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Sample records for 3d crystal structure

  1. 3D printed low-loss THz waveguide based on Kagome photonic crystal structure.

    PubMed

    Yang, Jing; Zhao, Jiayu; Gong, Cheng; Tian, Haolin; Sun, Lu; Chen, Ping; Lin, Lie; Liu, Weiwei

    2016-10-03

    A low-loss hollow core terahertz waveguide based on Kagome photonic crystal structure has been designed and fabricated by 3D printing. The 3D printed waveguide has been characterized by using THz time-domain spectroscopy. The results demonstrate that the obtained waveguide features average power propagation loss of 0.02 cm-1 for 0.2-1.0 THz (the minimum is about 0.002 cm-1 at 0.75 THz). More interesting, it could be simply mechanically spliced without any additional alignment, while maintaining the excellent performance. The 3D printing technique will be a promising solution to fabricate Kagome THz waveguide with well controllable characteristics and low cost.

  2. The crystal structure of Aspergillus fumigatus cyclophilin reveals 3D domain swapping of a central element.

    PubMed

    Limacher, Andreas; Kloer, Daniel P; Flückiger, Sabine; Folkers, Gerd; Crameri, Reto; Scapozza, Leonardo

    2006-02-01

    The crystal structure of Aspergillus fumigatus cyclophilin (Asp f 11) was solved by the multiwavelength anomalous dispersion method and was refined to a resolution of 1.85 A with R and R(free) values of 18.9% and 21.4%, respectively. Many cyclophilin structures have been solved to date, all showing the same monomeric conformation. In contrast, the structure of A. fumigatus cyclophilin reveals dimerization by 3D domain swapping and represents one of the first proteins with a swapped central domain. The domain-swapped element consists of two beta strands and a subsequent loop carrying a conserved tryptophan. The tryptophan binds into the active site, inactivating cis-trans isomerization. This might be a means of biological regulation. The two hinge loops leave the protein prone to misfolding. In this context, alternative forms of 3D domain swapping that can lead to N- or C-terminally swapped dimers, oligomers, and aggregates are discussed.

  3. Spectral element method for band-structure calculations of 3D phononic crystals

    NASA Astrophysics Data System (ADS)

    Shi, Linlin; Liu, Na; Zhou, Jianyang; Zhou, Yuanguo; Wang, Jiamin; Huo Liu, Qing

    2016-11-01

    The spectral element method (SEM) is a special kind of high-order finite element method (FEM) which combines the flexibility of a finite element method with the accuracy of a spectral method. In contrast to the traditional FEM, the SEM exhibits advantages in the high-order accuracy as the error decreases exponentially with the increase of interpolation degree by employing the Gauss-Lobatto-Legendre (GLL) polynomials as basis functions. In this study, the spectral element method is developed for the first time for the determination of band structures of 3D isotropic/anisotropic phononic crystals (PCs). Based on the Bloch theorem, we present a novel, intuitive discretization formulation for Navier equation in the SEM scheme for periodic media. By virtue of using the orthogonal Legendre polynomials, the generalized eigenvalue problem is converted to a regular one in our SEM implementation to improve the efficiency. Besides, according to the specific geometry structure, 8-node and 27-node hexahedral elements as well as an analytic mesh have been used to accurately capture curved PC models in our SEM scheme. To verify its accuracy and efficiency, this study analyses the phononic-crystal plates with square and triangular lattice arrangements, and the 3D cubic phononic crystals consisting of simple cubic (SC), bulk central cubic (BCC) and faced central cubic (FCC) lattices with isotropic or anisotropic scatters. All the numerical results considered demonstrate that SEM is superior to the conventional FEM and can be an efficient alternative method for accurate determination of band structures of 3D phononic crystals.

  4. Review on Chalcogenide 3D Nano-structured Crystals: Synthesis and Growth Mechanism.

    PubMed

    Qiu, Qi

    2015-01-01

    Three dimensional (3D) nano-structured crystals have received extensive attention for their superior properties over zero dimensional (0D), one dimensional (1D), or two dimensional (2D) nanomaterials in many areas. This review is generalized for the group of chalcogenide nanoflowers (NFs) by the synthetic techniques, such as solvothermal, wet chemical, sol-gel, surface oxidation, microwave, coating, electrochemical, and several other methods. The formation mechanism was also described for the purpose of opening up new food for thoughts to bring up new functionality of materials by tuning the morphology of crystals. The pH value or the template plays fundamental role in forming the nano-flowered structure. Moreover, the correlations between the surface area (SA), contact angle (CA), and the NFs are also discussed within the context. Here, we also discussed some patents relevant to the topic.

  5. 3D lattice distortions and defect structures in ion-implanted nano-crystals

    DOE PAGES

    Hofmann, Felix; Robinson, Ian K.; Tarleton, Edmund; ...

    2017-04-06

    The ability of Focused Ion Beam (FIB) techniques to cut solid matter at the nano-scale revolutionized the study of material structure across the life-, earth- and material sciences. But a detailed understanding of the damage caused by the ion beam and its effect on material properties remains elusive. We examine this damage in 3D using coherent X-ray diffraction to measure the full lattice strain tensor in FIB-milled gold nano-crystals. We also found that even very low ion doses, previously thought to be negligible, cause substantial lattice distortions. At higher doses, extended self-organized defect structures appear. Combined with detailed numerical calculations,more » these observations allow fundamental insight into the nature of the damage created and the structural instabilities that lead to a surprisingly inhomogeneous morphology.« less

  6. Structural Color for Additive Manufacturing: 3D-Printed Photonic Crystals from Block Copolymers.

    PubMed

    Boyle, Bret M; French, Tracy A; Pearson, Ryan M; McCarthy, Blaine G; Miyake, Garret M

    2017-03-28

    The incorporation of structural color into 3D printed parts is reported, presenting an alternative to the need for pigments or dyes for colored parts produced through additive manufacturing. Thermoplastic build materials composed of dendritic block copolymers were designed, synthesized, and used to additively manufacture plastic parts exhibiting structural color. The reflection properties of the photonic crystals arise from the periodic nanostructure formed through block copolymer self-assembly during polymer processing. The wavelength of reflected light could be tuned across the visible spectrum by synthetically controlling the block copolymer molecular weight and manufacture parts that reflected violet, green, or orange light with the capacity to serve as selective optical filters and light guides.

  7. The crystal structure of the dimeric colicin M immunity protein displays a 3D domain swap.

    PubMed

    Usón, Isabel; Patzer, Silke I; Rodríguez, Dayté Dayana; Braun, Volkmar; Zeth, Kornelius

    2012-04-01

    Bacteriocins are proteins secreted by many bacterial cells to kill related bacteria of the same niche. To avoid their own suicide through reuptake of secreted bacteriocins, these bacteria protect themselves by co-expression of immunity proteins in the compartment of colicin destination. In Escherichia coli the colicin M (Cma) is inactivated by the interaction with the Cma immunity protein (Cmi). We have crystallized and solved the structure of Cmi at a resolution of 1.95Å by the recently developed ab initio phasing program ARCIMBOLDO. The monomeric structure of the mature 10kDa protein comprises a long N-terminal α-helix and a four-stranded C-terminal β-sheet. Dimerization of this fold is mediated by an extended interface of hydrogen bond interactions between the α-helix and the four-stranded β-sheet of the symmetry related molecule. Two intermolecular disulfide bridges covalently connect this dimer to further lock this complex. The Cmi protein resembles an example of a 3D domain swapping being stalled through physical linkage. The dimer is a highly charged complex with a significant surplus of negative charges presumably responsible for interactions with Cma. Dimerization of Cmi was also demonstrated to occur in vivo. Although the Cmi-Cma complex is unique among bacteria, the general fold of Cmi is representative for a class of YebF-like proteins which are known to be secreted into the external medium by some Gram-negative bacteria.

  8. Image Forces on 3-D Dislocation Structures in Crystals of Finite Volume

    SciTech Connect

    El-Azab, Anter ); V.V. Bulatov

    1999-01-01

    The present work aims at studying the image stress and image Peach-Koehler force fields for three-dimensional dislocation configurations in a single crystal of finite volume. It is shown that the image stress field is significant within the entire crystal volume, and that the image Peach-Koehler force can be of the same order of magnitude as the direct interaction force calculated from the infinite domain solution. The results demonstrate that image stress gives rise to long-range interaction forces that are important in meso-scale dynamics of dislocation structures.

  9. Image forces on 3d dislocation structures in crystals of finite volume

    SciTech Connect

    El-Azab, A.

    1999-07-01

    The present work aims at studying the image stress and image Peach-Koehler force fields for three-dimensional dislocation configurations in a single crystal of finite volume. It is shown that the image stress field is significant within the entire crystal volume, and that the image Peach-Koehler force can be of the same order of magnitude as the direct interaction force calculated from the infinite domain solution. The results demonstrate that image stress gives rise to long-range interaction forces that are important in meso-scale dynamics of dislocation structures.

  10. The crystal structure of human CD21: Implications for Epstein-Barr virus and C3d binding.

    PubMed

    Prota, Andrea E; Sage, David R; Stehle, Thilo; Fingeroth, Joyce D

    2002-08-06

    Human complement receptor type 2 (CD21) is the cellular receptor for Epstein-Barr virus (EBV), a human tumor virus. The N-terminal two short consensus repeats (SCR1-SCR2) of the receptor interact with the EBV glycoprotein gp350/220 and also with the natural CD21 ligand C3d. Here we present the crystal structure of the CD21 SCR1-SCR2 fragment in the absence of ligand and demonstrate that it is able to bind EBV. Based on a functional analysis of wild-type and mutant CD21 and molecular modeling, we identify a likely region for EBV attachment and demonstrate that this region is not involved in the interaction with C3d. A comparison with the previously determined structure of CD21 SCR1-SCR2 in complex with C3d shows that, in both cases, CD21 assumes compact V-shaped conformations. However, our analysis reveals a surprising degree of flexibility at the SCR1-SCR2 interface, suggesting interactions between the two domains are not specific. We present evidence that the V-shaped conformation is induced by deglycosylation of the protein, and that physiologic glycosylation of CD21 would result in a more extended conformation, perhaps with additional epitopes for C3d binding.

  11. Crystal, magnetic and electronic structures of 3d-5d ordered double perovskite Ba2CoReO6

    NASA Astrophysics Data System (ADS)

    Musa Saad H.-E., M.; Rammeh, N.

    2016-12-01

    A comprehensive study on crystal, magnetic and electronic structures of ordered double perovskite Ba2CoReO6 was carried out using X-ray powder diffraction (XRD) and superconducting quantum interference device (SQUID). Also, the density functional theory (DFT) calculations were performed by full potential linear muffin-tin orbital (FP-LMTO) method within the localized spin density approximation (LSDA+U) and generalized gradient approximation (GGA+U). At room temperature, the crystal structure of Ba2CoReO6 is face-centered cubic, space group Fm 3 bar m , containing an almost completely ordered arrangement of CoO6-ReO6 octahedra. Magnetic structure showed an antiferromagnetic (AF) behavior below TN=41 K. The magnetic and electronic structures are consistent with the electronic configurations Co2+(3d7)-Re6+(5d1) having a total spin magnetic moment of about 2.0 μB/f.u. DFT electronic structures predicted half-metallic yields from 3d-t2g↓ and 5d-t2g↓ through O2-.

  12. The Calculation of the Band Structure in 3D Phononic Crystal with Hexagonal Lattice

    NASA Astrophysics Data System (ADS)

    Aryadoust, Mahrokh; Salehi, H.

    2015-12-01

    In this article, the propagation of acoustic waves in the phononic crystals (PCs) of three dimensions with the hexagonal (HEX) lattice is studied theoretically. The PCs are constituted of nickel (Ni) spheres embedded in epoxy. The calculations of the band structure and the density of states are performed using the plane wave expansion (PWE) method in the irreducible part of the Brillouin zone (BZ). In this study, we analyse the dependence of the band structures inside (the complete band gap width) on c/a and filling fraction in the irreducible part of the first BZ. Also, we have analysed the band structure of the ALHA and MLHKM planes. The results show that the maximum width of absolute elastic band gap (AEBG) (0.045) in the irreducible part of the BZ of HEX lattice is formed for c/a=6 and filling fraction equal to 0.01. In addition, the maximum of the first and second AEBG widths are 0.0884 and 0.0474, respectively, in the MLHKM plane, and the maximum of the first and second AEBG widths are 0.0851 and 0.0431, respectively, in the ALHA plane.

  13. 3D lattice distortions and defect structures in ion-implanted nano-crystals

    PubMed Central

    Hofmann, Felix; Tarleton, Edmund; Harder, Ross J.; Phillips, Nicholas W.; Ma, Pui-Wai; Clark, Jesse N.; Robinson, Ian K.; Abbey, Brian; Liu, Wenjun; Beck, Christian E.

    2017-01-01

    Focussed Ion Beam (FIB) milling is a mainstay of nano-scale machining. By manipulating a tightly focussed beam of energetic ions, often gallium (Ga+), FIB can sculpt nanostructures via localised sputtering. This ability to cut solid matter on the nano-scale revolutionised sample preparation across the life, earth and materials sciences. Despite its widespread usage, detailed understanding of the FIB-induced structural damage, intrinsic to the technique, remains elusive. Here we examine the defects caused by FIB in initially pristine objects. Using Bragg Coherent X-ray Diffraction Imaging (BCDI), we are able to spatially-resolve the full lattice strain tensor in FIB-milled gold nano-crystals. We find that every use of FIB causes large lattice distortions. Even very low ion doses, typical of FIB imaging and previously thought negligible, have a dramatic effect. Our results are consistent with a damage microstructure dominated by vacancies, highlighting the importance of free-surfaces in determining which defects are retained. At larger ion fluences, used during FIB-milling, we observe an extended dislocation network that causes stresses far beyond the bulk tensile strength of gold. These observations provide new fundamental insight into the nature of the damage created and the defects that lead to a surprisingly inhomogeneous morphology. PMID:28383028

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

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2016-01-01

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

  15. Seven 3d-4f coordination polymers of macrocyclic oxamide with polycarboxylates: Syntheses, crystal structures and magnetic properties

    NASA Astrophysics Data System (ADS)

    Xin, Na; Sun, Ya-Qiu; Zheng, Yan-Feng; Xu, Yan-Yan; Gao, Dong-Zhao; Zhang, Guo-Ying

    2016-11-01

    Seven new 3d-4f heterometallic coordination polymers, [Ln(CuL)2(Hbtca)(btca)(H2O)]·2H2O (Ln = TbIII1, PrIII2, SmIII3, EuIII4, YbIII5), [Nd(NiL)(nip)(Rnip)]·0·25H2O·0.25CH3OH (R= 0.6CH3, 0.4H) 6 and [Nd2(NiL)(nip)3(H2O)]·2H2O 7(CuL or NiL, H2L = 2, 3-dioxo-5, 6, 14, 15-dibenzo-1, 4, 8, 12-tetraazacyclo-pentadeca-7, 13-dien; H2btca = benzotriazole-5-carboxylic acid; H2nip = 5-nitroisophthalic acid) have been synthesized by a solvothermal method and characterized by single-crystal X-ray diffraction. Complexes 1-5 exhibit a double-strand meso-helical chain structures formed by [LnIIICuII2] units via the oxamide and benzotriazole-5-carboxylate bridges, while complex 6 exhibits a four-strand meso-helical chain formed by NdNi unit via the oxamide and 5-nitroisophthalate bridges. Complex 7 consists of a 2D layer framework formed by four-strand meso-helical chain via the nip2- bridges. Moreover, the magnetic properties of them were investigated, and the best-fit analysis of χMT versus T show that the anisotropic contribution of Ln(III) ions (arising from the spin-orbit coupling or the crystal field perturbation) dominates (weak exchange limit) in these complexes(for 3, λ = 214.6 cm-1, zj' = -0.33 cm-1, gav = 1.94; for 5, Δ = 6.98 cm-1, zj' = 1.53 cm-1, gav = 1.85).

  16. Optically rewritable 3D liquid crystal displays.

    PubMed

    Sun, J; Srivastava, A K; Zhang, W; Wang, L; Chigrinov, V G; Kwok, H S

    2014-11-01

    Optically rewritable liquid crystal display (ORWLCD) is a concept based on the optically addressed bi-stable display that does not need any power to hold the image after being uploaded. Recently, the demand for the 3D image display has increased enormously. Several attempts have been made to achieve 3D image on the ORWLCD, but all of them involve high complexity for image processing on both hardware and software levels. In this Letter, we disclose a concept for the 3D-ORWLCD by dividing the given image in three parts with different optic axis. A quarter-wave plate is placed on the top of the ORWLCD to modify the emerging light from different domains of the image in different manner. Thereafter, Polaroid glasses can be used to visualize the 3D image. The 3D image can be refreshed, on the 3D-ORWLCD, in one-step with proper ORWLCD printer and image processing, and therefore, with easy image refreshing and good image quality, such displays can be applied for many applications viz. 3D bi-stable display, security elements, etc.

  17. 3D-graphite structure

    SciTech Connect

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

    2011-01-15

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

  18. 3D structured illumination microscopy

    NASA Astrophysics Data System (ADS)

    Dougherty, William M.; Goodwin, Paul C.

    2011-03-01

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

  19. Crystal Structure of the Mycoplasma arthritidis-Derived Mitogen in Apo Form Reveals a 3D Domain-Swapped Dimer

    SciTech Connect

    Liu, L.; Li, Z; Guo, Y; VanVranken, S; Mourad, W; Li, H

    2010-01-01

    Mycoplasma arthritidis-derived mitogen (MAM) is a superantigen that can activate large fractions of T cells bearing particular V{beta} elements of T cell receptor. Here, we report the crystal structure of a MAM mutant K201A in apo form (unliganded) at 2.8-{angstrom} resolutions. We also partially refined the crystal structures of the MAM wild type and another MAM mutant L50A in apo forms at low resolutions. Unexpectedly, the structures of these apo MAM molecules display a three-dimensional domain-swapped dimer. The entire C-terminal domains of these MAM molecules are involved in the domain swapping. Functional analyses demonstrated that the K201A and L50A mutants do not show altered ability to bind to their host receptors and that they stimulate the activation of T cells as efficiently as does the wild type. Structural comparisons indicated that the 'reconstituted' MAM monomer from the domain-swapped dimer displays large differences at the hinge regions from the MAM{sub wt} molecule in the receptor-bound form. Further comparison indicated that MAM has a flexible N-terminal loop, implying that conformational changes could occur upon receptor binding.

  20. Uranyl and uranyl-3d block cation complexes with 1,3-adamantanedicarboxylate: crystal structures, luminescence, and magnetic properties.

    PubMed

    Thuéry, Pierre; Rivière, Eric; Harrowfield, Jack

    2015-03-16

    The reaction of 1,3-adamantanedicarboxylic acid (LH2) with uranyl nitrate under solvo-hydrothermal conditions, either alone or in the presence of additional metal cations (Co(2+), Ni(2+), or Cu(2+)) gives a series of nine complexes displaying a wide range of architectures. While [UO2(L)(H2O)]·1.25CH3CN (1) and [UO2(L)(DMF)] (2) are one-dimensional (1D) species analogous to that previously known, [H2NMe2]2[(UO2)2(L)3]·1.5H2O (3), which includes dimethylammonium counterions generated in situ, is a three-dimensional (3D) framework, and [UO2(L)(NMP)] (4) (NMP = N-methyl-2-pyrrolidone) is a braid-shaped 1D polymer. When 3d block metal ions are present and bound to 2,2'-bipyridine (bipy) coligands, their role is reduced to that of decorating species attached to uranyl-containing 1D polymers, as in [UO2M(L)2(bipy)2]·0.5H2O with M = Co (5) or Ni (6), and [(UO2)2Cu2(L)3(NO3)2(bipy)2]·0.5H2O (9), or of counterions, as in [Ni(bipy)3][(UO2)4(O)2(L)3]·3H2O (7), in which a two-dimensional (2D) assembly is built from tetranuclear uranyl-containing building units. In contrast, the heterometallic 3D framework [UO2Cu(L)2] (8) can be isolated in the absence of bipy. The emission spectra measured in the solid state display the usual uranyl vibronic fine structure, with various degrees of resolution and quenching, except for that of complex 7, which shows emission from the nickel(II) centers. The magnetic properties of complexes 5, 6, 8, and 9 were investigated, showing, in particular, the presence of zero-field splitting effects in 6 and weak antiferromagnetic interactions in 9.

  1. New five coordinated supramolecular structured cadmium complex as precursor for CdO nanoparticles: Synthesis, crystal structure, theoretical and 3D Hirshfeld surface analyses

    NASA Astrophysics Data System (ADS)

    Ghanbari Niyaky, S.; Montazerozohori, M.; Masoudiasl, A.; White, J. M.

    2017-03-01

    In this paper, a combined experimental and theoretical study on a new CdLBr2 complex (L = N1-(2-bromobenzylidene)-N2-(2-((E)-(2-bromobenzylidene) amino)ethyl) ethane-1,2-diamine) synthesized via template method, is described. The crystal structure analysis of the complex indicates that, the Cd(II) ion is centered in a distorted square pyramidal space constructed by three iminic nitrogens of the ligand as well as two bromide anions. More analysis of crystal packing proposed a supramolecular structure stabilized by some non-covalent interactions such as Br⋯Br and Xsbnd H⋯Br (X = N and C) in solid state. Furthermore, 3D Hirshfeld surface analyses and DFT studies were applied for theoretical investigation of the complexes. Theoretical achievements were found in a good agreement with respect to the experimental data. To evaluate the nature of bonding and the strength of the intra and inter-molecular interactions a natural bond orbital (NBO) analysis on the complex structure was performed. Time dependent density functional theory (TD-DFT) was also applied to predict the electronic spectral data of the complex as compared with the experimental ones. CdLBr2 complex as nano-structure compound was also prepared under ultrasonic conditions and characterized by scanning electron microscopy (SEM) and X-ray powder diffraction (XRPD). Finally, it was found that the cadmium complex can be used as a suitable precursor for preparation of CdO nanoparticles via calcination process at 600 °C under air atmosphere.

  2. 3D holographic polymer photonic crystal for superprism application

    NASA Astrophysics Data System (ADS)

    Chen, Jiaqi; Jiang, Wei; Chen, Xiaonan; Wang, Li; Zhang, Sasa; Chen, Ray T.

    2007-02-01

    Photonic crystal based superprism offers a new way to design new optical components for beam steering and DWDM application. 3D photonic crystals are especially attractive as they could offer more control of the light beam based on the needs. A polygonal prism based holographic fabrication method has been demonstrated for a three-dimensional face-centered-cubic (FCC)-type submicron polymer photonic crystal using SU8 as the photo-sensitive material. Therefore antivibration equipment and complicated optical alignment system are not needed and the requirement for the coherence of the laser source is relaxed compared with the traditional holographic setup. By changing the top-cut prism structure, the polarization of the laser beam, the exposure and development conditions we can achieve different kinds of triclinic or orthorhombic photonic crystals on demand. Special fabrication treatments have been introduced to ensure the survivability of the fabricated large area (cm2) nano-structures. Scanning electron microscopy and diffraction results proved the good uniformity of the fabricated structures. With the proper design of the refraction prism we have achieved a partial bandgap for S+C band (1460-1565nm) in the [111] direction. The transmission and reflection spectra obtained by Fourier transform infrared spectroscopy (FTIR) are in good agreement with simulated band structure. The superprism effects around 1550nm wavelength for the fabricated 3D polymer photonic crystal have been theoretically calculated and such effects can be used for beam steering purpose.

  3. Syntheses, crystal structures, and characterization of three 1D, 2D and 3D complexes based on mixed multidentate N- and O-donor ligands

    SciTech Connect

    Yang, Huai-Xia; Liang, Zhen; Hao, Bao-Lian; Meng, Xiang-Ru

    2014-10-15

    Three new 1D to 3D complexes, namely, ([Ni(btec)(Himb){sub 2}(H{sub 2}O){sub 2}]·6H{sub 2}O){sub n} (1), ([Cd(btec){sub 0.5}(imb)(H{sub 2}O)]·1.5H{sub 2}O){sub n} (2), and ([Zn(btec){sub 0.5}(imb)]·H{sub 2}O){sub n} (3) (H{sub 4}btec=1,2,4,5-benzenetetracarboxylic acid, imb=2-(1H-imidazol-1-methyl)-1H-benzimidazole) have been synthesized by adjusting the central metal ions. Single-crystal X-ray diffraction analyses reveal that complex 1 possesses a 1D chain structure which is further extended into the 3D supramolecular architecture via hydrogen bonds. Complex 2 features a 2D network with Schla¨fli symbol (5{sup 3}·6{sup 2}·7)(5{sup 2}·6{sup 4}). Complex 3 presents a 3D framework with a point symbol of (4·6{sup 4}·8)(4{sup 2}·6{sup 2}·8{sup 2}). Moreover, their IR spectra, PXRD patterns, thermogravimetric curves, and luminescent emissions were studied at room temperature. - Graphical abstract: Three new 1D to 3D complexes with different structural and topological motifs have been obtained by modifying the central metal ions. Additionally, their IR, TG analyses and fluorescent properties are also investigated. - Highlights: • Three complexes based on mixed multidentate N- and O-donor ligands. • The complexes are characterized by IR, luminescence and TGA techniques. • Benzenetetracarboxylates display different coordination modes in complexes 1–3. • Changing the metal ions can result in complexes with completely different structures.

  4. Large Area Printing of 3D Photonic Crystals

    NASA Astrophysics Data System (ADS)

    Watkins, James J.; Beaulieu, Michael R.; Hendricks, Nicholas R.; Kothari, Rohit

    2014-03-01

    We have developed a readily scalable print, lift, and stack approach for producing large area, 3D photonic crystal (PC) structures. UV-assisted nanoimprint lithography (UV-NIL) was used to pattern grating structures comprised of highly filled nanoparticle polymer composite resists with tune-able refractive indices (RI). The gratings were robust and upon release from a support substrate were oriented and stacked to yield 3D PCs. The RI of the composite resists was tuned between 1.58 and 1.92 at 800 nm while maintaining excellent optical transparency. The grating structure dimensions, line width, depth, and pitch, were easily varied by simply changing the imprint mold. For example, a 6 layer log-pile stack was prepared using a composite resist a RI of 1.72 yielding 72 % reflection at 900 nm. The process is scalable for roll-to-roll (R2R) production. Center for Hierarchical Manufacturing - an NSF Nanoscale Science and Engineering Center.

  5. Structure and magnetism of a binuclear Cu(II) pyrophosphate: transition to a 3D magnetic behaviour studied by single crystal EPR.

    PubMed

    Sartoris, Rosana P; Nascimento, Otaciro R; Santana, Ricardo C; Perec, Mireille; Baggio, Ricardo F; Calvo, Rafael

    2015-03-14

    A binuclear Cu(II) compound [Cu2(bpa)2(P2O7)(H2O)2]·2.5H2O, 1, (bpa = 2,2'-bipyridylamine), with pairs of Cu(II) ions bridged by one pyrophosphate tetra-anion, was synthesized and crystallized. Its triclinic structure was determined by single-crystal X-ray diffraction. Electron paramagnetic resonance (EPR) spectra of single crystal samples of 1 were recorded for a fixed orientation of the magnetic field (B0) as a function of temperature (T) between 4.7 and 293 K, and at T = 4.7, 50 and 293 K, as a function of the orientation of B0. Below ∼8 K, the spectra are assigned to two types of mononuclear crystal defects hyperfine-coupled to one copper and two nitrogen nuclei. The g-matrices and hyperfine couplings at these T provide information about the structures of these defects. Above 10 K, the spectrum is dominated by the response of the bulk binuclear Cu(II) material, showing hyperfine interactions with two copper nuclei, collapsing to a single peak above 18 K when the units are magnetically connected, and the magnetic behaviour becomes 3D. We attribute the results above 10 K to the interplay of an AFM intrabinuclear exchange interaction J0 = -28(3) cm(-1) (defined as Hex = -J0S1·S2), and three orders of magnitude weaker exchange coupling with average magnitude |J1| ≥ 0.022 cm(-1) between Cu(II) ions in neighbouring binuclear units. The interplays between structure, exchange couplings, magnetic dimension and spin dynamics in the binuclear compound are discussed. A previously unreported situation, where the structure of the spectra arising from the anisotropic spin-spin interaction term (D) within the binuclear unit is averaged out, but the forbidden half field transition is not, is observed and explained.

  6. A new 3D Co(II)–organic framework with acylamide-containing tetracarboxylate ligand: Solvothermal synthesis, crystal structure, gas adsorption and magnetic property

    SciTech Connect

    Zhang, Qingfu Zhang, Haina; Geng, Aijing; Wang, Suna; Zhang, Chong

    2014-04-01

    A new cobalt(II)–organic framework, [Co{sub 2}(L)(py){sub 2}(DMSO)]{sub n}• 0.5nDMF• 2nDMSO (1) [H{sub 4}L=5,5'-((naphthalene-2,6-dicarbonyl)bis(azanediyl))diisophthalic acid, py=pyridine, DMSO=dimethyl sulfoxide, DMF=N,N-dimethylformamide], has been solvothermally synthesized and characterized by elemental analysis, IR, TGA, PXRD and single-crystal X-ray crystallography. The structural analysis reveals that complex 1 is a 3D framework built from nanosized acylamide-containing tetracarboxylate ligands (L{sup 4−}) and dinuclear [Co{sub 2}(CO{sub 2}){sub 4}] secondary building units (SBUs), exhibiting a uninodal (4,4)-connected crb topology with the Schläfli symbol of (4• 6{sup 5}). The desolvated complex (1a) displays higher adsorption capability for CO{sub 2} than N{sub 2}, which may be due to the relatively strong binding affinity between the CO{sub 2} molecules and acylamide groups in the framework. The magnetic investigation shows that the dominant antiferromagnetic interaction is observed in complex 1. - Graphical abstract: A new 3D Co(II)–organic framework with nanosized acylamide-containing tetracarboxylate ligand was solvothermally synthesized and structurally characterized, its thermal stability, gas adsorption and magnetic property were studied. - Highlights: • A new 3D Co(II)–organic framework with nanosized acylamide-containing tetracarboxylate ligand has been solvothermally synthesized and characterized. • Complex 1 exhibits a uninodal (4,4)-connected crb topology. • The thermal stability, gas adsorption and magnetic property were studied.

