d(4), 3d(5), and 3d(6) metal ions has been considered and conditions for the IS state realization have been formulated. The regions of the mixed high-, intermediate-, and low-spin states have been found. The possibility of coexistence of the different spin states of 3d ions in the octahedral complexes has been considered using crystallography data for the YBaCo(2)O(5.5) layered cobaltite. PMID:21936547

  1. Electron flood gun damage effects in 3D secondary ion mass spectrometry imaging of organics.

    PubMed

    Havelund, Rasmus; Seah, Martin P; Shard, Alexander G; Gilmore, Ian S

    2014-09-01

    Electron flood guns used for charge compensation in secondary ion mass spectrometry (SIMS) cause chemical degradation. In this study, the effect of electron flood gun damage on argon cluster depth profiling is evaluated for poly(vinylcarbazole), 1,4-bis((1-naphthylphenyl)amino)biphenyl and Irganox 3114. Thin films of these three materials are irradiated with a range of doses from a focused beam of 20 eV electrons used for charge neutralization. SIMS chemical images of the irradiated surfaces show an ellipsoidal damaged area, approximately 3 mm in length, created by the electron beam. In depth profiles obtained with 5 keV Ar(2000)(+) sputtering from the vicinity of the damaged area, the characteristic ion signal intensity rises from a low level to a steady state. For the damaged thin films, the ion dose required to sputter through the thin film to the substrate is higher than for undamaged areas. It is shown that a damaged layer is formed and this has a sputtering yield that is reduced by up to an order of magnitude and that the thickness of the damaged layer, which increases with the electron dose, can be as much as 20 nm for Irganox 3114. The study emphasizes the importance of minimizing the neutralizing electron dose prior to the analysis. PMID:24912434

  2. Automated Segmentation of the Right Ventricle in 3D Echocardiography: A Kalman Filter State Estimation Approach.

    PubMed

    Bersvendsen, Jorn; Orderud, Fredrik; Massey, Richard John; Fosså, Kristian; Gerard, Olivier; Urheim, Stig; Samset, Eigil

    2016-01-01

    As the right ventricle's (RV) role in cardiovascular diseases is being more widely recognized, interest in RV imaging, function and quantification is growing. However, there are currently few RV quantification methods for 3D echocardiography presented in the literature or commercially available. In this paper we propose an automated RV segmentation method for 3D echocardiographic images. We represent the RV geometry by a Doo-Sabin subdivision surface with deformation modes derived from a training set of manual segmentations. The segmentation is then represented as a state estimation problem and solved with an extended Kalman filter by combining the RV geometry with a motion model and edge detection. Validation was performed by comparing surface-surface distances, volumes and ejection fractions in 17 patients with aortic insufficiency between the proposed method, magnetic resonance imaging (MRI), and a manual echocardiographic reference. The algorithm was efficient with a mean computation time of 2.0 s. The mean absolute distances between the proposed and manual segmentations were 3.6 ± 0.7 mm. Good agreements of end diastolic volume, end systolic volume and ejection fraction with respect to MRI ( -26±24 mL , -16±26 mL and 0 ± 10%, respectively) and a manual echocardiographic reference (7 ± 30 mL, 13 ± 17 mL and -5±7% , respectively) were observed. PMID:26168434

  3. Benchmarking of state-of-the-art needle detection algorithms in 3D ultrasound data volumes

    NASA Astrophysics Data System (ADS)

    Pourtaherian, Arash; Zinger, Svitlana; de With, Peter H. N.; Korsten, Hendrikus H. M.; Mihajlovic, Nenad

    2015-03-01

    Ultrasound-guided needle interventions are widely practiced in medical diagnostics and therapy, i.e. for biopsy guidance, regional anesthesia or for brachytherapy. Needle guidance using 2D ultrasound can be very challenging due to the poor needle visibility and the limited field of view. Since 3D ultrasound transducers are becoming more widely used, needle guidance can be improved and simplified with appropriate computer-aided analyses. In this paper, we compare two state-of-the-art 3D needle detection techniques: a technique based on line filtering from literature and a system employing Gabor transformation. Both algorithms utilize supervised classification to pre-select candidate needle voxels in the volume and then fit a model of the needle on the selected voxels. The major differences between the two approaches are in extracting the feature vectors for classification and selecting the criterion for fitting. We evaluate the performance of the two techniques using manually-annotated ground truth in several ex-vivo situations of different complexities, containing three different needle types with various insertion angles. This extensive evaluation provides better understanding on the limitations and advantages of each technique under different acquisition conditions, which is leading to the development of improved techniques for more reliable and accurate localization. Benchmarking results that the Gabor features are better capable of distinguishing the needle voxels in all datasets. Moreover, it is shown that the complete processing chain of the Gabor-based method outperforms the line filtering in accuracy and stability of the detection results.

  4. Design and fabrication of a foldable 3D silicon based package for solid state lighting applications

    NASA Astrophysics Data System (ADS)

    Sokolovskij, R.; Liu, P.; van Zeijl, H. W.; Mimoun, B.; Zhang, G. Q.

    2015-05-01

    Miniaturization of solid state lighting (SSL) luminaires as well as reduction of packaging and assembly costs are of prime interest for the SSL lighting industry. A novel silicon based LED package for lighting applications is presented in this paper. The proposed design consists of 5 rigid Si tiles connected by flexible polyimide hinges with embedded interconnects (ICs). Electrical, optical and thermal characteristics were taken into consideration during design. The fabrication process involved polyimide (PI) application and patterning, aluminium interconnect integration in the flexible hinge, LED reflector cavity formation and metalization followed by through wafer DRIE etching for chip formation and release. A method to connect chip front to backside without TSVs was also integrated into the process. Post-fabrication wafer level assembly included LED mounting and wirebond, phosphor-based colour conversion and silicone encapsulation. The package formation was finalized by vacuum assisted wrapping around an assembly structure to form a 3D geometry, which is beneficial for omnidirectional lighting. Bending tests were performed on the flexible ICs and optical performance at different temperatures was evaluated. It is suggested that 3D packages can be expanded to platforms for miniaturized luminaire applications by combining monolithic silicon integration and system-in-package (SiP) technologies.

  5. Data acquisition electronics and reconstruction software for real time 3D track reconstruction within the MIMAC project

    NASA Astrophysics Data System (ADS)

    Bourrion, O.; Bosson, G.; Grignon, C.; Bouly, J. L.; Richer, J. P.; Guillaudin, O.; Mayet, F.; Billard, J.; Santos, D.

    2011-11-01

    Directional detection of non-baryonic Dark Matter requires 3D reconstruction of low energy nuclear recoils tracks. A gaseous micro-TPC matrix, filled with either 3He, CF4 or C4H10 has been developed within the MIMAC project. A dedicated acquisition electronics and a real time track reconstruction software have been developed to monitor a 512 channel prototype. This auto-triggered electronic uses embedded processing to reduce the data transfer to its useful part only, i.e. decoded coordinates of hit tracks and corresponding energy measurements. An acquisition software with on-line monitoring and 3D track reconstruction is also presented.

  6. 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.

  7. 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.

  8. Thermal and Residual Excited-State Population in a 3D Transmon Qubit.

    PubMed

    Jin, X Y; Kamal, A; Sears, A P; Gudmundsen, T; Hover, D; Miloshi, J; Slattery, R; Yan, F; Yoder, J; Orlando, T P; Gustavsson, S; Oliver, W D

    2015-06-19

    Remarkable advancements in coherence and control fidelity have been achieved in recent years with cryogenic solid-state qubits. Nonetheless, thermalizing such devices to their milliKelvin environments has remained a long-standing fundamental and technical challenge. In this context, we present a systematic study of the first-excited-state population in a 3D transmon superconducting qubit mounted in a dilution refrigerator with a variable temperature. Using a modified version of the protocol developed by Geerlings et al., we observe the excited-state population to be consistent with a Maxwell-Boltzmann distribution, i.e., a qubit in thermal equilibrium with the refrigerator, over the temperature range 35-150 mK. Below 35 mK, the excited-state population saturates at approximately 0.1%. We verified this result using a flux qubit with ten times stronger coupling to its readout resonator. We conclude that these qubits have effective temperature T(eff)=35  mK. Assuming T(eff) is due solely to hot quasiparticles, the inferred qubit lifetime is 108  μs and in plausible agreement with the measured 80  μs. PMID:26196969

  9. Ultra-high voltage electron microscopy of primitive algae illuminates 3D ultrastructures of the first photosynthetic eukaryote

    PubMed Central

    Takahashi, Toshiyuki; Nishida, Tomoki; Saito, Chieko; Yasuda, Hidehiro; Nozaki, Hisayoshi

    2015-01-01

    A heterotrophic organism 1–2 billion years ago enslaved a cyanobacterium to become the first photosynthetic eukaryote, and has diverged globally. The primary phototrophs, glaucophytes, are thought to retain ancestral features of the first photosynthetic eukaryote, but examining the protoplast ultrastructure has previously been problematic in the coccoid glaucophyte Glaucocystis due to its thick cell wall. Here, we examined the three-dimensional (3D) ultrastructure in two divergent species of Glaucocystis using ultra-high voltage electron microscopy. Three-dimensional modelling of Glaucocystis cells using electron tomography clearly showed that numerous, leaflet-like flattened vesicles are distributed throughout the protoplast periphery just underneath a single-layered plasma membrane. This 3D feature is essentially identical to that of another glaucophyte genus Cyanophora, as well as the secondary phototrophs in Alveolata. Thus, the common ancestor of glaucophytes and/or the first photosynthetic eukaryote may have shown similar 3D structures. PMID:26439276

  10. 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

  11. 3D electron density imaging using single scattered x rays with application to breast CT and mammographic screening

    NASA Astrophysics Data System (ADS)

    van Uytven, Eric Peter

    Screening mammography is the current standard in detecting breast cancer. However, its fundamental disadvantage is that it projects a 3D object into a 2D image. Small lesions are difficult to detect when superimposed over layers of normal tissue. Commercial Computed Tomography (CT) produces a true 3D image yet has a limited role in mammography due to relatively low resolution and contrast. With the intent of enhancing mammography and breast CT, we have developed an algorithm which can produce 3D electron density images using a single projection. Imaging an object with x rays produces a characteristic scattered photon spectrum at the detector plane. A known incident beam spectrum, beam shape, and arbitrary 3D matrix of electron density values enable a theoretical scattered photon distribution to be calculated. An iterative minimization algorithm is used to make changes to the electron density voxel matrix to reduce regular differences between the theoretical and the experimentally measured distributions. The object is characterized by the converged electron density image. This technique has been validated in simulation using data produced by the EGSnrc Monte Carlo code system. At both mammographic and CT energies, a scanning polychromatic pencil beam was used to image breast tissue phantoms containing lesion-like inhomogeneities. The resulting Monte Carlo data is processed using a Nelder-Mead iterative algorithm (MATLAB) to produce the 3D matrix of electron density values. Resulting images have confirmed the ability of the algorithm to detect various 1x1x2.5 mm3 lesions with calcification content as low as 0.5% (p<0.005) at a dose comparable to mammography.

  12. 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

  13. A method for 3D electron density imaging using single scattered x-rays with application to mammographic screening

    NASA Astrophysics Data System (ADS)

    Van Uytven, Eric; Pistorius, Stephen; Gordon, Richard

    2008-10-01

    Screening mammography is the current standard in detecting breast cancer. However, its fundamental disadvantage is that it projects a 3D object into a 2D image. Small lesions are difficult to detect when superimposed over layers of normal, heterogeneous tissue. In this work, we examine the potential of single scattered photon electron density imaging in a mammographic environment. Simulating a low-energy (<20 keV) scanning pencil beam, we have developed an algorithm capable of producing 3D electron density images from a single projection. We have tested the algorithm by imaging parts of a simulated mammographic accreditation phantom containing lesions of various sizes. The results indicate that the group of imaged lesions differ significantly from background breast tissue (p < 0.005), confirming that electron density imaging may be a useful diagnostic test for the presence of breast cancer.

  14. 3D geomechanical-numerical modelling of the absolute stress state for geothermal reservoir exploration

    NASA Astrophysics Data System (ADS)

    Reiter, Karsten; Heidbach, Oliver; Moeck, Inga

    2013-04-01

    For the assessment and exploration of a potential geothermal reservoir, the contemporary in-situ stress is of key importance in terms of well stability and orientation of possible fluid pathways. However, available data, e.g. Heidbach et al. (2009) or Zang et al. (2012), deliver only point wise information of parts of the six independent components of the stress tensor. Moreover most measurements of the stress orientation and magnitude are done for hydrocarbon industry obvious in shallow depth. Interpolation across long distances or extrapolation into depth is unfavourable, because this would ignore structural features, inhomogeneity's in the crust or other local effects like topography. For this reasons geomechanical numerical modelling is the favourable method to quantify orientations and magnitudes of the 3D stress field for a geothermal reservoir. A geomechanical-numerical modelling, estimating the 3D absolute stress state, requires the initial stress state as model constraints. But in-situ stress measurements within or close by a potential reservoir are rare. For that reason a larger regional geomechanical-numerical model is necessary, which derive boundary conditions for the wanted local reservoir model. Such a large scale model has to be tested against in-situ stress measurements, orientations and magnitudes. Other suitable and available data, like GPS measurements or fault slip rates are useful to constrain kinematic boundary conditions. This stepwise approach from regional to local scale takes all stress field factors into account, from first over second up to third order. As an example we present a large scale crustal and upper mantle 3D-geomechanical-numerical model of the Alberta Basin and the surroundings, which is constructed to describe continuously the full stress tensor. In-situ stress measurements are the most likely data, because they deliver the most direct information's of the stress field and they provide insights into different depths, a

  15. 3D hydrodynamics and shear rates' variability in the United States Pharmacopeia Paddle Dissolution Apparatus.

    PubMed

    Ameur, Houari; Bouzit, Mohamed

    2013-08-16

    The 3D hydrodynamics and shear rates distributions within the United States Pharmacopeia Apparatus 2 have been investigated in this paper. With the help of a CFD package, several geometric modifications to the device were evaluated in this study. Specially, we examine the influence of impeller clearance, blade diameter, shape of the vessel base and shape of the lower part of blade. Increasing the impeller clearance was observed to exacerbate the heterogeneity in shear and would likely result in greater variability in dissolution measurements. Use of moderate blade diameter and dished bottom were observed to reduce shear heterogeneity in the regions where tablets are most likely to visit during testing. The comparative analysis shows better reproducibility and accelerated dissolution rates with the modified vessel shape, the dished bottom can enhance mixing near the vessel base when compared with the flat bottom. Increasing length of the lower edge of the paddle was observed to generate high radial pumping and to enlarge the dead zone located at the center of the vessel base. PMID:23680733

  16. 3D imaging and quantitative analysis of small solubilized membrane proteins and their complexes by transmission electron microscopy

    PubMed Central

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

    2013-01-01

    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. PMID:23267047

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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. PMID:24113529

  2. State-Specific Reactions of Cu(+)((1)S,(3)D) with SF6 and SF5Cl.

    PubMed

    Taylor, William S; Redmon, Xavier S; Scheuter, Benjamin A

    2016-04-21

    State-specific reactions of Cu(+)((1)S,(3)D) were carried out in a selected ion drift cell apparatus with SF6 and SF5Cl. Copper ions were prepared in a glow discharge utilizing Ne as the working gas. Analysis of Cu(+) states using ion mobility mass spectrometry (IMS) indicated the presence of both Cu(+)(3d(10)) and Cu(+)(3d(9)4s(1)) configurations attributable to the (1)S ground and (3)D first excited states of this metal ion, respectively. State-specific product formation in reactions of these ions with the two neutral substrates of interest here was determined using IMS along with both known and calculated energetic requirements for product formation. These experiments indicate that Cu(+)((1)S) associates with both SF6 and SF5Cl; however, the process is approximately four times as efficient with the latter neutral under these conditions. Association is also observed as a minor product between Cu(+)((3)D) and both neutral reactants. Inefficient formation of SF3(+) occurs as the sole bimolecular product from SF6 via Cu(+)((3)D). In contrast, Cu(+)((3)D) reacts with SF5Cl in rapid parallel bimolecular processes yielding SF3(+) and CuCl(+). These results also indicate that CuCl(+) initiates additional higher-order processes which result in SF5(+) and SF4Cl(+). The energetics associated with the formation of SF3(+) suggest that a copper halide neutral byproduct must also be formed, requiring a more complex mechanism than simple dissociative charge-transfer. PMID:27014999

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

    NASA Astrophysics Data System (ADS)

    Hwang, Seyeon

    The 3 dimensional printing (3DP), called to additive manufacturing (AM) or rapid prototyping (RP), is emerged to revolutionize manufacturing and completely transform how products are designed and fabricated. A great deal of research activities have been carried out to apply this new technology to a variety of fields. In spite of many endeavors, much more research is still required to perfect the processes of the 3D printing techniques especially in the area of the large-scale additive manufacturing and flexible printed electronics. The principles of various 3D printing processes are briefly outlined in the Introduction Section. New types of thermoplastic polymer composites aiming to specified functional applications are also introduced in this section. Chapter 2 shows studies about the metal/polymer composite filaments for fused deposition modeling (FDM) process. Various metal particles, copper and iron particles, are added into thermoplastics polymer matrices as the reinforcement filler. The thermo-mechanical properties, such as thermal conductivity, hardness, tensile strength, and fracture mechanism, of composites are tested to figure out the effects of metal fillers on 3D printed composite structures for the large-scale printing process. In Chapter 3, carbon/polymer composite filaments are developed by a simple mechanical blending process with an aim of fabricating the flexible 3D printed electronics as a single structure. Various types of carbon particles consisting of multi-wall carbon nanotube (MWCNT), conductive carbon black (CCB), and graphite are used as the conductive fillers to provide the thermoplastic polyurethane (TPU) with improved electrical conductivity. The mechanical behavior and conduction mechanisms of the developed composite materials are observed in terms of the loading amount of carbon fillers in this section. Finally, the prototype flexible electronics are modeled and manufactured by the FDM process using Carbon/TPU composite filaments and

  4. A modular hierarchical approach to 3D electron microscopy image segmentation.

    PubMed

    Liu, Ting; Jones, Cory; Seyedhosseini, Mojtaba; Tasdizen, Tolga

    2014-04-15

    The study of neural circuit reconstruction, i.e., connectomics, is a challenging problem in neuroscience. Automated and semi-automated electron microscopy (EM) image analysis can be tremendously helpful for connectomics research. In this paper, we propose a fully automatic approach for intra-section segmentation and inter-section reconstruction of neurons using EM images. A hierarchical merge tree structure is built to represent multiple region hypotheses and supervised classification techniques are used to evaluate their potentials, based on which we resolve the merge tree with consistency constraints to acquire final intra-section segmentation. Then, we use a supervised learning based linking procedure for the inter-section neuron reconstruction. Also, we develop a semi-automatic method that utilizes the intermediate outputs of our automatic algorithm and achieves intra-segmentation with minimal user intervention. The experimental results show that our automatic method can achieve close-to-human intra-segmentation accuracy and state-of-the-art inter-section reconstruction accuracy. We also show that our semi-automatic method can further improve the intra-segmentation accuracy. PMID:24491638

  5. 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

  6. 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

  7. Do's and don'ts of cryo-electron microscopy: a primer on sample preparation and high quality data collection for macromolecular 3D reconstruction.

    PubMed

    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

  8. 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

  9. 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

  10. 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.

  11. 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. PMID:22051087

  12. 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.

  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. PMID:26876163

  14. 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.

  15. 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.

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

    PubMed

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

    2014-08-15

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

  17. 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

  18. Structural, electronic and magnetic properties of 3d transition metals embedded graphene-like carbon nitride sheet: A DFT + U study

    NASA Astrophysics Data System (ADS)

    Zhang, Shuai; Chi, Runze; Li, Chong; Jia, Yu

    2016-03-01

    Using first-principles calculations, we have investigated the structural, electronic and magnetic properties of 3d transition-metals (TMs) embedded two dimensional graphene-like carbon nitride sheet (TMs@g-CN). Our results show that TMs embed in the cavity of g-CN sheet regularly and keep intact of the planar structure, though there is Jahn-Teller distortion inevitably. Additionally, the nonmagnetic and semiconducting sheet can be significantly modulated to be magnetic and metallic behaviors induced by the resonant impurity states between TMs 3d and g-CN 2p orbitals. Moreover, we also explore the magnetic coupling of TMs@g-CN and find that it varies dramatically with the change of the distance between TMs, i.e., from ferromagnetic (FM) to antiferromagnetic (AFM) transition. Finally, the underlying physical mechanism of the above findings is discussed.

  19. Duo gating on a 3D topological insulator - independent tuning of both topological surface states

    NASA Astrophysics Data System (ADS)

    Li, Chuan; de Ronde, Bob; Snelder, Marieke; Stehno, Martin; Huang, Yingkai; Golden, Mark; Brinkman, Alexander; ICE Team; IOP Collaboration

    ABSTRACT: Topological insulators are associated with a trove of exciting physics, such as the ability to host robust anyons, Majorana Bound States, which can be used for quantum computation. For future Majorana devices it is desirable to have the Fermi energy tuned as close as possible to the Dirac point of the topological surface state. Based on previous work on gating BSTS, we report the experimental progress towards gate-tuning of the top and bottom topological surface states of BiSbTeSe2 crystal flakes. When the Fermi level is moved across the Dirac point conduction is shown to change from electron dominated transport to hole dominated transport independently for either surface. In the high magnetic field, one can tune the system precisely between the different landau levels of both surfaces, thus a full gating map of the possible landau levels combination is established. In addition, we provide a simple capacitance model to explain the general hysteresis behaviors in topological insulator systems.

  20. 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

  1. State of the art of current 3-D scoliosis classifications: a systematic review from a clinical perspective.

    PubMed

    Donzelli, Sabrina; Poma, Salvatore; Balzarini, Luca; Borboni, Alberto; Respizzi, Stefano; Villafane, Jorge Hugo; Zaina, Fabio; Negrini, Stefano

    2015-01-01

    Scoliosis is a complex three dimensional (3D) deformity: the current lack of a 3D classification could hide something fundamental for scoliosis prognosis and treatment. A clear picture of the actually existing 3D classifications lacks. The aim of this systematic review was to identify all the 3D classification systems proposed until now in the literature with the aim to identify similarities and differences mainly in a clinical perspective.After a MEDLINE Data Base review, done in November 2013 using the search terms "Scoliosis/classification" [Mesh] and "scoliosis/classification and Imaging, three dimensional" [Mesh], 8 papers were included with a total of 1164 scoliosis patients, 23 hyperkyphosis and 25 controls, aged between 8 and 20 years, with curves from 10° to 81° Cobb, and various curve patterns. Six studies looked at the whole 3D spine and found classificatory parameters according to planes, angles and rotations, including: Plane of Maximal Curvature (PMC), Best Fit Plane, Cobb angles in bodily plane and PMC, Axial rotation of the apical vertebra and of the PMC, and geometric 3D torsion. Two studies used the regional (spinal) Top View of the spine and found classificatory parameters according to its geometrical properties (area, direction and barycenter) including: Ratio of the frontal and the sagittal size, Phase, Directions (total, thoracic and lumbar), and Shift. It was possible to find similarities among 10 out of the 16 the sub-groups identified by different authors with different methods in different populations.In summation, the state of the art of 3D classification systems include 8 studies which showed some comparability, even though of low level. The most useful one in clinical everyday practice, is far from being defined. More than 20 years passed since the definition of the third dimension of the scoliosis deformity, now the time has come for clinicians and bioengineers to start some real clinical application, and develop means to make this

  2. 2D approaches to 3D watermarking: state-of-the-art and perspectives

    NASA Astrophysics Data System (ADS)

    Mitrea, M.; Duţă, S.; Prêteux, F.

    2006-02-01

    With the advent of the Information Society, video, audio, speech, and 3D media represent the source of huge economic benefits. Consequently, there is a continuously increasing demand for protecting their related intellectual property rights. The solution can be provided by robust watermarking, a research field which exploded in the last 7 years. However, the largest part of the scientific effort was devoted to video and audio protection, the 3D objects being quite neglected. In the absence of any standardisation attempt, the paper starts by summarising the approaches developed in this respect and by further identifying the main challenges to be addressed in the next years. Then, it describes an original oblivious watermarking method devoted to the protection of the 3D objects represented by NURBS (Non uniform Rational B Spline) surfaces. Applied to both free form objects and CAD models, the method exhibited very good transparency (no visible differences between the marked and the unmarked model) and robustness (with respect to both traditional attacks and to NURBS processing).

  3. 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.

  4. 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

  5. [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

  6. 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.

  7. 3D Structure Determination of Native Mammalian Cells using Cryo-FIB and Cryo-electron Tomography

    PubMed Central

    Wang, Ke; Strunk, Korrinn; Zhao, Gongpu; Gray, Jennifer L.; Zhang, Peijun

    2012-01-01

    Cryo-electron tomography (cryo-ET) has enabled high resolution three-dimensional (3D) structural analysis of virus and host cell interactions and many cell signaling events; these studies, however, have largely been limited to very thin, peripheral regions of eukaryotic cells or to small prokaryotic cells. Recent efforts to make thin, vitreous sections using cryo-ultramicrotomy have been successful, however, this method is technically very challenging and with many artifacts. Here, we report a simple and robust method for creating in situ, frozen-hydrated cell lamellas using a focused ion beam at cryogenic temperature (cryo-FIB), allowing access to any interior cellular regions of interest. We demonstrate the utility of cryo-FIB with high resolution 3D cellular structures from both bacterial cells and large mammalian cells. The method will not only facilitate high-throughput 3D structural analysis of biological specimens, but is also broadly applicable to sample preparation of thin films and surface materials without the need for FIB “lift-out”. PMID:22796867

  8. 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

  9. 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.

  10. 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

  11. EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

    PubMed Central

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

    2015-01-01

    Advances in high resolution electron cryomicroscopy (cryo-EM) have been accompanied by the development of validation metrics to independently assess map quality and model geometry. EMRinger 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 will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM. PMID:26280328

  12. Electronic energy states

    NASA Technical Reports Server (NTRS)

    1976-01-01

    One-electron wave functions are reviewed and approximate solutions of two-electron systems are given in terms of these one-electron functions. The symmetry effects associated with electron spin are reviewed and the effects of electron exchange on energy levels of the two-electron system are given. The coupling of electronic orbital and spin angular momentum is considered next and the Lande interval rule for Russell-Saunders or LS coupling is derived. The configurations possible for various multi-electron LS couplings are enumerated (examples from the first two rows of the periodic table are given), and the meaning of the spectroscopic nomenclature is discussed, particularly with respect to the degeneracies of the electron states involved. Next the nomenclature, symmetries, and degeneracies for electron states of diatomic molecules are discussed, and some examples for N2, O2, and NO are presented. The electronic partition functions and derivative thermodynamic properties are expressed in terms of these energies and degeneracies, and examples are given for some of the simple gas species encountered in the earth's atmosphere.

  13. Electron scattering from large molecules: a 3d finite element R-matrix approach

    NASA Astrophysics Data System (ADS)

    Tonzani, Stefano; Greene, Chris H.

    2005-05-01

    To solve the Schr"odinger equation for scattering of a low energy electron from a molecule, we present a three-dimensional finite element R-matrix method [S. Tonzani and C. H. Greene, J. Chem. Phys. 122 01411, (2005)]. Using the static exchange and local density approximations, we can use directly the molecular potentials extracted from ab initio codes (GAUSSIAN 98 in the work described here). A local polarization potential based on density functional theory [F. A. Gianturco and A. Rodriguez-Ruiz, Phys. Rev. A 47, 1075 (1993)] approximately describes the long range attraction to the molecular target induced by the scattering electron without adjustable parameters. We have used this approach successfully in calculations of cross sections for small and medium sized molecules (like SF6, XeF6, C60 and Uracil). This method will be useful to treat the electron-induced dynamics of extended molecular systems, possibly of biological interest, where oth er more complex ab initio methods are difficult to apply.

  14. Simulation of unsteady state performance of a secondary air system by the 1D-3D-Structure coupled method

    NASA Astrophysics Data System (ADS)

    Wu, Hong; Li, Peng; Li, Yulong

    2016-02-01

    This paper describes the calculation method for unsteady state conditions in the secondary air systems in gas turbines. The 1D-3D-Structure coupled method was applied. A 1D code was used to model the standard components that have typical geometric characteristics. Their flow and heat transfer were described by empirical correlations based on experimental data or CFD calculations. A 3D code was used to model the non-standard components that cannot be described by typical geometric languages, while a finite element analysis was carried out to compute the structural deformation and heat conduction at certain important positions. These codes were coupled through their interfaces. Thus, the changes in heat transfer and structure and their interactions caused by exterior disturbances can be reflected. The results of the coupling method in an unsteady state showed an apparent deviation from the existing data, while the results in the steady state were highly consistent with the existing data. The difference in the results in the unsteady state was caused primarily by structural deformation that cannot be predicted by the 1D method. Thus, in order to obtain the unsteady state performance of a secondary air system more accurately and efficiently, the 1D-3D-Structure coupled method should be used.

  15. State-of-the-art of 3D cultures (organs-on-a-chip) in safety testing and pathophysiology.

    PubMed

    Alépée, Natalie; Bahinski, Anthony; Daneshian, Mardas; De Wever, Bart; Fritsche, Ellen; Goldberg, Alan; Hansmann, Jan; Hartung, Thomas; Haycock, John; Hogberg, Helena; Hoelting, Lisa; Kelm, Jens M; Kadereit, Suzanne; McVey, Emily; Landsiedel, Robert; Leist, Marcel; Lübberstedt, Marc; Noor, Fozia; Pellevoisin, Christian; Petersohn, Dirk; Pfannenbecker, Uwe; Reisinger, Kerstin; Ramirez, Tzutzuy; Rothen-Rutishauser, Barbara; Schäfer-Korting, Monika; Zeilinger, Katrin; Zurich, Marie-Gabriele

    2014-01-01

    Integrated approaches using different in vitro methods in combination with bioinformatics can (i) increase the success rate and speed of drug development; (ii) improve the accuracy of toxicological risk assessment; and (iii) increase our understanding of disease. Three-dimensional (3D) cell culture models are important building blocks of this strategy which has emerged during the last years. The majority of these models are organotypic, i.e., they aim to reproduce major functions of an organ or organ system. This implies in many cases that more than one cell type forms the 3D structure, and often matrix elements play an important role. This review summarizes the state of the art concerning commonalities of the different models. For instance, the theory of mass transport/metabolite exchange in 3D systems and the special analytical requirements for test endpoints in organotypic cultures are discussed in detail. In the next part, 3D model systems for selected organs--liver, lung, skin, brain--are presented and characterized in dedicated chapters. Also, 3D approaches to the modeling of tumors are presented and discussed. All chapters give a historical background, illustrate the large variety of approaches, and highlight up- and downsides as well as specific requirements. Moreover, they refer to the application in disease modeling, drug discovery and safety assessment. Finally, consensus recommendations indicate a roadmap for the successful implementation of 3D models in routine screening. It is expected that the use of such models will accelerate progress by reducing error rates and wrong predictions from compound testing. PMID:25027500

  16. Calorimetric approach for 3D dosimetry of high intensity therapeutic electron beams

    NASA Astrophysics Data System (ADS)

    Lamanna, E.; Fiorillo, A. S.; Vena, R.; Berdondini, A.; Bettuzzi, M.; Brancaccio, R.; Casali, F.; Morigi, M. P.; Bilokon, H.; Barca, G.; Castrovillari, F.; Siaka, Y. F. T.

    2009-12-01

    The technique of High Dose Rate Intra-Operative Radiation Therapy (HDR-IORT) consists in the delivery of irradiation immediately after the removal of a cancerous mass, where the same incision is used to focalize the radiation to the tumour bed. Given its particular characteristics, IORT requires dose measurements that are different from those requested in external radiotherapy treatments. The main reason lies in the fact that in this case a single high dose must be delivered to a target volume whose extension and depth will be determined directly during the operation. Because of this peculiar characteristics, until now there is not a dosimetric system able to detect the electron beam giving at once a realtime response and an extensive spatial measure of the absorbed dose. Within the framework of a research project of the INFN (Italian National Institute of Nuclear Physics), we proposed a new system to overcome the problems, Dosiort. The final set-up is a solid phantom having a density approximately 1 g/cm3 with sensitive layers of scintillating fibres at fixed positions in a calorimetric configuration for the containment of electrons of energy 4-12 MeV. The prototype will be able to define the physical and geometrical characteristics of the electron beam (energy, isotropy, homogeneity, etc) and to measure the parameters needed to select the energy, the intensity and the Monitor Units (MU) for the exposition: percentage Depth Dose; beam profiles; isodose curves; values of dose per MU. In this work we present the results obtained by using two orthogonal layers of the calorimetric phantom Dosiort, in particular we report the measurement of the dynamic range of the read-out system and the first qualitative study of the results which can be extracted from the measurements taken in a test beam.

  17. Nonlinear, nonlaminar - 3D computation of electron motion through the output cavity of a klystron.

    NASA Technical Reports Server (NTRS)

    Albers, L. U.; Kosmahl, H. G.

    1971-01-01

    The accurate computation is discussed of electron motion throughout the output cavity of a klystron amplifier. The assumptions are defined whereon the computation is based, and the equations of motion are reviewed, along with the space charge fields derived from a Green's function potential of a solid cylinder. The integration process is then examined with special attention to its most difficult and important aspect - namely, the accurate treatment of the dynamic effect of space charge forces on the motion of individual cell rings of equal volume and charge. The correct treatment is demonstrated upon four specific examples, and a few comments are given on the results obtained.-

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

    DOE PAGESBeta

    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.

