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Sample records for 3d electronic structure

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

    PubMed

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

    2015-07-17

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

  2. 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.

  3. 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.

  4. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

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

  5. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

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

  6. 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

  7. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGES

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

    2015-05-05

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    PubMed

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Behm, Jane M.; Morse, Michael D.

    1994-06-01

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

  12. 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.

  13. 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.

  14. 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

  15. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography.

    PubMed

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

    2005-11-01

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

  16. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography.

    PubMed

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

    2005-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Lin, He; Duan, Haiming

    2008-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Goel, Satyender; Masunov, Artëm E.

    2008-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  1. 3D Reconstruction of the Glycocalyx Structure in Mammalian Capillaries using Electron Tomography

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2015-10-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-10-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  7. 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

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

    PubMed

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

    2012-01-01

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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

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

    PubMed

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

    2003-09-30

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

  14. Self assembled structures for 3D integration

    NASA Astrophysics Data System (ADS)

    Rao, Madhav

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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed

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

    2010-02-28

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

  18. 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.

  19. 3D electron microscopy of biological nanomachines: principles and applications.

    PubMed

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

    2007-11-01

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

  20. 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.

  1. 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

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

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

  4. 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.

  5. 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.

  6. 3D structure and nuclear targets

    NASA Astrophysics Data System (ADS)

    Dupré, Raphaël; Scopetta, Sergio

    2016-06-01

    Recent experimental and theoretical ideas are laying the ground for a new era in the knowledge of the parton structure of nuclei. We report on two promising directions beyond inclusive deep inelastic scattering experiments, aimed at, among other goals, unveiling the three-dimensional structure of the bound nucleon. The 3D structure in coordinate space can be accessed through deep exclusive processes, whose non-perturbative content is parametrized in terms of generalized parton distributions. In this way the distribution of partons in the transverse plane will be obtained, providing a pictorial view of the realization of the European Muon Collaboration effect. In particular, we show how, through the generalized parton distribution framework, non-nucleonic degrees of freedom in nuclei can be unveiled. Analogously, the momentum space 3D structure can be accessed by studying transverse-momentum-dependent parton distributions in semi-inclusive deep inelastic scattering processes. The status of measurements is also summarized, in particular novel coincidence measurements at high-luminosity facilities, such as Jefferson Laboratory. Finally the prospects for the next years at future facilities, such as the 12GeV Jefferson Laboratory and the Electron Ion Collider, are presented.

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

    DOE PAGES

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

    2016-08-18

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

  8. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  9. Experimental electronic structure and Fermi-surface instability of the correlated 3d sulphide BaVS3 : High-resolution angle-resolved photoemission spectroscopy

    NASA Astrophysics Data System (ADS)

    Mitrovic, S.; Fazekas, P.; Søndergaard, C.; Ariosa, D.; Barišić, N.; Berger, H.; Cloëtta, D.; Forró, L.; Höchst, H.; Kupčić, I.; Pavuna, D.; Margaritondo, G.

    2007-04-01

    The correlated 3d sulphide BaVS3 exhibits an interesting coexistence of one-dimensional and three-dimensional properties. Our experiments determine the electronic band structure and shed light on this puzzle. High-resolution angle-resolved photoemission measurements in a 4-eV -wide range below the Fermi energy level uncover and investigate the coexistence of a1g wide-band and eg narrow-band d electrons, which lead to the complicated electronic properties of this material. We explore the effects of strong correlations and the Fermi surface instability associated with the metal-insulator transition.

  10. The hybridizations of cobalt 3 d bands with the electron band structure of the graphene/cobalt interface on a tungsten substrate

    NASA Astrophysics Data System (ADS)

    Hwang, Jinwoong; Hwang, Choongyu; Chung, Nak-Kwan; N'Diaye, A. D.; Schmid, A. K.; Denlinger, Jonathan

    2016-08-01

    The interface between graphene and a ferromagnetic substrate has attracted recent research interests due to its potential for spintronic applications. We report an angle-resolved photoemission spectroscopy study on the interface between graphene and cobalt epitaxially grown on a tungsten substrate. We find that the electron band structure of the interface exhibits clear discontinuities at the crossing points with cobalt 3 d bands. These observations indicate strong hybridizations between the electronic states in the interface and provide an important clue to understand the intriguing electromagnetic properties of the graphene/ferromagnet interface.

  11. 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.

  12. Structured light field 3D imaging.

    PubMed

    Cai, Zewei; Liu, Xiaoli; Peng, Xiang; Yin, Yongkai; Li, Ameng; Wu, Jiachen; Gao, Bruce Z

    2016-09-01

    In this paper, we propose a method by means of light field imaging under structured illumination to deal with high dynamic range 3D imaging. Fringe patterns are projected onto a scene and modulated by the scene depth then a structured light field is detected using light field recording devices. The structured light field contains information about ray direction and phase-encoded depth, via which the scene depth can be estimated from different directions. The multidirectional depth estimation can achieve high dynamic 3D imaging effectively. We analyzed and derived the phase-depth mapping in the structured light field and then proposed a flexible ray-based calibration approach to determine the independent mapping coefficients for each ray. Experimental results demonstrated the validity of the proposed method to perform high-quality 3D imaging for highly and lowly reflective surfaces. PMID:27607639

  13. 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

  14. 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

  15. 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.

  16. Structural, mechanical and electronic properties of 3d transition metal nitrides in cubic zincblende, rocksalt and cesium chloride structures: a first-principles investigation.

    PubMed

    Liu, Z T Y; Zhou, X; Khare, S V; Gall, D

    2014-01-15

    We report systematic results from ab initio calculations with density functional theory on three cubic structures, zincblende (zb), rocksalt (rs) and cesium chloride (cc), of the ten 3d transition metal nitrides. We computed lattice constants, elastic constants, their derived moduli and ratios that characterize mechanical properties. Experimental measurements exist in the literature of lattice constants for rs-ScN, rs-TiN and rs-VN and of elastic constants for rs-TiN and rs-VN, all of which are in good agreement with our computational results. Similarly, computed Vickers hardness (HV) values for rs-TiN and rs-VN are consistent with earlier experimental results. Several trends were observed in our rich data set of 30 compounds. All nitrides, except for zb-CrN, rs-MnN, rs-FeN, cc-ScN, cc-CrN, cc-NiN and cc-ZnN, were found to be mechanically stable. A clear correlation in the atomic density with the bulk modulus (B) was observed with maximum values of B around FeN, MnN and CrN. The shear modulus, Young's modulus, HV and indicators of brittleness showed similar trends and all showed maxima for cc-VN. The calculated value of HV for cc-VN was about 30 GPa, while the next highest values were for rs-ScN and rs-TiN, about 24 GPa. A relation (H(V) is proportional to θ(D)(2)) between HV and Debye temperature (θD) was investigated and verified for each structure type. A tendency for anti-correlation of the elastic constant C44, which strongly influences stability and hardness, with the number of electronic states around the Fermi energy was observed.

  17. A Ca(2+)-dependent global conformational change in the 3D structure of phosphorylase kinase obtained from electron microscopy.

    PubMed

    Nadeau, Owen W; Carlson, Gerald M; Gogol, Edward P

    2002-01-01

    Phosphorylase kinase (PhK), a Ca(2+)-dependent regulatory enzyme of the glycogenolytic cascade in skeletal muscle, is a 1.3 MDa hexadecameric oligomer comprising four copies of four distinct subunits, termed alpha, beta, gamma, and delta, the last being endogenous calmodulin. The structures of both nonactivated and Ca(2+)-activated PhK were determined to elucidate Ca(2+)-induced structural changes associated with PhK's activation. Reconstructions of both conformers of the kinase, each including over 11,000 particles, yielded bridged, bilobal structures with resolutions estimated by Fourier shell correlation at 24 A using a 0.5 correlation cutoff, or at 18 A by the 3sigma (corrected for D(2) symmetry) threshold curve. Extensive Ca(2+)-induced structural changes were observed in regions encompassing both the lobes and bridges, consistent with changes in subunit interactions upon activation. The relative placement of the alpha, beta, gamma, and delta subunits in the nonactivated three-dimensional structure, relying upon previous two-dimensional localizations, is in agreement with the known effects of Ca(2+) on subunit conformations and interactions in the PhK complex. PMID:11796107

  18. Motif3D: Relating protein sequence motifs to 3D structure.

    PubMed

    Gaulton, Anna; Attwood, Teresa K

    2003-07-01

    Motif3D is a web-based protein structure viewer designed to allow sequence motifs, and in particular those contained in the fingerprints of the PRINTS database, to be visualised on three-dimensional (3D) structures. Additional functionality is provided for the rhodopsin-like G protein-coupled receptors, enabling fingerprint motifs of any of the receptors in this family to be mapped onto the single structure available, that of bovine rhodopsin. Motif3D can be used via the web interface available at: http://www.bioinf.man.ac.uk/dbbrowser/motif3d/motif3d.html.

  19. Discovering Structural Regularity in 3D Geometry

    PubMed Central

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

    2010-01-01

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

  20. 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.

  1. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

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

    2015-07-15

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

  2. 3D Structure of Tillage Soils

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Ramasamy, Mouli; Varadan, Vijay K.

    2016-04-01

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

  4. 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

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

    PubMed Central

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

    2015-01-01

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

  6. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

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

    2016-07-01

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

  7. 3D-GNOME: an integrated web service for structural modeling of the 3D genome

    PubMed Central

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

    2016-01-01

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

  8. Spectroscopy of jet-cooled AlMn and trends in the electronic structure of the 3d transition metal aluminides

    NASA Astrophysics Data System (ADS)

    Behm, Jane M.; Morse, Michael D.

    1994-10-01

    Jet-cooled diatomic AlMn has been spectroscopically investigated and is shown to possess a 5Πi ground state deriving from the Al (3s23p1,2P0)+Mn (3d54s2,6S) separated atom limit. This implies that the aluminum atom favors a 3pπ approach to the manganese atom, a result that is in agreement with previous studies on the related AlCa and AlZn molecules. The ground state bond length has been measured as 2.6384±0.0010 Å, a value which includes corrections due to spin-uncoupling effects in the X 5Πi state. It is suggested that the 5Πi state emerges as the ground state due to a particularly favorable configuration interaction with a low-lying 5Πi state that derives from the interaction of Al (3s23p1,2P0)+Mn [3d6(5D)4s1,6D]. Combination of the atoms in this excited state leads to a strong σ2 covalent bond via a 3pσAl-4sσMn interaction, which causes this excited electronic state to drop in energy so that it is expected to lie within a few thousand cm-1 of the ground electronic state. Following a discussion of the spectroscopic results on AlMn, an overall summary of the spectroscopic results on the 3d series of transition metal aluminides is presented, along with predictions of the ground electronic states of the as yet unobserved AlSc, AlTi, and AlFe molecules.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  10. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

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

    2015-07-15

    X. Zhao and co-workers develop on page 4035 a new biocompatible hydrogel system that is extremely tough and stretchable and can be 3D printed into complex structures, such as the multilayer mesh shown. Cells encapsulated in the tough and printable hydrogel maintain high viability. 3D-printed structures of the tough hydrogel can sustain high mechanical loads and deformations. PMID:26172844

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

    PubMed Central

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

    2015-01-01

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

  12. 3D Structure of the Dihydropyridine Receptor of Skeletal Muscle.

    PubMed

    Samsó, Montserrat

    2015-01-01

    Excitation contraction coupling, the rapid and massive Ca(2+) release under control of an action potential that triggers muscle contraction, takes places at specialized regions of the cell called triad junctions. There, a highly ordered supramolecular complex between the dihydropyridine receptor (DHPR) and the ryanodine receptor (RyR1) mediates the quasi-instantaneous conversion from T-tubule depolarization into Ca(2+) release from the sarcoplasmic reticulum (SR). The DHPR has several key modules required for EC coupling: the voltage sensors and II-III loop in the alpha1s subunit, and the beta subunit. To gain insight into their molecular organization, this review examines the most updated 3D structure of the DHPR as obtained by transmission electron microscopy and image reconstruction. Although structure determination of a heteromeric membrane protein such as the DHPR is challenging, novel technical advances in protein expression and 3D labeling facilitated this task. The 3D structure of the DHPR complex consists of a main body with five irregular corners around its perimeter encompassing the transmembrane alpha 1s subunit besides the intracellular beta subunit, an extended extracellular alpha 2 subunit, and a bulky intracellular II-III loop. The structural definition attained at 19 Å resolution enabled docking of the atomic coordinates of structural homologs of the alpha1s and beta subunits. These structural features, together with their relative location with respect to the RyR1, are discussed in the context of the functional data. PMID:26913147

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

    PubMed Central

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

    2010-01-01

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

  14. 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.

  15. 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.

  16. 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.

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

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

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

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

    PubMed Central

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

    2008-01-01

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

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

    PubMed

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

    2012-01-01

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

  20. 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

  1. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

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

  2. Axonemal radial spokes: 3D structure, function and assembly.

    PubMed

    Pigino, Gaia; Ishikawa, Takashi

    2012-02-01

    The radial spoke (RS) is a complex of at least 23 proteins that works as a mechanochemical transducer between the central-pair apparatus and the peripheral microtubule doublets in eukaryotic flagella and motile cilia. The RS contributes to the regulation of the activity of dynein motors, and thus to flagellar motility. Despite numerous biochemical, physiological and structural studies, the mechanism of the function of the radial spoke remains unclear. Detailed knowledge of the 3D structure of the RS protein complex is needed in order to understand how RS regulates dynein activity. Here we review the most important findings on the structure of the RS, including results of our recent cryo-electron tomographic analysis of the RS protein complex. PMID:22754630

  3. 3D visualization of middle ear structures

    NASA Astrophysics Data System (ADS)

    Vogel, Uwe; Schmitt, Thomas

    1998-06-01

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

  4. Maintenance of a bone collagen phenotype by osteoblast-like cells in 3D periodic porous titanium (Ti-6Al-4 V) structures fabricated by selective electron beam melting.

    PubMed

    Hrabe, Nikolas W; Heinl, Peter; Bordia, Rajendra K; Körner, Carolin; Fernandes, Russell J

    2013-01-01

    Regular 3D periodic porous Ti-6Al-4 V structures were fabricated by the selective electron beam melting method (EBM) over a range of relative densities (0.17-0.40) and pore sizes (500-1500 µm). Structures were seeded with human osteoblast-like cells (SAOS-2) and cultured for four weeks. Cells multiplied within these structures and extracellular matrix collagen content increased. Type I and type V collagens typically synthesized by osteoblasts were deposited in the newly formed matrix with time in culture. High magnification scanning electron microscopy revealed cells attached to surfaces on the interior of the structures with an increasingly fibrous matrix. The in-vitro results demonstrate that the novel EBM-processed porous structures, designed to address the effect of stress-shielding, are conducive to osteoblast attachment, proliferation and deposition of a collagenous matrix characteristic of bone.

  5. 3D-Fun: predicting enzyme function from structure.

    PubMed

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

    2008-07-01

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

  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. Automated RNA 3D Structure Prediction with RNAComposer.

    PubMed

    Biesiada, Marcin; Purzycka, Katarzyna J; Szachniuk, Marta; Blazewicz, Jacek; Adamiak, Ryszard W

    2016-01-01

    RNAs adopt specific structures to perform their activities and these are critical to virtually all RNA-mediated processes. Because of difficulties in experimentally assessing structures of large RNAs using NMR, X-ray crystallography, or cryo-microscopy, there is currently great demand for new high-resolution 3D structure prediction methods. Recently we reported on RNAComposer, a knowledge-based method for the fully automated RNA 3D structure prediction from a user-defined secondary structure. RNAComposer method is especially suited for structural biology users. Since our initial report in 2012, both servers, freely available at http://rnacomposer.ibch.poznan.pl and http://rnacomposer.cs.put.poznan.pl have been often visited. Therefore this chapter provides guidance for using RNAComposer and discusses points that should be considered when predicting 3D RNA structure. An application example presents current scope and limitations of RNAComposer. PMID:27665601

  8. Formal representation of 3D structural geological models

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. Hybrid additive manufacturing of 3D electronic systems

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  14. Multifunctional 3D printing of heterogeneous hydrogel structures

    PubMed Central

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

    2016-01-01

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

  15. Multifunctional 3D printing of heterogeneous hydrogel structures

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  16. Multifunctional 3D printing of heterogeneous hydrogel structures.

    PubMed

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

    2016-01-01

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

  17. Multifunctional 3D printing of heterogeneous hydrogel structures.

    PubMed

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

    2016-09-15

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

  18. 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.

  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. 3D annotation and manipulation of medical anatomical structures

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

  1. 3D Ultrasonic Wave Simulations for Structural Health Monitoring

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  2. Assembly of graphene sheets into 3D macroscopic structures.

    PubMed

    Yin, Shengyan; Niu, Zhiqiang; Chen, Xiaodong

    2012-08-20

    Integration of graphene sheets, 2D nanoscale building blocks, into 3D macroscopic assemblies and ultimately into a functional system is essential to explore the advanced properties of individual graphene sheets for macroscopic applications. This Concept paper summarizes different ways, such as flow-directed assembly, layer-by-layer deposition, template-directed method, and leavening strategy to assemble graphene sheets into the layered and porous 3D macroscopic structures. The obtained structures show unique properties, such as flexible network, high specific surface area, and outstanding electrical and mechanical properties. Furthermore, the functional systems based on such graphene 3D macroscopic structures have shown enhanced performance in the applications of energy storage, catalysis, environmental remediation, and sensing.

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

    NASA Astrophysics Data System (ADS)

    Doerschuk, Peter C.; Johnson, John E.

    2000-11-01

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

  4. The first 3D malonate bridged copper [Cu(O{sub 2}C-CH{sub 2}-CO{sub 2}H){sub 2}{center_dot}2H{sub 2}O]: Structure, properties and electronic structure

    SciTech Connect

    Seguatni, A.; Fakhfakh, M.; Smiri, L.S.; Gressier, P.; Boucher, F.; Jouini, N.

    2012-03-15

    A new inorganic-organic compound [Cu(O{sub 2}C-CH{sub 2}-CO{sub 2}H){sub 2}{center_dot}2H{sub 2}O] ([Cumal]) was hydrothermally synthesized and characterized by IR spectroscopy, thermal analysis and single crystal X-ray diffraction. [Cumal] is the first three-dimensional compound existing in the system Cu(II)-malonic acid-H{sub 2}O. Its framework is built up through carboxyl bridged copper where CuO{sub 6} octahedra are elongated with an almost D{sub 4h} symmetry (4+2) due to the Jahn-Teller effect. The magnetic properties were studied by measuring its magnetic susceptibility in the temperature range of 2-300 K indicating the existence of weak ferromagnetic interactions. The electronic structure of [Cumal] was calculated within the density functional theory (DFT) framework. Structural features are well reproduced using DFT structural optimizations and the optical spectra, calculated within the dielectric formalism, explain very well the light blue colour of the compound. It is shown that a GGA+U approach with a U{sub eff} value of about 6 eV is necessary for a better correlation with the experiment. - Graphical abstract: [Cu(O{sub 2}C-CH{sub 2}-CO{sub 2}H){sub 2}{center_dot}2H{sub 2}O]: the first 3D hybrid organic-inorganic compound built up carboxyl groups. The network presents a diamond-like structure achieved via carboxyl. Highlights: Black-Right-Pointing-Pointer A new organic-inorganic material with an unprecedented topology is synthesized. Black-Right-Pointing-Pointer Crystallographic structure is determined using single crystal X-ray diffraction. Black-Right-Pointing-Pointer Electronic structure is obtained from DFT, GGA+U calculation. Black-Right-Pointing-Pointer Framework can be described as formed from CuC{sub 4} tetrahedron sharing four corners. Black-Right-Pointing-Pointer This structure can be classified as an extended diamond structure.

  5. 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.

  6. 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.

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

    PubMed Central

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

    2013-01-01

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

  8. RNAComposer and RNA 3D structure prediction for nanotechnology.

    PubMed

    Biesiada, Marcin; Pachulska-Wieczorek, Katarzyna; Adamiak, Ryszard W; Purzycka, Katarzyna J

    2016-07-01

    RNAs adopt specific, stable tertiary architectures to perform their activities. Knowledge of RNA tertiary structure is fundamental to understand RNA functions beginning with transcription and ending with turnover. Contrary to advanced RNA secondary structure prediction algorithms, which allow good accuracy when experimental data are integrated into the prediction, tertiary structure prediction of large RNAs still remains a significant challenge. However, the field of RNA tertiary structure prediction is rapidly developing and new computational methods based on different strategies are emerging. RNAComposer is a user-friendly and freely available server for 3D structure prediction of RNA up to 500 nucleotide residues. RNAComposer employs fully automated fragment assembly based on RNA secondary structure specified by the user. Importantly, this method allows incorporation of distance restraints derived from the experimental data to strengthen the 3D predictions. The potential and limitations of RNAComposer are discussed and an application to RNA design for nanotechnology is presented.

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

    PubMed

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

    2016-07-01

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

  10. 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

  11. 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.

  12. 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.

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

    PubMed

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

    2004-01-01

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

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

    PubMed

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

    2015-07-29

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

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

    PubMed Central

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

    2015-01-01

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

  16. Unique structure of iC3b resolved at a resolution of 24 Å by 3D-electron microscopy.

    PubMed

    Alcorlo, Martin; Martínez-Barricarte, Ruben; Fernández, Francisco J; Rodríguez-Gallego, César; Round, Adam; Vega, M Cristina; Harris, Claire L; de Cordoba, Santiago Rodríguez; Llorca, Oscar

    2011-08-01

    Activation of C3, deposition of C3b on the target surface, and subsequent amplification by formation of a C3-cleaving enzyme (C3-convertase; C3bBb) triggers the effector functions of complement that result in inflammation and cell lysis. Concurrently, surface-bound C3b is proteolyzed to iC3b by factor I and appropriate cofactors. iC3b then interacts with the complement receptors (CR) of the Ig superfamily, CR2 (CD21), CR3 (CD11b/CD18), and CR4 (CD11c/CD18) on leukocytes, down-modulating inflammation, enhancing B cell-mediated immunity, and targeting pathogens for clearance by phagocytosis. Using EM and small-angle X-ray scattering, we now present a medium-resolution structure of iC3b (24 Å). iC3b displays a unique conformation with structural features distinct from any other C3 fragment. The macroglobulin ring in iC3b is similar to that in C3b, whereas the TED (thioester-containing domain) domain and the remnants of the CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domain have moved to locations more similar to where they were in native C3. A consequence of this large conformational change is the disruption of the factor B binding site, which renders iC3b unable to assemble a C3-convertase. This structural model also justifies the decreased interaction between iC3b and complement regulators and the recognition of iC3b by the CR of the Ig superfamily, CR2, CR3, and CR4. These data further illustrate the extraordinary conformational versatility of C3 to accommodate a great diversity of functional activities.

  17. Unique structure of iC3b resolved at a resolution of 24 Å by 3D-electron microscopy.

    PubMed

    Alcorlo, Martin; Martínez-Barricarte, Ruben; Fernández, Francisco J; Rodríguez-Gallego, César; Round, Adam; Vega, M Cristina; Harris, Claire L; de Cordoba, Santiago Rodríguez; Llorca, Oscar

    2011-08-01

    Activation of C3, deposition of C3b on the target surface, and subsequent amplification by formation of a C3-cleaving enzyme (C3-convertase; C3bBb) triggers the effector functions of complement that result in inflammation and cell lysis. Concurrently, surface-bound C3b is proteolyzed to iC3b by factor I and appropriate cofactors. iC3b then interacts with the complement receptors (CR) of the Ig superfamily, CR2 (CD21), CR3 (CD11b/CD18), and CR4 (CD11c/CD18) on leukocytes, down-modulating inflammation, enhancing B cell-mediated immunity, and targeting pathogens for clearance by phagocytosis. Using EM and small-angle X-ray scattering, we now present a medium-resolution structure of iC3b (24 Å). iC3b displays a unique conformation with structural features distinct from any other C3 fragment. The macroglobulin ring in iC3b is similar to that in C3b, whereas the TED (thioester-containing domain) domain and the remnants of the CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domain have moved to locations more similar to where they were in native C3. A consequence of this large conformational change is the disruption of the factor B binding site, which renders iC3b unable to assemble a C3-convertase. This structural model also justifies the decreased interaction between iC3b and complement regulators and the recognition of iC3b by the CR of the Ig superfamily, CR2, CR3, and CR4. These data further illustrate the extraordinary conformational versatility of C3 to accommodate a great diversity of functional activities. PMID:21788512

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

    DOE PAGES

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

    2016-06-10

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

  19. Formation of coherent structures in 3D laminar mixing flows

    NASA Astrophysics Data System (ADS)

    Speetjens, Michel; Clercx, Herman

    2009-11-01

    Mixing under laminar flow conditions is key to a wide variety of industrial systems of size extending from microns to meters. Examples range from the traditional (and still very relevant) mixing of viscous fluids via compact processing equipment down to emerging micro-fluidics applications. Profound insight into laminar mixing mechanisms is imperative for further advancement of mixing technology (particularly for complex micro-fluidics systems) yet remains limited to date. The present study concentrates on a fundamental transport phenomenon of potential relevance to laminar mixing: the formation of coherent structures in the web of 3D fluid trajectories due to fluid inertia. Such coherent structures geometrically determine the transport properties of the flow and better understanding of their formation and characteristics may offer ways to control and manipulate the mixing properties of laminar flows. The formation of coherent structures and its impact upon 3D transport properties is demonstrated by way of examples.

  20. Gene3D: comprehensive structural and functional annotation of genomes.

    PubMed

    Yeats, Corin; Lees, Jonathan; Reid, Adam; Kellam, Paul; Martin, Nigel; Liu, Xinhui; Orengo, Christine

    2008-01-01

    Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources. The main structural annotation is generated through scanning these sequences against the CATH structural domain database profile-HMM library. CATH is a database of manually derived PDB-based structural domains, placed within a hierarchy reflecting topology, homology and conservation and is able to infer more ancient and divergent homology relationships than sequence-based approaches. This data is supplemented with Pfam-A, other non-domain structural predictions (i.e. coiled coils) and experimental data from UniProt. In order to enhance the investigations possible with this data, we have also incorporated a variety of protein annotation resources, including protein-protein interaction data, GO functional assignments, KEGG pathways, FUNCAT functional descriptions and links to microarray expression data. All of this data can be accessed through a newly re-designed website that has a focus on flexibility and clarity, with searches that can be restricted to a single genome or across the entire sequence database. Currently Gene3D contains over 3.5 million domain assignments for nearly 5 million proteins including 527 completed genomes. This is available at: http://gene3d.biochem.ucl.ac.uk/ PMID:18032434

  1. 3-D Numerical Modeling of a Complex Salt Structure

    SciTech Connect

    House, L.; Larsen, S.; Bednar, J.B.

    2000-02-17

    Reliably processing, imaging, and interpreting seismic data from areas with complicated structures, such as sub-salt, requires a thorough understanding of elastic as well as acoustic wave propagation. Elastic numerical modeling is an essential tool to develop that understanding. While 2-D elastic modeling is in common use, 3-D elastic modeling has been too computationally intensive to be used routinely. Recent advances in computing hardware, including commodity-based hardware, have substantially reduced computing costs. These advances are making 3-D elastic numerical modeling more feasible. A series of example 3-D elastic calculations were performed using a complicated structure, the SEG/EAGE salt structure. The synthetic traces show that the effects of shear wave propagation can be important for imaging and interpretation of images, and also for AVO and other applications that rely on trace amplitudes. Additional calculations are needed to better identify and understand the complex wave propagation effects produced in complicated structures, such as the SEG/EAGE salt structure.

  2. 3D printed components with ultrasonically arranged microscale structure

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  5. All dispenser printed flexible 3D structured thermoelectric generators

    NASA Astrophysics Data System (ADS)

    Cao, Z.; Shi, J. J.; Torah, R. N.; Tudor, M. J.; Beeby, S. P.

    2015-12-01

    This work presents a vertically fabricated 3D thermoelectric generator (TEG) by dispenser printing on flexible polyimide substrate. This direct-write technology only involves printing of electrodes, thermoelectric active materials and structure material, which needs no masks to transfer the patterns onto the substrate. The dimension for single thermoelectric element is 2 mm × 2 mm × 0.5 mm while the distance between adjacent cubes is 1.2 mm. The polymer structure layer was used to support the electrodes which are printed to connect the top ends of the thermoelectric material and ensure the flexibility as well. The advantages and the limitations of the dispenser printed 3D TEGs will also be evaluated in this paper. The proposed method is potential to be a low-cost and scalable fabrication solution for TEGs.