  7. Microwave assistant one pot synthesis, crystal structure, antifungal activities and 3D-QSAR of novel 1,2,4-triazolo[4,3-a]pyridines.

    PubMed

    Liu, Xing-Hai; Sun, Zhao-Hui; Yang, Ming-Yan; Tan, Cheng-Xia; Weng, Jian-Quan; Zhang, Yong-Gang; Ma, Yi

    2014-09-01

    A series of novel 1,2,4-triazolo[4,3-a]pyridines were synthesized, and their structures were characterized by (1) H NMR, MS, elemental analysis, and single-crystal X-ray diffraction analysis. The antifungal activities were evaluated. The antifungal activity results indicated that the compound 2b, 2g, 2p, and 2i exhibited good activities. The activity of compound 2b, 2g, 2p, and 2i can compare with the commercial pesticide. The 3D-QSAR model was developed using CoMFA method. Both the steric and electronic field distributions of CoMFA are in good agreement in this work and will be very helpful in designing a new set of analogues.

  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. Identifying Structure-Property Relationships Through DREAM.3D Representative Volume Elements and DAMASK Crystal Plasticity Simulations: An Integrated Computational Materials Engineering Approach

    NASA Astrophysics Data System (ADS)

    Diehl, Martin; Groeber, Michael; Haase, Christian; Molodov, Dmitri A.; Roters, Franz; Raabe, Dierk

    2017-03-01

    Predicting, understanding, and controlling the mechanical behavior is the most important task when designing structural materials. Modern alloy systems—in which multiple deformation mechanisms, phases, and defects are introduced to overcome the inverse strength-ductility relationship—give raise to multiple possibilities for modifying the deformation behavior, rendering traditional, exclusively experimentally-based alloy development workflows inappropriate. For fast and efficient alloy design, it is therefore desirable to predict the mechanical performance of candidate alloys by simulation studies to replace time- and resource-consuming mechanical tests. Simulation tools suitable for this task need to correctly predict the mechanical behavior in dependence of alloy composition, microstructure, texture, phase fractions, and processing history. Here, an integrated computational materials engineering approach based on the open source software packages DREAM.3D and DAMASK (Düsseldorf Advanced Materials Simulation Kit) that enables such virtual material development is presented. More specific, our approach consists of the following three steps: (1) acquire statistical quantities that describe a microstructure, (2) build a representative volume element based on these quantities employing DREAM.3D, and (3) evaluate the representative volume using a predictive crystal plasticity material model provided by DAMASK. Exemplarily, these steps are here conducted for a high-manganese steel.

  10. RADICAL SITES IN M. TUBERCULOSIS KATG IDENTIFIED USING EPR SPECTROSCOPY, THE 3-D CRYSTAL STRUCTURE AND ELECTRON-TRANSFER COUPLINGS†

    PubMed Central

    Ranguelova, Kalina; Girotto, Stefania; Gerfen, Gary J.; Yu, Shengwei; Suarez, Javier; Metlitsky, Leonid; Magliozzo, Richard S.

    2007-01-01

    Catalase-peroxidase (KatG) from Mycobacterium tuberculosis, a Class I peroxidase, exhibits high catalase activity and peroxidase activity with various substrates, and is responsible for activation of the commonly used antitubercular drug, isoniazid (INH). KatG readily forms amino acid based radicals during turnover with alkyl peroxides and this work focuses on extending the identification and characterization of radicals forming on the millisecond to seconds time scale. Rapid freeze- quench electron paramagnetic resonance spectroscopy (RFQ-EPR) reveals a change in the structure of the initially formed radical in the presence of INH. Heme-pocket binding of the drug, and knowledge that KatG[Y229F] lacks this signal provides evidence for radical formation on residue Y229. High-field RFQ-EPR spectroscopy confirmed a tryptophanyl radical signal and new analyses of X-band RFQ-EPR spectra also established its presence. High-field EPR spectroscopy also confirmed that the majority radical species is a tyrosyl radical. Site-directed mutagenesis, along with simulations of EPR spectra based on X-ray structural data for particular tyrosine and tryptophan residues enabled assignments based on predicted hyperfine coupling parameters. KatG mutants W107F, Y229F and the double mutant W107F/Y229F showed alteration in type and yield of radical species. Results are consistent with formation of a tyrosyl radical reasonably assigned to residue Y229 within the first few milliseconds of turnover. This is followed by a mixture of tyrosyl and tryptophanyl radical species, and finally to only a tyrosyl radical on residue Y353, which lies more distant from the heme. Radical processing of enzyme lacking the Trp107-Tyr229-Met255 adduct, found as a unique structural feature of catalase-peroxidases, is suggested to be a reasonable assignment of the phenomena. PMID:17204474

  11. 3-D phononic crystals with ultra-wide band gaps

    PubMed Central

    Lu, Yan; Yang, Yang; Guest, James K.; Srivastava, Ankit

    2017-01-01

    In this paper gradient based topology optimization (TO) is used to discover 3-D phononic structures that exhibit ultra-wide normalized all-angle all-mode band gaps. The challenging computational task of repeated 3-D phononic band-structure evaluations is accomplished by a combination of a fast mixed variational eigenvalue solver and distributed Graphic Processing Unit (GPU) parallel computations. The TO algorithm utilizes the material distribution-based approach and a gradient-based optimizer. The design sensitivity for the mixed variational eigenvalue problem is derived using the adjoint method and is implemented through highly efficient vectorization techniques. We present optimized results for two-material simple cubic (SC), body centered cubic (BCC), and face centered cubic (FCC) crystal structures and show that in each of these cases different initial designs converge to single inclusion network topologies within their corresponding primitive cells. The optimized results show that large phononic stop bands for bulk wave propagation can be achieved at lower than close packed spherical configurations leading to lighter unit cells. For tungsten carbide - epoxy crystals we identify all angle all mode normalized stop bands exceeding 100%, which is larger than what is possible with only spherical inclusions. PMID:28233812

  12. 3-D phononic crystals with ultra-wide band gaps

    NASA Astrophysics Data System (ADS)

    Lu, Yan; Yang, Yang; Guest, James K.; Srivastava, Ankit

    2017-02-01

    In this paper gradient based topology optimization (TO) is used to discover 3-D phononic structures that exhibit ultra-wide normalized all-angle all-mode band gaps. The challenging computational task of repeated 3-D phononic band-structure evaluations is accomplished by a combination of a fast mixed variational eigenvalue solver and distributed Graphic Processing Unit (GPU) parallel computations. The TO algorithm utilizes the material distribution-based approach and a gradient-based optimizer. The design sensitivity for the mixed variational eigenvalue problem is derived using the adjoint method and is implemented through highly efficient vectorization techniques. We present optimized results for two-material simple cubic (SC), body centered cubic (BCC), and face centered cubic (FCC) crystal structures and show that in each of these cases different initial designs converge to single inclusion network topologies within their corresponding primitive cells. The optimized results show that large phononic stop bands for bulk wave propagation can be achieved at lower than close packed spherical configurations leading to lighter unit cells. For tungsten carbide - epoxy crystals we identify all angle all mode normalized stop bands exceeding 100%, which is larger than what is possible with only spherical inclusions.

  13. Two novel lead(II) carboxyphosphonates with a layered and a 3D framework structure: syntheses, crystal structures, reversible dehydration/hydration, and luminescence properties.

    PubMed

    Chu, Wei; Sun, Zhen-Gang; Jiao, Cheng-Qi; Zhu, Yan-Yu; Sun, Shou-Hui; Tian, Hui; Zheng, Ming-Jing

    2013-06-14

    Two novel lead(II) carboxyphosphonates with a layered and a 3D framework structure, namely, [Pb2Cl3(H2L)]·H2O (1) and [Pb2(HL)(HBTC)] (2) (H3L = H2O3PCH2-NC5H9-COOH, H3BTC = 1,3,5-benzenetricarboxylic acid), have been synthesized under hydrothermal conditions and structurally characterized. For compound 1, the interconnection of Pb(1)O2Cl3, Pb(2)O2Cl3, and CPO3 polyhedra via corner- and edge-sharing forms a 1D chain. The adjacent chains connect with each other by sharing the chloride anion, thereby generating a 2D layered structure in the ab-plane. The lattice water molecules are located between adjacent layers. Compound 2 exhibits a 3D pillared-layered structure. The Pb(1)O5, Pb(2)O5, and CPO3 polyhedra are interconnected into a 1D double chain via corner- and edge-sharing, which is further linked to adjacent chains through carboxyphosphonate ligands to form a 2D double layer structure. Neighboring double layers are bridged through the second linkers HBTC(2-), leading to a 3D pillared-layered structure with a 1D channel system along the a-axis. An interesting feature of compound 1 is the presence of the dehydration/hydration properties. It is worth noting that compound 2 can be stable up to a high temperature. The luminescent properties of compounds 1 and 2 have also been studied.

  14. Reduction of Thermal Conductivity by Nanoscale 3D Phononic Crystal

    PubMed Central

    Yang, Lina; Yang, Nuo; Li, Baowen

    2013-01-01

    We studied how the period length and the mass ratio affect the thermal conductivity of isotopic nanoscale three-dimensional (3D) phononic crystal of Si. Simulation results by equilibrium molecular dynamics show isotopic nanoscale 3D phononic crystals can significantly reduce the thermal conductivity of bulk Si at high temperature (1000 K), which leads to a larger ZT than unity. The thermal conductivity decreases as the period length and mass ratio increases. The phonon dispersion curves show an obvious decrease of group velocities in 3D phononic crystals. The phonon's localization and band gap is also clearly observed in spectra of normalized inverse participation ratio in nanoscale 3D phononic crystal. PMID:23378898

  15. Reduction of thermal conductivity by nanoscale 3D phononic crystal.

    PubMed

    Yang, Lina; Yang, Nuo; Li, Baowen

    2013-01-01

    We studied how the period length and the mass ratio affect the thermal conductivity of isotopic nanoscale three-dimensional (3D) phononic crystal of Si. Simulation results by equilibrium molecular dynamics show isotopic nanoscale 3D phononic crystals can significantly reduce the thermal conductivity of bulk Si at high temperature (1000 K), which leads to a larger ZT than unity. The thermal conductivity decreases as the period length and mass ratio increases. The phonon dispersion curves show an obvious decrease of group velocities in 3D phononic crystals. The phonon's localization and band gap is also clearly observed in spectra of normalized inverse participation ratio in nanoscale 3D phononic crystal.

  16. 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

  17. High-resolution 3D structural and optical analyses of hybrid or composite materials by means of scanning probe microscopy combined with the ultramicrotome technique: an example of application to engineering of liquid crystals doped with fluorescent quantum dots

    NASA Astrophysics Data System (ADS)

    Mochalov, Konstantin E.; Efimov, Anton E.; Bobrovsky, Alexey Yu.; Agapov, Igor I.; Chistyakov, Anton A.; Oleinikov, Vladimir A.; Nabiev, Igor

    2013-05-01

    Combination of nanometer-scale 3D structural analysis with optical characterization of the same material is a challenging task. Its results may be important for nanophotonics, materials science, and quality control. We have developed a new technique for complementary high-resolution structural and optical characterization followed by optical spectroscopic and microscopic measurements accompanied by reconstruction of the 3D structure in the same area of the sample. The 3D structure is reconstructed by combination of ultramicrotomic and SPM techniques allowing the study of the 3D distribution of implanted nanoparticles and their effect on the matrix structure. The combination of scanning probe nanotomography (SPN) and optical microspectroscopy makes it possible to direct estimate how the 3D structural characteristics of materials affect their macroscopic optical properties. The technique developed has been applied to the engineering of materials made from cholesteric liquid crystals and fluorescent quantum dots (QDs). These materials permit photochemical patterning and image recording through the changes in the dissymmetry factor of circular polarization of QD emission. The differences in the polarisation images and morphological characteristics of the liquid crystal matrix have proved to be correlated with the arrangement of the areas of homogeneous distribution and nonhomogeneous clustering of QDs. The reconstruction of the 3D structure of the liquid crystal matrix in the areas of homogeneous QD distribution has shown that QDs embedded into cholesteric liquid crystal matrices do not perturb their periodic planar texture. The combined optical/SPM/ultramicrotome technique will be indispensable for evaluating the effects of inorganic nanoparticles on the organisation of organic and liquid crystal matrices, biomedical materials, cells, and tissues.

  18. 3D cone-sheet and crystal-settling models reveal magma-reservoir structure of the Carlingford central complex, Ireland

    NASA Astrophysics Data System (ADS)

    Schauroth, Jenny; Burchardt, Steffi; Meade, Fiona; Troll, Valentin R.

    2014-05-01

    The Palaeogene Carlingford central complex, northeast Ireland, hosts a swarm of mostly basaltic cone-sheets with several lithological subsets (Halsall, 1974). The two most abundant sets are aphyric and highly porphyritic cone-sheets with up to 80% of cm-sized plagioclase phenocrysts. The abundance of highly porphyritic cone-sheets seems to systematically increase with altitude compared to the aphyric type (Meade, 2008). We hypothesised that this observation might be explained by the zonation of the source magma reservoir. In order to test this hypothesis, we modelled the 3D cone-sheet structure at depth and the settling of plagioclase phenocrysts. The 3D model of the Carlingford cone-sheet swarm reveals that lithological types of Carlingford cone-sheets are not systematically distributed in space. Using the method proposed by Burchardt et al. (2013), we constructed the likely source reservoir of the cone-sheets, which is saucer-shaped, elongated in NW direction, 7 km long and 3 km wide, and located at a depth of 1 km below the present-day land surface. Our calculation of the terminal velocity of the plagioclase phenocrysts shows that the large phenocrysts in the porphyritic cone-sheets were too big to float at the conditions present in the Carlingford magma reservoir. We can therefore exclude vertical magma-chamber stratification as an explanation for the formation and distribution of porphyritic and aphyric cone-sheets. Instead, we envisage the formation of a crystal mush at the base and sides of the Carlingford magma reservoir. Cone-sheet injection and magma-cha,ber replenishments have remobilised plagioclase cumulates, which may explain the occurrence and distribution of aphyric and highly porphyritic cone-sheets. REFERENCES Burchardt, S., Troll, V. R., Mathieu, L., Emeleus, H. C., Donaldson, C., 2013, Scientific Reports 3, 2891. Halsall, T.J., 1974, The minor intrusions and structure of the Carlingford complex, Eire (PhD thesis): University of Leicester. Meade

  19. Controllable liquid crystal gratings for an adaptive 2D/3D auto-stereoscopic display

    NASA Astrophysics Data System (ADS)

    Zhang, Y. A.; Jin, T.; He, L. C.; Chu, Z. H.; Guo, T. L.; Zhou, X. T.; Lin, Z. X.

    2017-02-01

    2D/3D switchable, viewpoint controllable and 2D/3D localizable auto-stereoscopic displays based on controllable liquid crystal gratings are proposed in this work. Using the dual-layer staggered structure on the top substrate and bottom substrate as driven electrodes within a liquid crystal cell, the ratio between transmitting region and shielding region can be selectively controlled by the corresponding driving circuit, which indicates that 2D/3D switch and 3D video sources with different disparity images can reveal in the same auto-stereoscopic display system. Furthermore, the controlled region in the liquid crystal gratings presents 3D model while other regions maintain 2D model in the same auto-stereoscopic display by the corresponding driving circuit. This work demonstrates that the controllable liquid crystal gratings have potential applications in the field of auto-stereoscopic display.

  20. 3D Structures of Responsive Nanocompartmentalized Microgels.

    PubMed

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

    2016-11-09

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

  1. Inferential modeling of 3D chromatin structure.

    PubMed

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-04-30

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

  2. 3D plasmonic crystal metamaterials for ultra-sensitive biosensing

    NASA Astrophysics Data System (ADS)

    Aristov, Andrey I.; Manousidaki, Maria; Danilov, Artem; Terzaki, Konstantina; Fotakis, Costas; Farsari, Maria; Kabashin, Andrei V.

    2016-05-01

    We explore the excitation of plasmons in 3D plasmon crystal metamaterials and report the observation of a delocalized plasmon mode, which provides extremely high spectral sensitivity (>2600 nm per refractive index unit (RIU) change), outperforming all plasmonic counterparts excited in 2D nanoscale geometries, as well as a prominent phase-sensitive response (>3*104 deg. of phase per RIU). Combined with a large surface for bioimmobilization provided by the 3D matrix, the proposed sensor architecture promises a new important landmark in the advancement of plasmonic biosensing technology.

  3. 3D plasmonic crystal metamaterials for ultra-sensitive biosensing

    PubMed Central

    Aristov, Andrey I.; Manousidaki, Maria; Danilov, Artem; Terzaki, Konstantina; Fotakis, Costas; Farsari, Maria; Kabashin, Andrei V.

    2016-01-01

    We explore the excitation of plasmons in 3D plasmon crystal metamaterials and report the observation of a delocalized plasmon mode, which provides extremely high spectral sensitivity (>2600 nm per refractive index unit (RIU) change), outperforming all plasmonic counterparts excited in 2D nanoscale geometries, as well as a prominent phase-sensitive response (>3*104 deg. of phase per RIU). Combined with a large surface for bioimmobilization provided by the 3D matrix, the proposed sensor architecture promises a new important landmark in the advancement of plasmonic biosensing technology. PMID:27151104

  4. Automated modeling of RNA 3D structure.

    PubMed

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

    2014-01-01

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

  5. 3D coordination networks based on supramolecular chains as building units: synthesis and crystal structures of two silver(I) pyridyldiethynides.

    PubMed

    Zhang, Tianle; Kong, Jianxi; Hu, Yuejie; Meng, Xianggao; Yin, Hongbing; Hu, Dongshuang; Ji, Changpeng

    2008-04-21

    Two silver(I) pyridyldiethynides, [Ag2(3,5-C2PyC2).4CF3CO2Ag.4H2O] ( A) and [Ag 2(3,5-C2PyC2).3AgNO3.H2O](B), were synthesized by reactions of 3,5-diethynylpyridine with silver trifluoroacetate and silver nitrate in high yield, respectively. X-ray crystallographic studies revealed that in A pyridyldiethynide groups connect Ag 11 cluster units to generate 1D supramolecular chains as bridging ligands, where each ethynide group interacts with four silver atoms. These supramolecular chains bearing pyridyl groups are linked by silver ions to form wavelike layers, which are further connected by trifluoroacetate ligands to afford a 3D coordination network. However, B exhibits a different structural feature, where two ethynide groups in one pyridyldiethynide ligand coordinate to three and four silver atoms, respectively. These silver ethynide cluster units are linked through silver-ethynide and argentophilic interactions, leading to a double silver chain by sharing silver atoms in these units. In B, the silver double chains are further connected by bridging pyridyldiethynide groups to generate 2D networks, which interact through the Ag-N coordination bonds between silver atoms and pyridyl groups in the adjacent layers to generate a 3D coordination network. In these two compounds, trifluoroacetate and nitrate groups exhibit different bonding modes, indicating that the counterion is an important factor influencing the structures of supramolecular chains and coordination networks.

  6. Crystal structure and carrier transport properties of a new 3D mixed-valence Cu(I)-Cu(II) coordination polymer including pyrrolidine dithiocarbamate ligand.

    PubMed

    Okubo, Takashi; Tanaka, Naoya; Kim, Kyung Ho; Anma, Haruho; Seki, Shu; Saeki, Akinori; Maekawa, Masahiko; Kuroda-Sowa, Takayoshi

    2011-03-14

    A novel mixed-valence Cu(i)-Cu(ii) coordination polymer having an infinite three-dimensional (3D) structure, {[Cu(I)(4)Cu(II)(2)Br(4)(Pyr-dtc)(4)]·CHCl(3)}(n) (1) (Pyr-dtc(-) = pyrrolidine dithiocarbamate), has been prepared and structurally characterized via X-ray diffraction. This complex consists of 1D Cu(i)-Br chains and bridging mononuclear copper(ii) units of Cu(II)(Pyr-dtc)(2), which form an infinite 3D network. A magnetic study indicates that this complex includes copper(ii) ions exhibiting a weak antiferromagnetic interaction (θ = -0.086 K) between the unpaired electrons of the copper(ii) ions present in the diamagnetic Cu(i)-Br chains. The carrier transport properties of 1 are investigated using an impedance spectroscopy technique and flash-photolysis time-resolved microwave conductivity measurement (FP-TRMC). The impedance spectroscopy reveals that this complex exhibits intriguing semiconducting properties at a small activation energy (E(a) = 0.29 eV (bulk)). The sum of the mobilities of the negative and positive carriers estimated via FP-TRMC is Σμ∼ 0.4 cm(2) V(-1) s(-1).

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. Microfabricating 3D Structures by Laser Origami

    DTIC Science & Technology

    2011-11-09

    technique generates 3D microstructures by controlled out-of- plane folding of 2D patterns through a variety of laser-based digital fabrication...processes. Digital microfabrication techniques such as laser direct-write (LDW) offer a viable alternative for generating 3D self-folding designs. These...folding at the microscale where manual or mechanized actuation of the smaller struc- tures is not practical. LDW techniques allow micromachining and

  13. Synthesis, crystal structure and properties of a new 3D supramolecular unsymmetrical tetradentate Schiff bases copper (II) framework with stable tunnels

    NASA Astrophysics Data System (ADS)

    Al-Noaimi, Mousa; Awwadi, Firas F.; Al-Razagg, Raiid; Esmadi, Fatima T.

    2016-12-01

    Flexible unsymmetrical Schiff base ligand (L) which is derived from the half unit Y = C6H5COCH2C(Ndbnd CH2C6H4NH2)CH3 (obtained from the reaction of benzoylacetone and 2-aminobenzylamine) and 2- quinolinecarboxaldehyde have been successfully co-assembled with Cu(ClO4)2 to give out the [Cu(L)]ClO4 complex. The complex crystallizes in two different space groups; P21/n and P-1. The crystal structure of the P-1 phase indicates the presence of tunnels; the volume of these tunnels is 157 Å3 which is big enough to accommodate solvent molecules. The X-ray data indicates that these tunnels are most probably filled by highly disordered solvent molecules or solvent molecules with partial occupancy. The tunneled structure is stabilized via π-π stacking interactions to give a supramolecular MOF with 1D rhomboidal tunnels array. The copper(II) atom assumes a distorted-square pyrimidal coordination geometry where the perchlorate is located on the apex of the pyramide. In addition, this work presents and discusses the spectroscopic (IR, UV/vis), electro-chemical (cyclic voltammetry) behavior of the Cu(II) complexes. The Cu(II) oxidation state is stabilized by the novel tetradentate ligands, showing Cu(I/II) couple around 0.1 vs. Cp2Fe/Cp2Fe+.

  14. 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

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

    PubMed

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

    2015-07-01

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

  16. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

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

    2016-07-08

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

  17. 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

  18. Spherical 3D photonic crystal with conducting nanoshell and particle core

    NASA Astrophysics Data System (ADS)

    Zamudio-Lara, A.; Sánchez-Mondragón, J.; Escobedo-Alatorre, J.; Pérez-Careta, E.; Torres-Cisneros, M.; Tecpoyotl-Torres, Margarita; Vázquez-Buenos Aires, O.

    2009-06-01

    We discuss a structured 3D Dielectric Photonic Crystal with both a metallic core and a metallic shell. We discuss the role of each one, the stack, the core as well as the cavity formed between the core and the shell. The low frequency metallic core features becomes much more significant as it gets smaller and get diluted by the cavity.

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

    PubMed Central

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

    2017-01-01

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

  20. Two-dimensional 3d-4f heterometallic coordination polymers: syntheses, crystal structures, and magnetic properties of six new Co(II)-Ln(III) compounds.

    PubMed

    Díaz-Gallifa, Pau; Fabelo, Oscar; Pasán, Jorge; Cañadillas-Delgado, Laura; Lloret, Francesc; Julve, Miguel; Ruiz-Pérez, Catalina

    2014-06-16

    Six new heterometallic cobalt(II)-lanthanide(III) complexes of formulas [Ln(bta)(H2O)2]2[Co(H2O)6]·10H2O [Ln = Nd(III) (1) and Eu(III) (2)] and [Ln2Co(bta)2(H2O)8]n·6nH2O [Ln = Eu(III) (3), Sm(III) (4), Gd(III) (5), and Tb(III) (6)] (H4bta = 1,2,4,5-benzenetretracaboxylic acid) have been synthesized and characterized via single-crystal X-ray diffraction. 1 and 2 are isostructural compounds with a structure composed of anionic layers of [Ln(bta)(H2O)2]n(n-) sandwiching mononuclear [Co(H2O)6](2+) cations plus crystallization water molecules, which are interlinked by electrostatic forces and hydrogen bonds, leading to a supramolecular three-dimensional network. 3-6 are also isostructural compounds, and their structure consists of neutral layers of formula [Ln2Co(bta)2(H2O)8]n and crystallization water molecules, which are connected through hydrogen bonds to afford a supramolecular three-dimensional network. Heterometallic chains formed by the regular alternation of two nine-coordinate lanthanide(III) polyhedra [Ln(III)O9] and one compressed cobalt(II) octahedron [Co(II)O6] along the crystallographic c-axis are cross-linked by bta ligands within each layer of 3-6. Magnetic susceptibility measurements on polycrystalline samples for 3-6 have been carried out in the temperature range of 2.0-300 K. The magnetic behavior of these types of Ln(III)-Co(II) complexes, which have been modeled by using matrix dagonalization techniques, reveals the lack of magnetic coupling for 3 and 4, and the occurrence of weak antiferromagnetic interactions within the Gd(III)-Gd(III) (5) and Tb(III)-Tb(III) (6) dinuclear units through the exchange pathway provided by the double oxo(carboxylate) and double syn-syn carboxylate bridges.

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

    PubMed

    Miao, Zhichao; Westhof, Eric

    2017-03-30

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

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

    PubMed

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

    2017-05-01

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

  3. Fast-response liquid-crystal lens for 3D displays

    NASA Astrophysics Data System (ADS)

    Liu, Yifan; Ren, Hongwen; Xu, Su; Li, Yan; Wu, Shin-Tson

    2014-02-01

    Three-dimensional (3D) display has become an increasingly important technology trend for information display applications. Dozens of different 3D display solutions have been proposed. The autostereoscopic 3D display based on lenticular microlens array is a promising approach, and fast-switching microlens array enables this system to display both 3D and conventional 2D images. Here we report two different fast-response microlens array designs. The first one is a blue phase liquid crystal lens driven by the Pedot: PSS resistive film electrodes. This BPLC lens exhibits several attractive features, such as polarization insensitivity, fast response time, simple driving scheme, and relatively low driving voltage, as compared to other BPLC lens designs. The second lens design has a double-layered structure. The first layer is a polarization dependent polymer microlens array, and the second layer is a thin twisted-nematic (TN) liquid crystal cell. When the TN cell is switched on/off, the traversing light through the polymeric lens array is either focused or defocused, so that 2D/3D images are displayed correspondingly. This lens design has low driving voltage, fast response time, and simple driving scheme. Simulation and experiment demonstrate that the performance of both switchable lenses meet the requirement of 3D display system design.

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

    NASA Astrophysics Data System (ADS)

    Singh, Suryabhan; Bhim, Anupam

    2016-12-01

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

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

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

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

  6. 3D Rare earth porous coordination frameworks with formamide generated in situ syntheses: Crystal structure and down- and up-conversion luminescence

    SciTech Connect

    Ma, Xue; Tian, Jing; Yang, Hong-Y.; Zhao, Kai; Li, Xia

    2013-05-01

    The reaction of RE(NO)₃·6H₂O and formamide yielded the coordination polymers, [RE(HCOO)₄]⁻[NH₂CHNH₂]⁺ (RE=Y 1, Eu 2, Gd 3, Tb 4, Dy 5, Er 6, and Yb 7). They possess 3D porous frameworks with the 1D rhombic channels occupied by [NH₂CHNH₂]⁺ cations. Complexes 2 and 4 display the characteristic down-conversion emissions corresponding to ⁵D₀→⁷FJ (J=1–4) transitions of Eu(III) ion and ⁵D₄→⁷FJ (J=6–3) transitions of Tb(III) ion, respectively. Longer lifetime values of 2.128±0.002 ms (⁵D₀) for 2 and 2.132±0.002 ms (⁵D₄) for 4 have been observed. The up-conversion spectra of the Y:Yb,Er and Gd:Yb,Er codoped complexes exhibit three emission bands around 410 (⁴H9/2→⁴I15/2, blue), 518–570 (⁴S3/2, ²H11/2→⁴I15/2, green), and 655 nm (⁴F9/2→⁴I15/2, red). - Graphical Abstract: The complexes [RE(HCOO)₄]⁻[NH₂CHNH₂]⁺ possess 3D porous frameworks. Eu(III) and Tb(III) complexes show characteristic emission of Ln(III) ions. The up-conversion emission of the Y:Yb,Er and Gd:Yb,Er codoped complexes was observed. Highlights: •The reaction of RE(NO)₃·6H₂O and formamide produced complexes [RE(HCOO)₄]⁻[NH₂CHNH₂]⁺. • The complexes possess 3D frameworks with the 1D channels occupied by [NH₂CHNH₂]+ cations. • Eu(III)/Tb(III) complexes display the characteristic down-conversion emission of Ln(III) ions. • The Y:Yb,Er and Gd:Yb,Er doped complexes exhibit the up-conversion emission.