  19. Micromachined VLSI 3D electronics. Final report for period September 1, 2000 - March 31, 2001

    SciTech Connect

    Beetz, C.P.; Steinbeck, J.; Hsueh, K.L.

    2001-03-31

    The phase I program investigated the construction of electronic interconnections through the thickness of a silicon wafer. The novel aspects of the technology are that the length-to-width ratio of the channels is as high as 100:1, so that the minimum amount of real estate is used for contact area. Constructing a large array of these through-wafer interconnections will enable two circuit die to be coupled on opposite sides of a silicon circuit board providing high speed connection between the two.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. ICON: 3D reconstruction with 'missing-information' restoration in biological electron tomography.

    PubMed

    Deng, Yuchen; Chen, Yu; Zhang, Yan; Wang, Shengliu; Zhang, Fa; Sun, Fei

    2016-07-01

    Electron tomography (ET) plays an important role in revealing biological structures, ranging from macromolecular to subcellular scale. Due to limited tilt angles, ET reconstruction always suffers from the 'missing wedge' artifacts, thus severely weakens the further biological interpretation. In this work, we developed an algorithm called Iterative Compressed-sensing Optimized Non-uniform fast Fourier transform reconstruction (ICON) based on the theory of compressed-sensing and the assumption of sparsity of biological specimens. ICON can significantly restore the missing information in comparison with other reconstruction algorithms. More importantly, we used the leave-one-out method to verify the validity of restored information for both simulated and experimental data. The significant improvement in sub-tomogram averaging by ICON indicates its great potential in the future application of high-resolution structural determination of macromolecules in situ. PMID:27079261

  7. 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

  8. 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.

  9. The implications of free 3D scanning in the conservation state assessment of old wood painted icon

    NASA Astrophysics Data System (ADS)

    Munteanu, Marius; Sandu, Ion

    2016-06-01

    The present paper presents the conservation state and the making of a 3D model of a XVIII-th century orthodox icon on wood support, using free available software and cloud computing. In order to create the 3D model of the painting layer of the icon a number of 70 pictures were taken using a Nikon DSLR D3300, 24.2 MP in setup with a Hama Star 75 photo tripod, in loops 360° around the painting, at three different angles. The pictures were processed with Autodesk I23D Catch, which automatically finds and matches common features among all of the uploaded photographs in order to create the 3D scene, using the power and speed of cloud computing. The obtained 3D model was afterwards analyzed and processed in order to obtain a final version, which can now be use to better identify, to map and to prioritize the future conservation processes and finally can be shared online as an animation.

  10. Nonlinear, nonlaminar-3D computation of electron motion through the output cavity of a klystron

    NASA Technical Reports Server (NTRS)

    Albers, L. U.; Kosmahl, H. G.

    1971-01-01

    The equations of motion used in the computation are discussed along with the space charge fields and the integration process. The following assumptions were used as a basis for the computation: (1) The beam is divided into N axisymmetric discs of equal charge and each disc into R rings of equal charge. (2) The velocity of each disc, its phase with respect to the gap voltage, and its radius at a specified position in the drift tunnel prior to the interaction gap is known from available large signal one dimensional programs. (3) The fringing rf fields are computed from exact analytical expressions derived from the wave equation assuming a known field shape between the tunnel tips at a radius a. (4) The beam is focused by an axisymmetric magnetic field. Both components of B, that is B sub z and B sub r, are taken into account. (5) Since this integration does not start at the cathode but rather further down the stream prior to entering the output cavity it is assumed that each electron moved along a laminar path from the cathode to the start of integration.

  11. 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.

  12. Automated tracing of filaments in 3D electron tomography reconstructions using Sculptor and Situs.

    PubMed

    Rusu, Mirabela; Starosolski, Zbigniew; Wahle, Manuel; Rigort, Alexander; Wriggers, Willy

    2012-05-01

    The molecular graphics program Sculptor and the command-line suite Situs are software packages for the integration of biophysical data across spatial resolution scales. Herein, we provide an overview of recently developed tools relevant to cryo-electron tomography (cryo-ET), with an emphasis on functionality supported by Situs 2.7.1 and Sculptor 2.1.1. We describe a work flow for automatically segmenting filaments in cryo-ET maps including denoising, local normalization, feature detection, and tracing. Tomograms of cellular actin networks exhibit both cross-linked and bundled filament densities. Such filamentous regions in cryo-ET data sets can then be segmented using a stochastic template-based search, VolTrac. The approach combines a genetic algorithm and a bidirectional expansion with a tabu search strategy to localize and characterize filamentous regions. The automated filament segmentation by VolTrac compares well to a manual one performed by expert users, and it allows an efficient and reproducible analysis of large data sets. The software is free, open source, and can be used on Linux, Macintosh or Windows computers. PMID:22433493

  13. Solid state synthesis of chitosan and its unsaturated derivatives for laser microfabrication of 3D scaffolds

    NASA Astrophysics Data System (ADS)

    Akopova, T. A.; Demina, T. S.; Bagratashvili, V. N.; Bardakova, K. N.; Novikov, M. M.; Selezneva, I. I.; Istomin, A. V.; Svidchenko, E. A.; Cherkaev, G. V.; Surin, N. M.; Timashev, P. S.

    2015-07-01

    Chitosans with various degrees of deacetylation and molecular weights and their allyl substituted derivatives were obtained through a solvent-free reaction under shear deformation in an extruder. Structure and physical-chemical analysis of the samples were carried out using nuclear magnetic resonance (NMR), ultraviolet (UV) and infrared radiation (IR) spectroscopy. Photosensitive materials based on the synthesized polymers were successfully used for microfabrication of 3D well-defined architectonic structures by laser stereolithography. Study on the metabolic activity of NCTC L929 cultured in the presence of the cured chitosan extracts indicates that the engineered biomaterials could support adhesion, spreading and growth of adherent-dependent cells, and thus could be considered as biocompatible scaffolds.

  14. Protein Thermodynamics from the 3D Topological Structure of the Native State

    NASA Astrophysics Data System (ADS)

    Wood, Gregory; Dallakayan, Sargis; Jacobs, Donald

    2004-03-01

    Thermodynamic stability is calculated from the new Distance Constraint Model (DCM)[1]. Microscopic interactions are treated as constraints to which entropy and energies are assigned. From the 3D structure, an ensemble of mechanical frameworks are constructed representing distinct topologies of fluctuating constraints. For each framework, total energy is additive over all constraints while total entropy is additive over a select set of independent constraints. Independent constraints are identified via a graph theoretical algorithm, Floppy Inclusion and Rigid Substructure Topography (FIRST) [2]. Using Monte Carlo sampling a free energy landscape is calculated in constraint space. Excellent fits to heat capacity data for ubiquitin are achieved. Work supported by NIH GM48680-0952. [1] D. J. Jacobs, S. Dallakyan, G. G. Wood and A. Heckathorne, cond-mat/0309207 (to appear in PRE) [2] D. J. Jacobs, A. Rader, L. A. Kuhn and M. F. Thorpe, Proteins 44 150 (2001)

  15. 3-D TECATE/BREW: Thermal, stress, and birefringent ray-tracing codes for solid-state laser design

    SciTech Connect

    Gelinas, R.J.; Doss, S.K.; Nelson, R.G.

    1994-07-20

    This report describes the physics, code formulations, and numerics that are used in the TECATE (totally Eulerian code for anisotropic thermo-elasticity) and BREW (birefringent ray-tracing of electromagnetic waves) codes for laser design. These codes resolve thermal, stress, and birefringent optical effects in 3-D stationary solid-state systems. This suite of three constituent codes is a package referred to as LASRPAK.

  16. Electronic properties of 3d transitional metal pnictides: A comparative study by optical spectroscopy

    NASA Astrophysics Data System (ADS)

    Cheng, B.; Hu, B. F.; Chen, R. Y.; Xu, G.; Zheng, P.; Luo, J. L.; Wang, N. L.

    2012-10-01

    Single-crystalline KFe2As2 and CaT2As2 (T=Fe, Co, Ni, and Cu) are synthesized and investigated by resistivity, susceptibility, and optical spectroscopy. It is found that CaCu2As2 exhibits a similar transition to the lattice abrupt collapse transitions discovered in CaFe2(As1-xPx)2 and Ca1-xRxFe2As2 (R = rare-earth element). The resistivity of KFe2As2 and CaT2As2 (T=Fe, Co, Ni, and Cu) approximately follows the similar T2 dependence at low temperature, but the magnetic behaviors vary with different samples. Optical measurement reveals that the optical response of CaCu2As2 is not sensitive to the transition at 50 K, with no indication of development of a new energy gap below the transition temperature. Using Drude-Lorentz model, we find that two Drude terms, a coherent one and an incoherent one, can fit the low-energy optical conductivity of KFe2As2 and CaT2As2 (T=Fe, Co, and Ni) very well. However, in CaCu2As2, which is a sp-band metal, the low-energy optical conductivity can be well described by a coherent Drude term. Lack of the incoherent Drude term in CaCu2As2 may be attributed to a weaker electronic correlation than in KFe2As2 and CaT2As2 (T=Fe, Co, and Ni). Spectral weight analysis of these samples indicates that the unconventional spectral weight transfer, which is related to Hund's coupling energy JH, is only observed in iron pnictides, supporting the viewpoint that JH may be a key clue in the search for the mechanism of magnetism and superconductivity in pnictides.

  17. 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?

  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 PAGESBeta

    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. 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

  1. 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

  2. Electronic structure evolution of single bilayer Bi(1 1 1) film on 3D topological insulator Bi2Se x Te3-x surfaces.

    PubMed

    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

    2016-06-29

    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. PMID:27166645

  3. 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.

  4. Structural, electronic, and magnetic properties of 3D metal trioxide and tetraoxide superhalogen cluster-doped monolayer BN

    NASA Astrophysics Data System (ADS)

    Meng, Jingjing; Li, Dan; Niu, Yuan; Zhao, Hongmin; Liang, Chunjun; He, Zhiqun

    2016-07-01

    The structural, electronic, and magnetic properties of monolayer BN doped with 3D metal trioxide and tetraoxide superhalogen clusters are investigated using first-principle calculations. TMO3(4)-doped monolayer BN exhibits a low negative formation energy, whereas TM atoms embedded in monolayer BN show a high positive formation energy. TMO3(4) clusters are embedded more easily in monolayer BN than TM atoms. Compared with TMO3-doped structures, TMO4-doped structures have a higher structural stability because of their higher binding energies. Given their low negative formation energies, TMO4-doped structures are more favored for specific applications than TMO3-doped structures and TM atom-doped structures. Large magnetic moments per supercell and significant ferromagnetic couplings between a TM atom and neighboring B and N atoms on the BN layer were observed in all TMO4-doped structures, except for TiO4-doped structures.

  5. Universal bounds on charged states in 2d CFT and 3d gravity

    NASA Astrophysics Data System (ADS)

    Benjamin, Nathan; Dyer, Ethan; Fitzpatrick, A. Liam; Kachru, Shamit

    2016-08-01

    We derive an explicit bound on the dimension of the lightest charged state in two dimensional conformal field theories with a global abelian symmetry. We find that the bound scales with c and provide examples that parametrically saturate this bound. We also prove that any such theory must contain a state with charge-to-mass ratio above a minimal lower bound. We comment on the implications for charged states in three dimensional theories of gravity.

  6. Electronic Structure, Donor and Acceptor Transitions, and Magnetism of 3d Impurities in In2O3 and ZnO

    SciTech Connect

    Raebiger, H.; Lany, S,; Zunger, A.

    2009-01-01

    3d transition impurities in wide-gap oxides may function as donor/acceptor defects to modify carrier concentrations, and as magnetic elements to induce collective magnetism. Previous first-principles calculations have been crippled by the LDA error, where the occupation of the 3d-induced levels is incorrect due to spurious charge spilling into the misrepresented host conduction band, and have only considered magnetism and carrier doping separately. We employ a band-structure-corrected theory, and present simultaneously the chemical trends for electronic properties, carrier doping, and magnetism along the series of 3d{sup 1}-3d{sup 8} transition-metal impurities in the representative wide-gap oxide hosts In{sub 2}O{sub 3} and ZnO. We find that most 3d impurities in In{sub 2}O{sub 3} are amphoteric, whereas in ZnO, the early 3d's (Sc, Ti, and V) are shallow donors, and only the late 3d's (Co and Ni) have acceptor transitions. Long-range ferromagnetic interactions emerge due to partial filling of 3d resonances inside the conduction band and, in general, require electron doping from additional sources.

  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. Macroscopic Degeneracy of Zero-Mode Rotating Surface States in 3D Dirac and Weyl Semimetals under Radiation.

    PubMed

    González, José; Molina, Rafael A

    2016-04-15

    We investigate the development of novel surface states when 3D Dirac or Weyl semimetals are placed under circularly polarized electromagnetic radiation. We find that the hybridization between inverted Floquet bands opens, in general, a gap, which closes at so-called exceptional points found for complex values of the momentum. This corresponds to the appearance of midgap surface states in the form of evanescent waves decaying from the surface exposed to the radiation. We observe a phenomenon reminiscent of Landau quantization by which the midgap surface states get a large degeneracy proportional to the radiation flux traversing the surface of the semimetal. We show that all of these surface states carry angular current, leading to an angular modulation of their charge that rotates with the same frequency of the radiation, which should manifest in the observation of a macroscopic chiral current in the irradiated surface. PMID:27127980

  9. Macroscopic Degeneracy of Zero-Mode Rotating Surface States in 3D Dirac and Weyl Semimetals under Radiation

    NASA Astrophysics Data System (ADS)

    González, José; Molina, Rafael A.

    2016-04-01

    We investigate the development of novel surface states when 3D Dirac or Weyl semimetals are placed under circularly polarized electromagnetic radiation. We find that the hybridization between inverted Floquet bands opens, in general, a gap, which closes at so-called exceptional points found for complex values of the momentum. This corresponds to the appearance of midgap surface states in the form of evanescent waves decaying from the surface exposed to the radiation. We observe a phenomenon reminiscent of Landau quantization by which the midgap surface states get a large degeneracy proportional to the radiation flux traversing the surface of the semimetal. We show that all of these surface states carry angular current, leading to an angular modulation of their charge that rotates with the same frequency of the radiation, which should manifest in the observation of a macroscopic chiral current in the irradiated surface.

  10. Comparison of 3D Classical Trajectory and Transition-State Theory Reaction Cross Sections

    DOE R&D Accomplishments Database

    Koeppl, G. W.; Karplus, Martin

    1970-10-01

    Although there is excellent agreement for a system such as H+H{sub 2} --> H{sub 2}+H, in which both the potential and the particle masses are symmetric, significant deviations occur for more asymmetric reactions. A detailed analysis show that the calculated differences are from the violation of two assumptions of transition-state theory.

  11. Generating multi-GeV electron bunches using single stage laser wakefield acceleration in a 3D nonlinear regime

    NASA Astrophysics Data System (ADS)

    Lu, W.; Tzoufras, M.; Joshi, C.; Tsung, F. S.; Mori, W. B.; Vieira, J.; Fonseca, R. A.; Silva, L. O.

    2007-06-01

    The extraordinary ability of space-charge waves in plasmas to accelerate charged particles at gradients that are orders of magnitude greater than in current accelerators has been well documented. We develop a phenomenological framework for laser wakefield acceleration (LWFA) in the 3D nonlinear regime, in which the plasma electrons are expelled by the radiation pressure of a short pulse laser, leading to nearly complete blowout. Our theory provides a recipe for designing a LWFA for given laser and plasma parameters and estimates the number and the energy of the accelerated electrons whether self-injected or externally injected. These formulas apply for self-guided as well as externally guided pulses (e.g. by plasma channels). We demonstrate our results by presenting a sample particle-in-cell (PIC) simulation of a 30fs, 200 TW laser interacting with a 0.75 cm long plasma with density 1.5×1018cm-3 to produce an ultrashort (10 fs) monoenergetic bunch of self-injected electrons at 1.5 GeV with 0.3 nC of charge. For future higher-energy accelerator applications, we propose a parameter space, which is distinct from that described by Gordienko and Pukhov [Phys. Plasmas 12, 043109 (2005)PHPAEN1070-664X10.1063/1.1884126] in that it involves lower plasma densities and wider spot sizes while keeping the intensity relatively constant. We find that this helps increase the output electron beam energy while keeping the efficiency high.

  12. 3D collapse of rotating stellar iron cores in general relativity including deleptonization and a nuclear equation of state.

    PubMed

    Ott, C D; Dimmelmeier, H; Marek, A; Janka, H-T; Hawke, I; Zink, B; Schnetter, E

    2007-06-29

    We present 2D and 3D simulations of the collapse of rotating stellar iron cores in general relativity employing a nuclear equation of state and an approximate treatment of deleptonization. We compare fully general relativistic and conformally flat evolutions and find that the latter treatment is sufficiently accurate for the core-collapse supernova problem. We focus on gravitational wave (GW) emission from rotating collapse, bounce, and early postbounce phases. Our results indicate that the GW signature of these phases is much more generic than previously estimated. We also track the growth of a nonaxisymmetric instability in one model, leading to strong narrow-band GW emission. PMID:17678077

  13. 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.

  14. 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.

  15. 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.

  16. 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)

  17. 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

  18. 3D Ion and Electron Distribution Function Measurements from the Fast Plasma Investigation on the Magnetospheric Multiscale Mission

    NASA Astrophysics Data System (ADS)

    Giles, B. L.; Pollock, C. J.; Avanov, L. A.; Barrie, A. C.; Burch, J. L.; Chandler, M. O.; Clark, G. B.; Coffey, V. N.; Dickson, C.; Dorelli, J.; Ergun, R. E.; Fuselier, S. A.; Gershman, D. J.; Gliese, U.; Holland, M. P.; Jacques, A. D.; Kreisler, S.; Lavraud, B.; MacDonald, E.; Mauk, B.; Moore, T. E.; Mukai, T.; Nakamura, R.; Paterson, W. R.; Rager, A. C.; Saito, Y.; Salo, C.; Sauvaud, J. A.; Torbert, R. B.; Vinas, A. F.; Yokota, S.

    2015-12-01

    The primary focus of the Magnetospheric Multiscale (MMS) mission, launched in March 2015, is magnetic reconnection and associated processes. Understanding hinges critically on the kinetic physics that allows reconnection to take place. The Fast Plasma Investigation (FPI) provides electron and ion distribution functions at 4.5s cadence and, for select periods of time, at cadences of 30ms for electrons and 150ms for ions. These select time periods are chosen after in situ acquisition based on inspection of the low resolution data. Thus the FPI provides, independent of spacecraft spin rate, the time resolution needed to resolve the small, fast-moving reconnection diffusion regions. The first mission phase focuses on the dayside magnetopause and this presentation is intended to demonstrate the capabilities of FPI to resolve the important spatial scales relevant to the reconnection process. Magnetopause and other boundary crossings will be examined and the phase-space trajectories identified at the tetrahedral satellite locations through analysis of the 3D distribution functions.

  19. Influence of spatial disorder on the superconducting state of a 3D superconductor

    NASA Astrophysics Data System (ADS)

    Parra, Carolina; Niestemski, Francis; Giraldo-Gallo, Paula; Contryman, Alex W.; Geballe, Theodore H.; Fisher, Ian R.; Manoharan, Hari C.

    2014-03-01

    We present the first measurements of the local tunneling density of states on the three-dimensional superconductor BaPb1 - x BixO3 as a function of Bi doping. Scanning tunneling spectroscopy measurements are performed on a sequence of samples which exhibit a field-tuned superconductor-to-insulator (SIT) transition. Our study shows that gap variations in the superconducting (SC) state (as a sign of SC disorder level) increase when the system moves towards the SIT phase boundary, with spatial inhomogeneity comparable in size to the material's coherence length. We demonstrate that this highly inhomogeneous local gap size is always finite at every location, even for Bi concentration closest to the SIT, where local insulating behavior is expected and globally confirmed in transport experiments. Our results also suggest a method for increasing the critical temperature for this material by reducing its spatial disorder in the appropriate part of the phase diagram.

  20. High-Resolution 3D Structure Determination of Kaliotoxin by Solid-State NMR Spectroscopy

    PubMed Central

    Korukottu, Jegannath; Schneider, Robert; Vijayan, Vinesh; Lange, Adam; Pongs, Olaf; Becker, Stefan; Baldus, Marc; Zweckstetter, Markus

    2008-01-01

    High-resolution solid-state NMR spectroscopy can provide structural information of proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy. Here we demonstrate that it is possible to determine a protein structure by solid-state NMR to a resolution comparable to that by solution NMR. Using an iterative assignment and structure calculation protocol, a large number of distance restraints was extracted from 1H/1H mixing experiments recorded on a single uniformly labeled sample under magic angle spinning conditions. The calculated structure has a coordinate precision of 0.6 Å and 1.3 Å for the backbone and side chain heavy atoms, respectively, and deviates from the structure observed in solution. The approach is expected to be applicable to larger systems enabling the determination of high-resolution structures of amyloid or membrane proteins. PMID:18523586

  1. A fully implicit method for 3D quasi-steady state magnetic advection-diffusion.

    SciTech Connect

    Siefert, Christopher; Robinson, Allen Conrad

    2009-09-01

    We describe the implementation of a prototype fully implicit method for solving three-dimensional quasi-steady state magnetic advection-diffusion problems. This method allows us to solve the magnetic advection diffusion equations in an Eulerian frame with a fixed, user-prescribed velocity field. We have verified the correctness of method and implementation on two standard verification problems, the Solberg-White magnetic shear problem and the Perry-Jones-White rotating cylinder problem.

  2. Development of a State-Wide 3-D Seismic Tomography Velocity Model for California

    NASA Astrophysics Data System (ADS)

    Thurber, C. H.; Lin, G.; Zhang, H.; Hauksson, E.; Shearer, P.; Waldhauser, F.; Hardebeck, J.; Brocher, T.

    2007-12-01

    We report on progress towards the development of a state-wide tomographic model of the P-wave velocity for the crust and uppermost mantle of California. The dataset combines first arrival times from earthquakes and quarry blasts recorded on regional network stations and travel times of first arrivals from explosions and airguns recorded on profile receivers and network stations. The principal active-source datasets are Geysers-San Pablo Bay, Imperial Valley, Livermore, W. Mojave, Gilroy-Coyote Lake, Shasta region, Great Valley, Morro Bay, Mono Craters-Long Valley, PACE, S. Sierras, LARSE 1 and 2, Loma Prieta, BASIX, San Francisco Peninsula and Parkfield. Our beta-version model is coarse (uniform 30 km horizontal and variable vertical gridding) but is able to image the principal features in previous separate regional models for northern and southern California, such as the high-velocity subducting Gorda Plate, upper to middle crustal velocity highs beneath the Sierra Nevada and much of the Coast Ranges, the deep low-velocity basins of the Great Valley, Ventura, and Los Angeles, and a high- velocity body in the lower crust underlying the Great Valley. The new state-wide model has improved areal coverage compared to the previous models, and extends to greater depth due to the data at large epicentral distances. We plan a series of steps to improve the model. We are enlarging and calibrating the active-source dataset as we obtain additional picks from investigators and perform quality control analyses on the existing and new picks. We will also be adding data from more quarry blasts, mainly in northern California, following an identification and calibration procedure similar to Lin et al. (2006). Composite event construction (Lin et al., in press) will be carried out for northern California for use in conventional tomography. A major contribution of the state-wide model is the identification of earthquakes yielding arrival times at both the Northern California Seismic

  3. First-principles calculations of the electronic structure and magnetic properties of 3d transition-metal impurities in bcc and amorphous iron

    NASA Astrophysics Data System (ADS)

    Kontsevoi, O. Yu.; Gubanov, V. A.

    1995-06-01

    We present the results of the first-principles calculations of electronic structure, magnetic moments, and effective-exchange-interaction parameters for 3d impurities in ferromagnetic bcc and amorphous iron as obtained by the self-consistent tight-binding linear-muffin-tin-orbital recursion method. Impurities in bcc Fe have been modeled both in the single-site approximation and taking into account up to four shells of the nearest-to-the-impurity neighbors. The results for crystalline iron agree well with the previous more precise Korringa-Kohn-Rostoker Green's function calculations [Phys. Rev. B 40, 8203 (1989)], and confirm the sufficient accuracy of the method developed. The perturbations of electronic states for Fe atoms in different coordinational shells around impurity are considered. Peculiarities of impurity electronic states in amorphous Fe and their influence on magnetic behavior of the system are discussed. The role of impurities in possible stabilization of ferromagnetic ordering in amorphous Fe is investigated in terms of effective-exchange-interaction parameters calculated for the nearest-to-impurity host atoms.

  4. A novel numerical flux for the 3D Euler equations with general equation of state

    NASA Astrophysics Data System (ADS)

    Toro, Eleuterio F.; Castro, Cristóbal E.; Lee, Bok Jik

    2015-12-01

    Here we extend the flux vector splitting approach recently proposed in E.F. Toro and M.E. Vázquez-Cendón (2012) [42]. The scheme was originally presented for the 1D Euler equations for ideal gases and its extension presented in this paper is threefold: (i) we solve the three-dimensional Euler equations on general meshes; (ii) we use a general equation of state; and (iii) we achieve high order of accuracy in both space and time through application of the semi-discrete ADER methodology on general meshes. The resulting methods are systematically assessed for accuracy, robustness and efficiency on a carefully selected suite of test problems. Formal high accuracy is assessed through convergence rates studies for schemes of up to 4th order of accuracy in both space and time on unstructured meshes.

  5. Suppression law of quantum states in a 3D photonic fast Fourier transform chip.

    PubMed

    Crespi, Andrea; Osellame, Roberto; Ramponi, Roberta; Bentivegna, Marco; Flamini, Fulvio; Spagnolo, Nicolò; Viggianiello, Niko; Innocenti, Luca; Mataloni, Paolo; Sciarrino, Fabio

    2016-01-01

    The identification of phenomena able to pinpoint quantum interference is attracting large interest. Indeed, a generalization of the Hong-Ou-Mandel effect valid for any number of photons and optical modes would represent an important leap ahead both from a fundamental perspective and for practical applications, such as certification of photonic quantum devices, whose computational speedup is expected to depend critically on multi-particle interference. Quantum distinctive features have been predicted for many particles injected into multimode interferometers implementing the Fourier transform over the optical modes. Here we develop a scalable approach for the implementation of the fast Fourier transform algorithm using three-dimensional photonic integrated interferometers, fabricated via femtosecond laser writing technique. We observe the suppression law for a large number of output states with four- and eight-mode optical circuits: the experimental results demonstrate genuine quantum interference between the injected photons, thus offering a powerful tool for diagnostic of photonic platforms. PMID:26843135

  6. Suppression law of quantum states in a 3D photonic fast Fourier transform chip

    PubMed Central

    Crespi, Andrea; Osellame, Roberto; Ramponi, Roberta; Bentivegna, Marco; Flamini, Fulvio; Spagnolo, Nicolò; Viggianiello, Niko; Innocenti, Luca; Mataloni, Paolo; Sciarrino, Fabio

    2016-01-01

    The identification of phenomena able to pinpoint quantum interference is attracting large interest. Indeed, a generalization of the Hong–Ou–Mandel effect valid for any number of photons and optical modes would represent an important leap ahead both from a fundamental perspective and for practical applications, such as certification of photonic quantum devices, whose computational speedup is expected to depend critically on multi-particle interference. Quantum distinctive features have been predicted for many particles injected into multimode interferometers implementing the Fourier transform over the optical modes. Here we develop a scalable approach for the implementation of the fast Fourier transform algorithm using three-dimensional photonic integrated interferometers, fabricated via femtosecond laser writing technique. We observe the suppression law for a large number of output states with four- and eight-mode optical circuits: the experimental results demonstrate genuine quantum interference between the injected photons, thus offering a powerful tool for diagnostic of photonic platforms. PMID:26843135

  7. 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

  8. 3D interactive tractography-informed resting-state fMRI connectivity

    PubMed Central

    Chamberland, Maxime; Bernier, Michaël; Fortin, David; Whittingstall, Kevin; Descoteaux, Maxime

    2015-01-01

    In the past decade, the fusion between diffusion magnetic resonance imaging (dMRI) and functional magnetic resonance imaging (fMRI) has opened the way for exploring structure-function relationships in vivo. As it stands, the common approach usually consists of analysing fMRI and dMRI datasets separately or using one to inform the other, such as using fMRI activation sites to reconstruct dMRI streamlines that interconnect them. Moreover, given the large inter-individual variability of the healthy human brain, it is possible that valuable information is lost when a fixed set of dMRI/fMRI analysis parameters such as threshold values are assumed constant across subjects. By allowing one to modify such parameters while viewing the results in real-time, one can begin to fully explore the sensitivity of structure-function relations and how they differ across brain areas and individuals. This is especially important when interpreting how structure-function relationships are altered in patients with neurological disorders, such as the presence of a tumor. In this study, we present and validate a novel approach to achieve this: First, we present an interactive method to generate and visualize tractography-driven resting-state functional connectivity, which reduces the bias introduced by seed size, shape and position. Next, we demonstrate that structural and functional reconstruction parameters explain a significant portion of intra- and inter-subject variability. Finally, we demonstrate how our proposed approach can be used in a neurosurgical planning context. We believe this approach will promote the exploration of structure-function relationships in a subject-specific aspect and will open new opportunities for connectomics. PMID:26321901

  9. Experimental investigation of photoionization cross section for the 3d 2D excited states of lithium and sodium

    NASA Astrophysics Data System (ADS)

    Nadeem, Ali; Shah, Mehmood; Shahzada, Shaista; Ahmed, Mushtaq; Haq, Sami-ul-

    2013-09-01

    We report experimentally measured photoionization cross sections for the 3 d 2D excited states of lithium and sodium at first ionization threshold. The experiments were performed using two dye lasers simultaneously pumped by the second harmonic of a Nd:YAG laser. The vapor contentment and the detection system was a thermionic diode ion detector operating in a space charge limited mode. Photoionization cross sections of the excited states were deduced from the dependence of ion signal intensity on the ionizing laser energies as 19 ± 3 Mb and 21.5 ± 3.5 Mb for lithium and sodium respectively, which are in good agreement with the previously computed theoretical results.

  10. Association of intracellular and synaptic organization in cochlear inner hair cells revealed by 3D electron microscopy

    PubMed Central

    Bullen, Anwen; West, Timothy; Moores, Carolyn; Ashmore, Jonathan; Fleck, Roland A.; MacLellan-Gibson, Kirsty; Forge, Andrew

    2015-01-01

    ABSTRACT The ways in which cell architecture is modelled to meet cell function is a poorly understood facet of cell biology. To address this question, we have studied the cytoarchitecture of a cell with highly specialised organisation, the cochlear inner hair cell (IHC), using multiple hierarchies of three-dimensional (3D) electron microscopy analyses. We show that synaptic terminal distribution on the IHC surface correlates with cell shape, and the distribution of a highly organised network of membranes and mitochondria encompassing the infranuclear region of the cell. This network is juxtaposed to a population of small vesicles, which represents a potential new source of neurotransmitter vesicles for replenishment of the synapses. Structural linkages between organelles that underlie this organisation were identified by high-resolution imaging. Taken together, these results describe a cell-encompassing network of membranes and mitochondria present in IHCs that support efficient coding and transmission of auditory signals. Such techniques also have the potential for clarifying functionally specialised cytoarchitecture of other cell types. PMID:26045447

  11. 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.

  12. 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

  13. Steady-state first pass perfusion (SSFPP): A new approach to 3D first-pass myocardial perfusion imaging

    PubMed Central

    Giri, Shivraman; Xue, Hui; Maiseyeu, Andrei; Kroeker, Randall; Rajagopalan, Sanjay; White, Richard D.; Zuehlsdorff, Sven; Raman, Subha V.; Simonetti, Orlando P

    2013-01-01

    Purpose To describe and characterize a new approach to first-pass myocardial perfusion utilizing balanced steady-state free precession acquisition without the use of saturation recovery or other magnetization preparation. Theory The balanced steady-state free precession sequence is inherently sensitive to contrast agent enhancement of the myocardium. This sensitivity can be used to advantage in first-pass myocardial perfusion imaging by eliminating the need for magnetization preparation. Methods Bloch equation simulations, phantom experiments, and in vivo 2D imaging studies were run comparing the proposed technique with three other methods: saturation recovery spoiled gradient echo, saturation recovery steady-state free precession, and steady-state spoiled gradient echo without magnetization preparation. Additionally, an acquisition-reconstruction strategy for 3D perfusion imaging is proposed and initial experience with this approach is demonstrated in healthy subjects and one patient. Results Phantom experiments verified simulation results showing the sensitivity of the balanced steady-state free precession sequence to contrast agent enhancement in solid tissue is similar to that of magnetization-prepared acquisitions. Images acquired in normal volunteers showed the proposed technique provided superior signal and signal-to-noise ratio compared with all other sequences at baseline as well as post-contrast. Conclusion A new approach to first-pass myocardial perfusion is presented that obviates the need for magnetization preparation and provides high signal-to-noise ratio. PMID:23440705

  14. Simultaneous ionization-excitation of helium to the 3s, 3p, and 3d states of He+

    NASA Astrophysics Data System (ADS)

    Zatsarinny, Oleg; Bartschat, Klaus

    2015-05-01

    We extended our work on ionization of helium with simultaneous excitation to the n = 2 states to include the n = 3 manifold of the residual ion. This requires the inclusion of pseudo-states constructed on the 3s, 3p, and 3d ionic core. We used a parallelized version of the B-spline R-matrix (BSR) package to perform a calculation with 1,254 target states, resulting in up to 3,027 coupled channels and matrices of rank up to 200,000 to be diagonalized. The triple-differential cross section (TDCS) was extracted by the projection method. We obtain excellent agreement with experiment regarding the angular dependence of the TDCS for all kinematical situations available for comparison. Some discrepancies remain for the absolute magnitude. Results for the n = 2 states are stable and closely agree with previous predictions. Work supported by the United States National Science Foundation under grants No. PHY-1212450, PHY-1430245 and the XSEDE allocation PHY-090031.