  6. Advancements in 3D Structural Analysis of Geothermal Systems

    SciTech Connect

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

    2013-06-23

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

  7. Cancer3D: understanding cancer mutations through protein structures

    PubMed Central

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

    2015-01-01

    The new era of cancer genomics is providing us with extensive knowledge of mutations and other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. The database also helps users analyze the distribution patterns of the mutations as well as their relationship to changes in drug activity through two algorithms: e-Driver and e-Drug. These algorithms use knowledge of modular structure of genes and proteins to separately study each region. This approach allows users to find novel candidate driver regions or drug biomarkers that cannot be found when similar analyses are done on the whole-gene level. The Cancer3D database provides access to the results of such analyses based on data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). In addition, it displays mutations from over 14 700 proteins mapped to more than 24 300 structures from PDB. This helps users visualize the distribution of mutations and identify novel three-dimensional patterns in their distribution. PMID:25392415

  8. 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

  9. 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.

  10. Fabrication of 3-D Submicron Glass Structures by FIB

    NASA Astrophysics Data System (ADS)

    Chao, C. H.; Shen, S. C.; Wu, J. R.

    2009-10-01

    The fabrication characteristic of focused ion beam (FIB) for Pyrex glass was investigated. FIB has several advantages such as high resolution, high material removal rates, low forward scattering, and direct fabrication in selective area without any etching mask. In this study, FIB-etched Pyrex glass was used for fast fabrication of 3-D submicron structures. A glass structure with 0.39 μm in width was fabricated. The experimental results in terms of limiting beam size, ion dose (ion/cm2), and beam current are discussed. The influence of XeF2 gas on FIB glass fabrication was investigated.

  11. Automatic structural matching of 3D image data

    NASA Astrophysics Data System (ADS)

    Ponomarev, Svjatoslav; Lutsiv, Vadim; Malyshev, Igor

    2015-10-01

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

  12. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

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

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

    PubMed

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

    2012-07-01

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

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

    PubMed

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

    2006-01-01

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

  15. 3D geophysical investigations of shallow karstic structures

    NASA Astrophysics Data System (ADS)

    Rousset, D.; Genthon, P.; Perroud, H.; Sénéchal, G.

    2003-04-01

    The accurate determination of shallow kastified areas is of major importance for the quantitative modelling of fluid transfer as well as for geotechnical issues. Near surface geophysics offers a broad range of tools dedicated to the study of voids and other cavities filled with water or sediments. We present the results of various geophysical studies (seismics, GPR, 2-D and 3-D DC resitivity) in the Baget area, a hydrologically well monitored zone, in the vicinity of Moulis underground laboratory in the Central Pyrenees. The studied area is a 1Km long segment of a narrow EW valley, located on the boundary between limestones and shales, with emphasis on a 100m long anomalous zone. begin{itemize} Seismics doesn't allow to derive a focused image of the very shallow (< 2m) structure but amplitude anomalies suggest the presence of scattering structures in the valley. GPR data clearly show the sedimentary filling of the valley, overlying the generally transparent limestone basement. Two highly reflective zones evidence the presence of heterogeneities. 2-D DC resistivity exhibits very different results whether the lines are in the direction of the valley or perpendicular to it. Results suggest a strong influence of the topography leading to completely erroneous conclusions without complementary data. The presentation is focused on GPR and DC resitivity methods. The limitations of 3-D DC inversion is partly overcome by transforming the data from pole-pole pattern to dipole-dipole, allowing us to get more details on the shallow and short wavelenght structures with conventional software. Voids are indicated by the presence of a temporary river and speleological exploration but the results of the study show the absence of big cavities under the surface, within the first meters of limestone. GPR and DC resitivity studies reveal the presence of shallow metric heterogeneities which can be the water conduit system. 3-D investigation is necessary to get consistent results.

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

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

    Human and natural forces are rapidly modifying the global distribution and structure of terrestrial ecosystems on which all of life depends, altering the global carbon cycle, affecting our climate now and for the foreseeable future, causing steep reductions in species diversity, and endangering Earth s sustainability. To understand changes and trends in terrestrial ecosystems and their functioning as carbon sources and sinks, and to characterize the impact of their changes on climate, habitat and biodiversity, new space assets are urgently needed to produce high spatial resolution global maps of the three-dimensional (3D) structure of vegetation, its biomass above ground, the carbon stored within and the implications for atmospheric green house gas concentrations and climate. These needs were articulated in a 2007 National Research Council (NRC) report (NRC, 2007) recommending a new satellite mission, DESDynI, carrying an L-band Polarized Synthetic Aperture Radar (Pol-SAR) and a multi-beam lidar (Light RAnging And Detection) operating at 1064 nm. The objectives of this paper are to articulate the importance of these new, multi-year, 3D vegetation structure and biomass measurements, to briefly review the feasibility of radar and lidar remote sensing technology to meet these requirements, to define the data products and measurement requirements, and to consider implications of mission durations. The paper addresses these objectives by synthesizing research results and other input from a broad community of terrestrial ecology, carbon cycle, and remote sensing scientists and working groups. We conclude that: (1) current global biomass and 3-D vegetation structure information is unsuitable for both science and management and policy. The only existing global datasets of biomass are approximations based on combining land cover type and representative carbon values, instead of measurements of actual biomass. Current measurement attempts based on radar and multispectral

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

    NASA Astrophysics Data System (ADS)

    Jaiswal, Neeru; Kishtawal, C. M.

    2016-05-01

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

  18. Lithographically-generated 3D lamella layers and their structural color

    NASA Astrophysics Data System (ADS)

    Zhang, Sichao; Chen, Yifang; Lu, Bingrui; Liu, Jianpeng; Shao, Jinhai; Xu, Chen

    2016-04-01

    Inspired by the structural color from the multilayer nanophotonic structures in Morpho butterfly wing scales, 3D lamellae layers in dielectric polymers (polymethyl methacrylate, PMMA) with n ~ 1.5 were designed and fabricated by standard top-down electron beam lithography with one-step exposure followed by an alternating development/dissolution process of PMMA/LOR (lift-off resist) multilayers. This work offers direct proof of the structural blue/green color via lithographically-replicated PMMA/air multilayers, analogous to those in real Morpho butterfly wings. The success of nanolithography in this work for the 3D lamellae structures in dielectric polymers not only enables us to gain deeper insight into the mysterious blue color of the Morpho butterfly wings, but also breaks through the bottleneck in technical development toward broad applications in gas/liquid sensors, 3D meta-materials, coloring media, and infrared imaging devices, etc.

  19. 3D Imaging of Diatoms with Ion-abrasion Scanning Electron Microscopy

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2015-10-01

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

  1. Dual multispectral and 3D structured light laparoscope

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  2. 3D Shape and Indirect Appearance by Structured Light Transport.

    PubMed

    OToole, Matthew; Mather, John; Kutulakos, Kiriakos N

    2016-07-01

    We consider the problem of deliberately manipulating the direct and indirect light flowing through a time-varying, general scene in order to simplify its visual analysis. Our approach rests on a crucial link between stereo geometry and light transport: while direct light always obeys the epipolar geometry of a projector-camera pair, indirect light overwhelmingly does not. We show that it is possible to turn this observation into an imaging method that analyzes light transport in real time in the optical domain, prior to acquisition. This yields three key abilities that we demonstrate in an experimental camera prototype: (1) producing a live indirect-only video stream for any scene, regardless of geometric or photometric complexity; (2) capturing images that make existing structured-light shape recovery algorithms robust to indirect transport; and (3) turning them into one-shot methods for dynamic 3D shape capture.

  3. Edge singularities and structure of the 3-D Williams expansion

    NASA Astrophysics Data System (ADS)

    Apel, Thomas; Leguillon, Dominique; Pester, Cornelia; Yosibash, Zohar

    2008-08-01

    The elastic solution in a vicinity of a re-entrant wedge can be described by a Williams like expansion in terms of powers of the distance to a point on the edge. This expansion has a particular structure due to the invariance of the problem by translation parallel to the edge. We show here that some terms, so-called primary solutions, derive directly from solutions to the 2-D corner problem posed in the orthogonal cross section of the domain. The others, baptized shadow functions, derive of the primary solutions by integration along the axis parallel to the edge. This 3-D Williams expansion is shown to be equivalent to the edge expansion proposed by Costabel et al. [M. Costabel, M. Dauge, Z. Yosibash, A quasidual function method for extracting edge stress intensity functions, SIAM J. Math. Anal. 35 (5) (2004) 1177-1202]. To cite this article: T. Apel et al., C. R. Mecanique 336 (2008).

  4. 3D Global Coronal Density Structure and Associated Magnetic Field near Solar Maximum

    NASA Astrophysics Data System (ADS)

    Kramar, Maxim; Airapetian, Vladimir; Lin, Haosheng

    2016-08-01

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

  5. 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

  6. 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.

  7. 3D complex: a structural classification of protein complexes.

    PubMed

    Levy, Emmanuel D; Pereira-Leal, Jose B; Chothia, Cyrus; Teichmann, Sarah A

    2006-11-17

    Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

  8. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

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

  9. 3D Wilson cycle: structural inheritance and subduction polarity reversals

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Hong, Seongik

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

  11. 3D Imaging with Structured Illumination for Advanced Security Applications

    SciTech Connect

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

    2015-09-01

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

  12. Studies of the 3D Structure of the Nucleon at JLab

    NASA Astrophysics Data System (ADS)

    Avakian, Harut

    2016-08-01

    Studies of the 3D structure of the nucleon encoded in transverse momentum dependent distribution and fragmentation functions of partons and generalized parton distributions are among the key objectives of the JLab 12 GeV upgrade and the electron ion collider. Main challenges in extracting 3D partonic distributions from precision measurements of hard scattering processes include clear understanding of leading twist QCD fundamentals, higher twist effects, and also correlations of hadron production in target and current fragmentation regions. In this contribution we discuss some ongoing studies and future measurements of spin-orbit correlations at Jefferson Lab.

  13. An Efficient 3D Imaging using Structured Light Systems

    NASA Astrophysics Data System (ADS)

    Lee, Deokwoo

    Structured light 3D surface imaging has been crucial in the fields of image processing and computer vision, particularly in reconstruction, recognition and others. In this dissertation, we propose the approaches to development of an efficient 3D surface imaging system using structured light patterns including reconstruction, recognition and sampling criterion. To achieve an efficient reconstruction system, we address the problem in its many dimensions. In the first, we extract geometric 3D coordinates of an object which is illuminated by a set of concentric circular patterns and reflected to a 2D image plane. The relationship between the original and the deformed shape of the light patterns due to a surface shape provides sufficient 3D coordinates information. In the second, we consider system efficiency. The efficiency, which can be quantified by the size of data, is improved by reducing the number of circular patterns to be projected onto an object of interest. Akin to the Shannon-Nyquist Sampling Theorem, we derive the minimum number of circular patterns which sufficiently represents the target object with no considerable information loss. Specific geometric information (e.g. the highest curvature) of an object is key to deriving the minimum sampling density. In the third, the object, represented using the minimum number of patterns, has incomplete color information (i.e. color information is given a priori along with the curves). An interpolation is carried out to complete the photometric reconstruction. The results can be approximately reconstructed because the minimum number of the patterns may not exactly reconstruct the original object. But the result does not show considerable information loss, and the performance of an approximate reconstruction is evaluated by performing recognition or classification. In an object recognition, we use facial curves which are deformed circular curves (patterns) on a target object. We simply carry out comparison between the

  14. Subtractive 3D printing of optically active diamond structures.

    PubMed

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

    2014-05-21

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

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

    PubMed

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

    2014-07-01

    A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins. PMID:25069136

  16. The 3D structure of Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Patsourakos, Spiros

    2016-07-01

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

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

    PubMed Central

    Russo, Christopher J.; Passmore, Lori A.

    2014-01-01

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

  18. 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.

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

    PubMed Central

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

    2014-01-01

    Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function. PMID:24748753

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

    PubMed

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

    2011-09-14

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

  1. 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.

  2. 3D structures of membrane proteins from genomic sequencing

    PubMed Central

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

    2012-01-01

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

  3. 3D Vegetation Structure Extraction from Lidar Remote Sensing

    NASA Astrophysics Data System (ADS)

    Ni-Meister, W.

    2006-05-01

    Vegetation structure data are critical not only for biomass estimation and global carbon cycle studies, but also for ecosystem disturbance, species habitat and ecosystem biodiversity studies. However those data are rarely available at the global scale. Multispectral passive remote sensing has shown little success on this direction. The upcoming lidar remote sensing technology shows a great potential to measure vegetation vertical structure data globally. In this study, we present and test a Bayesian Stochastic Inversion (BSI) approach to invert a full canopy Geometric Optical and Radiative Transfer (GORT) model to retrieve 3-D vegetation structure parameters from large footprint (15m-25m diameter) vegetation lidar data. BSI approach allows us to take into account lidar-directly derived structure parameters, such as tree height and the upper and lower bounds of crown height and their uncertainties as the prior knowledge in the inversion. It provides not only the optimal estimates of model parameters, but also their uncertainties. We first assess the accuracy of vegetation structure parameter retrievals from vegetation lidar data through a comprehensive GORT input parameter sensitivity analysis. We calculated the singular value decomposition (SVD) of Jacobian matrix, which contains the partial derivatives of the combined model with respect to all relevant model input parameters and. Our analysis shows that with the prior knowledge of tree height, crown depth and crown shape, lidar waveforms is most sensitive to the tree density, then to the tree size and the least to the foliage area volume density. It indicates that tree density can be retrieved with the most accuracy and then the tree size, the least is the foliage area volume density. We also test the simplified BSI approach through a synthetic experiment. The synthetic lidar waveforms were generated based the vegetation structure data obtained from the Boreal Ecosystem Atmosphere Study (BOREAS). With the exact

  4. Optical 3D-coordinate measuring system using structured light

    NASA Astrophysics Data System (ADS)

    Schreiber, Wolfgang; Notni, Gunther; Kuehmstedt, Peter; Gerber, Joerg; Kowarschik, Richard M.

    1996-09-01

    The paper is aimed at the description of an optical shape measuring technique based on a consistent principle using fringe projection technique. We demonstrate a real 3D- coordinate measuring system where the sale of coordinates is given only by the illumination-structures. This method has the advantages that the aberration of the observing system and the depth-dependent imaging scale have no influence on the measuring accuracy and, moreover, the measurements are independent of the position of the camera with respect to the object under test. Furthermore, it is shown that the influence of specular effects of the surface on the measuring result can be eliminated. Moreover, we developed a very simple algorithm to calibrate the measuring system. The measuring examples show that a measuring accuracy of 10-4 (i.e. 10 micrometers ) within an object volume of 100 X 100 X 70 mm3 is achievable. Furthermore, it is demonstrated that the set of coordinate values can be processed in CNC- and CAD-systems.

  5. Slat Cove Unsteadiness Effect of 3D Flow Structures

    NASA Technical Reports Server (NTRS)

    Choudhari, Meelan M.; Khorrami, Mehdi R.

    2006-01-01

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

  6. 3D Soil Images Structure Quantification using Relative Entropy

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  7. 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-05-20

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

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

    NASA Astrophysics Data System (ADS)

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

    2003-06-01

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

  10. 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.

  11. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    PubMed

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

    2016-05-01

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

  12. Postprocessing techniques for 3D non-linear structures

    NASA Technical Reports Server (NTRS)

    Gallagher, Richard S.

    1987-01-01

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

  13. 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.

  14. 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.

  15. 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

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

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Gheorghe, Radu; Tchouprakov, Andrei; Sokolov, Roman

    2013-02-01

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

  19. 3-D structure and dynamics of microtubule self-organization

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Ou-Yang, H. Daniel

    2008-03-01

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

  20. 3D nano-structures for laser nano-manipulation.

    PubMed

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

    2013-01-01

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

  1. 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

  2. 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.

  3. 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

  4. Low-Cost Impact Detection and Location for Automated Inspections of 3D Metallic Based Structures

    PubMed Central

    Morón, Carlos; Portilla, Marina P.; Somolinos, José A.; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  5. PROMALS3D web server for accurate multiple protein sequence and structure alignments.

    PubMed

    Pei, Jimin; Tang, Ming; Grishin, Nick V

    2008-07-01

    Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087

  6. 3D structuring of biocompatible and biodegradable polymers via stereolithography.

    PubMed

    Gill, Andrew A; Claeyssens, Frederik

    2011-01-01

    The production of user-defined 3D microstructures from biocompatible and biodegradable materials via free-form fabrication is an important step to create off-the-shelf technologies to be used as tissue engineering scaffolds. One method of achieving this is the microstereolithography of block copolymers, allowing high resolution microstructuring of materials with tuneable physical properties. A versatile protocol for the production and photofunctionalisation of pre-polymers for microstereolithography is presented along with a discussion of the possible microstereolithography set-ups and previous work in the field.

  7. Multi Length Scale Imaging of Flocculated Estuarine Sediments; Insights into their Complex 3D Structure

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    Suspended estuarine sediments form flocs that are compositionally complex, fragile and irregularly shaped. The fate and transport of suspended particulate matter (SPM) is determined by the size, shape, density, porosity and stability of these flocs and prediction of SPM transport requires accurate measurements of these three-dimensional (3D) physical properties. However, the multi-scaled nature of flocs in addition to their fragility makes their characterisation in 3D problematic. Correlative microscopy is a strategy involving the spatial registration of information collected at different scales using several imaging modalities. Previously, conventional optical microscopy (COM) and transmission electron microscopy (TEM) have enabled 2-dimensional (2D) floc characterisation at the gross (> 1 µm) and sub-micron scales respectively. Whilst this has proven insightful there remains a critical spatial and dimensional gap preventing the accurate measurement of geometric properties and an understanding of how structures at different scales are related. Within life sciences volumetric imaging techniques such as 3D micro-computed tomography (3D µCT) and focused ion beam scanning electron microscopy [FIB-SEM (or FIB-tomography)] have been combined to characterise materials at the centimetre to micron scale. Combining these techniques with TEM enables an advanced correlative study, allowing material properties across multiple spatial and dimensional scales to be visualised. The aims of this study are; 1) to formulate an advanced correlative imaging strategy combining 3D µCT, FIB-tomography and TEM; 2) to acquire 3D datasets; 3) to produce a model allowing their co-visualisation; 4) to interpret 3D floc structure. To reduce the chance of structural alterations during analysis samples were first 'fixed' in 2.5% glutaraldehyde/2% formaldehyde before being embedding in Durcupan resin. Intermediate steps were implemented to improve contrast and remove pore water, achieved by the

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

    Rezania, Vahid; Tuszynski, Jack

    2016-01-01

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

  10. 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.

  11. 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

  12. 3s- and 3p-core level excitations in 3d-transition metal oxides from electron-energy-loss spectroscopy

    NASA Astrophysics Data System (ADS)

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

    1995-03-01

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

  13. 3D Printing: 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles (Adv. Mater. 19/2016).

    PubMed

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

    2016-05-01

    On page 3712, E. Fantino, A. Chiappone, and co-workers fabricate conductive 3D hybrid structures by coupling the photo-reduction of metal precursors with 3D printing technology. The generated structures consist of metal nanoparticles embedded in a polymer matrix shaped into complex multilayered architectures. 3D conductive structures are fabricated with a digital light-processing printer incorporating silver salt into photocurable formulations. PMID:27167030

  14. 3D Printing: 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles (Adv. Mater. 19/2016).

    PubMed

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

    2016-05-01

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

  15. Use of laser 3D surface digitizer in data collection and 3D modeling of anatomical structures

    NASA Astrophysics Data System (ADS)

    Tse, Kelly; Van Der Wall, Hans; Vu, Dzung H.

    2006-02-01

    A laser digitizer (Konica-Minolta Vivid 910) is used to obtain 3-dimensional surface scans of anatomical structures with a maximum resolution of 0.1mm. Placing the specimen on a turntable allows multiple scans allaround because the scanner only captures data from the portion facing its lens. A computer model is generated using 3D modeling software such as Geomagic. The 3D model can be manipulated on screen for repeated analysis of anatomical features, a useful capability when the specimens are rare or inaccessible (museum collection, fossils, imprints in rock formation.). As accurate measurements can be performed on the computer model, instead of taking measurements on actual specimens only at the archeological excavation site e.g., a variety of quantitative data can be later obtained on the computer model in the laboratory as new ideas come to mind. Our group had used a mechanical contact digitizer (Microscribe) for this purpose, but with the surface digitizer, we have been obtaining data sets more accurately and more quickly.

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

    PubMed

    Guo, Fei; Jiang, Wen

    2014-01-01

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

  17. 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

  18. Nano-Structural Elucidation in Carbon Black Loaded NR Vulcanizate by 3D-TEM and In Situ WAXD Measurements

    SciTech Connect

    Ikeda,Y.; Kato, A.; Shimanuki, J.; Kohjiya, S.; Tosaka, M.; Poompradub, S.; Toki, S.; Hsiao, B.

    2007-01-01

    Three dimensional (3D) visualization of nanometer structure of carbon black dispersion in rubbery matrix has successfully been studied and reported in this paper. Use of 3D-TEM, which is computerized tomography combined with transmission electron microscopy (TEM), enabled us to reconstruct 3D images of carbon black aggregates in natural rubber (NR) matrix. The TEM measurements were conducted by a bright-field method on thin samples without any electron staining. The sample was subject to uni-axial tilting (+65 degree to -65 degree with 2 degree increment) in the sample chamber, and 66 TEM images were taken on each sample. These TEM images were used for computerized tomography to reconstruct the 3D image. This technique is designated as 3D-TEM. The nano-structural features observed by 3D-TEM were in conformity with the electron-conductivity results, and the percolation behavior was recognized. These results were further supplemented by in situ wide-angle X-ray diffraction (WAXD), i.e., simultaneous WAXD and tensile measurements on the sample to observe the strain-induced crystallization in NR vulcanizate. Upon tensile elongation, the crystallization was clearly observed in WAXD in the presence of carbon black, and it contributed to the tensile properties. In order to understand the performances of filled NR vulcanizates, it surely is necessary to know the structural states of the mixed nano-filler and the crystallites produced upon elongation.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  20. 3D imaging and quantitative analysis of small solubilized membrane proteins and their complexes by transmission electron microscopy.

    PubMed

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

    2013-02-01

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

  1. Multiple 3D RNA Structure Superposition Using Neighbor Joining.

    PubMed

    Hoksza, David; Svozil, Daniel

    2015-01-01

    Recent advances in RNA research and the steady growth of available RNA structures call for bioinformatics methods for handling and analyzing RNA structural data. Recently, we introduced SETTER-a fast and accurate method for RNA pairwise structure alignment. In this paper, we describe MultiSETTER, SETTER extension for multiple RNA structure alignment. MultiSETTER combines SETTER's decomposition of RNA structures into non-overlapping structural subunits with the multiple sequence alignment algorithm ClustalW adapted for the structure alignment. The accuracy of MultiSETTER was assessed by the automatic classification of RNA structures and its comparison to SCOR annotations. In addition, MultiSETTER classification was also compared to multiple sequence alignment-based and secondary structure alignment-based classifications provided by LocARNA and RNADistance tools, respectively. MultiSETTER precompiled Windows libraries, as well as the C++ source code, are freely available from http://siret.cz/multisetter.

  2. A procedure to average 3D anatomical structures.

    PubMed

    Subramanya, K; Dean, D

    2000-12-01

    Creating a feature-preserving average of three dimensional anatomical surfaces extracted from volume image data is a complex task. Unlike individual images, averages present right-left symmetry and smooth surfaces which give insight into typical proportions. Averaging multiple biological surface images requires careful superimposition and sampling of homologous regions. Our approach to biological surface image averaging grows out of a wireframe surface tessellation approach by Cutting et al. (1993). The surface delineating wires represent high curvature crestlines. By adding tile boundaries in flatter areas the 3D image surface is parametrized into anatomically labeled (homology mapped) grids. We extend the Cutting et al. wireframe approach by encoding the entire surface as a series of B-spline space curves. The crestline averaging algorithm developed by Cutting et al. may then be used for the entire surface. Shape preserving averaging of multiple surfaces requires careful positioning of homologous surface regions such as these B-spline space curves. We test the precision of this new procedure and its ability to appropriately position groups of surfaces in order to produce a shape-preserving average. Our result provides an average that well represents the source images and may be useful clinically as a deformable model or for animation.

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

    PubMed

    Nelson, A C

    1986-01-01

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

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

    PubMed

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

    2015-09-01

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

  5. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    PubMed

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

    2016-05-01

    Coupling the photoreduction of a metal precursor with 3D-printing technology is shown to allow the fabrication of conductive 3D hybrid structures consisting of metal nanoparticles and organic polymers shaped in complex multilayered architectures. 3D conductive structures are fabricated incorporating silver nitrate into a photocurable oligomer in the presence of suitable photoinitiators and exposing them to a digital light system. PMID:26992060

  6. 3D Modeling of Branching Structures for Anatomical Instruction

    PubMed Central

    Mattingly, William A.; Chariker, Julia H.; Paris, Richard; Chang, Dar-jen; Pani, John R.

    2015-01-01

    Branching tubular structures are prevalent in many different organic and synthetic settings. From trees and vegetation in nature, to vascular structures throughout human and animal biology, these structures are always candidates for new methods of graphical and visual expression. We present a modeling tool for the creation and interactive modification of these structures. Parameters such as thickness and position of branching structures can be modified, while geometric constraints ensure that the resulting mesh will have an accurate anatomical structure by not having inconsistent geometry. We apply this method to the creation of accurate representations of the different types of retinal cells in the human eye. This method allows a user to quickly produce anatomically accurate structures with low polygon counts that are suitable for rendering at interactive rates on commodity computers and mobile devices. PMID:27087764

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

    PubMed

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

    2014-09-10

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

  8. 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

  9. 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.

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

    PubMed

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

    2016-07-01

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

  11. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and 3-dimensional structural information

    PubMed Central

    Pei, Jimin; Grishin, Nick V.

    2015-01-01

    SUMMARY Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of 3-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408

  12. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

    PubMed

    Pei, Jimin; Grishin, Nick V

    2014-01-01

    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408

  13. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

    PubMed

    Pei, Jimin; Grishin, Nick V

    2014-01-01

    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D.

  14. 3D imaging of the early embryonic chicken heart with focused ion beam scanning electron microscopy.

    PubMed

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

    2014-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-02-01

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

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Huang, T. S.

    1982-01-01

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

  18. The 3D Structure of the Galactic Bulge

    NASA Astrophysics Data System (ADS)

    Zoccali, Manuela; Valenti, Elena

    2016-06-01

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

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

    PubMed Central

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

    2002-01-01

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

  20. 3D structure determination of protein using TEM single particle analysis.

    PubMed

    Sato, Chikara; Mio, Kazuhiro; Kawata, Masaaki; Ogura, Toshihiko

    2014-11-01

    Proteins play important roles in cell functions such as enzymes, cell trafficking, neurotransmission, muscle contraction and hormone secretion. However, some proteins are very difficult to be crystallized and their structures are undetermined. Several techniques have been developed to elucidate the structure of macromolecules; X-ray or electron crystallography, nuclear magnetic resonance spectroscopy, and high-resolution electron microscopy. Among them, electron microscopy based single particle reconstruction (SPA) technique is a computer-aided structure determination method. This method reconstructs the 3D structure from projection images of dispersed protein. A large number of two-dimensional particle images are picked up from EM films, aligned and classified to generate 2D averages, and used to reconstruct the 3D structure by assigning the Euler angle of each 2D average. Due to the necessity of elaborate collaboration between the classical biology and the innovative information technology including parallel computing, scientists needed to break unseen barriers to get a start of this analysis. However, recent progresses in electron microscopes, mathematical algorithms, and computational abilities greatly reduced the height of barriers and expanded targets that are considered to be primarily addressable using single particle analysis. Membrane proteins are one of these targets to which the single particle analysis is successfully applied for the understanding of their 3D structures. For this purpose, we have developed various SPA methods [1-5] and applied them to different proteins [6-8].Here, we introduce reconstructed proteins, and discuss the availability of this technique. The intramembrane-cleaving proteases (I-CLiPs) that sever the transmembrane domains of their substrates have been identified in a range of organisms and play a variety of roles in biological conditions. I-CLiPs have been classified into three groups: serine-, aspartyl- and metalloprotease

  1. 3-D Structure of Molecules of Biological Significance

    ERIC Educational Resources Information Center

    Bennett, Alice S.; Schwenk, Karl

    1974-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  4. 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.