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

    PubMed

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

    2012-01-01

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  10. Hydrogen in polar intermetallics: Syntheses and structures of the ternary Ca5Bi3D0.93, Yb5Bi3Hx, and Sm5Bi3H~1 by powder neutron or single crystal X-ray diffraction

    SciTech Connect

    Leon-Escamilla, E. Alejandro; Dervenagas, Panagiotis; Stasis, Constantine; Corbett, John D.

    2010-01-01

    The syntheses of the title compounds are described in detail. Structural characterizations from refinements of single crystal X-ray diffraction data for Yb{sub 5}Bi{sub 3}H{sub x} and Sm{sub 5}Bi{sub 3}H{sub 1} and of powder neutron diffraction data for Ca{sub 5}Bi{sub 3}D{sub 0.93(3)} are reported. These confirm that all three crystallize with the heavy atom structure type of {beta}-Yb{sub 5}Sb{sub 3}, and the third gives the first proof that the deuterium lies in the center of nominal calcium tetrahedra, isostructural with the Ca{sub 5}Sb{sub 3}F-type structure. These Ca and Yb phases are particularly stable with respect to dissociation to Mn{sub 5}Si{sub 3}-type product plus H{sub 2}. Some contradictions in the literature regarding Yb{sub 5}Sb{sub 3} and Yb{sub 5}Sb{sub 3}H{sub x} phases are considered in terms of adventitious hydrogen impurities that are generated during reactions in fused silica containers at elevated temperatures.

  11. 3-D rare earth-doped colloidal photonic crystals

    NASA Astrophysics Data System (ADS)

    Clara Gonçalves, M.; Fortes, Luis M.; Almeida, Rui M.; Chiasera, Alessandro; Chiappini, Andrea; Ferrari, Maurizio

    2009-07-01

    Three-dimensional photonic bandgap structures have been synthesized by a colloidal/sol-gel route, starting with the self-organization of polystyrene microspheres into opal structures by vertical convective self-assembly, followed by sol-gel infiltration of the interstices with silica or titania doped with Er 3+ and Yb 3+ ions and the removal of the polymeric template by heat treatment. The structural and optical properties of the opals and inverse opals prepared by this method have been studied by scanning electron microscopy and near infra-red spectroscopy. The SEM images show that the photonic crystals contain ordered domains up to ˜600 μm 2. Variable incidence reflectivity spectra have been measured for the opals, infiltrated opals and inverse opals. The corresponding effective refractive indices ( neff) were calculated based on effective-medium approaches. Photoluminescence measurements of the emission of Er 3+ ions at ˜1.5 μm from titania inverse opal structures were performed and are compared with those characteristic of the same ions in bulk titania material in the absence of a photonic bandgap structure.

  12. The 3D Structure of the Proton

    NASA Astrophysics Data System (ADS)

    Kaiser, Ralf

    2012-09-01

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

  13. 3D Animations for Exploring Nucleon Structure

    NASA Astrophysics Data System (ADS)

    Gorman, Waverly; Burkardt, Matthias

    2016-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  15. Multiple Colors Output on Voile through 3D Colloidal Crystals with Robust Mechanical Properties.

    PubMed

    Meng, Yao; Tang, Bingtao; Ju, Benzhi; Wu, Suli; Zhang, Shufen

    2017-01-25

    Distinguished from the chromatic mechanism of dyes and pigments, structural color is derived from physical interactions of visible light with structures that are periodic at the scale of the wavelength of light. Using colloidal crystals with coloring functions for fabrics has resulted in significant improvements compared with chemical colors because the structural color from colloidal crystals bears many unique and fascinating optical properties, such as vivid iridescence and nonphotobleaching. However, the poor mechanical performance of the structural color films cannot meet actual requirements because of the weak point contact of colloidal crystal particles. Herein, we demonstrate in this study the patterning on voile fabrics with high mechanical strength on account of the periodic array lock effect of polymers, and multiple structural color output was simultaneously achieved by a simple two-phase self-assembly method for printing voile fabrics with 3D colloidal crystals. The colored voile fabrics exhibit high color saturation, good mechanical stability, and multiple-color patterns printable. In addition, colloidal crystals are promising potential substitutes for organic dyes and pigments because colloidal crystals are environmentally friendly.

  16. Ligational behaviour of (E)-2-amino-N‧-[1-(2-hydroxyphenyl)ethylidene]benzohydrazide towards later 3d metal ions: X-ray crystal structure of nickel(IV) complex

    NASA Astrophysics Data System (ADS)

    Gudasi, Kalagouda B.; Patil, Siddappa A.; Bakale, Raghavendra P.; Nethaji, Munirathinum

    2014-05-01

    Ligational behaviour of (E)-2-amino-N‧-[1-(2-hydroxyphenyl)ethylidene]benzohydrazide (Aheb) towards later 3d metal ions[copper(II), cobalt(II), manganese(II), zinc(II), cadmium(II) and nickel(IV)] has been studied. Their structures have been elucidated on the basis of spectral (IR, 1H NMR, UV-Vis, EPR and FAB-mass), elemental analyses, conductance measurements, magnetic moments, and thermal studies. During complexation Ni(II) ion has got oxidized to Ni(IV). The changes in the bond parameters of the ligand on complexation has been discussed by comparing the crystal structure of the ligand with that of its Ni(IV) complex. The X-ray single crystal analysis of [Ni(aheb)2]Cl2·4H2O has confirmed an octahedral geometry around the metal ion. EPR spectra of the Cu(II) complex in polycrystalline state at room (300 K) and liquid nitrogen temperature (77 K) were recorded and their salient features are reported.

  17. Capillary Force Driven Self-Assembly of Anisotropic Hierarchical Structures Prepared by Femtosecond Laser 3D Printing and Their Applications in Crystallizing Microparticles.

    PubMed

    Lao, Zhaoxin; Hu, Yanlei; Zhang, Chenchu; Yang, Liang; Li, Jiawen; Chu, Jiaru; Wu, Dong

    2015-12-22

    The hierarchical structures are the derivation of various functionalities in the natural world and have inspired broad practical applications in chemical systhesis and biological manipulation. However, traditional top-down fabrication approaches suffered from low complexity. We propose a laser printing capillary-assisted self-assembly (LPCS) strategy for fabricating regular periodic structures. Microscale pillars are first produced by the localized femtosecond laser polymerization and are subsequently self-assembled into periodic hierarchical architectures with the assistance of controlled capillary force. Moreover, based on anisotropic assemblies of micropillars, the LPCS method is further developed for the preparation of more complicated and advanced functional microstructures. Pillars cross section, height, and spatial arrangement can be tuned to guide capillary force, and diverse assemblies with different configurations are thus achieved. Finally, we developed a strategy for growing micro/nanoparticles in designed spatial locations through solution-evaporation self-assembly induced by morphology. Due to the high flexibility of LPCS method, the special arrangements, sizes, and distribution density of the micro/nanoparticles can be controlled readily. Our method will be employed not only to fabricate anisotropic hierarchical structures but also to design and manufacture organic/inorganic microparticles.

  18. Fluorescence Enhancement on Large Area Self-Assembled Plasmonic-3D Photonic Crystals.

    PubMed

    Chen, Guojian; Wang, Dongzhu; Hong, Wei; Sun, Lu; Zhu, Yongxiang; Chen, Xudong

    2017-03-01

    Discontinuous plasmonic-3D photonic crystal hybrid structures are fabricated in order to evaluate the coupling effect of surface plasmon resonance and the photonic stop band. The nanostructures are prepared by silver sputtering deposition on top of hydrophobic 3D photonic crystals. The localized surface plasmon resonance of the nanostructure has a symbiotic relationship with the 3D photonic stop band, leading to highly tunable characteristics. Fluorescence enhancements of conjugated polymer and quantum dot based on these hybrid structures are studied. The maximum fluorescence enhancement for the conjugated polymer of poly(5-methoxy-2-(3-sulfopropoxy)-1,4-phenylenevinylene) potassium salt by a factor of 87 is achieved as compared with that on a glass substrate due to the enhanced near-field from the discontinuous plasmonic structures, strong scattering effects from rough metal surface with photonic stop band, and accelerated decay rates from metal-coupled excited state of the fluorophore. It is demonstrated that the enhancement induced by the hybrid structures has a larger effective distance (optimum thickness ≈130 nm) than conventional plasmonic systems. It is expected that this approach has tremendous potential in the field of sensors, fluorescence-imaging, and optoelectronic applications.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  20. Virtual and Printed 3D Models for Teaching Crystal Symmetry and Point Groups

    ERIC Educational Resources Information Center

    Casas, Lluís; Estop, Euge`nia

    2015-01-01

    Both, virtual and printed 3D crystal models can help students and teachers deal with chemical education topics such as symmetry and point groups. In the present paper, two freely downloadable tools (interactive PDF files and a mobile app) are presented as examples of the application of 3D design to study point-symmetry. The use of 3D printing to…

  1. 3-D visualization of geologic structures and processes

    NASA Astrophysics Data System (ADS)

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

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

  2. Finding Organized Structures in 3-D LADAR Data

    DTIC Science & Technology

    2004-12-01

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

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

    PubMed

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

    2017-01-01

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

  4. Direct-Write 3D Nanoprinting of Plasmonic Structures

    DOE PAGES

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

    2016-11-23

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

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

    PubMed

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

    2017-03-08

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

  6. Direct-Write 3D Nanoprinting of Plasmonic Structures

    SciTech Connect

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

    2016-11-23

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

  7. 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/.

  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. FEM modeling of 3D photonic crystals and photonic crystal waveguides

    NASA Astrophysics Data System (ADS)

    Burger, Sven; Klose, Roland; Schaedle, Achim; Schmidt, Frank; Zschiedrich, Lin W.

    2005-03-01

    We present a finite-element simulation tool for calculating light fields in 3D nano-optical devices. This allows to solve challenging problems on a standard personal computer. We present solutions to eigenvalue problems, like Bloch-type eigenvalues in photonic crystals and photonic crystal waveguides, and to scattering problems, like the transmission through finite photonic crystals. The discretization is based on unstructured tetrahedral grids with an adaptive grid refinement controlled and steered by an error-estimator. As ansatz functions we use higher order, vectorial elements (Nedelec, edge elements). For a fast convergence of the solution we make use of advanced multi-grid algorithms adapted for the vectorial Maxwell's equations.

  10. Toward mobile 3D visualization for structural biologists.

    PubMed

    Tanramluk, Duangrudee; Akavipat, Ruj; Charoensawan, Varodom

    2013-12-01

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

  11. A full field, 3-D velocimeter for microgravity crystallization experiments

    NASA Technical Reports Server (NTRS)

    Brodkey, Robert S.; Russ, Keith M.

    1991-01-01

    The programming and algorithms needed for implementing a full-field, 3-D velocimeter for laminar flow systems and the appropriate hardware to fully implement this ultimate system are discussed. It appears that imaging using a synched pair of video cameras and digitizer boards with synched rails for camera motion will provide a viable solution to the laminar tracking problem. The algorithms given here are simple, which should speed processing. On a heavily loaded VAXstation 3100 the particle identification can take 15 to 30 seconds, with the tracking taking less than one second. It seeems reasonable to assume that four image pairs can thus be acquired and analyzed in under one minute.

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

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

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

    PubMed Central

    2013-01-01

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

  16. 3D WHOLE-PROMINENCE FINE STRUCTURE MODELING

    SciTech Connect

    Gunár, Stanislav; Mackay, Duncan H.

    2015-04-20

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

  17. Automated 3D structure composition for large RNAs

    PubMed Central

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

    2012-01-01

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

  18. Automated 3D structure composition for large RNAs.

    PubMed

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

    2012-08-01

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

  19. Designing 3D Structure by 5-7 Kirigami

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  20. Fabrication of 3D polymer photonic crystals for near-IR applications

    NASA Astrophysics Data System (ADS)

    Yao, Peng; Qiu, Liang; Shi, Shouyuan; Schneider, Garrett J.; Prather, Dennis W.; Sharkawy, Ahmed; Kelmelis, Eric

    2008-02-01

    Photonic crystals[1, 2] have stirred enormous research interest and became a growing enterprise in the last 15 years. Generally, PhCs consist of periodic structures that possess periodicity comparable with the wavelength that the PhCs are designed to modulate. If material and periodic pattern are properly selected, PhCs can be applied to many applications based on their unique properties, including photonic band gaps (PBG)[3], self-collimation[4], super prism[5], etc. Strictly speaking, PhCs need to possess periodicity in three dimensions to maximize their advantageous capabilities. However, many current research is based on scaled two-dimensional PhCs, mainly due to the difficulty of fabrication such three-dimensional PhCs. Many approaches have been explored for the fabrication of 3D photonic crystals, including layer-by-layer surface micromachining[6], glancing angle deposition[7], 3D micro-sculpture method[8], self-assembly[9] and lithographical methods[10-12]. Among them, lithographic methods became increasingly accepted due to low costs and precise control over the photonic crystal structure. There are three mostly developed lithographical methods, namely X-ray lithography[10], holographic lithography[11] and two-photon polymerization[12]. Although significant progress has been made in developing these lithography-based technologies, these approaches still suffer from significant disadvantages. X-ray lithography relies on an expensive radiation source. Holographic lithography lacks the flexibility to create engineered defects, and multi-photon polymerization is not suitable for parallel fabrication. In our previous work, we developed a multi-layer photolithography processes[13, 14] that is based on multiple resist application and enhanced absorption upon exposure. Using a negative lift-off resist (LOR) and 254nm DUV source, we have demonstrated fabrication of 3D arbitrary structures with feature size of several microns. However, severe intermixing problem

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

  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. 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

  5. Polymorphism, crystal nucleation and growth in the phase-field crystal model in 2D and 3D

    NASA Astrophysics Data System (ADS)

    Tóth, Gyula I.; Tegze, György; Pusztai, Tamás; Tóth, Gergely; Gránásy, László

    2010-09-01

    We apply a simple dynamical density functional theory, the phase-field crystal (PFC) model of overdamped conservative dynamics, to address polymorphism, crystal nucleation, and crystal growth in the diffusion-controlled limit. We refine the phase diagram for 3D, and determine the line free energy in 2D and the height of the nucleation barrier in 2D and 3D for homogeneous and heterogeneous nucleation by solving the respective Euler-Lagrange (EL) equations. We demonstrate that, in the PFC model, the body-centered cubic (bcc), the face-centered cubic (fcc), and the hexagonal close-packed structures (hcp) compete, while the simple cubic structure is unstable, and that phase preference can be tuned by changing the model parameters: close to the critical point the bcc structure is stable, while far from the critical point the fcc prevails, with an hcp stability domain in between. We note that with increasing distance from the critical point the equilibrium shapes vary from the sphere to specific faceted shapes: rhombic dodecahedron (bcc), truncated octahedron (fcc), and hexagonal prism (hcp). Solving the equation of motion of the PFC model supplied with conserved noise, solidification starts with the nucleation of an amorphous precursor phase, into which the stable crystalline phase nucleates. The growth rate is found to be time dependent and anisotropic; this anisotropy depends on the driving force. We show that due to the diffusion-controlled growth mechanism, which is especially relevant for crystal aggregation in colloidal systems, dendritic growth structures evolve in large-scale isothermal single-component PFC simulations. An oscillatory effective pair potential resembling those for model glass formers has been evaluated from structural data of the amorphous phase obtained by instantaneous quenching. Finally, we present results for eutectic solidification in a binary PFC model.

  6. 3D genome structure modeling by Lorentzian objective function.

    PubMed

    Trieu, Tuan; Cheng, Jianlin

    2016-11-29

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

  7. 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.

  8. Spectral selectivity of 3D magnetophotonic crystal film fabricated from single butterfly wing scales.

    PubMed

    Peng, Wenhong; Zhu, Shenmin; Zhang, Wang; Yang, Qingqing; Zhang, Di; Chen, Zhixin

    2014-06-07

    3D magnetophotonic crystal (3D-MPC) film is an excellent platform for tailoring the magneto-optical response of magnetic materials. However, its fabrication is a great challenge due to the limitation of commonly used artificial synthesis methods. Inspired by the unique structures of biospecies, we hereby manipulate the pristine single wing scales of Morpho didius precisely and successfully fabricate Fe3O4 films with photonic structure. The synthesis strategy involves the fabrication of Fe2O3 film from a single wing scale using an improved sol-gel method followed by a subsequent reduction. The intrinsic hierarchical photonic structures as well as the anisotropic optical properties of the pristine butterfly wing scale have been retained in the obtained Fe2O3 and Fe3O4 films. When investigated under an external magnetic field, a spectral blue shift about 43 nm is observed in the designated orientation of the Fe3O4 film, which is useful for the design and creation of novel magnetic-optical modulator devices. Furthermore, these single scales can be used as building blocks to fabricate designable and more complicated assembled nano systems. This biomimetic technique combined with the variety of structures of butterfly wing scales provides an effective approach to produce magneto-photonic films with desired structure, paving a new way for theoretical research and practical applications.

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

    PubMed

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

    2011-09-01

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

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

    PubMed

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

    2016-01-01

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

  11. Instability and Wave Propagation in Structured 3D Composites

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  12. 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.

  13. 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

  14. 3D-modeling of deformed halite hopper crystals by Object Based Image Analysis

    NASA Astrophysics Data System (ADS)

    Leitner, Christoph; Hofmann, Peter; Marschallinger, Robert

    2014-12-01

    Object Based Image Analysis (OBIA) is an established method for analyzing multiscale and multidimensional imagery in a range of disciplines. In the present study this method was used for the 3D reconstruction of halite hopper crystals in a mudrock sample, based on Computed Tomography data. To quantitatively assess the reliability of OBIA results, they were benchmarked against a corresponding "gold standard", a reference 3D model of the halite crystals that was derived by manual expert digitization of the CT images. For accuracy assessment, classical per-scene statistics were extended to per-object statistics. The strength of OBIA was to recognize all objects similar to halite hopper crystals and in particular to eliminate cracks. Using a support vector machine (SVM) classifier on top of OBIA, unsuitable objects like halite crystal clusters, polyhalite-coated crystals and spherical halite crystals were effectively dismissed, but simultaneously the number of well-shaped halites was reduced.

  15. 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.

  16. Liquid crystal lens array for 3D microscopy and endoscope application

    NASA Astrophysics Data System (ADS)

    Huang, Yi-Pai; Hsieh, Po-Yuan; Hassanfiroozi, Amir; Chu, Chao-Yu; Hsuan, Yun; Martinez, Manuel; Javidi, Bahram

    2016-06-01

    In this paper, we demonstrate two liquid crystal (LC) lens array devices for 3D microscope and 3D endoscope applications respectively. Compared with the previous 3D biomedical system, the proposed LC lens arrays are not only switchable between 2D and 3D modes, but also are able to adjust focus in both modes. The multi-function liquid crystal lens (MFLC-lens) array with dual layer electrode has diameter 1.42 mm, which is much smaller than the conventional 3D endoscope with double fixed lenses. The hexagonal liquid crystal micro-lens array (HLC-MLA) instead of fixed micro-lens array in 3D light field microscope can extend the effective depth of field from 60 um to 780 um. To achieve the LC lens arrays, a high-resistance layer needs to be coated on the electrodes to generate an ideal gradient electric-field distribution, which can induce a lens-like form of LC molecules. The parameters and characteristics of high-resistance layer are investigated and discussed with an aim to optimize the performance of liquid crystal lens arrays.

  17. 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.

  18. 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

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

  20. 3D reconstruction methods of coronal structures by radio observations

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  1. 2D and 3D crystallization of a bacterial homologue of human vitamin C membrane transport proteins.

    PubMed

    Jeckelmann, Jean-Marc; Harder, Daniel; Ucurum, Zöhre; Fotiadis, Dimitrios

    2014-10-01

    Most organisms are able to synthesize vitamin C whereas humans are not. In order to contribute to the elucidation of the molecular working mechanism of vitamin C transport through biological membranes, we cloned, overexpressed, purified, functionally characterized, and 2D- and 3D-crystallized a bacterial protein (UraDp) with 29% of amino acid sequence identity to the human sodium-dependent vitamin C transporter 1 (SVCT1). Ligand-binding experiments by scintillation proximity assay revealed that uracil is a substrate preferably bound to UraDp. For structural analysis, we report on the production of tubular 2D crystals and present a first projection structure of UraDp from negatively stained tubes. On the other hand the successful growth of UraDp 3D crystals and their crystallographic analysis is described. These 3D crystals, which diffract X-rays to 4.2Å resolution, pave the way towards the high-resolution crystal structure of a bacterial homologue with high amino acid sequence identity to human SVCT1.

  2. Cancer3D: understanding cancer mutations through protein structures.

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2017-02-01

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

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

    PubMed

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

    2014-09-23

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

  5. Extreme low thermal conductivity in nanoscale 3D Si phononic crystal with spherical pores.

    PubMed

    Yang, Lina; Yang, Nuo; Li, Baowen

    2014-01-01

    In this work, we propose a nanoscale three-dimensional (3D) Si phononic crystal (PnC) with spherical pores, which can reduce the thermal conductivity of bulk Si by a factor up to 10,000 times at room temperature. Thermal conductivity of Si PnCs depends on the porosity, for example, the thermal conductivity of Si PnCs with porosity 50% is 300 times smaller than that of bulk Si. The phonon participation ratio spectra demonstrate that more phonons are localized as the porosity increases. The thermal conductivity is insensitive to the temperature changes from room temperature to 1100 K. The extreme-low thermal conductivity could lead to a larger value of ZT than unity as the periodic structure affects very little the electric conductivity.

  6. 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

  7. Manufacturing of a 3D complex hyperstable Cesic structure

    NASA Astrophysics Data System (ADS)

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

    2007-09-01

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

  8. Novel 3D bismuth-based coordination polymers: Synthesis, structure, and second harmonic generation properties

    NASA Astrophysics Data System (ADS)

    Wibowo, Arief C.; Smith, Mark D.; Yeon, Jeongho; Halasyamani, P. Shiv; zur Loye, Hans-Conrad

    2012-11-01

    Two new 3D bismuth containing coordination polymers are reported along with their single crystal structures and SHG properties. Compound 1: Bi2O2(pydc) (pydc=pyridine-2, 5-dicarboxylate), crystallizes in the monoclinic, polar space group, P21 (a=9.6479(9) Å, b=4.2349(4) Å, c=11.9615(11) Å, β=109.587(1)°), which contains Bi2O2 chains that are connected into a 3D structure via the pydc ligands. Compound 2: Bi4Na4(1R3S-cam)8(EtOH)3.1(H2O)3.4 (1R3S cam=1R3S-camphoric acid) crystallizes in the monoclinic, polar space group, P21 (a=19.0855(7) Å, b=13.7706(5) Å, c=19.2429(7) Å, β=90.701(1)°) and is a true 3D coordination polymer. These are two example of SHG compounds prepared using unsymmetric ligands (compound 1) or chiral ligands (compound 2), together with metals that often exhibit stereochemically-active lone pairs, such as Bi3+, a synthetic approach that resulted in polar, non-centrosymmetric, 3D metal-organic coordination polymer.

  9. 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.

  10. 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.

  11. 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.

  12. 3-D Attenuation Structure around the SAFOD site, Parkfield, California

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  13. 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.

  14. 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.

  15. One-, Two-, and Three-Dimensional Heterospin Complexes Consisting of 4-(N-tert-Butyloxylamino)pyridine (4NOpy), Dicyanamide Ion (DCA), and 3d Metal Ions: Crystal Structures and Magnetic Properties of [M(II)(4NOpy)x(DCA)y(CH3CN)z]n (M = Mn, Co, Ni, Cu, Zn).

    PubMed

    Ogawa, Hiraku; Mori, Koya; Murashima, Kensuke; Karasawa, Satoru; Koga, Noboru

    2016-01-19

    Solutions of 3d metal ion salts, M(NO3)2, 4-(N-tert-butyloxylamino)pyridine (4NOpy), and dicyanamide (DCA) in CH3CN were mixed to afford single crystals of the polymeric complexes [M(II)(4NOpy)x(DCA)y(CH3CN)z]n (M(II) = Mn (1), Co (2), Ni (3), Cu (4a and 4b), Zn (5)). X-ray crystallography revealed that the crystal structures are a three-dimensional (3-D) network for 1, 2-D networks for 2, 3, 4a, and 5, and a 1-D chain for 4b. Crystals of 2, 3, 4a, and 5 contained CH3CN molecules as crystal solvents, which were readily desorbed in the ambient atmosphere. After desorption of the CH3CN molecules, the crystal structures of 2 and 3 were confirmed to be slightly shrunk without destruction of the crystal lattice. Crystals of 2, 3, 4a, and 5 after desorption of crystal solvents were used for investigations of the magnetic properties. Complex 1 showed antiferromagnetic interactions to form a ferrimagnetic chain and exhibited the magnetic behavior of a 2-D (or 3-D) spin-canted antiferromagnet with TN = 12 K. Complex 2 containing anisotropic Co(II) ions also showed the behavior of a 1-D (or 2-D) spin-canted antiferromagnet with TN = 6 K. In 3, 4a, and 4b, the aminoxyl of 4NOpy ferromagnetically interacted with the metal ion with coupling constants of JM-NO/kB = 45, 45, and 43 K, respectively. In 5, the magnetic couplings between the aminoxyls in 4NOpy through the diamagnetic Zn(II) ion were weakly antiferromagntic (JNO-NO = -1.2 K). DCA might be a weak antiferromagnetic connector for the metal chains.

  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. Co-axial association of recombinant eye lens aquaporin-0 observed in loosely packed 3D crystals.

    PubMed

    Palanivelu, Dinesh V; Kozono, David E; Engel, Andreas; Suda, Kitaru; Lustig, Ariel; Agre, Peter; Schirmer, Tilman

    2006-01-27

    Aquaporin-0 (AQP0) is the major membrane protein in vertebrate eye lenses. It has been proposed that AQP0 tetramers mediate contact between membranes of adjacent lens fiber cells, which would be consistent with the extraordinarily narrow inter-cellular spacing. We have obtained 3D crystals of recombinant bovine AQP0 that diffract to 7.0 A resolution. The crystal packing was determined by molecular replacement and shows that, within the cubic lattice, AQP0 tetramers are associated head-to-head along their 4-fold axes. Oligomeric states larger than the tetramer were also observed in solution by native gel electrophoresis and analytical ultracentrifugation methods. In the crystals, there are no direct contacts between octamers, and it can thus be inferred that crystalline order is mediated solely by the detergent belts surrounding the membrane protein. Across the tetramer-tetramer interface, extracellular loops A and C interdigitate at the center and the perimeter of the octamer, respectively. The octamer structure is compared with that of the recently determined structure of truncated ovine AQP0 derived from electron diffraction of 2D crystals. Intriguingly, also in these crystals, octamers are observed, but with significantly different relative tetramer-tetramer orientations. The interactions observed in the loosely packed 3D crystals reported here may in fact represent an in vivo association mode between AQP0 tetramers from juxtaposed membranes in the eye lens.

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

    PubMed

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

    2011-01-01

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

  20. Mineral crystal alignment in mineralized fracture callus determined by 3D small-angle X-ray scattering

    NASA Astrophysics Data System (ADS)

    Liu, Yifei; Manjubala, Inderchand; Roschger, Paul; Schell, Hanna; Duda, Georg N.; Fratzl, Peter

    2010-10-01

    Callus tissue formed during bone fracture healing is a mixture of different tissue types as revealed by histological analysis. But the structural characteristics of mineral crystals within the healing callus are not well known. Since two-dimensional (2D) scanning small-angle X-ray scattering (sSAXS) patterns showed that the size and orientation of callus crystals vary both spatially and temporally [1] and 2D electron microscopic analysis implies an anisotropic property of the callus morphology, the mineral crystals within the callus are also expected to vary in size and orientation in 3D. Three-dimensional small-angle X-ray scattering (3D SAXS), which combines 2D SAXS patterns collected at different angles of sample tilting, has been previously applied to investigate bone minerals in horse radius [2] and oim/oim mouse femur/tibia [3]. We implement a similar 3D SAXS method but with a different way of data analysis to gather information on the mineral alignment in fracture callus. With the proposed accurate yet fast assessment of 3D SAXS information, it was shown that the plate shaped mineral particles in the healing callus were aligned in groups with their predominant orientations occurring as a fiber texture.

  1. 3D Printing of Hierarchical Silk Fibroin Structures.

    PubMed

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

    2016-12-21

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

  2. Diagnosis and control of 3D elastic mechanical structures

    NASA Astrophysics Data System (ADS)

    Krajcin, Idriz; Soeffker, Dirk

    2005-05-01

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

  3. 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.

  4. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGES

    Zhang, Xing; Zhang, Lei; Tong, Huimin; ...

    2015-05-05

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

  5. 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.

  6. 3D inverted colloidal crystals in realistic cell migration assays for drug screening applications.

    PubMed

    da Silva, Joakim; Lautenschläger, Franziska; Kuo, Cheng-Hwa R; Guck, Jochen; Sivaniah, Easan

    2011-12-01

    Screening drugs for their specific impact on cell mechanics, in addition to targeting adhesion and proteolysis, will be important for successfully moderating migration in infiltrative disorders including cancer metastasis. We present 3D inverted colloidal crystals made of hydrogel as a realistic cell migration assay, where the geometry and stiffness can be set independently to mimic the tissue requirements in question. We show the utility of this 3D assay for drug screening purposes, specifically in contrast to conventional 2D migration studies, by surveying the effects of commonly used cytoskeletal toxins that impact cell mechanics. This assay allows studying large cell numbers for good statistics but at single-cell resolution.

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

    NASA Astrophysics Data System (ADS)

    Lehtimaeki, R.

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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Zhu, Litao; Jiang, Tianzi

    2004-05-01

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

  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. 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.