  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. Preliminary Pseudo 3-D Imagery of the State Line Fault, Stewart Valley, Nevada Using Seismic Reflection Data

    NASA Astrophysics Data System (ADS)

    Saldaña, S. C.; Snelson, C. M.; Taylor, W. J.; Beachly, M.; Cox, C. M.; Davis, R.; Stropky, M.; Phillips, R.; Robins, C.; Cothrun, C.

    2007-12-01

    The Pahrump Fault system is located in the central Basin and Range region and consists of three main fault zones: the Nopah range front fault zone, the State Line fault zone and the Spring Mountains range fault zone. The State Line fault zone is made up north-west trending dextral strike-slip faults that run parallel to the Nevada- California border. Previous geologic and geophysical studies conducted in and around Stewart Valley, located ~90 km from Las Vegas, Nevada, have constrained the location of the State Line fault zone to within a few kilometers. The goals of this project were to use seismic methods to definitively locate the northwestern most trace of the State Line fault and produce pseudo 3-D seismic cross-sections that can then be used to characterize the subsurface geometry and determine the slip of the State Line fault. During July 2007, four seismic lines were acquired in Stewart Valley: two normal and two parallel to the mapped traces of the State Line fault. Presented here are preliminary results from the two seismic lines acquired normal to the fault. These lines were acquired utilizing a 144-channel geode system with each of the 4.5 Hz vertical geophones set out at 5 m intervals to produce a 595 m long profile to the north and a 715 m long profile to the south. The vibroseis was programmed to produce an 8 s linear sweep from 20-160 Hz. These data returned excellent signal to noise and reveal subsurface lithology that will subsequently be used to resolve the subsurface geometry of the State Line fault. This knowledge will then enhance our understanding of the evolution of the State Line fault. Knowing how the State Line fault has evolved gives insight into the stick-slip fault evolution for the region and may improve understanding of how stress has been partitioned from larger strike-slip systems such as the San Andreas fault.

  17. State-resolved three-dimensional electron-momentum correlation in nonsequential double ionization of benzene

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    We report state-resolved electron-momentum correlation measurement of strong-field nonsequential double ionization in benzene. With a novel coincidence detection apparatus, highly efficient triple coincidence (electron-electron dication) and quadruple coincidence (electron-electron-cation-cation) are used to resolve the final ionic states and to characterize three-dimensional (3D) electron-momentum correlation. The primary states associated with dissociative and nondissociative dications are assigned. A 3D momentum anticorrelation is observed for the electrons in coincidence with dissociative benzene dication states whereas such a correlation is absent for nondissociative dication states.

  18. Task-Independent Cognitive State Transition Detection From Cortical Neurons During 3-D Reach-to-Grasp Movements.

    PubMed

    Kang, Xiaoxu; Sarma, Sridevi V; Santaniello, Sabato; Schieber, Marc; Thakor, Nitish V

    2015-07-01

    Complex reach, grasp, and object manipulation tasks require sequential, temporal coordination of movements by neurons in the brain. Detecting cognitive state transitions associated with motor tasks from sequential neural data is pivotal in rehabilitation engineering. The cognitive state detectors proposed thus far rely on task-dependent (TD) models, i.e., the detection strategy exploits a priori knowledge of the movement tasks to determine the actual cognitive states, regardless of whether these cognitive states actually depend on the movement tasks or not. This approach, however, is not viable when the tasks are not known a priori (e.g., the subject performs many different tasks) or there is paucity of neural data for each task. Moreover, some cognitive states (e.g., holding) may be invariant to the movement tasks performed. Here we propose a real-time (online) task-independent (TI) framework to detect cognitive state transitions from spike trains and kinematic measurements. We constructed this detection framework using 452 single-unit neural spike recordings collected via multielectrode arrays in the premotor dorsal and ventral (PMd and PMv) cortical regions of two nonhuman primates performing 3-D multiobject reach-to-grasp tasks. We used the detection latency and accuracy of state transitions to measure the performance. We find that, in both online and offline detection modes: 1) TI models have significantly better performance than corresponding TD models when using neuronal data alone and 2) during movements, the addition of the kinematics history to the TI models further improves detection performance. These findings suggest that TI models may accurately detect cognitive state transitions. Our framework could pave the way for a TI control of neural prosthesis from cortical neurons. PMID:25643410

  19. Interactions of Pluronic nanocarriers with 2D and 3D cell cultures: Effects of PEO block length and aggregation state.

    PubMed

    Arranja, Alexandra; Denkova, Antonia G; Morawska, Karolina; Waton, Gilles; van Vlierberghe, Sandra; Dubruel, Peter; Schosseler, François; Mendes, Eduardo

    2016-02-28

    This work reveals how the physicochemical properties of Pluronic block copolymers influence significantly their interactions with cancer cells, whether in monolayer or spheroid cultures, and how different clinical applications can be foreseen. Two-dimensional (2D) and three-dimensional (3D) cell culture models were used to investigate the interactions of Pluronic carriers with different PEO block length and aggregation state (unimers versus cross-linked micelles) in HeLa and U87 cancer cells. Stabilized micelles of Pluronic P94 or F127 were obtained by polymerization of a crosslinking agent in the micelles hydrophobic core. Nanocarriers were functionalized with a fluorescent probe for visualization, and with a chelator for radiolabeling with Indium-111 and gamma-quantification. The 2D cell models revealed that the internalization pathways and ultimate cellular localization of the Pluronic nanocarriers depended largely on both the PEO block size and aggregation state of the copolymers. The smaller P94 unimers with an average radius of 2.1nm and the shortest PEO block mass (1100gmol(-1)) displayed the highest cellular uptake and retention. 3D tumor spheroids were used to assess the penetration capacity and toxicity potential of the nanocarriers. Results showed that cross-linked F127 micelles were more efficiently delivered across the tumor spheroids, and the penetration depth depends mostly on the transcellular transport of the carriers. The Pluronic P94-based carriers with the shortest PEO block length induced spheroid toxicity, which was significantly influenced by the spheroid cellular type. PMID:26792572

  20. A hybrid 3D-Var data assimilation scheme for joint state and parameter estimation: application to morphodynamic modelling

    NASA Astrophysics Data System (ADS)

    Smith, P.; Nichols, N. K.; Dance, S.

    2011-12-01

    Data assimilation is typically used to provide initial conditions for state estimation; combining model predictions with observational data to produce an updated model state that most accurately characterises the true system state whilst keeping the model parameters fixed. This updated model state is then used to initiate the next model forecast. However, even with perfect initial data, inaccurate representation of model parameters will lead to the growth of model error and therefore affect the ability of our model to accurately predict the true system state. A key question in model development is how to estimate parameters a priori. In most cases, parameter estimation is addressed as a separate issue to state estimation and model calibration is performed offline in a separate calculation. Here we demonstrate how, by employing the technique of state augmentation, it is possible to use data assimilation to estimate uncertain model parameters concurrently with the model state as part of the assimilation process. We present a novel hybrid data assimilation algorithm developed for application to parameter estimation in morphodynamic models. The new approach is based on a computationally inexpensive 3D-Var scheme, where the specification of the covariance matrices is crucial for success. For combined state-parameter estimation, it is particularly important that the cross-covariances between the parameters and the state are given a good a priori specification. Early experiments indicated that in order to yield reliable estimates of the true parameters, a flow dependent representation of the state-parameter cross covariances is required. By combining ideas from 3D-Var and the extended Kalman filter we have developed a novel hybrid assimilation scheme that captures the flow dependent nature of the state-parameter cross covariances without the computational expense of explicitly propagating the full system covariance matrix. We will give details of the formulation of this

  1. 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

  2. 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.

  3. From microscales to macroscales in 3D: selfconsistent equation of state for supernova and neutron star models

    NASA Astrophysics Data System (ADS)

    Newton, W. G.; Stone, J. R.; Mezzacappa, A.

    2006-09-01

    First results from a fully self-consistent, temperature-dependent equation of state that spans the density range of neutron stars and supernova cores above neutron drip density are presented. The equation of state (EoS) is calculated using a mean-field Hartree-Fock method in three dimensions (3D). The nuclear interaction is represented by the phenomenological Skyrme model in this work, but the EoS can be obtained in our framework for any suitable form of the nucleon-nucleon effective interaction. The scheme we employ naturally allows effects such as (i) neutron drip, which results in an external neutron gas, (ii) the variety of exotic nuclear shapes expected for extremely neutron heavy nuclei, and (iii) the subsequent dissolution of these nuclei into nuclear matter. In this way, the equation of state is calculated across phase transitions without recourse to interpolation techniques between density regimes described by different physical models. EoS tables are calculated in the wide range of densities, temperature and proton/neutron ratios on the ORNL NCCS XT3, using up to 2000 processors simultaneously.

  4. 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

  5. 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.

  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. A 3D in vitro model to explore the inter-conversion between epithelial and mesenchymal states during EMT and its reversion.

    PubMed

    Bidarra, S J; Oliveira, P; Rocha, S; Saraiva, D P; Oliveira, C; Barrias, C C

    2016-01-01

    Epithelial-to-mesenchymal transitions (EMT) are strongly implicated in cancer dissemination. Intermediate states, arising from inter-conversion between epithelial (E) and mesenchymal (M) states, are characterized by phenotypic heterogeneity combining E and M features and increased plasticity. Hybrid EMT states are highly relevant in metastatic contexts, but have been largely neglected, partially due to the lack of physiologically-relevant 3D platforms to study them. Here we propose a new in vitro model, combining mammary E cells with a bioengineered 3D matrix, to explore phenotypic and functional properties of cells in transition between E and M states. Optimized alginate-based 3D matrices provided adequate 3D microenvironments, where normal epithelial morphogenesis was recapitulated, with formation of acini-like structures, similar to those found in native mammary tissue. TGFβ1-driven EMT in 3D could be successfully promoted, generating M-like cells. TGFβ1 removal resulted in phenotypic switching to an intermediate state (RE cells), a hybrid cell population expressing both E and M markers at gene/protein levels. RE cells exhibited increased proliferative/clonogenic activity, as compared to M cells, being able to form large colonies containing cells with front-back polarity, suggesting a more aggressive phenotype. Our 3D model provides a powerful tool to investigate the role of the microenvironment on metastable EMT stages. PMID:27255191

  8. A 3D in vitro model to explore the inter-conversion between epithelial and mesenchymal states during EMT and its reversion

    PubMed Central

    Bidarra, S. J.; Oliveira, P.; Rocha, S.; Saraiva, D. P.; Oliveira, C.; Barrias, C. C.

    2016-01-01

    Epithelial-to-mesenchymal transitions (EMT) are strongly implicated in cancer dissemination. Intermediate states, arising from inter-conversion between epithelial (E) and mesenchymal (M) states, are characterized by phenotypic heterogeneity combining E and M features and increased plasticity. Hybrid EMT states are highly relevant in metastatic contexts, but have been largely neglected, partially due to the lack of physiologically-relevant 3D platforms to study them. Here we propose a new in vitro model, combining mammary E cells with a bioengineered 3D matrix, to explore phenotypic and functional properties of cells in transition between E and M states. Optimized alginate-based 3D matrices provided adequate 3D microenvironments, where normal epithelial morphogenesis was recapitulated, with formation of acini-like structures, similar to those found in native mammary tissue. TGFβ1-driven EMT in 3D could be successfully promoted, generating M-like cells. TGFβ1 removal resulted in phenotypic switching to an intermediate state (RE cells), a hybrid cell population expressing both E and M markers at gene/protein levels. RE cells exhibited increased proliferative/clonogenic activity, as compared to M cells, being able to form large colonies containing cells with front-back polarity, suggesting a more aggressive phenotype. Our 3D model provides a powerful tool to investigate the role of the microenvironment on metastable EMT stages. PMID:27255191

  9. Flexible, solid-state, ion-conducting membrane with 3D garnet nanofiber networks for lithium batteries.

    PubMed

    Fu, Kun Kelvin; Gong, Yunhui; Dai, Jiaqi; Gong, Amy; Han, Xiaogang; Yao, Yonggang; Wang, Chengwei; Wang, Yibo; Chen, Yanan; Yan, Chaoyi; Li, Yiju; Wachsman, Eric D; Hu, Liangbing

    2016-06-28

    Beyond state-of-the-art lithium-ion battery (LIB) technology with metallic lithium anodes to replace conventional ion intercalation anode materials is highly desirable because of lithium's highest specific capacity (3,860 mA/g) and lowest negative electrochemical potential (∼3.040 V vs. the standard hydrogen electrode). In this work, we report for the first time, to our knowledge, a 3D lithium-ion-conducting ceramic network based on garnet-type Li6.4La3Zr2Al0.2O12 (LLZO) lithium-ion conductor to provide continuous Li(+) transfer channels in a polyethylene oxide (PEO)-based composite. This composite structure further provides structural reinforcement to enhance the mechanical properties of the polymer matrix. The flexible solid-state electrolyte composite membrane exhibited an ionic conductivity of 2.5 × 10(-4) S/cm at room temperature. The membrane can effectively block dendrites in a symmetric Li | electrolyte | Li cell during repeated lithium stripping/plating at room temperature, with a current density of 0.2 mA/cm(2) for around 500 h and a current density of 0.5 mA/cm(2) for over 300 h. These results provide an all solid ion-conducting membrane that can be applied to flexible LIBs and other electrochemical energy storage systems, such as lithium-sulfur batteries. PMID:27307440

  10. 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

  11. 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

  12. Spatial 3D infrastructure: display-independent software framework, high-speed rendering electronics, and several new displays

    NASA Astrophysics Data System (ADS)

    Chun, Won-Suk; Napoli, Joshua; Cossairt, Oliver S.; Dorval, Rick K.; Hall, Deirdre M.; Purtell, Thomas J., II; Schooler, James F.; Banker, Yigal; Favalora, Gregg E.

    2005-03-01

    We present a software and hardware foundation to enable the rapid adoption of 3-D displays. Different 3-D displays - such as multiplanar, multiview, and electroholographic displays - naturally require different rendering methods. The adoption of these displays in the marketplace will be accelerated by a common software framework. The authors designed the SpatialGL API, a new rendering framework that unifies these display methods under one interface. SpatialGL enables complementary visualization assets to coexist through a uniform infrastructure. Also, SpatialGL supports legacy interfaces such as the OpenGL API. The authors" first implementation of SpatialGL uses multiview and multislice rendering algorithms to exploit the performance of modern graphics processing units (GPUs) to enable real-time visualization of 3-D graphics from medical imaging, oil & gas exploration, and homeland security. At the time of writing, SpatialGL runs on COTS workstations (both Windows and Linux) and on Actuality"s high-performance embedded computational engine that couples an NVIDIA GeForce 6800 Ultra GPU, an AMD Athlon 64 processor, and a proprietary, high-speed, programmable volumetric frame buffer that interfaces to a 1024 x 768 x 3 digital projector. Progress is illustrated using an off-the-shelf multiview display, Actuality"s multiplanar Perspecta Spatial 3D System, and an experimental multiview display. The experimental display is a quasi-holographic view-sequential system that generates aerial imagery measuring 30 mm x 25 mm x 25 mm, providing 198 horizontal views.

  13. Wavelengths of the 3p-3d transitions of the Co- and Fe-like ions: The effects of electron correlation

    SciTech Connect

    Chen, Mau Hsiung

    1987-09-02

    The experimental observations of the 3p/sup 6/ 3d/sup 9/ /sup 2/D - 3p/sup 5/ 3d/sup 10/ /sup 2/p transitions of the Co-like ions and 3p/sup 6/ 3d/sup 8/ /sup 3/F/sub 4/ - 3p/sup 5/ 3d/sup 9/ /sup 3/F/sub 3/ of the Fe-like ions have recently been extended to highly charged ions of heavy elements up to uranium (Z = 92). A comparison between the observed energies and calculated values from the Dirac-Fock model indicated persistent discrepancies of 3 to 4 eV for all ions. Systematic multiconfiguration Dirac-Fock calculations for these transitions have been carried out with emphases on the effects of electron correlation. The previously found discrepancies theory and experiment have mostly removed after the inclusion of the electron-electron correlation effects in the theoretical calculations. 13 refs.

  14. 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.

  15. Single electron states in polyethylene

    SciTech Connect

    Wang, Y.; MacKernan, D.; Cubero, D. E-mail: n.quirke@imperial.ac.uk; Coker, D. F.; Quirke, N. E-mail: n.quirke@imperial.ac.uk

    2014-04-21

    We report computer simulations of an excess electron in various structural motifs of polyethylene at room temperature, including lamellar and interfacial regions between amorphous and lamellae, as well as nanometre-sized voids. Electronic properties such as density of states, mobility edges, and mobilities are computed on the different phases using a block Lanczos algorithm. Our results suggest that the electronic density of states for a heterogeneous material can be approximated by summing the single phase density of states weighted by their corresponding volume fractions. Additionally, a quantitative connection between the localized states of the excess electron and the local atomic structure is presented.

  16. Single electron states in polyethylene

    NASA Astrophysics Data System (ADS)

    Wang, Y.; MacKernan, D.; Cubero, D.; Coker, D. F.; Quirke, N.

    2014-04-01

    We report computer simulations of an excess electron in various structural motifs of polyethylene at room temperature, including lamellar and interfacial regions between amorphous and lamellae, as well as nanometre-sized voids. Electronic properties such as density of states, mobility edges, and mobilities are computed on the different phases using a block Lanczos algorithm. Our results suggest that the electronic density of states for a heterogeneous material can be approximated by summing the single phase density of states weighted by their corresponding volume fractions. Additionally, a quantitative connection between the localized states of the excess electron and the local atomic structure is presented.

  17. Predicting the natural state of fractured carbonate reservoirs: An Andector Field, West Texas test of a 3-D RTM simulator

    SciTech Connect

    Tuncay, K.; Romer, S.; Ortoleva, P.; Hoak, T.; Sundberg, K.

    1998-12-31

    The power of the reaction, transport, mechanical (RTM) modeling approach is that it directly uses the laws of geochemistry and geophysics to extrapolate fracture and other characteristics from the borehole or surface to the reservoir interior. The objectives of this facet of the project were to refine and test the viability of the basin/reservoir forward modeling approach to address fractured reservoir in E and P problems. The study attempts to resolve the following issues: role of fracturing and timing on present day location and characteristics; clarifying the roles and interplay of flexure dynamics, changing rock rheological properties, fluid pressuring and tectonic/thermal histories on present day reservoir location and characteristics; and test the integrated RTM modeling/geological data approach on a carbonate reservoir. Sedimentary, thermal and tectonic data from Andector Field, West Texas, were used as input to the RTM basin/reservoir simulator to predict its preproduction state. The results were compared with data from producing reservoirs to test the RTM modeling approach. The effects of production on the state of the field are discussed in a companion report. The authors draw the following conclusions: RTM modeling is an important new tool in fractured reservoir E and P analysis; the strong coupling of RTM processes and the geometric and tensorial complexity of fluid flow and stresses require the type of fully coupled, 3-D RTM model for fracture analysis as pioneered in this project; flexure analysis cannot predict key aspects of fractured reservoir location and characteristics; fracture history over the lifetime of a basin is required to understand the timing of petroleum expulsion and migration and the retention properties of putative reservoirs.

  18. 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.

  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. Inductor and TSV Design of 20-V Boost Converter for Low Power 3D Solid State Drive with NAND Flash Memories

    NASA Astrophysics Data System (ADS)

    Yasufuku, Tadashi; Ishida, Koichi; Miyamoto, Shinji; Nakai, Hiroto; Takamiya, Makoto; Sakurai, Takayasu; Takeuchi, Ken

    Two essential technologies for a 3D Solid State Drive (3D-SSD) with a boost converter are presented in this paper. The first topic is the spiral inductor design which determines the performance of the boost converter, and the second is the effect of TSV's on the boost converter. These techniques are very important in achieving a 3D-SSD with a boost converter. In the design of the inductor, the on-board inductor from 250nH to 320nH is the best design feature that meets all requirements, including high output voltage above 20V, fast rise time, low energy consumption, and area smaller than 25mm2. The use of a boost converter with the proposed inductor leads to a reduction of the energy consumption during the write operation of the proposed 1.8-V 3D-SSD by 68% compared with the conventional 3.3-V 3D-SSD with the charge pump. The feasibility of 3D-SSD's with Through Silicon Vias (TSV's) connections is also discussed. In order to maintain the advantages of the boost converter over the charge pump, the reduction of the parasitic resistance of TSV's is very important.

  1. 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.

  2. 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.

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

    DOE PAGESBeta

    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

  4. Breath-held MR cholangiopancreatography (MRCP) using a 3D Dixon fat-water separated balanced steady state free precession sequence.

    PubMed

    Glockner, James F; Saranathan, Manojkumar; Bayram, Ersin; Lee, Christine U

    2013-10-01

    A novel 3D breath-held Dixon fat-water separated balanced steady state free precession (b-SSFP) sequence for MR cholangiopancreatography (MRCP) is described and its potential clinical utility assessed in a series of patients. The main motivation is to develop a robust breath-held alternative to the respiratory gated 3D Fast Spin Echo (FSE) sequence, the current clinical sequence of choice for MRCP. Respiratory gated acquisitions are susceptible to motion artifacts and blurring in patients with significant diaphragmatic drift, erratic respiratory rhythms or sleep apnea. A two point Dixon fat-water separation scheme was developed which eliminates signal loss arising from B0 inhomogeneity effects and minimizes artifacts from perturbation of the b-SSFP steady state. Preliminary results from qualitative analysis of 49 patients demonstrate robust performance of the 3D Dixon b-SSFP sequence with diagnostic image quality acquired in a 20-24s breath-hold. PMID:23876262

  5. Improved robustness study of a shock ignited target, with DUED code including non-local electron transport and 3D laser ray-tracing

    NASA Astrophysics Data System (ADS)

    Atzeni, Stefano; Marocchino, Alberto; Schiavi, Angelo

    2016-03-01

    Accurate descriptions of laser power coupling to the plasma and electron energy transport are crucial for designing shock-ignition targets and assessing their robustness (in particular with regard to laser and positioning errors). To this purpose, the 2D DUED laser fusion code has been improved with the inclusion of a 3D laser ray-tracing scheme and a model for non-local electron transport. 2D simulations with the upgraded code are presented; the dependence of the fusion yield vs target displacement is studied. Two different irradiation configurations are considered.

  6. Bound state solution of Dirac equation for 3D harmonics oscillator plus trigonometric scarf noncentral potential using SUSY QM approach

    SciTech Connect

    Cari, C. Suparmi, A.

    2014-09-30

    Dirac equation of 3D harmonics oscillator plus trigonometric Scarf non-central potential for spin symmetric case is solved using supersymmetric quantum mechanics approach. The Dirac equation for exact spin symmetry reduces to Schrodinger like equation. The relativistic energy and wave function for spin symmetric case are simply obtained using SUSY quantum mechanics method and idea of shape invariance.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Alcolea Palafox, M.; Iza, N.

    2012-11-01

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

  9. A new 3D grid method for accurate electronic structure calculation of polyatomic molecules: The Voronoi-cell finite difference method

    NASA Astrophysics Data System (ADS)

    Son, Sang-Kil; Chu, Shih-I.

    2008-05-01

    We introduce a new computational method on unstructured grids in the three-dimensional (3D) spaces to investigate the electronic structure of polyatomic molecules. The Voronoi-cell finite difference (VFD) method realizes a simple discrete Laplacian operator on unstructured grids based on Voronoi cells and their natural neighbors. The feature of unstructured grids enables us to choose intuitive pictures for an optimal molecular grid system. The new VFD method achieves highly adaptability by the Voronoi-cell diagram and yet simplicity by the finite difference scheme. It has no limitation in local refinement of grids in the vicinity of nuclear positions and provides an explicit expression at each grid without any integration. This method augmented by unstructured molecular grids is suitable for solving the Schr"odinger equation with the realistic 3D Coulomb potentials regardless of symmetry of molecules. For numerical examples, we test accuracies for electronic structures of one-electron polyatomic systems: linear H2^+ and triangular H3^++. We also extend VFD to the density functional theory (DFT) for many-electron polyatomic molecules.

  10. 3D bioprinting of skin: a state-of-the-art review on modelling, materials, and processes.

    PubMed

    Vijayavenkataraman, S; Lu, W F; Fuh, J Y H

    2016-01-01

    The skin is the largest organ of the body, having a complex multi-layered structure and guards the underlying muscles, bones, ligaments, and internal organs. It serves as the first line of defence to any external stimuli, hence it is the most vulnerable to injury and warrants the need for rapid and reliable regeneration methods. Tissue engineered skin substitutes help overcome the limitations of traditional skin treatment methods, in terms of technology, time, and cost. While there is commendable progress in the treating of superficial wounds and injuries with skin substitutes, treatment of full-thickness injuries, especially with third or fourth degree burns, still looks murkier. Engineering multi-layer skin architecture, conforming to the native skin structure is a tougher goal to achieve with the current tissue engineering methods, if not impossible, restoring all the functions of the native skin. The testing of drugs and cosmetics is another area, where engineered skins are very much needed, with bans being imposed on product testing on animals. Given this greater need, 3D bioprinting is a promising technology that can achieve rapid and reliable production of biomimetic cellular skin substitutes, satisfying both clinical and industrial needs. This paper reviews all aspects related to the 3D bioprinting of skin, right from imaging the injury site, 3D model creation, biomaterials that are used and their suitability, types of cells and their functions, actual bioprinting technologies, along with the challenges and future prospects. PMID:27606434

  11. Spatially Resolved Energetic Electron Properties for the 21 May 2004 Flare from Radio Observations and 3D Simulations

    NASA Astrophysics Data System (ADS)

    Kuznetsov, A. A.; Kontar, E. P.

    2015-01-01

    We investigated in detail the 21 May 2004 flare using simultaneous observations of the Nobeyama Radioheliograph, the Nobeyama Radiopolarimeters, the Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI), and the Solar and Heliospheric Observatory (SOHO). The flare images in different spectral ranges reveal a well-defined single flaring loop in this event. We simulated the gyrosynchrotron microwave emission using the recently developed interactive IDL tool GX Simulator. By comparing the simulation results with the observations, we deduced the spatial and spectral properties of the non-thermal electron distribution. The microwave emission has been found to be produced by the high-energy electrons (> 100 keV) with a relatively hard spectrum ( δ≃2); the electrons were strongly concentrated near the loop top. At the same time, the number of high-energy electrons near the footpoints was too low to be detected in the RHESSI images and spatially unresolved data. The SOHO Extreme-ultraviolet Imaging Telescope images and the low-frequency microwave spectra suggest the presence of an extended "envelope" of the loop with lower magnetic field. Most likely, the energetic electron distribution in the considered flare reflects the localized (near the loop top) particle acceleration (injection) process accompanied by trapping and scattering.

  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. 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].

  14. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.

    PubMed

    Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R; Murshudov, Garib N; Short, Judith M; Scheres, Sjors H W; Henderson, Richard

    2013-12-01

    Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an

  15. 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. PMID:26568395

  16. Layered nano-gratings by electron beam writing to form 3-level diffractive optical elements for 3D phase-offset holographic lithography

    NASA Astrophysics Data System (ADS)

    Yuan, Liang (Leon); Herman, Peter R.

    2015-11-01

    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 1st 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.

  17. 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.

  18. Hierarchical graphene nanocones over 3D platform of carbon fabrics: A route towards fully foldable graphene based electron source

    NASA Astrophysics Data System (ADS)

    Maiti, Uday N.; Maiti, Soumen; Das, Nirmalya S.; Chattopadhyay, Kalyan K.

    2011-10-01

    A three dimensional field emitter comprising hierarchical nanostructures of graphene over flexible fabric substrate is presented. The nanostructuring is realized through plasma treatment of graphene, coaxially deposited over individual carbon fiber by means of simple aqueous phase electrophoretic deposition technique. Hierarchical graphene nanocone, acting as a cold electron emitter, exhibits outstanding electron emission performance with a turn-on field as low as 0.41 V μm-1 and a threshold field down to 0.81 V μm-1. Electric field modification around the special woven like geometry of the underlying base fabric substrate serves as the booster to the nanostructured graphene related field amplification at the electron emission site. Superb robustness in the emission stability can be attributed to suppressed joule heating on behalf of higher inborn accessible surface area of graphene nanocone as well as excellent electrical and thermal conductivity of both the graphene and carbon fabrics. Superior flexibility of this high-performance graphene based emitter ensures their potential use in completely foldable and wearable field emission devices.A three dimensional field emitter comprising hierarchical nanostructures of graphene over flexible fabric substrate is presented. The nanostructuring is realized through plasma treatment of graphene, coaxially deposited over individual carbon fiber by means of simple aqueous phase electrophoretic deposition technique. Hierarchical graphene nanocone, acting as a cold electron emitter, exhibits outstanding electron emission performance with a turn-on field as low as 0.41 V μm-1 and a threshold field down to 0.81 V μm-1. Electric field modification around the special woven like geometry of the underlying base fabric substrate serves as the booster to the nanostructured graphene related field amplification at the electron emission site. Superb robustness in the emission stability can be attributed to suppressed joule heating on

  19. Optimization of 3D conformal electron beam therapy in inhomogeneous media by concomitant fluence and energy modulation

    NASA Astrophysics Data System (ADS)

    Åsell, Mats; Hyödynmaa, Simo; Gustafsson, Anders; Brahme, Anders

    1997-11-01

    The possibilities of using simultaneous fluence and energy modulation techniques in electron beam therapy to shape the dose distribution and almost eliminate the influences of tissue inhomogeneities have been investigated. By using a radiobiologically based optimization algorithm the radiobiological properties of the tissues can be taken into account when trying to find the best possible dose delivery. First water phantoms with differently shaped surfaces were used to study the effect of surface irregularities. We also studied water phantoms with internal inhomogeneities consisting of air or cortical bone. It was possible to improve substantially the dose distribution by fluence modulation in these cases. In addition to the fluence modulation the most suitable single electron energy in each case was also determined. Finally, the simultaneous use of several preselected electron beam energies was also tested, each with an individually optimized fluence profile. One to six electron energies were used, resulting in a slow improvement in complication-free cure with increasing number of beam energies. To apply these techniques to a more clinically relevant situation a post-operative breast cancer patient was studied. For simplicity this patient was treated with only one anterior beam portal to clearly illustrate the effect of inhomogeneities like bone and lung on the dose distribution. It is shown that by using fluence modulation the influence of dose inhomogeneities can be significantly reduced. When two or more electron beam energies with individually optimized fluence profiles are used the dose conformality to the internal target volume is further increased, particularly for targets with complex shapes.

  20. 3D Breath-Held Cardiac Function With Projection Reconstruction in Steady State Free Precession Validated Using 2D Cine MRI

    PubMed Central

    Peters, Dana C.; Ennis, Daniel B.; Rohatgi, Pratik; Syed, Mushabbar A.; McVeigh, Elliot R.; Arai, Andrew E.

    2007-01-01

    Purpose: To develop and validate a three-dimensional (3D) single breath-hold, projection reconstruction (PR), balanced steady state free precession (SSFP) method for cardiac function evaluation against a two-dimensional (2D) multislice Fourier (Cartesian) transform (FT) SSFP method. Materials and Methods: The 3D PR SSFP sequence used projections in the x-y plane and partitions in z, providing 70–80 msec temporal resolution and 1.7 × 1.7 × 8–10 mm in a 24-heartbeat breath hold. A total of 10 volunteers were imaged with both methods, and the measurements of global cardiac function were compared. Results: Mean signal-to-noise ratios (SNRs) for the blood and myocardium were 114 and 42 (2D) and 59 and 21 (3D). Bland-Altman analysis comparing the 2D and 3D ejection fraction (EF), left ventricular end diastolic volume (LVEDV) and end systolic volume (LVESV), and end diastolic myocardial mass (LVEDM) provided values of bias ±2 SD of 0.6% ± 7.7 % for LVEF, 5.9 mL ± 20 mL for LVEDV, −2.8 mL ± 12 mL for LVESV, and −0.61 g ± 13 g for LVEDM. 3D interobserver variability was greater than 2D for LVEDM and LVESV. Conclusion: In a single breath hold, the 3D PR method provides comparable information to the standard 2D FT method, which employs 10–12 breath holds. PMID:15332248

  1. 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.

  2. 3 D characterization of gold nanoparticles supported on heavy metal oxide catalysts by HAADF-STEM electron tomography.

    PubMed

    González, J C; Hernández, J C; López-Haro, M; del Río, E; Delgado, J J; Hungría, A B; Trasobares, S; Bernal, S; Midgley, P A; Calvino, José Juan

    2009-01-01

    Living on the edge: Three-dimensional reconstructions from electron tomography data recorded from Au/Ce(0.50)Tb(0.12)Zr(0.38)O(2-x) catalysts show that gold nanoparticles (see picture; yellow) are preferentially located on stepped facets and nanocrystal boundaries. An epitaxial relationship between the metal and support plays a key role in the structural stabilization of the gold nanoparticles. PMID:19544338

  3. 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.