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

    PubMed Central

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

    2010-01-01

    There have been steady improvements in protein structure prediction during the past 2 decades. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. First, a systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein. Then, an efficient process was applied for iterative coarse-grain model generation and evaluation at the Cα or backbone level. In this process, we construct models using interresidue spatial restraints derived from alignments by multidimensional scaling, evaluate and select models through clustering and static scoring functions, and iteratively improve the selected models by integrating spatial restraints and previous models. Finally, the full-atom models were evaluated using molecular dynamics simulations based on structural changes under simulated heating. We have continuously improved the performance of MUFOLD by using a benchmark of 200 proteins from the Astral database, where no template with >25% sequence identity to any target protein is included. The average root-mean-square deviation of the best models from the native structures is 4.28 Å, which shows significant and systematic improvement over our previous methods. The computing time of MUFOLD is much shorter than many other tools, such as Rosetta. MUFOLD demonstrated some success in the 2008 community-wide experiment for protein structure prediction CASP8. PMID:19927325

  6. 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

  7. 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

  8. 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.

  9. Nanoimprint of a 3D structure on an optical fiber for light wavefront manipulation

    NASA Astrophysics Data System (ADS)

    Calafiore, Giuseppe; Koshelev, Alexander; Allen, Frances I.; Dhuey, Scott; Sassolini, Simone; Wong, Edward; Lum, Paul; Munechika, Keiko; Cabrini, Stefano

    2016-09-01

    Integration of complex photonic structures onto optical fiber facets enables powerful platforms with unprecedented optical functionalities. Conventional nanofabrication technologies, however, do not permit viable integration of complex photonic devices onto optical fibers owing to their low throughput and high cost. In this paper we report the fabrication of a three-dimensional structure achieved by direct nanoimprint lithography on the facet of an optical fiber. Nanoimprint processes and tools were specifically developed to enable a high lithographic accuracy and coaxial alignment of the optical device with respect to the fiber core. To demonstrate the capability of this new approach, a 3D beam splitter has been designed, imprinted and optically characterized. Scanning electron microscopy and optical measurements confirmed the good lithographic capabilities of the proposed approach as well as the desired optical performance of the imprinted structure. The inexpensive solution presented here should enable advancements in areas such as integrated optics and sensing, achieving enhanced portability and versatility of fiber optic components.

  10. Nanoimprint of a 3D structure on an optical fiber for light wavefront manipulation.

    PubMed

    Calafiore, Giuseppe; Koshelev, Alexander; Allen, Frances I; Dhuey, Scott; Sassolini, Simone; Wong, Edward; Lum, Paul; Munechika, Keiko; Cabrini, Stefano

    2016-09-16

    Integration of complex photonic structures onto optical fiber facets enables powerful platforms with unprecedented optical functionalities. Conventional nanofabrication technologies, however, do not permit viable integration of complex photonic devices onto optical fibers owing to their low throughput and high cost. In this paper we report the fabrication of a three-dimensional structure achieved by direct nanoimprint lithography on the facet of an optical fiber. Nanoimprint processes and tools were specifically developed to enable a high lithographic accuracy and coaxial alignment of the optical device with respect to the fiber core. To demonstrate the capability of this new approach, a 3D beam splitter has been designed, imprinted and optically characterized. Scanning electron microscopy and optical measurements confirmed the good lithographic capabilities of the proposed approach as well as the desired optical performance of the imprinted structure. The inexpensive solution presented here should enable advancements in areas such as integrated optics and sensing, achieving enhanced portability and versatility of fiber optic components.

  11. Delineation of nuclear structures in 3D multicellular systems

    SciTech Connect

    2013-09-13

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  13. Imaging solar coronal magnetic structures in 3D

    NASA Astrophysics Data System (ADS)

    Cartledge, N. P.

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

  14. Designing self-assembling 3D structures of microcapsules

    NASA Astrophysics Data System (ADS)

    Li, Like; Shum, Henry; Shklyaev, Oleg; Yashin, Victor; Balazs, Anna

    Self-assembly of complex, three-dimensional structures is commonly achieved by biological cells but difficult to realize in synthetic systems with micron-scale or larger components. Some previous modeling studies have considered only the planar self-assembly of microcapsules on a substrate. In this work, nanoparticles released from the capsules bind to the substrate and to the shells of nearby capsules. The non-uniform nanoparticle deposition on a capsule's surface leads to adhesion gradients, which drive the capsules to effectively ``climb'' on top of one another and self-organize in the vertical direction. We determine conditions that favor this structural organization. In particular, we study how the vertical structuring depends on the background fluid flow, the topography of the microcapsules and the underlying surface, the capsule-capsule interaction and that between the capsules and the substrate. The findings can provide design rules for the autonomous creation of novel nanocomposites, where the layers are formed from nanoparticle-containing and nanoparticle-decorated microcapsules.

  15. 3D Printing for Spacecraft Multi-Functional Structures

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    1999-11-22

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

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

    PubMed Central

    Wang, Jianwei; Zhang, Yong

    2016-01-01

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

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

    PubMed

    Wang, Jianwei; Zhang, Yong

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Wang, Jianwei; Zhang, Yong

    2016-04-01

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

  20. 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

  1. 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.

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

    PubMed

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

    2015-05-08

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  5. 3d Modeling of cultural heritage objects with a structured light system.

    NASA Astrophysics Data System (ADS)

    Akca, Devrim

    3D modeling of cultural heritage objects is an expanding application area. The selection of the right technology is very important and strictly related to the project requirements, budget and user's experience. The triangulation based active sensors, e.g. structured light systems are used for many kinds of 3D object reconstruction tasks and in particular for 3D recording of cultural heritage objects. This study presents the experiences in the results of two such projects in which a close-range structured light system is used for the 3D digitization. The paper includes the essential steps of the 3D object modeling pipeline, i.e. digitization, registration, surface triangulation, editing, texture mapping and visualization. The capabilities of the used hardware and software are addressed. Particular emphasis is given to a coded structured light system as an option for data acquisition.

  6. 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.

  7. 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.

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

    PubMed

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

    2015-08-26

    3D printing of metallic microarchitectures with controlled internal structures is realized at room temperature in ambient air conditions by the manipulation of metal ion concentration and pulsed electric potentials in the electrolyte meniscus during the meniscus-guided electrodeposition. Precise control of the printing nozzle enables the drawing of complex 3D microarchitectures with well-defined geometries and positions. PMID:25917532

  9. Formation of 3D structures in a volumetric photocurable material via a holographic method

    NASA Astrophysics Data System (ADS)

    Vorzobova, N. D.; Bulgakova, V. G.; Veselov, V. O.

    2015-12-01

    The principle of forming 3D polymer structures is considered, based on the display of the 3D intensity distribution of radiation formed by a hologram in the bulk of a photocurable material. The conditions are determined for limiting the cure depth and reproducing the projected wavefront configuration.

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

    NASA Technical Reports Server (NTRS)

    Riggs, H. R.

    2000-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Allen, R.

    2003-04-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets. PMID:26824922

  14. X-Ray Nanofocus CT: Visualising Of Internal 3D-Structures With Submicrometer Resolution

    NASA Astrophysics Data System (ADS)

    Weinekoetter, Christian

    2008-09-01

    High-resolution X-ray Computed Tomography (CT) allows the visualization and failure analysis of the internal micro structure of objects—even if they have complicated 3D-structures where 2D X-ray microscopy would give unclear information. During the past several years, computed tomography has progressed to higher resolution and quicker reconstruction of the 3D-volume. Most recently it even allows a three-dimensional look into the inside of materials with submicron resolution. With the use of nanofocus® tube technology, nanoCT®-systems are pushing forward into application fields that were exclusive to high cost and rare available synchrotron techniques. The study was performed with the new nanotom, a very compact laboratory system which allows the analysis of samples up to 120 mm in diameter and weighing up to 1 kg with exceptional voxel-resolution down to <500 nm (<0.5 microns). It is the first 180 kV nanofocus® computed tomography system in the world which is tailored specifically to the highest-resolution applications in the fields of material science, micro electronics, geology and biology. Therefore it is particularly suitable for nanoCT-examinations e.g. of synthetic materials, metals, ceramics, composite materials, mineral and organic samples. There are a few physical effects influencing the CT quality, such as beam-hardening within the sample or ring-artefacts, which can not be completely avoided. To optimize the quality of high resolution 3D volumes, the nanotom® includes a variety of effective software tools to reduce ring-artefacts and correct beam hardenings or drift effects which occurred during data acquisition. The resulting CT volume data set can be displayed in various ways, for example by virtual slicing and sectional views in any direction of the volume. By the fact that this requires only a mouse click, this technique will substitute destructive mechanical slicing and cutting in many applications. The initial CT results obtained with the

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

    NASA Astrophysics Data System (ADS)

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

    1997-11-01

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

  16. 3D lidar imaging for detecting and understanding plant responses and canopy structure.

    PubMed

    Omasa, Kenji; Hosoi, Fumiki; Konishi, Atsumi

    2007-01-01

    Understanding and diagnosing plant responses to stress will benefit greatly from three-dimensional (3D) measurement and analysis of plant properties because plant responses are strongly related to their 3D structures. Light detection and ranging (lidar) has recently emerged as a powerful tool for direct 3D measurement of plant structure. Here the use of 3D lidar imaging to estimate plant properties such as canopy height, canopy structure, carbon stock, and species is demonstrated, and plant growth and shape responses are assessed by reviewing the development of lidar systems and their applications from the leaf level to canopy remote sensing. In addition, the recent creation of accurate 3D lidar images combined with natural colour, chlorophyll fluorescence, photochemical reflectance index, and leaf temperature images is demonstrated, thereby providing information on responses of pigments, photosynthesis, transpiration, stomatal opening, and shape to environmental stresses; these data can be integrated with 3D images of the plants using computer graphics techniques. Future lidar applications that provide more accurate dynamic estimation of various plant properties should improve our understanding of plant responses to stress and of interactions between plants and their environment. Moreover, combining 3D lidar with other passive and active imaging techniques will potentially improve the accuracy of airborne and satellite remote sensing, and make it possible to analyse 3D information on ecophysiological responses and levels of various substances in agricultural and ecological applications and in observations of the global biosphere. PMID:17030540

  17. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  18. 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

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  20. Sensitivity of an MT Array to 3D Structure Outside the Array Footprint

    NASA Astrophysics Data System (ADS)

    Booker, J. R.; Mackie, R. L.; Burd, A. I.; Pomposiello, M. C.; Favetto, A. B.

    2015-12-01

    Standard data collection strategy in magnetotellurics (MT) is to deploy a profile or array of sites that spans the target of interest. There is no expectation that structure can be imaged outside the area covered by sites. We have inverted two MT arrays for 3D structure under Argentina. The two arrays do not overlap, but serendipitously the 3D model for the northern array overlaps the position of a prominent 3D deep conductive structure seen in the inversion of the southern array. To our surprise this deep southern feature is also imaged by the northern array even though it is well outside the footprint of the northern array. It therefore appears that typical intuition about one's ability to image structure outside the span of the sites is not always true. We present model studies to demonstrate why this is so and under what conditions one can expect a 3D array to be capable of imaging structure outside the array.

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

    PubMed

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

    2012-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  3. 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.

  4. 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.

  5. Mu-Synthesis robust control of 3D bar structure vibration using piezo-stack actuators

    NASA Astrophysics Data System (ADS)

    Mystkowski, Arkadiusz; Koszewnik, Andrzej Piotr

    2016-10-01

    This paper presents an idea for the Mu-Synthesis robust control of 3D bar structure vibration with using a piezo-stack actuators. A model of the 3D bar structure with uncertain parameters is presented as multi-input multi-output (MIMO) dynamics. Nominal stability and nominal performances of the open-loop 3D bar structure dynamic model is developed. The uncertain model-based robust controller is derived due to voltage control signal saturation and selected parameter perturbations. The robust control performances and robustness of the system due to uncertainties influence is evaluated by using singular values and a small gain theorem. Finally, simulation investigations and experimental results shown that system response of the 3D bar structure dynamic model with taken into account perturbed parameters met desired robust stability and system limits. The proposed robust controller ensures a good dynamics of the closed-loop system, robustness, and vibration attenuation.

  6. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    ERIC Educational Resources Information Center

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

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

  8. Design of novel 3D gene activated PEG scaffolds with ordered pore structure.

    PubMed

    Orsi, Silvia; Guarnieri, Daniela; Netti, Paolo A

    2010-03-01

    The ability to genetically modify cells seeded inside synthetic hydrogel scaffolds offers a suitable approach to induce and control tissue repair and regeneration guiding cell fate. In fact the transfected cells can act as local in vivo bioreactor, secreting plasmid encoded proteins that augment tissue regeneration processes. We have realized a DNA bioactivated high porous poly(ethylene glycol) (PEG) matrix by polyethyleneimine (PEI)/DNA complexes adsorption. As the design of the microarchitectural features of a scaffold also contributes to promote and influence cell fate, we appropriately designed the inner structure of gene activated PEG hydrogels by gelatine microparticles templating. Microarchitectural properties of the scaffold were analysed by scanning electron microscopy. 3D cell migration and transfection were monitored through time-lapse videomicroscopy and confocal laser scanning microscopy.

  9. 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

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Nuroh, K.

    2008-12-01

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

  13. 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

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

    SciTech Connect

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

    2004-04-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  16. 3D Plant cell architecture of Arabidopsis thaliana (Brassicaceae) using focused ion beam–scanning electron microscopy1

    PubMed Central

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

    2014-01-01

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

  17. 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

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

    PubMed

    Franzini-Armstrong, Clara

    2015-01-01

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

  19. 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.

  20. 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

  1. 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.

  2. 3-D wave propagation solution of a stable resonator, free-electron laser

    NASA Astrophysics Data System (ADS)

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

    1983-11-01

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

  3. 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

  4. 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

  5. 3D-Mapping of Dolomitized Structures in Lower Cambrian Phosphorites

    NASA Astrophysics Data System (ADS)

    Hippler, Dorothee; Stammeier, Jessica A.; Brunner, Roland; Rosc, Jördis; Franz, Gerhard; Dietzel, Martin

    2016-04-01

    Dolomitization is a widespread phenomenon in ancient sedimentary rocks, particularly close to the Precambrian-Cambrian boundary. Dolomite can form in synsedimentary or hydrothermal environments, preferentially via the replacement of solid carbonate precursor phases. Synsedimentary dolomite formation is often associated with microbial activity, such as bacterial sulfate reduction or methanogenesis. In this study, we investigate dolomitic phosphorites from the Lowermost Cambrian Tal Group, Mussoori Syncline, Lesser Himalaya, India, using micro-CT 3D-mapping, in order to unravel the complex diagenetic history of the rocks. The selected sample shows alternating layering of phosphatic mudstones and sparitic dolostone, in which brecciated layers of phosphorite or phosphatic mudstones are immersed in a dolomite-rich matrix. Lamination occurs on a sub-millimetre scale, with lamination sometimes wavy to crinkly. This fabric is interpreted as former microbial mats, providing the environment for early diagenetic phosphatization. Preliminary electron backscatter imaging with scanning microscopy revealed that dolomite crystals often occur in spherical to ellipsoidal structures, typically with a high porosity. This dolomite is associated with botryoidal apatite, organic matter and small amounts of calcite. Micro-CT 3D-mappings reveal that dolomite structures are cigar-shaped, elongated and up to 600 μm long. They are further arranged in a Mikado-like oriented framework spanning a layer thickness of a few millimetres. Analyses of ambient pore space, with similar elongated outlines and filled with organic matter, suggest a potential coherence of ambient pore space and shape of the dolomite structures. Allowing for other associated mineral phases, such as pyrite and silicates, and their spatial distribution, the present approach can be used to unravel distinct diagenetic reaction pathways, and might thus constrain the proxy potential of these Lower Cambrian dolomitic phosphorites

  6. Self-Discovery of Structural Geology Concepts using Interactive 3D Visualization

    NASA Astrophysics Data System (ADS)

    Billen, M. I.; Saunders, J.

    2010-12-01

    Mastering structural geology concepts that depend on understanding three-dimensional (3D) geometries and imagining relationships among unseen subsurface structures are fundamental skills for geologists. Traditionally these skills are developed first, through use of 2D drawings of 3D structures that can be difficult to decipher or 3D physical block models that show only a limited set of relationships on the surfaces of the blocks, followed by application and testing of concepts in field settings. We hypothesize that this learning process can be improved by providing repeated opportunities to evaluate and explore synthetic 3D structures using interactive 3D visualization software. We present laboratory modules designed for undergraduate structural geology curriculum using a self-discovery approach to teach concepts such as: the Rule of V’s, structure separation versus fault slip, and the more general dependence of structural exposure on surface topography. The laboratory modules are structured to allow students to discover and articulate each concept from observations of synthetic data both on traditional maps and using the volume visualization software 3DVisualizer. Modules lead students through exploration of data (e.g., a dipping layered structure exposed in ridge-valley topography or obliquely offset across a fault) by allowing them to interactively view (rotate, pan, zoom) the exposure of structures on topographic surfaces and to toggle on/off the full 3D structure as a transparent colored volume. This tool allows student to easily visually understand the relationships between, for example a dipping structure and its exposure on valley walls, as well as how the structure extends beneath the surface. Using this method gives students more opportunities to build a mental library of previously-seen relationships from which to draw-on when applying concepts in the field setting. These laboratory modules, the data and software are freely available from KeckCAVES.

  7. Vascular Structure Identification in Intraoperative 3D Contrast-Enhanced Ultrasound Data.

    PubMed

    Ilunga-Mbuyamba, Elisee; Avina-Cervantes, Juan Gabriel; Lindner, Dirk; Cruz-Aceves, Ivan; Arlt, Felix; Chalopin, Claire

    2016-04-08

    In this paper, a method of vascular structure identification in intraoperative 3D Contrast-Enhanced Ultrasound (CEUS) data is presented. Ultrasound imaging is commonly used in brain tumor surgery to investigate in real time the current status of cerebral structures. The use of an ultrasound contrast agent enables to highlight tumor tissue, but also surrounding blood vessels. However, these structures can be used as landmarks to estimate and correct the brain shift. This work proposes an alternative method for extracting small vascular segments close to the tumor as landmark. The patient image dataset involved in brain tumor operations includes preoperative contrast T1MR (cT1MR) data and 3D intraoperative contrast enhanced ultrasound data acquired before (3D-iCEUS(start) and after (3D-iCEUS(end) tumor resection. Based on rigid registration techniques, a preselected vascular segment in cT1MR is searched in 3D-iCEUS(start) and 3D-iCEUS(end) data. The method was validated by using three similarity measures (Normalized Gradient Field, Normalized Mutual Information and Normalized Cross Correlation). Tests were performed on data obtained from ten patients overcoming a brain tumor operation and it succeeded in nine cases. Despite the small size of the vascular structures, the artifacts in the ultrasound images and the brain tissue deformations, blood vessels were successfully identified.

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

    NASA Technical Reports Server (NTRS)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

    3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.

  9. Vascular Structure Identification in Intraoperative 3D Contrast-Enhanced Ultrasound Data

    PubMed Central

    Ilunga-Mbuyamba, Elisee; Avina-Cervantes, Juan Gabriel; Lindner, Dirk; Cruz-Aceves, Ivan; Arlt, Felix; Chalopin, Claire

    2016-01-01

    In this paper, a method of vascular structure identification in intraoperative 3D Contrast-Enhanced Ultrasound (CEUS) data is presented. Ultrasound imaging is commonly used in brain tumor surgery to investigate in real time the current status of cerebral structures. The use of an ultrasound contrast agent enables to highlight tumor tissue, but also surrounding blood vessels. However, these structures can be used as landmarks to estimate and correct the brain shift. This work proposes an alternative method for extracting small vascular segments close to the tumor as landmark. The patient image dataset involved in brain tumor operations includes preoperative contrast T1MR (cT1MR) data and 3D intraoperative contrast enhanced ultrasound data acquired before (3D-iCEUSstart) and after (3D-iCEUSend) tumor resection. Based on rigid registration techniques, a preselected vascular segment in cT1MR is searched in 3D-iCEUSstart and 3D-iCEUSend data. The method was validated by using three similarity measures (Normalized Gradient Field, Normalized Mutual Information and Normalized Cross Correlation). Tests were performed on data obtained from ten patients overcoming a brain tumor operation and it succeeded in nine cases. Despite the small size of the vascular structures, the artifacts in the ultrasound images and the brain tissue deformations, blood vessels were successfully identified. PMID:27070610

  10. 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.

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

    DOE PAGES

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

    2015-03-18

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

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

    NASA Astrophysics Data System (ADS)

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

    1990-05-01

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

  13. Laser fabrication of 2D and 3D metal nanoparticle structures and arrays.

    PubMed

    Kuznetsov, A I; Kiyan, R; Chichkov, B N

    2010-09-27

    A novel method for fabrication of 2D and 3D metal nanoparticle structures and arrays is proposed. This technique is based on laser-induced transfer of molten metal nanodroplets from thin metal films. Metal nanoparticles are produced by solidification of these nanodroplets. The size of the transferred nanoparticles can be controllably changed in the range from 180 nm to 1500 nm. Several examples of complex 2D and 3D microstructures generated form gold nanoparticles are demonstrated. PMID:20941016

  14. Low-resolution characterization of the 3D structure of the Euglena gracilis photoreceptor

    SciTech Connect

    Barsanti, Laura; Coltelli, Primo; Evangelista, Valtere; Passarelli, Vincenzo; Frassanito, Anna Maria; Vesentini, Nicoletta; Gualtieri, Paolo

    2008-10-24

    This paper deals with the first characterization of the structure of the photoreceptive organelle of the unicellular alga Euglena gracilis (Euglenophyta). This organelle has a three-dimensional organization consisting of up to 50 closely stacked membrane lamellae. Ionically induced unstacking of the photoreceptor lamellae revealed ordered arrays well suited to structural analysis by electron microscopy and image analysis, which ultimately yielded a low-resolution picture of the structure. Each lamella is formed by the photoreceptive membrane protein of the cell assembled within the membrane layer in a hexagonal lattice. The first order diffraction spots in the calculated Fourier transform reveals the presence of 6-fold symmetrized topography (better resolution about 90 A). The 2D and 3D structural data are very similar with those recently published on proteorodopsin, a membrane protein used by marine bacterio-plankton as light-driven proton pump. In our opinion these similarity indicate that a photoreceptive protein belonging to the same superfamily of proteorodopsin could form the Euglena photoreceptor.

  15. Air-structured optical fibre drawn from a 3D-printed preform

    NASA Astrophysics Data System (ADS)

    Cook, Kevin; Leon-Saval, Sergio; Canning, John; Reid, Zane; Hossain, Md. Arafat; Peng, Gang-Ding

    2015-09-01

    We report the first optical fibre drawn from a 3D-printed preform. An air-structured polymer preform is printed using a modified butadiene plastic called Bendlay as opposed to the more-common Acrylonitrile Butadiene Styrene (ABS). The preform is subsequently drawn to fibre form at a relatively low temperature of 160 °C and maintains its air-structured cladding holes. Such ability to freely-design and 3D-print complex preform structures, such as photonic bandgap and photonic crystal structures, opens up an exciting new front in optical fibre fabrication.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  17. Tailored complex 3D vortex lattice structures by perturbed multiples of three-plane waves.

    PubMed

    Xavier, Jolly; Vyas, Sunil; Senthilkumaran, Paramasivam; Joseph, Joby

    2012-04-20

    As three-plane waves are the minimum number required for the formation of vortex-embedded lattice structures by plane wave interference, we present our experimental investigation on the formation of complex 3D photonic vortex lattice structures by a designed superposition of multiples of phase-engineered three-plane waves. The unfolding of the generated complex photonic lattice structures with higher order helical phase is realized by perturbing the superposition of a relatively phase-encoded, axially equidistant multiple of three noncoplanar plane waves. Through a programmable spatial light modulator assisted single step fabrication approach, the unfolded 3D vortex lattice structures are experimentally realized, well matched to our computer simulations. The formation of higher order intertwined helices embedded in these 3D spiraling vortex lattice structures by the superposition of the multiples of phase-engineered three-plane waves interference is also studied.

  18. Single cell detection using 3D magnetic rolled-up structures.

    PubMed

    Ger, Tzong-Rong; Huang, Hao-Ting; Huang, Chen-Yu; Lai, Mei-Feng

    2013-11-01

    A 3D rolled-up structure made of a SiO2 layer and a fishbone-like magnetic thin film was proposed here as a biosensor. The magnetoresistance (MR) measurement results of the sensor suggest that the presence of the stray field, which is induced by the magnetic nanoparticles, significantly increased the switching field. Comparing the performance of the 2D sensor and 3D sensor designed in this study, the response in switching field variation was 12.14% in the 2D sensor and 62.55% in the 3D sensor. The response in MR ratio variation was 4.55% in the 2D sensor and 82.32% in the 3D sensor. In addition, the design of the 3D sensor structure also helped to attract and trap a single magnetic cell due to its stronger stray field compared with the 2D structure. The 3D magnetic biosensor designed here can provide important information for future biochip research and applications.

  19. Stereomicroscopic 3D-pattern profiling of murine and human intestinal inflammation reveals unique structural phenotypes

    PubMed Central

    Rodriguez-Palacios, Alex; Kodani, Tomohiro; Kaydo, Lindsey; Pietropaoli, Davide; Corridoni, Daniele; Howell, Scott; Katz, Jeffry; Xin, Wei; Pizarro, Theresa T.; Cominelli, Fabio

    2015-01-01

    Histology is fundamental to assess two-dimensional intestinal inflammation; however, inflammatory bowel diseases (IBDs) are often indistinguishable microscopically on the basis of mucosal biopsies. Here, we use stereomicroscopy (SM) to rapidly profile the entire intestinal topography and assess inflammation. We examine the mucosal surface of >700 mice (encompassing >16 strains and various IBD-models), create a profiling catalogue of 3D-stereomicroscopic abnormalities and demonstrate that mice with comparable histological scores display unique sub-clusters of 3D-structure-patterns of IBD pathology, which we call 3D-stereoenterotypes, and which are otherwise indiscernible histologically. We show that two ileal IBD-stereoenterotypes (‘cobblestones' versus ‘villous mini-aggregation') cluster separately within two distinct mouse lines of spontaneous ileitis, suggesting that host genetics drive unique and divergent inflammatory 3D-structural patterns in the gut. In humans, stereomicroscopy reveals ‘liquefaction' lesions and hierarchical fistulous complexes, enriched with clostridia/segmented filamentous bacteria, running under healthy mucosa in Crohn's disease. We suggest that stereomicroscopic (3D-SMAPgut) profiling can be easily implemented and enable the comprehensive study of inflammatory 3D structures, genetics and flora in IBD. PMID:26154811

  20. Gene3D: structural assignments for the biologist and bioinformaticist alike

    PubMed Central

    Buchan, Daniel W. A.; Rison, Stuart C. G.; Bray, James E.; Lee, David; Pearl, Frances; Thornton, Janet M.; Orengo, Christine A.

    2003-01-01

    The Gene3D database (http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/) provides structural assignments for genes within complete genomes. These are available via the internet from either the World Wide Web or FTP. Assignments are made using PSI-BLAST and subsequently processed using the DRange protocol. The DRange protocol is an empirically benchmarked method for assessing the validity of structural assignments made using sequence searching methods where appropriate assignment statistics are collected and made available. Gene3D links assignments to their appropriate entries in relevent structural and classification resources (PDBsum, CATH database and the Dictionary of Homologous Superfamilies). Release 2.0 of Gene3D includes 62 genomes, 2 eukaryotes, 10 archaea and 40 bacteria. Currently, structural assignments can be made for between 30 and 40 percent of any given genome. In any genome, around half of those genes assigned a structural domain are assigned a single domain and the other half of the genes are assigned multiple structural domains. Gene3D is linked to the CATH database and is updated with each new update of CATH. PMID:12520054

  1. 3-D seismic velocity and attenuation structures in the geothermal field

    SciTech Connect

    Nugraha, Andri Dian; Syahputra, Ahmad; Fatkhan,; Sule, Rachmat

    2013-09-09

    We conducted delay time tomography to determine 3-D seismic velocity structures (Vp, Vs, and Vp/Vs ratio) using micro-seismic events in the geothermal field. The P-and S-wave arrival times of these micro-seismic events have been used as input for the tomographic inversion. Our preliminary seismic velocity results show that the subsurface condition of geothermal field can be fairly delineated the characteristic of reservoir. We then extended our understanding of the subsurface physical properties through determining of attenuation structures (Qp, Qs, and Qs/Qp ratio) using micro-seismic waveform. We combined seismic velocities and attenuation structures to get much better interpretation of the reservoir characteristic. Our preliminary attanuation structures results show reservoir characterization can be more clearly by using the 3-D attenuation model of Qp, Qs, and Qs/Qp ratio combined with 3-D seismic velocity model of Vp, Vs, and Vp/Vs ratio.