  18. 3D Seismic Imaging over a Potential Collapse Structure

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  1. Direct laser-writing of ferroelectric single-crystal waveguide architectures in glass for 3D integrated optics

    PubMed Central

    Stone, Adam; Jain, Himanshu; Dierolf, Volkmar; Sakakura, Masaaki; Shimotsuma, Yasuhiko; Miura, Kiyotaka; Hirao, Kazuyuki; Lapointe, Jerome; Kashyap, Raman

    2015-01-01

    Direct three-dimensional laser writing of amorphous waveguides inside glass has been studied intensely as an attractive route for fabricating photonic integrated circuits. However, achieving essential nonlinear-optic functionality in such devices will also require the ability to create high-quality single-crystal waveguides. Femtosecond laser irradiation is capable of crystallizing glass in 3D, but producing optical-quality single-crystal structures suitable for waveguiding poses unique challenges that are unprecedented in the field of crystal growth. In this work, we use a high angular-resolution electron diffraction method to obtain the first conclusive confirmation that uniform single crystals can be grown inside glass by femtosecond laser writing under optimized conditions. We confirm waveguiding capability and present the first quantitative measurement of power transmission through a laser-written crystal-in-glass waveguide, yielding loss of 2.64 dB/cm at 1530 nm. We demonstrate uniformity of the crystal cross-section down the length of the waveguide and quantify its birefringence. Finally, as a proof-of-concept for patterning more complex device geometries, we demonstrate the use of dynamic phase modulation to grow symmetric crystal junctions with single-pass writing. PMID:25988599

  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. Determination and validation of mTOR kinase-domain 3D structure by homology modeling.

    PubMed

    Lakhlili, Wiame; Chevé, Gwénaël; Yasri, Abdelaziz; Ibrahimi, Azeddine

    2015-01-01

    The AKT/mammalian target of rapamycin (mTOR) pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D) structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  5. 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.

  6. 3D Soil Images Structure Quantification using Relative Entropy

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  7. Slat Cove Unsteadiness Effect of 3D Flow Structures

    NASA Technical Reports Server (NTRS)

    Choudhari, Meelan M.; Khorrami, Mehdi R.

    2006-01-01

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

  8. Viewing zone duplication of multi-projection 3D display system using uniaxial crystal.

    PubMed

    Lee, Chang-Kun; Park, Soon-Gi; Moon, Seokil; Lee, Byoungho

    2016-04-18

    We propose a novel multiplexing technique for increasing the viewing zone of a multi-view based multi-projection 3D display system by employing double refraction in uniaxial crystal. When linearly polarized images from projector pass through the uniaxial crystal, two possible optical paths exist according to the polarization states of image. Therefore, the optical paths of the image could be changed, and the viewing zone is shifted in a lateral direction. The polarization modulation of the image from a single projection unit enables us to generate two viewing zones at different positions. For realizing full-color images at each viewing zone, a polarization-based temporal multiplexing technique is adopted with a conventional polarization switching device of liquid crystal (LC) display. Through experiments, a prototype of a ten-view multi-projection 3D display system presenting full-colored view images is implemented by combining five laser scanning projectors, an optically clear calcite (CaCO3) crystal, and an LC polarization rotator. For each time sequence of temporal multiplexing, the luminance distribution of the proposed system is measured and analyzed.

  9. A 3D hybrid praseodymium-antimony-oxochloride compound: single-crystal-to-single-crystal transformation and photocatalytic properties.

    PubMed

    Zou, Guo-Dong; Zhang, Gui-Gang; Hu, Bing; Li, Jian-Rong; Feng, Mei-Ling; Wang, Xin-Chen; Huang, Xiao-Ying

    2013-11-04

    A 3D organic-inorganic hybrid compound, (2-MepyH)3[{Fe(1,10-phen)3}3][{Pr4Sb12O18(OH)Cl(11.5)}(TDC)(4.5)({Pr4Sb12O18(OH)Cl(9.5)} Cl)]·3(2-Mepy)·28H2O (1; 2-Mepy=2-methylpyridine, 1,10-phen=1,10-phenanthroline, H2TDC=thiophene-2,5-dicarboxylic acid), was hydrothermally synthesized and structurally characterized. Unusually, two kinds of high-nuclearity clusters, namely [(Pr4Sb12O18(OH)Cl11)(COO)5](5-) and [(Pr4Sb12O18(OH)Cl9)Cl(COO)5](4-), coexist in the structure of compound 1; two of the latter clusters are doubly bridged by two μ2-Cl(-) moieties to form a new centrosymmetric dimeric cluster. An unprecedented spontaneous and reversible single-crystal-to-single-crystal transformation was observed, which simultaneously involved a notable organic-ligand movement between the metal ions and an alteration of the bridging ion in the dimeric cluster, induced by guest-release/re-adsorption, thereby giving rise to the interconversion between compound 1 and the compound (2-MepyH)3[{Fe(1,10-phen)3}3][{Pr4Sb12O18(OH)Cl(11.5)}(TDC)4({Pr4Sb12O18Cl(10.5)(TDC)(0.5)(H2O)(1.5)}O(0.5))]·25H2O (1'). The mechanism of this transformation has also been discussed in great detail. Photocatalytic H2-evolution activity was observed for compound 1' under UV light with Pt as a co-catalyst and MeOH as a sacrificial electron donor.

  10. 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

  11. Globular and Optically Transparent Photonic Crystals Based on 3D-opal Matrix and REE

    NASA Astrophysics Data System (ADS)

    Ivicheva, S. N.; Kargin, Yu. F.; Gorelik, V. S.

    By repeatedly filling the octahedral and tetrahedral pores of 3D-silica opal matrices with silica sol doped with rare-earth elements with subsequent heat treatment globular photonic crystals filled with mesoporous glass and optically transparent photonic crystals (quantytes) containing 10-30 ppm REE were produced, depending on the annealing temperature. Voids of fcc lattice formed by amorphous spherical globules of SiO2 in globular photonic crystals are filled (up to 70%) by mesoporous glass doped with rare earth elements. Pores in the transparent photonic crystals disappear during sintering of globules of silica and mesoporous glass, but the periodic arrangement of REE-enriched silica areas (quantum dots) is retained. The reflection and luminescence spectra of photonic crystals filled with sols doped with europium Eu3+ and terbium Tb3+ were experimentally studied. A significant increase in the photoluminescence intensity of Eu3+ ions at the approach of the spectral position of the transition 5D0 → 7F2 to the edge of the bandgaps of the photonic crystal was determined. The authors come to the conclusion that a lowering of the threshold for lasing transitions in ions of rare elements is possible.

  12. High-resistance liquid-crystal lens array for rotatable 2D/3D autostereoscopic display.

    PubMed

    Chang, Yu-Cheng; Jen, Tai-Hsiang; Ting, Chih-Hung; Huang, Yi-Pai

    2014-02-10

    A 2D/3D switchable and rotatable autostereoscopic display using a high-resistance liquid-crystal (Hi-R LC) lens array is investigated in this paper. Using high-resistance layers in an LC cell, a gradient electric-field distribution can be formed, which can provide a better lens-like shape of the refractive-index distribution. The advantages of the Hi-R LC lens array are its 2D/3D switchability, rotatability (in the horizontal and vertical directions), low driving voltage (~2 volts) and fast response (~0.6 second). In addition, the Hi-R LC lens array requires only a very simple fabrication process.

  13. Computerized 3-D reconstruction of complicated anatomical structure

    NASA Astrophysics Data System (ADS)

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

    1992-06-01

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

  14. 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.

  15. 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.

  16. Cylindrical liquid crystal lenses system for autostereoscopic 2D/3D display

    NASA Astrophysics Data System (ADS)

    Chen, Chih-Wei; Huang, Yi-Pai; Chang, Yu-Cheng; Wang, Po-Hao; Chen, Po-Chuan; Tsai, Chao-Hsu

    2012-06-01

    The liquid crystal lenses system, which could be electrically controlled easily for autostereoscopic 2D/3D switchable display was proposed. The High-Resistance liquid crystal (HRLC) lens utilized less controlled electrodes and coated a high-resistance layer between the controlled-electrodes was proposed and was used in this paper. Compare with the traditional LC lens, the HR-LC Lens could provide smooth electric-potential distribution within the LC layer under driving status. Hence, the proposed HR-LC Lens had less circuit complexity, low driving voltage, and good optical performance also could be obtained. In addition, combining with the proposed driving method called dual-directional overdriving method, the above method could reduce the switching time by applying large voltage onto cell. Consequently, the total switching time could be further reduced to around 2second. It is believed that the LC lens system has high potential in the future.

  17. 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.

  18. Digital holographic tomography method for 3D observation of domain patterns in ferroelectric single crystals

    NASA Astrophysics Data System (ADS)

    Mokrý, Pavel; Psota, Pavel; Steiger, Kateřina; Václavík, Jan; Vápenka, David; Doleček, Roman; Vojtíšek, Petr; Sládek, Juraj; Lédl, Vít.

    2016-11-01

    We report on the development and implementation of the digital holographic tomography for the three-dimensio- nal (3D) observations of the domain patterns in the ferroelectric single crystals. Ferroelectric materials represent a group of materials, whose macroscopic dielectric, electromechanical, and elastic properties are greatly in uenced by the presence of domain patterns. Understanding the role of domain patterns on the aforementioned properties require the experimental techniques, which allow the precise 3D measurements of the spatial distribution of ferroelectric domains in the single crystal. Unfortunately, such techniques are rather limited at this time. The most frequently used piezoelectric atomic force microscopy allows 2D observations on the ferroelectric sample surface. Optical methods based on the birefringence measurements provide parameters of the domain patterns averaged over the sample volume. In this paper, we analyze the possibility that the spatial distribution of the ferroelectric domains can be obtained by means of the measurement of the wavefront deformation of the transmitted optical wave. We demonstrate that the spatial distribution of the ferroelectric domains can be determined by means of the measurement of the spatial distribution of the refractive index. Finally, it is demonstrated that the measurements of wavefront deformations generated in ferroelectric polydomain systems with small variations of the refractive index provide data, which can be further processed by means of the conventional tomographic methods.

  19. Colloidal and polyelectrolyte inks for direct-write assembly of 3D periodic structures

    NASA Astrophysics Data System (ADS)

    Gratson, Gregory Michael

    Novel inks were developed for the direct-write assembly of 3D periodic structures with varying feature size. Specifically, two ink designs were pursued: (1) a model colloidal ink (feature size > 100 mum) and (2) a polyelectrolyte ink (feature size ˜ 1 mum). The rheological properties of both inks were specifically tailored for our direct-write assembly process, which involves ink deposition through a fine scale nozzle that is robotically controlled using a 3-axis stage. Central to this approach is the design of inks that are capable of flowing through deposition nozzles of varying size and then "setting" immediately to facilitate shape retention of the deposited features. In addition, the inks must contain a high solid volume fraction to minimize drying-induced shrinkage after assembly is complete. First, a model colloidal ink based on monodisperse silica microspheres was designed for 3D periodic structures. These colloidal inks suffer difficulties (e.g., nozzle clogging) when used to fabricate structures with feature sizes below ˜ 100 mum, so a different ink design was pursued based on polyelectrolyte complexes. These inks rapidly solidified upon deposition into an IPA/water coagulation reservoir, and the exact coagulation mechanism depended strongly on reservoir composition. The water/IPA ratio in the reservoir (83--88 % IPA) was carefully tailored to produce filaments that could maintain their shape while spanning unsupported regions in the structure, yet were flexible enough to adhere to the substrate or underlying layers. Several micro-periodic structures of varying design were fabricated, revealing the facile nature of our approach. 3D micro-periodic scaffolds were used to create photonic crystals with high refractive index contrast. Silica chemical vapor deposition was performed under ambient conditions to produce a thin inorganic layer around the polymer, which facilitated further high-temperature steps. The polymer was removed through burnout at 475

  20. 3D photonic crystal-based biosensor functionalized with quantum dot-based aptamer for thrombine detection

    NASA Astrophysics Data System (ADS)

    Lim, Chae Young; Choi, Eunpyo; Park, Youngkyu; Park, Jungyul

    2013-05-01

    In this paper, we propose a new technique for protein detection by using the enhancement of intensity in quantum dots (Qdot) whose emission is guided by 3D photonic crystal (PC) structures. For easy to use, we design the emitted light from the sensor can be recovered, when the chemical antibody (aptamer) conjugated with guard DNA (g-DNA) labeled with a quencher (Black FQ) hybridizes with the target proteins. In detail, we synthesis a Qdot-aptamer complex and then immobilize these complex on the PC surfaces. Next, we perform the hybridization of the Qdot-aptamer complex with g-DNA labeled with the quencher. It induces the quenching effect of fluoresce intensity in the Qdot-aptamer. In presence of target protein (thrombin), the Qdot-aptamer complex prefers to form the thrombin-aptamer complex: this results in the release of Black FQ-g-DNA and the quenched light intensity recovers into the original high intensity with Qdot. The intensity recovery varies quantitatively according to the level of the target protein concentration. This proposed sensor shows much higher detection sensitivity than the general fluorescent detection mechanism, which is functionalized on the flat surfaces because of the light guiding effect from 3D photonic crystal structures.

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

    NASA Astrophysics Data System (ADS)

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

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

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

    PubMed Central

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-01

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

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

    PubMed

    Takagishi, Kensuke; Umezu, Shinjiro

    2017-01-05

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

  4. Structure-based 3D QSAR and design of novel acetylcholinesterase inhibitors

    NASA Astrophysics Data System (ADS)

    Sippl, Wolfgang; Contreras, Jean-Marie; Parrot, Isabelle; Rival, Yveline M.; Wermuth, Camille G.

    2001-05-01

    The paper describes the construction, validation and application of a structure-based 3D QSAR model of novel acetylcholinesterase (AChE) inhibitors. Initial use was made of four X-ray structures of AChE complexed with small, non-specific inhibitors to create a model of the binding of recently developed aminopyridazine derivatives. Combined automated and manual docking methods were applied to dock the co-crystallized inhibitors into the binding pocket. Validation of the modelling process was achieved by comparing the predicted enzyme-bound conformation with the known conformation in the X-ray structure. The successful prediction of the binding conformation of the known inhibitors gave confidence that we could use our model to evaluate the binding conformation of the aminopyridazine compounds. The alignment of 42 aminopyridazine compounds derived by the docking procedure was taken as the basis for a 3D QSAR analysis applying the GRID/GOLPE method. A model of high quality was obtained using the GRID water probe, as confirmed by the cross-validation method (q2 LOO=0.937, q2 L50% O=0.910). The validated model, together with the information obtained from the calculated AChE-inhibitor complexes, were considered for the design of novel compounds. Seven designed inhibitors which were synthesized and tested were shown to be highly active. After performing our modelling study the X-ray structure of AChE complexed with donepezil, an inhibitor structurally related to the developed aminopyirdazines, has been made available. The good agreement found between the predicted binding conformation of the aminopyridazines and the one observed for donepezil in the crystal structure further supports our developed model.

  5. Holographic fabrication of 3D photonic crystal templates with 4, 5, and 6-fold rotational symmetry using a single beam and single exposure

    NASA Astrophysics Data System (ADS)

    Lowell, David; George, David; Lutkenhaus, Jeffery; Philipose, Usha; Zhang, Hualiang; Lin, Yuankun

    2016-03-01

    A method of fabricating large-volume three-dimensional (3D) photonic crystal and quasicrystal templates using holographic lithography is presented. Fabrication is accomplished using a single-beam and single exposure by a reflective optical element (ROE). The ROE is 3D printed support structure which holds reflecting surfaces composed of silicon or gallium arsenide. Large-volume 3D photonic crystal and quasicrystal templates with 4-fold, 5-fold, and 6-fold symmetry were fabricated and found to be in good agreement with simulation. Although the reflective surfaces were setup away from the Brewster's angle, the interference among the reflected s and p-polarizations still generated bicontinuous structures, demonstrating the flexibility of the ROE. The ROE, being a compact and inexpensive alternative to diffractive optical elements and top-cut prisms, facilitates the large-scale integration of holographically fabricated photonic structures into on-chip applications.

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

    PubMed

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

    2013-02-07

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

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

    PubMed Central

    Rezania, Vahid; Tuszynski, Jack

    2016-01-01

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

  8. New skeletal 3D polymeric inorganic cluster [W4S16Cu16Cl16]n with Cu in mixed-valence states: solid-state synthesis, crystal structure, and third-order nonlinear optical properties.

    PubMed

    Cai, Ya; Wang, Yan; Li, Yizhi; Wang, Xiaoshu; Xin, Xinquan; Liu, Caiming; Zheng, Hegen

    2005-12-12

    A new 3D polymeric inorganic cluster with Cu in mixed-valence states was synthesized by the solid-state reaction of (NH4)2WS4, S8, CuCl, and Et4NCl; S8 may be regarded as the oxidizing agent converting Cu(I) to Cu(II) and causing the polymerization of [WS4]2-. The third-order nonlinear optical (NLO) properties are determined, and the results show that the cluster exhibits both large NLO absorptive and strong refractive behaviors.

  9. Crystal growth and electronic properties of a 3D Rashba material, BiTeI, with adjusted carrier concentrations.

    PubMed

    Kanou, Manabu; Sasagawa, Takao

    2013-04-03

    3D Rashba materials can be a leading player in spin-related novel phenomena, ranging from the metallic extreme (unconventional superconductivity) to the transport intermediate (spin Hall effects) to the novel insulating variant (3D topological insulating states). As the essential backbone for both fundamental and applied research of such a 3D Rashba material, this study established the growth of sizeable single crystals of a candidate compound BiTeI with adjusted carrier concentrations. Three techniques (standard vertical Bridgman, modified horizontal Bridgman, and vapour transport) were employed, and BiTeI crystals (>1 × 1 × 0.2 mm(3)) with fundamentally different electronic states from metallic to insulating were successfully grown by the chosen technique. The 3D Rashba electronic states, including the Fermi surface topology, for the corresponding carrier concentrations of the obtained BiTeI crystals were revealed by relativistic first-principles calculations.

  10. Photonic liquid crystal fibers tuning by four electrode system produced with 3D printing technology

    NASA Astrophysics Data System (ADS)

    Ertman, Slawomir; Bednarska, Karolina; Czapla, Aleksandra; Woliński, Tomasz R.

    2015-09-01

    Photonic liquid crystal fiber has been intensively investigated in last few years. It has been proved that guiding properties of such fibers could be tuned with an electric field. In particular efficient tuning could be obtained if multi-electrode system allowing for dynamic change of not only intensity of the electric field, but also its direction. In this work we report a simple to build four electrode system, which is based on a precisely aligned four cylindrical microelectrodes. As an electrodes we use enameled copper wire with diameter adequate to the diameter of the fiber to be tuned. To ensure uniform and parallel alignment of the wires a special micro-profiles has been designed and then produced with filament 3D printer. The possibility of the dynamic change of the electric field direction in such scalable and cost effective electrode assembly has been experimentally confirmed.

  11. Fabrication of 3-D Photonic Band Gap Crystals Via Colloidal Self-Assembly

    NASA Technical Reports Server (NTRS)

    Subramaniam, Girija; Blank, Shannon

    2005-01-01

    The behavior of photons in a Photonic Crystals, PCs, is like that of electrons in a semiconductor in that, it prohibits light propagation over a band of frequencies, called Photonic Band Gap, PBG. Photons cannot exist in these band gaps like the forbidden bands of electrons. Thus, PCs lend themselves as potential candidates for devices based on the gap phenomenon. The popular research on PCs stem from their ability to confine light with minimal losses. Large scale 3-D PCs with a PBG in the visible or near infra red region will make optical transistors and sharp bent optical fibers. Efforts are directed to use PCs for information processing and it is not long before we can have optical integrated circuits in the place of electronic ones.

  12. Simulation of light transport in scintillators based on 3D characterization of crystal surfaces.

    PubMed

    Roncali, Emilie; Cherry, Simon R

    2013-04-07

    In the development of positron emission tomography (PET) detectors, understanding and optimizing scintillator light collection is critical for achieving high performance, particularly when the design incorporates depth-of-interaction (DOI) encoding or time-of-flight information. Monte-Carlo simulations play an important role in guiding research in detector designs and popular software such as GATE now include models of light transport in scintillators. Although current simulation toolkits are able to provide accurate models of perfectly polished surfaces, they do not successfully predict light output for other surface finishes, for example those often used in DOI-encoding detectors. The lack of accuracy of those models mainly originates from a simplified description of rough surfaces as an ensemble of micro-facets determined by the distribution of their normal, typically a gaussian distribution. The user can specify the standard deviation of this distribution, but this parameter does not provide a full description of the surface reflectance properties. We propose a different approach based on 3D measurements of the surface using atomic force microscopy. Polished and rough (unpolished) crystals were scanned to compute the surface reflectance properties. The angular distributions of reflectance and reflected rays were computed and stored in look-up tables (LUTs). The LUTs account for the effect of incidence angle and were integrated in a light transport model. Crystals of different sizes were simulated with and without reflector. The simulated maximum light output and the light output as a function of DOI showed very good agreement with experimental characterization of the crystals, indicating that our approach provides an accurate model of polished and rough surfaces and could be used to predict light collection in scintillators. This model is based on a true 3D representation of the surface, makes no assumption about the surface and provides insight on the optical

  13. Simulation of light transport in scintillators based on 3D characterization of crystal surfaces

    NASA Astrophysics Data System (ADS)

    Roncali, Emilie; Cherry, Simon R.

    2013-04-01

    In the development of positron emission tomography (PET) detectors, understanding and optimizing scintillator light collection is critical for achieving high performance, particularly when the design incorporates depth-of-interaction (DOI) encoding or time-of-flight information. Monte-Carlo simulations play an important role in guiding research in detector designs and popular software such as GATE now include models of light transport in scintillators. Although current simulation toolkits are able to provide accurate models of perfectly polished surfaces, they do not successfully predict light output for other surface finishes, for example those often used in DOI-encoding detectors. The lack of accuracy of those models mainly originates from a simplified description of rough surfaces as an ensemble of micro-facets determined by the distribution of their normal, typically a Gaussian distribution. The user can specify the standard deviation of this distribution, but this parameter does not provide a full description of the surface reflectance properties. We propose a different approach based on 3D measurements of the surface using atomic force microscopy. Polished and rough (unpolished) crystals were scanned to compute the surface reflectance properties. The angular distributions of reflectance and reflected rays were computed and stored in look-up tables (LUTs). The LUTs account for the effect of incidence angle and were integrated in a light transport model. Crystals of different sizes were simulated with and without reflector. The simulated maximum light output and the light output as a function of DOI showed very good agreement with experimental characterization of the crystals, indicating that our approach provides an accurate model of polished and rough surfaces and could be used to predict light collection in scintillators. This model is based on a true 3D representation of the surface, makes no assumption about the surface and provides insight on the optical

  14. Hands-on Symmetry, Building and Using 3-D Crystal Models in Mineralogy

    NASA Astrophysics Data System (ADS)

    Cole, K.

    2002-12-01

    Symmetry has historically been the most difficult subject in mineralogy and because so much of the science of mineralogy and crystallography builds on the fundamentals of form and symmetry, it is essential students understand it well. I concluded in recent years that better manipulatives might hold the key to better student comprehension. Mineralogy lab exercises related to symmetry typically involve the use of line drawings of 3-D crystal shapes sometimes augmented with a selection of small wooden models. Many students find the line drawings difficult to envision as 3-D solids. This makes the leap to identifying symmetry elements almost impossible for them and very time consuming for the instructor. The few line drawings for which models were available to my students were readily understood. Following the purchase of a new chop saw, I discovered that it is easy to cut most crystal models from scrap lumber and spent two weeks calculating, cutting, and finishing wooden models. For each of the line drawings used in my symmetry labs two models were cut, 200 models total. Models were also cut to show form development, distorted growth, enantiomorphism, and twinning. The models were cut to a final size of 5 to 15 cm and can be written on with chalk. The large model size and chalkability allowed students to more easily identify, mark, and erase mirrors, axes, forms, etc. Use of these models resulted in 50% less lab time needed in teaching the concepts of symmetry and form and 75% less time for students to complete the exercises. Scores on the symmetry labs averaged 55% to 65% in 1999-2001. The Fall 2002 averages were 85% and the errors made were much more trivial in nature, a dramatic improvement indeed.

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

    PubMed Central

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

    2010-01-01

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

  16. Crystal structure and prediction.

    PubMed

    Thakur, Tejender S; Dubey, Ritesh; Desiraju, Gautam R

    2015-04-01

    The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

  17. Crystal Structure and Prediction

    NASA Astrophysics Data System (ADS)

    Thakur, Tejender S.; Dubey, Ritesh; Desiraju, Gautam R.

    2015-04-01

    The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

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

    PubMed Central

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

    2015-01-01

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

  19. Laser Scanning Holographic Lithography for Flexible 3D Fabrication of Multi-Scale Integrated Nano-structures and Optical Biosensors.

    PubMed

    Yuan, Liang Leon; Herman, Peter R

    2016-02-29

    Three-dimensional (3D) periodic nanostructures underpin a promising research direction on the frontiers of nanoscience and technology to generate advanced materials for exploiting novel photonic crystal (PC) and nanofluidic functionalities. However, formation of uniform and defect-free 3D periodic structures over large areas that can further integrate into multifunctional devices has remained a major challenge. Here, we introduce a laser scanning holographic method for 3D exposure in thick photoresist that combines the unique advantages of large area 3D holographic interference lithography (HIL) with the flexible patterning of laser direct writing to form both micro- and nano-structures in a single exposure step. Phase mask interference patterns accumulated over multiple overlapping scans are shown to stitch seamlessly and form uniform 3D nanostructure with beam size scaled to small 200 μm diameter. In this way, laser scanning is presented as a facile means to embed 3D PC structure within microfluidic channels for integration into an optofluidic lab-on-chip, demonstrating a new laser HIL writing approach for creating multi-scale integrated microsystems.

  20. Laser Scanning Holographic Lithography for Flexible 3D Fabrication of Multi-Scale Integrated Nano-structures and Optical Biosensors

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    Three-dimensional (3D) periodic nanostructures underpin a promising research direction on the frontiers of nanoscience and technology to generate advanced materials for exploiting novel photonic crystal (PC) and nanofluidic functionalities. However, formation of uniform and defect-free 3D periodic structures over large areas that can further integrate into multifunctional devices has remained a major challenge. Here, we introduce a laser scanning holographic method for 3D exposure in thick photoresist that combines the unique advantages of large area 3D holographic interference lithography (HIL) with the flexible patterning of laser direct writing to form both micro- and nano-structures in a single exposure step. Phase mask interference patterns accumulated over multiple overlapping scans are shown to stitch seamlessly and form uniform 3D nanostructure with beam size scaled to small 200 μm diameter. In this way, laser scanning is presented as a facile means to embed 3D PC structure within microfluidic channels for integration into an optofluidic lab-on-chip, demonstrating a new laser HIL writing approach for creating multi-scale integrated microsystems.

  1. Laser Scanning Holographic Lithography for Flexible 3D Fabrication of Multi-Scale Integrated Nano-structures and Optical Biosensors

    PubMed Central

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

    2016-01-01

    Three-dimensional (3D) periodic nanostructures underpin a promising research direction on the frontiers of nanoscience and technology to generate advanced materials for exploiting novel photonic crystal (PC) and nanofluidic functionalities. However, formation of uniform and defect-free 3D periodic structures over large areas that can further integrate into multifunctional devices has remained a major challenge. Here, we introduce a laser scanning holographic method for 3D exposure in thick photoresist that combines the unique advantages of large area 3D holographic interference lithography (HIL) with the flexible patterning of laser direct writing to form both micro- and nano-structures in a single exposure step. Phase mask interference patterns accumulated over multiple overlapping scans are shown to stitch seamlessly and form uniform 3D nanostructure with beam size scaled to small 200 μm diameter. In this way, laser scanning is presented as a facile means to embed 3D PC structure within microfluidic channels for integration into an optofluidic lab-on-chip, demonstrating a new laser HIL writing approach for creating multi-scale integrated microsystems. PMID:26922872

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

    PubMed

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

    2016-11-04

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

  3. Hydrogen in polar intermetallics: Syntheses and structures of the ternary Ca{sub 5}Bi{sub 3}D{sub 0.93}, Yb{sub 5}Bi{sub 3}H{sub x}, and Sm{sub 5}Bi{sub 3}H{sub a}pprox{sub 1} by powder neutron or single crystal X-ray diffraction

    SciTech Connect

    Alejandro Leon-Escamilla, E.; Dervenagas, Panagiotis; Stassis, Constantine; Corbett, John D.

    2010-01-15

    The syntheses of the title compounds are described in detail. Structural characterizations from refinements of single crystal X-ray diffraction data for Yb{sub 5}Bi{sub 3}H{sub x} and Sm{sub 5}Bi{sub 3}H{sub a}pprox{sub 1} and of powder neutron diffraction data for Ca{sub 5}Bi{sub 3}D{sub 0.93(3)} are reported. These confirm that all three crystallize with the heavy atom structure type of beta-Yb{sub 5}Sb{sub 3}, and the third gives the first proof that the deuterium lies in the center of nominal calcium tetrahedra, isostructural with the Ca{sub 5}Sb{sub 3}F-type structure. These Ca and Yb phases are particularly stable with respect to dissociation to Mn{sub 5}Si{sub 3}-type product plus H{sub 2}. Some contradictions in the literature regarding Yb{sub 5}Sb{sub 3} and Yb{sub 5}Sb{sub 3}H{sub x} phases are considered in terms of adventitious hydrogen impurities that are generated during reactions in fused silica containers at elevated temperatures. - Graphical abstract: The structure of Ca{sub 5}Bi{sub 3}H{sub 0.93} occurs in the novel Ca{sub 5}Sb{sub 3}F structure type with D centered in the shaded calcium tetrahedra.

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

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

    PubMed

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

    2016-11-29

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

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

    USGS Publications Warehouse

    Rodriguez, Brian D.