  4. 3D electrostatic gyrokinetic electron and fully kinetic ion simulation of lower-hybrid drift instability of Harris current sheet

    DOE PAGESBeta

    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

  5. 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.

  6. A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography.

    PubMed

    Kuybeda, Oleg; Frank, Gabriel A; Bartesaghi, Alberto; Borgnia, Mario; Subramaniam, Sriram; Sapiro, Guillermo

    2013-02-01

    The limitation of using low electron doses in non-destructive cryo-electron tomography of biological specimens can be partially offset via averaging of aligned and structurally homogeneous subsets present in tomograms. This type of sub-volume averaging is especially challenging when multiple species are present. Here, we tackle the problem of conformational separation and alignment with a "collaborative" approach designed to reduce the effect of the "curse of dimensionality" encountered in standard pair-wise comparisons. Our new approach is based on using the nuclear norm as a collaborative similarity measure for alignment of sub-volumes, and by exploiting the presence of symmetry early in the processing. We provide a strict validation of this method by analyzing mixtures of intact simian immunodeficiency viruses SIV mac239 and SIV CP-MAC. Electron microscopic images of these two virus preparations are indistinguishable except for subtle differences in conformation of the envelope glycoproteins displayed on the surface of each virus particle. By using the nuclear norm-based, collaborative alignment method presented here, we demonstrate that the genetic identity of each virus particle present in the mixture can be assigned based solely on the structural information derived from single envelope glycoproteins displayed on the virus surface. PMID:23110852

  7. Local Diagnosis of Reconnection in 3D

    NASA Astrophysics Data System (ADS)

    Scudder, J. D.; Karimabadi, H.; Daughton, W. S.; Roytershteyn, V.

    2014-12-01

    We demonstrate (I,II) an approach to find reconnection sites in 3D where there is no flux function for guidance, and where local observational signatures for the ``violation of frozen flux'' are under developed, if not non-existent. We use 2D and 3D PIC simulations of asymmetric guide field reconnection to test our observational hierarchy of single spacecraft kinetic diagnostics - all possible with present state of the art instrumentation. The proliferation of turbulent, electron inertial scale layers in the realistic 3D case demonstrates that electron demagnetization, while necessary, is not sufficient to identify reconnection sites. An excellent local, observable, single spacecraft proxy is demonstrated for the size of the theoretical frozen flux violation. Since even frozen flux violations need not imply reconnection is at hand, a new calibrated dimensionless method is used to determine the importance of such violations. This measure is available in 2D and 3D to help differentiate reconnection layers from weaker frozen flux violating layers. We discuss the possibility that this technique can be implemented on MMS. A technique to highlight flow geometries conducive to reconnection in 3D simulations is also suggested, that may also be implementable with the MMS flotilla. We use local analysis with multiple necessary, but theoretically independent electron kinetic conditions to help reduce the probability of misidentification of any given layer as a reconnection site. Since these local conditions are all necessary for the site, but none is known to be sufficient, the multiple tests help to greatly reduce false positive identifications. The selectivity of the results of this approach using PIC simulations of 3D asymmetric guide field reconnection will be shown using varying numbers of simultaneous conditions. Scudder, J.D., H. Karimabadi, W. Daughton and V. Roytershteyn I, II, submitted Phys. Plasma., 2014

  8. Polarized electron correlations near auto-ionizing states of zinc atoms

    NASA Astrophysics Data System (ADS)

    Williams, James; Pravica, Luka; Samarin, Sergey

    2015-09-01

    Multi-electron metal atoms find new applications in diverse structures with spin and momentum-dependent properties having significance in determining material functionalities. Electron correlations effects are determined from scattering kinematics of spin-polarized electrons exciting zinc atoms near autoionizing states up to 16 eV. Previous studies of the 4p 3 , 1P1 , 4 d,5 d,6d3D1 , 2 , 3 and 4 d,5d1D1 excited states observed photon decay intensities and scattered electron energies and angles in the energy region of the 3d94s24 p autoionizing states up to 12 eV. Strong electron correlations and active roles of 3 d electrons were evident. Our observations of the 53S excited state for electron energies up to 16 eV show dominant 3 d core-excited negative-ion resonances and strong Post-Collision Interaction (PCI). For low energies of scattered and ejected electrons, after near-threshold excitation of the 3d94s24 p autoionizing states, a large transfer of orbital angular momentum is evident. Results include angular differential elastic scattering and excitation functions, ``integrated'' Stokes polarization parameters and spin up/down asymmetries indicating spin-orbit interaction and electron exchange effects. School of Physics

  9. A review of state-of-the-art stereology for better quantitative 3D morphology in cardiac research.

    PubMed

    Mühlfeld, Christian; Nyengaard, Jens Randel; Mayhew, Terry M

    2010-01-01

    The aim of stereological methods in biomedical research is to obtain quantitative information about three-dimensional (3D) features of tissues, cells, or organelles from two-dimensional physical or optical sections. With immunogold labeling, stereology can even be used for the quantitative analysis of the distribution of molecules within tissues and cells. Nowadays, a large number of design-based stereological methods offer an efficient quantitative approach to intriguing questions in cardiac research, such as "Is there a significant loss of cardiomyocytes during progression from ventricular hypertrophy to heart failure?" or "Does a specific treatment reduce the degree of fibrosis in the heart?" Nevertheless, the use of stereological methods in cardiac research is rare. The present review article demonstrates how some of the potential pitfalls in quantitative microscopy may be avoided. To this end, we outline the concepts of design-based stereology and illustrate their practical applications to a wide range of biological questions in cardiac research. We hope that the present article will stimulate researchers in cardiac research to incorporate design-based stereology into their study designs, thus promoting an unbiased quantitative 3D microscopy. PMID:19144544

  10. 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.

  11. Toroidal mode number estimation of the edge-localized modes using the KSTAR 3-D electron cyclotron emission imaging system.

    PubMed

    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

    2014-06-01

    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* of filaments at the plasma outboard midplane. Equilibrium reconstruction verifies that α* 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. PMID:24985817

  12. 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.

  13. Interchain electron states in polyethylene

    NASA Astrophysics Data System (ADS)

    Serra, S.; Tosatti, E.; Iarlori, S.; Scandolo, S.; Santoro, G.

    2000-08-01

    We present a theoretical study of the nature of the lowest empty conduction-band states in crystalline polyethylene (PE), conducted through density-functional electronic structure calculations. Results reveal that the wave function of the conduction-band edge is of interchain character, as opposed to the intrachain character of all the filled valence-band states. Thus, while a hole added to neutral PE will mainly belong to the PE chain backbone bonds, an added electron in PE will mostly reside between the chains, and far from the existing bonds. Moreover, the added electron state charge centroid is predicted to move further out from the chain backbone towards the low-density interstitial region, if and when the chains are pried apart. This suggests that injected electrons will naturally flow to low-density regions inside real PE, and that the experimentally established propensity of PE to expel electrons out of the bulk, should be directly related to the interchain nature of the conduction states.

  14. Simultaneous Acquisition of 2D and 3D Solid-State NMR Experiments for Sequential Assignment of Oriented Membrane Protein Samples

    PubMed Central

    Gopinath, T.; Mote, Kaustubh R; Veglia, Gianluigi

    2016-01-01

    We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins aligned in mechanically or magnetically lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living 15N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through 15N-15N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish 15N-15N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments. PMID:25749871

  15. Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples.

    PubMed

    Gopinath, T; Mote, Kaustubh R; Veglia, Gianluigi

    2015-05-01

    We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living (15)N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through (15)N-(15)N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish (15)N-(15)N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments. PMID:25749871

  16. Patient-Specific Artery Shrinkage and 3D Zero-Stress State in Multi-Component 3D FSI Models for Carotid Atherosclerotic Plaques Based on In Vivo MRI Data

    PubMed Central

    Huang, Xueying; Yang, Chun; Yuan, Chun; Liu, Fei; Canton, Gador; Zheng, Jie; Woodard, Pamela K.; Sicard, Gregorio A.; Tang, Dalin

    2009-01-01

    Image-based computational models for atherosclerotic plaques have been developed to perform mechanical analysis to quantify critical flow and stress/strain conditions related to plaque rupture which often leads directly to heart attack or stroke. An important modeling issue is how to determine zero stress state from in vivo plaque geometries. This paper presents a method to quantify human carotid artery axial and inner circumferential shrinkages by using patient-specific ex vivo and in vivo MRI images. A shrink-stretch process based on patient-specific in vivo plaque morphology and shrinkage data was introduced to shrink the in vivo geometry first to find the zero-stress state (opening angle was ignored to reduce the complexity), and then stretch and pressurize to recover the in vivo plaque geometry with computed initial stress, strain, flow pressure and velocity conditions. Effects of the shrink-stretch process on plaque stress/strain distributions were demonstrated based on patient-specific data using 3D models with fluid-structure interactions (FSI). The average artery axial and inner circumferential shrinkages were 25% and 7.9%, respectively, based on a data set obtained from 10 patients. Maximum values of maximum principal stress and strain increased 349.8% and 249% respectively with 33% axial stretch. Influence of inner circumferential shrinkage (7.9%) was not very noticeable under 33% axial stretch, but became more noticeable under smaller axial stretch. Our results indicated that accurate knowledge of artery shrinkages and the shrink-stretch process will considerably improve the accuracy of computational predictions made based on results from those in vivo MRI-based FSI models. PMID:19444328

  17. Patient-specific artery shrinkage and 3D zero-stress state in multi-component 3D FSI models for carotid atherosclerotic plaques based on in vivo MRI data.

    PubMed

    Huang, Xueying; Yang, Chun; Yuan, Chun; Liu, Fei; Canton, Gador; Zheng, Jie; Woodard, Pamela K; Sicard, Gregorio A; Tang, Dalin

    2009-06-01

    Image-based computational models for atherosclerotic plaques have been developed to perform mechanical analysis to quantify critical flow and stress/strain conditions related to plaque rupture which often leads directly to heart attack or stroke. An important modeling issue is how to determine zero stress state from in vivo plaque geometries. This paper presents a method to quantify human carotid artery axial and inner circumferential shrinkages by using patient-specific ex vivo and in vivo MRI images. A shrink-stretch process based on patient-specific in vivo plaque morphology and shrinkage data was introduced to shrink the in vivo geometry first to find the zero-stress state (opening angle was ignored to reduce the complexity), and then stretch and pressurize to recover the in vivo plaque geometry with computed initial stress, strain, flow pressure and velocity conditions. Effects of the shrink-stretch process on plaque stress/strain distributions were demonstrated based on patient-specific data using 3D models with fluid-structure interactions (FSI). The average artery axial and inner circumferential shrinkages were 25% and 7.9%, respectively, based on a data set obtained from 10 patients. Maximum values of maximum principal stress and strain increased 349.8% and 249% respectively with 33% axial stretch. Influence of inner circumferential shrinkage (7.9%) was not very noticeable under 33% axial stretch, but became more noticeable under smaller axial stretch. Our results indicated that accurate knowledge of artery shrinkages and the shrink-stretch process will considerably improve the accuracy of computational predictions made based on results from those in vivo MRI-based FSI models. PMID:19444328

  18. 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.

  19. 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.

  20. Drawing the geometry of 3d transition metal-boron pairs in silicon from electron emission channeling experiments

    NASA Astrophysics Data System (ADS)

    Silva, D. J.; Wahl, U.; Correia, J. G.; Augustyns, V.; Lima, T. A. L.; Costa, A.; Bosne, E.; da Silva, M. R.; Araújo, J. P.; Pereira, L. M. C.

    2016-03-01

    Although the formation of transition metal-boron pairs is currently well established in silicon processing, the geometry of these complexes is still not completely understood. We investigated the lattice location of the transition metals manganese, iron, cobalt and nickel in n- and p+ -type silicon by means of electron emission channeling. For manganese, iron and cobalt, we observed an increase of sites near the ideal tetrahedral interstitial position by changing the doping from n- to p+ -type Si. Such increase was not observed for Ni. We ascribe this increase to the formation of pairs with boron, driven by Coulomb interactions, since the majority of iron, manganese and cobalt is positively charged in p+ -type silicon while Ni is neutral. We propose that breathing mode relaxation around the boron ion within the pair causes the observed displacement from the ideal tetrahedral interstitial site. We discuss the application of the emission channeling technique in this system and, in particular, how it provides insight on the geometry of such pairs.

  1. 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.

  2. 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.

  3. 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

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

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    Apollo's 3-dimensional graphics hardware, but does not take advantage of the shading and hidden line/surface removal capabilities of the Apollo DN10000. Although this implementation does not offer a capability for putting text on plots, it does support the use of a mouse to translate, rotate, or zoom in on views. The version 3.6b+ Apollo implementations of PLOT3D (ARC-12789) and PLOT3D/TURB3D (ARC-12785) were developed for use on Apollo computers running UNIX System V with BSD 4.3 extensions and the graphics library GMR3D Version 2.0. The standard distribution media for each of these programs is a 9-track, 6250 bpi magnetic tape in TAR format. Customers purchasing one implementation version of PLOT3D or PLOT3D/TURB3D will be given a $200 discount on each additional implementation version ordered at the same time. Version 3.6b+ of PLOT3D and PLOT3D/TURB3D are also supported for the following computers and graphics libraries: 1) generic UNIX Supercomputer and IRIS, suitable for CRAY 2/UNICOS, CONVEX, and Alliant with remote IRIS 2xxx/3xxx or IRIS 4D (ARC-12779, ARC-12784); 2) VAX computers running VMS Version 5.0 and DISSPLA Version 11.0 (ARC-12777, ARC-12781); 3) generic UNIX and DISSPLA Version 11.0 (ARC-12788, ARC-12778); and (4) Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D workstations (ARC-12783, ARC-12782). Silicon Graphics Iris, IRIS 4D, and IRIS 2xxx/3xxx are trademarks of Silicon Graphics Incorporated. VAX and VMS are trademarks of Digital Electronics Corporation. DISSPLA is a trademark of Computer Associates. CRAY 2 and UNICOS are trademarks of CRAY Research, Incorporated. CONVEX is a trademark of Convex Computer Corporation. Alliant is a trademark of Alliant. Apollo and GMR3D are trademarks of Hewlett-Packard, Incorporated. UNIX is a registered trademark of AT&T.

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

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    Apollo's 3-dimensional graphics hardware, but does not take advantage of the shading and hidden line/surface removal capabilities of the Apollo DN10000. Although this implementation does not offer a capability for putting text on plots, it does support the use of a mouse to translate, rotate, or zoom in on views. The version 3.6b+ Apollo implementations of PLOT3D (ARC-12789) and PLOT3D/TURB3D (ARC-12785) were developed for use on Apollo computers running UNIX System V with BSD 4.3 extensions and the graphics library GMR3D Version 2.0. The standard distribution media for each of these programs is a 9-track, 6250 bpi magnetic tape in TAR format. Customers purchasing one implementation version of PLOT3D or PLOT3D/TURB3D will be given a $200 discount on each additional implementation version ordered at the same time. Version 3.6b+ of PLOT3D and PLOT3D/TURB3D are also supported for the following computers and graphics libraries: 1) generic UNIX Supercomputer and IRIS, suitable for CRAY 2/UNICOS, CONVEX, and Alliant with remote IRIS 2xxx/3xxx or IRIS 4D (ARC-12779, ARC-12784); 2) VAX computers running VMS Version 5.0 and DISSPLA Version 11.0 (ARC-12777, ARC-12781); 3) generic UNIX and DISSPLA Version 11.0 (ARC-12788, ARC-12778); and (4) Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D workstations (ARC-12783, ARC-12782). Silicon Graphics Iris, IRIS 4D, and IRIS 2xxx/3xxx are trademarks of Silicon Graphics Incorporated. VAX and VMS are trademarks of Digital Electronics Corporation. DISSPLA is a trademark of Computer Associates. CRAY 2 and UNICOS are trademarks of CRAY Research, Incorporated. CONVEX is a trademark of Convex Computer Corporation. Alliant is a trademark of Alliant. Apollo and GMR3D are trademarks of Hewlett-Packard, Incorporated. UNIX is a registered trademark of AT&T.

  6. X-Ray Emission Spectra and Electronic Structures of Red Phosphorus, 3d Transition-Metal Phosphides and III V Compounds

    NASA Astrophysics Data System (ADS)

    Sugiura, Chikara

    1995-07-01

    The P Kβ emission spectra in fluorescence from red amorphous phosphorus, 3d transition-metal phosphides TiP, CrP, FeP, Fe2P, Fe3P, CoP, Co2P, Ni5P4, Ni2P, Ni3P, Cu3P, ZnP2 (black) and Zn3P2, and the semiconducting phosphides of the III-V type, BP, AlP, GaP and InP are measured with a high-resolution two-crystal vacuum spectrometer equipped with Ge(111) crystals. The influence of the metal atoms appears distinctly on the P Kβ fluorescence emission spectra. The measured spectra are compared with available X-ray emission and XPS valence-band spectra and theoretical energy-band calculations on a common energy scale. It is shown that considerable p-d, s mixing occurs in the valence bands of the 3d transition-metal phosphides and the P 3p states mix fairly with the P 3s states in the valence bands of red phosphorus, Gap and InP

  7. Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming.

    PubMed

    Beagan, Jonathan A; Gilgenast, Thomas G; Kim, Jesi; Plona, Zachary; Norton, Heidi K; Hu, Gui; Hsu, Sarah C; Shields, Emily J; Lyu, Xiaowen; Apostolou, Effie; Hochedlinger, Konrad; Corces, Victor G; Dekker, Job; Phillips-Cremins, Jennifer E

    2016-05-01

    Pluripotent genomes are folded in a topological hierarchy that reorganizes during differentiation. The extent to which chromatin architecture is reconfigured during somatic cell reprogramming is poorly understood. Here we integrate fine-resolution architecture maps with epigenetic marks and gene expression in embryonic stem cells (ESCs), neural progenitor cells (NPCs), and NPC-derived induced pluripotent stem cells (iPSCs). We find that most pluripotency genes reconnect to target enhancers during reprogramming. Unexpectedly, some NPC interactions around pluripotency genes persist in our iPSC clone. Pluripotency genes engaged in both "fully-reprogrammed" and "persistent-NPC" interactions exhibit over/undershooting of target expression levels in iPSCs. Additionally, we identify a subset of "poorly reprogrammed" interactions that do not reconnect in iPSCs and display only partially recovered, ESC-specific CTCF occupancy. 2i/LIF can abrogate persistent-NPC interactions, recover poorly reprogrammed interactions, reinstate CTCF occupancy, and restore expression levels. Our results demonstrate that iPSC genomes can exhibit imperfectly rewired 3D-folding linked to inaccurately reprogrammed gene expression. PMID:27152443

  8. 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.

  9. NeuroMorph: a toolset for the morphometric analysis and visualization of 3D models derived from electron microscopy image stacks.

    PubMed

    Jorstad, Anne; Nigro, Biagio; Cali, Corrado; Wawrzyniak, Marta; Fua, Pascal; Knott, Graham

    2015-01-01

    Serialelectron microscopy imaging is crucial for exploring the structure of cells and tissues. The development of block face scanning electron microscopy methods and their ability to capture large image stacks, some with near isotropic voxels, is proving particularly useful for the exploration of brain tissue. This has led to the creation of numerous algorithms and software for segmenting out different features from the image stacks. However, there are few tools available to view these results and make detailed morphometric analyses on all, or part, of these 3D models. We have addressed this issue by constructing a collection of software tools, called NeuroMorph, with which users can view the segmentation results, in conjunction with the original image stack, manipulate these objects in 3D, and make measurements of any region. This approach to collecting morphometric data provides a faster means of analysing the geometry of structures, such as dendritic spines and axonal boutons. This bridges the gap that currently exists between rapid reconstruction techniques, offered by computer vision research, and the need to collect measurements of shape and form from segmented structures that is currently done using manual segmentation methods. PMID:25240318

  10. Novel magnetic and electronic states in manganite-iridate heterostructures

    NASA Astrophysics Data System (ADS)

    Nichols, John; Lee, Shinbuhm; Petrie, Jon; Meyer, Tricia; Gao, Xiang; Guo, Erjia; Freeland, John; Yi, Di; Liu, Jian; Haskel, Daniel; Ward, Thomas Zac; Eres, Gyula; Lauter, Valeria; Fitzsimmons, Michael R.; Lee, Ho Nyung

    Strong correlation between spin, charge, lattice, and orbital order parameters has proven to give rise to exotic physical phenomena, while epitaxial design of materials with strong interfacial coupling is an efficient technique to tune such parameters. Although there have been numerous studies of interfaces between 3 d-3 d and 4 d-3 d compounds, only few studies reported work on 3 d and 5 d materials and there has been no report on strong interfacial coupling in such systems. We have synthesized high quality [(AMnO3)m /(SrIrO3)n ]z (A = Sr, La) heterostructures by pulsed laser epitaxy on SrTiO3 (001) substrates and have observed interesting novel magnetic and electronic ground states, which are highly sensitive to the degree of dimensional confinement in the heterostructures. Based on studies with x-ray diffraction, SQUID, dc-transport, x-ray circular dichroism, and polarized neutron reflectometry measurements, we will report intriguing magnetic and transport properties that provide the first evidence of strong interfacial coupling between 5 d and 3 d materials. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division.

  11. In vivo measurement of arterial and venous oxygenation in the rat using 3D spectral-spatial electron paramagnetic resonance imaging.

    PubMed

    Kuppusamy, P; Shankar, R A; Zweier, J L

    1998-07-01

    Electron paramagnetic resonance imaging (EPRI) instrumentation, enabling the performance of three-dimensional spectral-spatial images of free radicals, has been developed to study spatially defined differences in tissue metabolism and oxygenation. Using this instrumentation 3D images of nitroxides in rat tail were obtained. The images visualize the arterial and venous vasculature in the tail segment. Based on the exchange broadening influence of oxygen on the EPR linewidth of nitroxides, we performed localized oxygen measurements in the in vivo rat. An oxygen concentration of 300+/-30 microM was measured in the arteries and 50+/-20 microM in the veins. These results demonstrate the feasibility of performing in vivo, non-invasive measurements and mapping of localized oxygenation in small animals using spectral-spatial EPR imaging techniques. PMID:9703045

  12. 3D RVE models able to capture and quantify the dispersion, agglomeration and orientation state of CNT in CNT/PP nanocomposites

    NASA Astrophysics Data System (ADS)

    Bhuiyan, Md; Pucha, Raghuram; Kalaitzidou, Kyriaki

    2016-02-01

    The focus of this study is to investigate the capabilities of 3D RVE models in predicting the tensile modulus of carbon nanotube polypropylene (CNT/PP) composites which differ slightly in the dispersion, agglomeration and orientation states of CNT within the PP matrix. The composites are made using melt mixing followed by either injection molding or melt spinning of fibers. The dispersion, agglomeration and orientation of CNT within the PP are experimentally altered by using a surfactant and by forcing the molten material to flow through a narrow orifice (melt spinning) that promotes alignment of CNT along the flow/drawing direction. An elaborate image analysis technique is used to quantify the CNT characteristics in terms of probability distribution functions (PDF). The PDF are then introduced to the 3D RVE models which also account for the CNT-PP interfacial interactions. It is concluded that the 3D RVE models can accurately distinguish among the different cases (dispersion, distribution, geometry and alignment of CNT) as the predicted tensile modulus is in good agreement with the experimentally determined one.

  13. Novel symmetrical coralloid Cu 3D superstructures: Solid-state synthesis from a Cu-carboxylate MOF and their in-situ thermal conversion

    SciTech Connect

    Chen Lingyun; Shen Yongming; Bai Junfeng; Wang Chunzhao

    2009-08-15

    We describe here a one-step solid-state process for the synthesis of metal three-dimensional (3D) superstructures from a metal-organic framework (MOF). Novel symmetrical coralloid Cu 3D superstructures with surface interspersed with clusters of Cu nanoparticles were successfully synthesized by thermolysis of the [Cu{sub 3}(btc){sub 2}] (btc=benzene-1,3,5-tricarboxylato) MOF in a one-end closed horizontal tube furnace (OCTF). The obtained products were characterized by TGA, FT-IR, XRD, EDX, SEM, TEM, HRTEM and SAED. Different reaction conditions were discussed. Furthermore, the synthesized Cu samples were converted into CuO microstructures by in-situ calcination in the air. In addition, the possible formation mechanism was also proposed. This method is a simple and facile route, which builds a direct linkage between metal-carboxylate MOF crystals and metal nano- or microstructures and also opens a new application field of MOFs. - Graphical abstract: Novel symmetrical coralloid Cu 3D superstructures were synthesized by thermolysis of the [Cu{sub 3}(btc){sub 2}] (btc=benzene-1,3,5-tricarboxylato) MOF microcrystals in a one-end closed horizontal tube furnace (OCTF).

  14. SU-D-213-05: Design, Evaluation and First Applications of a Off-Site State-Of-The-Art 3D Dosimetry System

    SciTech Connect

    Malcolm, J; Mein, S; McNiven, A; Letourneau, D; Oldham, M

    2015-06-15

    Purpose: To design, construct and commission a prototype in-house three dimensional (3D) dose verification system for stereotatic body radiotherapy (SBRT) verification at an off-site partner institution. To investigate the potential of this system to achieve sufficient performance (1mm resolution, 3% noise, within 3% of true dose reading) for SBRT verification. Methods: The system was designed utilizing a parallel ray geometry instigated by precision telecentric lenses and an LED 630nm light source. Using a radiochromic dosimeter, a 3D dosimetric comparison with our gold-standard system and treatment planning software (Eclipse) was done for a four-field box treatment, under gamma passing criteria of 3%/3mm/10% dose threshold. Post off-site installation, deviations in the system’s dose readout performance was assessed by rescanning the four-field box irradiated dosimeter and using line-profiles to compare on-site and off-site mean and noise levels in four distinct dose regions. As a final step, an end-to-end test of the system was completed at the off-site location, including CT-simulation, irradiation of the dosimeter and a 3D dosimetric comparison of the planned (Pinnacle{sup 3}) to delivered dose for a spinal SBRT treatment(12 Gy per fraction). Results: The noise level in the high and medium dose regions of the four field box treatment was relatively 5% pre and post installation. This reflects the reduction in positional uncertainty through the new design. This At 1mm dose voxels, the gamma pass rates(3%,3mm) for our in-house gold standard system and the off-site system were comparable at 95.8% and 93.2% respectively. Conclusion: This work will describe the end-to-end process and results of designing, installing, and commissioning a state-of-the-art 3D dosimetry system created for verification of advanced radiation treatments including spinal radiosurgery.

  15. Effect of site preference of 3d atoms on the electronic structure and half-metallicity of Heusler alloy Mn2YAl

    NASA Astrophysics Data System (ADS)

    Luo, Hongzhi; Zhu, Zhiyong; Ma, Li; Xu, Shifeng; Zhu, Xiaoxi; Jiang, Chengbao; Xu, Huibin; Wu, Guangheng

    2008-03-01

    The site preference of 3d atoms Y in Mn2YAl (Y = V, Fe, Co) alloys and its influence on their electronic structures and magnetism have been studied by first-principles calculations. The results prove that elements with more valence electrons than Mn tend to enter the A (0, 0, 0) and C (½, ½, ½) sites and elements with fewer electrons prefer the B (¼, ¼, ¼) site (Wyckoff positions). Meanwhile, it is found that for Mn2VAl and Mn2FeAl, a high spin polarization can be obtained whether the Y atom enters the (A, C) or the B site. In particular, Mn2VAl is half-metallic whether it forms the Cu2MnAl type or the Hg2CuTi type of structure. And a 100% spin polarization can be retained even when a 25% Mn-V antisite disorder occurs. This is quite preferable in practical applications. It is also found that the higher-valent element such as Co at the B (¼, ¼, ¼) site has opposite effects and tends to close the energy gap. Finally, a systemic summarization on the electronic and magnetic properties of Mn2YAl (Y = Ti, V, Cr, Mn, Fe and Co) alloys was made. All of them except for Mn2TiAl are predicted as half-metals. The calculated total spin moment is an integral value and increases from -3µB/f.u. for Mn2TiAl to +2µB/f.u. for Mn2CoAl with increasing number of valence electrons. This agrees with the Slater-Pauling curve quite well. All the Mn2YAl alloys studied here are ferrimagnets.

  16. Data-driven techniques for detecting dynamical state changes in noisily measured 3D single-molecule trajectories.

    PubMed

    Calderon, Christopher P

    2014-01-01

    Optical microscopes and nanoscale probes (AFM, optical tweezers, etc.) afford researchers tools capable of quantitatively exploring how molecules interact with one another in live cells. The analysis of in vivo single-molecule experimental data faces numerous challenges due to the complex, crowded, and time changing environments associated with live cells. Fluctuations and spatially varying systematic forces experienced by molecules change over time; these changes are obscured by "measurement noise" introduced by the experimental probe monitoring the system. In this article, we demonstrate how the Hierarchical Dirichlet Process Switching Linear Dynamical System (HDP-SLDS) of Fox et al. [IEEE Transactions on Signal Processing 59] can be used to detect both subtle and abrupt state changes in time series containing "thermal" and "measurement" noise. The approach accounts for temporal dependencies induced by random and "systematic overdamped" forces. The technique does not require one to subjectively select the number of "hidden states" underlying a trajectory in an a priori fashion. The number of hidden states is simultaneously inferred along with change points and parameters characterizing molecular motion in a data-driven fashion. We use large scale simulations to study and compare the new approach to state-of-the-art Hidden Markov Modeling techniques. Simulations mimicking single particle tracking (SPT) experiments are the focus of this study. PMID:25397733

  17. Orphan spin operators enable the acquisition of multiple 2D and 3D magic angle spinning solid-state NMR spectra

    NASA Astrophysics Data System (ADS)

    Gopinath, T.; Veglia, Gianluigi

    2013-05-01

    We propose a general method that enables the acquisition of multiple 2D and 3D solid-state NMR spectra for U-13C, 15N-labeled proteins. This method, called MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), makes it possible to detect four coherence transfer pathways simultaneously, utilizing orphan (i.e., neglected) spin operators of nuclear spin polarization generated during 15N-13C cross polarization (CP). In the MEIOSIS experiments, two phase-encoded free-induction decays are decoded into independent nuclear polarization pathways using Hadamard transformations. As a proof of principle, we show the acquisition of multiple 2D and 3D spectra of U-13C, 15N-labeled microcrystalline ubiquitin. Hadamard decoding of CP coherences into multiple independent spin operators is a new concept in solid-state NMR and is extendable to many other multidimensional experiments. The MEIOSIS method will increase the throughput of solid-state NMR techniques for microcrystalline proteins, membrane proteins, and protein fibrils.

  18. The Three-Dimensional Micro- and Nanostructure of the Aortic Medial Lamellar Unit Measured Using 3D Confocal & Electron Microscopy Imaging

    PubMed Central

    O’Connell, Mary K; Murthy, Sushila; Phan, Samson; Xu, Chengpei; Buchanan, JoAnn; Spilker, Ryan; Dalman, Ronald L; Zarins, Christopher K; Denk, Winfried; Taylor, Charles A

    2009-01-01

    Changes in arterial wall composition and function underlie all forms of vascular disease. The fundamental structural and functional unit of the aortic wall is the medial lamellar unit (MLU). While the basic composition and organization of the MLU is known, three-dimensional (3D) microstructural details are tenuous, due (in part) to lack of three-dimensional data at micro- and nano-scales. We applied novel electron and confocal microscopy techniques to obtain 3D volumetric information of aortic medial microstructure at micro- and nano-scales with all constituents present. For the rat abdominal aorta, we show that medial elastin has three primary forms: with approximately 71% of total elastin as thick, continuous lamellar sheets, 27% as thin, protruding interlamellar elastin fibers (IEFs), and 2% as thick radial struts. Elastin pores are not simply holes in lamellar sheets, but are indented and gusseted openings in lamellae. Smooth Muscle Cells (SMCs) weave throughout the interlamellar elastin framework, with cytoplasmic extensions abutting IEFs, resulting in approximately 20° radial tilt (relative to the lumen surface) of elliptical SMC nuclei. Collagen fibers are organized as large, parallel bundles tightly enveloping SMC nuclei. Quantification of the orientation of collagen bundles, SMC nuclei, and IEFs reveal that all three primary medial constituents have predominantly circumferential orientation, correlating with reported circumferentially dominant values of physiological stress, collagen fiber recruitment, and tissue stiffness. This high resolution three-dimensional view of the aortic media reveals MLU microstructure details that suggest a highly complex and integrated mural organization that correlates with aortic mechanical properties. PMID:18248974

  19. 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)

  20. 3D Imaging of Nickel Oxidation States using Full Field X-ray Absorption Near Edge Structure Nanotomography

    SciTech Connect

    Nelson, George; Harris, William; Izzo, John; Grew, Kyle N.

    2012-01-20

    Reduction-oxidation (redox) cycling of the nickel electrocatalyst phase in the solid oxide fuel cell (SOFC) anode can lead to performance degradation and cell failure. A greater understanding of nickel redox mechanisms at the microstructural level is vital to future SOFC development. Transmission x-ray microscopy (TXM) provides several key techniques for exploring oxidation states within SOFC electrode microstructure. Specifically, x-ray nanotomography and x-ray absorption near edge structure (XANES) spectroscopy have been applied to study samples of varying nickel (Ni) and nickel oxide (NiO) compositions. The imaged samples are treated as mock SOFC anodes containing distinct regions of the materials in question. XANES spectra presented for the individual materials provide a basis for the further processing and analysis of mixed samples. Images of composite samples obtained are segmented, and the distinct nickel and nickel oxide phases are uniquely identified using full field XANES spectroscopy. Applications to SOFC analysis are discussed.