  2. Using CATH-Gene3D to Analyze the Sequence, Structure, and Function of Proteins.

    PubMed

    Sillitoe, Ian; Lewis, Tony; Orengo, Christine

    2015-01-01

    The CATH database is a classification of protein structures found in the Protein Data Bank (PDB). Protein structures are chopped into individual units of structural domains, and these domains are grouped together into superfamilies if there is sufficient evidence that they have diverged from a common ancestor during the process of evolution. A sister resource, Gene3D, extends this information by scanning sequence profiles of these CATH domain superfamilies against many millions of known proteins to identify related sequences. Thus the combined CATH-Gene3D resource provides confident predictions of the likely structural fold, domain organisation, and evolutionary relatives of these proteins. In addition, this resource incorporates annotations from a large number of external databases such as known enzyme active sites, GO molecular functions, physical interactions, and mutations. This unit details how to access and understand the information contained within the CATH-Gene3D Web pages, the downloadable data files, and the remotely accessible Web services.

  3. Estimating the complexity of 3D structural models using machine learning methods

    NASA Astrophysics Data System (ADS)

    Mejía-Herrera, Pablo; Kakurina, Maria; Royer, Jean-Jacques

    2016-04-01

    Quantifying the complexity of 3D geological structural models can play a major role in natural resources exploration surveys, for predicting environmental hazards or for forecasting fossil resources. This paper proposes a structural complexity index which can be used to help in defining the degree of effort necessary to build a 3D model for a given degree of confidence, and also to identify locations where addition efforts are required to meet a given acceptable risk of uncertainty. In this work, it is considered that the structural complexity index can be estimated using machine learning methods on raw geo-data. More precisely, the metrics for measuring the complexity can be approximated as the difficulty degree associated to the prediction of the geological objects distribution calculated based on partial information on the actual structural distribution of materials. The proposed methodology is tested on a set of 3D synthetic structural models for which the degree of effort during their building is assessed using various parameters (such as number of faults, number of part in a surface object, number of borders, ...), the rank of geological elements contained in each model, and, finally, their level of deformation (folding and faulting). The results show how the estimated complexity in a 3D model can be approximated by the quantity of partial data necessaries to simulated at a given precision the actual 3D model without error using machine learning algorithms.

  4. System for conveyor belt part picking using structured light and 3D pose estimation

    NASA Astrophysics Data System (ADS)

    Thielemann, J.; Skotheim, Ø.; Nygaard, J. O.; Vollset, T.

    2009-01-01

    Automatic picking of parts is an important challenge to solve within factory automation, because it can remove tedious manual work and save labor costs. One such application involves parts that arrive with random position and orientation on a conveyor belt. The parts should be picked off the conveyor belt and placed systematically into bins. We describe a system that consists of a structured light instrument for capturing 3D data and robust methods for aligning an input 3D template with a 3D image of the scene. The method uses general and robust pre-processing steps based on geometric primitives that allow the well-known Iterative Closest Point algorithm to converge quickly and robustly to the correct solution. The method has been demonstrated for localization of car parts with random position and orientation. We believe that the method is applicable for a wide range of industrial automation problems where precise localization of 3D objects in a scene is needed.

  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. Development of portable 3D optical measuring system using structured light projection method

    NASA Astrophysics Data System (ADS)

    Aoki, Hiroshi

    2014-05-01

    Three-dimensional (3D) scanners are becoming increasingly common in many industries. However most of these scanning technologies have drawbacks for practical use due to size, weight, accessibility, and ease-of-use. Depending on the application, speed, flexibility and portability can often be deemed more important than accuracy. We have developed a solution to address this market requirement and overcome the aforementioned limitations. To counteract shortcomings such as heavy weight and large size, an optical sensor is used that consists of a laser projector, a camera system, and a multi-touch screen. Structured laser light is projected onto the measured object with a newly designed laser projector employing a single Micro Electro Mechanical Systems (MEMS) mirror. The optical system is optimized for the combination of a Laser Diode (LD), the MEMS mirror and the size of measurement area to secure the ideal contrast of structured light. Also, we developed a new calibration algorithm for this sensor with MEMS laser projector that uses an optical camera model for point cloud calculation. These technical advancements make the sensor compact, save power consumption, and reduce heat generation yet still allows for rapid calculation. Due to the principle of the measurement, structured light triangulation utilizing phase-shifting technology, resolution is improved. To meet requirements for practical applications, the optics, electronics, image processing, display and data management capabilities have been integrated into a single compact unit.

  7. 3D printing of weft knitted textile based structures by selective laser sintering of nylon powder

    NASA Astrophysics Data System (ADS)

    Beecroft, M.

    2016-07-01

    3D printing is a form of additive manufacturing whereby the building up of layers of material creates objects. The selective laser sintering process (SLS) uses a laser beam to sinter powdered material to create objects. This paper builds upon previous research into 3D printed textile based material exploring the use of SLS using nylon powder to create flexible weft knitted structures. The results show the potential to print flexible textile based structures that exhibit the properties of traditional knitted textile structures along with the mechanical properties of the material used, whilst describing the challenges regarding fineness of printing resolution. The conclusion highlights the potential future development and application of such pieces.

  8. 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

  9. Electronic structure studies of topological materials

    NASA Astrophysics Data System (ADS)

    Zhou, Shuyun

    Three-dimensional (3D) Dirac fermions are a new class of topological quantum materials. In 3D Dirac semimetals, the conduction and valence bands touch each other at discrete points in the momentum space and show linear dispersions along all momentum directions, forming 3D Dirac cones which are protected by the crystal symmetry. Here I will present our recent studies of the electronic structures of novel materials which host 3D Dirac fermions by using angle-resolved photoemission spectroscopy.

  10. Quasi-3D Waveform Inversion for Velocity Structures and Source Process Analyses Using its Results

    NASA Astrophysics Data System (ADS)

    Hikima, K.; Koketsu, K.

    2007-12-01

    In this study, we propose an efficient waveform inversion method for 2-D velocity structures and 3-D velocity structures are constructed by interpolating the results of the 2-D inversions. We apply these methods to a source process study of the 2003 Miyagi-ken Hokubu earthquake. We will first construct a velocity model, then determine the source processes of this earthquake sequence using the Green's function calculated with the resultant 3-D velocity model. We formulate the inversion procedure in a 2-D cross section. In a 2-D problem, an earthquake is forced to be a line source. Therefore, we introduce approximate transformation from a line source to a point source (Vidale and Helmberger, 1987). We use the 2-D velocity-stress staggered-grid finite difference scheme, so that the source representation is somewhat different from the original 'source box method' and we apply additional corrections to calculated waveforms. The boundary shapes of layers are expressed by connected nodes and we invert observed waveforms for layer thicknesses at the nodes. We perform 2-D velocity inversions along cross sections which involve a medium-size earthquake and observation points. We assemble the results for many stations and interpolated them to construct the 3-D velocity model. Finally, we calculate waveforms from the target earthquake by the 3-D finite difference method with this velocity model to confirm the validity of the model. We next perform waveform inversions for source processes of the 2003 Miyagi-ken Hokubu earthquake sequence using the resultant 3-D velocity model. We divide the fault plane into northern and southern subplanes, so that the southern subplane includes the hypocenter of the mainshock and the largest foreshock. The strike directions of the northern and southern subplanes were N-S and NE-SW, respectively. The Green's functions for these source inversions are calculated using the reciprocal theorem. We determine the slip models using the 3- D structure and

  11. Acquisition of 3d Information for Vanished Structure by Using Only AN Ancient Picture

    NASA Astrophysics Data System (ADS)

    Kunii, Y.; Sakamoto, R.

    2016-06-01

    In order to acquire 3D information for reconstruction of vanished historical structure, grasp of 3D shape of such structure was attempted by using an ancient picture. Generally, 3D information of a structure is acquired by photogrammetric theory which requires two or more pictures. This paper clarifies that the geometrical information of the structure was obtained only from an ancient picture, and 3D information was acquired. This kind of method was applied for an ancient picture of the Old Imperial Theatre. The Old Imperial Theatre in the picture is constituted by two-point perspective. Therefore, estimated value of focal length of camera, length of camera to the Old Imperial Theatre and some parameters were calculated by estimation of field angle, using body height as an index of length and some geometrical information. Consequently, 3D coordinate of 120 measurement points on the surface of the Old Imperial Theatre were calculated respectively, and 3DCG modeling of the Old Imperial Theatre was realized.

  12. Characterisation of the surface structure of 3D printed scaffolds for cell infiltration and surgical suturing.

    PubMed

    Ruiz-Cantu, Laura; Gleadall, Andrew; Faris, Callum; Segal, Joel; Shakesheff, Kevin; Yang, Jing

    2016-03-01

    3D printing is of great interest for tissue engineering scaffolds due to the ability to form complex geometries and control internal structures, including porosity and pore size. The porous structure of scaffolds plays an important role in cell ingrowth and nutrition infusion. Although the internal porosity and pore size of 3D printed scaffolds have been frequently studied, the surface porosity and pore size, which are critical for cell infiltration and mass transport, have not been investigated. The surface geometry can differ considerably from the internal scaffold structure depending on the 3D printing process. It is vital to be able to control the surface geometry of scaffolds as well as the internal structure to fabricate optimal architectures. This work presents a method to control the surface porosity and pore size of 3D printed scaffolds. Six scaffold designs have been printed with surface porosities ranging from 3% to 21%. We have characterised the overall scaffold porosity and surface porosity using optical microscopy and microCT. It has been found that surface porosity has a significant impact on cell infiltration and proliferation. In addition, the porosity of the surface has been found to have an effect on mechanical properties and on the forces required to penetrate the scaffold with a surgical suturing needle. To the authors' knowledge, this study is the first to investigate the surface geometry of extrusion-based 3D printed scaffolds and demonstrates the importance of surface geometry in cell infiltration and clinical manipulation. PMID:26930179

  13. 3D OCT imaging in clinical settings: toward quantitative measurements of retinal structures

    NASA Astrophysics Data System (ADS)

    Zawadzki, Robert J.; Fuller, Alfred R.; Zhao, Mingtao; Wiley, David F.; Choi, Stacey S.; Bower, Bradley A.; Hamann, Bernd; Izatt, Joseph A.; Werner, John S.

    2006-02-01

    The acquisition speed of current FD-OCT (Fourier Domain - Optical Coherence Tomography) instruments allows rapid screening of three-dimensional (3D) volumes of human retinas in clinical settings. To take advantage of this ability requires software used by physicians to be capable of displaying and accessing volumetric data as well as supporting post processing in order to access important quantitative information such as thickness maps and segmented volumes. We describe our clinical FD-OCT system used to acquire 3D data from the human retina over the macula and optic nerve head. B-scans are registered to remove motion artifacts and post-processed with customized 3D visualization and analysis software. Our analysis software includes standard 3D visualization techniques along with a machine learning support vector machine (SVM) algorithm that allows a user to semi-automatically segment different retinal structures and layers. Our program makes possible measurements of the retinal layer thickness as well as volumes of structures of interest, despite the presence of noise and structural deformations associated with retinal pathology. Our software has been tested successfully in clinical settings for its efficacy in assessing 3D retinal structures in healthy as well as diseased cases. Our tool facilitates diagnosis and treatment monitoring of retinal diseases.

  14. Characterisation of the surface structure of 3D printed scaffolds for cell infiltration and surgical suturing.

    PubMed

    Ruiz-Cantu, Laura; Gleadall, Andrew; Faris, Callum; Segal, Joel; Shakesheff, Kevin; Yang, Jing

    2016-03-01

    3D printing is of great interest for tissue engineering scaffolds due to the ability to form complex geometries and control internal structures, including porosity and pore size. The porous structure of scaffolds plays an important role in cell ingrowth and nutrition infusion. Although the internal porosity and pore size of 3D printed scaffolds have been frequently studied, the surface porosity and pore size, which are critical for cell infiltration and mass transport, have not been investigated. The surface geometry can differ considerably from the internal scaffold structure depending on the 3D printing process. It is vital to be able to control the surface geometry of scaffolds as well as the internal structure to fabricate optimal architectures. This work presents a method to control the surface porosity and pore size of 3D printed scaffolds. Six scaffold designs have been printed with surface porosities ranging from 3% to 21%. We have characterised the overall scaffold porosity and surface porosity using optical microscopy and microCT. It has been found that surface porosity has a significant impact on cell infiltration and proliferation. In addition, the porosity of the surface has been found to have an effect on mechanical properties and on the forces required to penetrate the scaffold with a surgical suturing needle. To the authors' knowledge, this study is the first to investigate the surface geometry of extrusion-based 3D printed scaffolds and demonstrates the importance of surface geometry in cell infiltration and clinical manipulation.

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

    PubMed

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

    2010-04-15

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

  16. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    PubMed Central

    Hayat, Sikander; Sander, Chris; Marks, Debora S.

    2015-01-01

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953

  17. The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture.

    PubMed

    Markaki, Yolanda; Smeets, Daniel; Fiedler, Susanne; Schmid, Volker J; Schermelleh, Lothar; Cremer, Thomas; Cremer, Marion

    2012-05-01

    Three-dimensional structured illumination microscopy (3D-SIM) has opened up new possibilities to study nuclear architecture at the ultrastructural level down to the ~100 nm range. We present first results and assess the potential using 3D-SIM in combination with 3D fluorescence in situ hybridization (3D-FISH) for the topographical analysis of defined nuclear targets. Our study also deals with the concern that artifacts produced by FISH may counteract the gain in resolution. We address the topography of DAPI-stained DNA in nuclei before and after 3D-FISH, nuclear pores and the lamina, chromosome territories, chromatin domains, and individual gene loci. We also look at the replication patterns of chromocenters and the topographical relationship of Xist-RNA within the inactive X-territory. These examples demonstrate that an appropriately adapted 3D-FISH/3D-SIM approach preserves key characteristics of the nuclear ultrastructure and that the gain in information obtained by 3D-SIM yields new insights into the functional nuclear organization. PMID:22508100

  18. Structural response to 3D simulated earthquake motions in San Bernardino Valley

    USGS Publications Warehouse

    Safak, E.; Frankel, A.

    1994-01-01

    Structural repsonse to one- and three-dimensional (3D) simulated motions in San Bernardino Valley from a hypothetical earthquake along the San Andreas fault with moment magnitude 6.5 and rupture length of 30km is investigated. The results show that the ground motions and the structural response vary dramatically with the type of simulation and the location. -from Authors

  19. 3D topography of biologic tissue by multiview imaging and structured light illumination

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Zhang, Shiwu; Xu, Ronald

    2014-02-01

    Obtaining three-dimensional (3D) information of biologic tissue is important in many medical applications. This paper presents two methods for reconstructing 3D topography of biologic tissue: multiview imaging and structured light illumination. For each method, the working principle is introduced, followed by experimental validation on a diabetic foot model. To compare the performance characteristics of these two imaging methods, a coordinate measuring machine (CMM) is used as a standard control. The wound surface topography of the diabetic foot model is measured by multiview imaging and structured light illumination methods respectively and compared with the CMM measurements. The comparison results show that the structured light illumination method is a promising technique for 3D topographic imaging of biologic tissue.

  20. CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures.

    PubMed

    Vlahovicek, Kristian; Pintar, Alessandro; Parthasarathi, Laavanya; Carugo, Oliviero; Pongor, Sándor

    2005-07-01

    The WWW servers at http://www.icgeb.org/protein/ are dedicated to the analysis of protein 3D structures submitted by the users as the Protein Data Bank (PDB) files. CX computes an atomic protrusion index that makes it possible to highlight the protruding atoms within a protein 3D structure. DPX calculates a depth index for the buried atoms and makes it possible to analyze the distribution of buried residues. CX and DPX return PDB files containing the calculated indices that can then be visualized using standard programs, such as Swiss-PDBviewer and Rasmol. PRIDE compares 3D structures using a fast algorithm based on the distribution of inter-atomic distances. The options include pairwise as well as multiple comparisons, and fold recognition based on searching the CATH fold database. PMID:15980464

  1. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

    Madura, Thomas; Gull, Theodore R.; Clementel, Nicola; Paardekooper, Jan-Pieter; Kruip, Chael; Corcoran, Michael F.; Hamaguchi, Kenji; Teodoro, Mairan

    2015-01-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (>120 MSun), highly eccentric (e ~ 0.9) binary Eta Carinae. Using a consumer-grade 3D printer (Makerbot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of Eta Carinae's inner (r ~110 AU) wind-wind collision interface at multiple orbital phases. These 3D prints reveal important, previously unknown 'finger-like' structures at orbital phases shortly after periastron (φ ~1.045) that protrude radially outward from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. Rayleigh-Taylor) that arise at the interface between the radiatively-cooled layer of dense post-shock primary-star wind and the hot, adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unknown physical features highlight the important role 3D printing can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  2. Advanced methods for 3-D inelastic structural analysis for hot engine structures

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.

    1989-01-01

    Three-dimensional Inelastic Analysis Methods are described. These methods were incorporated into a series of new computer codes embodying a progression of mathematical models (mechanics of materials, specialty finite element, boundary element) for streamlined analysis of hot engine structures such as: (1) combustor liners, (2) turbine blades, and (3) turbine vanes. These models address the effects of high temperatures and thermal/mechanical loadings on the local (stress/strain) and global (displacements, frequencies, amplitudes, buckling) structural behavior of the three respective components. The methods and the three computer codes, referred to as MOMM (Mechanics Of Materials Model), MHOST (MARC-Hot Section Technology), and BEST3D (Boundary Element Stress Technology), have been developed and are briefly described.

  3. Introduction of DC line structures into a superconducting microwave 3D cavity

    SciTech Connect

    Kong, Wei-Cheng; Deng, Guang-Wei; Li, Shu-Xiao; Li, Hai-Ou; Cao, Gang; Xiao, Ming; Guo, Guo-Ping

    2015-02-15

    We report a technique that can noninvasively add multiple DC wires into a 3D superconducting microwave cavity for electronic devices that require DC electrical terminals. We studied the influence of our DC lines on the cavity performance systematically. We found that the quality factor of the cavity is reduced if any of the components of the electrical wires cross the cavity equipotential planes. Using this technique, we were able to incorporate a quantum dot (QD) device into a 3D cavity. We then controlled and measured the QD transport signal using the DC lines. We have also studied the heating effects of the QD by the microwave photons in the cavity.

  4. Synthesis on structure and properties of zinc nanocrystal in high ordered 3D nanostructures

    SciTech Connect

    Sathyaseelan, B.; Manigandan, A.; Anbarasu, V.; Sivakumar, K.

    2015-06-24

    The wet impregnation method was employed to prepare ZnO encapsulated in mesoporous silica (ZnO/KIT-6). The prepared ZnO/KIT-6 samples have been studied by X-ray diffraction, transmission electron microscope, and nitrogen adsorption–desorption isotherm. The low angle powder XRD patterns of Calcined ZnO/KIT-6 materials showed a phase that can be indexed to cubic Ia3d. Tem images revealed well ordered cubic 3D nanoporous chennels. The ZnO encapsulated in KIT-6 can be used as light-emitting diodes and ultraviolet nanolasers.

  5. 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.

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

    PubMed

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

    2015-07-01

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

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

    PubMed

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

    2015-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-09-01

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

  9. Direct-growth carbon nanotubes on 3D structural microelectrodes for electrophysiological recording.

    PubMed

    Pan, Alice Ian; Lin, Min-Hsuan; Chung, Hui-Wen; Chen, Hsin; Yeh, Shih-Rung; Chuang, Yung-Jen; Chang, Yen-Chung; Yew, Tri-Rung

    2016-01-01

    A novel 3D carbon nanotube (CNT) microelectrode was developed through direct growth of CNTs on a gold pin-shaped 3D microelectrode at a low temperature (400 °C) for applications in neural and cardiac recording. With an electroplated Ni catalyst layer covering the entire surface of the pin-shaped structure, CNTs were synthesized on a 3D microelectrode by catalytic thermal chemical vapor deposition (CVD). According to the analyses by electrochemical impedance spectroscopy, the impedance of 3D microelectrodes after CNT growth and UV/O3 treatment decreased from 9.3 Ω mm(-2) to 1.2 Ω mm(-2) and the capacitance increased largely from 2.2 mF cm(-2) to 73.3 mF cm(-2). The existence of UVO3-treated CNT led to a large improvement of interfacial capacitance, contributing to the decrease of impedance. The electrophysiological detection capability of this 3D CNT microelectrode was demonstrated by the distinguished P waves, QRS complex and T waves in the electrocardiogram of the zebrafish heart and the action potential recorded from individual rat hippocampal neurons. The compatibility of integration with ICs, high resolution in space, electrophysiological signals, and non-invasive long-term recording suggest that the 3D CNT microelectrode exhibits promising potential for applications in electrophysiological research and clinical trials.

  10. Direct-growth carbon nanotubes on 3D structural microelectrodes for electrophysiological recording.

    PubMed

    Pan, Alice Ian; Lin, Min-Hsuan; Chung, Hui-Wen; Chen, Hsin; Yeh, Shih-Rung; Chuang, Yung-Jen; Chang, Yen-Chung; Yew, Tri-Rung

    2016-01-01

    A novel 3D carbon nanotube (CNT) microelectrode was developed through direct growth of CNTs on a gold pin-shaped 3D microelectrode at a low temperature (400 °C) for applications in neural and cardiac recording. With an electroplated Ni catalyst layer covering the entire surface of the pin-shaped structure, CNTs were synthesized on a 3D microelectrode by catalytic thermal chemical vapor deposition (CVD). According to the analyses by electrochemical impedance spectroscopy, the impedance of 3D microelectrodes after CNT growth and UV/O3 treatment decreased from 9.3 Ω mm(-2) to 1.2 Ω mm(-2) and the capacitance increased largely from 2.2 mF cm(-2) to 73.3 mF cm(-2). The existence of UVO3-treated CNT led to a large improvement of interfacial capacitance, contributing to the decrease of impedance. The electrophysiological detection capability of this 3D CNT microelectrode was demonstrated by the distinguished P waves, QRS complex and T waves in the electrocardiogram of the zebrafish heart and the action potential recorded from individual rat hippocampal neurons. The compatibility of integration with ICs, high resolution in space, electrophysiological signals, and non-invasive long-term recording suggest that the 3D CNT microelectrode exhibits promising potential for applications in electrophysiological research and clinical trials. PMID:26588673

  11. 3D multi-layered fibrous cellulose structure using an electrohydrodynamic process for tissue engineering.

    PubMed

    Kim, Minseong; Kim, GeunHyung

    2015-11-01

    Micro/nanofibrous structures have been applied widely in various tissue-engineering applications because the topological structures are similar to the extracellular matrix (ECM), which encourages a high degree of cell adhesion and growth. However, it has been difficult to produce a three-dimensional (3D) fibrous structure using controllable macro-pores. Recently, cellulose has been considered a high-potential natural-origin biomaterial, but its use in 3D biomedical structures has been limited due to its narrow processing window. Here, we suggest a new 3D cellulose scaffold consisting of multi-layered struts made of submicron-sized entangled fibers that were fabricated using an electrohydrodynamic direct jet (EHDJ) process that is spin-printing. By optimizing processing conditions (electric field strength, cellulose feeding rate, and distance between nozzle and target), we can achieve a multi-layered cellulose structure consisting of the cylindrically entangled cellulose fibers. To compare the properties of the fabricated 3D cellulose structure, we used a PCL fibrous scaffold, which has a similar fibrous morphology and pore geometry, as a control. The physical and in vitro biocompatibilities of both fibrous scaffolds were assessed using human dermal fibroblasts, and the cellulose structure showed higher cell adhesion and metabolic activities compared with the control. These results suggest the EHDJ process to be an effective fabricating tool for tissue engineering and the cellulose scaffold has high potential as a tissue regenerative material.

  12. Modeling 3D soil and sediment distributions for assessing catchment structure and hydrological feedbacks

    NASA Astrophysics Data System (ADS)

    Maurer, Thomas; Brück, Yasemine; Hinz, Christoph; Gerke, Horst H.

    2015-04-01

    Structural heterogeneity, namely the spatial distribution of soils and sediments (represented by mineral particles), characterizes catchment hydrological behavior. In natural catchments, local geology and the specific geomorphic processes determine the characteristics and spatial distribution of structures. In constructed catchments, structural features are determined primarily by the construction processes and the geological origin of the parent material. Objectives are scenarios of 3D catchment structures in form of complete 3D description of soil hydraulic properties generated from the knowledge of the formation processes. The constructed hydrological catchment 'Hühnerwasser' (Lower Lusatia, Brandenburg, Germany) was used for the calibration and validation of model results due to its well-known conditions. For the modelling of structural features, a structure generator was used to model i) quasi-deterministic sediment distributions using input data from a geological model of the parent material excavation site; ii) sediment distributions that are conditioned to measurement data from soil sampling; and iii) stochastic component sediment distributions. All three approaches allow a randomization within definable limits. Furthermore, the spoil cone / spoil ridge orientation, internal layering, surface compaction and internal spoil cone compaction were modified. These generated structural models were incorporated in a gridded 3D volume model constructed with the GOCAD software. For selected scenarios, the impact of structure variation was assessed by hydrological modelling with HYDRUS 2D/3D software. For that purpose, 3D distributions of soil hydraulic properties were estimated based on generated sediment properties using adapted pedotransfer functions. Results from the hydrological model were compared them to measured discharges from the catchment. The impact of structural feature variation on flow behaviour was analysed by comparing different simulation scenarios

  13. Structure light telecentric stereoscopic vision 3D measurement system based on Scheimpflug condition

    NASA Astrophysics Data System (ADS)

    Mei, Qing; Gao, Jian; Lin, Hui; Chen, Yun; Yunbo, He; Wang, Wei; Zhang, Guanjin; Chen, Xin

    2016-11-01

    We designed a new three-dimensional (3D) measurement system for micro components: a structure light telecentric stereoscopic vision 3D measurement system based on the Scheimpflug condition. This system creatively combines the telecentric imaging model and the Scheimpflug condition on the basis of structure light stereoscopic vision, having benefits of a wide measurement range, high accuracy, fast speed, and low price. The system measurement range is 20 mm×13 mm×6 mm, the lateral resolution is 20 μm, and the practical vertical resolution reaches 2.6 μm, which is close to the theoretical value of 2 μm and well satisfies the 3D measurement needs of micro components such as semiconductor devices, photoelectron elements, and micro-electromechanical systems. In this paper, we first introduce the principle and structure of the system and then present the system calibration and 3D reconstruction. We then present an experiment that was performed for the 3D reconstruction of the surface topography of a wafer, followed by a discussion. Finally, the conclusions are presented.

  14. 2D and 3D multipactor modeling in dielectric-loaded accelerator structures

    NASA Astrophysics Data System (ADS)

    Sinitsyn, Oleksandr; Nusinovich, Gregory; Antonsen, Thomas

    2010-11-01

    Multipactor (MP) is known as the avalanche growth of the number of secondary electrons emitted from a solid surface exposed to an RF electric field under vacuum conditions. MP is a severe problem in modern rf systems and, therefore, theoretical and experimental studies of MP are of great interest to the researchers working in various areas of physics and engineering. In this work we present results of MP studies in dielectric-loaded accelerator (DLA) structures. First, we show simulation results obtained with the use of the 2D self-consistent MP model (O. V. Sinitsyn, et. al., Phys. Plasmas, vol. 16, 073102 (2009)) and compare those to experimental ones obtained during recent extensive studies of DLA structures performed by Argonne National Laboratory, Naval Research Laboratory, SLAC National Accelerator Laboratory and Euclid TechLabs (C. Jing, et al., IEEE Trans. Plasma Sci., vol. 38, pp. 1354-1360 (2010)). Then we present some new results of 3D analysis of MP which include studies of particle trajectories and studies of MP development at the early stage.

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

    DOEpatents

    Zemla, Adam T.