    2017-03-31

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

  8. 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.

  9. 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.

  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. 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…

  12. 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.

  13. 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

  14. A 3D POM-MOF composite based on Ni(ΙΙ) ion and 2,2‧-bipyridyl-3,3‧-dicarboxylic acid: Crystal structure and proton conductivity

    NASA Astrophysics Data System (ADS)

    Wei, Meilin; Wang, Xiaoxiang; Sun, Jingjing; Duan, Xianying

    2013-06-01

    We have succeeded in constructing a 3D POM-MOF, {H[Ni(Hbpdc)(H2O)2]2[PW12O40]·8H2O}n (H2bpdc=2,2'-bipyridyl-3,3'-dicarboxylic acid), by the controllable self-assembly of H2bpdc, Keggin-anions and Ni2+ ions based on the electrostatic and coordination interactions. Interestingly, Hbpdc- as polydentate organic ligands and Keggin-anion as polydentate inorganic ligands are covalently linked transition-metal nickel at the same time. The title complex represents a new example of introducing the metal N-heterocyclic multi-carboxylic acid frameworks into POMs chemistry. Based on Keggin-anions being immobilized as part of the metal N-heterocyclic multi-carboxylic acid framework, the title complex realizes four approaches in the 1D hydrophilic channel used to engender proton conductivity in MOFs. Its water adsorption isotherm at room temperature and pressure shows that the water content in it was 31 cm3 g-1 at the maximum allowable humidity, corresponding to 3.7 water molecules per unit formula. It exhibits good proton conductivities (10-4-10-3 S cm-1) at 100 °C in the relative humidity range 35-98%. The corresponding activation energy (Ea) of conductivity was estimated to be 1.01 eV.

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2010-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  18. Subtractive 3D Printing of Optically Active Diamond Structures

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  20. 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.

  1. 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

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

    PubMed

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

    2016-08-01

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

  3. A 3D POM–MOF composite based on Ni(ΙΙ) ion and 2,2´-bipyridyl-3,3´-dicarboxylic acid: Crystal structure and proton conductivity

    SciTech Connect

    Wei, Meilin; Wang, Xiaoxiang; Sun, Jingjing; Duan, Xianying

    2013-06-01

    We have succeeded in constructing a 3D POM–MOF, (H[Ni(Hbpdc)(H₂O)₂]₂[PW₁₂O₄₀]·8H₂O)n (H₂bpdc=2,2´-bipyridyl-3,3´-dicarboxylic acid), by the controllable self-assembly of H₂bpdc, Keggin-anions and Ni²⁺ ions based on the electrostatic and coordination interactions. Interestingly, Hbpdc⁻ as polydentate organic ligands and Keggin-anion as polydentate inorganic ligands are covalently linked transition-metal nickel at the same time. The title complex represents a new example of introducing the metal N-heterocyclic multi-carboxylic acid frameworks into POMs chemistry. Based on Keggin-anions being immobilized as part of the metal N-heterocyclic multi-carboxylic acid framework, the title complex realizes four approaches in the 1D hydrophilic channel used to engender proton conductivity in MOFs. Its water adsorption isotherm at room temperature and pressure shows that the water content in it was 31 cm³ g⁻¹ at the maximum allowable humidity, corresponding to 3.7 water molecules per unit formula. It exhibits good proton conductivities (10⁻⁴–10⁻³ S cm⁻¹) at 100 °C in the relative humidity range 35–98%. The corresponding activation energy (E{sub a}) of conductivity was estimated to be 1.01 eV. - Graphical abstract: A POM–MOF composite constructed by Keggin-type polyanion, Ni²⁺ and H₂bpdc shows good proton conductivities of 10⁻⁴–10⁻³ S cm⁻¹ at 100 °C under 35–98% RH. - Highlights: • A POM–MOF was constructed by combining metal N-heterocyclic multi-carboxylic acid framework and Keggin anion. • It opens a pathway for design and synthesis of multifunctional hybrid materials based on two building units. • Three types of potential proton-carriers have been assembled in the 1D hydrophilic channels of the POM–MOF. • It achieved such proton conductivities as 10⁻⁴–10⁻³ S cm⁻¹ at 100 °C in the RH range 35–98%.

  4. Rapid Prototyping across the Spectrum: RF to Optical 3D Electromagnetic Structures

    DTIC Science & Technology

    2015-11-17

    fabricated using 3D printer . The fill factor decreases radially outwards and the voids are visible in the unit cells as you approach the periphery of the...with thin walls) [29]. Figure 6: Examples of lenses fabricated with AM (a) GRIN lens fabricated using 3D printer . The fill factor decreases...AFRL-RW-EG-TP-2015-002 Rapid Prototyping across the Spectrum: RF to Optical 3D Electromagnetic Structures Jeffery W. Allen Monica S. Allen Brett

  5. 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.

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

    SciTech Connect

    ANDERSON, C. A.

    1999-11-22

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

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

    PubMed Central

    Wang, Jianwei; Zhang, Yong

    2016-01-01

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

  8. 2D and 3D photonic crystal materials for photocatalysis and electrochemical energy storage and conversion.

    PubMed

    Collins, Gillian; Armstrong, Eileen; McNulty, David; O'Hanlon, Sally; Geaney, Hugh; O'Dwyer, Colm

    2016-01-01

    This perspective reviews recent advances in inverse opal structures, how they have been developed, studied and applied as catalysts, catalyst support materials, as electrode materials for batteries, water splitting applications, solar-to-fuel conversion and electrochromics, and finally as photonic photocatalysts and photoelectrocatalysts. Throughout, we detail some of the salient optical characteristics that underpin recent results and form the basis for light-matter interactions that span electrochemical energy conversion systems as well as photocatalytic systems. Strategies for using 2D as well as 3D structures, ordered macroporous materials such as inverse opals are summarized and recent work on plasmonic-photonic coupling in metal nanoparticle-infiltrated wide band gap inverse opals for enhanced photoelectrochemistry are provided.

  9. 2D and 3D photonic crystal materials for photocatalysis and electrochemical energy storage and conversion

    PubMed Central

    Collins, Gillian; Armstrong, Eileen; McNulty, David; O’Hanlon, Sally; Geaney, Hugh; O’Dwyer, Colm

    2016-01-01

    Abstract This perspective reviews recent advances in inverse opal structures, how they have been developed, studied and applied as catalysts, catalyst support materials, as electrode materials for batteries, water splitting applications, solar-to-fuel conversion and electrochromics, and finally as photonic photocatalysts and photoelectrocatalysts. Throughout, we detail some of the salient optical characteristics that underpin recent results and form the basis for light-matter interactions that span electrochemical energy conversion systems as well as photocatalytic systems. Strategies for using 2D as well as 3D structures, ordered macroporous materials such as inverse opals are summarized and recent work on plasmonic–photonic coupling in metal nanoparticle-infiltrated wide band gap inverse opals for enhanced photoelectrochemistry are provided. PMID:27877904

  10. 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.

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

    PubMed

    Trewhella, Jill

    2016-10-01

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

  12. Single-Crystal to Single-Crystal Phase Transition and Segmented Thermochromic Luminescence in a Dynamic 3D Interpenetrated Ag(I) Coordination Network.

    PubMed

    Yan, Zhi-Hao; Li, Xiao-Yu; Liu, Li-Wei; Yu, Si-Qi; Wang, Xing-Po; Sun, Di

    2016-02-01

    A new 3D Ag(I)-based coordination network, [Ag2(pz)(bdc)·H2O]n (1; pz = pyrazine and H2bdc = benzene-1,3-dicarboxylic acid), was constructed by one-pot assembly and structurally established by single-crystal X-ray diffraction at different temperatures. Upon cooling from 298 to 93 K, 1 undergo an interesting single-crystal to single-crystal phase transition from orthorhombic Ibca (Z = 16) to Pccn (Z = 32) at around 148 K. Both phases show a rare 2-fold-interpenetrated 4-connected lvt network but incorporate different [Ag2(COO)2] dimeric secondary building units. It is worth mentioning that complex 1 shows red- and blue-shifted luminescences in the 290-170 and 140-80 K temperature ranges, respectively. The variable-temperature single-crystal X-ray crystallographic studies suggest that the argentophilic interactions and rigidity of the structure dominated the luminescence chromism trends at the respective temperature ranges. Upon being mechanically ground, 1 exhibits a slight mechanoluminescence red shift from 589 to 604 nm at 298 K.

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

    PubMed Central

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

    2013-01-01

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

  14. 3D nano-structures for laser nano-manipulation

    PubMed Central

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

    2013-01-01

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

  15. 3-D Structure of Sunspots using Imaging Spectroscopy

    NASA Technical Reports Server (NTRS)

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

    2006-01-01

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

  16. Probing the intrinsic optical Bloch-mode emission from a 3D photonic crystal

    NASA Astrophysics Data System (ADS)

    Hsieh, Mei-Li; Bur, James A.; Du, Qingguo; John, Sajeev; Lin, Shawn-Yu

    2016-10-01

    We report experimental observation of intrinsic Bloch-mode emission from a 3D tungsten photonic crystal at low thermal excitation. After the successful removal of conventional metallic emission (normal emission), it is possible to make an accurate comparison of the Bloch-mode and the normal emission. For all biases, we found that the emission intensity of the Bloch-mode is higher than that of the normal emission. The Bloch-mode emission also exhibits a slower dependence on (\\hslash ω /{k}bT) than that of the normal emission. The observed higher emission intensity and a different T-dependence is attributed to Bloch-mode assisted emission where emitters have been located into a medium having local density of states different than the isotropic case. Furthermore, our finite-difference time-domain (FDTD) simulation shows the presence of localized spots at metal-air boundaries and corners, having intense electric field. The enhanced plasmonic field and local non-equilibrium could induce a strong thermally stimulated emission and may be the cause of our unusual observation.

  17. Light-directing chiral liquid crystal nanostructures: from 1D to 3D.

    PubMed

    Bisoyi, Hari Krishna; Li, Quan

    2014-10-21

    Endowing external, remote, and dynamic control to self-organized superstructures with desired functionalities is a principal driving force in the bottom-up nanofabrication of molecular devices. Light-driven chiral molecular switches or motors in liquid crystal (LC) media capable of self-organizing into optically tunable one-dimensional (1D) and three-dimensional (3D) superstructures represent such an elegant system. As a consequence, photoresponsive cholesteric LCs (CLCs), i.e., self-organized 1D helical superstructures, and LC blue phases (BPs), i.e., self-organized 3D periodic cubic lattices, are emerging as a new generation of multifunctional supramolecular 1D and 3D photonic materials in their own right because of their fundamental academic interest and technological significance. These smart stimuli-responsive materials can be facilely fabricated from achiral LC hosts by the addition of a small amount of a light-driven chiral molecular switch or motor. The photoresponsiveness of these materials is a result of both molecular interaction and geometry changes in the chiral molecular switch upon light irradiation. The doped photoresponsive CLCs undergo light-driven pitch modulation and/or helix inversion, which has many applications in color filters, polarizers, all-optical displays, optical lasers, sensors, energy-saving smart devices, and so on. Recently, we have conceptualized and rationally synthesized different light-driven chiral molecular switches that have very high helical twisting powers (HTPs) and exhibit large changes in HTP in different states, thereby enabling wide phototunability of the systems by the addition of very small amounts of the molecular switches into commercially available achiral LCs. The light-driven chiral molecular switches are based on well-recognized azobenzene, dithienylcyclopentene, and spirooxazine derivatives. We have demonstrated high-resolution and lightweight photoaddressable displays without patterned electronics on

  18. 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).

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

    SciTech Connect

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

    1996-01-01

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

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

    SciTech Connect

    Kerr, J.; Jones, G.L.

    1996-12-31

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-02-01

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

  2. 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.

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

    PubMed

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

    2015-08-26

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

  4. 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

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

    PubMed

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

    2010-11-01

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

  6. 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.

  7. Experimental studies of cobalt ferrite nanoparticles doped silica matrix 3D magneto-photonic crystals

    NASA Astrophysics Data System (ADS)

    Abou Diwan, E.; Royer, F.; Kekesi, R.; Jamon, D.; Blanc-Mignon, M. F.; Neveu, S.; Rousseau, J. J.

    2013-05-01

    In this paper, we present the synthesis and the optical properties of 3D magneto-photonic structures. The elaboration process consists in firstly preparing then infiltrating polystyrene direct opals with a homogeneous solution of sol-gel silica precursors doped by cobalt ferrite nanoparticles, and finally dissolving the polystyrene spheres. Scanning Electron Microscopy (SEM) images of the prepared samples clearly evidence a periodic arrangement. Using a home-made polarimetric optical bench, the transmittance as a function of the wavelength, the Faraday rotation as a function of the applied magnetic field, and the Faraday ellipticity as a function of the wavelength and as a function of the applied magnetic field were measured. The existence of deep photonic band gaps (PBG), the unambiguous magnetic character of the samples and the qualitative modification of the Faraday ellipticity in the area of the PBG are evidenced.

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

    PubMed

    Omasa, Kenji; Hosoi, Fumiki; Konishi, Atsumi

    2007-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  10. 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.

  11. Crystal engineering in 3D: Converting nanoscale lamellar manganese oxide to cubic spinel while affixed to a carbon architecture

    DOE PAGES

    Donakowski, Martin D.; Wallace, Jean M.; Sassin, Megan B.; ...

    2016-06-17

    Here, by applying differential pair distribution function (DPDF) analyses to the energy–storage relevant MnOx/carbon system— but in a 3D architectural rather than powder–composite configuration—we can remove contributions of the carbon nanofoam paper scaffold and quantify the multiphasic oxide speciation as the nanoscale, disordered MnOx grafted to the carbon walls (MnOx@CNF) structurally rearranges in situ from birnessite AMnOx (A = Na+; Li+) to tetragonal Mn3O4 to spinel LiMn2O4. The first reaction step involves topotactic exchange of interlayer Na+ by Li+ in solution followed by thermal treatments to crystal engineer the –10–nm–thick 2D layered oxide throughout the macroscale nanofoam paper into amore » spinel phase. The oxide remains affixed to the walls of the nanofoam throughout the phase transformations. The DPDF fits are improved by retention of one plane of birnessite–like oxide after conversion to spinel. We support the DPDF–derived assignments by X–ray photoelectron spectroscopy and Raman spectroscopy, the latter of which tracks how crystal engineering the oxide affects the disorder of the carbon substrate. We further benchmark MnOx@CNF with nonaqueous electrochemical measurements versus lithium as the oxide converts from X–ray–amorphous birnessite to interlayer-registered LiMnOx to spinel. The lamellar AMnOx displays pseudocapacitive electrochemical behavior, with a doubling of specific capacitance for the interlayer–registered LiMnOx, while the spinel LiMn2O4@CNF displays a faradaic electrochemical response characteristic of Li–ion insertion. Our results highlight the need for holistic understanding when crystal engineering an (atomistic) charge–storing phase within the (architectural) structure of practical electrodes.« less

  12. 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.

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

    PubMed

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

    2013-01-01

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

  14. Sparsity-based Ankylography for Recovering 3D molecular structures from single-shot 2D scattered light intensity

    PubMed Central

    Mutzafi, Maor; Shechtman, Yoav; Eldar, Yonina C.; Cohen, Oren; Segev, Mordechai

    2015-01-01

    Deciphering the three-dimensional (3D) structure of complex molecules is of major importance, typically accomplished with X-ray crystallography. Unfortunately, many important molecules cannot be crystallized, hence their 3D structure is unknown. Ankylography presents an alternative, relying on scattering an ultrashort X-ray pulse off a single molecule before it disintegrates, measuring the far-field intensity on a two-dimensional surface, followed by computation. However, significant information is absent due to lower dimensionality of the measurements and the inability to measure the phase. Recent Ankylography experiments attracted much interest, but it was counter-argued that Ankylography is valid only for objects containing a small number of volume pixels. Here, we propose a sparsity-based approach to reconstruct the 3D structure of molecules. Sparsity is natural for Ankylography, because molecules can be represented compactly in stoichiometric basis. Utilizing sparsity, we surpass current limits on recoverable information by orders of magnitude, paving the way for deciphering the 3D structure of macromolecules. PMID:26289358

  15. 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.

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

    PubMed Central

    Li, Haotian; Huang, Yangyu

    2017-01-01

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

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

    PubMed

    Li, Haotian; Huang, Yangyu; Xiao, Yi

    2017-01-01

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

  18. Study of the structure of 3D-ordered macroporous GaN-ZnS:Mn nanocomposite films

    SciTech Connect

    Kurdyukov, D. A. Shishkin, I. I.; Grudinkin, S. A.; Sitnikova, A. A.; Zamoryanskaya, M. V.; Golubev, V. G.

    2015-05-15

    A film-type 3D-ordered macroporous GaN-ZnS:Mn nanocomposite with the structure of an inverted opal is fabricated. Structural studies of the nanocomposite are performed, and it is shown that GaN and ZnS:Mn introduced into the pores of the silica opal are nanocrystallites misoriented with respect to each other. It is shown that the nanocomposite is a structurally perfect 3D photonic crystal. The efficiency of using a buffer of GaN crystallites to preclude interaction between the surface of the spherical a-SiO{sub 2} particles forming the opal matrix and chemically active substances introduced into the pores is demonstrated.

  19. 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.

  20. 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.

  1. Bulk crystal growth and electronic characterization of the 3D Dirac semimetal Na{sub 3}Bi

    SciTech Connect

    Kushwaha, Satya K.; Krizan, Jason W.; Cava, R. J.; Feldman, Benjamin E.; Gyenis, András; Randeria, Mallika T.; Xiong, Jun; Xu, Su-Yang; Alidoust, Nasser; Belopolski, Ilya; Liang, Tian; Zahid Hasan, M.; Ong, N. P.; Yazdani, A.

    2015-04-01

    High quality hexagon plate-like Na{sub 3}Bi crystals with large (001) plane surfaces were grown from a molten Na flux. The freshly cleaved crystals were analyzed by low temperature scanning tunneling microscopy and angle-resolved photoemission spectroscopy, allowing for the characterization of the three-dimensional (3D) Dirac semimetal (TDS) behavior and the observation of the topological surface states. Landau levels were observed, and the energy-momentum relations exhibited a linear dispersion relationship, characteristic of the 3D TDS nature of Na{sub 3}Bi. In transport measurements on Na{sub 3}Bi crystals, the linear magnetoresistance and Shubnikov-de Haas quantum oscillations are observed for the first time.

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

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

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

  3. 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.

  4. 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

  5. 3D high-resolution two-photon crosslinked hydrogel structures for biological studies.

    PubMed

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

    2017-03-25

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

    Qiu, Peihua; Mukherjee, Partha Sarathi

    2012-08-01

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

  8. A 3D profile function suitable for integration of neutron time-of-flight single crystal diffraction peaks

    NASA Astrophysics Data System (ADS)

    Gutmann, Matthias J.

    2017-03-01

    A 3D profile function is presented suitable to integrate reflections arising in time-of-flight (TOF) single crystal neutron diffraction experiments. In order to account for the large asymmetry of the peak shape in the TOF direction, a 3D Gaussian ellipsoid in the pixel (x, z) and time-of-flight coordinates is convoluted with a rising and falling exponential along the time-of-flight direction. An analytic expression is derived, making it suitable for least-squares fitting. The application of this function in detector space or reciprocal space is straightforward.

  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. Micro-Structured Two-Component 3D Metamaterials with Negative Thermal-Expansion Coefficient from Positive Constituents

    NASA Astrophysics Data System (ADS)

    Qu, Jingyuan; Kadic, Muamer; Naber, Andreas; Wegener, Martin

    2017-01-01

    Controlling the thermal expansion of materials is of great technological importance. Uncontrolled thermal expansion can lead to failure or irreversible destruction of structures and devices. In ordinary crystals, thermal expansion is governed by the asymmetry of the microscopic binding potential, which cannot be adjusted easily. In artificial crystals called metamaterials, thermal expansion can be controlled by structure. Here, following previous theoretical work, we fabricate three-dimensional (3D) two-component polymer micro-lattices by using gray-tone laser lithography. We perform cross-correlation analysis of optical microscopy images taken at different sample temperatures. The derived displacement-vector field reveals that the thermal expansion and resulting bending of the bi-material beams leads to a rotation of the 3D chiral crosses arranged onto a 3D checkerboard pattern within one metamaterial unit cell. These rotations can compensate the expansion of the all positive constituents, leading to an effectively near-zero thermal length-expansion coefficient, or over-compensate the expansion, leading to an effectively negative thermal length-expansion coefficient. This evidences a striking level of thermal-expansion control.

  11. Micro-Structured Two-Component 3D Metamaterials with Negative Thermal-Expansion Coefficient from Positive Constituents

    PubMed Central

    Qu, Jingyuan; Kadic, Muamer; Naber, Andreas; Wegener, Martin

    2017-01-01

    Controlling the thermal expansion of materials is of great technological importance. Uncontrolled thermal expansion can lead to failure or irreversible destruction of structures and devices. In ordinary crystals, thermal expansion is governed by the asymmetry of the microscopic binding potential, which cannot be adjusted easily. In artificial crystals called metamaterials, thermal expansion can be controlled by structure. Here, following previous theoretical work, we fabricate three-dimensional (3D) two-component polymer micro-lattices by using gray-tone laser lithography. We perform cross-correlation analysis of optical microscopy images taken at different sample temperatures. The derived displacement-vector field reveals that the thermal expansion and resulting bending of the bi-material beams leads to a rotation of the 3D chiral crosses arranged onto a 3D checkerboard pattern within one metamaterial unit cell. These rotations can compensate the expansion of the all positive constituents, leading to an effectively near-zero thermal length-expansion coefficient, or over-compensate the expansion, leading to an effectively negative thermal length-expansion coefficient. This evidences a striking level of thermal-expansion control. PMID:28079161

  12. Micro-Structured Two-Component 3D Metamaterials with Negative Thermal-Expansion Coefficient from Positive Constituents.

    PubMed

    Qu, Jingyuan; Kadic, Muamer; Naber, Andreas; Wegener, Martin

    2017-01-12

    Controlling the thermal expansion of materials is of great technological importance. Uncontrolled thermal expansion can lead to failure or irreversible destruction of structures and devices. In ordinary crystals, thermal expansion is governed by the asymmetry of the microscopic binding potential, which cannot be adjusted easily. In artificial crystals called metamaterials, thermal expansion can be controlled by structure. Here, following previous theoretical work, we fabricate three-dimensional (3D) two-component polymer micro-lattices by using gray-tone laser lithography. We perform cross-correlation analysis of optical microscopy images taken at different sample temperatures. The derived displacement-vector field reveals that the thermal expansion and resulting bending of the bi-material beams leads to a rotation of the 3D chiral crosses arranged onto a 3D checkerboard pattern within one metamaterial unit cell. These rotations can compensate the expansion of the all positive constituents, leading to an effectively near-zero thermal length-expansion coefficient, or over-compensate the expansion, leading to an effectively negative thermal length-expansion coefficient. This evidences a striking level of thermal-expansion control.

  13. Fabrication of fully undercut ZnO-based photonic crystal membranes with 3D optical confinement

    NASA Astrophysics Data System (ADS)

    Hoffmann, Sandro Phil; Albert, Maximilian; Meier, Cedrik

    2016-09-01

    For studying nonlinear photonics, a highly controllable emission of photons with specific properties is essential. Two-dimensional photonic crystals (PhCs) have proven to be an excellent candidate for manipulating photon emission due to resonator-based effects. Additionally, zinc oxide (ZnO) has high susceptibility coefficients and therefore shows pronounced nonlinear effects. However, in order to fabricate such a cavity, a fully undercut ZnO membrane is required, which is a challenging problem due to poor selectivity of the known etching chemistry for typical substrates such as sapphire or ZnO. The aim of this paper is to demonstrate and characterize fully undercut photonic crystal membranes based on a thin ZnO film sandwiched between two layers of silicon dioxide (SiO2) on silicon substrates, from the initial growth of the heterostructure throughout the entire fabrication process. This process leads to a fully undercut ZnO-based membrane with adjustable optical confinement in all three dimensions. Finally, photonic resonances within the tailored photonic band gap are achieved due to optimized PhC-design (in-plane) and total internal reflection in the z-direction. The presented approach enables a variety of photon based resonator structures in the UV regime for studying nonlinear effects, including photon-exciton coupling and all-optical switching.

  14. 3D-Printed High-Density Droplet Array Chip for Miniaturized Protein Crystallization Screening under Vapor Diffusion Mode.

    PubMed

    Liang, Yi-Ran; Zhu, Li-Na; Gao, Jie; Zhao, Hong-Xia; Zhu, Ying; Ye, Sheng; Fang, Qun

    2017-03-23

    Here we describe the combination of three-dimensional (3D) printed chip and automated microfluidic droplet-based screening techniques for achieving massively parallel, nanoliter-scale protein crystallization screening under vapor diffusion mode. We fabricated high-density microwell array chips for sitting-drop vapor diffusion crystallization utilizing the advantage of the 3D-printing technique in producing high-aspect-ratio chips. To overcome the obstacle of 3D-printed microchips in performing long-term reactions caused by their porousness and gas permeability properties in chip body, we developed a two-step postprocessing method, including paraffin filling and parylene coating, to achieve high sealability and stability. We also developed a simple method especially suitable for controlling the vapor diffusion speed of nanoliter-scale droplets by changing the layer thickness of covering oil. With the above methods, 84 tests of nanoliter-scale protein crystallization under vapor diffusion mode were successfully achieved in the 7 × 12 droplet array chip with a protein consumption of 10 nL for each test, which is 20-100 times lower than that in the conventional large-volume screening system. Such a nanoliter-scale vapor diffusion system was applied to two model proteins with commercial precipitants and displayed advantages over that under microbatch mode. It identified more crystallization conditions, especially for the protein samples with lower concentrations.

  15. A 3-D Puzzle Approach to Building Protein-DNA Structures.

    PubMed

    Hinton, Deborah M

    2017-02-02

    Despite recent advances in structural analysis, it is still challenging to obtain a high resolution structure for a complex of RNA polymerase, transcriptional factors, and DNA. However, using biochemical constraints, 3-D printed models of available structures, and computer modeling, one can build biologically relevant models of such supramolecular complexes.

  16. 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.

  17. 3D and 4D atlas system of living human body structure.

    PubMed

    Suzuki, N; Takatsu, A; Hattori, A; Ezumi, T; Oda, S; Yanai, T; Tominaga, H

    1998-01-01

    A reference system for accessing anatomical information from a complete 3D structure of the whole body "living human", including 4D cardiac dynamics, was reconstructed with 3D and 4D data sets obtained from normal volunteers. With this system, we were able to produce a human atlas in which sectional images can be accessed from any part of the human body interactively by real-time image generation.

  18. Cryogenic optical localization provides 3D protein structure data with Angstrom resolution.

    PubMed

    Weisenburger, Siegfried; Boening, Daniel; Schomburg, Benjamin; Giller, Karin; Becker, Stefan; Griesinger, Christian; Sandoghdar, Vahid

    2017-02-01

    We introduce Cryogenic Optical Localization in 3D (COLD), a method to localize multiple fluorescent sites within a single small protein with Angstrom resolution. We demonstrate COLD by determining the conformational state of the cytosolic Per-ARNT-Sim domain from the histidine kinase CitA of Geobacillus thermodenitrificans and resolving the four biotin sites of streptavidin. COLD provides quantitative 3D information about small- to medium-sized biomolecules on the Angstrom scale and complements other techniques in structural biology.

  19. Linear-time protein 3-D structure searching with insertions and deletions

    PubMed Central

    2010-01-01

    Background Two biomolecular 3-D structures are said to be similar if the RMSD (root mean square deviation) between the two molecules' sequences of 3-D coordinates is less than or equal to some given constant bound. Tools for searching for similar structures in biomolecular 3-D structure databases are becoming increasingly important in the structural biology of the post-genomic era. Results We consider an important, fundamental problem of reporting all substructures in a 3-D structure database of chain molecules (such as proteins) which are similar to a given query 3-D structure, with consideration of indels (i.e., insertions and deletions). This problem has been believed to be very difficult but its exact computational complexity has not been known. In this paper, we first prove that the problem in unbounded dimensions is NP-hard. We then propose a new algorithm that dramatically improves the average-case time complexity of the problem in 3-D in case the number of indels k is bounded by a constant. Our algorithm solves the above problem for a query of size m and a database of size N in average-case O(N) time, whereas the time complexity of the previously best algorithm was O(Nmk+1). Conclusions Our results show that although the problem of searching for similar structures in a database based on the RMSD measure with indels is NP-hard in the case of unbounded dimensions, it can be solved in 3-D by a simple average-case linear time algorithm when the number of indels is bounded by a constant. PMID:20047663

  20. Efficient Design Tool for 2D and 3D NIMS Photonic Crystals

    DTIC Science & Technology

    2008-01-28

    and  Le‐Wei  Li, “Analysis  of  Probe‐fed  Conformal  Microstrip   Antennas  on Finite Ground Plane and Substrate”, IEEE Transactions on  Antennas  and...approach will be very  flexible   in handling many different  types of photonic crystals of  various geometrical  structures. Most  importantly,  the...Because of many different choices of the basis functions for the volume cells, the approach will be very flexible in handling many different types of

  1. Measuring nonlinear stresses generated by defects in 3D colloidal crystals

    NASA Astrophysics Data System (ADS)

    Lin, Neil Y. C.; Bierbaum, Matthew; Schall, Peter; Sethna, James P.; Cohen, Itai

    2016-11-01

    The mechanical, structural and functional properties of crystals are determined by their defects, and the distribution of stresses surrounding these defects has broad implications for the understanding of transport phenomena. When the defect density rises to levels routinely found in real-world materials, transport is governed by local stresses that are predominantly nonlinear. Such stress fields however, cannot be measured using conventional bulk and local measurement techniques. Here, we report direct and spatially resolved experimental measurements of the nonlinear stresses surrounding colloidal crystalline defect cores, and show that the stresses at vacancy cores generate attractive interactions between them. We also directly visualize the softening of crystalline regions surrounding dislocation cores, and find that stress fluctuations in quiescent polycrystals are uniformly distributed rather than localized at grain boundaries, as is the case in strained atomic polycrystals. Nonlinear stress measurements have important implications for strain hardening, yield and fatigue.