  1. Systematic measurement of the relative electron-impact excitation cross section of the 3d{yields}2p{sup 1}P{sub 1} resonance and {sup 3}D{sub 1} intercombination lines in mid-Z neonlike ions

    SciTech Connect

    Brown, G. V.; Beiersdorfer, P.; Widmann, K.

    2001-03-01

    The relative electron-impact cross sections for exciting the 3d{yields}2p{sup 1}P{sub 1} resonance and {sup 3}D{sub 1} intercombination lines have been measured in nine neonlike ions between Cr{sup 14+} and Kr{sup 26+}. The ratio drops from about 4.4 for Cr{sup 14+} to less than unity for Kr{sup 26+} in response to an increase in relativistic effects. A measurement of the dependence of this ratio on electron energy is presented for Fe{sup 16+}. No dependence on electron energy is found. The measured ratios are generally lower than theory, showing that the relative intensity of the intercombination line is larger than predicted and illustrating the difficulty to predict electron-impact excitation cross sections in the intermediate coupling regime at the level needed for spectral diagnostics.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  4. 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.

  5. 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.

  6. 3D Kitaev spin liquids

    NASA Astrophysics Data System (ADS)

    Hermanns, Maria

    The Kitaev honeycomb model has become one of the archetypal spin models exhibiting topological phases of matter, where the magnetic moments fractionalize into Majorana fermions interacting with a Z2 gauge field. In this talk, we discuss generalizations of this model to three-dimensional lattice structures. Our main focus is the metallic state that the emergent Majorana fermions form. In particular, we discuss the relation of the nature of this Majorana metal to the details of the underlying lattice structure. Besides (almost) conventional metals with a Majorana Fermi surface, one also finds various realizations of Dirac semi-metals, where the gapless modes form Fermi lines or even Weyl nodes. We introduce a general classification of these gapless quantum spin liquids using projective symmetry analysis. Furthermore, we briefly outline why these Majorana metals in 3D Kitaev systems provide an even richer variety of Dirac and Weyl phases than possible for electronic matter and comment on possible experimental signatures. Work done in collaboration with Kevin O'Brien and Simon Trebst.

  7. Noncontrast MR Angiography for Comprehensive Assessment of Abdominopelvic Arteries using Quadruple Inversion-Recovery Preconditioning and 3D balanced Steady-State Free Precession Imaging

    PubMed Central

    Atanasova, Iliyana P.; Kim, Daniel; Lim, Ruth P.; Storey, Pippa; Kim, Sooah; Guo, Hua; Lee, Vivian S.

    2011-01-01

    Purpose To develop a non-contrast MR angiography (MRA) method for comprehensive evaluation of abdominopelvic arteries in a single 3D acquisition. Materials and Methods A non-contrast MRA (NC MRA) pulse sequence was developed using 4 inversion-recovery (IR) pulses and 3D balanced steady-state free precession (b-SSFP) readout to provide arterial imaging from renal to external iliac arteries. Respiratory triggered, high spatial resolution (1.3 × 1.3 × 1.7 mm3) non-contrast angiograms were obtained in seven volunteers and ten patients referred for gadolinium-enhanced MRA (CE MRA). Images were assessed for diagnostic quality by two radiologists. Quantitative measurements of arterial signal contrast were also performed. Results NC MRA imaging was successfully completed in all subjects in 7.0 ± 2.3 minutes. In controls, image quality of NC MRA averaged 2.79 ± 0.39 on a scale of 0 to 3, where 3 is maximum. Image quality of NC MRA (2.65 ± 0.41) was comparable to that of CE MRA (2.9 ± 0.32) in all patients. Contrast ratio measurements in patients demonstrated that NC MRA provides arterial contrast comparable to source CE MRA images with adequate venous and excellent background tissue suppression. Conclusion The proposed non-contrast MRA pulse sequence provides high quality visualization of abdominopelvic arteries within clinically feasible scan times. PMID:21591013

  8. How do monomeric components of a polymer gel dosimeter respond to ionising radiation: A steady-state radiolysis towards preparation of a 3D polymer gel dosimeter

    NASA Astrophysics Data System (ADS)

    Kozicki, Marek

    2011-12-01

    Ionising radiation-induced reactions of aqueous single monomer solutions and mixtures of poly(ethylene glycol) diacrylate (PEGDA) and N, N'-methylenebisacrylamide (Bis) in a steady-state condition are presented below and above gelation doses in order to highlight reactions in irradiated 3D polymer gel dosimeters, which are assigned for radiotherapy dosimetry. Both monomers are shown to undergo radical polymerisation and cross-linking, which result in the measured increase in molecular weight and radius of gyration of the formed polydisperse polymer coils. The formation of nanogels was also observed for Bis solutions at a low concentration. In the case of PEGDA-Bis mixtures, co-polymerisation is suggested as well. At a sufficiently high radiation dose, the formation of a polymer network was observed for both monomers and their mixture. For this reason a sol-gel analysis for PEGDA and Bis was performed gravimetrically and a proposition of an alternative to this method employing a nuclear magnetic resonance technique is made. The two monomers were used for preparation of 3D polymer gel dosimeters having the acronyms PABIG and PABIG nx. The latter is presented for the first time in this work and is a type of the formerly established PABIG polymer gel dosimeter. The elementary characteristics of the new composition are presented, underlining the ease of its preparation, low dose threshold, and slightly increased sensitivity but lower quasi-linear range of dose response in comparison to PABIG.

  9. TRACE 3-D documentation

    SciTech Connect

    Crandall, K.R.

    1987-08-01

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

  10. 3-D crustal structure of the western United States: application of Rayleigh-wave ellipticity extracted from noise cross-correlations

    NASA Astrophysics Data System (ADS)

    Lin, Fan-Chi; Tsai, Victor C.; Schmandt, Brandon

    2014-08-01

    We present a new 3-D seismic model of the western United States crust derived from a joint inversion of Rayleigh-wave phase velocity and ellipticity measurements using periods from 8 to 100 s. Improved constraints on upper-crustal structure result from use of short-period Rayleigh-wave ellipticity, or Rayleigh-wave H/V (horizontal to vertical) amplitude ratios, measurements determined using multicomponent ambient noise cross-correlations. To retain the amplitude ratio information between vertical and horizontal components, for each station, we perform daily noise pre-processing (temporal normalization and spectrum whitening) simultaneously for all three components. For each station pair, amplitude measurements between cross-correlations of different components (radial-radial, radial-vertical, vertical-radial and vertical-vertical) are then used to determine the Rayleigh-wave H/V ratios at the two station locations. We use all EarthScope/USArray Tranportable Array data available between 2007 January and 2011 June to determine the Rayleigh-wave H/V ratios and their uncertainties at all station locations and construct new Rayleigh-wave H/V ratio maps in the western United States between periods of 8 and 24 s. Combined with previous longer period earthquake Rayleigh-wave H/V ratio measurements and Rayleigh-wave phase velocity measurements from both ambient noise and earthquakes, we invert for a new 3-D crustal and upper-mantle model in the western United States. Correlation between the inverted model and known geological features at all depths suggests good resolution in five crustal layers. Use of short-period Rayleigh-wave H/V ratio measurements based on noise cross-correlation enables resolution of distinct near surface features such as the Columbia River Basalt flows, which overlie a thick sedimentary basin.

  11. 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

  12. 3D Band Diagram and Photoexcitation of 2D–3D Semiconductor Heterojunctions

    DOE PAGESBeta

    Li, Bo; Shi, Gang; Lei, Sidong; He, Yongmin; Gao, Weilu; Gong, Yongji; Ye, Gonglan; Zhou, Wu; Keyshar, Kunttal; Hao, Ji; et al

    2015-08-17

    The emergence of a rich variety of two-dimensional (2D) layered semiconductor materials has enabled the creation of atomically thin heterojunction devices. Junctions between atomically thin 2D layers and 3D bulk semiconductors can lead to junctions that are fundamentally electronically different from the covalently bonded conventional semiconductor junctions. In this paper, we propose a new 3D band diagram for the heterojunction formed between n-type monolayer MoS2 and p-type Si, in which the conduction and valence band-edges of the MoS2 monolayer are drawn for both stacked and in-plane directions. This new band diagram helps visualize the flow of charge carriers inside themore » device in a 3D manner. Our detailed wavelength-dependent photocurrent measurements fully support the diagrams and unambiguously show that the band alignment is type I for this 2D-3D heterojunction. Photogenerated electron–hole pairs in the atomically thin monolayer are separated and driven by an external bias and control the “on/off” states of the junction photodetector device. Finally, two photoresponse regimes with fast and slow relaxation are also revealed in time-resolved photocurrent measurements, suggesting the important role played by charge trap states.« less

  13. 3D Band Diagram and Photoexcitation of 2D–3D Semiconductor Heterojunctions

    SciTech Connect

    Li, Bo; Shi, Gang; Lei, Sidong; He, Yongmin; Gao, Weilu; Gong, Yongji; Ye, Gonglan; Zhou, Wu; Keyshar, Kunttal; Hao, Ji; Dong, Pei; Ge, Liehui; Lou, Jun; Kono, Junichiro; Vajtai, Robert; Ajayan, Pulickel M.

    2015-08-17

    The emergence of a rich variety of two-dimensional (2D) layered semiconductor materials has enabled the creation of atomically thin heterojunction devices. Junctions between atomically thin 2D layers and 3D bulk semiconductors can lead to junctions that are fundamentally electronically different from the covalently bonded conventional semiconductor junctions. In this paper, we propose a new 3D band diagram for the heterojunction formed between n-type monolayer MoS2 and p-type Si, in which the conduction and valence band-edges of the MoS2 monolayer are drawn for both stacked and in-plane directions. This new band diagram helps visualize the flow of charge carriers inside the device in a 3D manner. Our detailed wavelength-dependent photocurrent measurements fully support the diagrams and unambiguously show that the band alignment is type I for this 2D-3D heterojunction. Photogenerated electron–hole pairs in the atomically thin monolayer are separated and driven by an external bias and control the “on/off” states of the junction photodetector device. Finally, two photoresponse regimes with fast and slow relaxation are also revealed in time-resolved photocurrent measurements, suggesting the important role played by charge trap states.

  14. 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.

  15. A Step-by-Step Assembly of a 3D Coordination Polymer in the Solid-State by Desolvation and [2+2] Cycloaddition Reactions.

    PubMed

    Medishetty, Raghavender; Tandiana, Rika; Wu, Jien; Bai, Zhaozhi; Du, Yonghua; Vittal, Jagadese J

    2015-08-17

    Two solid-state structural transformations that occur in a stepwise and a controlled manner are described. A combination of desolvation and cycloaddition reactions has been employed to synthesise a 3D coordination polymer (CP) from 1D CP [Cd(bdc)(4-spy)2 (H2 O)]⋅2 H2 O⋅2 DMF (bdc=1,4-benzenedicarboxylate, 4-spy=4-styrylpyridine) presumably via a 2D layered structure, [Cd2 (bdc)2 (4-spy)4 ]. In the absence of single crystals to follow the course of the photocycloaddition reaction, thermogravimetry, XAFS and NOESY NMR experiments were used to propose the formation of layered and pillared layered structures. Further, the present strategy enables us to synthesise new multidimensional architectures that are otherwise inaccessible by the self-assembly process. PMID:26150356

  16. 3D-full wave and kinetics numerical modelling of electron cyclotron resonance ion sources plasma: steps towards self-consistency

    NASA Astrophysics Data System (ADS)

    Mascali, David; Torrisi, Giuseppe; Neri, Lorenzo; Sorbello, Gino; Castro, Giuseppe; Celona, Luigi; Gammino, Santo

    2015-01-01

    Electron Cyclotron Resonance (ECR) ion Sources are the most performing machines for the production of intense beams of multi-charged ions in fundamental science, applied physics and industry. Investigation of plasma dynamics in ECRIS still remains a challenge. A better comprehension of electron heating, ionization and diffusion processes, ion confinement and ion beam formation is mandatory in order to increase ECRIS performances both in terms of output beams currents, charge states, beam quality (emittance minimization, beam halos suppression, etc.). Numerical solution of Vlasov equation via kinetic codes coupled to FEM solvers is ongoing at INFN-LNS, based on a PIC strategy. Preliminary results of the modeling will be shown about wave-plasma interaction and electron-ion confinement: the obtained results are very helpful to better understand the influence of the different parameters (especially RF frequency and power) on the ion beam formation mechanism.

  17. Sol-gel synthesis, phase composition, morphological and structural characterization of Ca10(PO4)6(OH)2: XRD, FTIR, SEM, 3D SEM and solid-state NMR studies

    NASA Astrophysics Data System (ADS)

    Kareiva, Simonas; Klimavicius, Vytautas; Momot, Aleksandr; Kausteklis, Jonas; Prichodko, Aleksandra; Dagys, Laurynas; Ivanauskas, Feliksas; Sakirzanovas, Simas; Balevicius, Vytautas; Kareiva, Aivaras

    2016-09-01

    Aqueous sol-gel chemistry route based on ammonium-hydrogen phosphate as the phosphorus precursor, calcium acetate monohydrate as source of calcium ions, and 1,2-ethylendiaminetetraacetic acid (EDTA), or 1,2-diaminocyclohexanetetracetic acid (DCTA), or tartaric acid (TA), or ethylene glycol (EG), or glycerol (GL) as complexing agents have been used to prepare calcium hydroxyapatite (Ca10(PO4)6(OH)2, CHAp). The phase transformations, composition, and structural changes in the polycrystalline samples were studied by infrared spectroscopy (FTIR), X-ray powder diffraction analysis (XRD), and scanning electron microscopy (SEM). The local short-range (nano- and mezo-) scale effects in CHAp were studied using solid-state NMR spectroscopy. The spatial 3D data from the SEM images of CHAp samples obtained by TA, EG and GL sol-gel routes were recovered for the first time to our knowledge.

  18. Lifetime of inner-shell hole states of Ar (2p) and Kr (3d) using equation-of-motion coupled cluster method

    SciTech Connect

    Ghosh, Aryya; Vaval, Nayana; Pal, Sourav

    2015-07-14

    Auger decay is an efficient ultrafast relaxation process of core-shell or inner-shell excited atom or molecule. Generally, it occurs in femto-second or even atto-second time domain. Direct measurement of lifetimes of Auger process of single ionized and double ionized inner-shell state of an atom or molecule is an extremely difficult task. In this paper, we have applied the highly correlated complex absorbing potential-equation-of-motion coupled cluster (CAP-EOMCC) approach which is a combination of CAP and EOMCC approach to calculate the lifetime of the states arising from 2p inner-shell ionization of an Ar atom and 3d inner-shell ionization of Kr atom. We have also calculated the lifetime of Ar{sup 2+}(2p{sup −1}3p{sup −1}) {sup 1}D, Ar{sup 2+}(2p{sup −1}3p{sup −1}) {sup 1}S, and Ar{sup 2+}(2p{sup −1}3s{sup −1}) {sup 1}P double ionized states. The predicted results are compared with the other theoretical results as well as experimental results available in the literature.

  19. Modelling of the steady state thermal behaviour of a permanent magnet direct current motor with commutator. 3D finite elements study

    NASA Astrophysics Data System (ADS)

    Bernard, R.; Glises, R.; Chamagne, D.; Cuchet, D.; Kauffmann, J. M.

    1999-08-01

    The aim of this work concerns the development and the validation of a thermal steady state model applied to a permanent magnet direct current motor with commutator. The rated power of the machine is 120 W. Design has been realized thanks to the thermal modulus of the computation software with the finite element method Flux3D. It is shown in this work how it is possible to use only the heat equation to simulate the thermal behaviour of the motor. It implies calculating of new fluid conductivities (considering also all thermal modes) by comparison of calculated and experimental temperatures. To realize these 3D modelizations, it is necessary to know and to locate all the losses of the motor which are considered as thermal sources. The experimental temperatures are given by 40 chromel-alumel thermocouples of 100 μm diameter located in the rotor and the stator of the machine. Numerical computations use Dirichlet boundary layer conditions given by an IR camera. Ce travail concerne le développement et la validation d'un modèle de simulation du comportement thermique tridimensionnel en régime permanent d'un moteur électrique de 120 watt à courant continu, à aimants permanents et à collecteur. Le logiciel est développé à partir du code de calculs par éléments finis Flux3D. L'équation de la chaleur modélise l'ensemble des transferts thermiques du moteur. Cela nécessite de recaler certains paramètres fluides par comparaison des températures simulées et expérimentales. Une séparation détaillée des différentes pertes est nécessaire pour obtenir une bonne précision finale. Un banc d'essais thermiques permet d'obtenir à l'aide de 40 thermocouples (chromel-alumel de 100 μm de diamètre) les températures au stator et au rotor. Une caméra thermographique infrarouge donne les conditions aux limites de Dirichlet nécessaires à la modélisation.

  20. Bootstrapping 3D fermions

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  1. Multi-scale Finite-Frequency Travel-time Tomography Applied to Imaging 3-D Velocity Structure of the Upper Mantle Beneath the Southwest United States

    NASA Astrophysics Data System (ADS)

    Yin, Y.; Hung, S.

    2007-12-01

    Seismic tomographic imaging has played a key component to unravel the deep processes that caused the surface morphology and rift magmatism in the southwest United States. Several studies used teleseismic body- wave arrivals recorded by the La Ristra experiment, a dense broadband array of 950-km in length deployed during 1999-2001 and run through the Great Plains, the Rio Grande Rift, and the Colorado Plateau, to construct a 2-D tomographic image of the upper mantle structure beneath this linear array (e.g., Gao et al., 2004). However, because of the inevitable smoothing and damping imposed in the tomographic model, the resulting velocity contrast is too weak to explain distinct P and S waveform changes across the array (Song and Helmberger, 2007). In this study, we include all the data from the La Ristra and available nearby arrays and reexamine finite- frequency travel time delays measured by inter-station cross correlation of waveforms at both high- (0.3-2 Hz for P and 0.1-0.5 Hz for S) and low-frequencies (0.03-0.125 Hz for P and 0.03-0.1 Hz for S). Differing from the previous models that rely on classical ray theory and simple grid parameterization, our inversion considers more realistic 3-D sensitivity kernels for relative travel-time delays and a wavelet-based, multi-scale parameterization that enables to yield robust features with spatially-varying resolutions. Our preliminary P-wave model reveals a prominent low-velocity zone extending from near surface to the depth of 300 km beneath the Rio Grande Rift, while the upper mantle which underlies the Great Plains and the Colorado Plateau is seismically fast. We will demonstrate the difference and improvement of 3-D tomographic models through the use of finite-frequency kernels and multi-scale parameterization.

  2. 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

  3. 3D finite element simulation of microstructure evolution in blade forging of Ti-6Al-4V alloy based on the internal state variable models

    NASA Astrophysics Data System (ADS)

    Luo, Jiao; Wu, Bin; Li, Miao-Quan

    2012-02-01

    The physically-based internal state variable (ISV) models were used to describe the changes of dislocation density, grain size, and flow stress in the high temperature deformation of titanium alloys in this study. The constants of the present models could be identified based on experimental results, which were conducted at deformation temperatures ranging from 1093 K to 1303 K, height reductions ranging from 20% to 60%, and the strain rates of 0.001, 0.01, 0.1, 1.0, and 10.0 s-1. The physically-based internal state variable models were implemented into the commercial finite element (FE) code. Then, a three-dimensional (3D) FE simulation system coupling of deformation, heat transfer, and microstructure evolution was developed for the blade forging of Ti-6Al-4V alloy. FE analysis was carried out to simulate the microstructure evolution in the blade forging of Ti-6Al-4V alloy. Finally, the blade forging tests of Ti-6Al-4V alloy were performed to validate the results of FE simulation. According to the tensile tests, it is seen that the mechanical properties, such as tensile strength and elongation, satisfy the application requirements well. The maximum and minimum differences between the calculated and experimental grain size of primary α phase are 11.71% and 4.23%, respectively. Thus, the industrial trials show a good agreement with FE simulation of blade forging.

  4. Biocompatible 3D Matrix with Antimicrobial Properties.

    PubMed

    Ion, Alberto; Andronescu, Ecaterina; Rădulescu, Dragoș; Rădulescu, Marius; Iordache, Florin; Vasile, Bogdan Ștefan; Surdu, Adrian Vasile; Albu, Madalina Georgiana; Maniu, Horia; Chifiriuc, Mariana Carmen; Grumezescu, Alexandru Mihai; Holban, Alina Maria

    2016-01-01

    The aim of this study was to develop, characterize and assess the biological activity of a new regenerative 3D matrix with antimicrobial properties, based on collagen (COLL), hydroxyapatite (HAp), β-cyclodextrin (β-CD) and usnic acid (UA). The prepared 3D matrix was characterized by Scanning Electron Microscopy (SEM), Fourier Transform Infrared Microscopy (FT-IRM), Transmission Electron Microscopy (TEM), and X-ray Diffraction (XRD). In vitro qualitative and quantitative analyses performed on cultured diploid cells demonstrated that the 3D matrix is biocompatible, allowing the normal development and growth of MG-63 osteoblast-like cells and exhibited an antimicrobial effect, especially on the Staphylococcus aureus strain, explained by the particular higher inhibitory activity of usnic acid (UA) against Gram positive bacterial strains. Our data strongly recommend the obtained 3D matrix to be used as a successful alternative for the fabrication of three dimensional (3D) anti-infective regeneration matrix for bone tissue engineering. PMID:26805790

  5. Ab initio and long-range investigation of the Ω(+/-) states of NaK dissociating adiabatically up to Na(3s 2S1/2) + K(3d 2D3/2)

    NASA Astrophysics Data System (ADS)

    Allouche, A. R.; Aubert-Frécon, M.

    2011-07-01

    A theoretical investigation of the electronic structure of the NaK molecule including spin-orbit effects has been performed for the 34 Ω(+/-) states dissociating adiabatically into the limits up to Na(3s2S1/2) + K(3d2D3/2) from both an ab initio approach and a long-range model. Equilibrium distances, transition energies, harmonic frequencies as well as depths of wells and heights of humps are reported for all the states. Formulas for calculating the long-range energies for all the 0+/-, 1, 2, and 3 states under investigation are also displayed. They are expressed in terms of the Cn (n = 6,8, …) long-range coefficients and exchange integrals for the 2S+1Λ(+) parent states, available from literature. As present data could help experimentalists we make available extensive tables of energy values versus internuclear distances in our database at the web address: http://www-lasim.univ-lyon1.fr/spip.php?rubrique99.

  6. 3D microscope

    NASA Astrophysics Data System (ADS)

    Iizuka, Keigo

    2008-02-01

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

  7. Creep modulation of Omori law generated by a Coulomb stress perturbation in a 3-D rate-and-state asperity model

    NASA Astrophysics Data System (ADS)

    Dublanchet, P.; Bernard, P.; Favreau, P.

    2013-09-01

    We present numerical simulations conducted with a quasi-dynamic, 3-D rate-and-state asperity model and an analytical approach in order to study the behavior of a seismic asperity surrounded by aseismic creep in response to external Coulomb stress perturbations. This work is inspired by the observation of Omori decay characterizing the recurrence time of isolated repeating earthquakes, such as at the Parkfield segment of the San Andreas Fault during the postseismic phase of the 2004 Mw6 event. Based on the numerical results and on an analysis of phase diagrams, we identify two possible regimes that characterize the response of an asperity surrounded by aseismic creep to a stress step, depending on an effective steady state friction parameter A. For the specific perturbation used in this study, we observe that when A is positive, the relaxation of the system is governed by the response of the creeping segments of the fault, and the asperity ruptures in an Omori sequence. In this regime, we demonstrate that the duration of the relaxation process depends on A. Furthermore, we show that this effective strengthening behavior is equivalent to a subcritical density of asperities meaning that the shape of the Omori decay is controlled by the relative proportion of seismic and aseismic material within the fault. On the other hand, a fault characterized by effective steady state weakening (A<0) behaves like a spring and slider system that loses the memory of the stress perturbation once the first aftershock occurred, at least in the simulations presented here.

  8. Theoretical studies of electronically excited states

    SciTech Connect

    Besley, Nicholas A.

    2014-10-06

    Time-dependent density functional theory is the most widely used quantum chemical method for studying molecules in electronically excited states. However, excited states can also be computed within Kohn-Sham density functional theory by exploiting methods that converge the self-consistent field equations to give excited state solutions. The usefulness of single reference self-consistent field based approaches for studying excited states is demonstrated by considering the calculation of several types of spectroscopy including the infrared spectroscopy of molecules in an electronically excited state, the rovibrational spectrum of the NO-Ar complex, core electron binding energies and the emission spectroscopy of BODIPY in water.

  9. 3-D Technology Approaches for Biological Ecologies

    NASA Astrophysics Data System (ADS)

    Liu, Liyu; Austin, Robert; U. S-China Physical-Oncology Sciences Alliance (PS-OA) Team

    Constructing three dimensional (3-D) landscapes is an inevitable issue in deep study of biological ecologies, because in whatever scales in nature, all of the ecosystems are composed by complex 3-D environments and biological behaviors. Just imagine if a 3-D technology could help complex ecosystems be built easily and mimic in vivo microenvironment realistically with flexible environmental controls, it will be a fantastic and powerful thrust to assist researchers for explorations. For years, we have been utilizing and developing different technologies for constructing 3-D micro landscapes for biophysics studies in in vitro. Here, I will review our past efforts, including probing cancer cell invasiveness with 3-D silicon based Tepuis, constructing 3-D microenvironment for cell invasion and metastasis through polydimethylsiloxane (PDMS) soft lithography, as well as explorations of optimized stenting positions for coronary bifurcation disease with 3-D wax printing and the latest home designed 3-D bio-printer. Although 3-D technologies is currently considered not mature enough for arbitrary 3-D micro-ecological models with easy design and fabrication, I hope through my talk, the audiences will be able to sense its significance and predictable breakthroughs in the near future. This work was supported by the State Key Development Program for Basic Research of China (Grant No. 2013CB837200), the National Natural Science Foundation of China (Grant No. 11474345) and the Beijing Natural Science Foundation (Grant No. 7154221).

  10. Influence of disorder on ageing and memory effects in non-equilibrium critical dynamics of 3D Ising model relaxing from an ordered state

    NASA Astrophysics Data System (ADS)

    Prudnikov, Vladimir V.; Prudnikov, Pavel V.; Pospelov, Evgeny A.

    2016-04-01

    We have performed a numerical investigation of the influence of disorder on the dynamical non-equilibrium evolution of a 3D site-diluted Ising model from a low-temperature initial state with magnetization m 0  =  1. It is shown that two-time dependences of the autocorrelation and integrated response functions for systems with spin concentrations p  =  1.0, 0.95, 0.8, 0.6 and 0.5 demonstrate ageing properties with anomalous slowing-down relaxation and violation of the fluctuation-dissipation ratio. It was revealed that during non-equilibrium critical dynamics in the long-time regime t-{{t}\\text{w}}\\gg {{t}\\text{w}}\\gg 1 the autocorrelation functions for diluted systems are extremely slow due to the pinning of domain walls on impurity sites. We have found that the fluctuation-dissipation ratio {{X}∞}=0 for diluted systems with spin concentration p  <  1 while the pure system is characterized by {{X}∞}=0.784(7) . The autocorrelation function power-law delay becomes the same as for the time dependence of the magnetization in the critical point and is characterized by exponent -β /zν . Also, for diluted systems we reveal memory effects for critical evolution in the ageing regime with realization of cyclic temperature change and quenching at T<{{T}\\text{c}} .

  11. Three-step laser excitation of the odd-parity 5s5d 3D → 5s nf 3F states of cadmium

    NASA Astrophysics Data System (ADS)

    Nadeem, Ali; Shah, M.; Haq, S. U.; Shahzada, S.; Mumtaz, M.; Waheed, A.; Nawaz, M.; Ahmed, M.; Baig, M. A.

    2014-07-01

    We report new experimental data on the term energies and effective quantum numbers of the highly excited odd parity states of cadmium in the 71 773-72 500 cm-1 energy range. The experiment was performed using three dye lasers simultaneously pumped by the second harmonic (532 nm) of the Nd;YAG laser. The vapor containment and detection system was a thermionic diode ion detector working in a space charge limited mode. The new observations include the 5snf3F3 (12 ⩽ n ⩽ 52), 5snf3F4 (13 ⩽ n ⩽ 33) and 5snf3F2 (12 ⩽ n ⩽ 22) Rydberg series excited from the 5s5d3D multiplet. A two parameter fit to the transitions energies of the 5snf3F3 series yields the binding energy of the 5snd 2D2 level as 13 042.178 ± 0.02 cm-1 and consequently the first ionization of cadmium is determined as 72 540.05 ± 0.13 cm-1, which is in good agreement with the previously reported value.

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

    SciTech Connect

    Mason, W.E.

    1992-03-04

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

  13. 3D Printed Bionic Ears

    PubMed Central

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

    2013-01-01

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

  14. 3D printed bionic ears.

    PubMed

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

    2013-06-12

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

  15. Density functional study of the stable oxidation states and the binding of oxygen in MO4 clusters of the 3d elements.

    PubMed

    Uzunova, Ellie L

    2011-10-01

    The tetraoxide clusters with stoichiometry MO(4), and the structural isomers with side-on and end-on bonded dioxygen, are studied by DFT with the B1LYP functional. Diperoxides M(O(2))(2) are the most stable clusters at the beginning (Sc, Ti) and at the end of the row (Co-Cu), the latter being planar. For V, Cr, and Mn, the dioxoperoxides O(2)M(O(2)) are the most stable isomers. Low-spin states are dominant for the nonplanar diperoxides M(O(2))(2) and dioxoperoxides O(2)M(O(2)), and the local magnetic moment at the metal cations is small. The local charge on the metal cation center is higher in the diperoxides of Sc and Ti; it drops significantly in the dioxoperoxides of V and Cr. The iron dioxosuperoxide in the (3)A'' state, which contains end-on bonded dioxygen, OOFeO(2), is an exception with higher charge on Fe. In the planar diperoxides of Co, Ni, and Cu, oxygen-to-metal charge transfer is significant, and the local charge on the metal cation is close to 1. In all tetraoxygen clusters of the 3d elements, the cation center remains strongly electrophilic and interacts with Ar atoms from the inert-gas matrix, where the clusters are trapped for IR spectral studies. Significant frequency shifts in the matrix are found for the dioxoperoxide of vanadium, O(2)V(O(2)), the dioxosuperoxide of iron, OOFeO(2), and the nickel diperoxide, Ni(O(2))(2). PMID:21875076

  16. Multiviewer 3D monitor

    NASA Astrophysics Data System (ADS)

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

    1998-09-01

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

  17. 3D Audio System

    NASA Technical Reports Server (NTRS)

    1992-01-01

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

  18. High-Pressure Single-Crystal Structures of 3D Lead-Halide Hybrid Perovskites and Pressure Effects on their Electronic and Optical Properties.

    PubMed

    Jaffe, Adam; Lin, Yu; Beavers, Christine M; Voss, Johannes; Mao, Wendy L; Karunadasa, Hemamala I

    2016-04-27

    We report the first high-pressure single-crystal structures of hybrid perovskites. The crystalline semiconductors (MA)PbX3 (MA = CH3NH3 (+), X = Br(-) or I(-)) afford us the rare opportunity of understanding how compression modulates their structures and thereby their optoelectronic properties. Using atomic coordinates obtained from high-pressure single-crystal X-ray diffraction we track the perovskites' precise structural evolution upon compression. These structural changes correlate well with pressure-dependent single-crystal photoluminescence (PL) spectra and high-pressure bandgaps derived from density functional theory. We further observe dramatic piezochromism where the solids become lighter in color and then transition to opaque black with compression. Indeed, electronic conductivity measurements of (MA)PbI3 obtained within a diamond-anvil cell show that the material's resistivity decreases by 3 orders of magnitude between 0 and 51 GPa. The activation energy for conduction at 51 GPa is only 13.2(3) meV, suggesting that the perovskite is approaching a metallic state. Furthermore, the pressure response of mixed-halide perovskites shows new luminescent states that emerge at elevated pressures. We recently reported that the perovskites (MA)Pb(Br x I1-x )3 (0.2 < x < 1) reversibly form light-induced trap states, which pin their PL to a low energy. This may explain the low voltages obtained from solar cells employing these absorbers. Our high-pressure PL data indicate that compression can mitigate this PL redshift and may afford higher steady-state voltages from these absorbers. These studies show that pressure can significantly alter the transport and thermodynamic properties of these technologically important semiconductors. PMID:27163050

  19. High-Pressure Single-Crystal Structures of 3D Lead-Halide Hybrid Perovskites and Pressure Effects on their Electronic and Optical Properties

    PubMed Central

    2016-01-01

    We report the first high-pressure single-crystal structures of hybrid perovskites. The crystalline semiconductors (MA)PbX3 (MA = CH3NH3+, X = Br– or I–) afford us the rare opportunity of understanding how compression modulates their structures and thereby their optoelectronic properties. Using atomic coordinates obtained from high-pressure single-crystal X-ray diffraction we track the perovskites’ precise structural evolution upon compression. These structural changes correlate well with pressure-dependent single-crystal photoluminescence (PL) spectra and high-pressure bandgaps derived from density functional theory. We further observe dramatic piezochromism where the solids become lighter in color and then transition to opaque black with compression. Indeed, electronic conductivity measurements of (MA)PbI3 obtained within a diamond-anvil cell show that the material’s resistivity decreases by 3 orders of magnitude between 0 and 51 GPa. The activation energy for conduction at 51 GPa is only 13.2(3) meV, suggesting that the perovskite is approaching a metallic state. Furthermore, the pressure response of mixed-halide perovskites shows new luminescent states that emerge at elevated pressures. We recently reported that the perovskites (MA)Pb(BrxI1–x)3 (0.2 < x < 1) reversibly form light-induced trap states, which pin their PL to a low energy. This may explain the low voltages obtained from solar cells employing these absorbers. Our high-pressure PL data indicate that compression can mitigate this PL redshift and may afford higher steady-state voltages from these absorbers. These studies show that pressure can significantly alter the transport and thermodynamic properties of these technologically important semiconductors. PMID:27163050

  20. Design of smart 3D-digital X-ray microtomographic scanners for non-destructive testing of materials and components of electronic devices with a multilayered structure

    NASA Astrophysics Data System (ADS)

    Syryamkin, V. I.; Suntsov, S. B.; Klestov, S. A.; Echina, E. S.