    2011-09-20

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

  16. Mixed-Mode Fracture and Fatigue Analysis of Cracked 3D Complex Structures using a 3D SGBEM-FEM Alternating Method

    NASA Astrophysics Data System (ADS)

    Bhavanam, Sharada

    The aim of this thesis is to numerically evaluate the mixed-mode Stress Intensity Factors (SIFs) of complex 3D structural geometries with arbitrary 3D cracks using the Symmetric Galerkin Boundary Element Method-Finite Element Method (SGBEM-FEM) Alternating Method. Various structural geometries with different loading scenarios and crack configurations were examined in this thesis to understand the behavior and trends of the mixed-mode SIFs as well as the fatigue life for these complex structural geometries. Although some 3D structures have empirical and numerical solutions that are readily available in the open literature, some do not; therefore this thesis presents the results of fracture and fatigue analyses of these 3D complex structures using the SGBEM-FEM Alternating Method to serve as reference for future studies. Furthermore, there are advantages of using the SGBEM-FEM Alternating Method compared to traditional FEM methods. For example, the fatigue-crack-growth and fatigue life can be better estimated for a structure because different fatigue models (i.e. Walker, Paris, and NASGRO) can be used within the same framework of the SGBEM-FEM Alternating Method. The FEM (un-cracked structure)/BEM(crack model) meshes are modeled independently, which speeds up the computation process and reduces the cost of human labor. A simple coarse mesh can be used for all fracture and fatigue analyses of complex structures. In this thesis, simple coarse meshes were used for 3D complex structures, which were below 5000 elements as compared to traditional FEM, which require meshes where the elements range on the order of ˜250,000 to ˜106 and sometimes even more than that.

  17. Precision structural engineering of self-rolled-up 3D nanomembranes guided by transient quasi-static FEM modeling.

    PubMed

    Huang, Wen; Koric, Seid; Yu, Xin; Hsia, K Jimmy; Li, Xiuling

    2014-11-12

    Micro- and nanoscale tubular structures can be formed by strain-induced self-rolled-up nanomembranes. Precision engineering of the shape and dimension determines the performance of devices based on this platform for electronic, optical, and biological applications. A transient quasi-static finite element method (FEM) with moving boundary conditions is proposed as a general approach to design diverse types of three-dimensional (3D) rolled-up geometries. This method captures the dynamic release process of membranes through etching driven by mismatch strain and accurately predicts the final dimensions of rolled-up structures. Guided by the FEM modeling, experimental demonstration using silicon nitride membranes was achieved with unprecedented precision including controlling fractional turns of a rolled-up membrane, anisotropic rolling to form helical structures, and local stress control for 3D hierarchical architectures.

  18. 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.

  19. Multi-scale modelling of strongly heterogeneous 3D composite structures using spatial Voronoi tessellation

    NASA Astrophysics Data System (ADS)

    El Said, Bassam; Ivanov, Dmitry; Long, Andrew C.; Hallett, Stephen R.

    2016-03-01

    3D composite materials are characterized by complex internal yarn architectures, leading to complex deformation and failure development mechanisms. Net-shaped preforms, which are originally periodic in nature, lose their periodicity when the fabric is draped, deformed on a tool, and consolidated to create geometrically complex composite components. As a result, the internal yarn architecture, which dominates the mechanical behaviour, becomes dependent on the structural geometry. Hence, predicting the mechanical behaviour of 3D composites requires an accurate representation of the yarn architecture within structural scale models. When applied to 3D composites, conventional finite element modelling techniques are limited to either homogenised properties at the structural scale, or the unit cell scale for a more detailed material property definition. Consequently, these models fail to capture the complex phenomena occurring across multiple length scales and their effects on a 3D composite's mechanical response. Here a multi-scale modelling approach based on a 3D spatial Voronoi tessellation is proposed. The model creates an intermediate length scale suitable for homogenisation to deal with the non-periodic nature of the final material. Information is passed between the different length scales to allow for the effect of the structural geometry to be taken into account on the smaller scales. The stiffness and surface strain predictions from the proposed model have been found to be in good agreement with experimental results. The proposed modelling framework has been used to gain important insight into the behaviour of this category of materials. It has been observed that the strain and stress distributions are strongly dependent on the internal yarn architecture and consequently on the final component geometry. Even for simple coupon tests, the internal architecture and geometric effects dominate the mechanical response. Consequently, the behaviour of 3D woven

  20. 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

  1. Deposit3D: a tool for automating structure depositions to the Protein Data Bank

    SciTech Connect

    Badger, J. Hendle, J.; Burley, S. K.; Kissinger, C. R.

    2005-09-01

    This paper describes a Python script that may be used to gather all required structure-annotation information into an mmCIF file for upload through the RCSB PDB ADIT structure-deposition interface. Almost all successful protein structure-determination projects in the public sector culminate in a structure deposition to the Protein Data Bank (PDB). In order to expedite the deposition proces, Deposit3D has been developed. This command-line script calculates or gathers all the required structure-deposition information and outputs this data into a mmCIF file for subsequent upload through the RCSB PDB ADIT interface. Deposit3D might be particularly useful for structural genomics pipeline projects because it allows workers involved with various stages of a structure-determination project to pool their different categories of annotation information before starting a deposition session.

  2. Segmented images and 3D images for studying the anatomical structures in MRIs

    NASA Astrophysics Data System (ADS)

    Lee, Yong Sook; Chung, Min Suk; Cho, Jae Hyun

    2004-05-01

    For identifying the pathological findings in MRIs, the anatomical structures in MRIs should be identified in advance. For studying the anatomical structures in MRIs, an education al tool that includes the horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is necessary. Such an educational tool, however, is hard to obtain. Therefore, in this research, such an educational tool which helps medical students and doctors study the anatomical structures in MRIs was made as follows. A healthy, young Korean male adult with standard body shape was selected. Six hundred thirteen horizontal MRIs of the entire body were scanned and inputted to the personal computer. Sixty anatomical structures in the horizontal MRIs were segmented to make horizontal segmented images. Coronal, sagittal MRIs and coronal, sagittal segmented images were made. 3D images of anatomical structures in the segmented images were reconstructed by surface rendering method. Browsing software of the MRIs, segmented images, and 3D images was composed. This educational tool that includes horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is expected to help medical students and doctors study anatomical structures in MRIs.

  3. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints

    PubMed Central

    Magnus, Marcin; Boniecki, Michał J.; Dawson, Wayne; Bujnicki, Janusz M.

    2016-01-01

    RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb. PMID:27095203

  4. 3D flexible NiTi-braided elastomer composites for smart structure applications

    NASA Astrophysics Data System (ADS)

    Heller, L.; Vokoun, D.; Šittner, P.; Finckh, H.

    2012-04-01

    While outstanding functional properties of thin NiTi wires are nowadays well recognized and beneficially utilized in medical NiTi devices, development of 2D/3D wire structures made out of these NiTi wires remains challenging and mostly unexplored. The research is driven by the idea of creating novel 2D/3D smart structures which inherit the functional properties of NiTi wires and actively utilize geometrical deformations within the structure to create new/improved functional properties. Generally, textile technology provides attractive processing methods for manufacturing 2D/3D smart structures made out of NiTi wires. Such structures may be beneficially combined with soft elastomers to create smart deformable composites. Following this route, we carried out experimental work focused on development of 3D flexible NiTi-braided elastomer composites involving their design, laboratory manufacture and thermomechanical testing. We describe the manufacturing technology and structural properties of these composites; and perform thermomechanical tests on the composites, focusing particularly on quasistatic tensile properties, energy absorption, damping and actuation under tensile loading. Functional thermomechanical properties of the composites are discussed with regard to the mechanical properties of the components and architecture of the composites. It is found that the composites indeed inherit all important features of the thermomechanical behavior of NiTi wires but, due to their internal architecture, outperform single NiTi wires in some features such as the magnitude of recoverable strain, superelastic damping capacity and thermally induced actuation strain.

  5. 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

  6. Seismic source inversion using Green's reciprocity and a 3-D structural model for the Japanese Islands

    NASA Astrophysics Data System (ADS)

    Simutė, S.; Fichtner, A.

    2015-12-01

    We present a feasibility study for seismic source inversions using a 3-D velocity model for the Japanese Islands. The approach involves numerically calculating 3-D Green's tensors, which is made efficient by exploiting Green's reciprocity. The rationale for 3-D seismic source inversion has several aspects. For structurally complex regions, such as the Japan area, it is necessary to account for 3-D Earth heterogeneities to prevent unknown structure polluting source solutions. In addition, earthquake source characterisation can serve as a means to delineate existing faults. Source parameters obtained for more realistic Earth models can then facilitate improvements in seismic tomography and early warning systems, which are particularly important for seismically active areas, such as Japan. We have created a database of numerically computed 3-D Green's reciprocals for a 40°× 40°× 600 km size area around the Japanese Archipelago for >150 broadband stations. For this we used a regional 3-D velocity model, recently obtained from full waveform inversion. The model includes attenuation and radial anisotropy and explains seismic waveform data for periods between 10 - 80 s generally well. The aim is to perform source inversions using the database of 3-D Green's tensors. As preliminary steps, we present initial concepts to address issues that are at the basis of our approach. We first investigate to which extent Green's reciprocity works in a discrete domain. Considering substantial amounts of computed Green's tensors we address storage requirements and file formatting. We discuss the importance of the initial source model, as an intelligent choice can substantially reduce the search volume. Possibilities to perform a Bayesian inversion and ways to move to finite source inversion are also explored.

  7. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression.

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation.

  8. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression

    PubMed Central

    Jacob, J. Augustin; Kumar, N. Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  9. Advanced resin systems and 3D textile preforms for low cost composite structures

    NASA Technical Reports Server (NTRS)

    Shukla, J. G.; Bayha, T. D.

    1993-01-01

    Advanced resin systems and 3D textile preforms are being evaluated at Lockheed Aeronautical Systems Company (LASC) under NASA's Advanced Composites Technology (ACT) Program. This work is aimed towards the development of low-cost, damage-tolerant composite fuselage structures. Resin systems for resin transfer molding and powder epoxy towpreg materials are being evaluated for processability, performance and cost. Three developmental epoxy resin systems for resin transfer molding (RTM) and three resin systems for powder towpregging are being investigated. Various 3D textile preform architectures using advanced weaving and braiding processes are also being evaluated. Trials are being conducted with powdered towpreg, in 2D weaving and 3D braiding processes for their textile processability and their potential for fabrication in 'net shape' fuselage structures. The progress in advanced resin screening and textile preform development is reviewed here.

  10. Structure of complement receptor 2 in complex with its C3d ligand.

    PubMed

    Szakonyi, G; Guthridge, J M; Li, D; Young, K; Holers, V M; Chen, X S

    2001-06-01

    Complement receptor 2 (CR2/CD21) is an important receptor that amplifies B lymphocyte activation by bridging the innate and adaptive immune systems. CR2 ligands include complement C3d and Epstein-Barr virus glycoprotein 350/220. We describe the x-ray structure of this CR2 domain in complex with C3d at 2.0 angstroms. The structure reveals extensive main chain interactions between C3d and only one short consensus repeat (SCR) of CR2 and substantial SCR side-side packing. These results provide a detailed understanding of receptor-ligand interactions in this protein family and reveal potential target sites for molecular drug design. PMID:11387479

  11. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression.

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  12. 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.

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

    NASA Astrophysics Data System (ADS)

    Hagelberg, Frank

    2003-03-01

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

  14. 3D shape shearography with integrated structured light projection for strain inspection of curved objects

    NASA Astrophysics Data System (ADS)

    Anisimov, Andrei G.; Groves, Roger M.

    2015-05-01

    Shearography (speckle pattern shearing interferometry) is a non-destructive testing technique that provides full-field surface strain characterization. Although real-life objects especially in aerospace, transport or cultural heritage are not flat (e.g. aircraft leading edges or sculptures), their inspection with shearography is of interest for both hidden defect detection and material characterization. Accurate strain measuring of a highly curved or free form surface needs to be performed by combining inline object shape measuring and processing of shearography data in 3D. Previous research has not provided a general solution. This research is devoted to the practical questions of 3D shape shearography system development for surface strain characterization of curved objects. The complete procedure of calibration and data processing of a 3D shape shearography system with integrated structured light projector is presented. This includes an estimation of the actual shear distance and a sensitivity matrix correction within the system field of view. For the experimental part a 3D shape shearography system prototype was developed. It employs three spatially-distributed shearing cameras, with Michelson interferometers acting as the shearing devices, one illumination laser source and a structured light projector. The developed system performance was evaluated with a previously reported cylinder specimen (length 400 mm, external diameter 190 mmm) loaded by internal pressure. Further steps for the 3D shape shearography prototype and the technique development are also proposed.

  15. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

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

    2016-08-19

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

  16. RNAssess--a web server for quality assessment of RNA 3D structures.

    PubMed

    Lukasiak, Piotr; Antczak, Maciej; Ratajczak, Tomasz; Szachniuk, Marta; Popenda, Mariusz; Adamiak, Ryszard W; Blazewicz, Jacek

    2015-07-01

    Nowadays, various methodologies can be applied to model RNA 3D structure. Thus, the plausible quality assessment of 3D models has a fundamental impact on the progress of structural bioinformatics. Here, we present RNAssess server, a novel tool dedicated to visual evaluation of RNA 3D models in the context of the known reference structure for a wide range of accuracy levels (from atomic to the whole molecule perspective). The proposed server is based on the concept of local neighborhood, defined as a set of atoms observed within a sphere localized around a central atom of a particular residue. A distinctive feature of our server is the ability to perform simultaneous visual analysis of the model-reference structure coherence. RNAssess supports the quality assessment through delivering both static and interactive visualizations that allows an easy identification of native-like models and/or chosen structural regions of the analyzed molecule. A combination of results provided by RNAssess allows us to rank analyzed models. RNAssess offers new route to a fast and efficient 3D model evaluation suitable for the RNA-Puzzles challenge. The proposed automated tool is implemented as a free and open to all users web server with an user-friendly interface and can be accessed at: http://rnassess.cs.put.poznan.pl/. PMID:26068469

  17. From 1D chain to 3D network: A theoretical study on TiO{sub 2} low dimensional structures

    SciTech Connect

    Guo, Ling-ju; He, Tao; Zeng, Zhi

    2015-06-14

    We have performed a systematic study on a series of low dimensional TiO{sub 2} nanostructures under density functional theory methods. The geometries, stabilities, growth mechanism, and electronic structures of 1D chain, 2D ring, 2D ring array, and 3D network of TiO{sub 2} nanostructures are analyzed. Based on the Ti{sub 2}O{sub 4} building unit, a series of 1D TiO{sub 2} nano chains and rings can be built. Furthermore, 2D ring array and 3D network nanostructures can be constructed from 1D chains and rings. Among non-periodic TiO{sub 2} chain and ring structures, one series of ring structures is found to be more stable. The geometry model of the 2D ring arrays and 3D network structures in this work has provided a theoretical understanding on the structure information in experiments. Based on these semiconductive low dimensional structures, moreover, it can help to understand and design new hierarchical TiO{sub 2} nanostructure in the future.

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

    NASA Astrophysics Data System (ADS)

    Rioux, Marc

    1994-10-01

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

  19. A reduced-coordinate approach to modeling RNA 3-D structures

    SciTech Connect

    Tung, Chang-Shung

    1997-09-01

    With the realization of RNA molecules capable of performing very specific functions (e.g., catalytic RNAs and RNAs that bind ligand with affinity and specificity of an anti-body) and contrary to the traditional view that structure of RNA molecules being functionally passive, it has become clear that studying the 3-dimensional (3-D) folding of RNA molecules is a very important task. In the absence of sufficient number of experimentally determined RNA structures available up-to-date, folding of RNA structures computationally provides an alternative approach in studying the 3-D structure of RNA molecules. We have developed a computational approach for folding RNA 3-D structures. The method is conceptually simple and general. It consists of two major components. The first being the arrangement of all helices in space. Once the helices are positioned and oriented in space, structures of the connecting loops are modeled and inserted between the helices. Any number of structural constraints derived either experimentally or theoretically can be used to guide the folding processes. A conformational sampling approach is developed with structural equilibration using the Metropolis Monte Carlo simulation. The lengths of various loop sizes (ranging from 1 base to 7 bases) are calculated based on a set of RNA structures deposited in PDB as well as a set of loop structures constructed using our method. The validity of using the averaged loop lengths of the connecting loops as distance constraints for arranging the helices in space is studied.

  20. About the automated pattern creation of 3D jacquard double needle bed warp knitted structures

    NASA Astrophysics Data System (ADS)

    Renkens, W.; Kyosev, Y.

    2016-07-01

    Three dimensional structures can be produced on jacquard warp knitting machines with double needle bed. This work presents theoretical considerations about the modelling and simulation of these structures. After that a method is described, how to obtain production parameters from the simulation data. The analysis demonstrates, that the automated pattern creation of 3D structures is not always possible and not all mathematical solutions of the problem can be knittable.

  1. Proteopedia: A Collaborative, Virtual 3D Web-Resource for Protein and Biomolecule Structure and Function

    ERIC Educational Resources Information Center

    Hodis, Eran; Prilusky, Jaime, Sussman, Joel L.

    2010-01-01

    Protein structures are hard to represent on paper. They are large, complex, and three-dimensional (3D)--four-dimensional if conformational changes count! Unlike most of their substrates, which can easily be drawn out in full chemical formula, drawing every atom in a protein would usually be a mess. Simplifications like showing only the surface of…

  2. Ion Beam Etching: Replication of Micro Nano-structured 3D Stencil Masks

    SciTech Connect

    Weber, Patrick; Guibert, Edouard; Mikhailov, Serguei; Bruegger, Juergen; Villanueva, Guillermo

    2009-03-10

    Ion beam LIGA allows the etching of 3D nano-structures by direct writing with a nano-sized beam. However, this is a relatively time consuming process. We propose here another approach for etching structures on large surfaces and faster, compared to the direct writing process. This approach consists of replicating 3D structured masks, by scanning an unfocused ion beam. A polymer substrate is placed behind the mask, as in UV photolithography. But the main advantage is that the 3D structure of the mask can be replicated into the polymer. For that purpose, the masks (developped at LMIS1, EPFL) are made of a silicon nitride membrane 100 nm thick, on which 3D gold structures up to 200 nm thick, are deposited. The 3D Au structures are made with the nanostencil method, based on successive gold deposition. The IMA institute, from HE-Arc, owns a High Voltage Engineering 1.7 MV Tandetron with both solid and gaseous negative ion sources, able to generate ions from almost every chemical element in a broad range of energies comprised between 400 keV and 6.8 MeV. The beam composition and energy are chosen in such a way, that ions lose a significant fraction of their energy when passing through the thickest regions of the mask. Ions passing through thinner regions of the mask loose a smaller fraction of their energy and etch the polymer with larger thicknesses, allowing a replication of the mask into the polymer. For our trials, we have used a carbon beam with an energy of 500 keV. The beam was focussed to a diameter of 5 mm with solid slits, in order to avoid border effects and thus ensure a homogeneous dose distribution on the beam diameter. The feasibility of this technique has been demonstrated, allowing industrial applications for micro-mould fabrication, micro-fluidics and micro-optics.

  3. Holographic particle velocimetry - A 3D measurement technique for vortex interactions, coherent structures and turbulence

    NASA Astrophysics Data System (ADS)

    Meng, Hui; Hussain, Fazle

    1991-10-01

    To understand the topology and dynamics of coherent structures (CS), the interactions of CS with fine-scale turbulence, and the effects of CS on entrainment, mixing and combustion, experimental tools are needed that can measure velocity (preferably vorticity) vector fields in both 3D space and time. While traditional measurement techniques are not able to serve this purpose, holographic particle velocimetry (HPV) appears to be promising. In a demonstration experiment, the instantaneous 3D velocity vector fields in some simple vortical flows have been obtained using the HPV technique. In this preliminary report, the principles of the HPV technique are illustrated and the key issues in its implementation are discussed.

  4. Research of aluminium alloy aerospace structure aperture measurement based on 3D digital speckle correlation method

    NASA Astrophysics Data System (ADS)

    Bai, Lu; Wang, Hongbo; Zhou, Jiangfan; Yang, Rong; Zhang, Hui

    2014-11-01

    In this paper, the aperture change of the aluminium alloy aerospace structure under real load is researched. Static experiments are carried on which is simulated the load environment of flight course. Compared with the traditional methods, through experiments results, it's proved that 3D digital speckle correlation method has good adaptability and precision on testing aperture change, and it can satisfy measurement on non-contact,real-time 3D deformation or stress concentration. The test results of new method is compared with the traditional method.

  5. Non-contact 3D fingerprint scanner using structured light illumination

    NASA Astrophysics Data System (ADS)

    Troy, Mike; Hassebrook, Laurence; Yalla, Veeraganesh; Daley, Raymond

    2011-03-01

    As crime prevention and national security remain a top priority, requirements for the use of fingerprints for identification continue to grow. While the size of fingerprint databases continues to expand, new technologies that can improve accuracy and ultimately matching performance will become more critical to maintain the effectiveness of the systems. FlashScan3D has developed non-contact, fingerprint scanners based on the principles of Structured Light Illumination (SLI) that capture 3Dimensional data of fingerprints quickly, accurately and independently of an operator. FlashScan3D will present findings from various research projects performed for the US Army and the Department of Homeland Security.

  6. A Patterned 3D Silicon Anode Fabricated by Electrodeposition on a Virus-Structured Current Collector

    SciTech Connect

    Chen, X L; Gerasopoulos, K; Guo, J C; Brown, A; Wang, Chunsheng; Ghodssi, Reza; Culver, J N

    2010-11-09

    Electrochemical methods were developed for the deposition of nanosilicon onto a 3D virus-structured nickel current collector. This nickel current collector is composed of self-assembled nanowire-like rods of genetically modified tobacco mosaic virus (TMV1cys), chemically coated in nickel to create a complex high surface area conductive substrate. The electrochemically depo­sited 3D silicon anodes demonstrate outstanding rate performance, cycling stability, and rate capability. Electrodeposition thus provides a unique means of fabricating silicon anode materials on complex substrates at low cost.

  7. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  8. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells

    PubMed Central

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L.; Han, Jessica H.; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H.; Bussey, Kimberly J.; Meldrum, Deirdre R.

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an ‘epigenetic’ drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat’s differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  9. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-08-09

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action.

  10. 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

  11. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    PubMed Central

    Zenou, M.; Sa’ar, A.; Kotler, Z.

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  12. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures.

    PubMed

    Zenou, M; Sa'ar, A; Kotler, Z

    2015-11-25

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures.

  13. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    NASA Astrophysics Data System (ADS)

    Zenou, M.; Sa'Ar, A.; Kotler, Z.

    2015-11-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures.

  14. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures.

    PubMed

    Zenou, M; Sa'ar, A; Kotler, Z

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  15. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data.

    PubMed

    Lee, Woonghee; Petit, Chad M; Cornilescu, Gabriel; Stark, Jaime L; Markley, John L

    2016-06-01

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27-98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

  16. Influence of 3D anisotropic structures on bipole-quadrupole DC resistivity (BQ-DC) measurements

    NASA Astrophysics Data System (ADS)

    Loewer, A.; Junge, A.; Guenther, T.; Grinat, M.; Hering, P.

    2015-12-01

    3D modelling of BQ-DC measurements can show a rather strong directional distortion of the electric current density for an inhomogeneous subsurface. Anisotropic structures increase this effect. Depending on the anisotropy direction, current density might vary by 90° between the interior and exterior of an anisotropic body. In combination with 3D effects currents might even flow into the opposite direction compared to those expected for a homogeneous half space. This effect can produce negative potential differences (in combination with positive geometry factors) at the surface which cannot be explained by an isotropic resistivity distribution and thus those data cannot be used by an isotropic inversion. Consequently, anisotropic forward modelling is necessary to explain such observations. In nature anisotropic resistivity can appear in the context of strongly foliated structures. Such structures exist in the Rhenish Massif, Germany, where extensive shallow greywacke shales with different strength of foliation are found. In this area a field campaign was performed in 2014 to provide evidence for the existence of anisotropic resistivity structures. Two perpendicular bipole current injections at 15 locations produced individual potential distributions. The potential differences were recorded for two orthogonal directions each at 30 positions for an array set up within the survey area. We use the apparent resistivity tensor after Bibby 1986 to display the BQ-DC data. It uses the hypothetical current densities of each of the two bipole sources calculated for an equivalent homogenous half space at the location of the quadrupole measurement to derive a resistivity tensor. The spatial behavior of modelled tensors gives evidence of the anisotropic body although the structure is covered by an isotropic layer. The data are explained by a 3D anisotropic resistivity distribution using a 3D isotropic inversion scheme combined with 3D anisotropic forward-modelling.

  17. EK3D: an E. coli K antigen 3-dimensional structure database

    PubMed Central

    Kunduru, Bharathi Reddy; Nair, Sanjana Anilkumar; Rathinavelan, Thenmalarchelvi

    2016-01-01

    A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial outer membrane surface, which is a potential drug & vaccine target. It plays a key role in host–pathogen interactions as well as host immune evasion and thus, mandates detailed structural information. Nonetheless, acquiring structural information of K antigens is not straightforward due to their innate enormous conformational flexibility. Here, we have developed a manually curated database of K antigens corresponding to various E. coli serotypes, which differ from each other in their monosaccharide composition, linkage between the monosaccharides and their stereoisomeric forms. Subsequently, we have modeled their 3D structures and developed an organized repository, namely EK3D that can be accessed through www.iith.ac.in/EK3D/. Such a database would facilitate the development of antibacterial drugs to combat E. coli infections as it has evolved resistance against 2 major drugs namely, third-generation cephalosporins and fluoroquinolones. EK3D also enables the generation of polymeric K antigens of varying lengths and thus, provides comprehensive information about E. coli K antigens. PMID:26615200

  18. Fabrication of 3D microfluidic structures inside glass by femtosecond laser micromachining

    NASA Astrophysics Data System (ADS)

    Sugioka, Koji; Cheng, Ya

    2014-01-01

    Femtosecond lasers have opened up new avenues in materials processing due to their unique characteristics of ultrashort pulse widths and extremely high peak intensities. One of the most important features of femtosecond laser processing is that a femtosecond laser beam can induce strong absorption in even transparent materials due to nonlinear multiphoton absorption. This makes it possible to directly create three-dimensional (3D) microfluidic structures in glass that are of great use for fabrication of biochips. For fabrication of the 3D microfluidic structures, two technical approaches are being attempted. One of them employs femtosecond laser-induced internal modification of glass followed by wet chemical etching using an acid solution (Femtosecond laser-assisted wet chemical etching), while the other one performs femtosecond laser 3D ablation of the glass in distilled water (liquid-assisted femtosecond laser drilling). This paper provides a review on these two techniques for fabrication of 3D micro and nanofluidic structures in glass based on our development and experimental results.

  19. EK3D: an E. coli K antigen 3-dimensional structure database.

    PubMed

    Kunduru, Bharathi Reddy; Nair, Sanjana Anilkumar; Rathinavelan, Thenmalarchelvi

    2016-01-01

    A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial outer membrane surface, which is a potential drug & vaccine target. It plays a key role in host-pathogen interactions as well as host immune evasion and thus, mandates detailed structural information. Nonetheless, acquiring structural information of K antigens is not straightforward due to their innate enormous conformational flexibility. Here, we have developed a manually curated database of K antigens corresponding to various E. coli serotypes, which differ from each other in their monosaccharide composition, linkage between the monosaccharides and their stereoisomeric forms. Subsequently, we have modeled their 3D structures and developed an organized repository, namely EK3D that can be accessed through www.iith.ac.in/EK3D/. Such a database would facilitate the development of antibacterial drugs to combat E. coli infections as it has evolved resistance against 2 major drugs namely, third-generation cephalosporins and fluoroquinolones. EK3D also enables the generation of polymeric K antigens of varying lengths and thus, provides comprehensive information about E. coli K antigens. PMID:26615200

  20. The theoretical 3D structure of Bacillus thuringiensis Cry5Ba.

    PubMed

    Xia, Li-Qiu; Zhao, Xin-Min; Ding, Xue-Zhi; Wang, Fa-Xiang; Sun, Yun-Jun

    2008-09-01

    Cry5Ba is a delta-endotoxin produced by Bacillus thuringiensis PS86A1 NRRL B-18900. It is active against nematodes and has great potential for nematode control. Here, we predict the first theoretical model of the three-dimensional (3D) structure of a Cry5Ba toxin by homology modeling on the structure of the Cry1Aa toxin, which is specific to Lepidopteran insects. Cry5Ba resembles the previously reported Cry1Aa toxin structure in that they share a common 3D structure with three domains, but there are some distinctions, with the main differences being located in the loops of domain I. Cry5Ba exhibits a changeable extending conformation structure, and this special structure may also be involved in pore-forming and specificity determination. A fuller understanding of the 3D structure will be helpful in the design of mutagenesis experiments aimed at improving toxicity, and lead to a deep understanding of the mechanism of action of nematicidal toxins.

  1. Parametric estimation of 3D tubular structures for diffuse optical tomography

    PubMed Central

    Larusson, Fridrik; Anderson, Pamela G.; Rosenberg, Elizabeth; Kilmer, Misha E.; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L.