  2. 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.

  3. Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy.

    PubMed

    Punjani, Ali; Brubaker, Marcus A; Fleet, David J

    2017-04-01

    Discovering the 3D atomic-resolution structure of molecules such as proteins and viruses is one of the foremost research problems in biology and medicine. Electron Cryomicroscopy (cryo-EM) is a promising vision-based technique for structure estimation which attempts to reconstruct 3D atomic structures from a large set of 2D transmission electron microscope images. This paper presents a new Bayesian framework for cryo-EM structure estimation that builds on modern stochastic optimization techniques to allow one to scale to very large datasets. We also introduce a novel Monte-Carlo technique that reduces the cost of evaluating the objective function during optimization by over five orders of magnitude. The net result is an approach capable of estimating 3D molecular structure from large-scale datasets in about a day on a single CPU workstation.

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

    PubMed

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

    2013-11-07

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

  5. 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

  6. Efficient global wave propagation adapted to 3-D structural complexity: a pseudospectral/spectral-element approach

    NASA Astrophysics Data System (ADS)

    Leng, Kuangdai; Nissen-Meyer, Tarje; van Driel, Martin

    2016-12-01

    We present a new, computationally efficient numerical method to simulate global seismic wave propagation in realistic 3-D Earth models. We characterize the azimuthal dependence of 3-D wavefields in terms of Fourier series, such that the 3-D equations of motion reduce to an algebraic system of coupled 2-D meridian equations, which is then solved by a 2-D spectral element method (SEM). Computational efficiency of such a hybrid method stems from lateral smoothness of 3-D Earth models and axial singularity of seismic point sources, which jointly confine the Fourier modes of wavefields to a few lower orders. We show novel benchmarks for global wave solutions in 3-D structures between our method and an independent, fully discretized 3-D SEM with remarkable agreement. Performance comparisons are carried out on three state-of-the-art tomography models, with seismic period ranging from 34 s down to 11 s. It turns out that our method has run up to two orders of magnitude faster than the 3-D SEM, featured by a computational advantage expanding with seismic frequency.

  7. 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

  8. 3D-printing and mechanics of bio-inspired articulated and multi-material structures.

    PubMed

    Porter, Michael M; Ravikumar, Nakul; Barthelat, Francois; Martini, Roberto

    2016-12-21

    3D-printing technologies allow researchers to build simplified physical models of complex biological systems to more easily investigate their mechanics. In recent years, a number of 3D-printed structures inspired by the dermal armors of various fishes have been developed to study their multiple mechanical functionalities, including flexible protection, improved hydrodynamics, body support, or tail prehensility. Natural fish armors are generally classified according to their shape, material and structural properties as elasmoid scales, ganoid scales, placoid scales, carapace scutes, or bony plates. Each type of dermal armor forms distinct articulation patterns that facilitate different functional advantages. In this paper, we highlight recent studies that developed 3D-printed structures not only to inform the design and application of some articulated and multi-material structures, but also to explain the mechanics of the natural biological systems they mimic.

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

    PubMed

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

    2016-04-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  11. 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.

  12. 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.

  13. Mechanism of Enzymatic Reaction and Protein-Protein Interactions of PLD from a 3D Structural Model

    PubMed Central

    Mahankali, Madhu; Alter, Gerald; Gomez-Cambronero, Julian

    2014-01-01

    The phospholipase D (PLD) superfamily catalyzes the hydrolysis of cell membrane phospholipids generating the key intracellular lipid second messenger phosphatidic acid. However, there is not yet any resolved structure either from a crystallized protein or from NMR of any mammalian PLDs. We propose here a 3D model of the PLD2 by combining homology and ab initio 3 dimensional structural modeling methods, and docking conformation. This model is in agreement with the biochemical and physiological behavior of PLD in cells. For the lipase activity, the N- and C-terminal histidines of the HKD motifs (His 442/His 756) form a catalytic pocket, which accommodates phosphatidylcholine head group (but not phosphatidylethanolamine or phosphatidyl serine). The model explains the mechanism of the reaction catalysis, with nucleophilic attacks of His 442 and water, the latter aided by His 756. Further, the secondary structure regions superimposed with bacterial PLD crystal structure, which indicated an agreement structure model obtained. It also explains protein-protein interactions, such as PLD2-Rac2 transmodulation (with a 1:2 stoichiometry), PLD2 GEF activity on Rac2 that is relevant for actin polymerization and cell migration, and a biding site for phosphoinositides. Since tumor-aggravating properties have been found in mice overexpressing PLD2 enzyme, the 3D model of PLD2 will be also useful, to a large extent, in developing pharmaceuticals to modulate its in vivo activity. PMID:25308783

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

    NASA Astrophysics Data System (ADS)

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

    2009-01-01

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

  15. 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.

  16. Definition of subsurface stratigraphy, structure and rock properties from 3-D seismic data

    NASA Astrophysics Data System (ADS)

    Hart, Bruce S.

    1999-10-01

    This paper summarizes how three-dimensional (3-D) seismic technology is being used, primarily in the petroleum industry, to define subsurface structure, stratigraphy and rock properties. A 3-D seismic data volume: (a) provides a more accurate image of the subsurface than can be obtained with 2-D seismic methods; (b) is continuous, and so has a much greater spatial sampling than is obtained with 2-D seismic or other subsurface data (e.g., wells); and (c) can be viewed and interpreted interactively from a variety of perspectives, thus enhancing the interpreter's ability to generate an accurate description of subsurface features of interest. Seismic interpretation was once the almost exclusive realm of geophysicists, however, most 3-D seismic interpretation today is conducted by multidisciplinary teams that integrate geophysical, geological, petrophysical and engineering data and concepts into the 3-D seismic interpretation. These factors, plus proper survey design, help to increase the chances of success of a 3-D seismic interpretation project. Although there are cases where the technology is not appropriate or cannot be applied (for economic reasons or otherwise), the general success of 3-D seismic has led it to become a mainstay of the petroleum industry. The approach and technology, first developed in that industry, have potential applications in other applied and fundamental earth science disciplines, including mining, environmental geology, structural geology and stratigraphy.

  17. Calculation of the Slip System Activity in Deformed Zinc Single Crystals Using Digital 3-D Image Correlation Data

    SciTech Connect

    Florando, J; Rhee, M; Arsenlis, A; LeBlanc, M; Lassila, D

    2006-02-21

    A 3-D image correlation system, which measures the full-field displacements in 3 dimensions, has been used to experimentally determine the full deformation gradient matrix for two zinc single crystals. Based on the image correlation data, the slip system activity for the two crystals has been calculated. The results of the calculation show that for one crystal, only the primary slip system is active, which is consistent with traditional theory. The other crystal however, shows appreciable deformation on slip systems other than the primary. An analysis has been conducted which confirms the experimental observation that these other slip system deform in such a manner that the net result is slip which is approximately one third the magnitude and directly orthogonal to the primary system.

  18. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.

    PubMed

    McGuire, Ross; Verhoeven, Stefan; Vass, Márton; Vriend, Gerrit; de Esch, Iwan J P; Lusher, Scott J; Leurs, Rob; Ridder, Lars; Kooistra, Albert J; Ritschel, Tina; de Graaf, Chris

    2017-02-27

    3D-e-Chem-VM is an open source, freely available Virtual Machine ( http://3d-e-chem.github.io/3D-e-Chem-VM/ ) that integrates cheminformatics and bioinformatics tools for the analysis of protein-ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb).

  19. 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.

  20. Novel scanning electron microscopy methods for analyzing the 3D structure of the Golgi apparatus.

    PubMed

    Koga, Daisuke; Ushiki, Tatsuo; Watanabe, Tsuyoshi

    2017-01-01

    The structure of the Golgi apparatus has been extensively examined by light and electron microscopy, but details of its three-dimensional (3D) structure have remained unclear because of the technical limitations of conventional microscopy techniques. To overcome this problem, we have developed several novel scanning electron microscopy (SEM) methods for observing the 3D structure of subcellular organelles including the Golgi apparatus: (1) an osmium maceration method that facilitates SEM observation of membranous organelles, including the Golgi apparatus, by selectively removing soluble cytoplasmic proteins, (2) an osmium impregnation/maceration method that combines an osmium impregnation method with the osmium maceration method to determine the polarity of the Golgi apparatus by SEM, (3) a correlative light and SEM method that combines a cryosectioning technique with the osmium maceration method to enable correlation of the immunocytochemical distribution of molecules with the 3D ultrastructure of the Golgi apparatus, and (4) array tomography based on the systematic collection and integration of SEM images of serial ultrathin sections on glass slides for revealing the 3D ultrastructure of the entire Golgi apparatus. Together, the novel SEM techniques listed above can reveal the complete 3D structure of the Golgi apparatus in different cell types.

  1. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

    PubMed Central

    2017-01-01

    3D-e-Chem-VM is an open source, freely available Virtual Machine (http://3d-e-chem.github.io/3D-e-Chem-VM/) that integrates cheminformatics and bioinformatics tools for the analysis of protein–ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein–ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb). PMID:28125221

  2. Observation of solid-solid transitions in 3D crystals of colloidal superballs

    NASA Astrophysics Data System (ADS)

    Meijer, Janne-Mieke; Pal, Antara; Ouhajji, Samia; Lekkerkerker, Henk N. W.; Philipse, Albert P.; Petukhov, Andrei V.

    2017-02-01

    Self-organization in anisotropic colloidal suspensions leads to a fascinating range of crystal and liquid crystal phases induced by shape alone. Simulations predict the phase behaviour of a plethora of shapes while experimental realization often lags behind. Here, we present the experimental phase behaviour of superball particles with a shape in between that of a sphere and a cube. In particular, we observe the formation of a plastic crystal phase with translational order and orientational disorder, and the subsequent transformation into rhombohedral crystals. Moreover, we uncover that the phase behaviour is richer than predicted, as we find two distinct rhombohedral crystals with different stacking variants, namely hollow-site and bridge-site stacking. In addition, for slightly softer interactions we observe a solid-solid transition between the two. Our investigation brings us one step closer to ultimately controlling the experimental self-assembly of superballs into functional materials, such as photonic crystals.

  3. Observation of solid–solid transitions in 3D crystals of colloidal superballs

    PubMed Central

    Meijer, Janne-Mieke; Pal, Antara; Ouhajji, Samia; Lekkerkerker, Henk N. W.; Philipse, Albert P.; Petukhov, Andrei V.

    2017-01-01

    Self-organization in anisotropic colloidal suspensions leads to a fascinating range of crystal and liquid crystal phases induced by shape alone. Simulations predict the phase behaviour of a plethora of shapes while experimental realization often lags behind. Here, we present the experimental phase behaviour of superball particles with a shape in between that of a sphere and a cube. In particular, we observe the formation of a plastic crystal phase with translational order and orientational disorder, and the subsequent transformation into rhombohedral crystals. Moreover, we uncover that the phase behaviour is richer than predicted, as we find two distinct rhombohedral crystals with different stacking variants, namely hollow-site and bridge-site stacking. In addition, for slightly softer interactions we observe a solid–solid transition between the two. Our investigation brings us one step closer to ultimately controlling the experimental self-assembly of superballs into functional materials, such as photonic crystals. PMID:28186101

  4. 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

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

    PubMed

    Hayat, Sikander; Sander, Chris; Marks, Debora S; Elofsson, Arne

    2015-04-28

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

  6. Crystal engineering in 3D: Converting nanoscale lamellar manganese oxide to cubic spinel while affixed to a carbon architecture

    SciTech Connect

    Donakowski, Martin D.; Wallace, Jean M.; Sassin, Megan B.; Chapman, Karena W.; Parker, Joseph F.; Long, Jeffrey W.; Rolison, Debra R.

    2016-06-17

    Here, by applying differential pair distribution function (DPDF) analyses to the energy–storage relevant MnOx/carbon system— but in a 3D architectural rather than powder–composite configuration—we can remove contributions of the carbon nanofoam paper scaffold and quantify the multiphasic oxide speciation as the nanoscale, disordered MnOx grafted to the carbon walls (MnOx@CNF) structurally rearranges in situ from birnessite AMnOx (A = Na+; Li+) to tetragonal Mn3O4 to spinel LiMn2O4. The first reaction step involves topotactic exchange of interlayer Na+ by Li+ in solution followed by thermal treatments to crystal engineer the –10–nm–thick 2D layered oxide throughout the macroscale nanofoam paper into a spinel phase. The oxide remains affixed to the walls of the nanofoam throughout the phase transformations. The DPDF fits are improved by retention of one plane of birnessite–like oxide after conversion to spinel. We support the DPDF–derived assignments by X–ray photoelectron spectroscopy and Raman spectroscopy, the latter of which tracks how crystal engineering the oxide affects the disorder of the carbon substrate. We further benchmark MnOx@CNF with nonaqueous electrochemical measurements versus lithium as the oxide converts from X–ray–amorphous birnessite to interlayer-registered LiMnOx to spinel. The lamellar AMnOx displays pseudocapacitive electrochemical behavior, with a doubling of specific capacitance for the interlayer–registered LiMnOx, while the spinel LiMn2O4@CNF displays a faradaic electrochemical response characteristic of Li–ion insertion. Our results highlight the need for holistic understanding when crystal engineering an (atomistic) charge–storing phase within the (architectural) structure of practical electrodes.

  7. 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.

  8. Structure-From-Motion in 3D Space Using 2D Lidars

    PubMed Central

    Choi, Dong-Geol; Bok, Yunsu; Kim, Jun-Sik; Shim, Inwook; Kweon, In So

    2017-01-01

    This paper presents a novel structure-from-motion methodology using 2D lidars (Light Detection And Ranging). In 3D space, 2D lidars do not provide sufficient information for pose estimation. For this reason, additional sensors have been used along with the lidar measurement. In this paper, we use a sensor system that consists of only 2D lidars, without any additional sensors. We propose a new method of estimating both the 6D pose of the system and the surrounding 3D structures. We compute the pose of the system using line segments of scan data and their corresponding planes. After discarding the outliers, both the pose and the 3D structures are refined via nonlinear optimization. Experiments with both synthetic and real data show the accuracy and robustness of the proposed method. PMID:28165372

  9. 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.

  10. 3D Dewetting for Crystal Patterning: Toward Regular Single-Crystalline Belt Arrays and Their Functionality.

    PubMed

    Wu, Yuchen; Feng, Jiangang; Su, Bin; Jiang, Lei

    2016-03-16

    Arrays of unidirectional dewetting behaviors can be generated by using 3D-wettability-difference micropillars, yielding highly ordered organic single-crystalline belt arrays. These patterned organic belts show an improved mobility record and can be used as flexible pressure sensors with high sensitivity.

  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. Enhanced genome annotation using structural profiles in the program 3D-PSSM.

    PubMed

    Kelley, L A; MacCallum, R M; Sternberg, M J

    2000-06-02

    A method (three-dimensional position-specific scoring matrix, 3D-PSSM) to recognise remote protein sequence homologues is described. The method combines the power of multiple sequence profiles with knowledge of protein structure to provide enhanced recognition and thus functional assignment of newly sequenced genomes. The method uses structural alignments of homologous proteins of similar three-dimensional structure in the structural classification of proteins (SCOP) database to obtain a structural equivalence of residues. These equivalences are used to extend multiply aligned sequences obtained by standard sequence searches. The resulting large superfamily-based multiple alignment is converted into a PSSM. Combined with secondary structure matching and solvation potentials, 3D-PSSM can recognise structural and functional relationships beyond state-of-the-art sequence methods. In a cross-validated benchmark on 136 homologous relationships unambiguously undetectable by position-specific iterated basic local alignment search tool (PSI-Blast), 3D-PSSM can confidently assign 18 %. The method was applied to the remaining unassigned regions of the Mycoplasma genitalium genome and an additional 13 regions were assigned with 95 % confidence. 3D-PSSM is available to the community as a web server: http://www.bmm.icnet.uk/servers/3dpssm

  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. Towards an efficient compression of 3D coordinates of macromolecular structures

    PubMed Central

    Valasatava, Yana; Bradley, Anthony R.; Rose, Alexander S.; Duarte, Jose M.; Prlić, Andreas

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format. PMID:28362865

  15. Towards an efficient compression of 3D coordinates of macromolecular structures.

    PubMed

    Valasatava, Yana; Bradley, Anthony R; Rose, Alexander S; Duarte, Jose M; Prlić, Andreas; Rose, Peter W

    2017-01-01

    The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format.

  16. 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.

  17. Simulation approach of atomic layer deposition in large 3D structures

    NASA Astrophysics Data System (ADS)

    Schwille, Matthias C.; Barth, Jonas; Schössler, Timo; Schön, Florian; Bartha, Johann W.; Oettel, Martin

    2017-04-01

    We present a new simulation method predicting thicknesses of thin films obtained by atomic layer deposition in high aspect ratio 3D geometries as they appear in MEMS manufacturing. The method features a Monte-Carlo computation of film deposition in free molecular flow, as well as in the Knudsen and diffusive gas regime, applicable for large structures. We compare our approach to analytic and simulation results from the literature. The capability of the method is demonstrated by a comparison to experimental film thicknesses in a large 3D structure. Finally, the feasability to extract process parameters, i.e. sticking coefficients is shown.

  18. Integral scaling behavior of different morphologies of 3D xenon crystals

    NASA Astrophysics Data System (ADS)

    Singer, H. M.; Bilgram, J. H.

    2006-07-01

    Three-dimensional crystals have been observed in situ during the growth from supercooled melt. Depending on growth conditions three crystal morphologies were formed: dendrites, doublons and seaweed. Fractal dimensions of contour and area have been determined using correlation and box dimension techniques. Algorithms have been developed on the basis of fractal geometry to extract quantities from contour and area of projections of a crystal to characterise the crystal morphology. A method is presented to find hidden length scales in apparently scale invariant physical systems. We show that intrinsic length scales found by this method can be used to characterise morphologies of xenon crystals. It is shown that scaling relations by conventional tools of fractal geometry omit important intrinsical behavior and provide only averaged quantities.

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

    PubMed

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-10-01

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

  20. 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

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

    PubMed

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

    2016-07-08

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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  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. Protein-protein interaction networks studies and importance of 3D structure knowledge.

    PubMed

    Lu, Hui-Chun; Fornili, Arianna; Fraternali, Franca

    2013-12-01

    Protein-protein interaction networks (PPINs) are a powerful tool to study biological processes in living cells. In this review, we present the progress of PPIN studies from abstract to more detailed representations. We will focus on 3D interactome networks, which offer detailed information at the atomic level. This information can be exploited in understanding not only the underlying cellular mechanisms, but also how human variants and disease-causing mutations affect protein functions and complexes' stability. Recent studies have used structural information on PPINs to also understand the molecular mechanisms of binding partner selection. We will address the challenges in generating 3D PPINs due to the restricted number of solved protein structures. Finally, some of the current use of 3D PPINs will be discussed, highlighting their contribution to the studies in genotype-phenotype relationships and in the optimization of targeted studies to design novel chemical compounds for medical treatments.

  9. 3D watershed-based segmentation of internal structures within MR brain images

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2000-06-01

    In this paper an image-based method founded on mathematical morphology is presented in order to facilitate the segmentation of cerebral structures on 3D magnetic resonance images (MRIs). The segmentation is described as an immersion simulation, applied to the modified gradient image, modeled by a generated 3D region adjacency graph (RAG). The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions are identified in order to attribute an influence zone only to relevant minima of the image. This stage uses contrasted regions from morphological reconstruction and labeled flat regions constrained by the RAG. The goal of the decision stage is to precisely locate the contours of regions detected by the marker extraction. This decision is performed by a 3D extension of the watershed transform. Upon completion of the segmentation, the outcome of the preceding process is presented to the user for manual selection of the structures of interest (SOI). Results of this approach are described and illustrated with examples of segmented 3D MRIs of the human head.

  10. Voxel-coding method for quantification of vascular structure from 3D images

    NASA Astrophysics Data System (ADS)

    Soltanian-Zadeh, Hamid; Shahrokni, Ali; Zoroofi, Reza A.

    2001-05-01

    This paper presents an image processing method for information extraction from 3D images of vasculature. It automates the study of vascular structures by extracting quantitative information such as skeleton, length, diameter, and vessel-to- tissue ratio for different vessels as well as their branches. Furthermore, it generates 3D visualization of vessels based on desired anatomical characteristics such as vessel diameter or 3D connectivity. Steps of the proposed approach are as follows. (1) Preprocessing, in which intensity adjustment, optimal thresholding, and median filtering are done. (2) 3D thinning, in which medial axis and skeleton of the vessels are found. (3) Branch labeling, in which different branches are identified and each voxel is assigned to the corresponding branch. (4) Quantitation, in which length of each branch is estimated, based on the number of voxels assigned to it, and its diameter is calculated using the medial axis direction. (5) Visualization, in which vascular structure is shown in 3D, using color coding and surface rendering methods. We have tested and evaluated the proposed algorithms using simulated images of multi-branch vessels and real confocal microscopic images of the vessels in rat brains. Experimental results illustrate performance of the methods and usefulness of the results for medical image analysis applications.

  11. 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.

  12. In situ 3D topographic and shape analysis by synchrotron radiation X-ray microtomography for crystal form identification in polymorphic mixtures

    NASA Astrophysics Data System (ADS)

    Yin, Xian-Zhen; Xiao, Ti-Qiao; Nangia, Ashwini; Yang, Shuo; Lu, Xiao-Long; Li, Hai-Yan; Shao, Qun; He, You; York, Peter; Zhang, Ji-Wen

    2016-04-01

    Polymorphism denotes the existence of more than one crystal structure of a substance, and great practical and theoretical interest for the chemical and pharmaceutical industries. In many cases, it is challenging to produce a pure crystal form and establish a sensitive detection method for the identification of crystal form in a mixture of polymorphs. In this study, an accurate and sensitive method based on synchrotron radiation X-ray computed microtomography (SR-μCT) was devised to identify the polymorphs of clopidogrel bisulphate (CLP). After 3D reconstruction, crystal particles were extracted and dozens of structural parameters were calculated. Whilst, the particle shapes of the two crystal forms were all irregular, the surface of CLP II was found to be rougher than CLP I. In order to classify the crystal form based on the quantitative morphological property of particles, Volume Bias Percentage based on Surface Smoothing (VBP) was defined and a new method based on VBP was successfully developed, with a total matching rate of 99.91% for 4544 particles and a lowest detectable limit of 1%. More important for the mixtures in solid pharmaceutical formulations, the interference of excipients can be avoided, a feature cannot achieved by other available analytical methods.

  13. Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

    PubMed Central

    Shi, Ya-Zhou; Jin, Lei; Wang, Feng-Hua; Zhu, Xiao-Long; Tan, Zhi-Jie

    2015-01-01

    A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a three-bead coarse-grained predictive model with implicit salt/solvent potentials. In this study, we further develop the model by improving the implicit-salt electrostatic potential and including a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in divalent/monovalent ion solutions. The model presented here can predict 3D structures of RNA hairpins with bulges/internal loops (<77 nucleotides) from their sequences at the corresponding experimental ion conditions with an overall improved accuracy compared to the experimental data; the model also makes reliable predictions for the flexibility of RNA hairpins with bulge loops of different lengths at several divalent/monovalent ion conditions. In addition, the model successfully predicts the stability of RNA hairpins with various loops/stems in divalent/monovalent ion solutions. PMID:26682822

  14. A 3D Optical Surface Profilometer Using a Dual-Frequency Liquid Crystal-Based Dynamic Fringe Pattern Generator

    PubMed Central

    Joo, Kyung-Il; Kim, Mugeon; Park, Min-Kyu; Park, Heewon; Kim, Byeonggon; Hahn, JoonKu; Kim, Hak-Rin

    2016-01-01

    We propose a liquid crystal (LC)-based 3D optical surface profilometer that can utilize multiple fringe patterns to extract an enhanced 3D surface depth profile. To avoid the optical phase ambiguity and enhance the 3D depth extraction, 16 interference patterns were generated by the LC-based dynamic fringe pattern generator (DFPG) using four-step phase shifting and four-step spatial frequency varying schemes. The DFPG had one common slit with an electrically controllable birefringence (ECB) LC mode and four switching slits with a twisted nematic LC mode. The spatial frequency of the projected fringe pattern could be controlled by selecting one of the switching slits. In addition, moving fringe patterns were obtainable by applying voltages to the ECB LC layer, which varied the phase difference between the common and the selected switching slits. Notably, the DFPG switching time required to project 16 fringe patterns was minimized by utilizing the dual-frequency modulation of the driving waveform to switch the LC layers. We calculated the phase modulation of the DFPG and reconstructed the depth profile of 3D objects using a discrete Fourier transform method and geometric optical parameters. PMID:27801812

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

  16. Graphene originated 3D structures grown on the assembled nickel particles

    NASA Astrophysics Data System (ADS)

    Paronyan, Tereza; Harutyunyan, Avetik; Honda Research Institute USA Inc. Team

    2013-03-01

    Recently, the fabrication of various morphologies of graphene originated structures became very important due to the perspective of wide range of new applications. Particularly, free standing 3D structured graphene foams could be imperative in energy related areas . Here, we present the new approach of the CVD growth of 3D graphene network by using primarily sintered Ni particle's (~40 μm size) assembles as a template-catalyst via decomposition of low rate of CH4 at 1100° C based on synthesis method described earlier. SEM and Raman spectra analysis revealed the formation of graphene structure containing a single up to few layers grown on the sintered metal particles served as a catalyst-template. After etching the metal frame without using any support polymer, 3D free-standing graphene microporous structure was formed demonstrating high BET surface area. Two probe measurements of frame resistance were ~2-8 Ω. Our approach allows controllable tune the pore size and thereby the surface area of 3D graphene network through the variation of the template-catalyst particles size.

  17. 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.

  18. 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.

  19. 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.

  20. Studies of the 3D Structure of the Nucleon at Jlab

    SciTech Connect

    Avakian, Harut

    2016-07-01

    Studies of the 3D structure of the nucleon encoded in Transverse Momentum Dependent distribution and fragmentation functions of partons and Generalized Parton Distributions are among the key objectives of the JLab 12 GeV upgrade and the Electron Ion Collider. Main challenges in extracting 3D partonic distributions from precision measurements of hard scattering processes include clear understanding of leading twist QCD fundamentals, higher twist effects, and also correlations of hadron production in target and current fragmentation regions. In this contribution we discuss some ongoing studies and future measurements of spin-orbit correlations at Jefferson Lab.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Recursive estimation of 3D motion and surface structure from local affine flow parameters.

    PubMed

    Calway, Andrew

    2005-04-01

    A recursive structure from motion algorithm based on optical flow measurements taken from an image sequence is described. It provides estimates of surface normals in addition to 3D motion and depth. The measurements are affine motion parameters which approximate the local flow fields associated with near-planar surface patches in the scene. These are integrated over time to give estimates of the 3D parameters using an extended Kalman filter. This also estimates the camera focal length and, so, the 3D estimates are metric. The use of parametric measurements means that the algorithm is computationally less demanding than previous optical flow approaches and the recursive filter builds in a degree of noise robustness. Results of experiments on synthetic and real image sequences demonstrate that the algorithm performs well.

  6. 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

  7. 3D electrical structure of porphyry copper deposit: A case study of Shaxi copper deposit

    NASA Astrophysics Data System (ADS)

    Chen, Xiang-Bin; Lü, Qing-Tian; Yan, Jia-Yong

    2012-06-01

    Located in Lu-Zong ore concentration area, middle-lower Yangtze metallogenic belt, ShaXi porphyry copper deposit is a typical hydrothermal deposit. To investigate the distribution of deep ore bodies and spatial characteristics of host structures, an AMT survey was conducted in mining area. Eighteen pseudo-2D resistivity sections were constructed through careful processing and inversion. These sections clearly show resistivity difference between the Silurian sandstones formation and quartz diorite porphyry and this porphyry copper formation was controlled by the highly resistive anticlines. Using 3D block Kriging interpolation method and 3D visualization techniques, we constructed a detailed 3D resistivity model of quartz diorite porphyry which shows the shape and spatial distribution of deep ore bodies. This case study can serve as a good example for future ore prospecting in and around this mining area.

  8. 3D shape measurement of shoeprint impression with structured illumination and fringe pattern analysis

    NASA Astrophysics Data System (ADS)

    Su, Xianyu; Cao, Yiping; Xiang, Liqun; Chen, Wenjing

    2002-06-01

    The shoeprint impressions of suspect left at the crime scene can sometimes tell investigators what type of shoes to be looked for. These shoeprint impressions as one of the important evidence are useful in the detection of criminals. In this paper we propose a novel technique for identifying and analyzing the 3D characteristics of shoeprint impressions. We also design 3D shoeprint impression analysis system based on the combination the 3D shape measurement with structured illumination and fringe pattern analysis. We give a detail discussion on the principle and configuration of the system. Laboratory experiments show the technique is efficient in the detection of shoeprint and in the offering the reference for judicial evidence.

  9. Human Sinoatrial Node Structure: 3D Microanatomy of Sinoatrial Conduction Pathways

    PubMed Central

    Csepe, Thomas A.; Zhao, Jichao; Hansen, Brian J.; Li, Ning; Sul, Lidiya V.; Lim, Praise; Wang, Yufeng; Simonetti, Orlando P.; Kilic, Ahmet; Mohler, Peter J.; Janssen, Paul ML.; Fedorov, Vadim V.