    2015-10-01

    The article studies the operating procedures of an X-ray microtomographic scanner and the module of reconstruction and analysis 3D-image of a test sample in particular. An algorithm for 3D-image reconstruction based on image shadow projections and mathematical methods of the processing are described. Chapter 1 describes the basic principles of X-ray tomography and general procedures of the device developed. Chapters 2 and 3 are devoted to the problem of resources saving by the system during the X-ray tomography procedure, which is achieved by preprocessing of the initial shadow projections. Preprocessing includes background noise removing from the images, which reduces the amount of shadow projections in general and increases the efficiency of the group shadow projections compression. Chapter 4 covers general procedures of defect search, which is based on vector analysis principles. In conclusion, the main applications of X-ray tomography are presented.

  1. Design of smart 3D-digital X-ray microtomographic scanners for non-destructive testing of materials and components of electronic devices with a multilayered structure

    SciTech Connect

    Syryamkin, V. I. Klestov, S. A. Echina, E. S.; Suntsov, S. B.

    2015-10-27

    The article studies the operating procedures of an X-ray microtomographic scanner and the module of reconstruction and analysis 3D-image of a test sample in particular. An algorithm for 3D-image reconstruction based on image shadow projections and mathematical methods of the processing are described. Chapter 1 describes the basic principles of X-ray tomography and general procedures of the device developed. Chapters 2 and 3 are devoted to the problem of resources saving by the system during the X-ray tomography procedure, which is achieved by preprocessing of the initial shadow projections. Preprocessing includes background noise removing from the images, which reduces the amount of shadow projections in general and increases the efficiency of the group shadow projections compression. Chapter 4 covers general procedures of defect search, which is based on vector analysis principles. In conclusion, the main applications of X-ray tomography are presented.

  2. Anomalous confined electron states in graphene superlattices

    SciTech Connect

    Anh Le, H.; Chien Nguyen, D.; Nam Do, V.

    2014-07-07

    We show that periodic scalar potentials can induce the localization of some electronic states in graphene. Particularly, localized states are found at energies outside the potential variation range and embedded in the continuum spectrum of delocalized ones. The picture of the connection of wave functions with typical symmetries defined in relevant-edge nanoribbons is employed to explain the formation of the electronic structure and to characterize/classify eigen-states in graphene superlattices.

  3. 3D Surgical Simulation

    PubMed Central

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

    2009-01-01

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

  4. Charge and electronic states of cuprite: Experiment and theory

    NASA Astrophysics Data System (ADS)

    Kim, Miyoung

    The bonding characteristics of cuprite have been studied by the using convergent beam electron diffraction (CBED) method. The low-order structure factors are closely related to the valence electron density, and the CBED is one of the most accurate methods of measuring the low order structure factors. The multipole model is used for converting the structure factors into charge density. The multipole expansion takes into account non-spherical valence electron density due to atomic bonding based on the crystal symmetry. The charge transfer from copper to oxygen is determined from the multipole fitting parameters. The hybridization state between 4s-3d orbitals of copper is also estimated. Electronic states of CU2O are investigated by studying the fine structure of the electron-energy loss spectrum (EELS). The cross section of the near edge structure is proportional to the density of state times an atomic transition site-projected matrix element which generally varies slowly in the region of interest. Both the fine structure of Cu- L2'3 and O-K of Cu2O are significantly different from those of CuO, which shows the sensitivity of EELS fine structure to the crystal bonding. Full-potential Linearized Augmented Plane Wave (FLAPW) calculations have been used to compare experimental results with theory. The structure factors and bonding charge density are compared with the results obtained by the CBED method, and the density of states is compared with the EELS. The FLAPW method has also been used in the local density approximations CLDA) to calculate values of the mean inner Coulomb potential V 0 for Si, Ge and MgO. These values are compared with recent measurements by electron holography. The supercell calculations are performed for crystal slabs, so that the effects of different crystal orientations and surface structures on V0 can be evaluated.

  5. 3D polarimetric purity

    NASA Astrophysics Data System (ADS)

    Gil, José J.; San José, Ignacio

    2010-11-01

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

  6. 3D field harmonics

    SciTech Connect

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

    1991-03-30

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

  7. 'Bonneville' in 3-D!

    NASA Technical Reports Server (NTRS)

    2004-01-01

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

  8. Organ-Mounted Electronics: An Universal and Easy-to-Use Model for the Pressure of Arbitrary-Shape 3D Multifunctional Integumentary Cardiac Membranes (Adv. Healthcare Mater. 8/2016).

    PubMed

    Su, Yewang; Liu, Zhuangjian; Xu, Lizhi

    2016-04-01

    Recently developed concepts for 3D, organ-mounted electronics for cardiac applications require an universal and easy-to-use mechanical model to calculate the average pressure associated with operation of the device, which is crucial for evaluation of design efficacy and optimization. A simple, accurate, easy-to-use, and universal model to quantify the average pressure for arbitrarily shaped organs is proposed by Y. Su and colleagues on page 889. Cover designed by Zhenhai Li. PMID:27091775

  9. 3D cryo-electron reconstruction of BmrA, a bacterial multidrug ABC transporter in an inward-facing conformation and in a lipidic environment.

    PubMed

    Fribourg, Pierre Frederic; Chami, Mohamed; Sorzano, Carlos Oscar S; Gubellini, Francesca; Marabini, Roberto; Marco, Sergio; Jault, Jean-Michel; Lévy, Daniel

    2014-05-15

    ABC (ATP-binding cassette) membrane exporters are efflux transporters of a wide diversity of molecule across the membrane at the expense of ATP. A key issue regarding their catalytic cycle is whether or not their nucleotide-binding domains (NBDs) are physically disengaged in the resting state. To settle this controversy, we obtained structural data on BmrA, a bacterial multidrug homodimeric ABC transporter, in a membrane-embedded state. BmrA in the apostate was reconstituted in lipid bilayers forming a mixture of ring-shaped structures of 24 or 39 homodimers. Three-dimensional models of the ring-shaped structures of 24 or 39 homodimers were calculated at 2.3 nm and 2.5 nm resolution from cryo-electron microscopy, respectively. In these structures, BmrA adopts an inward-facing open conformation similar to that found in mouse P-glycoprotein structure with the NBDs separated by 3 nm. Both lipidic leaflets delimiting the transmembrane domains of BmrA were clearly resolved. In planar membrane sheets, the NBDs were even more separated. BmrA in an ATP-bound conformation was determined from two-dimensional crystals grown in the presence of ATP and vanadate. A projection map calculated at 1.6 nm resolution shows an open outward-facing conformation. Overall, the data are consistent with a mechanism of drug transport involving large conformational changes of BmrA and show that a bacterial ABC exporter can adopt at least two open inward conformations in lipid membrane. PMID:24630999

  10. Characterizing Properties and Performance of 3D Printed Plastic Scintillators

    NASA Astrophysics Data System (ADS)

    McCormick, Jacob

    2015-10-01

    We are determining various characteristics of the performance of 3D printed scintillators. A scintillator luminesces when an energetic particle raises electrons to an excited state by depositing some of its energy in the atom. When these excited electrons fall back down to their stable states, they emit the excess energy as light. We have characterized the transmission spectrum, emission spectrum, and relative intensity of light produced by 3D printed scintillators. We are also determining mechanical properties such as tensile strength and compressibility, and the refractive index. The emission and transmission spectra were measured using a monochromator. By observing the transmission spectrum, we can see which optical wavelengths are absorbed by the scintillator. This is then used to correct the emission spectrum, since this absorption is present in the emission spectrum. Using photomultiplier tubes in conjunction with integration hardware (QDC) to measure the intensity of light emitted by 3D printed scintillators, we compare with commercial plastic scintillators. We are using the characterizations to determine if 3D printed scintillators are a viable alternative to commercial scintillators for use at Jefferson Lab in nuclear and accelerated physics detectors. I would like to thank Wouter Deconinck, as well as the Parity group at the College of William and Mary for all advice and assistance with my research.

  11. A pseudo-3D approach based on electron backscatter diffraction and backscatter electron imaging to study the character of phase boundaries between Mg and long period stacking ordered phase in a Mg–2Y–Zn alloy

    SciTech Connect

    Afshar, Mehran Zaefferer, Stefan

    2015-03-15

    In Mg–2 at.% Y–1 at.% Zn alloys, the LPSO (Long Period Stacking Ordered) phase is important to improve mechanical properties of the material. The aim of this paper is to present a study on the phase boundary character in these two-phase alloys. Using EBSD pattern analysis it was found that the 24R structure is the dominant LPSO phase structure in the current alloy. The phase boundary character between the Mg matrix and the LPSO phase was investigated using an improved pseudo-3D EBSD (electron backscatter diffraction) technique in combination with BSE or SE (backscatter or secondary electron) imaging. A large amount of very low-angle phase boundaries was detected. The (0 0 0 2) plane in the Mg matrix which is parallel to the (0 0 0 24) plane in the LPSO phase was found to be the most frequent plane for these phase boundaries. This plane is supposed to be the habit plane of the eutectic co-solidification of the Mg matrix and the LPSO phase. - Highlights: • It is shown that for the investigated alloy the LPSO phase has mainly 24R crystal structure. • A new method is presented which allows accurate determination of the 5-parameter grain or phase boundary character. • It is found that the low-angle phase boundaries appearing in the alloy all have basal phase boundary planes.

  12. Method for optimal sensor deployment on 3D terrains utilizing a steady state genetic algorithm with a guided walk mutation operator based on the wavelet transform.

    PubMed

    Unaldi, Numan; Temel, Samil; Asari, Vijayan K

    2012-01-01

    One of the most critical issues of Wireless Sensor Networks (WSNs) is the deployment of a limited number of sensors in order to achieve maximum coverage on a terrain. The optimal sensor deployment which enables one to minimize the consumed energy, communication time and manpower for the maintenance of the network has attracted interest with the increased number of studies conducted on the subject in the last decade. Most of the studies in the literature today are proposed for two dimensional (2D) surfaces; however, real world sensor deployments often arise on three dimensional (3D) environments. In this paper, a guided wavelet transform (WT) based deployment strategy (WTDS) for 3D terrains, in which the sensor movements are carried out within the mutation phase of the genetic algorithms (GAs) is proposed. The proposed algorithm aims to maximize the Quality of Coverage (QoC) of a WSN via deploying a limited number of sensors on a 3D surface by utilizing a probabilistic sensing model and the Bresenham's line of sight (LOS) algorithm. In addition, the method followed in this paper is novel to the literature and the performance of the proposed algorithm is compared with the Delaunay Triangulation (DT) method as well as a standard genetic algorithm based method and the results reveal that the proposed method is a more powerful and more successful method for sensor deployment on 3D terrains. PMID:22666078

  13. Method for Optimal Sensor Deployment on 3D Terrains Utilizing a Steady State Genetic Algorithm with a Guided Walk Mutation Operator Based on the Wavelet Transform

    PubMed Central

    Unaldi, Numan; Temel, Samil; Asari, Vijayan K.

    2012-01-01

    One of the most critical issues of Wireless Sensor Networks (WSNs) is the deployment of a limited number of sensors in order to achieve maximum coverage on a terrain. The optimal sensor deployment which enables one to minimize the consumed energy, communication time and manpower for the maintenance of the network has attracted interest with the increased number of studies conducted on the subject in the last decade. Most of the studies in the literature today are proposed for two dimensional (2D) surfaces; however, real world sensor deployments often arise on three dimensional (3D) environments. In this paper, a guided wavelet transform (WT) based deployment strategy (WTDS) for 3D terrains, in which the sensor movements are carried out within the mutation phase of the genetic algorithms (GAs) is proposed. The proposed algorithm aims to maximize the Quality of Coverage (QoC) of a WSN via deploying a limited number of sensors on a 3D surface by utilizing a probabilistic sensing model and the Bresenham's line of sight (LOS) algorithm. In addition, the method followed in this paper is novel to the literature and the performance of the proposed algorithm is compared with the Delaunay Triangulation (DT) method as well as a standard genetic algorithm based method and the results reveal that the proposed method is a more powerful and more successful method for sensor deployment on 3D terrains. PMID:22666078

  14. Nearly free electron states in MXenes

    NASA Astrophysics Data System (ADS)

    Khazaei, Mohammad; Ranjbar, Ahmad; Ghorbani-Asl, Mahdi; Arai, Masao; Sasaki, Taizo; Liang, Yunye; Yunoki, Seiji

    2016-05-01

    Using a set of first-principles calculations, we studied the electronic structures of two-dimensional transition metal carbides and nitrides, so called MXenes, functionalized with F, O, and OH. Our projected band structures and electron localization function analyses reveal the existence of nearly free electron (NFE) states in a variety of MXenes. The NFE states are spatially located just outside the atomic structure of MXenes and are extended parallel to the surfaces. Moreover, we found that the OH-terminated MXenes offer the NFE states energetically close to the Fermi level. In particular, the NFE states in some of the OH-terminated MXenes, such as T i2C (OH) 2,Z r2C (OH) 2,Z r2N (OH) 2,H f2C (OH) 2,H f2N (OH) 2,N b2C (OH) 2 , and T a2C (OH) 2 , are partially occupied. This is in remarkable contrast to graphene, graphane, and Mo S2 , in which their NFE states are located far above the Fermi level and thus they are unoccupied. As a prototype of such systems, we investigated the electron transport properties of H f2C (OH) 2 and found that the NFE states in H f2C (OH) 2 provide almost perfect transmission channels without nuclear scattering for electron transport. Our results indicate that these systems might find applications in nanoelectronic devices. Our findings provide new insights into the unique electronic band structures of MXenes.

  15. Topology dictionary for 3D video understanding.

    PubMed

    Tung, Tony; Matsuyama, Takashi

    2012-08-01

    This paper presents a novel approach that achieves 3D video understanding. 3D video consists of a stream of 3D models of subjects in motion. The acquisition of long sequences requires large storage space (2 GB for 1 min). Moreover, it is tedious to browse data sets and extract meaningful information. We propose the topology dictionary to encode and describe 3D video content. The model consists of a topology-based shape descriptor dictionary which can be generated from either extracted patterns or training sequences. The model relies on 1) topology description and classification using Reeb graphs, and 2) a Markov motion graph to represent topology change states. We show that the use of Reeb graphs as the high-level topology descriptor is relevant. It allows the dictionary to automatically model complex sequences, whereas other strategies would require prior knowledge on the shape and topology of the captured subjects. Our approach serves to encode 3D video sequences, and can be applied for content-based description and summarization of 3D video sequences. Furthermore, topology class labeling during a learning process enables the system to perform content-based event recognition. Experiments were carried out on various 3D videos. We showcase an application for 3D video progressive summarization using the topology dictionary. PMID:22745004

  16. Mapping the 3D Geometry of the San Leandro Block of the Hayward Fault Zone Using Geologic, Geophysical and Remote Sensing Data, California State University, East Bay Campus

    NASA Astrophysics Data System (ADS)

    McEvilly, A.; Abimbola, A.; Chan, J. H.; Strayer, L. M.

    2015-12-01

    California State University, East Bay (CSUEB), located in Hayward, California, lies atop the San Leandro block (SLB) in the Hayward fault zone. The SLB is a J-K aged lithotectonic assemblage dominated by gabbro and intercalated with minor volcanics and sediments. It is bound by the subparallel northwest-trending western Hayward and eastern Chabot (CF) faults and pervasively cut by anastomosing secondary faults. The block itself is ~30 km along strike and 2-3 km wide. Previous studies suggest the block dips steeply to the northeast and extends to a depth of at least 7 km. In May of 2015, as part of an ongoing collaborative effort led by the USGS to create a 3D velocity model of the San Francisco Bay Area, researchers from CSUEB and the USGS conducted a seismic survey on the CSUEB campus. The primary goal of this pilot study was to locate the trace of the CF on the CSUEB campus and to determine bedrock depth. We deployed a 60-channel, 300m profile using 4.5Hz sensors spaced at 5m intervals. Active seismic sources were used at each geophone location. A 226kg accelerated weight-drop was used to generate P and Rayleigh waves for P-wave tomography and multichannel analysis of surface waves (MASW), and a 3.5kg sledgehammer and block were used to generate S and Love waves for S-wave tomography and multichannel analysis of Love waves (MALW). Preliminary P-wave tomography, MASW, and MALW results from this pilot study suggest the location of an eastward-dipping CF as well as the presence of a high-velocity unit at about 20m depth, presumably an unmapped sliver of bedrock from the San Leandro block. Further studies planned for the fall of 2015 include additional seismic lines and surface mapping along the Chabot fault on and near the CSUEB campus. These new geophysical, GPS, and field geological data will be integrated with LiDAR imagery and existing geological, gravity and magnetic maps to create a 3-dimensional model of the portion of the SLB that contains the CSUEB campus.

  17. Fermionic thermocoherent state: Efficiency of electron transport

    NASA Astrophysics Data System (ADS)

    Karmakar, Anirban; Gangopadhyay, Gautam

    2016-02-01

    On the basis of the fermionic coherent state of Cahill and Glauber [Phys. Rev. A 59, 1538 (1999)], 10.1103/PhysRevA.59.1538, we have introduced here the fermionic thermocoherent state in terms of the quasiprobability distribution which shows the appropriate thermal and coherent limits as in the bosonic case or the Glauber-Lachs state. It is shown that the fermionic thermocoherent state can be realized as a displaced thermal state of fermions. Its relation with the fermionic displaced number state and the fermion-added coherent state are explored in the spirit of the bosonic case. We have investigated the nature of the average current and the suppression of noise due to the thermocoherent character of the source. The theory is applied to the problem of electronic conduction. A modification of the Landauer conductance formula is suggested which reflects the role of nonzero coherence of the source in electron transport.

  18. Prominent rocks - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

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

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

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

  19. 'Diamond' in 3-D

    NASA Technical Reports Server (NTRS)

    2004-01-01

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

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

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

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

  20. Magnetism In 3d Transition Metals at High Pressures

    SciTech Connect

    Iota, V

    2006-02-09

    This research project examined the changes in electronic and magnetic properties of transition metals and oxides under applied pressures, focusing on complex relationship between magnetism and phase stability in these correlated electron systems. As part of this LDRD project, we developed new measurement techniques and adapted synchrotron-based electronic and magnetic measurements for use in the diamond anvil cell. We have performed state-of-the-art X-ray spectroscopy experiments at the dedicated high-pressure beamline HP-CAT (Sector 16 Advanced Photon Source, Argonne National Laboratory), maintained in collaboration with of University of Nevada, Las Vegas and Geophysical Laboratory of The Carnegie Institution of Washington. Using these advanced measurements, we determined the evolution of the magnetic order in the ferromagnetic 3d transition metals (Fe, Co and Ni) under pressure, and found that at high densities, 3d band broadening results in diminished long range magnetic coupling. Our experiments have allowed us to paint a unified picture of the effects of pressure on the evolution of magnetic spin in 3d electron systems. The technical and scientific advances made during this LDRD project have been reported at a number of scientific meetings and conferences, and have been submitted for publication in technical journals. Both the technical advances and the physical understanding of correlated systems derived from this LDRD are being applied to research on the 4f and 5f electron systems under pressure.

  1. Description of electronic excited states using electron correlation operator.

    PubMed

    Nichols, Bryan; Rassolov, Vitaly A

    2013-09-14

    The electron correlation energy in a chemical system is defined as a difference between the energy of an exact energy for a given Hamiltonian, and a mean-field, or single determinant, approximation to it. A promising way to model electron correlation is through the expectation value of a linear two-electron operator for the Kohn-Sham single determinant wavefunction. For practical reasons, it is desirable for such an operator to be universal, i.e., independent of the positions and types of nuclei in a molecule. The correlation operator models the effect of electron correlation on the interaction energy in a electron pair. We choose an operator expanded in a small number of Gaussians as a model for electron correlation, and test it by computing atomic and molecular adiabatic excited states. The computations are performed within the Δ Self-Consistent Field (ΔSCF) formalism, and are compared to the time-dependent density functional theory model with popular density functionals. The simplest form of the correlation operator contains only one parameter derived from the helium atom ground state correlation energy. The correlation operator approach significantly outperforms other methods in computation of atomic excitation energies. The accuracy of molecular excitation energies computed with the correlation operator is limited by the shortcomings of the ΔSCF methodology in describing excited states. PMID:24050332

  2. Intense steady state electron beam generator

    DOEpatents

    Hershcovitch, Ady; Kovarik, Vincent J.; Prelec, Krsto

    1990-01-01

    An intense, steady state, low emittance electron beam generator is formed by operating a hollow cathode discharge plasma source at critical levels in combination with an extraction electrode and a target electrode that are operable to extract a beam of fast primary electrons from the plasma source through a negatively biased grid that is critically operated to repel bulk electrons toward the plasma source while allowing the fast primary electrons to move toward the target in the desired beam that can be successfully transported for relatively large distances, such as one or more meters away from the plasma source.

  3. Intense steady state electron beam generator

    DOEpatents

    Hershcovitch, A.; Kovarik, V.J.; Prelec, K.

    1990-07-17

    An intense, steady state, low emittance electron beam generator is formed by operating a hollow cathode discharge plasma source at critical levels in combination with an extraction electrode and a target electrode that are operable to extract a beam of fast primary electrons from the plasma source through a negatively biased grid that is critically operated to repel bulk electrons toward the plasma source while allowing the fast primary electrons to move toward the target in the desired beam that can be successfully transported for relatively large distances, such as one or more meters away from the plasma source. 2 figs.

  4. Study of the collagen structure in the superficial zone and physiological state of articular cartilage using a 3D confocal imaging technique

    PubMed Central

    Wu, Jian P; Kirk, Thomas B; Zheng, Ming H

    2008-01-01

    Introduction The collagen structure in the superficial zone of articular cartilage is critical to the tissue's durability. Early osteoarthritis is often characterized with fissures on the articular surface. This is closely related to the disruption of the collagen network. However, the traditional histology can not offer visualization of the collagen structure in articular cartilage because it uses conventional optical microscopy that does not have insufficient imaging resolution to resolve collagen from proteoglycans in hyaline articular cartilage. This study examines the 3D collagen network of articular cartilage scored from 0 to 2 in the scoring system of International Cartilage Repair Society, and aims to develop a 3D histology for assessing early osteoarthritis. Methods Articular cartilage was visually classified into five physiological groups: normal cartilage, aged cartilage, cartilage with artificial and natural surface disruption, and fibrillated. The 3D collagen matrix of the cartilage was acquired using a 3D imaging technique developed previously. Traditional histology was followed to grade the physiological status of the cartilage in the scoring system of International Cartilage Repair Society. Results Normal articular cartilage contains interwoven collagen bundles near the articular surface, approximately within the lamina splendens. However, its collagen fibres in the superficial zone orient predominantly in a direction spatially oblique to the articular surface. With age and disruption of the articular surface, the interwoven collagen bundles are gradually disappeared, and obliquely oriented collagen fibres change to align predominantly in a direction spatially perpendicular to the articular surface. Disruption of the articular surface is well related to the disappearance of the interwoven collagen bundles. Conclusion A 3D histology has been developed to supplement the traditional histology and study the subtle changes in the collagen network in the

  5. A high capacity 3D steganography algorithm.

    PubMed

    Chao, Min-Wen; Lin, Chao-hung; Yu, Cheng-Wei; Lee, Tong-Yee

    2009-01-01

    In this paper, we present a very high-capacity and low-distortion 3D steganography scheme. Our steganography approach is based on a novel multilayered embedding scheme to hide secret messages in the vertices of 3D polygon models. Experimental results show that the cover model distortion is very small as the number of hiding layers ranges from 7 to 13 layers. To the best of our knowledge, this novel approach can provide much higher hiding capacity than other state-of-the-art approaches, while obeying the low distortion and security basic requirements for steganography on 3D models. PMID:19147891

  6. Interface induced states at the boundary between a 3D topological insulator Bi2Se3 and a ferromagnetic insulator EuS

    NASA Astrophysics Data System (ADS)

    Eremeev, S. V.; Men`shov, V. N.; Tugushev, V. V.; Chulkov, E. V.

    2015-06-01

    By means of relativistic density functional theory (DFT) calculations we study electron band structure of the topological insulator (TI) Bi2Se3 thin films deposited on the ferromagnetic insulator (FMI) EuS substrate. In the Bi2Se3/EuS heterostructure, the gap opened in the spectrum of the topological state has a hybridization character and is shown to be controlled by the Bi2Se3 film thickness, while magnetic contribution to the gap is negligibly small. We also analyzed the effect of Eu doping on the magnetization of the Bi2Se3 film and demonstrated that the Eu impurity induces magnetic moments on neighboring Se and Bi atoms an order of magnitude larger than the substrate-induced moments. Recent magnetic and magneto-transport measurements in EuS/Bi2Se3 heterostructure are discussed.

  7. Molecular, electronic structure and conformational flexibility of the 1,6-dihydropyrimidine, 4,5-dihydrofuro[2,3-d]pyrimidine and their oxo, imino and methylene derivatives

    NASA Astrophysics Data System (ADS)

    Shishkin, Oleg V.; Antonov, Dmitry M.

    1996-11-01

    Molecular and electronic structures of 1,6-dihydropyrimidine, 4,5-dihydrofuro[2,3-d]pyrimidine and their oxo, imino and methylene derivatives have been studied using the semiempirical quantum-chemical method AM1. The equilibrium geometry of all molecules is planar. These results were confirmed by X-ray structural investigations of the 1-oxo- and 1-imino derivatives of 2,5-dimethyl-3-(2,2,2-trichloroethyl)-4,5-dihydrofuro[2,3-d]pyrimidine. However, the dihydropyrimidine ring in all compounds possesses a degree of conformational flexibility. The transition from a planar equilibrium conformation to a distorted sofa with the CNCC torsion angle ± 20° causes an increase of energy less than 1.5 kcal mol -1. The factors that determine this property of the dihydroheterocycle (bending strain, non-aromaticity, conjugation, 1,2-allylic strain) have been considered.

  8. Micro stereo lithography and fabrication of 3D microdevices

    NASA Astrophysics Data System (ADS)

    Varadan, Vijay K.; Varadan, Vasundara V.

    1999-08-01

    Micro Stereo Lithography (MSL) is a poor man's LIGA for fabricating high aspect ratio MEMS devices in UV curable semiconducting polymers using either two computer-controlled low inertia galvanometric mirrors with the aid of focusing lens or an array of optical fibers. For 3D MEMS devices, the polymers need to have conductive and possibly piezoelectric or ferroelectric properties. Such polymers are being developed at Penn State resulting in microdevices for fluid and drug delivery. Applications may include implanted medical delivery systems, chemical and biological instruments, fluid delivery in engines, pump coolants and refrigerants for local cooling of electronic components. With the invention of organic thin film transistor, now it is possible to fabricate 3D polymeric MEMS devices with built-in-electronics similar to silicon based microelectronics. In this paper, a brief introduction of MSL system is presented followed by a detailed design and development of micro pumps using this approach.

  9. Extra Dimensions: 3D in PDF Documentation

    NASA Astrophysics Data System (ADS)

    Graf, Norman A.

    2012-12-01

    Experimental science is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universal 3D (U3D) and the ISO PRC file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. Until recently, Adobe's Acrobat software was also capable of incorporating 3D content into PDF files from a variety of 3D file formats, including proprietary CAD formats. However, this functionality is no longer available in Acrobat X, having been spun off to a separate company. Incorporating 3D content now requires the additional purchase of a separate plug-in. In this talk we present alternatives based on open source libraries which allow the programmatic creation of 3D content in PDF format. While not providing the same level of access to CAD files as the commercial software, it does provide physicists with an alternative path to incorporate 3D content into PDF files from such disparate applications as detector geometries from Geant4, 3D data sets, mathematical surfaces or tesselated volumes.

  10. Medical 3D Printing for the Radiologist.

    PubMed

    Mitsouras, Dimitris; Liacouras, Peter; Imanzadeh, Amir; Giannopoulos, Andreas A; Cai, Tianrun; Kumamaru, Kanako K; George, Elizabeth; Wake, Nicole; Caterson, Edward J; Pomahac, Bohdan; Ho, Vincent B; Grant, Gerald T; Rybicki, Frank J

    2015-01-01

    While use of advanced visualization in radiology is instrumental in diagnosis and communication with referring clinicians, there is an unmet need to render Digital Imaging and Communications in Medicine (DICOM) images as three-dimensional (3D) printed models capable of providing both tactile feedback and tangible depth information about anatomic and pathologic states. Three-dimensional printed models, already entrenched in the nonmedical sciences, are rapidly being embraced in medicine as well as in the lay community. Incorporating 3D printing from images generated and interpreted by radiologists presents particular challenges, including training, materials and equipment, and guidelines. The overall costs of a 3D printing laboratory must be balanced by the clinical benefits. It is expected that the number of 3D-printed models generated from DICOM images for planning interventions and fabricating implants will grow exponentially. Radiologists should at a minimum be familiar with 3D printing as it relates to their field, including types of 3D printing technologies and materials used to create 3D-printed anatomic models, published applications of models to date, and clinical benefits in radiology. Online supplemental material is available for this article. PMID:26562233

  11. Two electronic states in spherical quantum nanolayer

    NASA Astrophysics Data System (ADS)

    Aghekyan, N. G.; Kazaryan, E. M.; Kostanyan, A. A.; Sarkisyan, H. A.

    2010-10-01

    In this paper two electronic states in spherical quantum nanolayer are discussed. The Coulomb interaction between the electrons is discussed as perturbation. For confinement potential of the nanolayer the three-dimensional radial analog of Smorodinsky-Winternitz potential is considered. The problem is discussed within the frameworks of Russell-Saunders coupling scheme, thus, the spin-orbit interaction is considered weak. Therefore the eigenfunctions of the system is represented as a multiplication of its coordinate wave function and spin wave function. For this system the analogue of helium atom theory is represented. The eigenfunctions and energy states are obtained for one and two electron cases in the spherical quantum nanolayer. For the spherical nanolayer the dependence of perturbation energy, unperturbed system energy and the total energy for the ground state upon the inner radius is represented when the outer radius is fixed.

  12. Floating electron states in covalent semiconductors.

    PubMed

    Matsushita, Yu-ichiro; Furuya, Shinnosuke; Oshiyama, Atsushi

    2012-06-15

    We report first-principles electronic-structure calculations that clarify the floating nature of electron states in covalent semiconductors. It is found that wave functions of several conduction- and valence-band states, including the conduction-band minima, do not distribute near atomic sites, as was taken for granted, but float in interstitial channels in most semiconductors. The directions and shapes of the interstitial channels depend on the crystal symmetry so that mysterious variation of the energy gaps in SiC polymorphs is naturally explained by considering the floating nature. PMID:23004300

  13. Verification of Long Period Surface Waves from Ambient Noise and Its Application in Constructing 3D Shear Wave Structure of Lithosphere in United States

    NASA Astrophysics Data System (ADS)

    Xie, J.; Yang, Y.; Ni, S.; Zhao, K.

    2015-12-01

    In the past decade, ambient noise tomography (ANT) has become an estimated method to construct the earth's interior structures thanks to its advantage in extracting surface waves from cross-correlations of ambient noise without using earthquake data. However, most of previous ambient noise tomography studies concentrate on short and intermediate periods (<50sec) due to the dominant energy of the microseism at these periods. Studies of long period surface waves from cross-correlation of ambient noise are limited. In this study, we verify the accuracy of the long period (50-250sec) surface wave (Rayleigh wave) from ambient noise by comparing both dispersion curves and seismic waveforms from ambient noise with those from earthquake records quantitatively. After that, we calculate vertical-vertical cross-correlation functions among more than1800 USArray Transportable Array stations and extract high quality interstation phase velocity dispersion curves from them at 10-200 sec periods. Then, we adopt a finite frequency ambient noise tomography method based on Born approximation to obtain high resolution phase velocity maps using the obtained dispersion measurements at 10-150 sec periods. Afterward, we extract local dispersion curves from these dispersion maps and invert them for 1D shear wave velocity profiles at individual grids using a Bayesian Monte Carlo method. Finally, a 3D shear velocity model is constructed by assembling all the 1D Vs profiles. Our 3D model is overall similar to other models constructed using earthquake surface waves and body waves. In summary, we demonstrate that the long period surface waves can be extracted from ambient noise, and the long period dispersion measurements from ambient noise are as accurate as those from earthquake data and can be used to construct 3D lithospheric structure from surface down to lithosphere/asthenosphere depths.