    2013-01-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction. PMID:23411913

  2. Image enhancement and segmentation of fluid-filled structures in 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Chalana, Vikram; Dudycha, Stephen; McMorrow, Gerald

    2003-05-01

    Segmentation of fluid-filled structures, such as the urinary bladder, from three-dimensional ultrasound images is necessary for measuring their volume. This paper describes a system for image enhancement, segmentation and volume measurement of fluid-filled structures on 3D ultrasound images. The system was applied for the measurement of urinary bladder volume. Results show an average error of less than 10% in the estimation of the total bladder volume.

  3. Optical fibre sensing in metals by embedment in 3D printed metallic structures

    NASA Astrophysics Data System (ADS)

    Maier, R. R. J.; Havermann, D.; Schneller, O.; Mathew, J.; Polyzos, D.; MacPherson, W. N.; Hand, D. P.

    2014-05-01

    Additive manufacturing or 3D printing of structural components in metals has potential to revolutionise the manufacturing industry. Embedded sensing in such structures opens a route towards SMART metals, providing added functionality, intelligence and enhanced performance in many components. Such embedded sensors would be capable of operating at extremely high temperatures by utilizing regenerated fibre Bragg gratings and in-fibre Fabry-Perot cavities.

  4. 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

  5. ModeRNA: a tool for comparative modeling of RNA 3D structure

    PubMed Central

    Rother, Magdalena; Rother, Kristian; Puton, Tomasz; Bujnicki, Janusz M.

    2011-01-01

    RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative modeling of RNA 3D structures. As an input, ModeRNA requires a 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template. It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post-translational modifications in proteins. ModeRNA can also model DNA structures or use them as templates. It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available. PMID:21300639

  6. 3D interactive model of lumbar spinal structures of anesthetic interest.

    PubMed

    Prats-Galino, Alberto; Reina, Miguel A; Mavar Haramija, Marija; Puigdellivol-Sánchez, Anna; Juanes Méndez, Juan A; De Andrés, José A

    2015-03-01

    A 3D model of lumbar structures of anesthetic interest was reconstructed from human magnetic resonance (MR) images and embedded in a Portable Document Format (PDF) file, which can be opened by freely available software and used offline. The MR images were analyzed using a specific 3D software platform for biomedical data. Models generated from manually delimited volumes of interest and selected MR images were exported to Virtual Reality Modeling Language format and were presented in a PDF document containing JavaScript-based functions. The 3D file and the corresponding instructions and license files can be downloaded freely at http://diposit.ub.edu/dspace/handle/2445/44844?locale=en. The 3D PDF interactive file includes reconstructions of the L3-L5 vertebrae, intervertebral disks, ligaments, epidural and foraminal fat, dural sac and nerve root cuffs, sensory and motor nerve roots of the cauda equina, and anesthetic approaches (epidural medial, spinal paramedial, and selective nerve root paths); it also includes a predefined sequential educational presentation. Zoom, 360° rotation, selective visualization, and transparency graduation of each structure and clipping functions are available. Familiarization requires no specialized informatics knowledge. The ease with which the document can be used could make it valuable for anatomical and anesthetic teaching and demonstration of patient information. PMID:25352014

  7. New insights into high resolution DEM structural analysis with Coltop3D software

    NASA Astrophysics Data System (ADS)

    Metzger, R.; Jaboyedoff, M.; Oppikofer, T.

    2009-04-01

    Modern measurement devices such a terrestrial laser scanning (TLS) systems allow for collecting tremendous amount of (x,y,z) points (up to 20 millions) within a few minutes. However, data analysis still may be impaired because of software limitations, which are usually not designed to handle such huge data sets. To overcome this shortcoming, a software - Coltop3D - was written from scratch. Coltop3D aims at providing the geosciences community a powerful tool to visually handle seamlessly large point clouds and large regular grids DEM, at allowing for straightforward visual analysis of the data with different colour scheme, and at providing specific geologist and/or geoscientist treatment methods such as structural analysis. The main features of Coltop3D are as follow: 1) Ability to handle huge data sets (up to 150 millions points); 2) Coloring the surface with a color scheme linking computer graphics HSV wheel and Schmidt-Lambert stereonet projection; 3) Ability to select a subset of a point cloud with complex geometric shapes; 4) Ability to select a subset of a point cloud with dip and dip direction values; 5) Creating density stereonets with selected subset; 6) Easily import from or export point cloud data to third party software. Besides the technical and basic capabilities of Coltop3D, specific case studies such as structural analysis and rock fall analysis will be presented.

  8. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications. PMID:25982877

  9. A lightweight tangible 3D interface for interactive visualization of thin fiber structures.

    PubMed

    Jackson, Bret; Lau, Tung Yuen; Schroeder, David; Toussaint, Kimani C; Keefe, Daniel F

    2013-12-01

    We present a prop-based, tangible interface for 3D interactive visualization of thin fiber structures. These data are commonly found in current bioimaging datasets, for example second-harmonic generation microscopy of collagen fibers in tissue. Our approach uses commodity visualization technologies such as a depth sensing camera and low-cost 3D display. Unlike most current uses of these emerging technologies in the games and graphics communities, we employ the depth sensing camera to create a fish-tank stereoscopic virtual reality system at the scientist's desk that supports tracking of small-scale gestures with objects already found in the work space. We apply the new interface to the problem of interactive exploratory visualization of three-dimensional thin fiber data. A critical task for the visual analysis of these data is understanding patterns in fiber orientation throughout a volume.The interface enables a new, fluid style of data exploration and fiber orientation analysis by using props to provide needed passive-haptic feedback, making 3D interactions with these fiber structures more controlled. We also contribute a low-level algorithm for extracting fiber centerlines from volumetric imaging. The system was designed and evaluated with two biophotonic experts who currently use it in their lab. As compared to typical practice within their field, the new visualization system provides a more effective way to examine and understand the 3D bioimaging datasets they collect.

  10. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications.

  11. Generation of 3-D surface maps in waste storage silos using a structured light source

    NASA Technical Reports Server (NTRS)

    Burks, B. L.; Rowe, J. C.; Dinkins, M. A.; Christensen, B.; Selleck, C.; Jacoboski, D.; Markus, R.

    1992-01-01

    Surface contours inside the large waste storage tanks typical of the Department of Energy (DOE) complex are, in general, highly irregular. In addition to pipes and other pieces of equipment in the tanks, the surfaces may have features such as mounds, fissures, crystalline structures, and mixed solid and liquid forms. Prior to remediation activities, it will be necessary to characterize the waste to determine the most effective remediation approaches. Surface contour data will be required both prior to and during remediation. The use is described of a structured light source to generate 3-D surface contour maps of the interior of waste storage silos at the Feed Materials Production Center at Fernald, OH. The landscape inside these large waste storage tanks bears a strong resemblance to some of the landscapes that might be encountered during lunar or planetary exploration. Hence, these terrestrial 3-D mapping techniques may be directly applicable to extraterrestrial exploration. In further development, it will be demonstrated that these 3-D data can be used for robotic task planning just as 3-D surface contour data of a satellite could be used to plan maintenance tasks for a space-based servicing robot.

  12. Optimal Image Stitching for Concrete Bridge Bottom Surfaces Aided by 3d Structure Lines

    NASA Astrophysics Data System (ADS)

    Liu, Yahui; Yao, Jian; Liu, Kang; Lu, Xiaohu; Xia, Menghan

    2016-06-01

    Crack detection for bridge bottom surfaces via remote sensing techniques is undergoing a revolution in the last few years. For such applications, a large amount of images, acquired with high-resolution industrial cameras close to the bottom surfaces with some mobile platform, are required to be stitched into a wide-view single composite image. The conventional idea of stitching a panorama with the affine model or the homographic model always suffers a series of serious problems due to poor texture and out-of-focus blurring introduced by depth of field. In this paper, we present a novel method to seamlessly stitch these images aided by 3D structure lines of bridge bottom surfaces, which are extracted from 3D camera data. First, we propose to initially align each image in geometry based on its rough position and orientation acquired with both a laser range finder (LRF) and a high-precision incremental encoder, and these images are divided into several groups with the rough position and orientation data. Secondly, the 3D structure lines of bridge bottom surfaces are extracted from the 3D cloud points acquired with 3D cameras, which impose additional strong constraints on geometrical alignment of structure lines in adjacent images to perform a position and orientation optimization in each group to increase the local consistency. Thirdly, a homographic refinement between groups is applied to increase the global consistency. Finally, we apply a multi-band blending algorithm to generate a large-view single composite image as seamlessly as possible, which greatly eliminates both the luminance differences and the color deviations between images and further conceals image parallax. Experimental results on a set of representative images acquired from real bridge bottom surfaces illustrate the superiority of our proposed approaches.

  13. Pipeline inwall 3D measurement system based on the cross structured light

    NASA Astrophysics Data System (ADS)

    Shen, Da; Lin, Zhipeng; Xue, Lei; Zheng, Qiang; Wang, Zichi

    2014-01-01

    In order to accurately realize the defect detection of pipeline inwall, this paper proposes a measurement system made up of cross structured light, single CCD camera and a smart car, etc. Based on structured light measurement technology, this paper mainly introduces the structured light measurement system, the imaging mathematical model, and the parameters and method of camera calibration. Using these measuring principles and methods, the camera in remote control car platform achieves continuous shooting of objects and real-time rebound processing as well as utilizing established model to extract 3D point cloud coordinate to reconstruct pipeline defects, so it is possible to achieve 3D automatic measuring, and verifies the correctness and feasibility of this system. It has been found that this system has great measurement accuracy in practice.

  14. Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure

    NASA Astrophysics Data System (ADS)

    Prilusky, Jaime; Hodis, Eran; Sussman, Joel L.

    Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other structures. Proteopedia ( http://www.proteopedia.org ) presents 3D biomolecule structures in a broadly accessible manner to a diverse scientific audience through easy-to-use molecular visualization tools integrated into a wiki environment that anyone with a user account can edit. We describe recent advances in the web resource in the areas of content and software. In terms of content, we describe a large growth in user-added content as well as improvements in automatically-generated content for all PDB entry pages in the resource. In terms of software, we describe new features ranging from the capability to create pages hidden from public view to the capability to export pages for offline viewing. New software features also include an improved file-handling system and availability of biological assemblies of protein structures alongside their asymmetric units.

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

    PubMed

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

    1993-12-01

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

  16. Ripple modulated electronic structure of a 3D topological insulator

    NASA Astrophysics Data System (ADS)

    Madhavan, Vidya

    2013-03-01

    Many of the unusual properties of topological insulators can only be realized through a delicate tuning of the Dirac surface state rendering their detection thus far elusive. We have discovered that the surface state dispersion of a prototypical topological insulator can be continuously tuned via a novel topographical route. STM images of Bi2Te3 show one-dimensional (striped) ripples with 100nm periodicity. By combining information from Landau level spectra and Fourier transform of interference patterns we show that the ripples induce spatial modulations in the surface state dispersion. We describe how the ripples create topological channels for chiral spin modes at the boundaries such that placing the Fermi energy between the Landau levels of these periodic stripes would result in the first experimental realization of the ideal 1D dissipationless quantum wire. This ability to tune the surface state dispersion locally opens the door to a host of new phenomena in topological insulators.

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

    PubMed

    Berg, Sigrid; Rønnekleiv, Arne

    2012-07-01

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

  18. 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

  19. Topological evolutionary computing in the optimal design of 2D and 3D structures

    NASA Astrophysics Data System (ADS)

    Burczynski, T.; Poteralski, A.; Szczepanik, M.

    2007-10-01

    An application of evolutionary algorithms and the finite-element method to the topology optimization of 2D structures (plane stress, bending plates, and shells) and 3D structures is described. The basis of the topological evolutionary optimization is the direct control of the density material distribution (or thickness for 2D structures) by the evolutionary algorithm. The structures are optimized for stress, mass, and compliance criteria. The numerical examples demonstrate that this method is an effective technique for solving problems in computer-aided optimal design.

  20. 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

  1. 3D structure and conductive thermal field of the Upper Rhine Graben

    NASA Astrophysics Data System (ADS)

    Freymark, Jessica; Sippel, Judith; Scheck-Wenderoth, Magdalena; Bär, Kristian; Stiller, Manfred; Fritsche, Johann-Gerhard; Kracht, Matthias

    2016-04-01

    The Upper Rhine Graben (URG) was formed as part of the European Cenozoic Rift System in a complex extensional setting. At present-day, it has a large socioeconomic relevance as it provides a great potential for geothermal energy production in Germany and France. For the utilisation of this energy resource it is crucial to understand the structure and the observed temperature anomalies in the rift basin. In the framework of the EU-funded "IMAGE" project (Integrated Methods for Advanced Geothermal Exploration), we apply a data-driven numerical modelling approach to quantify the processes and properties controlling the spatial distribution of subsurface temperatures. Typically, reservoir-scale numerical models are developed for predictions on the subsurface hydrothermal conditions and for reducing the risk of drilling non-productive geothermal wells. One major problem related to such models is setting appropriate boundary conditions that define, for instance, how much heat enters the reservoir from greater depths. Therefore, we first build a regional lithospheric-scale 3D structural model, which covers not only the entire URG but also adjacent geological features like the Black Forest and the Vosges Mountains. In particular, we use a multidisciplinary dataset (e.g. well data, seismic reflection data, existing structural models, gravity) to construct the geometries of the sediments, the crust and the lithospheric mantle that control the spatial distribution of thermal conductivity and radiogenic heat production and hence temperatures. By applying a data-based and lithology-dependent parameterisation of this lithospheric-scale 3D structural model and a 3D finite element method, we calculate the steady-state conductive thermal field for the entire region. Available measured temperatures (down to depths of up to 5 km) are considered to validate the 3D thermal model. We present major characteristics of the lithospheric-scale 3D structural model and results of the 3D

  2. 3D structure tensor analysis of light microscopy data for validating diffusion MRI

    PubMed Central

    Khan, Ahmad Raza; Cornea, Anda; Leigland, Lindsey A.; Kohama, Steven G.; Jespersen, Sune Nørhøj; Kroenke, Christopher D.

    2015-01-01

    Diffusion magnetic resonance imaging (d-MRI) is a powerful non-invasive and non-destructive technique for characterizing brain tissue on the microscopic scale. However, the lack of validation of d-MRI by independent experimental means poses an obstacle to accurate interpretation of data acquired using this method. Recently, structure tensor analysis has been applied to light microscopy images, and this technique holds promise to be a powerful validation strategy for d-MRI. Advantages of this approach include its similarity to d-MRI in terms of averaging the effects of a large number of cellular structures, and its simplicity, which enables it to be implemented in a high-throughput manner. However, a drawback of previous implementations of this technique arises from it being restricted to 2D. As a result, structure tensor analyses have been limited to tissue sectioned in a direction orthogonal to the direction of interest. Here we describe the analytical framework for extending structure tensor analysis to 3D, and utilize the results to analyze serial image “stacks” acquired with confocal microscopy of rhesus macaque hippocampal tissue. Implementation of 3D structure tensor procedures requires removal of sources of anisotropy introduced in tissue preparation and confocal imaging. This is accomplished with image processing steps to mitigate the effects of anisotropic tissue shrinkage, and the effects of anisotropy in the point spread function (PSF). In order to address the latter confound, we describe procedures for measuring the dependence of PSF anisotropy on distance from the microscope objective within tissue. Prior to microscopy, ex vivo d-MRI measurements performed on the hippocampal tissue revealed three regions of tissue with mutually orthogonal directions of least restricted diffusion that correspond to CA1, alveus and inferior longitudinal fasciculus. We demonstrate the ability of 3D structure tensor analysis to identify structure tensor orientations

  3. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases. PMID:26231917

  4. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases.

  5. A fast and low-loss 3-D magnetotelluric inversion method with parallel structure

    NASA Astrophysics Data System (ADS)

    Zhang, K.; Zhang, L.

    2013-12-01

    The 2D assumption is valid in some cases of interpretation, the approximation does not work in most cases, especially in areas with complex geo-electrical structure. A number of 3D magentotelluric inversion methods has been proposed, including RRI, CG, QA, NLCG. Each of those methods has its own advantages and disadvantages. However, as the 3D dataset and mesh grid require greater computer memory and calculation time than 2D methods, the efficiency of the inversion scheme become a key concern of 3D inversions. We chose NLCG as the optimization method for inversion. A parameter matrix related with the current resisitivity model and data error is proposed to approximate the Hessian matrix. So four forward calculation can be avoided each iteration. In addition, OPENMP parallel API is utilized to establish an effecient parallel inversion structure based on frequency to reduce computation time. And both synthetic and field data are used to test the efficiency of the inversion and the preconditioning method. The model consists of four square prisms residing in a halfspace. The total computation time of invertion is 706s (use one PC). Fiugre 1 shows the inversion result. The abnormal bodies can be distinguished clearly. Field data from the NIHE dataset in China is used to verify the reliability and efficiency of the 3D inversion method. The total computation time is about 25 minutes after 60 iterations on one PC. Totally, four electrical layers can be corresponded to the four stratum in 3D AMT inversion model, and the faults can be seen clearly. In addition, we can get more information about fault and alteration interface from constrained inversion result. Finally, the inversion method is very fast and low-loss, so it can be used in modern PC (need only one PC) with few hardware constraints. (a): initial model; (b): inversion depth slices (1-4km); (c): fitting error (a): AMT 3D slice; (b): CSAMT 2D model; (c): TEM 1D model; (d): SIP 2D model; (e) AMT 3D constrained

  6. Low-cost structured-light based 3D capture system design

    NASA Astrophysics Data System (ADS)

    Dong, Jing; Bengtson, Kurt R.; Robinson, Barrett F.; Allebach, Jan P.

    2014-03-01

    Most of the 3D capture products currently in the market are high-end and pricey. They are not targeted for consumers, but rather for research, medical, or industrial usage. Very few aim to provide a solution for home and small business applications. Our goal is to fill in this gap by only using low-cost components to build a 3D capture system that can satisfy the needs of this market segment. In this paper, we present a low-cost 3D capture system based on the structured-light method. The system is built around the HP TopShot LaserJet Pro M275. For our capture device, we use the 8.0 Mpixel camera that is part of the M275. We augment this hardware with two 3M MPro 150 VGA (640 × 480) pocket projectors. We also describe an analytical approach to predicting the achievable resolution of the reconstructed 3D object based on differentials and small signal theory, and an experimental procedure for validating that the system under test meets the specifications for reconstructed object resolution that are predicted by our analytical model. By comparing our experimental measurements from the camera-projector system with the simulation results based on the model for this system, we conclude that our prototype system has been correctly configured and calibrated. We also conclude that with the analytical models, we have an effective means for specifying system parameters to achieve a given target resolution for the reconstructed object.

  7. 3D structure tensor analysis of light microscopy data for validating diffusion MRI.

    PubMed

    Khan, Ahmad Raza; Cornea, Anda; Leigland, Lindsey A; Kohama, Steven G; Jespersen, Sune Nørhøj; Kroenke, Christopher D

    2015-05-01

    Diffusion magnetic resonance imaging (d-MRI) is a powerful non-invasive and non-destructive technique for characterizing brain tissue on the microscopic scale. However, the lack of validation of d-MRI by independent experimental means poses an obstacle to accurate interpretation of data acquired using this method. Recently, structure tensor analysis has been applied to light microscopy images, and this technique holds promise to be a powerful validation strategy for d-MRI. Advantages of this approach include its similarity to d-MRI in terms of averaging the effects of a large number of cellular structures, and its simplicity, which enables it to be implemented in a high-throughput manner. However, a drawback of previous implementations of this technique arises from it being restricted to 2D. As a result, structure tensor analyses have been limited to tissue sectioned in a direction orthogonal to the direction of interest. Here we describe the analytical framework for extending structure tensor analysis to 3D, and utilize the results to analyze serial image "stacks" acquired with confocal microscopy of rhesus macaque hippocampal tissue. Implementation of 3D structure tensor procedures requires removal of sources of anisotropy introduced in tissue preparation and confocal imaging. This is accomplished with image processing steps to mitigate the effects of anisotropic tissue shrinkage, and the effects of anisotropy in the point spread function (PSF). In order to address the latter confound, we describe procedures for measuring the dependence of PSF anisotropy on distance from the microscope objective within tissue. Prior to microscopy, ex vivo d-MRI measurements performed on the hippocampal tissue revealed three regions of tissue with mutually orthogonal directions of least restricted diffusion that correspond to CA1, alveus and inferior longitudinal fasciculus. We demonstrate the ability of 3D structure tensor analysis to identify structure tensor orientations that

  8. Topology optimization of 3D structures with design-dependent loads

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Liu, Shu-Tian; Zhang, Xiong

    2010-10-01

    Topology optimization of continuum structures with design-dependent loads has long been a challenge. In this paper, the topology optimization of 3D structures subjected to design-dependent loads is investigated. A boundary search scheme is proposed for 3D problems, by means of which the load surface can be identified effectively and efficiently, and the difficulties arising in other approaches can be overcome. The load surfaces are made up of the boundaries of finite elements and the loads can be directly applied to corresponding element nodes, which leads to great convenience in the application of this method. Finally, the effectiveness and efficiency of the proposed method is validated by several numerical examples.

  9. 1D nanorod-planted 3D inverse opal structures for use in dye-sensitized solar cells.

    PubMed

    Park, Yesle; Lee, Jung Woo; Ha, Su-Jin; Moon, Jun Hyuk

    2014-03-21

    The effectiveness of the 1D nanorod (NR)-planted 3D inverse opal (IO) structure as an electrode for dye-sensitized solar cells (DSSCs) is demonstrated here. The NRs were grown on the surface of a macroporous IO structure and their longitudinal growth increased the surface area of the structure proportional to the growth duration. NR/IO electrodes with various NR growth times were compared. A remarkable JSC was obtained for the DSSCs utilizing a NR/IO electrode. The improvement of the JSC was analyzed in terms of its efficiency in light harvesting and electron transport. The growth of the NRs improved the dye adsorption density and scattering property of the electrode, resulting in an improvement in the light harvesting efficiency. Electrochemical impedance analysis revealed that the NRs also improved its electron transport properties. Further growth of the NRs tended to limit the increase of the JSC, which could be attributed to an overlap between them. PMID:24356878

  10. 3D form line construction by structural field interpolation (SFI) of geologic strike and dip observations

    NASA Astrophysics Data System (ADS)

    Hillier, Michael; de Kemp, Eric; Schetselaar, Ernst

    2013-06-01

    Interpreting and modelling geometries of complex geologic structures from strike/dip measurements using manually-drafted structural form lines is labour intensive, irreproducible and inherently limited to two dimensions. Herein, the structural field interpolation (SFI) algorithm is presented that overcomes these limitations by constructing 3D structural form lines from the vector components of strike/dip measurements. The SFI interpolation algorithm employs an anisotropic inverse distance weighting scheme derived from eigen analysis of the poles to strike/dip measurements within a neighbourhood of user defined dimension and shape (ellipsoidal to spherical) and honours younging directions, when available. The eigen analysis also provides local estimates of the plunge vector and associated Woodcock distribution properties to assure plunge-normal structural form line reconstruction with unidirectional propagation of form lines across fold and fan structures. The method is advantageous for modelling geometries of geologic structures from a wide range of structurally anisotropic data. Modelled vector fields from three case studies are presented that reproduce the expected bedding-foliation geometry and provide reasonable representation of complex folds from local to regional scales. Results illustrate the potential for using vector fields to support geologic interpretation through the direct visualization of geometric trends of structural features in 3D.

  11. Computer modeling of 3D structures of cytochrome P450s.

    PubMed

    Chang, Y T; Stiffelman, O B; Loew, G H

    1996-01-01

    The understanding of structure-function relationship of enzymes requires detailed information of their three-dimensional structure. Protein structure determination by X-ray and NMR methods, the two most frequently used experimental procedures, are often difficult and time-consuming. Thus computer modeling of protein structures has become an increasingly active and attractive option for obtaining predictive models of three-dimensional protein structures. Specifically, for the ubiquitous metabolizing heme proteins, the cytochrome P450s, the X-ray structures of four isozymes of bacterial origin, P450cam, P450terp, P450BM-3 and P450eryF have now been determined. However, attempts to obtain the structure of mammalian forms by experimental means have thus far not been successful. Thus, there have been numerous attempts to construct models of mammalian P450s using homology modeling methods in which the known structures have been used to various extents and in various strategies to build models of P450 isozymes. In this paper, we review these efforts and then describe a strategy for structure building and assessment of 3D models of P450s recently developed in our laboratory that corrects many of the weaknesses in the previous procedures. The results are 3D models that for the first time are stable to unconstrained molecular dynamics simulations. The use of this method is demonstrated by the construction and validation of a 3D model for rabbit liver microsomal P450 isozyme 2B4, responsible for the oxidative metabolism of diverse xenobiotics including widely used inhalation anesthetics. Using this 2B4 model, the substrate access channel, substrate binding site and plausible surface regions for binding with P450 redox partners were identified. PMID:9010606

  12. A theoretical study of the structure and stability of borohydride on 3d transition metals

    NASA Astrophysics Data System (ADS)

    Arevalo, Ryan Lacdao; Escaño, Mary Clare Sison; Gyenge, Elod; Kasai, Hideaki

    2012-12-01

    The adsorption of borohydride on 3d transition metals (Cr, Mn, Fe, Co, Ni and Cu) was studied using first principles calculations within spin-polarized density functional theory. Magnetic effect on the stability of borohydride is noted. Molecular adsorption is favorable on Co, Ni and Cu, which is characterized by the strong s-dzz hybridization of the adsorbate-substrate states. Dissociated adsorption structure yielding one or two H adatom fragments on the surface is observed for Cr, Mn and Fe.

  13. 3D reconstruction of internal structure of animal body using near-infrared light

    NASA Astrophysics Data System (ADS)

    Tran, Trung Nghia; Yamamoto, Kohei; Namita, Takeshi; Kato, Yuji; Shimizu, Koichi

    2014-03-01

    To realize three-dimensional (3D) optical imaging of the internal structure of animal body, we have developed a new technique to reconstruct CT images from two-dimensional (2D) transillumination images. In transillumination imaging, the image is blurred due to the strong scattering in the tissue. We had developed a scattering suppression technique using the point spread function (PSF) for a fluorescent light source in the body. In this study, we have newly proposed a technique to apply this PSF for a light source to the image of unknown light-absorbing structure. The effectiveness of the proposed technique was examined in the experiments with a model phantom and a mouse. In the phantom experiment, the absorbers were placed in the tissue-equivalent medium to simulate the light-absorbing organs in mouse body. Near-infrared light was illuminated from one side of the phantom and the image was recorded with CMOS camera from another side. Using the proposed techniques, the scattering effect was efficiently suppressed and the absorbing structure can be visualized in the 2D transillumination image. Using the 2D images obtained in many different orientations, we could reconstruct the 3D image. In the mouse experiment, an anesthetized mouse was held in an acrylic cylindrical holder. We can visualize the internal organs such as kidneys through mouse's abdomen using the proposed technique. The 3D image of the kidneys and a part of the liver were reconstructed. Through these experimental studies, the feasibility of practical 3D imaging of the internal light-absorbing structure of a small animal was verified.

  14. 3D Structures: Microfluidic Stamping on Sheath Flow (Small 24/2016).

    PubMed

    Yoon, Dong Hyun; Tanaka, Daiki; Sekiguchi, Tetsushi; Shoji, Shuichi

    2016-06-01

    A microfluidic stamping method to form functional shapes on a cross section in fibre-shaped flow is presented by D. H. Yoon and co-workers on page 3224. Microfluidic stamping and overstamping allowed various cross sectional shapes on the three-dimensional flow. Dimension of the flows is controlled via a change in combination of 3D structures and fluidic conditions, which correspond to stamp type and stamping force. PMID:27306739

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  16. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures.

    PubMed

    Nadzirin, Nurul; Gardiner, Eleanor J; Willett, Peter; Artymiuk, Peter J; Firdaus-Raih, Mohd

    2012-07-01

    Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/. PMID:22573174

  17. Segmentation of bone structures in 3D CT images based on continuous max-flow optimization

    NASA Astrophysics Data System (ADS)

    Pérez-Carrasco, J. A.; Acha-Piñero, B.; Serrano, C.

    2015-03-01

    In this paper an algorithm to carry out the automatic segmentation of bone structures in 3D CT images has been implemented. Automatic segmentation of bone structures is of special interest for radiologists and surgeons to analyze bone diseases or to plan some surgical interventions. This task is very complicated as bones usually present intensities overlapping with those of surrounding tissues. This overlapping is mainly due to the composition of bones and to the presence of some diseases such as Osteoarthritis, Osteoporosis, etc. Moreover, segmentation of bone structures is a very time-consuming task due to the 3D essence of the bones. Usually, this segmentation is implemented manually or with algorithms using simple techniques such as thresholding and thus providing bad results. In this paper gray information and 3D statistical information have been combined to be used as input to a continuous max-flow algorithm. Twenty CT images have been tested and different coefficients have been computed to assess the performance of our implementation. Dice and Sensitivity values above 0.91 and 0.97 respectively were obtained. A comparison with Level Sets and thresholding techniques has been carried out and our results outperformed them in terms of accuracy.