    2016-01-01

    Introduction Despite a century of extensive study on the human sinoatrial node (SAN), the structure-to-function features of specialized SAN conduction pathways (SACP) are still unknown and debated. We report a new method for direct analysis of the SAN microstructure in optically-mapped human hearts with and without clinical history of SAN dysfunction. Methods Two explanted donor human hearts were coronary-perfused and optically-mapped. Structural analyses of histological sections parallel to epicardium (~13-21μm intervals) were integrated with optical maps to create 3D computational reconstructions of the SAN complex. High-resolution fiber fields were obtained using 3D Eigen-analysis of the structure tensor, and used to analyze SACP microstructure with a fiber-tracking approach. Results Optical mapping revealed normal SAN activation of the atria through a lateral SACP proximal to the crista terminalis in Heart #1 but persistent SAN exit block in diseased Heart #2. 3D structural analysis displayed a functionally-observed SAN border composed of fibrosis, fat, and/or discontinuous fibers between SAN and atria, which was only crossed by several branching myofiber tracts in SACP regions. Computational 3D fiber-tracking revealed that myofiber tracts of SACPs created continuous connections between SAN #1 and atria, but in SAN #2, SACP region myofiber tracts were discontinuous due to fibrosis and fat. Conclusions We developed a new integrative functional, structural and computational approach that allowed for the resolution of the specialized 3D microstructure of human SACPs for the first time. Application of this integrated approach will shed new light on the role of the specialized SAN microanatomy in maintaining sinus rhythm. PMID:26743207

  10. An extended 3D discrete-continuous model and its application on single- and bi-crystal micropillars

    NASA Astrophysics Data System (ADS)

    Huang, Minsheng; Liang, Shuang; Li, Zhenhuan

    2017-04-01

    A 3D discrete-continuous model (3D DCM), which couples the 3D discrete dislocation dynamics (3D DDD) and finite element method (FEM), is extended in this study. New schemes for two key information transfers between DDD and FEM, i.e. plastic-strain distribution from DDD to FEM and stress transfer from FEM to DDD, are suggested. The plastic strain induced by moving dislocation segments is distributed to an elementary spheroid (ellipsoid or sphere) via a specific new distribution function. The influence of various interfaces (such as free surfaces and grain boundaries (GBs)) on the plastic-strain distribution is specially considered. By these treatments, the deformation fields can be solved accurately even for dislocations on slip planes severely inclined to the FE mesh, with no spurious stress concentration points produced. In addition, a stress correction by singular and non-singular theoretical solutions within a cut-off sphere is introduced to calculate the stress on the dislocations accurately. By these schemes, the present DCM becomes less sensitive to the FE mesh and more numerically efficient, which can also consider the interaction between neighboring dislocations appropriately even though they reside in the same FE mesh. Furthermore, the present DCM has been employed to model the compression of single-crystal and bi-crystal micropillars with rigid and dislocation-absorbed GBs. The influence of internal GB on the jerky stress-strain response and deformation mode is studied in detail to shed more light on these important micro-plastic problems.

  11. Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity.

    PubMed

    Lee, Karen J I; Calder, Grant M; Hindle, Christopher R; Newman, Jacob L; Robinson, Simon N; Avondo, Jerome J H Y; Coen, Enrico S

    2016-12-26

    Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale.

  12. Modeling and characterization of 2-D and 3-D textile structural composites

    SciTech Connect

    Yang, J.M.

    1986-01-01

    This dissertation studies the analytical modeling and experimental characterization of various two-dimensional and three-dimensional textile structure composites. In the analytical approach, various theoretical models were established to predict the stiffness, strength, nonlinear deformation, and failure behavior of triaxial woven-fabric composites, 3-D braided composites, and multilayer multidirectional warp knit fabric composites in polymer and metal matrices. The structure performance maps of various textile structural composites were also established, based upon these analytical methods. In the experimental approach, extensive mechanical testing and microstructural characterization were performed to investigate the thermomechanical properties and failure behavior of 3-D braided FP/Al composites. Results of this research will serve as the basis for assessing the potential of textile composites for structural applications.

  13. 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

  14. Cryo-EM structure of a 3D DNA-origami object

    PubMed Central

    Bai, Xiao-chen; Martin, Thomas G.; Scheres, Sjors H. W.; Dietz, Hendrik

    2012-01-01

    A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback. PMID:23169645

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

    PubMed

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

    2013-02-01

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

  16. 3D scanning of internal structure in gel engineering materials with visual scanning microscopic light scattering

    NASA Astrophysics Data System (ADS)

    Watanabe, Yosuke; Gong, Jing; Masato, Makino; Kabir, M. Hasnat; Furukawa, Hidemitsu

    2014-04-01

    The 3D printing technology, causing much attention from the beginning of 2013, will be possibly an alternative method to fabricate the biological soft tissues. Recently our group of Yamagata University has developed the world-first 3D Gel Printer to fabricate the complicated gel-materials with high-strength and biocompatibility. However, there are no 3D scanners that collect the data from the internal structure of complicated gel objects such as eye lens. It means that a new system for scanning the internal structure is needed now. In this study, firstly, we have tried to investigate the gel network of synthetic and biological gel with scanning microscopic light scattering (SMILS). We calculated the Young's modulus of synthetic gels with the SMILS and with the tensile test, and precisely compared the results between them. The temperature dependences of the inside structure and the transparency are observed in the pig crystalline lens. The quantitative analysis indicates the importance of the internal structure of real object. Secondary, we show the new system named Gel-scanner that can provide the 2-dimentional data of the internal structure. From examining our findings, the scanning of internal structure will enable us to expect physical properties of the real object. We convince that the gelscanner will play major role in the various fields.

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

    PubMed

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

    2017-02-23

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

  18. Structural and functional imaging of 3D microfluidic mixers using optical coherence tomography.

    PubMed

    Xi, Chuanwu; Marks, Daniel L; Parikh, Devang S; Raskin, Lutgarde; Boppart, Stephen A

    2004-05-18

    To achieve high mixing efficiency in microfluidic devices, complex designs are often required. Microfluidic devices have been evaluated with light and confocal microscopy, but fluid-flow characteristics at different depths are difficult to separate from the en face images produced. By using optical coherence tomography (OCT), an imaging modality capable of imaging 3D microstructures at micrometer-scale resolutions over millimeter-size scales, we obtained 3D dynamic functional and structural data for three representative microfluidic mixers: a Y channel mixer, a 3D serpentine mixer, and a vortex mixer. In the serpentine mixer, OCT image analysis revealed that the mixing efficiency was linearly dependent on the Reynolds number, whereas it appeared to have exponential dependence when imaged with light microscopy. The visual overlap of fluid flows in light-microscopy images leads to an overestimation of the mixing efficiency, an effect that was eliminated with OCT imaging. Doppler OCT measurements determined velocity profiles at various points in the serpentine mixer. Mixing patterns in the vortex mixer were compared with light-microscopy and OCT image analysis. These results demonstrate that OCT can significantly improve the characterization of 3D microfluidic device structure and function.

  19. 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.

  20. 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.

  1. A generalized crystal-cutting method for modeling arbitrarily oriented crystals in 3D periodic simulation cells with applications to crystal-crystal interfaces

    NASA Astrophysics Data System (ADS)

    Kroonblawd, Matthew P.; Mathew, Nithin; Jiang, Shan; Sewell, Thomas D.

    2016-10-01

    A Generalized Crystal-Cutting Method (GCCM) is developed that automates construction of three-dimensionally periodic simulation cells containing arbitrarily oriented single crystals and thin films, two-dimensionally (2D) infinite crystal-crystal homophase and heterophase interfaces, and nanostructures with intrinsic N-fold interfaces. The GCCM is based on a simple mathematical formalism that facilitates easy definition of constraints on cut crystal geometries. The method preserves the translational symmetry of all Bravais lattices and thus can be applied to any crystal described by such a lattice including complicated, low-symmetry molecular crystals. Implementations are presented with carefully articulated combinations of loop searches and constraints that drastically reduce computational complexity compared to simple loop searches. Orthorhombic representations of monoclinic and triclinic crystals found using the GCCM overcome some limitations in standard distributions of popular molecular dynamics software packages. Stability of grain boundaries in β-HMX was investigated using molecular dynamics and molecular statics simulations with 2D infinite crystal-crystal homophase interfaces created using the GCCM. The order of stabilities for the four grain boundaries studied is predicted to correlate with the relative prominence of particular crystal faces in lab-grown β-HMX crystals. We demonstrate how nanostructures can be constructed through simple constraints applied in the GCCM framework. Example GCCM constructions are shown that are relevant to some current problems in materials science, including shock sensitivity of explosives, layered electronic devices, and pharmaceuticals.

  2. 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.

  3. 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.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Takizawa, Tokihiro; Okada, Hoshihito; Matsuse, Takehiro

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

  6. Effective 3D protein structure prediction with local adjustment genetic-annealing algorithm.

    PubMed

    Zhang, Xiao-Long; Lin, Xiao-Li

    2010-09-01

    The protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing the energy function. The protein folding structure prediction is computationally challenging and has been shown to be NP-hard problem when the 3D off-lattice AB model is employed. In this paper, the local adjustment genetic-annealing (LAGA) algorithm was used to search the ground state of 3D offlattice AB model for protein folding structure. The algorithm included an improved crossover strategy and an improved mutation strategy, where a local adjustment strategy was also used to enhance the searching ability. The experiments were carried out with the Fibonacci sequences. The experimental results demonstrate that the LAGA algorithm appears to have better performance and accuracy compared to the previous methods.

  7. Fabrication of 3D embedded hollow structures inside polymer dielectric PMMA with femtosecond laser

    NASA Astrophysics Data System (ADS)

    Zheng, Chong; Chen, Tao; Hu, Anming; Liu, Shibing; Li, Junwei

    2016-11-01

    Recent progresses in femtosecond laser (fs) manufacturing have already proved that fs laser is a powerful tool in three dimensional internal structure fabrications. However, most studies are mainly focused on realize such structures in inorganic transparent dielectric, such as photosensitive glass and fused silica, etc. In this study, we present two methods to fabricate embedded internal 3D structures in a polymer dielectric material polymethyl methacrylate (PMMA). Both continuous hollow structure such as microfluidic channels and discrete hollow structures such as single microcavities are successfully fabricated with the help of femtosecond lasers. Among them, complicated 3D microchannel with a total length longer than 10mm and diameters around 80μm to 200μm are fabricated with a low repetition rate Ti: sapphire femtosecond laser by direct laser writing at a speed ranging from 25μm/s to 2000μm/s microcavities which function as concave microball lenses (CMBLs) and can be applied in super-wide-angle imaging are fabricated with a high repetition rate femtosecond fiber laser due to the distinct heat accumulation effect after 5s irradiation with the tightly focused fs laser beam. These new approaches proved that femtosecond laser direct writing technology has great application potential in 3D integrated devices manufacturing in the future.

  8. Fragment-based strategy for structural optimization in combination with 3D-QSAR.

    PubMed

    Yuan, Haoliang; Tai, Wenting; Hu, Shihe; Liu, Haichun; Zhang, Yanmin; Yao, Sihui; Ran, Ting; Lu, Shuai; Ke, Zhipeng; Xiong, Xiao; Xu, Jinxing; Chen, Yadong; Lu, Tao

    2013-10-01

    Fragment-based drug design has emerged as an important methodology for lead discovery and drug design. Different with other studies focused on fragment library design and active fragment identification, a fragment-based strategy was developed in combination with three-dimensional quantitative structure-activity relationship (3D-QSAR) for structural optimization in this study. Based on a validated scaffold or fragment hit, a series of structural optimization was conducted to convert it to lead compounds, including 3D-QSAR modelling, active site analysis, fragment-based structural optimization and evaluation of new molecules. 3D-QSAR models and active site analysis provided sufficient information for confirming the SAR and pharmacophoric features for fragments. This strategy was evaluated through the structural optimization on a c-Met inhibitor scaffold 5H-benzo[4,5]cyclohepta[1,2-b]pyridin-5-one, which resulted in an c-Met inhibitor with high inhibitory activity. Our study suggested the effectiveness of this fragment-based strategy and the druggability of our newly explored active region. The reliability of this strategy indicated it could also be applied to facilitate lead optimization of other targets.

  9. Proteins without unique 3D structures: biotechnological applications of intrinsically unstable/disordered proteins.

    PubMed

    Uversky, Vladimir N

    2015-03-01

    Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins or regions that do not have unique 3D structures under functional conditions. Therefore, from the viewpoint of their lack of stable 3D structure, IDPs/IDPRs are inherently unstable. As much as structure and function of normal ordered globular proteins are determined by their amino acid sequences, the lack of unique 3D structure in IDPs/IDPRs and their disorder-based functionality are also encoded in the amino acid sequences. Because of their specific sequence features and distinctive conformational behavior, these intrinsically unstable proteins or regions have several applications in biotechnology. This review introduces some of the most characteristic features of IDPs/IDPRs (such as peculiarities of amino acid sequences of these proteins and regions, their major structural features, and peculiar responses to changes in their environment) and describes how these features can be used in the biotechnology, for example for the proteome-wide analysis of the abundance of extended IDPs, for recombinant protein isolation and purification, as polypeptide nanoparticles for drug delivery, as solubilization tools, and as thermally sensitive carriers of active peptides and proteins.

  10. Fragment-based strategy for structural optimization in combination with 3D-QSAR

    NASA Astrophysics Data System (ADS)

    Yuan, Haoliang; Tai, Wenting; Hu, Shihe; Liu, Haichun; Zhang, Yanmin; Yao, Sihui; Ran, Ting; Lu, Shuai; Ke, Zhipeng; Xiong, Xiao; Xu, Jinxing; Chen, Yadong; Lu, Tao

    2013-10-01

    Fragment-based drug design has emerged as an important methodology for lead discovery and drug design. Different with other studies focused on fragment library design and active fragment identification, a fragment-based strategy was developed in combination with three-dimensional quantitative structure-activity relationship (3D-QSAR) for structural optimization in this study. Based on a validated scaffold or fragment hit, a series of structural optimization was conducted to convert it to lead compounds, including 3D-QSAR modelling, active site analysis, fragment-based structural optimization and evaluation of new molecules. 3D-QSAR models and active site analysis provided sufficient information for confirming the SAR and pharmacophoric features for fragments. This strategy was evaluated through the structural optimization on a c-Met inhibitor scaffold 5H-benzo[4,5]cyclohepta[1,2-b]pyridin-5-one, which resulted in an c-Met inhibitor with high inhibitory activity. Our study suggested the effectiveness of this fragment-based strategy and the druggability of our newly explored active region. The reliability of this strategy indicated it could also be applied to facilitate lead optimization of other targets.

  11. Extended depth-of-focus 3D micro integral imaging display using a bifocal liquid crystal lens.

    PubMed

    Shen, Xin; Wang, Yu-Jen; Chen, Hung-Shan; Xiao, Xiao; Lin, Yi-Hsin; Javidi, Bahram

    2015-02-15

    We present a three dimensional (3D) micro integral imaging display system with extended depth of focus by using a polarized bifocal liquid crystal lens. This lens and other optical components are combined as the relay optical element. The focal length of the relay optical element can be controlled to project an elemental image array in multiple positions with various lenslet image planes, by applying different voltages to the liquid crystal lens. The depth of focus of the proposed system can therefore be extended. The feasibility of our proposed system is experimentally demonstrated. In our experiments, the depth of focus of the display system is extended from 3.82 to 109.43 mm.

  12. 3D Printed Modeling of the Mitral Valve for Catheter-Based Structural Interventions.

    PubMed

    Vukicevic, Marija; Puperi, Daniel S; Jane Grande-Allen, K; Little, Stephen H

    2017-02-01

    As catheter-based structural heart interventions become increasingly complex, the ability to effectively model patient-specific valve geometry as well as the potential interaction of an implanted device within that geometry will become increasingly important. Our aim with this investigation was to combine the technologies of high-spatial resolution cardiac imaging, image processing software, and fused multi-material 3D printing, to demonstrate that patient-specific models of the mitral valve apparatus could be created to facilitate functional evaluation of novel trans-catheter mitral valve repair strategies. Clinical 3D transesophageal echocardiography and computed tomography images were acquired for three patients being evaluated for a catheter-based mitral valve repair. Target anatomies were identified, segmented and reconstructed into 3D patient-specific digital models. For each patient, the mitral valve apparatus was digitally reconstructed from a single or fused imaging data set. Using multi-material 3D printing methods, patient-specific anatomic replicas of the mitral valve were created. 3D print materials were selected based on the mechanical testing of elastomeric TangoPlus materials (Stratasys, Eden Prairie, Minnesota, USA) and were compared to freshly harvested porcine leaflet tissue. The effective bending modulus of healthy porcine MV tissue was significantly less than the bending modulus of TangoPlus (p < 0.01). All TangoPlus varieties were less stiff than the maximum tensile elastic modulus of mitral valve tissue (3697.2 ± 385.8 kPa anterior leaflet; 2582.1 ± 374.2 kPa posterior leaflet) (p < 0.01). However, the slopes of the stress-strain toe regions of the mitral valve tissues (532.8 ± 281.9 kPa anterior leaflet; 389.0 ± 156.9 kPa posterior leaflet) were not different than those of the Shore 27, Shore 35, and Shore 27 with Shore 35 blend TangoPlus material (p > 0.95). We have demonstrated that patient-specific mitral valve models can be

  13. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

    PubMed

    Miao, Zhichao; Adamiak, Ryszard W; Antczak, Maciej; Batey, Robert T; Becka, Alexander J; Biesiada, Marcin; Boniecki, Michał J; Bujnicki, Janusz; Chen, Shi-Jie; Cheng, Clarence Yu; Chou, Fang-Chieh; Ferré-D'Amaré, Adrian R; Das, Rhiju; Dawson, Wayne K; Feng, Ding; Dokholyan, Nikolay V; Dunin-Horkawicz, Stanisław; Geniesse, Caleb; Kappel, Kalli; Kladwang, Wipapat; Krokhotin, Andrey; Łach, Grzegorz E; Major, François; Mann, Thomas H; Magnus, Marcin; Pachulska-Wieczorek, Katarzyna; Patel, Dinshaw J; Piccirilli, Joseph A; Popenda, Mariusz; Purzycka, Katarzyna J; Ren, Aiming; Rice, Greggory M; Santalucia, John; Sarzynska, Joanna; Szachniuk, Marta; Tandon, Arpit; Trausch, Jeremiah J; Tian, Siqi; Wang, Jian; Weeks, Kevin M; Williams, Benfeard; Xiao, Yi; Xu, Xiaojun; Zhang, Dong; Zok, Tomasz; Westhof, Eric

    2017-01-30

    RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF) and one set describes large conformational changes between ligand-free and ligand-bound states; the Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All the puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal notable need for algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.

  14. 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

  15. 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

  16. Functional classification of protein 3D structures from predicted local interaction sites.

    PubMed

    Parasuram, Ramya; Lee, Joslynn S; Yin, Pengcheng; Somarowthu, Srinivas; Ondrechen, Mary Jo

    2010-12-01

    A new approach to the functional classification of protein 3D structures is described with application to some examples from structural genomics. This approach is based on functional site prediction with THEMATICS and POOL. THEMATICS employs calculated electrostatic potentials of the query structure. POOL is a machine learning method that utilizes THEMATICS features and has been shown to predict accurate, precise, highly localized interaction sites. Extension to the functional classification of structural genomics proteins is now described. Predicted functionally important residues are structurally aligned with those of proteins with previously characterized biochemical functions. A 3D structure match at the predicted local functional site then serves as a more reliable predictor of biochemical function than an overall structure match. Annotation is confirmed for a structural genomics protein with the ribulose phosphate binding barrel (RPBB) fold. A putative glucoamylase from Bacteroides fragilis (PDB ID 3eu8) is shown to be in fact probably not a glucoamylase. Finally a structural genomics protein from Streptomyces coelicolor annotated as an enoyl-CoA hydratase (PDB ID 3g64) is shown to be misannotated. Its predicted active site does not match the well-characterized enoyl-CoA hydratases of similar structure but rather bears closer resemblance to those of a dehalogenase with similar fold.

  17. 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.

  18. Comparison of low cost 3D structured light scanners for face modeling.

    PubMed

    Bakirman, Tolga; Gumusay, Mustafa Umit; Reis, Hatice Catal; Selbesoglu, Mahmut Oguz; Yosmaoglu, Serra; Yaras, Mehmet Cem; Seker, Dursun Zafer; Bayram, Bulent

    2017-02-01

    This study aims to compare three different structured light scanner systems to generate accurate 3D human face models. Among these systems, the most dense and expensive one was denoted as the reference and the other two that were low cost and low resolution were compared according to the reference system. One female face and one male face were scanned with three light scanner systems. Point-cloud filtering, mesh generation, and hole-filling steps were carried out using a trial version of commercial software; moreover, the data evaluation process was realized using CloudCompare open-source software. Various filtering and mesh smoothing levels were applied on reference data to compare with other low-cost systems. Thus, the optimum reduction level of reference data was evaluated to continue further processes. The outcome of the presented study shows that low-cost structured light scanners have a great potential for 3D object modeling, including the human face. A considerable cheap structured light system has been used due to its capacity to obtain spatial and morphological information in the case study of 3D human face modeling. This study also discusses the benefits and accuracy of low-cost structured light systems.

  19. Low-cost impact detection and location for automated inspections of 3D metallic based structures.

    PubMed

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

    2015-05-28

    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.

  20. Rapid Fabrication of Cell-Laden Alginate Hydrogel 3D Structures by Micro Dip-Coating

    PubMed Central

    Ghanizadeh Tabriz, Atabak; Mills, Christopher G.; Mullins, John J.; Davies, Jamie A.; Shu, Wenmiao

    2017-01-01

    Development of a simple, straightforward 3D fabrication method to culture cells in 3D, without relying on any complex fabrication methods, remains a challenge. In this paper, we describe a new technique that allows fabrication of scalable 3D cell-laden hydrogel structures easily, without complex machinery: the technique can be done using only apparatus already available in a typical cell biology laboratory. The fabrication method involves micro dip-coating of cell-laden hydrogels covering the surface of a metal bar, into the cross-linking reagents calcium chloride or barium chloride to form hollow tubular structures. This method can be used to form single layers with thickness ranging from 126 to 220 µm or multilayered tubular structures. This fabrication method uses alginate hydrogel as the primary biomaterial and a secondary biomaterial can be added depending on the desired application. We demonstrate the feasibility of this method, with survival rate over 75% immediately after fabrication and normal responsiveness of cells within these tubular structures using mouse dermal embryonic fibroblast cells and human embryonic kidney 293 cells containing a tetracycline-responsive, red fluorescent protein (tHEK cells). PMID:28286747

  1. 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

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

    PubMed

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

    2013-01-01

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

  3. 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.

  4. Propagation of Coronal Mass Ejections in 3D and the Structure of the Inner Heliosphere

    NASA Astrophysics Data System (ADS)

    Gallagher, P. T.; Byrne, J. P.; Maloney, S. A.; McAteer, J.

    2011-12-01

    Solar coronal mass ejections (CMEs) are the most significant drivers of adverse space weather on Earth, but the physics governing their propagation through the heliosphere is not well understood. Although stereoscopic imaging of CMEs with NASA's Solar Terrestrial Relations Observatory (STEREO) has provided some insight into their three-dimensional (3D) propagation, the mechanisms governing their evolution remain unclear because of difficulties in reconstructing their true 3D structure. In this talk I will describe the use of an elliptical tie-pointing technique to reconstruct a CME front in 3D, enabling us to quantify its deflected trajectory from high latitudes along the ecliptic, and measure its increasing angular width and propagation. At large distances from the Sun (>7 R_sun), I will describe how its motion is determined by drag effects in the solar wind, using ENLIL simulations of the inner heliosphere. By combining a 3D reconstruction with modelling of the solar wind, we predict an arrival time within 30 mins of the in-situ detection of the CME at ACE

  5. 3D analysis of vortical structures in an abdominal aortic aneurysm by stereoscopic PIV

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  6. 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

  7. Design of a 3D Digital Liquid Crystal Particle Thermometry and Velocimetry (3DDLCPT/V) System

    NASA Astrophysics Data System (ADS)

    Grothe, Rob; Rixon, Greg; Dabiri, Dana

    2007-11-01

    A novel 3D Digital Liquid Crystal Particle Thermometry and Velocimetry (3DDLCPT/V) system has been designed and fabricated. By combining 3D Defocusing Particle Image Velocimetry (3DDPIV) and Digital Particle Image Thermometry (DPIT) into one system, this technique provides simultaneous temperature and velocity data using temperature-sensitive liquid crystal particles (LCP) as flow sensors. A custom water-filled prism corrects for astigmatism caused by off-axis imaging. New optics equations are derived to account for multi-surface refractions. This redesign also maximizes the use of the CCD area to more efficiently image the volume of interest. Six CCD cameras comprise the imaging system, with three allocated for velocity measurements and three for temperature measurements. The cameras are optically aligned to sub-pixel accuracy using a precision grid and high-resolution translation stages. Two high-intensity custom-designed xenon flashlamps provide illumination. Temperature calibration of the LCP is then performed. These results and proof-of-concept experiments will be discussed in detail.

  8. High-contrast step-index waveguides in borate nonlinear laser crystals by 3D laser writing.

    PubMed

    Rodenas, Airan; Kar, Ajoy K

    2011-08-29

    We report the ultrafast fabrication of high-contrast step-index channel waveguides in Nd(3+):YCa(4)O(BO(3))(3) borate laser crystals by means of 3D direct laser writing. Guiding up to 3.4 μm wavelength is demonstrated for the first time in a laser written crystalline waveguide. Modeling the measured fundamental modes at the wavelengths of 1.9 µm and 3.4 µm allowed us to estimate the high laser-induced refractive index increments (index contrasts) to be 0.010 (0.59%), and 0.005 (0.29%), respectively. Confocal µ-Raman spectral imaging of the waveguides cross-sections confirmed that the cores have very well defined step profiles, and that the increase in the refractive index can be linked to the localized creation of permanent intrinsic defects. These results indicate that this crystalline waveguides are a potential candidate for the development of 3D active waveguide circuits, due to the laser and electro-optic properties of rare earth doped borate crystals.

  9. Utilizing in-situ resources and 3D printing structures for a manned Mars mission

    NASA Astrophysics Data System (ADS)

    Kading, Benjamin; Straub, Jeremy

    2015-02-01

    This paper presents a manned Mars mission, which is based on the use of in-situ resources for the fabrication of structures. First, it provides an overview of the two-phase mission. In phase one, robotic construction units prepare a functional base for phase-two human habitation. Then, it describes a set of prospective structures that can be created utilizing additive manufacturing (commonly known as 3D printing) techniques and in situ materials. Next, the technological advancements required to allow this type of mission are considered and their feasibility is discussed. Specific focus is given to the topics of basalt 3D printing and the maintenance of the pressure environment. The process of the construction of the base is also discussed. Finally the proposed approach is analyzed through comparison to prior missions, before concluding.

  10. Analysis of the 3D Structure and Velocity of a CME on 2 January 2008

    NASA Astrophysics Data System (ADS)

    López, F. M.; Cremades, H.

    We perform an analysis of the 3D structure and velocity of a CME (coronal mass ejection) ejected on 2 January 2008. The event was imaged by both STEREO A and B spacecraft (mutual separation of ˜44°), providing polarized images of the event from two different points of view. To obtain information on the 3D structure of the CME from polarized images, a polarization technique (Moran & Davila, Science 305, 66, 2003) is applied. Aided by this method, we have constructed topographical maps which show the height of the various event features from the plane of the sky (i.e. toward or away from the observer) and have dinamically analyzed and compared the real and projected on the plane of the sky velocities.

  11. 3D modeling of doping from the atmosphere in floating zone silicon crystal growth

    NASA Astrophysics Data System (ADS)

    Sabanskis, A.; Surovovs, K.; Virbulis, J.

    2017-01-01

    Three-dimensional numerical simulations of the inert gas flow, melt flow and dopant transport in both phases are carried out for silicon single crystal growth using the floating zone method. The mathematical model allows to predict the cooling heat flux density at silicon surfaces and realistically describes the dopant transport in case of doping from the atmosphere. A very good agreement with experiment is obtained for the radial resistivity variation profiles by taking into account the temperature dependence of chemical reaction processes at the free surface.

  12. The calculation of static polarizabilities of 1-3D periodic compounds. the implementation in the crystal code.

    PubMed

    Ferrero, Mauro; Rérat, Michel; Orlando, Roberto; Dovesi, Roberto

    2008-07-15

    The Coupled Perturbed Hartree-Fock (CPHF) scheme has been implemented in the CRYSTAL06 program, that uses a gaussian type basis set, for systems periodic in 1D (polymers), 2D (slabs), 3D (crystals) and, as a limiting case, 0D (molecules), which enables comparison with molecular codes. CPHF is applied to the calculation of the polarizability alpha of LiF in different aggregation states: finite and infinite chains, slabs, and cubic crystal. Correctness of the computational scheme for the various dimensionalities and its numerical efficiency are confirmed by the correct trend of alpha: alpha for a finite linear chain containing N LiF units with large N tends to the value for the infinite chain, N parallel chains give the slab value when N is sufficiently large, and N superimposed slabs tend to the bulk value. CPHF results compare well with those obtained with a saw-tooth potential approach, previously implemented in CRYSTAL. High numerical accuracy can easily be achieved at relatively low cost, with the same kind of dependence on the computational parameters as for the SCF cycle. Overall, the cost of one component of the dielectric tensor is roughly the same as for the SCF cycle, and it is dominated by the calculation of two-electron four-center integrals.

  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. Analysis and 3D visualization of structures of animal brains obtained from histological sections

    NASA Astrophysics Data System (ADS)

    Forero-Vargas, Manuel G.; Fuentes, Veronica; Lopez, D.; Moscoso, A.; Merchan, Miguel A.