  14. Electronically excited states of PANH anions.

    PubMed

    Theis, Mallory L; Candian, Alessandra; Tielens, Alexander G G M; Lee, Timothy J; Fortenberry, Ryan C

    2015-06-14

    The singly deprotonated anion derivatives of nitrogenated polycyclic aromatic hydrocarbons (PANHs) are investigated for their electronically excited state properties. These include single deprotonation of the two unique arrangements of quinoline producing fourteen different isomers. This same procedure is also undertaken for single deprotonation of the three nitrogenation isomers of acridine and the three of pyrenidine. It is shown quantum chemically that the quinoline-class of PANH anion derivatives can only produce a candidate dipole-bound excited state each, a state defined as the interaction of an extra electron with the dipole moment of the corresponding neutral. However, the acridine- and pyrenidine-classes possess valence excited states as well as the possible dipole-bound excited states where the latter is only possible if the dipole moment is sufficiently large to retain the extra electron; the valence excitation is independent of the radical dipolar strength. As a result, the theoretical vertically computed electronic spectra of deprotonated PANH anion derivatives is fairly rich in the 1.5 eV to 2.5 eV range significantly opening the possibilities for these molecules to be applied to longer wavelength studies of visible and near-IR spectroscopy. Lastly, the study of these systems is also enhanced by the inclusion of informed orbital arrangements in a simply constructed basis set that is shown to be more complete and efficient than standard atom-centered functions. PMID:25975430

  15. Particle Acceleration in 3D Magnetic Reconnection

    NASA Astrophysics Data System (ADS)

    Dahlin, J.; Drake, J. F.; Swisdak, M.

    2015-12-01

    Magnetic reconnection is an important driver of energetic particles in phenomena such as magnetospheric storms and solar flares. Using kinetic particle-in-cell (PIC) simulations, we show that the stochastic magnetic field structure which develops during 3D reconnection plays a vital role in particle acceleration and transport. In a 2D system, electrons are trapped in magnetic islands which limits their energy gain. In a 3D system, however, the stochastic magnetic field enables the energetic electrons to access volume-filling acceleration regions and therefore gain energy much more efficiently than in the 2D system. We also examine the relative roles of two important acceleration drivers: parallel electric fields and a Fermi mechanism associated with reflection of charged particles from contracting field lines. We find that parallel electric fields are most important for accelerating low energy particles, whereas Fermi reflection dominates energetic particle production. We also find that proton energization is reduced in the 3D system.

  16. Electron Microscopy: an Analytical Tool for Solid State Physicists

    NASA Astrophysics Data System (ADS)

    van Tendeloo, Gustaaf

    2013-03-01

    For too long the electron microscope has been considered as ``a big magnifying glass.'' Modern electron microscopy however has evolved into an analytical technique, able to provide quantitative data on structure, composition, chemical bonding and magnetic properties. Using lens corrected instruments it is now possible to determine atom shifts at interfaces with a precision of a few picometer; chemical diffusion at these interfaces can be imaged down to atomic scale. The chemical nature of the surface atoms can be visualized and even the bonding state of the elements (e.g. Mn2+ versus Mn3+) can be detected on an atomic scale. Electron microscopy is by principle a projection technique, but the final dream is to obtain atomic info of materials in three dimensions. We will show that this is no longer a dream, but that it is possible using advanced microscopy. We will show evidence of determining the valence change Ce4+ versus Ce3+ at the surface of a CeO2 nanocrystal; the atomic shifts at the interface between LaAlO3 and SrTiO3 and the 3D relaxation of a Au nanocrystal.

  17. Initial state dependence of convoy electrons emitted from the excited ions by resonant coherent excitation

    NASA Astrophysics Data System (ADS)

    Azuma, T.; Nakano, Y.; Metoki, K.; Hatakeyama, A.; Nakai, Y.; Komaki, K.; Yamazaki, Y.; Takada, E.; Murakami, T.

    2009-11-01

    Convoy electrons emitted from 416 MeV/u heliumlike Ar16+ ions excited by three-dimensional resonant coherent excitation (3D-RCE) have been explored. The 1s electron in the ground state was excited to the 2p state by a periodic crystal field during the passage through a Si crystal and released into the continuum by collisions with target atoms to form a cusp-shaped peak in the energy distribution, referred to as convoy electron. Under the resonance condition, we found not only enhancement of the convoy electron yield but also significant narrowing in the energy distribution, reflecting the initial bound state momentum distribution of the excited ions. This suggests that RCE is well-suited to study fast ion collisions involving the specific excited state.

  18. 3D Spectroscopy in Astronomy

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  19. Electronics: State of the Art No. 2.

    ERIC Educational Resources Information Center

    Gosling, W.

    1979-01-01

    Reviewed is a brief history of electronics technology, from the early beginnings of vacuum devices to development of solid state devices, silicon fabrication in the use of transistors, and integrated circuits. Educational needs at the university or polytechnic level are discussed. (CS)

  20. 3D Elevation Program—Virtual USA in 3D

    USGS Publications Warehouse

    Lukas, Vicki; Stoker, J.M.

    2016-01-01

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

  1. Extra dimensions: 3D in PDF documentation

    SciTech Connect

    Graf, Norman A.

    2011-01-11

    Experimental science is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universal 3D (U3D) file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. By providing support for scripting and animation, temporal data can also be easily distributed to a wide, non-technical audience. We discuss how the field of radiation imaging could benefit from incorporating full 3D information about not only the detectors, but also the results of the experimental analyses, in its electronic publications. In this article, we present examples drawn from high-energy physics, mathematics and molecular biology which take advantage of this functionality. Furthermore, we demonstrate how 3D detector elements can be documented, using either CAD drawings or other sources such as GEANT visualizations as input.

  2. Extra dimensions: 3D in PDF documentation

    DOE PAGESBeta

    Graf, Norman A.

    2011-01-11

    Experimental science is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universalmore » 3D (U3D) file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. By providing support for scripting and animation, temporal data can also be easily distributed to a wide, non-technical audience. We discuss how the field of radiation imaging could benefit from incorporating full 3D information about not only the detectors, but also the results of the experimental analyses, in its electronic publications. In this article, we present examples drawn from high-energy physics, mathematics and molecular biology which take advantage of this functionality. Furthermore, we demonstrate how 3D detector elements can be documented, using either CAD drawings or other sources such as GEANT visualizations as input.« less

  3. BEAMS3D Neutral Beam Injection Model

    NASA Astrophysics Data System (ADS)

    McMillan, Matthew; Lazerson, Samuel A.

    2014-09-01

    With the advent of applied 3D fields in Tokamaks and modern high performance stellarators, a need has arisen to address non-axisymmetric effects on neutral beam heating and fueling. We report on the development of a fully 3D neutral beam injection (NBI) model, BEAMS3D, which addresses this need by coupling 3D equilibria to a guiding center code capable of modeling neutral and charged particle trajectories across the separatrix and into the plasma core. Ionization, neutralization, charge-exchange, viscous slowing down, and pitch angle scattering are modeled with the ADAS atomic physics database. Elementary benchmark calculations are presented to verify the collisionless particle orbits, NBI model, frictional drag, and pitch angle scattering effects. A calculation of neutral beam heating in the NCSX device is performed, highlighting the capability of the code to handle 3D magnetic fields. Notice: this manuscript has been authored by Princeton University under Contract Number DE-AC02-09CH11466 with the US Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.

  4. Effect of Resonant Magnetic Perturbations on 3D equilibria in the MST RFP

    NASA Astrophysics Data System (ADS)

    Munaretto, Stefano; Chapman, B. E.; Almagri, A. F.; Boguski, J.; Cianciosa, M.; den Hartog, D. J.; Dubois, A. M.; Goetz, J. A.; Hanson, J. D.; Holly, D. J.; McCollam, K. J.; Nishizawa, T.; Nornberg, M. D.; Norval, R. J.; Sarff, J. S.

    2015-11-01

    The orientation of 3D equilibria in the MST RFP can now be controlled with application of a resonant magnetic perturbation (RMP). This control has led to improved diagnosis revealing enhancements in both the central electron temperature and density. Coupled to a recent advance in the V3FIT code, reconstructions of the 3D equilibria have also been improved. The RMP also inhibits generation of high-energy (>20keV) electrons, which are otherwise produced with the 3D state. This state occurs when the normally broad spectrum of core-resonant m = 1 tearing modes condenses, with the innermost resonant mode growing to large amplitude ~ 8% of the axisymmetric field. As the dominant mode grows, eddy current in MST's conducting shell slows the mode's rotation, eventually leading to locking of the 3D structure. An m = 1 RMP with an amplitude br/B ~ 10% can force the 3D structure into any desired orientation relative to MST's diagnostics. Reduced stochasticity and improved confinement of high-energy electrons during the formations of the 3D structure are observed. This work is supported by the US DOE.

  5. Charge-compensation in 3d-transition-metal-oxide intercalation cathodes through the generation of localized electron holes on oxygen.

    PubMed

    Luo, Kun; Roberts, Matthew R; Hao, Rong; Guerrini, Niccoló; Pickup, David M; Liu, Yi-Sheng; Edström, Kristina; Guo, Jinghua; Chadwick, Alan V; Duda, Laurent C; Bruce, Peter G

    2016-07-01

    During the charging and discharging of lithium-ion-battery cathodes through the de- and reintercalation of lithium ions, electroneutrality is maintained by transition-metal redox chemistry, which limits the charge that can be stored. However, for some transition-metal oxides this limit can be broken and oxygen loss and/or oxygen redox reactions have been proposed to explain the phenomenon. We present operando mass spectrometry of (18)O-labelled Li1.2[Ni0.13(2+)Co0.13(3+)Mn0.54(4+)]O2, which demonstrates that oxygen is extracted from the lattice on charging a Li1.2[Ni0.13(2+)Co0.13(3+)Mn0.54(4+)]O2 cathode, although we detected no O2 evolution. Combined soft X-ray absorption spectroscopy, resonant inelastic X-ray scattering spectroscopy, X-ray absorption near edge structure spectroscopy and Raman spectroscopy demonstrates that, in addition to oxygen loss, Li(+) removal is charge compensated by the formation of localized electron holes on O atoms coordinated by Mn(4+) and Li(+) ions, which serve to promote the localization, and not the formation, of true O2(2-) (peroxide, O-O ~1.45 Å) species. The quantity of charge compensated by oxygen removal and by the formation of electron holes on the O atoms is estimated, and for the case described here the latter dominates. PMID:27325095

  6. Visualization of liver in 3-D

    NASA Astrophysics Data System (ADS)

    Chen, Chin-Tu; Chou, Jin-Shin; Giger, Maryellen L.; Kahn, Charles E., Jr.; Bae, Kyongtae T.; Lin, Wei-Chung

    1991-05-01

    Visualization of the liver in three dimensions (3-D) can improve the accuracy of volumetric estimation and also aid in surgical planning. We have developed a method for 3-D visualization of the liver using x-ray computed tomography (CT) or magnetic resonance (MR) images. This method includes four major components: (1) segmentation algorithms for extracting liver data from tomographic images; (2) interpolation techniques for both shape and intensity; (3) schemes for volume rendering and display, and (4) routines for electronic surgery and image analysis. This method has been applied to cases from a living-donor liver transplant project and appears to be useful for surgical planning.

  7. A 3D cellular context for the macromolecular world

    PubMed Central

    Patwardhan, Ardan; Ashton, Alun; Brandt, Robert; Butcher, Sarah; Carzaniga, Raffaella; Chiu, Wah; Collinson, Lucy; Doux, Pascal; Duke, Elizabeth; Ellisman, Mark H; Franken, Erik; Grünewald, Kay; Heriche, Jean-Karim; Koster, Abraham; Kühlbrandt, Werner; Lagerstedt, Ingvar; Larabell, Carolyn; Lawson, Catherine L; Saibil, Helen R; Sanz-García, Eduardo; Subramaniam, Sriram; Verkade, Paul; Swedlow, Jason R; Kleywegt, Gerard J

    2015-01-01

    We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community. PMID:25289590

  8. First-principles study on the magnetism and electronic structure in 3d transition metal (X=Sc, V, Cr, Mn, Fe, Ni, Cu) doped CoO

    NASA Astrophysics Data System (ADS)

    Liu, R. X.; Wang, X. C.; Chen, G. F.; Yang, B. H.

    2016-03-01

    We have studied the electronic structure and magnetism of the single transitional metal element X=Sc, V, Cr, Mn, Fe, Ni, Cu-doped CoO systems by first-principles calculations. At X=Sc, Cr, Cu, the binding energy of the doped systems is lower than pure CoO, suggesting that these systems are energetically stable. In the Sc, V, Cr, Mn, Fe, Ni, Cu-doped 2×2×2 CoO supercells, the total magnetic moments are 3.03, 5.64, 6.80, 7.70, 6.93, 2.30 and 1.96 μB, respectively. At X=Cr and Fe, the doped CoO systems are half-metallic with a high spin polarization. The large magnetic moment and high spin polarization in the Cr and Fe-doped CoO are important for the design of the spintronic devices.

  9. Unoccupied electronic states in adsorbate systems

    NASA Astrophysics Data System (ADS)

    Bertel, E.

    1991-11-01

    Experimental work on unoccupied electronic states in adsorbate systems on metallic substrates is reviewed with emphasis on recent developments. The first part is devoted to molecular adsorbates. Weakly chemisorbed hydrocarbons are briefly discussed. An exhaustive inverse photoemission (IPE) study of the CO bond to the transition metals Ni, Pb, and Pt is presented. Adsorbed NO is taken as an example to demonstrate the persisting discrepancies in the interpretation of IPE spectra. Atomic adsorbates are discussed in the second part. The quantum well state model is applied to interpret the surface states in reconstructing and non-reconstructing adsorption systems of alkali metals and hydrogen. A recent controversy on the unoccupied electronic states of the Cu(110)/O p(2×1) surface is critically reviewed. The quantum well state model is then compared to tight binding and local-density-functional calculations of the unoccupied bands and the deficiencies of the various approaches are pointed out. Finally, the relation between the surface state model and more chemically oriented models of surface bonding is briefly discussed.

  10. Modular 3-D Transport model

    EPA Science Inventory

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

  11. Market study: 3-D eyetracker

    NASA Technical Reports Server (NTRS)

    1977-01-01

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

  12. LLNL-Earth3D

    2013-10-01

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

  13. [3-D ultrasound in gastroenterology].

    PubMed

    Zoller, W G; Liess, H

    1994-06-01

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

  14. 3D World Building System

    SciTech Connect

    2013-10-30

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

  15. 3D World Building System

    ScienceCinema

    None

    2014-02-26

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

  16. 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 Central

    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. PMID:23869614

  17. The impacts of electronic state hybridization on the binding energy of single phosphorus donor electrons in extremely downscaled silicon nanostructures

    SciTech Connect

    The Anh, Le Manoharan, Muruganathan; Moraru, Daniel; Tabe, Michiharu; Mizuta, Hiroshi

    2014-08-14

    We present the density functional theory calculations of the binding energy of the Phosphorus (P) donor electrons in extremely downscaled single P-doped Silicon (Si) nanorods. In past studies, the binding energy of donor electrons was evaluated for the Si nanostructures as the difference between the ionization energy for the single P-doped Si nanostructures and the electron affinity for the un-doped Si nanostructures. This definition does not take into account the strong interaction of donor electron states and Si electron states explicitly at the conductive states and results in a monotonous increase in the binding energy by reducing the nanostructure's dimensions. In this paper, we introduce a new approach to evaluate the binding energy of donor electrons by combining the projected density of states (PDOS) analysis and three-dimensional analysis of associated electron wavefunctions. This enables us to clarify a gradual change of the spatial distribution of the 3D electron wavefunctions (3DWFs) from the donor electron ground state, which is fully localized around the P donor site to the first conductive state, which spreads over the outer Si nanorods contributing to current conduction. We found that the energy of the first conductive state is capped near the top of the atomistic effective potential at the donor site with respect to the surrounding Si atoms in nanorods smaller than about 27 a{sub 0}. This results in the binding energy of approximately 1.5 eV, which is virtually independent on the nanorod's dimensions. This fact signifies a good tolerance of the binding energy, which governs the operating temperature of the single dopant-based transistors in practice. We also conducted the computationally heavy transmission calculations of the single P-doped Si nanorods connected to the source and drain electrodes. The calculated transmission spectra are discussed in comparison with the atomistic effective potential distributions and the PDOS-3DWFs method.

  18. The impacts of electronic state hybridization on the binding energy of single phosphorus donor electrons in extremely downscaled silicon nanostructures

    NASA Astrophysics Data System (ADS)

    The Anh, Le; Moraru, Daniel; Manoharan, Muruganathan; Tabe, Michiharu; Mizuta, Hiroshi

    2014-08-01

    We present the density functional theory calculations of the binding energy of the Phosphorus (P) donor electrons in extremely downscaled single P-doped Silicon (Si) nanorods. In past studies, the binding energy of donor electrons was evaluated for the Si nanostructures as the difference between the ionization energy for the single P-doped Si nanostructures and the electron affinity for the un-doped Si nanostructures. This definition does not take into account the strong interaction of donor electron states and Si electron states explicitly at the conductive states and results in a monotonous increase in the binding energy by reducing the nanostructure's dimensions. In this paper, we introduce a new approach to evaluate the binding energy of donor electrons by combining the projected density of states (PDOS) analysis and three-dimensional analysis of associated electron wavefunctions. This enables us to clarify a gradual change of the spatial distribution of the 3D electron wavefunctions (3DWFs) from the donor electron ground state, which is fully localized around the P donor site to the first conductive state, which spreads over the outer Si nanorods contributing to current conduction. We found that the energy of the first conductive state is capped near the top of the atomistic effective potential at the donor site with respect to the surrounding Si atoms in nanorods smaller than about 27 a0. This results in the binding energy of approximately 1.5 eV, which is virtually independent on the nanorod's dimensions. This fact signifies a good tolerance of the binding energy, which governs the operating temperature of the single dopant-based transistors in practice. We also conducted the computationally heavy transmission calculations of the single P-doped Si nanorods connected to the source and drain electrodes. The calculated transmission spectra are discussed in comparison with the atomistic effective potential distributions and the PDOS-3DWFs method.

  19. Euro3D Science Conference

    NASA Astrophysics Data System (ADS)

    Walsh, J. R.

    2004-02-01

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

  20. PLOT3D user's manual

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

  1. 3D printing in dentistry.

    PubMed

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

    2015-12-01

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

  2. The importance of 3D dosimetry

    NASA Astrophysics Data System (ADS)

    Low, Daniel

    2015-01-01

    Radiation therapy has been getting progressively more complex for the past 20 years. Early radiation therapy techniques needed only basic dosimetry equipment; motorized water phantoms, ionization chambers, and basic radiographic film techniques. As intensity modulated radiation therapy and image guided therapy came into widespread practice, medical physicists were challenged with developing effective and efficient dose measurement techniques. The complex 3-dimensional (3D) nature of the dose distributions that were being delivered demanded the development of more quantitative and more thorough methods for dose measurement. The quality assurance vendors developed a wide array of multidetector arrays that have been enormously useful for measuring and characterizing dose distributions, and these have been made especially useful with the advent of 3D dose calculation systems based on the array measurements, as well as measurements made using film and portal imagers. Other vendors have been providing 3D calculations based on data from the linear accelerator or the record and verify system, providing thorough evaluation of the dose but lacking quality assurance (QA) of the dose delivery process, including machine calibration. The current state of 3D dosimetry is one of a state of flux. The vendors and professional associations are trying to determine the optimal balance between thorough QA, labor efficiency, and quantitation. This balance will take some time to reach, but a necessary component will be the 3D measurement and independent calculation of delivered radiation therapy dose distributions.

  3. Why LiFePO4 is a safe battery electrode: Coulomb repulsion induced electron-state reshuffling upon lithiation

    NASA Astrophysics Data System (ADS)

    Wang, Yung Jui; Liu, Xiaosong; Barbiellini, B.; Hafiz, Hasnain; Basak, Susmita; Liu, Jun; Richardson, Thomas; Shu, Guojiun; Chou, Fangcheng; Weng, Tsu-Chien; Nordlund, Dennis; Sokaras, Dimosthenis; Moritz, B.; Devereaux, T. P.; Qiao, Ruimin; Chuang, Yi-De; Bansil, Arun; Hussain, Zahid; Yang, Wanli

    We performed systematic experimental and theoretical studies based on soft X-ray emission, absorption, and hard X-ray Raman spectroscopy of LixFePO4. The results show a non-rigid electron-state reconfiguration of both the occupied and unoccupied Fe-3d and O-2p states during the (de)lithiation process. The critical 3d electron state configurations are consistent with the calculations based on MBJGGA+U framework, which improves the overall lineshape prediction compared with the conventionally used GGA+U method. The combined experimental and theoretical studies show that the non-rigid electron state reshuffling guarantees the stability of oxygen during the redox reaction throughout the charge and discharge process of LiFePO4 electrodes, leading to the intrinsic safe performance of the electrodes. Work supported by the US DOE.

  4. The role of amino acid electron-donor/acceptor atoms in host-cell binding peptides is associated with their 3D structure and HLA-binding capacity in sterile malarial immunity induction

    SciTech Connect

    Patarroyo, Manuel E.; Almonacid, Hannia; Moreno-Vranich, Armando

    2012-01-20

    Highlights: Black-Right-Pointing-Pointer Fundamental residues located in some HABPs are associated with their 3D structure. Black-Right-Pointing-Pointer Electron-donor atoms present in {beta}-turn, random, distorted {alpha}-helix structures. Black-Right-Pointing-Pointer Electron-donor atoms bound to HLA-DR53. Black-Right-Pointing-Pointer Electron-acceptor atoms present in regular {alpha}-helix structure bound to HLA-DR52. -- Abstract: Plasmodium falciparum malaria continues being one of the parasitic diseases causing the highest worldwide mortality due to the parasite's multiple evasion mechanisms, such as immunological silence. Membrane and organelle proteins are used during invasion for interactions mediated by high binding ability peptides (HABPs); these have amino acids which establish hydrogen bonds between them in some of their critical binding residues. Immunisation assays in the Aotus model using HABPs whose critical residues had been modified have revealed a conformational change thereby enabling a protection-inducing response. This has improved fitting within HLA-DR{beta}1{sup Asterisk-Operator} molecules where amino acid electron-donor atoms present in {beta}-turn, random or distorted {alpha}-helix structures preferentially bound to HLA-DR53 molecules, whilst HABPs having amino acid electron-acceptor atoms present in regular {alpha}-helix structure bound to HLA-DR52. This data has great implications for vaccine development.

  5. 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.

  6. Bioprinting of 3D hydrogels.

    PubMed

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

    2015-08-01

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

  7. Unassisted 3D camera calibration

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

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

  8. Arena3D: visualization of biological networks in 3D

    PubMed Central

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

    2008-01-01

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

  9. Electronic structure and bonding of the 3d transition metal borides, MB, M =Sc, Ti, V, Cr, Mn, Fe, Co, Ni, and Cu through all electron ab initio calculations

    NASA Astrophysics Data System (ADS)

    Tzeli, Demeter; Mavridis, Aristides

    2008-01-01

    The electronic structure and bonding of the ground and some low-lying states of all first row transition metal borides (MB), ScB, TiB, VB, CrB, MnB, FeB, CoB, NiB, and CuB have been studied by multireference configuration interaction (MRCI) methods employing a correlation consistent basis set of quintuple cardinality (5Z). It should be stressed that for all the above nine molecules, experimental results are essentially absent, whereas with the exception of ScB and CuB the remaining seven species are studied theoretically for the first time. We have constructed full potential energy curves at the MRCI/5Z level for a total of 27 low-lying states, subsequently used to extract binding energies, spectroscopic parameters, and bonding schemes. In addition, some 20 or more states for every MB species have been examined at the MRCI/4Z level of theory. The ground state symmetries and corresponding binding energies (in kcal/mol) are Σ-5(ScB), 76; Δ6(TiB), 65; Σ+7(VB), 55; Σ+6(CrB), 31; Π5(MnB), 20; Σ-4(FeB), 54; Δ3(CoB), 66; Σ+2(NiB), 79; and Σ+1(CuB), 49.

  10. Fdf in US3D

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  11. Multi-view and 3D deformable part models.

    PubMed

    Pepik, Bojan; Stark, Michael; Gehler, Peter; Schiele, Bernt

    2015-11-01

    As objects are inherently 3D, they have been modeled in 3D in the early days of computer vision. Due to the ambiguities arising from mapping 2D features to 3D models, 3D object representations have been neglected and 2D feature-based models are the predominant paradigm in object detection nowadays. While such models have achieved outstanding bounding box detection performance, they come with limited expressiveness, as they are clearly limited in their capability of reasoning about 3D shape or viewpoints. In this work, we bring the worlds of 3D and 2D object representations closer, by building an object detector which leverages the expressive power of 3D object representations while at the same time can be robustly matched to image evidence. To that end, we gradually extend the successful deformable part model [1] to include viewpoint information and part-level 3D geometry information, resulting in several different models with different level of expressiveness. We end up with a 3D object model, consisting of multiple object parts represented in 3D and a continuous appearance model. We experimentally verify that our models, while providing richer object hypotheses than the 2D object models, provide consistently better joint object localization and viewpoint estimation than the state-of-the-art multi-view and 3D object detectors on various benchmarks (KITTI [2] , 3D object classes [3] , Pascal3D+ [4] , Pascal VOC 2007 [5] , EPFL multi-view cars[6] ). PMID:26440264

  12. Effect of size on electronic states in a strained pyramidal InAs-GaAs quantum dot system

    SciTech Connect

    Ripan, G. H.; Woon, C. Y.; Gopir, G.

    2015-09-25

    The effect of size on electronic states in a strained pyramidal InAs-GaAs quantum dot system was studied. A comparison was made between two InAs quantum pyramids of different sizes embedded inside a cubic GaAs susbtrate material. Strain relaxation was carried out via the Metropolis Monte Carlo method and the calculated local strain tensors were then included to solve the energy values and the wave functions of the electronic states inside the two simulation cube. The 3D finite difference scheme was employed to solve the time independent Schrödinger equation based on the decoupled electron-hole model. Calculated energy values of the four lowest electronic states showed that the transitions between the electron and hole states widen as the size of the dot becomes smaller especially between the ground states. The confinement of electrons and holes become weaker as the size of the dot reduces.

  13. Why LiFePO4 is a safe battery electrode: Coulomb repulsion induced electron-state reshuffling upon lithiation.

    PubMed

    Liu, Xiaosong; Wang, Yung Jui; Barbiellini, Bernardo; Hafiz, Hasnain; Basak, Susmita; Liu, Jun; Richardson, Thomas; Shu, Guojiun; Chou, Fangcheng; Weng, Tsu-Chien; Nordlund, Dennis; Sokaras, Dimosthenis; Moritz, Brian; Devereaux, Thomas P; Qiao, Ruimin; Chuang, Yi-De; Bansil, Arun; Hussain, Zahid; Yang, Wanli

    2015-10-21

    LiFePO4 is a battery cathode material with high safety standards due to its unique electronic structure. We performed systematic experimental and theoretical studies based on soft X-ray emission, absorption, and hard X-ray Raman spectroscopy of LixFePO4 nanoparticles and single crystals. The results clearly show a non-rigid electron-state reconfiguration of both the occupied and unoccupied Fe-3d and O-2p states during the (de)lithiation process. We focus on the energy configurations of the occupied states of LiFePO4 and the unoccupied states of FePO4, which are the critical states where electrons are removed and injected during the charge and discharge process, respectively. In LiFePO4, the soft X-ray emission spectroscopy shows that, due to the Coulomb repulsion effect, the occupied Fe-3d states with the minority spin sit close to the Fermi level. In FePO4, the soft X-ray absorption and hard X-ray Raman spectroscopy show that the unoccupied Fe-3d states again sit close to the Fermi level. These critical 3d electron state configurations are consistent with the calculations based on modified Becke and Johnson potentials GGA+U (MBJGGA+U) framework, which improves the overall lineshape prediction compared with the conventionally used GGA+U method. The combined experimental and theoretical studies show that the non-rigid electron state reshuffling guarantees the stability of oxygen during the redox reaction throughout the charge and discharge process of LiFePO4 electrodes, leading to the intrinsic safe performance of the electrodes. PMID:26388021

  14. Wavefront construction in 3-D

    SciTech Connect

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

    1995-12-31

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

  15. Heterodyne 3D ghost imaging

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  16. 3-D Finite Element Heat Transfer

    1992-02-01

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

  17. Combinatorial 3D Mechanical Metamaterials

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  18. Shim3d Helmholtz Solution Package

    2009-01-29

    This suite of codes solves the Helmholtz Equation for the steady-state propagation of single-frequency electromagnetic radiation in an arbitrary 2D or 3D dielectric medium. Materials can be either transparent or absorptive (including metals) and are described entirely by their shape and complex dielectric constant. Dielectric boundaries are assumed to always fall on grid boundaries and the material within a single grid cell is considered to be uniform. Input to the problem is in the formmore » of a Dirichlet boundary condition on a single boundary, and may be either analytic (Gaussian) in shape, or a mode shape computed using a separate code (such as the included eigenmode solver vwave20), and written to a file. Solution is via the finite difference method using Jacobi iteration for 3D problems or direct matrix inversion for 2D problems. Note that 3D problems that include metals will require different iteration parameters than described in the above reference. For structures with curved boundaries not easily modeled on a rectangular grid, the auxillary codes helmholtz11(2D), helm3d (semivectoral), and helmv3d (full vectoral) are provided. For these codes the finite difference equations are specified on a topological regular triangular grid and solved using Jacobi iteration or direct matrix inversion as before. An automatic grid generator is supplied.« less

  19. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    -scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed technology is simple and compatible with standard epi-fluorescence microscopes used in biological and clinical laboratories. Thus, 3D multiplexed immunoplasmonics microscopy is ready for clinical applications as a cost-efficient alternative to immunofluorescence. Electronic supplementary information (ESI) available: Characterization of functionalized nanoparticles by UV-visible-NIR spectroscopy, standard dark field microscopy and reflected light microscopy. Immunofluorescence of cells. See DOI: 10.1039/c6nr01257d

  20. Diffractive optical element for creating visual 3D images.

    PubMed

    Goncharsky, Alexander; Goncharsky, Anton; Durlevich, Svyatoslav

    2016-05-01

    A method is proposed to compute and synthesize the microrelief of a diffractive optical element to produce a new visual security feature - the vertical 3D/3D switch effect. The security feature consists in the alternation of two 3D color images when the diffractive element is tilted up/down. Optical security elements that produce the new security feature are synthesized using electron-beam technology. Sample optical security elements are manufactured that produce 3D to 3D visual switch effect when illuminated by white light. Photos and video records of the vertical 3D/3D switch effect of real optical elements are presented. The optical elements developed can be replicated using standard equipment employed for manufacturing security holograms. The new optical security feature is easy to control visually, safely protected against counterfeit, and designed to protect banknotes, documents, ID cards, etc. PMID:27137530

  1. Determination of relative orientation between (1)H CSA tensors from a 3D solid-state NMR experiment mediated through (1)H/(1)H RFDR mixing under ultrafast MAS.

    PubMed

    Pandey, Manoj Kumar; Nishiyama, Yusuke

    2015-09-01

    To obtain piercing insights into inter and intramolecular H-bonding, and π-electron interactions measurement of (1)H chemical shift anisotropy (CSA) tensors is gradually becoming an obvious choice. While the magnitude of CSA tensors provides unique information about the local electronic environment surrounding the nucleus, the relative orientation between these tensors can offer further insights into the spatial arrangement of interacting nuclei in their respective three-dimensional (3D) space. In this regard, we present a 3D anisotropic/anisotropic/isotropic proton chemical shift (CSA/CSA/CS) correlation experiment mediated through (1)H/(1)H radio frequency-driven recoupling (RFDR) which enhances spin diffusion through recoupled (1)H-(1)H dipolar couplings under ultrafast magic angle spinning (MAS) frequency (70kHz). Relative orientation between two interacting 1H CSA tensors is obtained by fitting two-interacting (1)H CSA tensors by fitting two-dimensional (2D) (1)H/(1)H CSA/CSA spectral slices through extensive numerical simulations. To recouple (1)H CSAs in the indirect frequency dimensions of a 3D experiment we have employed γ-encoded radio frequency (RF) pulse sequence based on R-symmetry (R188(7)) with a series of phase-alternated 2700(°)-90180(°) composite-180° pulses on citric acid sample. Due to robustness of applied (1)H CSA recoupling sequence towards the presence of RF field inhomogeneity, we have successfully achieved an excellent (1)H/(1)H CSA/CSA cross-correlation efficiency between H-bonded sites of citric acid. PMID:26065628

  2. STAR3D: a stack-based RNA 3D structural alignment tool

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

    The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875

  3. STAR3D: a stack-based RNA 3D structural alignment tool.

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-11-16

    The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875

  4. From "sapienza" to "sapienza, State Archives in Rome". a Looping Effect Bringing Back to the Original Source Comunication and Culture by Innovative and Low Cost 3d Surveying, Imaging Systems and GIS Applications

    NASA Astrophysics Data System (ADS)

    Paolini, P.; Forti, G.; Catalani, G.; Lucchetti, S.; Menghini, A.; Mirandola, A.; Pistacchio, S.; Porzia, U.; Roberti, M.