  18. Integration of nano-scale components and supports in micromachined 3D silicon structures

    NASA Astrophysics Data System (ADS)

    Song, J.; Azimi, S.; Y Dang, Z.; Breese, M. B. H.

    2014-04-01

    We have developed a process for the three-dimensional (3D) machining of p-type silicon on a micro- and nano-scale using high-energy ion beam irradiation with one or more energies and fluences, followed by electrochemical anodization in hydrofluoric acid. We present a study of the dependence of our fabricated structures on irradiating ion energies, fluences, geometries and wafer resistivity. All these factors determine whether the micro- and nano-scale features are properly connected to the supports in the 3D silicon structures. If wrongly chosen, any of these factors may cause a breakage at the connection through localized over-etching. Under optimum irradiation and anodization conditions, free-standing patterned membranes can be fabricated with feature dimensions of 100 nm over areas of many square millimeters. This investigation is based on silicon structures but is relevant to any electro-assisted etching process for 3D fabrication, paving the way for achieving free-standing silicon photonics, mechanical resonators and micro-/nano-electromechanical systems.

  19. Enhanced hybrid search algorithm for protein structure prediction using the 3D-HP lattice model.

    PubMed

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

    2013-09-01

    The problem of protein structure prediction in the hydrophobic-polar (HP) lattice model is the prediction of protein tertiary structure. This problem is usually referred to as the protein folding problem. This paper presents a method for the application of an enhanced hybrid search algorithm to the problem of protein folding prediction, using the three dimensional (3D) HP lattice model. The enhanced hybrid search algorithm is a combination of the particle swarm optimizer (PSO) and tabu search (TS) algorithms. Since the PSO algorithm entraps local minimum in later evolution extremely easily, we combined PSO with the TS algorithm, which has properties of global optimization. Since the technologies of crossover and mutation are applied many times to PSO and TS algorithms, so enhanced hybrid search algorithm is called the MCMPSO-TS (multiple crossover and mutation PSO-TS) algorithm. Experimental results show that the MCMPSO-TS algorithm can find the best solutions so far for the listed benchmarks, which will help comparison with any future paper approach. Moreover, real protein sequences and Fibonacci sequences are verified in the 3D HP lattice model for the first time. Compared with the previous evolutionary algorithms, the new hybrid search algorithm is novel, and can be used effectively to predict 3D protein folding structure. With continuous development and changes in amino acids sequences, the new algorithm will also make a contribution to the study of new protein sequences. PMID:23824509

  20. 3-D Structure of the Slave and Rae Cratons Provides Clues to Their Construction

    NASA Astrophysics Data System (ADS)

    Snyder, D. B.

    2013-12-01

    Deep geologic structures within cratons that make up continental cores were long neglected. Recently acquired geophysical data from large observational arrays and geochemical data resulting from exploration for diamond has now made possible co-registration of large-scale (400-km depth), truly 3-dimensional data sets. P-waves, surface waves and magnetotelluric observations provide 3-D wavespeed and conductivity models. Multi-azimuthal receiver functions map seismic discontinuity surfaces in 3-D. Xenolith suites erupted in kimberlites provide rock samples at key lithospheric depths, albeit at sparsely distributed locations. These multi-disciplinary models are becoming available for several key cratons worldwide; here the deep structure of the Slave and Rae cratons of the Canadian Shield is described. Lithospheric layers with tapered, wedge-shaped margins are common. Slave craton layers are sub-horizontal and indicate construction of the craton core at 2.7 Ga by underthrusting and flat stacking of lithosphere. The central Rae craton has predominantly dipping discontinuities that indicate construction at 1.9 Ga by thrusting similar to that observed in crustal ';thick-skinned' fold-and-thrust belts. 3-D mapping of conductivity and metasomatism, the latter via mineral recrystallization and resetting of isotopic ages, overprints primary structures in both cratons. Distribution of more conductivitve mantle suggests that assumed causative pervasive metasomatism occurs at 100-200 km depths with ';chimneys' reaching to shallower depths, typically in locations where kimberlites or mineralization has occurred.

  1. MAP(2.0)3D: a sequence/structure based server for protein engineering.

    PubMed

    Verma, Rajni; Schwaneberg, Ulrich; Roccatano, Danilo

    2012-04-20

    The Mutagenesis Assistant Program (MAP) is a web-based tool to provide statistical analyses of the mutational biases of directed evolution experiments on amino acid substitution patterns. MAP analysis assists protein engineers in the benchmarking of random mutagenesis methods that generate single nucleotide mutations in a codon. Herein, we describe a completely renewed and improved version of the MAP server, the MAP(2.0)3D server, which correlates the generated amino acid substitution patterns to the structural information of the target protein. This correlation aids in the selection of a more suitable random mutagenesis method with specific biases on amino acid substitution patterns. In particular, the new server represents MAP indicators on secondary and tertiary structure and correlates them to specific structural components such as hydrogen bonds, hydrophobic contacts, salt bridges, solvent accessibility, and crystallographic B-factors. Three model proteins (D-amino oxidase, phytase, and N-acetylneuraminic acid aldolase) are used to illustrate the novel capability of the server. MAP(2.0)3D server is available publicly at http://map.jacobs-university.de/map3d.html.

  2. Minimizing camera-eye optical aberrations during the 3D reconstruction of retinal structures

    NASA Astrophysics Data System (ADS)

    Aldana-Iuit, Javier; Martinez-Perez, M. Elena; Espinosa-Romero, Arturo; Diaz-Uribe, Rufino

    2010-05-01

    3D reconstruction of blood vessels is a powerful visualization tool for physicians, since it allows them to refer to qualitative representation of their subject of study. In this paper we propose a 3D reconstruction method of retinal vessels from fundus images. The reconstruction method propose herein uses images of the same retinal structure in epipolar geometry. Images are preprocessed by RISA system for segmenting blood vessels and obtaining feature points for correspondences. The correspondence points process is solved using correlation. The LMedS analysis and Graph Transformation Matching algorithm are used for outliers suppression. Camera projection matrices are computed with the normalized eight point algorithm. Finally, we retrieve 3D position of the retinal tree points by linear triangulation. In order to increase the power of visualization, 3D tree skeletons are represented by surfaces via generalized cylinders whose radius correspond to morphological measurements obtained by RISA. In this paper the complete calibration process including the fundus camera and the optical properties of the eye, the so called camera-eye system is proposed. On one hand, the internal parameters of the fundus camera are obtained by classical algorithms using a reference pattern. On the other hand, we minimize the undesirable efects of the aberrations induced by the eyeball optical system assuming that contact enlarging lens corrects astigmatism, spherical and coma aberrations are reduced changing the aperture size and eye refractive errors are suppressed adjusting camera focus during image acquisition. Evaluation of two self-calibration proposals and results of 3D blood vessel surface reconstruction are presented.

  3. Novel 3D bismuth-based coordination polymers: Synthesis, structure, and second harmonic generation properties

    SciTech Connect

    Wibowo, Arief C.; Smith, Mark D.; Yeon, Jeongho; Halasyamani, P. Shiv; Loye, Hans-Conrad zur

    2012-11-15

    Two new 3D bismuth containing coordination polymers are reported along with their single crystal structures and SHG properties. Compound 1: Bi{sub 2}O{sub 2}(pydc) (pydc=pyridine-2, 5-dicarboxylate), crystallizes in the monoclinic, polar space group, P2{sub 1} (a=9.6479(9) A, b=4.2349(4) A, c=11.9615(11) A, {beta}=109.587(1) Degree-Sign ), which contains Bi{sub 2}O{sub 2} chains that are connected into a 3D structure via the pydc ligands. Compound 2: Bi{sub 4}Na{sub 4}(1R3S-cam){sub 8}(EtOH){sub 3.1}(H{sub 2}O){sub 3.4} (1R3S cam=1R3S-camphoric acid) crystallizes in the monoclinic, polar space group, P2{sub 1} (a=19.0855(7) A, b=13.7706(5) A, c=19.2429(7) A, {beta}=90.701(1) Degree-Sign ) and is a true 3D coordination polymer. These are two example of SHG compounds prepared using unsymmetric ligands (compound 1) or chiral ligands (compound 2), together with metals that often exhibit stereochemically-active lone pairs, such as Bi{sup 3+}, a synthetic approach that resulted in polar, non-centrosymmetric, 3D metal-organic coordination polymer. - Graphical Abstract: Structures of two new, polar, 3D Bismuth(III)-based coordination polymers: Bi{sub 2}O{sub 2}(pydc) (compound 1), and Bi{sub 4}Na{sub 4}(1R3S-cam){sub 8}(EtOH){sub 3.1}(H{sub 2}O){sub 3.4} (compound 2). Highlights: Black-Right-Pointing-Pointer New, polar, 3D Bismuth(III)-based coordination polymers. Black-Right-Pointing-Pointer First polar bismuth-based coordination polymers synthesized via a 'hybrid' strategy. Black-Right-Pointing-Pointer Combination of stereochemically-active lone pairs and unsymmetrical or chiral ligands. Black-Right-Pointing-Pointer Synthesis of class C-SHG materials based on Kurtz-Perry categories.

  4. [MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].

    PubMed

    Korkosh, V S; Zhorov, B S; Tikhonov, D B

    2016-01-01

    An integral part of modern evolutionary biology is comparative analysis of structure and function of macromolecules such as proteins. The first and critical step to understand evolution of homologous proteins is their amino acid sequence alignment. However, standard algorithms fop not provide unambiguous sequence alignments for proteins of poor homology. More reliable results can be obtained by comparing experimental 3D structures obtained at atomic resolution, for instance, with the aid of X-ray structural analysis. If such structures are lacking, homology modeling is used, which may take into account indirect experimental data on functional roles of individual amino-acid residues. An important problem is that the sequence alignment, which reflects genetic modifications, does not necessarily correspond to the functional homology. The latter depends on three-dimensional structures which are critical for natural selection. Since alignment techniques relying only on the analysis of primary structures carry no information on the functional properties of proteins, including 3D structures into consideration is very important. Here we consider several examples involving ion channels and demonstrate that alignment of their three-dimensional structures can significantly improve sequence alignments obtained by traditional methods.

  5. 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.

  6. 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

  7. 3-D Radar Imaging Reveals Deep Structures and Buried Craters Within the Martian Polar Caps

    NASA Astrophysics Data System (ADS)

    Putzig, N. E.; Foss, F. J., II; Campbell, B. A.; Phillips, R. J.; Smith, I. B.

    2015-12-01

    We use Shallow Radar (SHARAD) observations on thousands of orbital passes by the Mars Reconnaissance Orbiter to produce fully imaged 3-D data volumes encompassing both polar ice caps of Mars. Greatly clarifying the view of subsurface features, a completed volume for Planum Boreum provides new constraints on the nature and timing of emplacement of the northern polar deposits and their relationship to climate. The standard method of mapping subsurface features with single-pass 2-D radargrams has been very fruitful (see Brothers et al. 2015, JGR 120 in press, and references therein), but a full assessment of internal structures has been hindered by interfering off-nadir echoes from spiral troughs and other variable topography prevalent on both caps. By assembling the SHARAD radargrams into a volume and applying a 3-D imaging process (migration) borrowed from seismic processing techniques, we enhance the signal-to-noise ratio while repositioning the echoes to their proper locations, thereby unraveling the interference. As part of the process, we correct ionospheric distortions and delays of the radar echoes (Campbell et al. 2014, IEEE GRSL 11 #3). Interfaces painstakingly mapped in radargrams (e.g., the basal-unit surface, a buried chasma) are clearly visible in the 3-D volume, and new features are revealed. Structures may now be mapped through trough-rich regions, including a widespread sequence that provides corroborative evidence of recent ice ages (Smith et al. 2015, LPSC XLVI #2574). Distinctive radar signatures associated with known, partially buried craters also occur elsewhere in the volume but without surface expression. Presumably, these are fully buried craters that may provide a new means to estimate the age of the deposits. Preliminary work for Planum Australe demonstrates that the 3-D processing currently underway will illuminate deep structures that are broadly obfuscated in 2-D radargrams by a shallow scatterer (Campbell et al. 2015, LPSC XLVI #2366).

  8. 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.

  9. Monolithic 3D titania with ultrathin nanoshell structures for enhanced photocatalytic activity and recyclability

    NASA Astrophysics Data System (ADS)

    Ahn, Changui; Park, Junyong; Kim, Donghyuk; Jeon, Seokwoo

    2013-10-01

    nanoshell titania increases the photocatalytic performance more than three-fold relative to that of a thin film of equivalent sample size. Also, the monolithic form of titania enables it to be reused without any degradation of photocatalytic activity. The newly developed nanomaterials in this study can serve as an efficient and reusable photocatalyst for water purification systems. Electronic supplementary information (ESI) available: Further details of SEM images of 3D nanoshell titania and a P25 film, thickness of coated titania measured by AFM, photocatalytic performance of a P25 film and a thin film, a detailed unit cell model of 3D nanostructures for calculation of the theoretical surface area, and comparison data of photocatalytic performances with references. See DOI: 10.1039/c3nr03115b

  10. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    PubMed Central

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-01-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations. PMID:26346202

  11. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    NASA Astrophysics Data System (ADS)

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-09-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations.

  12. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers.

    PubMed

    Mao, Yiqi; Yu, Kai; Isakov, Michael S; Wu, Jiangtao; Dunn, Martin L; Jerry Qi, H

    2015-01-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations. PMID:26346202

  13. Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities

    PubMed Central

    Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong

    2016-01-01

    Three-dimensional (3D) genome structures vary from cell to cell even in an isogenic sample. Unlike protein structures, genome structures are highly plastic, posing a significant challenge for structure-function mapping. Here we report an approach to comprehensively identify 3D chromatin clusters that each occurs frequently across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data. Applying our method to a population of genome structures (at the macrodomain resolution) of lymphoblastoid cells, we identify an atlas of stable inter-chromosomal chromatin clusters. A large number of these clusters are enriched in binding of specific regulatory factors and are therefore defined as ‘Regulatory Communities.' We reveal two major factors, centromere clustering and transcription factor binding, which significantly stabilize such communities. Finally, we show that the regulatory communities differ substantially from cell to cell, indicating that expression variability could be impacted by genome structures. PMID:27240697

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

    NASA Astrophysics Data System (ADS)

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

    1996-06-01

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

  15. Combination of photogrammetric and geoelectric methods to assess 3d structures associated to natural hazards

    NASA Astrophysics Data System (ADS)

    Fargier, Yannick; Dore, Ludovic; Antoine, Raphael; Palma Lopes, Sérgio; Fauchard, Cyrille

    2016-04-01

    The extraction of subsurface materials is a key element for the economy of a nation. However, natural degradation of underground quarries is a major issue from an economic and public safety point of view. Consequently, the quarries stakeholders require relevant tools to define hazards associated to these structures. Safety assessment methods of underground quarries are recent and mainly based on rock physical properties. This kind of method leads to a certain homogeneity assumption of pillar internal properties that can cause an underestimation of the risk. Electrical Resistivity Imaging (ERI) is a widely used method that possesses two advantages to overcome this limitation. The first is to provide a qualitative understanding for the detection and monitoring of anomalies in the pillar body (e.g. faults). The second is to provide a quantitative description of the electrical resistivity distribution inside the pillar. This quantitative description can be interpreted with constitutive laws to help decision support (water content decreases the mechanical resistance of a chalk). However, conventional 2D and 3D Imaging techniques are usually applied to flat surface surveys or to surfaces with moderate topography. A 3D inversion of more complex media (case of the pillar) requires a full consideration of the geometry that was never taken into account before. The Photogrammetric technique presents a cost effective solution to obtain an accurate description of the external geometry of a complex media. However, this method has never been fully coupled with a geophysical method to enhance/improve the inversion process. Consequently we developed a complete procedure showing that photogrammetric and ERI tools can be efficiently combined to assess a complex 3D structure. This procedure includes in a first part a photogrammetric survey, a processing stage with an open source software and a post-processing stage finalizing a 3D surface model. The second part necessitates the

  16. The feasibility of photo-based 3D modeling for the structures by using a common digital camera

    NASA Astrophysics Data System (ADS)

    Li, Ping; Zhang, Jin-quan; Li, Wan-heng; Lv, Jian-ming; Wang, Xin-zheng

    2011-12-01

    This article explored the method of photo-based 3D modeling for the arc bridge structures by ordinary digital camera. Firstly, a series of processes had been studied by using ordinary digital camera that included the camera calibration, data acquisition, data management, and 3D orientation, setting scale and textures, etc., then the 3D model from photos can be built. The model can be measured, edited and close to the real structures. Take an interior masonry arch bridge as an example, build 3D model through the processes above by using camera HP CB350. The 3D model can be integrated with the loading conditions and material properties, to provide the detailed data for analyzing the structure. This paper has accumulated the experience in data acquisition and modeling methods. The methods can be applied to other structural analysis, and other conditions of 3D modeling with fast and economic advantages.

  17. Characterization of ABS specimens produced via the 3D printing technology for drone structural components

    NASA Astrophysics Data System (ADS)

    Ferro, Carlo Giovanni; Brischetto, Salvatore; Torre, Roberto; Maggiore, Paolo

    2016-07-01

    The Fused Deposition Modelling (FDM) technology is widely used in rapid prototyping. 3D printers for home desktop applications are usually employed to make non-structural objects. When the mechanical stresses are not excessive, this technology can also be successfully employed to produce structural objects, not only in prototyping stage but also in the realization of series pieces. The innovative idea of the present work is the application of this technology, implemented in a desktop 3D printer, to the realization of components for aeronautical use, especially for unmanned aerial systems. For this purpose, the paper is devoted to the statistical study of the performance of a desktop 3D printer to understand how the process performs and which are the boundary limits of acceptance. Mechanical and geometrical properties of ABS (Acrylonitrile Butadiene Styrene) specimens, such as tensile strength and stiffness, have been evaluated. ASTM638 type specimens have been used. A capability analysis has been applied for both mechanical and dimensional performances. Statistically stable limits have been determined using experimentally collected data.

  18. The first 3-D LaIII-SrII heterometallic complex: Synthesis, structure and luminescent properties

    NASA Astrophysics Data System (ADS)

    Hong, Zhiwei; Ran, Jingwen; Li, Tao; Chen, Yanmei

    2016-10-01

    The first 3-D LaIII-SrII heterometallic complex, namely [La2Sr(pda)4(H2O)4]n·6nH2O (1, H2pda = pyridine-2,6-dicarboxylic acid), has been successfully synthesized under solvothermal conditions. Single crystal X-ray diffraction analysis reveals that complex 1 features a 3-D porous framework and displays a new topology. The crystal structure can be simplified to a 4,6-connected 3-D network with Schläfli symbol of {34·42·88·9}2{34·42}. The crystals also have been characterized by X-ray powder diffraction, elemental analysis, thermal analysis, and IR spectroscopy. The infrared spectral analysis indicates that complex 1 is a carboxylate coordinated compound, several water molecules exist in the compound. The thermal study shows that there are ten water molecules in the crystal structure. The luminescent property has also been investigated. It shows a blue-purple fluorescence emission.

  19. 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.

  20. The lithospheric-scale 3D structural configuration of the North Alpine Foreland Basin constrained by gravity modelling and the calculation of the 3D load distribution

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

    The North Alpine Foreland Basin is situated in the northern front of the European Alps and extends over parts of France, Switzerland, Germany and Austria. It formed as a wedge shaped depression since the Tertiary in consequence of the Euro - Adriatic continental collision and the Alpine orogeny. The basin is filled with clastic sediments, the Molasse, originating from erosional processes of the Alps and underlain by Mesozoic sedimentary successions and a Paleozoic crystalline crust. For our study we have focused on the German part of the basin. To investigate the deep structure, the isostatic state and the load distribution of this region we have constructed a 3D structural model of the basin and the Alpine area using available depth and thickness maps, regional scale 3D structural models as well as seismic and well data for the sedimentary part. The crust (from the top Paleozoic down to the Moho (Grad et al. 2008)) has been considered as two-parted with a lighter upper crust and a denser lower crust; the partition has been calculated following the approach of isostatic equilibrium of Pratt (1855). By implementing a seismic Lithosphere-Asthenosphere-Boundary (LAB) (Tesauro 2009) the crustal scale model has been extended to the lithospheric-scale. The layer geometry and the assigned bulk densities of this starting model have been constrained by means of 3D gravity modelling (BGI, 2012). Afterwards the 3D load distribution has been calculated using a 3D finite element method. Our results show that the North Alpine Foreland Basin is not isostatically balanced and that the configuration of the crystalline crust strongly controls the gravity field in this area. Furthermore, our results show that the basin area is influenced by varying lateral load differences down to a depth of more than 150 km what allows a first order statement of the required compensating horizontal stress needed to prevent gravitational collapse of the system. BGI (2012). The International

  1. Direct observation in 3d of structural crossover in binary hard sphere mixtures

    NASA Astrophysics Data System (ADS)

    Statt, Antonia; Pinchaipat, Rattachai; Turci, Francesco; Evans, Robert; Royall, C. Patrick

    2016-04-01

    For binary fluid mixtures of spherical particles in which the two species are sufficiently different in size, the dominant wavelength of oscillations of the pair correlation functions is predicted to change from roughly the diameter of the large species to that of the small species along a sharp crossover line in the phase diagram [C. Grodon et al., J. Chem. Phys. 121, 7869 (2004)]. Using particle-resolved colloid experiments in 3d we demonstrate that crossover exists and that its location in the phase diagram is in quantitative agreement with the results of both theory and our Monte-Carlo simulations. In contrast with previous work [J. Baumgartl et al., Phys. Rev. Lett. 98, 198303 (2007)], where a correspondence was drawn between crossover and percolation of both species, in our 3d study we find that structural crossover is unrelated to percolation.

  2. Structured-Light Sensor Using Two Laser Stripes for 3D Reconstruction without Vibrations

    PubMed Central

    Usamentiaga, Rubén; Molleda, Julio; Garcia, Daniel F.

    2014-01-01

    3D reconstruction based on laser light projection is a well-known method that generally provides accurate results. However, when this method is used for inspection in uncontrolled environments, it is greatly affected by vibrations. This paper presents a structured-light sensor based on two laser stripes that provides a 3D reconstruction without vibrations. Using more than one laser stripe provides redundant information than is used to compensate for the vibrations. This work also proposes an accurate calibration process for the sensor based on standard calibration plates. A series of experiments are performed to evaluate the proposed method using a mechanical device that simulates vibrations. Results show excellent performance, with very good accuracy. PMID:25347586

  3. Creation of a long-lifespan ciliated epithelial tissue structure using a 3D collagen scaffold

    PubMed Central

    Wang, Yuchi; Wong, Lid B.; Mao, Hua

    2009-01-01

    We describe a method of using a 3D collagen gel scaffold applied at the air-liquid interface to culture dissociated primary tracheal-bronchial ciliated cells into a ciliated epithelial tissue structure (CETS). This 3D collagen gel culture system enables the induction of ciliogenesis and continuously provides support, maintenance, development, differentiation and propagation for the growth of cilia into the CETS. The CETS developed by this system resembles the ciliary metachronal motility and morphological, histological and physiopharmacological characteristics of cells found in native and in vivo ciliated epithelia. The CETS can be sustained for months with a straightforward and simple maintenance protocol. The integrity of the functional ciliary activity of this CETS enables the evaluation of long-term effects of many pulmonary drug candidates without using animals. PMID:19836831

  4. Micro-CT for the quantification of 3D voids within damaged structures

    SciTech Connect

    Patterson, Brian M; Hamilton, Christopher E; Cerreta, Ellen K; Dennis - Koller, Darcie; Bronkhorst, C. A.; Hansen, B. L.

    2011-01-26

    Micro X-ray Computed Tomography (MXCT) is widely used in the materials community to examine the internal structure of materials for voids and cracks due to damage or casting, or other defects. Most research in this area focuses on the qualitative aspect of the image, simply answering; Are there voids present? Here we present an ongoing study of the quantified incipient spall voids in Cu with different grain sizes, using a gas gun with various velocities. Data analysis packages for MXCT are just now becoming able to dimensionally measure and produce statistics on the voids-present. In order to make the size of the features in the 3D image quantifiable, the question, how many radiographs are required to render the object dimensionally accurate in 3D, must be answered. A series of data sets has been coUected, varying the number of radiographs collected in order to determine the appropriate number required.

  5. Analytical 3-D p-element for quadrilateral plates—Part 1: Thick isotropic plate structures

    NASA Astrophysics Data System (ADS)

    Zhu, B.; Leung, A. Y. T.; Li, Q. S.; Lu, J. W. Z.; Zhang, X. C.

    2007-06-01

    An analytical three-dimensional (3-D) p-version element for the vibration analysis of arbitrary quadrilateral thick plates is presented. With the additional hierarchical shape functions and analytically integrated element matrices, the computed accuracy is considerably improved. The computed natural frequencies of cantilever and simply supported square plates show that the convergence rate of the present element is very fast with respect to the number of hierarchical terms and it can predict very accurate modes. The element is applicable to the free vibration analysis of quadrilateral, polygonal plates as well as 3-D space structures. The continuous wavelet transform (CWT) is applied for the identification of damping ratios. Based on the Rayleigh damping model, the damped vibration response is obtained. A simple experiment is performed to verify the predicted vibration responses. The results show that the proposed element is also efficient for the vibration response analysis of plates.

  6. Shape optimization of 3D continuum structures via force approximation techniques

    NASA Technical Reports Server (NTRS)

    Vanderplaats, Garret N.; Kodiyalam, Srinivas

    1988-01-01

    The existing need to develop methods whereby the shape design efficiency can be improved through the use of high quality approximation methods is addressed. An efficient approximation method for stress constraints in 3D shape design problems is proposed based on expanding the nodal forces in Taylor series with respect to shape variations. The significance of this new method is shown through elementary beam theory calculations and via numerical computations using 3D solid finite elements. Numerical examples including the classical cantilever beam structure and realistic automotive parts like the engine connecting rod are designed for optimum shape using the proposed method. The numerical results obtained from these methods are compared with other published results, to assess the efficiency and the convergence rate of the proposed method.

  7. Determining the 3-D structure and motion of objects using a scanning laser range sensor

    NASA Technical Reports Server (NTRS)

    Nandhakumar, N.; Smith, Philip W.

    1993-01-01

    In order for the EVAHR robot to autonomously track and grasp objects, its vision system must be able to determine the 3-D structure and motion of an object from a sequence of sensory images. This task is accomplished by the use of a laser radar range sensor which provides dense range maps of the scene. Unfortunately, the currently available laser radar range cameras use a sequential scanning approach which complicates image analysis. Although many algorithms have been developed for recognizing objects from range images, none are suited for use with single beam, scanning, time-of-flight sensors because all previous algorithms assume instantaneous acquisition of the entire image. This assumption is invalid since the EVAHR robot is equipped with a sequential scanning laser range sensor. If an object is moving while being imaged by the device, the apparent structure of the object can be significantly distorted due to the significant non-zero delay time between sampling each image pixel. If an estimate of the motion of the object can be determined, this distortion can be eliminated; but, this leads to the motion-structure paradox - most existing algorithms for 3-D motion estimation use the structure of objects to parameterize their motions. The goal of this research is to design a rigid-body motion recovery technique which overcomes this limitation. The method being developed is an iterative, linear, feature-based approach which uses the non-zero image acquisition time constraint to accurately recover the motion parameters from the distorted structure of the 3-D range maps. Once the motion parameters are determined, the structural distortion in the range images is corrected.

  8. Kohn-Sham Band Structure Benchmark Including Spin-Orbit Coupling for 2D and 3D Solids

    NASA Astrophysics Data System (ADS)

    Huhn, William; Blum, Volker

    2015-03-01

    Accurate electronic band structures serve as a primary indicator of the suitability of a material for a given application, e.g., as electronic or catalytic materials. Computed band structures, however, are subject to a host of approximations, some of which are more obvious (e.g., the treatment of the exchange-correlation of self-energy) and others less obvious (e.g., the treatment of core, semicore, or valence electrons, handling of relativistic effects, or the accuracy of the underlying basis set used). We here provide a set of accurate Kohn-Sham band structure benchmarks, using the numeric atom-centered all-electron electronic structure code FHI-aims combined with the ``traditional'' PBE functional and the hybrid HSE functional, to calculate core, valence, and low-lying conduction bands of a set of 2D and 3D materials. Benchmarks are provided with and without effects of spin-orbit coupling, using quasi-degenerate perturbation theory to predict spin-orbit splittings. This work is funded by Fritz-Haber-Institut der Max-Planck-Gesellschaft.

  9. 3D visualization of deformation structures and potential fluid pathways at the Grimsel Test Site

    NASA Astrophysics Data System (ADS)

    Schneeberger, Raphael; Kober, Florian; Berger, Alfons; Spillmann, Thomas; Herwegh, Marco

    2015-04-01

    Knowledge on the ability of fluids to infiltrate subsurface rocks is of major importance for underground constructions, geothermal or radioactive waste disposal projects. In this study, we focus on the characterization of water infiltration pathways, their 3D geometries and origins. Based on surface and subsurface mapping in combination with drill core data, we developed by the use of MoveTM (Midland Valley Exploration Ltd.) a 3D structural model of the Grimsel Test Site (GTS). GTS is an underground laboratory operated by NAGRA, the Swiss organisation responsible for the management of nuclear waste. It is located within a suite of post-Variscan magmatic bodies comprising former granitic and granodioritic melts, which are dissected by mafic and aplitic dikes. During Alpine orogeny, the suite was tectonically overprinted within two stages of ductile deformation (Wehrens et al., in prep.) followed by brittle overprint of some of the shear zones during the retrograde exhumation history. It is this brittle deformation, which controls today's water infiltration network. However, the associated fractures, cataclasites and fault gouges are controlled themselves by aforementioned pre-existing mechanical discontinuities, whose origin ranges back as far as to the magmatic stage. For example, two sets of vertically oriented mafic dikes (E-W and NW-SE striking) and compositional heterogeneities induced by magmatic segregation processes in the plutonic host rocks served as nucleation sites for Alpine strain localization. Subsequently, NE-SW, E-W and NW-SE striking ductile shear zones were formed, in combination with high temperature fracturing while dissecting the host rocks in a complex 3D pattern (Wehrens et al, in prep.). Whether the ductile shear zones have been subjected to brittle reactivation and can serve as infiltration pathways or not, depends strongly on their orientations with respect to the principal stress field. Especially where deformation structures intersect

  10. Loading mode dependent effective properties of octet-truss lattice structures using 3D-printing

    NASA Astrophysics Data System (ADS)

    Challapalli, Adithya

    Cellular materials, often called lattice materials, are increasingly receiving attention for their ultralight structures with high specific strength, excellent impact absorption, acoustic insulation, heat dissipation media and compact heat exchangers. In alignment with emerging additive manufacturing (AM) technology, realization of the structural applications of the lattice materials appears to be becoming faster. Considering the direction dependent material properties of the products with AM, by directionally dependent printing resolution, effective moduli of lattice structures appear to be directionally dependent. In this paper, a constitutive model of a lattice structure, which is an octet-truss with a base material having an orthotropic material property considering AM is developed. In a case study, polyjet based 3D printing material having an orthotropic property with a 9% difference in the principal direction provides difference in the axial and shear moduli in the octet-truss by 2.3 and 4.6%. Experimental validation for the effective properties of a 3D printed octet-truss is done for uniaxial tension and compression test. The theoretical value based on the micro-buckling of truss member are used to estimate the failure strength. Modulus value appears a little overestimate compared with the experiment. Finite element (FE) simulations for uniaxial compression and tension of octettruss lattice materials are conducted. New effective properties for the octet-truss lattice structure are developed considering the observed behavior of the octet-truss structure under macroscopic compression and tension trough simulations.

  11. The “lnc” between 3D Chromatin Structure and X Chromosome Inactivation

    PubMed Central

    Pandya-Jones, Amy; Plath, Kathrin

    2016-01-01

    The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilities the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions. PMID:27062886

  12. 3D Geo-Structures Visualization Education Project (3dgeostructuresvis.ucdavis.edu)

    NASA Astrophysics Data System (ADS)

    Billen, M. I.

    2014-12-01

    Students of field-based geology must master a suite of challenging skills from recognizing rocks, to measuring orientations of features in the field, to finding oneself (and the outcrop) on a map and placing structural information on maps. Students must then synthesize this information to derive meaning from the observations and ultimately to determine the three-dimensional (3D) shape of the deformed structures and their kinematic history. Synthesizing this kind of information requires sophisticated visualizations skills in order to extrapolate observations into the subsurface or missing (eroded) material. The good news is that students can learn 3D visualization skills through practice, and virtual tools can help provide some of that practice. Here I present a suite of learning modules focused at developing students' ability to imagine (visualize) complex 3D structures and their exposure through digital topographic surfaces. Using the software 3DVisualizer, developed by KeckCAVES (keckcaves.org) we have developed visualizations of common geologic structures (e.g., syncline, dipping fold) in which the rock is represented by originally flat-lying layers of sediment, each with a different color, which have been subsequently deformed. The exercises build up in complexity, first focusing on understanding the structure in 3D (penetrative understanding), and then moving to the exposure of the structure at a topographic surface. Individual layers can be rendered as a transparent feature to explore how the layer extends above and below the topographic surface (e.g., to follow an eroded fold limb across a valley). The exercises are provided using either movies of the visualization (which can also be used for examples during lectures), or the data and software can be downloaded to allow for more self-driven exploration and learning. These virtual field models and exercises can be used as "practice runs" before going into the field, as make-up assignments, as a field

  13. Combining 3D structure with glycan array data provides insight into the origin of glycan specificity.

    PubMed

    Grant, Oliver C; Tessier, Matthew B; Meche, Lawrence; Mahal, Lara K; Foley, Bethany L; Woods, Robert J

    2016-07-01

    Defining how a glycan-binding protein (GBP) specifically selects its cognate glycan from among the ensemble of glycans within the cellular glycome is an area of intense study. Powerful insight into recognition mechanisms can be gained from 3D structures of GBPs complexed to glycans; however, such structures remain difficult to obtain experimentally. Here an automated 3D structure generation technique, called computational carbohydrate grafting, is combined with the wealth of specificity information available from glycan array screening. Integration of the array data with modeling and crystallography allows generation of putative co-complex structures that can be objectively assessed and iteratively altered until a high level of agreement with experiment is achieved. Given an accurate model of the co-complexes, grafting is also able to discern which binding determinants are active when multiple potential determinants are present within a glycan. In some cases, induced fit in the protein or glycan was necessary to explain the observed specificity, while in other examples a revised definition of the minimal binding determinants was required. When applied to a collection of 10 GBP-glycan complexes, for which crystallographic and array data have been reported, grafting provided a structural rationalization for the binding specificity of >90% of 1223 arrayed glycans. A webtool that enables researchers to perform computational carbohydrate grafting is available at www.glycam.org/gr (accessed 03 March 2016).

  14. Pseudocontact Shift-Driven Iterative Resampling for 3D Structure Determinations of Large Proteins.

    PubMed

    Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas

    2016-01-29

    Pseudocontact shifts (PCSs) induced by paramagnetic lanthanides produce pronounced effects in nuclear magnetic resonance spectra, which are easily measured and which deliver valuable long-range structure restraints. Even sparse PCS data greatly enhance the success rate of 3D (3-dimensional) structure predictions of proteins by the modeling program Rosetta. The present work extends this approach to 3D structures of larger proteins, comprising more than 200 residues, which are difficult to model by Rosetta without additional experimental restraints. The new algorithm improves the fragment assembly method of Rosetta by utilizing PCSs generated from paramagnetic lanthanide ions attached at four different sites as the only experimental restraints. The sparse PCS data are utilized at multiple stages, to identify native-like local structures, to rank the best structural models and to rebuild the fragment libraries. The fragment libraries are refined iteratively until convergence. The PCS-driven iterative resampling algorithm is strictly data dependent and shown to generate accurate models for a benchmark set of eight different proteins, ranging from 100 to 220 residues, using solely PCSs of backbone amide protons.

  15. Combining 3D structure with glycan array data provides insight into the origin of glycan specificity.

    PubMed

    Grant, Oliver C; Tessier, Matthew B; Meche, Lawrence; Mahal, Lara K; Foley, Bethany L; Woods, Robert J

    2016-07-01

    Defining how a glycan-binding protein (GBP) specifically selects its cognate glycan from among the ensemble of glycans within the cellular glycome is an area of intense study. Powerful insight into recognition mechanisms can be gained from 3D structures of GBPs complexed to glycans; however, such structures remain difficult to obtain experimentally. Here an automated 3D structure generation technique, called computational carbohydrate grafting, is combined with the wealth of specificity information available from glycan array screening. Integration of the array data with modeling and crystallography allows generation of putative co-complex structures that can be objectively assessed and iteratively altered until a high level of agreement with experiment is achieved. Given an accurate model of the co-complexes, grafting is also able to discern which binding determinants are active when multiple potential determinants are present within a glycan. In some cases, induced fit in the protein or glycan was necessary to explain the observed specificity, while in other examples a revised definition of the minimal binding determinants was required. When applied to a collection of 10 GBP-glycan complexes, for which crystallographic and array data have been reported, grafting provided a structural rationalization for the binding specificity of >90% of 1223 arrayed glycans. A webtool that enables researchers to perform computational carbohydrate grafting is available at www.glycam.org/gr (accessed 03 March 2016). PMID:26911287

  16. Learning the 3-D structure of objects from 2-D views depends on shape, not format

    PubMed Central

    Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

    2016-01-01

    Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

  17. New Approach for 3D Local Structure Refinement Using Non-Muffin-Tin XANES Analysis

    SciTech Connect

    Smolentsev, Grigory; Soldatov, Alexander V.; Feiters, Martin C.

    2007-02-02

    A new technique of 3D local structure refinement using full-potential X-ray absorption near edge structure (XANES) analysis is proposed and demonstrated in application to metalloorganic complexes of Ni. It can be applied to determine local structure in those cases where the muffin-tin approximation used in most full multiple scattering schemes fails. The method is based on the fitting of experimental XANES data using multidimensional interpolation of spectra as a function of structural parameters, recently proposed by us, and ab-initio full potential calculations of XANES using finite difference method. The small number of required ab-initio calculations is the main advantage of the approach, which allows one to use computationally time-expensive non-muffin-tin finite-difference method. The possibility to extract information on bond angles in addition to bond-lengths accessible to standard EXAFS is demonstrated and it opens new perspectives of quantitative XANES analysis as a 3D local structure probe.

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

    PubMed Central

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

    2015-01-01

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

  19. Fabrication of 3D photocatalytic α-Fe2O3 structure using direct ink writing method

    NASA Astrophysics Data System (ADS)

    Li, Yayun; Li, Bo; Li, Longtu

    2014-02-01

    Three-dimensional (3D) photocatalytic devices are economical and environmental, since they can be easily recycled and reused. In this paper, a kind of 3D photocatalytic device with a rod diameter of 250 μm was fabricated using the aqueous-based α-Fe2O3 ceramic inks by direct ink writing (DIW) method. The properties of the DIW woodpile samples were investigated by X-ray diffraction (XRD), scanning electron microscope (SEM) and optical microscope. The result shows that the ink with solid content of 71.4 wt.% exhibits a shear thinning behavior and proper viscoelastic properties, which ensure a feasible extrusion in the whole shaping process. The sample sintered at 800°C in air causes photocatalytic degradation of methylene blue (MB) solution under the ultraviolet (UV) light. The photocatalytic properties of the α-Fe2O3 woodpile structure was characterized by the UV-visible light spectrophotometer, and it was found to be better than that of bulk sample with same weight for its higher specific surface. The DIW technique would offer a potential method for the design and fabrication of 3D photocatalytic devices.

  20. Modeling the Impact of Drizzle and 3D Cloud Structure on Remote Sensing of Effective Radius

    NASA Technical Reports Server (NTRS)

    Platnick, Steven; Zinner, Tobias; Ackerman, S.

    2008-01-01

    Remote sensing of cloud particle size with passive sensors like MODIS is an important tool for cloud microphysical studies. As a measure of the radiatively relevant droplet size, effective radius can be retrieved with different combinations of visible through shortwave infrared channels. MODIS observations sometimes show significantly larger effective radii in marine boundary layer cloud fields derived from the 1.6 and 2.1 pm channel observations than for 3.7 pm retrievals. Possible explanations range from 3D radiative transport effects and sub-pixel cloud inhomogeneity to the impact of drizzle formation on the droplet distribution. To investigate the potential influence of these factors, we use LES boundary layer cloud simulations in combination with 3D Monte Carlo simulations of MODIS observations. LES simulations of warm cloud spectral microphysics for cases of marine stratus and broken stratocumulus, each for two different values of cloud condensation nuclei density, produce cloud structures comprising droplet size distributions with and without drizzle size drops. In this study, synthetic MODIS observations generated from 3D radiative transport simulations that consider the full droplet size distribution will be generated for each scene. The operational MODIS effective radius retrievals will then be applied to the simulated reflectances and the results compared with the LES microphysics.

  1. Color influence on accuracy of 3D scanners based on structured light

    NASA Astrophysics Data System (ADS)

    Voisin, Sophie; Page, David L.; Foufou, Sebti; Truchetet, Frédéric; Abidi, Mongi A.

    2006-02-01

    The characterization of commercial 3D scanners allows acquiring precise and useful data. The accuracy of range and, more recently, color for 3D scanners is usually studied separately, but when the 3D scanner is based on structured light with a color coding pattern, color influence on range accuracy should be investigated. The commercial product that we have tested has the particularity that it can acquire data under ambient light instead of a controlled environment as it is with most available scanners. Therefore, based on related work in the literature and on experiments we have done on a variety of standard illuminants, we have designed an interesting setup to control illuminant interference. Basically, the setup consists of acquiring the well-known Macbeth ColorChecker under a controlled environment and also ambient daylight. The results have shown variations with respect to the color. We have performed several statistical studies to show how the range results evolve with respect to the RGB and the HSV channels. In addition, a systematic noise error has also been identified. This noise depends on the object color. A subset of colors shows strong noise errors while other colors have minimal or even no systematic error under the same illuminant.

  2. Integration of 3D structure from disparity into biological motion perception independent of depth awareness.

    PubMed

    Wang, Ying; Jiang, Yi

    2014-01-01

    Images projected onto the retinas of our two eyes come from slightly different directions in the real world, constituting binocular disparity that serves as an important source for depth perception - the ability to see the world in three dimensions. It remains unclear whether the integration of disparity cues into visual perception depends on the conscious representation of stereoscopic depth. Here we report evidence that, even without inducing discernible perceptual representations, the disparity-defined depth information could still modulate the visual processing of 3D objects in depth-irrelevant aspects. Specifically, observers who could not discriminate disparity-defined in-depth facing orientations of biological motions (i.e., approaching vs. receding) due to an excessive perceptual bias nevertheless exhibited a robust perceptual asymmetry in response to the indistinguishable facing orientations, similar to those who could consciously discriminate such 3D information. These results clearly demonstrate that the visual processing of biological motion engages the disparity cues independent of observers' depth awareness. The extraction and utilization of binocular depth signals thus can be dissociable from the conscious representation of 3D structure in high-level visual perception.

  3. Algorithms for extraction of structural attitudes from 3D outcrop models

    NASA Astrophysics Data System (ADS)

    Duelis Viana, Camila; Endlein, Arthur; Ademar da Cruz Campanha, Ginaldo; Henrique Grohmann, Carlos

    2016-05-01

    The acquisition of geological attitudes on rock cuts using traditional field compass survey can be a time consuming, dangerous, or even impossible task depending on the conditions and location of outcrops. The importance of this type of data in rock-mass classifications and structural geology has led to the development of new techniques, in which the application of photogrammetric 3D digital models has had an increasing use. In this paper we present two algorithms for extraction of attitudes of geological discontinuities from virtual outcrop models: ply2atti and scanline, implemented with the Python programming language. The ply2atti algorithm allows for the virtual sampling of planar discontinuities appearing on the 3D model as individual exposed surfaces, while the scanline algorithm allows the sampling of discontinuities (surfaces and traces) along a virtual scanline. Application to digital models of a simplified test setup and a rock cut demonstrated a good correlation between the surveys undertaken using traditional field compass reading and virtual sampling on 3D digital models.

  4. Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.

    PubMed

    Tokheim, Collin; Bhattacharya, Rohit; Niknafs, Noushin; Gygax, Derek M; Kim, Rick; Ryan, Michael; Masica, David L; Karchin, Rachel

    2016-07-01

    The impact of somatic missense mutation on cancer etiology and progression is often difficult to interpret. One common approach for assessing the contribution of missense mutations in carcinogenesis is to identify genes mutated with statistically nonrandom frequencies. Even given the large number of sequenced cancer samples currently available, this approach remains underpowered to detect drivers, particularly in less studied cancer types. Alternative statistical and bioinformatic approaches are needed. One approach to increase power is to focus on localized regions of increased missense mutation density or hotspot regions, rather than a whole gene or protein domain. Detecting missense mutation hotspot regions in three-dimensional (3D) protein structure may also be beneficial because linear sequence alone does not fully describe the biologically relevant organization of codons. Here, we present a novel and statistically rigorous algorithm for detecting missense mutation hotspot regions in 3D protein structures. We analyzed approximately 3 × 10(5) mutations from The Cancer Genome Atlas (TCGA) and identified 216 tumor-type-specific hotspot regions. In addition to experimentally determined protein structures, we considered high-quality structural models, which increase genomic coverage from approximately 5,000 to more than 15,000 genes. We provide new evidence that 3D mutation analysis has unique advantages. It enables discovery of hotspot regions in many more genes than previously shown and increases sensitivity to hotspot regions in tumor suppressor genes (TSG). Although hotspot regions have long been known to exist in both TSGs and oncogenes, we provide the first report that they have different characteristic properties in the two types of driver genes. We show how cancer researchers can use our results to link 3D protein structure and the biologic functions of missense mutations in cancer, and to generate testable hypotheses about driver mechanisms. Our results

  5. Multimodal 3-D reconstruction of human anatomical structures using SurLens Visualization System.

    PubMed

    Adeshina, A M; Hashim, R; Khalid, N E A; Abidin, S Z Z

    2013-03-01

    In the medical diagnosis and treatment planning, radiologists and surgeons rely heavily on the slices produced by medical imaging devices. Unfortunately, these image scanners could only present the 3-D human anatomical structure in 2-D. Traditionally, this requires medical professional concerned to study and analyze the 2-D images based on their expert experience. This is tedious, time consuming and prone to error; expecially when certain features are occluding the desired region of interest. Reconstruction procedures was earlier proposed to handle such situation. However, 3-D reconstruction system requires high performance computation and longer processing time. Integrating efficient reconstruction system into clinical procedures involves high resulting cost. Previously, brain's blood vessels reconstruction with MRA was achieved using SurLens Visualization System. However, adapting such system to other image modalities, applicable to the entire human anatomical structures, would be a meaningful contribution towards achieving a resourceful system for medical diagnosis and disease therapy. This paper attempts to adapt SurLens to possible visualisation of abnormalities in human anatomical structures using CT and MR images. The study was evaluated with brain MR images from the department of Surgery, University of North Carolina, United States and CT abdominal pelvic, from the Swedish National Infrastructure for Computing. The MR images contain around 109 datasets each of T1-FLASH, T2-Weighted, DTI and T1-MPRAGE. Significantly, visualization of human anatomical structure was achieved without prior segmentation. SurLens was adapted to visualize and display abnormalities, such as an indication of walderstrom's macroglobulinemia, stroke and penetrating brain injury in the human brain using Magentic Resonance (MR) images. Moreover, possible abnormalities in abdominal pelvic was also visualized using Computed Tomography (CT) slices. The study shows SurLens' functionality as

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

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

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

  7. Structural and property studies on metal–organic compounds with 3-D supramolecular network

    SciTech Connect

    Zhang, Qi-Ying; Ma, Ke-Fang; Xiao, Hong-Ping; Li, Xin-Hua; Shi, Qian

    2014-07-01

    Two carboxylato-bridged allomeric compounds, ([Cu{sub 2}(dbsa){sub 2}(hmt) (H{sub 2}O){sub 4}]{sub 1/2}·2H{sub 2}O){sub n} (1), ([Ni(dbsa)(H{sub 2}O){sub 2}]{sub 1/2}[Ni(dbsa)(hmt)(H{sub 2}O){sub 2}]{sub 1/2}·2H{sub 2}O){sub n} (2) (H{sub 2}dbsa=meso-2,3-dibromosuccinic acid, hmt=hexamethylenetetramine) have been synthesized and characterized by X-ray structral analyses. The metal ions have two kinds of coordination fashion in one unit, and bridged by carboxylate and hmt ligands along with weak interactions existing in the solid structure, forming a 3-D supramolecular network. Variable-temperature magnetic property studies reveal the existence of antiferromagnetic interactions in 1 and 2 with g=2.2, J{sub 1}=−3.5 cm{sup −1}, J{sub 2}=−2.8 cm{sup −1} for 1, and g=2.1, J=−3.5 cm{sup −1} for 2. - Graphical abstract: Variable-temperature magnetic property studies of two 3-D supramolecular compounds reveal the existence of antiferromagnetic interactions between the metal ions, through the effective super-exchange media. - Highlights: • Two 3-D allomeric Cu(II) and Ni(II) metal–organic compounds have been prepared. • The 3-D networks were constructed by coordination bonds, weak interactions and hydrogen bond interactions. • There are antiferromagnetic super-exchange interactions between the metal ions.

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

    PubMed Central

    2013-01-01

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

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

    SciTech Connect

    Johnson, M.W.

    1990-01-01

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

  10. Antigenic and 3D structural characterization of soluble X4 and hybrid X4-R5 HIV-1 Env trimers

    PubMed Central

    2014-01-01

    Background HIV-1 is decorated with trimeric glycoprotein spikes that enable infection by engaging CD4 and a chemokine coreceptor, either CCR5 or CXCR4. The variable loop 3 (V3) of the HIV-1 envelope protein (Env) is the main determinant for coreceptor usage. The predominant CCR5 using (R5) HIV-1 Env has been intensively studied in function and structure, whereas the trimeric architecture of the less frequent, but more cytopathic CXCR4 using (X4) HIV-1 Env is largely unknown, as are the consequences of sequence changes in and near V3 on antigenicity and trimeric Env structure. Results Soluble trimeric gp140 Env constructs were used as immunogenic mimics of the native spikes to analyze their antigenic properties in the context of their overall 3D structure. We generated soluble, uncleaved, gp140 trimers from a prototypic T-cell line-adapted (TCLA) X4 HIV-1 strain (NL4-3) and a hybrid (NL4-3/ADA), in which the V3 spanning region was substituted with that from the primary R5 isolate ADA. Compared to an ADA (R5) gp140, the NL4-3 (X4) construct revealed an overall higher antibody accessibility, which was most pronounced for the CD4 binding site (CD4bs), but also observed for mAbs against CD4 induced (CD4i) epitopes and gp41 mAbs. V3 mAbs showed significant binding differences to the three constructs, which were refined by SPR analysis. Of interest, the NL4-3/ADA construct with the hybrid NL4-3/ADA CD4bs showed impaired CD4 and CD4bs mAb reactivity despite the presence of the essential elements of the CD4bs epitope. We obtained 3D reconstructions of the NL4-3 and the NL4-3/ADA gp140 trimers via electron microscopy and single particle analysis, which indicates that both constructs inherit a propeller-like architecture. The first 3D reconstruction of an Env construct from an X4 TCLA HIV-1 strain reveals an open conformation, in contrast to recently published more closed structures from R5 Env. Exchanging the X4 V3 spanning region for that of R5 ADA did not alter the open

  11. 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)

  12. Complex Crustal Structure Beneath Western Turkey Revealed by 3D Seismic Full Waveform Inversion (FWI)

    NASA Astrophysics Data System (ADS)

    Cubuk-Sabuncu, Yesim; Taymaz, Tuncay; Fichtner, Andreas

    2016-04-01

    We present a 3D radially anisotropic velocity model of the crust and uppermost mantle structure beneath the Sea of Marmara and surroundings based on the full waveform inversion method. The intense seismic activity and crustal deformation are observed in the Northwest Turkey due to transition tectonics between the strike-slip North Anatolian Fault (NAF) and the extensional Aegean region. We have selected and simulated complete waveforms of 62 earthquakes (Mw > 4.0) occurred during 2007-2015, and recorded at (Δ < 10°) distances. Three component earthquake data is obtained from broadband seismic stations of Kandilli Observatory and Earthquake Research Center (KOERI, Turkey), Hellenic Unified Seismic Network (HUSN, Greece) and Earthquake Research Center of Turkey (AFAD-DAD). The spectral-element solver of the wave equation, SES3D algorithm, is used to simulate seismic wave propagation in 3D spherical coordinates (Fichtner, 2009). The Large Scale Seismic Inversion Framework (LASIF) workflow tool is also used to perform full seismic waveform inversion (Krischer et al., 2015). The initial 3D Earth model is implemented from the multi-scale seismic tomography study of Fichtner et al. (2013). Discrepancies between the observed and simulated synthetic waveforms are determined using the time-frequency misfits which allows a separation between phase and amplitude information (Fichtner et al., 2008). The conjugate gradient optimization method is used to iteratively update the initial Earth model when minimizing the misfit. The inversion is terminated after 19 iterations since no further advances are observed in updated models. Our analysis revealed shear wave velocity variations of the shallow and deeper crustal structure beneath western Turkey down to depths of ~35-40 km. Low shear wave velocity anomalies are observed in the upper and mid crustal depths beneath major fault zones located in the study region. Low velocity zones also tend to mark the outline of young volcanic

  13. Error analysis for creating 3D face templates based on cylindrical quad-tree structure

    NASA Astrophysics Data System (ADS)

    Gutfeter, Weronika

    2015-09-01

    Development of new biometric algorithms is parallel to advances in technology of sensing devices. Some of the limitations of the current face recognition systems may be eliminated by integrating 3D sensors into these systems. Depth sensing devices can capture a spatial structure of the face in addition to the texture and color. This kind of data is yet usually very voluminous and requires large amount of computer resources for being processed (face scans obtained with typical depth cameras contain more than 150 000 points per face). That is why defining efficient data structures for processing spatial images is crucial for further development of 3D face recognition methods. The concept described in this work fulfills the aforementioned demands. Modification of the quad-tree structure was chosen because it can be easily transformed into less dimensional data structures and maintains spatial relations between data points. We are able to interpret data stored in the tree as a pyramid of features which allow us to analyze face images using coarse-to-fine strategy, often exploited in biometric recognition systems.

  14. Comparative 3D genome structure analysis of the fission and the budding yeast.

    PubMed

    Gong, Ke; Tjong, Harianto; Zhou, Xianghong Jasmine; Alber, Frank

    2015-01-01

    We studied the 3D structural organization of the fission yeast genome, which emerges from the tethering of heterochromatic regions in otherwise randomly configured chromosomes represented as flexible polymer chains in an nuclear environment. This model is sufficient to explain in a statistical manner many experimentally determined distinctive features of the fission yeast genome, including chromatin interaction patterns from Hi-C experiments and the co-locations of functionally related and co-expressed genes, such as genes expressed by Pol-III. Our findings demonstrate that some previously described structure-function correlations can be explained as a consequence of random chromatin collisions driven by a few geometric constraints (mainly due to centromere-SPB and telomere-NE tethering) combined with the specific gene locations in the chromosome sequence. We also performed a comparative analysis between the fission and budding yeast genome structures, for which we previously detected a similar organizing principle. However, due to the different chromosome sizes and numbers, substantial differences are observed in the 3D structural genome organization between the two species, most notably in the nuclear locations of orthologous genes, and the extent of nuclear territories for genes and chromosomes. However, despite those differences, remarkably, functional similarities are maintained, which is evident when comparing spatial clustering of functionally related genes in both yeasts. Functionally related genes show a similar spatial clustering behavior in both yeasts, even though their nuclear locations are largely different between the yeast species.

  15. MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures.

    PubMed

    Niknafs, Noushin; Kim, Dewey; Kim, Ryangguk; Diekhans, Mark; Ryan, Michael; Stenson, Peter D; Cooper, David N; Karchin, Rachel

    2013-11-01

    Mutation position imaging toolbox (MuPIT) interactive is a browser-based application for single-nucleotide variants (SNVs), which automatically maps the genomic coordinates of SNVs onto the coordinates of available three-dimensional (3D) protein structures. The application is designed for interactive browser-based visualization of the putative functional relevance of SNVs by biologists who are not necessarily experts either in bioinformatics or protein structure. Users may submit batches of several thousand SNVs and review all protein structures that cover the SNVs, including available functional annotations such as binding sites, mutagenes