    2016-04-01

    High Quality survey models, realized by multiple Low Cost methods and technologies, as a container to sharing Cultural and Archival Heritage, this is the aim guiding our research, here described in its primary applications. The SAPIENZA building, a XVI century masterpiece that represented the first unified headquarters of University in Rome, plays since year 1936, when the University moved to its newly edified campus, the role of the main venue for the State Archives. By the collaboration of a group of students of the Architecture Faculty, some integrated survey methods were applied on the monument with success. The beginning was the topographic survey, creating a reference on ground and along the monument for the upcoming applications, a GNNS RTK survey followed georeferencing points on the internal courtyard. Dense stereo matching photogrammetry is nowadays an accepted method for generating 3D survey models, accurate and scalable; it often substitutes 3D laser scanning for its low cost, so that it became our choice. Some 360° shots were planned for creating panoramic views of the double portico from the courtyard, plus additional single shots of some lateral spans and of pillars facing the court, as a single operation with a double finality: to create linked panotours with hotspots to web-linked databases, and 3D textured and georeferenced surface models, allowing to study the harmonic proportions of the classical architectural order. The use of free web Gis platforms, to load the work in Google Earth and the realization of low cost 3D prototypes of some representative parts, has been even performed.

  5. INCORPORATING DYNAMIC 3D SIMULATION INTO PRA

    SciTech Connect

    Steven R Prescott; Curtis Smith

    2011-07-01

    Through continued advancement in computational resources, development that was previously done by trial and error production is now performed through computer simulation. These virtual physical representations have the potential to provide accurate and valid modeling results and are being used in many different technical fields. Risk assessment now has the opportunity to use 3D simulation to improve analysis results and insights, especially for external event analysis. By using simulations, the modeler only has to determine the likelihood of an event without having to also predict the results of that event. The 3D simulation automatically determines not only the outcome of the event, but when those failures occur. How can we effectively incorporate 3D simulation into traditional PRA? Most PRA plant modeling is made up of components with different failure modes, probabilities, and rates. Typically, these components are grouped into various systems and then are modeled together (in different combinations) as a “system” with logic structures to form fault trees. Applicable fault trees are combined through scenarios, typically represented by event tree models. Though this method gives us failure results for a given model, it has limitations when it comes to time-based dependencies or dependencies that are coupled to physical processes which may themselves be space- or time-dependent. Since, failures from a 3D simulation are naturally time related, they should be used in that manner. In our simulation approach, traditional static models are converted into an equivalent state diagram representation with start states, probabilistic driven movements between states and terminal states. As the state model is run repeatedly, it converges to the same results as the PRA model in cases where time-related factors are not important. In cases where timing considerations are important (e.g., when events are dependent upon each other), then the simulation approach will typically

  6. Robust Electrografting on Self-Organized 3D Graphene Electrodes.

    PubMed

    Fortgang, Philippe; Tite, Teddy; Barnier, Vincent; Zehani, Nedjla; Maddi, Chiranjeevi; Lagarde, Florence; Loir, Anne-Sophie; Jaffrezic-Renault, Nicole; Donnet, Christophe; Garrelie, Florence; Chaix, Carole

    2016-01-20

    Improving graphene-based electrode fabrication processes and developing robust methods for its functionalization are two key research routes to develop new high-performance electrodes for electrochemical applications. Here, a self-organized three-dimensional (3D) graphene electrode processed by pulsed laser deposition with thermal annealing is reported. This substrate shows great performance in electron transfer kinetics regarding ferrocene redox probes in solution. A robust electrografting strategy for covalently attaching a redox probe onto these graphene electrodes is also reported. The modification protocol consists of a combination of diazonium salt electrografting and click chemistry. An alkyne-terminated phenyl ring is first electrografted onto the self-organized 3D graphene electrode by in situ electrochemical reduction of 4-ethynylphenyl diazonium. Then the ethynylphenyl-modified surface efficiently reacts with the redox probe bearing a terminal azide moiety (2-azidoethyl ferrocene) by means of Cu(I)-catalyzed alkyne-azide cycloaddition. Our modification strategy applied to 3D graphene electrodes was analyzed by means of atomic force microscopy, scanning electron microscopy, Raman spectroscopy, cyclic voltammetry, and X-ray photoelectron spectroscopy (XPS). For XPS chemical surface analysis, special attention was paid to the distribution and chemical state of iron and nitrogen in order to highlight the functionalization of the graphene-based substrate by electrochemically grafting a ferrocene derivative. Dense grafting was observed, offering 4.9 × 10(-10) mol cm(-2) surface coverage and showing a stable signal over 22 days. The electrografting was performed in the form of multilayers, which offers higher ferrocene loading than a dense monolayer on a flat surface. This work opens highly promising perspectives for the development of self-organized 3D graphene electrodes with various sensing functionalities. PMID:26710829

  7. CASTLE3D - A Computer Aided System for Labelling Archaeological Excavations in 3D

    NASA Astrophysics Data System (ADS)

    Houshiar, H.; Borrmann, D.; Elseberg, J.; Nüchter, A.; Näth, F.; Winkler, S.

    2015-08-01

    Documentation of archaeological excavation sites with conventional methods and tools such as hand drawings, measuring tape and archaeological notes is time consuming. This process is prone to human errors and the quality of the documentation depends on the qualification of the archaeologist on site. Use of modern technology and methods in 3D surveying and 3D robotics facilitate and improve this process. Computer-aided systems and databases improve the documentation quality and increase the speed of data acquisition. 3D laser scanning is the state of the art in modelling archaeological excavation sites, historical sites and even entire cities or landscapes. Modern laser scanners are capable of data acquisition of up to 1 million points per second. This provides a very detailed 3D point cloud of the environment. 3D point clouds and 3D models of an excavation site provide a better representation of the environment for the archaeologist and for documentation. The point cloud can be used both for further studies on the excavation and for the presentation of results. This paper introduces a Computer aided system for labelling archaeological excavations in 3D (CASTLE3D). Consisting of a set of tools for recording and georeferencing the 3D data from an excavation site, CASTLE3D is a novel documentation approach in industrial archaeology. It provides a 2D and 3D visualisation of the data and an easy-to-use interface that enables the archaeologist to select regions of interest and to interact with the data in both representations. The 2D visualisation and a 3D orthogonal view of the data provide cuts of the environment that resemble the traditional hand drawings. The 3D perspective view gives a realistic view of the environment. CASTLE3D is designed as an easy-to-use on-site semantic mapping tool for archaeologists. Each project contains a predefined set of semantic information that can be used to label findings in the data. Multiple regions of interest can be joined under

  8. From 3D view to 3D print

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  9. Quantum Electronic Transport of Topological Surface States in β-Ag2Se Nanowire.

    PubMed

    Kim, Jihwan; Hwang, Ahreum; Lee, Sang-Hoon; Jhi, Seung-Hoon; Lee, Sunghun; Park, Yun Chang; Kim, Si-In; Kim, Hong-Seok; Doh, Yong-Joo; Kim, Jinhee; Kim, Bongsoo

    2016-04-26

    Single-crystalline β-Ag2Se nanostructures, a new class of 3D topological insulators (TIs), were synthesized using the chemical vapor transport method. The topological surface states were verified by measuring electronic transport properties including the weak antilocalization effect, Aharonov-Bohm oscillations, and Shubnikov-de Haas oscillations. First-principles band calculations revealed that the band inversion in β-Ag2Se is caused by strong spin-orbit coupling and Ag-Se bonding hybridization. These investigations provide evidence of nontrivial surface state about β-Ag2Se TIs that have anisotropic Dirac cones. PMID:27018892

  10. 3-D Cavern Enlargement Analyses

    SciTech Connect

    EHGARTNER, BRIAN L.; SOBOLIK, STEVEN R.

    2002-03-01

    Three-dimensional finite element analyses simulate the mechanical response of enlarging existing caverns at the Strategic Petroleum Reserve (SPR). The caverns are located in Gulf Coast salt domes and are enlarged by leaching during oil drawdowns as fresh water is injected to displace the crude oil from the caverns. The current criteria adopted by the SPR limits cavern usage to 5 drawdowns (leaches). As a base case, 5 leaches were modeled over a 25 year period to roughly double the volume of a 19 cavern field. Thirteen additional leaches where then simulated until caverns approached coalescence. The cavern field approximated the geometries and geologic properties found at the West Hackberry site. This enabled comparisons are data collected over nearly 20 years to analysis predictions. The analyses closely predicted the measured surface subsidence and cavern closure rates as inferred from historic well head pressures. This provided the necessary assurance that the model displacements, strains, and stresses are accurate. However, the cavern field has not yet experienced the large scale drawdowns being simulated. Should they occur in the future, code predictions should be validated with actual field behavior at that time. The simulations were performed using JAS3D, a three dimensional finite element analysis code for nonlinear quasi-static solids. The results examine the impacts of leaching and cavern workovers, where internal cavern pressures are reduced, on surface subsidence, well integrity, and cavern stability. The results suggest that the current limit of 5 oil drawdowns may be extended with some mitigative action required on the wells and later on to surface structure due to subsidence strains. The predicted stress state in the salt shows damage to start occurring after 15 drawdowns with significant failure occurring at the 16th drawdown, well beyond the current limit of 5 drawdowns.

  11. CASPT2 study of inverse sandwich-type dinuclear 3d transition metal complexes of ethylene and dinitrogen molecules: similarities and differences in geometry, electronic structure, and spin multiplicity.

    PubMed

    Nakagaki, Masayuki; Sakaki, Shigeyoshi

    2015-07-01

    The spin multiplicities and coordination structures of inverse sandwich-type complexes (ISTCs) of ethylene and dinitrogen molecules with 3d transition metal elements (Sc to Ni), (μ-C2H4)[M(AIP)]2 and (μ-N2)[M(AIP)]2 (AIPH = (Z)-1-amino-3-iminoprop-1-ene; M = Sc to Ni) were investigated by the CASPT2 method. In both ethylene and dinitrogen ISTCs of the early 3d transition metals (Sc to Cr), sandwiched ethylene and dinitrogen ligands coordinate with two metal atoms in an η(2)-side-on form and their ground states have an open-shell singlet spin multiplicity. The η(1)-end-on coordination structure of dinitrogen ISTCs is considerably less stable than the η(2)-side-on form in these metals. For the late 3d transition metals (Mn to Ni), ethylene and dinitrogen ISTCs exhibit interesting similarities and differences in spin multiplicity and structure as follows: in ethylene ISTCs of Mn to Ni, the ground state has an open-shell singlet spin multiplicity like those of the ISTCs of early transition metals. However, the ethylene ligand is considerably distorted, in which the ethylene carbon atoms have a tetrahedral-like structure similar to sp(3) carbon and each of them coordinates with one metal in a μ-η(1):η(1) structure. These geometrical features are completely different from those of ISTCs of the early transition metals. In dinitrogen ISTCs of Mn to Ni, on the other hand, the ground state has a high spin multiplicity from nonet (Mn) to triplet (Ni). The η(2)-side-on coordination structure of the dinitrogen ligand is as stable as the η(1)-end-on form in the Mn complex but the η(1)-end-on structure is more stable than the η(2)-side-on form in the Fe to Ni complexes. All these interesting similarities and differences between ethylene and dinitrogen ISTCs and between the early and late transition metal elements arise from the occupation of several important molecular orbitals. PMID:26041561

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

    NASA Astrophysics Data System (ADS)

    Schild, Jonas; Seele, Sven; Masuch, Maic

    2012-03-01

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

  13. PLOT3D/AMES, DEC VAX VMS VERSION USING DISSPLA (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    well as 2-D and 3-D lines, but does not support graphics features requiring 3-D polygons (shading and hidden line removal, for example). Views can be manipulated using keyboard commands. This version of PLOT3D is potentially able to produce files for a variety of output devices; however, site-specific capabilities will vary depending on the device drivers supplied with the user's DISSPLA library. If ARCGRAPH (ARC-12350) is installed on the user's VAX, the VMS/DISSPLA version of PLOT3D can also be used to create files for use in GAS (Graphics Animation System, ARC-12379), an IRIS program capable of animating and recording images on film. The version 3.6b+ VMS/DISSPLA implementations of PLOT3D (ARC-12777) and PLOT3D/TURB3D (ARC-12781) were developed for use on VAX computers running VMS Version 5.0 and DISSPLA Version 11.0. The standard distribution media for each of these programs is a 9-track, 6250 bpi magnetic tape in DEC VAX BACKUP format. Customers purchasing one implementation version of PLOT3D or PLOT3D/TURB3D will be given a $200 discount on each additional implementation version ordered at the same time. Version 3.6b+ of PLOT3D and PLOT3D/TURB3D are also supported for the following computers and graphics libraries: (1) generic UNIX Supercomputer and IRIS, suitable for CRAY 2/UNICOS, CONVEX, and Alliant with remote IRIS 2xxx/3xxx or IRIS 4D (ARC-12779, ARC-12784); (2) Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D (ARC-12783, ARC12782); (3) generic UNIX and DISSPLA Version 11.0 (ARC-12788, ARC-12778); and (4) Apollo computers running UNIX and GMR3D Version 2.0 (ARC-12789, ARC-12785 which have no capabilities to put text on plots). Silicon Graphics Iris, IRIS 4D, and IRIS 2xxx/3xxx are trademarks of Silicon Graphics Incorporated. VAX and VMS are trademarks of Digital Electronics Corporation. DISSPLA is a trademark of Computer Associates. CRAY 2 and UNICOS are trademarks of CRAY Research, Incorporated. CONVEX is a trademark of Convex Computer Corporation. Alliant is a

  14. PLOT3D/AMES, DEC VAX VMS VERSION USING DISSPLA (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P. G.

    1994-01-01

    well as 2-D and 3-D lines, but does not support graphics features requiring 3-D polygons (shading and hidden line removal, for example). Views can be manipulated using keyboard commands. This version of PLOT3D is potentially able to produce files for a variety of output devices; however, site-specific capabilities will vary depending on the device drivers supplied with the user's DISSPLA library. If ARCGRAPH (ARC-12350) is installed on the user's VAX, the VMS/DISSPLA version of PLOT3D can also be used to create files for use in GAS (Graphics Animation System, ARC-12379), an IRIS program capable of animating and recording images on film. The version 3.6b+ VMS/DISSPLA implementations of PLOT3D (ARC-12777) and PLOT3D/TURB3D (ARC-12781) were developed for use on VAX computers running VMS Version 5.0 and DISSPLA Version 11.0. The standard distribution media for each of these programs is a 9-track, 6250 bpi magnetic tape in DEC VAX BACKUP format. Customers purchasing one implementation version of PLOT3D or PLOT3D/TURB3D will be given a $200 discount on each additional implementation version ordered at the same time. Version 3.6b+ of PLOT3D and PLOT3D/TURB3D are also supported for the following computers and graphics libraries: (1) generic UNIX Supercomputer and IRIS, suitable for CRAY 2/UNICOS, CONVEX, and Alliant with remote IRIS 2xxx/3xxx or IRIS 4D (ARC-12779, ARC-12784); (2) Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D (ARC-12783, ARC12782); (3) generic UNIX and DISSPLA Version 11.0 (ARC-12788, ARC-12778); and (4) Apollo computers running UNIX and GMR3D Version 2.0 (ARC-12789, ARC-12785 which have no capabilities to put text on plots). Silicon Graphics Iris, IRIS 4D, and IRIS 2xxx/3xxx are trademarks of Silicon Graphics Incorporated. VAX and VMS are trademarks of Digital Electronics Corporation. DISSPLA is a trademark of Computer Associates. CRAY 2 and UNICOS are trademarks of CRAY Research, Incorporated. CONVEX is a trademark of Convex Computer Corporation. Alliant is a

  15. Remote 3D Medical Consultation

    NASA Astrophysics Data System (ADS)

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

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

  16. Speaking Volumes About 3-D

    NASA Technical Reports Server (NTRS)

    2002-01-01

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

  17. Modeling the steady-state ISV (in situ vitrification) process: A 3-D finite element analysis of coupled thermal-electric fields

    SciTech Connect

    Langerman, M.A.

    1990-09-01

    Steady-state modeling considerations for simulating the in situ vitrification (ISV) process are documented based upon the finite element numerical approach. Recommendations regarding boundary condition specifications and mesh discretization are presented. The effects of several parameters on the ISV process response are calculated and the results discussed. The parameters investigated include: (1) electrode depth, (2) ambient temperature, (3) supplied current, (4) electrical conductivity, (5) electrode separation, and (6) soil/waste characterization. 13 refs., 29 figs., 1 tab.

  18. Spin Liquid State in the 3D Frustrated Antiferromagnet PbCuTe_{2}O_{6}: NMR and Muon Spin Relaxation Studies.

    PubMed

    Khuntia, P; Bert, F; Mendels, P; Koteswararao, B; Mahajan, A V; Baenitz, M; Chou, F C; Baines, C; Amato, A; Furukawa, Y

    2016-03-11

    PbCuTe_{2}O_{6} is a rare example of a spin liquid candidate featuring a three-dimensional magnetic lattice. Strong geometric frustration arises from the dominant antiferromagnetic interaction that generates a hyperkagome network of Cu^{2+} ions although additional interactions enhance the magnetic lattice connectivity. Through a combination of magnetization measurements and local probe investigations by NMR and muon spin relaxation down to 20 mK, we provide robust evidence for the absence of magnetic freezing in the ground state. The local spin susceptibility probed by the NMR shift hardly deviates from the macroscopic one down to 1 K pointing to a homogeneous magnetic system with a low defect concentration. The saturation of the NMR shift and the sublinear power law temperature (T) evolution of the 1/T_{1} NMR relaxation rate at low T point to a nonsinglet ground state favoring a gapless fermionic description of the magnetic excitations. Below 1 K a pronounced slowing down of the spin dynamics is witnessed, which may signal a reconstruction of spinon Fermi surface. Nonetheless, the compound remains in a fluctuating spin liquid state down to the lowest temperature of the present investigation. PMID:27015508

  19. Spin liquid state in the 3D frustrated antiferromagnet PbCuTe2O6: NMR and muon spin relaxation studies

    DOE PAGESBeta

    Khuntia, P.; Bert, F.; Mendels, P.; Koteswararao, B.; Mahajan, A. V.; Baenitz, M.; Chou, F. C.; Baines, C.; Amato, A.; Furukawa, Y.

    2016-03-11

    In this study, PbCuTe2O6 is a rare example of a spin liquid candidate featuring a three-dimensional magnetic lattice. Strong geometric frustration arises from the dominant antiferromagnetic interaction that generates a hyperkagome network of Cu2+ ions although additional interactions enhance the magnetic lattice connectivity. Through a combination of magnetization measurements and local probe investigations by NMR and muon spin relaxation down to 20 mK, we provide robust evidence for the absence of magnetic freezing in the ground state. The local spin susceptibility probed by the NMR shift hardly deviates from the macroscopic one down to 1 K pointing to a homogeneousmore » magnetic system with a low defect concentration. The saturation of the NMR shift and the sublinear power law temperature (T) evolution of the 1/T1 NMR relaxation rate at low T point to a nonsinglet ground state favoring a gapless fermionic description of the magnetic excitations. Below 1 K a pronounced slowing down of the spin dynamics is witnessed, which may signal a reconstruction of spinon Fermi surface. Nonetheless, the compound remains in a fluctuating spin liquid state down to the lowest temperature of the present investigation.« less

  20. Spin Liquid State in the 3D Frustrated Antiferromagnet PbCuTe2 O6 : NMR and Muon Spin Relaxation Studies

    NASA Astrophysics Data System (ADS)

    Khuntia, P.; Bert, F.; Mendels, P.; Koteswararao, B.; Mahajan, A. V.; Baenitz, M.; Chou, F. C.; Baines, C.; Amato, A.; Furukawa, Y.

    2016-03-01

    PbCuTe2O6 is a rare example of a spin liquid candidate featuring a three-dimensional magnetic lattice. Strong geometric frustration arises from the dominant antiferromagnetic interaction that generates a hyperkagome network of Cu2 + ions although additional interactions enhance the magnetic lattice connectivity. Through a combination of magnetization measurements and local probe investigations by NMR and muon spin relaxation down to 20 mK, we provide robust evidence for the absence of magnetic freezing in the ground state. The local spin susceptibility probed by the NMR shift hardly deviates from the macroscopic one down to 1 K pointing to a homogeneous magnetic system with a low defect concentration. The saturation of the NMR shift and the sublinear power law temperature (T ) evolution of the 1 /T1 NMR relaxation rate at low T point to a nonsinglet ground state favoring a gapless fermionic description of the magnetic excitations. Below 1 K a pronounced slowing down of the spin dynamics is witnessed, which may signal a reconstruction of spinon Fermi surface. Nonetheless, the compound remains in a fluctuating spin liquid state down to the lowest temperature of the present investigation.

  1. PLOT3D/AMES, GENERIC UNIX VERSION USING DISSPLA (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    well as 2-D and 3-D lines, but does not support graphics features requiring 3-D polygons (shading and hidden line removal, for example). Views can be manipulated using keyboard commands. This version of PLOT3D is potentially able to produce files for a variety of output devices; however, site-specific capabilities will vary depending on the device drivers supplied with the user's DISSPLA library. The version 3.6b+ UNIX/DISSPLA implementations of PLOT3D (ARC-12788) and PLOT3D/TURB3D (ARC-12778) were developed for use on computers running UNIX SYSTEM 5 with BSD 4.3 extensions. The standard distribution media for each ofthese programs is a 9track, 6250 bpi magnetic tape in TAR format. Customers purchasing one implementation version of PLOT3D or PLOT3D/TURB3D will be given a $200 discount on each additional implementation version ordered at the same time. Version 3.6b+ of PLOT3D and PLOT3D/TURB3D are also supported for the following computers and graphics libraries: (1) generic UNIX Supercomputer and IRIS, suitable for CRAY 2/UNICOS, CONVEX, Alliant with remote IRIS 2xxx/3xxx or IRIS 4D (ARC-12779, ARC-12784); (2) Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D (ARC-12783, ARC-12782); (3) VAX computers running VMS Version 5.0 and DISSPLA Version 11.0 (ARC-12777, ARC-12781); and (4) Apollo computers running UNIX and GMR3D Version 2.0 (ARC-12789, ARC-12785 which have no capabilities to put text on plots). Silicon Graphics Iris, IRIS 4D, and IRIS 2xxx/3xxx are trademarks of Silicon Graphics Incorporated. VAX and VMS are trademarks of Digital Electronics Corporation. DISSPLA is a trademark of Computer Associates. CRAY 2 and UNICOS are trademarks of CRAY Research, Incorporated. CONVEX is a trademark of Convex Computer Corporation. Alliant is a trademark of Alliant. Apollo and GMR3D are trademarks of Hewlett-Packard, Incorporated. System 5 is a trademark of Bell Labs, Incorporated. BSD4.3 is a trademark of the University of California at Berkeley. UNIX is a registered trademark of AT&T.

  2. PLOT3D/AMES, GENERIC UNIX VERSION USING DISSPLA (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    well as 2-D and 3-D lines, but does not support graphics features requiring 3-D polygons (shading and hidden line removal, for example). Views can be manipulated using keyboard commands. This version of PLOT3D is potentially able to produce files for a variety of output devices; however, site-specific capabilities will vary depending on the device drivers supplied with the user's DISSPLA library. The version 3.6b+ UNIX/DISSPLA implementations of PLOT3D (ARC-12788) and PLOT3D/TURB3D (ARC-12778) were developed for use on computers running UNIX SYSTEM 5 with BSD 4.3 extensions. The standard distribution media for each ofthese programs is a 9track, 6250 bpi magnetic tape in TAR format. Customers purchasing one implementation version of PLOT3D or PLOT3D/TURB3D will be given a $200 discount on each additional implementation version ordered at the same time. Version 3.6b+ of PLOT3D and PLOT3D/TURB3D are also supported for the following computers and graphics libraries: (1) generic UNIX Supercomputer and IRIS, suitable for CRAY 2/UNICOS, CONVEX, Alliant with remote IRIS 2xxx/3xxx or IRIS 4D (ARC-12779, ARC-12784); (2) Silicon Graphics IRIS 2xxx/3xxx or IRIS 4D (ARC-12783, ARC-12782); (3) VAX computers running VMS Version 5.0 and DISSPLA Version 11.0 (ARC-12777, ARC-12781); and (4) Apollo computers running UNIX and GMR3D Version 2.0 (ARC-12789, ARC-12785 which have no capabilities to put text on plots). Silicon Graphics Iris, IRIS 4D, and IRIS 2xxx/3xxx are trademarks of Silicon Graphics Incorporated. VAX and VMS are trademarks of Digital Electronics Corporation. DISSPLA is a trademark of Computer Associates. CRAY 2 and UNICOS are trademarks of CRAY Research, Incorporated. CONVEX is a trademark of Convex Computer Corporation. Alliant is a trademark of Alliant. Apollo and GMR3D are trademarks of Hewlett-Packard, Incorporated. System 5 is a trademark of Bell Labs, Incorporated. BSD4.3 is a trademark of the University of California at Berkeley. UNIX is a registered trademark of AT&T.

  3. 3D-Printed Microfluidics.

    PubMed

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

    2016-03-14

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

  4. A quasi steady state method for solving transient Darcy flow in complex 3D fractured networks accounting for matrix to fracture flow

    NASA Astrophysics Data System (ADS)

    Nœtinger, B.

    2015-02-01

    Modeling natural Discrete Fracture Networks (DFN) receives more and more attention in applied geosciences, from oil and gas industry, to geothermal recovery and aquifer management. The fractures may be either natural, or artificial in case of well stimulation. Accounting for the flow inside the fracture network, and accounting for the transfers between the matrix and the fractures, with the same level of accuracy is an important issue for calibrating the well architecture and for setting up optimal resources recovery strategies. Recently, we proposed an original method allowing to model transient pressure diffusion in the fracture network only [1]. The matrix was assumed to be impervious. A systematic approximation scheme was built, allowing to model the initial DFN by a set of N unknowns located at each identified intersection between fractures. The higher N, the higher the accuracy of the model. The main assumption was using a quasi steady state hypothesis, that states that the characteristic diffusion time over one single fracture is negligible compared with the characteristic time of the macroscopic problem, e.g. change of boundary conditions. In that context, the lowest order approximation N = 1 has the form of solving a transient problem in a resistor/capacitor network, a so-called pipe network. Its topology is the same as the network of geometrical intersections between fractures. In this paper, we generalize this approach in order to account for fluxes from matrix to fractures. The quasi steady state hypothesis at the fracture level is still kept. Then, we show that in the case of well separated time scales between matrix and fractures, the preceding model needs only to be slightly modified in order to incorporate these fluxes. The additional knowledge of the so-called matrix to fracture transfer function allows to modify the mass matrix that becomes a time convolution operator. This is reminiscent of existing space averaged transient dual porosity models.

  5. 3D Computations and Experiments

    SciTech Connect

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

    2004-04-05

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

  6. 3D Computations and Experiments

    SciTech Connect

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

    2003-05-12

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

  7. Exploring 3D structure of human gonadotropin hormone receptor at antagonist state using homology modeling, molecular dynamic simulation, and cross-docking studies.

    PubMed

    Sakhteman, Amirhossein; Khoddami, Minasadat; Negahdaripour, Manica; Mehdizadeh, Arash; Tatar, Mohsen; Ghasemi, Younes

    2016-09-01

    Human gonadotropin hormone receptor, a G-protein coupled receptor, is the target of many medications used in fertility disorders. Obtaining more structural information about the receptor could be useful in many studies related to drug design. In this study, the structure of human gonadotropin receptor was subjected to homology modeling studies and molecular dynamic simulation within a DPPC lipid bilayer for 100 ns. Several frames were thereafter extracted from simulation trajectories representing the receptor at different states. In order to find a proper model of the receptor at the antagonist state, all frames were subjected to cross-docking studies of some antagonists with known experimental values (Ki). Frame 194 revealed a reasonable correlation between docking calculated energy scores and experimental activity values (|r| = 0.91). The obtained correlation was validated by means of SSLR and showed the presence of no chance correlation for the obtained model. Different structural features reported for the receptor, such as two disulfide bridges and ionic lock between GLU90 and LYS 121 were also investigated in the final model. PMID:27561920

  8. Electron correlations in solid state physics

    SciTech Connect

    Freericks, J.K.

    1991-04-01

    Exactly solvable models of electron correlations in solid state physics are presented. These models include the spinless Falicov- Kimball model, the t-t{prime}-J model, and the Hubbard model. The spinless Falicov-Kimball model is analyzed in one-dimension. Perturbation theory and numerical techniques are employed to determine the phase diagram at zero temperature. A fractal structure is found where the ground-state changes (discontinuously) at each rational electron filling. The t-t{prime}-J model (strongly interacting limit of a Hubbard model) is studied on eight-site small clusters in the simple-cubic, body-centered-cubic, face-centered-cubic, and square lattices. Symmetry is used to simplify the problem and determine the exact many-body wavefunctions. Ground states are found that exhibit magnetic order or heavy-fermionic character. Attempts to extrapolate to the thermodynamic limit are also made. The Hubbard model is examined on an eight-site square-lattice cluster in the presence of and in the absence of a magnetic field'' that couples only to orbital motion. A new magnetic phase is discovered for the ordinary Hubbard model at half-filling. In the magnetic field'' case, it is found that the strongly frustrated Heisenberg model may be studied from adiabatic continuation of a tight-binding model (from weak to strong coupling) at one point. The full symmetries of the Hamiltonian are utilized to make the exact diagonalization feasibile. Finally, the presence of hidden'' extra symmetry for finite size clusters with periodic boundary conditions is analyzed for a variety of clusters. Moderately sized systems allow nonrigid transformations that map a lattice onto itself preserving its neighbor structure; similar operations are not present in smaller or larger systems. The additional symmetry requires particular representations of the space group to stick together explaining many puzzling degeneracies found in exact diagonalization studies.

  9. 3D IC for Future HEP Detectors

    SciTech Connect

    Thom, J.; Lipton, R.; Heintz, U.; Johnson, M.; Narain, M.; Badman, R.; Spiegel, L.; Triphati, M.; Deptuch, G.; Kenney, C.; Parker, S.; Ye, Z.; Siddons, D.

    2014-11-07

    Three dimensional integrated circuit technologies offer the possibility of fabricating large area arrays of sensors integrated with complex electronics with minimal dead area, which makes them ideally suited for applications at the LHC upgraded detectors and other future detectors. Here we describe ongoing R&D efforts to demonstrate functionality of components of such detectors. This also includes the study of integrated 3D electronics with active edge sensors to produce "active tiles" which can be tested and assembled into arrays of arbitrary size with high yield.

  10. 3D IC for future HEP detectors

    NASA Astrophysics Data System (ADS)

    Thom, J.; Lipton, R.; Heintz, U.; Johnson, M.; Narain, M.; Badman, R.; Spiegel, L.; Triphati, M.; Deptuch, G.; Kenney, C.; Parker, S.; Ye, Z.; Siddons, D. P.

    2014-11-01

    Three dimensional integrated circuit technologies offer the possibility of fabricating large area arrays of sensors integrated with complex electronics with minimal dead area, which makes them ideally suited for applications at the LHC upgraded detectors and other future detectors. We describe ongoing R&D efforts to demonstrate functionality of components of such detectors. This includes the study of integrated 3D electronics with active edge sensors to produce "active tiles" which can be tested and assembled into arrays of arbitrary size with high yield.

  11. Towards magnetic 3D x-ray imaging

    NASA Astrophysics Data System (ADS)

    Fischer, Peter; Streubel, R.; Im, M.-Y.; Parkinson, D.; Hong, J.-I.; Schmidt, O. G.; Makarov, D.

    2014-03-01

    Mesoscale phenomena in magnetism will add essential parameters to improve speed, size and energy efficiency of spin driven devices. Multidimensional visualization techniques will be crucial to achieve mesoscience goals. Magnetic tomography is of large interest to understand e.g. interfaces in magnetic multilayers, the inner structure of magnetic nanocrystals, nanowires or the functionality of artificial 3D magnetic nanostructures. We have developed tomographic capabilities with magnetic full-field soft X-ray microscopy combining X-MCD as element specific magnetic contrast mechanism, high spatial and temporal resolution due to the Fresnel zone plate optics. At beamline 6.1.2 at the ALS (Berkeley CA) a new rotation stage allows recording an angular series (up to 360 deg) of high precision 2D projection images. Applying state-of-the-art reconstruction algorithms it is possible to retrieve the full 3D structure. We will present results on prototypic rolled-up Ni and Co/Pt tubes and glass capillaries coated with magnetic films and compare to other 3D imaging approaches e.g. in electron microscopy. Supported by BES MSD DOE Contract No. DE-AC02-05-CH11231 and ERC under the EU FP7 program (grant agreement No. 306277).

  12. On the Electronically Excited States of Uracil

    SciTech Connect

    Epifanovsky, Evgeny; Kowalski, Karol; Fan, Peng-Dong; Valiev, Marat; Matsika, Spiridoula; Krylov, Anna

    2008-10-09

    Vertical excitation energies in uracil in the gas phase and in water solution are investigated by the equation-of-motion coupled-cluster and multi-reference configuration interaction methods. Basis set effects are found to be important for converged results. The analysis of electronic wave functions reveals that the lowest singlet states are predominantly of a singly excited character and are therefore well described by single-reference equation-of-motion methods augmented by a perturbative triples correction to account for dynamical correlation. Our best estimates