    2002-11-01

    This paper presents a new application for the analysis of histological sections and their 3D visualization. The process is performed in few steps. First, a manual process is necessary to determine the regions of interest, including image digitalization, drawing of borders and alignment between all images. Then, a reconstruction process is made. After sampling the contour, the structure of interest is displayed. The application is experimentally validated and some results on histological sections of a rodent's brain (hamster and rat) are shown.

  15. In silico 3D structure modeling and inhibitor binding studies of human male germ cell-associated kinase.

    PubMed

    Tanneeru, Karunakar; Balla, Ashok Raja; Guruprasad, Lalitha

    2015-01-01

    Human male germ cell-associated kinase (hMAK) is an androgen-inducible gene in prostate epithelial cells, and it acts as a coactivator of androgen receptor signaling in prostate cancer. The 3D structure of the hMAK kinase was modeled based on the crystal structure of CDK2 kinase using comparative modeling methods, and the ATP-binding site was characterized. We have collected five inhibitors of hMAK from the literature and docked into the ATP-binding site of the kinase domain. Solvated interaction energies (SIE) of inhibitor binding are calculated from the molecular dynamics simulations trajectories of protein-inhibitor complexes. The contribution from each active site residue in hMAK toward inhibitor binding revealed the nature and extent of interactions between inhibitors and individual residues. The main chain atoms of Met79 invariably form hydrogen bonds with all five inhibitors. The amino acids Leu7, Val15, and Leu129 stabilize the inhibitors via CH-pi interactions. The Asp140 in the active site and Glu77 in hinge region show characteristic hydrogen bonding interactions with inhibitors. From SIE, the residue-wise interactions revealed the nature of non-bonding contacts and modifications required to increase the inhibitor activity. Our work provides 3D model structure of hMAK and molecular basis for the mechanisms of hMAK inhibition at atomic level that aid in designing new potent inhibitors.

  16. 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.

  17. 3D Photonic Crystals Build Up By Self-Organization Of Nanospheres

    DTIC Science & Technology

    2006-05-23

    shown in Figure 4, the inverted structure for a fcc structure of spheres in a background with dielectric contrast 12 exhibits a CPBG, as illustrated in...0.70 0.75 0.80 0.85 0.90 0.95 fre qe nc y (c /a ) wavevector Figure 4. Calculated band structure for a fcc structure of spheres in a background...packed simple fcc structure . As illustrated in Figure 9, the maximum gap size appears when dielectric contrast is about 6, and the higher order gap

  18. 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.

  19. 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.

  20. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures

    PubMed Central

    Nadzirin, Nurul; Gardiner, Eleanor J.; Willett, Peter; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2012-01-01

    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

  1. 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.

  2. [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.

  3. 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.

  4. Modeling of elastic and plastic waves for HCP single crystals in a 3D formulation based on zinc single crystal

    NASA Astrophysics Data System (ADS)

    Krivosheina, Marina; Kobenko, Sergey; Tuch, Elena; Kozlova, Maria

    2016-11-01

    This paper investigates elastic and plastic waves in HCP single crystals through the numerical simulation of strain processes in anisotropic materials based on a zinc single crystal. Velocity profiles for compression waves in the back surfaces of single-crystal zinc plates with impact loading oriented in 0001 and 10 1 ¯0 are presented in this work as a part of results obtained in numerical simulations. The mathematical model implemented in this study reflects the following characteristics of the mechanical properties inherent in anisotropic (transtropic) materials: varying degree of anisotropy of elastic and plastic properties, which includes reverse anisotropy, dependence of distribution of all types of waves on the velocity orientation, and the anisotropy of compressibility. Another feature of elastic and plastic waves in HCP single crystals is that the shock wave does not split into an elastic precursor and "plastic" compression shock wave, which is inherent in zinc single crystals with loading oriented in 0001. The study compares numerical results obtained in a three-dimensional formulation with the results of velocity profiles from the back surfaces of target plates obtained in real experiments. These results demonstrate that the mathematical model is capable of describing the properties of the above-mentioned anisotropic (transtropic) materials.

  5. A Metal Organic Framework with Spherical Protein Nodes: Rational Chemical Design of 3D Protein Crystals.

    PubMed

    Sontz, Pamela A; Bailey, Jake B; Ahn, Sunhyung; Tezcan, F Akif

    2015-09-16

    We describe here the construction of a three-dimensional, porous, crystalline framework formed by spherical protein nodes that assemble into a prescribed lattice arrangement through metal-organic linker-directed interactions. The octahedral iron storage enzyme, ferritin, was engineered in its C3 symmetric pores with tripodal Zn coordination sites. Dynamic light scattering and crystallographic studies established that this Zn-ferritin construct could robustly self-assemble into the desired bcc-type crystals upon coordination of a ditopic linker bearing hydroxamic acid functional groups. This system represents the first example of a ternary protein-metal-organic crystalline framework whose formation is fully dependent on each of its three components.

  6. 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).

  7. Syntheses, structures, and photoluminescence of d 10 coordination architectures: From 1D to 3D complexes based on mixed ligands

    NASA Astrophysics Data System (ADS)

    Yuan, Gang; Shao, Kui-Zhan; Du, Dong-Ying; Wang, Xin-Long; Su, Zhong-Min

    2011-05-01

    Six new compounds, namely, {[Cd 3(Himpy) 3(tda) 2]·3H 2O} n ( 1), {[Zn 3(bipy) 2(tda) 2(H 2O) 2]·4H 2O} n ( 2), {[Cd 3(bipy) 3(tda) 2]·4H 2O} n ( 3), {[Cd 3(tda) 2(H 2O) 3Cl]·H 2O} n ( 4), {[Zn 2(tz)(tda)(H 2O) 2]·H 2O} n ( 5) and {[Cd 7(pz)(tda) 4(OAc)(H 2O) 7]·3H 2O} n ( 6) [H 3tda = 1H-1,2,3-triazole-4,5-dicarboxylic acid, Himpy = 2-(1H-imidazol-2-yl)pyridine, bipy = 2,2'-bipyridine, Htz = 1H-1,2,4-triazole, H 2pz = piperazine] have been prepared under hydrothermal condition and characterized by elemental analyses, infrared spectroscopy, powder X-ray diffraction and single-crystal X-ray diffraction analyses. Compound 1 is a 1D column-like structure and displays a 3D supramolecular network via the π···π stacking interaction. The compounds 2 and 3 exhibit similar 2D layer-like structure, which further extend to 3D supermolecular structure by the π···π stacking interaction. All of compounds 4- 6 display 3D framework with diverse topology constructed from the tda 3- ligands in different coordination modes and secondary ligands (or bridging atom) connecting metal ions. Furthermore, the thermal stabilities and photoluminescent properties of compounds 1- 6 were studied.

  8. Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA.

    PubMed

    Mrozek, Dariusz; Brożek, Miłosz; Małysiak-Mrozek, Bożena

    2014-02-01

    Searching for similar 3D protein structures is one of the primary processes employed in the field of structural bioinformatics. However, the computational complexity of this process means that it is constantly necessary to search for new methods that can perform such a process faster and more efficiently. Finding molecular substructures that complex protein structures have in common is still a challenging task, especially when entire databases containing tens or even hundreds of thousands of protein structures must be scanned. Graphics processing units (GPUs) and general purpose graphics processing units (GPGPUs) can perform many time-consuming and computationally demanding processes much more quickly than a classical CPU can. In this paper, we describe the GPU-based implementation of the CASSERT algorithm for 3D protein structure similarity searching. This algorithm is based on the two-phase alignment of protein structures when matching fragments of the compared proteins. The GPU (GeForce GTX 560Ti: 384 cores, 2GB RAM) implementation of CASSERT ("GPU-CASSERT") parallelizes both alignment phases and yields an average 180-fold increase in speed over its CPU-based, single-core implementation on an Intel Xeon E5620 (2.40GHz, 4 cores). In this paper, we show that massive parallelization of the 3D structure similarity search process on many-core GPU devices can reduce the execution time of the process, allowing it to be performed in real time. GPU-CASSERT is available at: http://zti.polsl.pl/dmrozek/science/gpucassert/cassert.htm.

  9. 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

  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.

    PubMed

    Mao, Yiqi; Yu, Kai; Isakov, Michael S; Wu, Jiangtao; Dunn, Martin L; Jerry Qi, H

    2015-09-08

    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

    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.

  13. 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

  14. 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.

  15. Development of biologically active compounds by combining 3D QSAR and structure-based design methods

    NASA Astrophysics Data System (ADS)

    Sippl, Wolfgang

    2002-11-01

    One of the major challenges in computational approaches to drug design is the accurate prediction of the binding affinity of novel biomolecules. In the present study an automated procedure which combines docking and 3D-QSAR methods was applied to several drug targets. The developed receptor-based 3D-QSAR methodology was tested on several sets of ligands for which the three-dimensional structure of the target protein has been solved - namely estrogen receptor, acetylcholine esterase and protein-tyrosine-phosphatase 1B. The molecular alignments of the studied ligands were determined using the docking program AutoDock and were compared with the X-ray structures of the corresponding protein-ligand complexes. The automatically generated protein-based ligand alignment obtained was subsequently taken as basis for a comparative field analysis applying the GRID/GOLPE approach. Using GRID interaction fields and applying variable selection procedures, highly predictive models were obtained. It is expected that concepts from receptor-based 3D QSAR will be valuable tools for the analysis of high-throughput screening as well as virtual screening data

  16. 3D Density Structure and LOS Observations of a Model CME

    NASA Astrophysics Data System (ADS)

    Manchester, W. B.; Lugaz, N.; Gombosi, T.; de Zeeuw, D.; Sokolov, I.; Toth, G.

    2004-12-01

    We present synthetic Thomson-scattered white-light images of a simulated coronal mass ejection (CME). The simulations are based on a 3-D MHD model of a CME propagating through a bimodal solar wind characteristic of solar minimum. The CME is driven by a 3-D Gibson-Low flux rope inserted in the helmet streamer of the steady-state corona. Synthetic coronograph images are produced that follow the evolution of the CME to 1 AU from several points of view. The white light images provide a basis for comparison with wide angle coronographs, like those of SMEI or STEREO. We find that a large amount of plasma is swept up from the solar wind by the CME-driven shock wave, which dominates the density structure far from the Sun. We also find that the shape of this compressed plasma is highly distorted by the variation in speed of the ambient solar wind. Comparisons of 2-D integrated images to the 3-D density structure show that the viewing angle severely effects the line-of-sight appearance of the CME, as well as the estimated mass of the CME from such 2D images.

  17. 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

  18. 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.

  19. Structured light 3D tracking system for measuring motions in PET brain imaging

    NASA Astrophysics Data System (ADS)

    Olesen, Oline V.; Jørgensen, Morten R.; Paulsen, Rasmus R.; Højgaard, Liselotte; Roed, Bjarne; Larsen, Rasmus

    2010-02-01

    Patient motion during scanning deteriorates image quality, especially for high resolution PET scanners. A new proposal for a 3D head tracking system for motion correction in high resolution PET brain imaging is set up and demonstrated. A prototype tracking system based on structured light with a DLP projector and a CCD camera is set up on a model of the High Resolution Research Tomograph (HRRT). Methods to reconstruct 3D point clouds of simple surfaces based on phase-shifting interferometry (PSI) are demonstrated. The projector and camera are calibrated using a simple stereo vision procedure where the projector is treated as a camera. Additionally, the surface reconstructions are corrected for the non-linear projector output prior to image capture. The results are convincing and a first step toward a fully automated tracking system for measuring head motions in PET imaging.

  20. Imaging and 3D reconstruction of cerebrovascular structures in embryonic zebrafish.

    PubMed

    Ethell, Douglas W; Cameron, D Joshua

    2014-04-22

    Zebrafish are a powerful tool to study developmental biology and pathology in vivo. The small size and relative transparency of zebrafish embryos make them particularly useful for the visual examination of processes such as heart and vascular development. In several recent studies transgenic zebrafish that express EGFP in vascular endothelial cells were used to image and analyze complex vascular networks in the brain and retina, using confocal microscopy. Descriptions are provided to prepare, treat and image zebrafish embryos that express enhanced green fluorescent protein (EGFP), and then generate comprehensive 3D renderings of the cerebrovascular system. Protocols include the treatment of embryos, confocal imaging, and fixation protocols that preserve EGFP fluorescence. Further, useful tips on obtaining high-quality images of cerebrovascular structures, such as removal the eye without damaging nearby neural tissue are provided. Potential pitfalls with confocal imaging are discussed, along with the steps necessary to generate 3D reconstructions from confocal image stacks using freely available open source software.

  1. Solution structure of the complex between CR2 SCR 1-2 and C3d of human complement: an X-ray scattering and sedimentation modelling study.

    PubMed

    Gilbert, Hannah E; Eaton, Julian T; Hannan, Jonathan P; Holers, V Michael; Perkins, Stephen J

    2005-02-25

    Complement receptor type 2 (CR2, CD21) forms a tight complex with C3d, a fragment of C3, the major complement component. Previous crystal structures of the C3d-CR2 SCR 1-2 complex and free CR2 SCR 1-2 showed that the two SCR domains of CR2 form contact with each other in a closed V-shaped structure. SCR 1 and SCR 2 are connected by an unusually long eight-residue linker peptide. Medium-resolution solution structures for CR2 SCR 1-2, C3d, and their complex were determined by X-ray scattering and analytical ultracentrifugation. CR2 SCR 1-2 is monomeric. For CR2 SCR 1-2, its radius of gyration R(G) of 2.12(+/-0.05) nm, its maximum length of 10nm and its sedimentation coefficient s20,w(o) of 1.40(+/-0.03) S do not agree with those calculated from the crystal structures, and instead suggest an open structure. Computer modelling of the CR2 SCR1-2 solution structure was based on the structural randomisation of the eight-residue linker peptide joining SCR 1 and SCR 2 to give 9950 trial models. Comparisons with the X-ray scattering curve indicated that the most favoured arrangements for the two SCR domains corresponded to an open V-shaped structure with no contacts between the SCR domains. For C3d, X-ray scattering and sedimentation velocity experiments showed that it exists as a monomer-dimer equilibrium with a dissociation constant of 40 microM. The X-ray scattering curve for monomeric C3d gave an R(G) value of 1.95 nm, and this together with its s20,w(o) value of 3.17 S gave good agreement with the monomeric C3d crystal structure. Modelling of the C3d dimer gave good agreements with its scattering and ultracentrifugation parameters. For the complex, scattering and ultracentrifugation experiments showed that there was no dimerisation, indicating that the C3d dimerisation site was located close to the CR2 SCR 1-2 binding site. The R(G) value of 2.44(+/-0.1) nm, its length of 9 nm and its s20,w(o) value of 3.45(+/-0.01) S showed that its structure was not much more

  2. Determining the 3-D structure and motion of objects using a scanning laser range sensor

    NASA Astrophysics Data System (ADS)

    Nandhakumar, N.; Smith, Philip W.

    1993-12-01

    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.

  3. 1d, 2d, and 3d periodic structures: Electromagnetic characterization, design, and measurement

    NASA Astrophysics Data System (ADS)

    Brockett, Timothy John

    Periodic structures have many useful applications in electromagnetics including phased arrays, frequency selective surfaces, and absorbing interfaces. Their unique properties can be used to provide increased performance in antenna gain, electromagnetic propagation, and electromagnetic absorption. In antenna arrays, repeating elements create a larger eective aperture, increasing the gain of the antenna and the ability to scan the direction of the main beam. Three-dimensional periodic structures, such as an array of shaped pillars such as columns, cones, or prisms have the potential of improving electromagnetic absorption, improving performance in applications such as solar cell eciency and absorbing interfaces. Furthermore, research into periodic structures is a continuing endeavor where novel approaches and analysis in appropriate applications can be sought. This dissertation will address the analysis, diagnostics, and enhancement of 1D, 2D, and 3D periodic structures for antenna array applications and solar cell technology. In particular, a unique approach to array design will be introduced to prevent the appearance of undesirable grating lobes in large antenna arrays that employ subarrays. This approach, named the distortion diagnostic procedure, can apply directly to 1D and 2D periodic structures in the form of planar antenna arrays. Interesting corollaries included here are developments in millimeter-wave antenna measurements including spiral planar scanning, phaseless measurements, and addressing antennas that feature an internal source. Finally, analysis and enhancement of 3D periodic structures in nanostructure photovoltaic arrays and absorbing interfaces will be examined for their behavior and basic operation in regards to improved absorption of electromagnetic waves.

  4. 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.

  5. 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

  6. 3D crustal and lithospheric structure of the Pyrenean orogenic wedge

    NASA Astrophysics Data System (ADS)

    Theunissen, Thomas; Chevrot, Sébastien; Sylvander, Matthieu; Monteiller, Vadim; Villasenor, Antonio; Benahmed, Sébastien; Calvet, Marie

    2013-04-01

    The Pyrenean orogenic wedge is the consequence of the collision between the Iberian microplate and the southwesternmost part of the Eurasian plate from 55 to 25 Ma (Eocene to Oligocene). The shortening began since Late Cretaceous, about 100 My ago, leading to about 75 km from the west to 125 km to the east of continental crustal shortening. Before this period of time, the region was characterized by a sedimentary basin associated with a very important thinning that later controlled the deformation during the shortening process. Mantle outcrops are therefore present along and north of the North Pyrenean Fault with a scattered localization to the west toward the Mauleon basin. Today, the horizontal deformation rate is very low and the recent seismicity, mainly normal faulting mechanisms, is certainly caused by coupling between erosion and isostatic readjustments. Images from seismic reflection, gravity modeling, local and teleseismic seismic waves inversions and magnetotellurics inversions are in agreement with the subduction of Iberia beneath Aquitania. The 3D crustal structure reveals the presence of an important thickening of the continental crust associated with the subduction of the Iberian lower crust through the north beneath Aquitania at the favor of a detachment. Lateral variations of the geometry (including that of the Moho) and the wave propagation properties are important. In order to better analyze waveforms from local, regional or teleseismic earthquakes and to better constrain the geodynamical evolution of the Pyrenean chain over the time, PYROPE and TOPO-IBERIA projects were born. Two temporary seismic arrays (using broadband seismometers), on the French and Spanish sides, have been deployed between 2010 and 2013. We present here preliminary results on 3D crustal structures (approximately in the window 40° N-45° N and -4° E and 5° E) from arrival-times of about 20000 earthquakes recorded at about 200 seismic stations between 1978 and 2012

  7. Introducing Defects in 3D Photonic Crystals: State of the Art

    DTIC Science & Technology

    2006-01-01

    for ma- nipulating the building blocks. Through the use of a nanorobot ,[48] the first diamond struc- ture formed out of colloidal microspheres was...placement of poly- styrene microspheres, point defects could be embedded into the resulting structure. The same nanorobot was also used to fabricate...robotically stacked and aligned with the nanorobot to form structures of up to 20 layers. An advantage of using microfabricated InP plates over microspheres

  8. Potassium uranyl borate 3D framework compound resulted from temperature directed hydroborate condensation: structure, spectroscopy, and dissolution studies.

    PubMed

    Xu, Xiaomei; Liu, Zhiyong; Yang, Shitong; Chen, Lanhua; Diwu, Juan; Alekseev, Evgeny V; Chai, Zhifang; Albrecht-Schmitt, Thomas E; Wang, Shuao

    2016-10-04

    The equatorial coordination nature of the uranyl unit has resulted in only three uranyl borate 3D framework compounds reported so far formed from boric acid flux reactions conducted at 190 °C while all others are 2D layers. Here in this work, by increasing the reaction temperature to 250 °C, a new potassium uranyl borate K[(UO2)B6O10(OH)] (KUBO-4) framework compound is synthesized that shares the same layer topology with the previously reported 2D layered KUBO-1. The 3D structure of KUBO-4 is achieved by interlayer hydroborate condensation. The KUBO-4 was further characterized with single crystal XRD, SHG and fluorescence spectra, and TG/DSC measurements. A deep understanding regarding the dissolution behaviours of uranyl borate is achieved via solubility studies of the KUBO-1 and KUBO-4 performed using a combination of ICP-MS, powder XRD, and fluorescence spectroscopy techniques. The results confirm the lack of stability of borates in aqueous solutions with the presence of coordinating ligands in the environment regardless of the structure types.

  9. 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

  10. Protein contact maps: A binary depiction of protein 3D structures

    NASA Astrophysics Data System (ADS)

    Emerson, Isaac Arnold; Amala, Arumugam

    2017-01-01

    In recent years, there has been a considerable interest in examining the structure and dynamics of complex networks. Proteins in 3D space may also be considered as complex systems emerged through the interactions of their constituent amino acids. This representation provides a powerful framework to uncover the general organized principle of protein contact network. Here we reviewed protein contact map in terms of protein structure prediction and analyses. In addition, we had also discussed the various computational techniques for the prediction of protein contact maps and the tools to visualize contact maps.

  11. Modal liquid crystal devices in optical tweezing: 3D control and oscillating potential wells.

    PubMed

    Hands, Philip J W; Tatarkova, Svetlana A; Kirby, Andrew K; Love, Gordon D

    2006-05-15

    We investigate the use of liquid crystal (LC) adaptive optics elements to provide full 3 dimensional particle control in an optical tweezer. These devices are suitable for single controllable traps, and so are less versatile than many of the competing technologies which can be used to control multiple particles. However, they have the advantages of simplicity and light efficiency. Furthermore, compared to binary holographic optical traps they have increased positional accuracy. The transmissive LC devices could be retro-fitted to an existing microscope system. An adaptive modal LC lens is used to vary the z-focal position over a range of up to 100 mum and an adaptive LC beam-steering device is used to deflect the beam (and trapped particle) in the x-y plane within an available radius of 10 mum. Furthermore, by modifying the polarisation of the incident light, these LC components also offer the opportunity for the creation of dual optical traps of controllable depth and separation.

  12. Modal liquid crystal devices in optical tweezing: 3D control and oscillating potential wells

    NASA Astrophysics Data System (ADS)

    Hands, Philip J. W.; Tatarkova, Svetlana A.; Kirby, Andrew K.; Love, Gordon D.

    2006-05-01

    We investigate the use of liquid crystal (LC) adaptive optics elements to provide full 3 dimensional particle control in an optical tweezer. These devices are suitable for single controllable traps, and so are less versatile than many of the competing technologies which can be used to control multiple particles. However, they have the advantages of simplicity and light efficiency. Furthermore, compared to binary holographic optical traps they have increased positional accuracy. The transmissive LC devices could be retro-fitted to an existing microscope system. An adaptive modal LC lens is used to vary the z-focal position over a range of up to 100 μm and an adaptive LC beam-steering device is used to deflect the beam (and trapped particle) in the x-y plane within an available radius of 10 μm. Furthermore, by modifying the polarisation of the incident light, these LC components also offer the opportunity for the creation of dual optical traps of controllable depth and separation.

  13. 3D visualization of XFEL beam focusing properties using LiF crystal X-ray detector

    PubMed Central

    Pikuz, Tatiana; Faenov, Anatoly; Matsuoka, Takeshi; Matsuyama, Satoshi; Yamauchi, Kazuto; Ozaki, Norimasa; Albertazzi, Bruno; Inubushi, Yuichi; Yabashi, Makina; Tono, Kensuke; Sato, Yuya; Yumoto, Hirokatsu; Ohashi, Haruhiko; Pikuz, Sergei; Grum-Grzhimailo, Alexei N.; Nishikino, Masaharu; Kawachi, Tetsuya; Ishikawa, Tetsuya; Kodama, Ryosuke

    2015-01-01

    Here, we report, that by means of direct irradiation of lithium fluoride a (LiF) crystal, in situ 3D visualization of the SACLA XFEL focused beam profile along the propagation direction is realized, including propagation inside photoluminescence solid matter. High sensitivity and large dynamic range of the LiF crystal detector allowed measurements of the intensity distribution of the beam at distances far from the best focus as well as near the best focus and evaluation of XFEL source size and beam quality factor M2. Our measurements also support the theoretical prediction that for X-ray photons with energies ~10 keV the radius of the generated photoelectron cloud within the LiF crystal reaches about 600 nm before thermalization. The proposed method has a spatial resolution ~ 0.4–2.0 μm for photons with energies 6–14 keV and potentially could be used in a single shot mode for optimization of different focusing systems developed at XFEL and synchrotron facilities. PMID:26634431

  14. 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

  15. A 3D model describing the initial structure of an artificial hydrological catchment

    NASA Astrophysics Data System (ADS)

    Maurer, T.; Schneider, A.; Buczko, U.; Gerke, H. H.

    2009-04-01

    The initial development stages of artificially constructed hydrologic catchments are characterized by the absence of vegetation, soil organic matter and soil horizons. This results in increased surface runoff and favors erosion processes that dominate the initial phase. Hydraulic conditions on artificial catchments thus are governed by rapidly changing surface structures as well as by the primary internal structural framework. Contemporary hydrological modeling does not consider any dynamic change of relevant structural features but rather assumes a stable, invariant landscape. The objective of this study was the digital visualization and quantitative description of the initial state and its early structural dynamics, exemplified for the small artificial hydrological catchment "Huehnerwasser" near Cottbus, Germany. Photogrammetric surveys of surface and internal structural units (clay basis liner) during the construction phase provided spatially and temporally resolved data for digital elevation models (DEM). Interpolated physical and chemical soil properties obtained at a borehole grid (e.g., texture) are used for the visualization of spatial distribution of relevant (hydraulic) parameters. The data are merged in a database and visualized in the 3D-GIS application GoCAD. The specific technological construction processes determines the internal structure of the artificial catchment. Resulting differences in bulk density and texture are supposed to have considerable impact on hydraulic properties. A structure generator program was implemented to reproduce the initial structure of the sediment layer as closely as possible. Results of the digital structure generation are checked with non-invasive geophysical measurements, on-site bore holes data and off-site 2D vertical spoil exploration. The accuracy of structure generator results will be compared with predictions of different interpolation methods. Thus, the structure model will serve as a basis for deriving the 3D

  16. Towards Automated Seismic Moment Tensor Inversion in Australia Using 3D Structural Model

    NASA Astrophysics Data System (ADS)

    Hingee, M.; Tkalcic, H.; Fichtner, A.; Sambridge, M.; Kennett, B. L.; Gorbatov, A.

    2009-12-01

    There is significant seismic activity in the region around Australia, largely due to the plate boundaries to the north and to the east of the mainland. This seismicity poses serious seismic and tsunamigenic hazard in a wider region, and risk to coastal areas of Australia, and is monitored by Geoscience Australia (GA) using a network of permanent broadband seismometers within Australia. Earthquake and tsunami warning systems were established by the Australian Government and have been using the waveforms from the GA seismological network. The permanent instruments are augmented by non-GA seismic stations based both within and outside of Australia. In particular, seismic moment tensor (MT) solutions for events around Australia as well as local distances are useful for both warning systems and geophysical studies in general. These monitoring systems, however, currently use only one dimensional, spherically-symmetric models of the Earth for source parameter determination. Recently, a novel 3D model of Australia and the surrounding area has been developed from spectral element simulations [1], taking into account not only velocity heterogeneities, but also radial anisotropy and seismic attenuation. This development, inter alia, introduces the potential of providing significant improvements in MT solution accuracy. Allowing reliable MT solutions with reduced dependence on non-GA stations is a secondary advantage. We studied the feasibility of using 1D versus 3D structural models. The accuracy of the 3D model has been investigated, confirming that these models are in most cases superior to the 1D models. A full MT inversion method using a point source approximation was developed as the first step, keeping in mind that for more complex source time functions, a finite source inversion will be needed. Synthetic experiments have been performed with random noise added to the signal to test the code in the both 1D and 3D setting, using a precomputed library of structural Greens

  17. Molecular Phylogeny and Predicted 3D Structure of Plant beta-D-N-Acetylhexosaminidase

    PubMed Central

    Hossain, Md. Anowar

    2014-01-01

    beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom. PMID:25165734

  18. Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase.

    PubMed

    Hossain, Md Anowar; Roslan, Hairul Azman

    2014-01-01

    beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom.

  19. 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

  20. Uncovering the structural basis of protein interactions with efficient clustering of 3-D interaction interfaces.

    PubMed

    Aung, Z; Tan, S-H; Ng, S-K; Tan, K-L

    2007-01-01

    The biological mechanisms with which proteins interact with one another are best revealed by studying the structural interfaces between interacting proteins. Protein-protein interfaces can be extracted from 3-D structural data of protein complexes and then clustered to derive biological insights. However, conventional protein interface clustering methods lack computational scalability and statistical support. In this work, we present a new method named "PPiClust" to systematically encode, cluster and analyze similar 3-D interface patterns in protein complexes efficiently. Experimental results showed that our method is effective in discovering visually consistent and statistically significant clusters of interfaces, and at the same time sufficiently time-efficient to be performed on a single computer. The interface clusters are also useful for uncovering the structural basis of protein interactions. Analysis of the resulting interface clusters revealed groups of structurally diverse proteins having similar interface patterns. We also found, in some of the interface clusters, the presence of well-known linear binding motifs which were non-contiguous in the primary sequences. These results suggest that PPiClust can discover not only statistically significant but also biologically significant protein interface clusters from protein complex structural data.

  1. Manipulating Heat Flow through 3 Dimensional Nanoscale Phononic Crystal Structure

    DTIC Science & Technology

    2014-06-02

    Nanoscale Phononic Crystal Structure 5a. CONTRACT NUMBER FA23861214047 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Baowen Li 5d...through computer simulation, how the three dimensional (3D) phononic crystal structures can confine phonon and thus reduce thermal conductivity...phononic crystal (PnC) with spherical pores, which can reduce thermal conductivity of bulk Si by a factor up to 10,000 times at room temperature. The

  2. Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

    NASA Astrophysics Data System (ADS)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

    NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

  3. The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

    PubMed

    Rose, Peter W; Prlić, Andreas; Altunkaya, Ali; Bi, Chunxiao; Bradley, Anthony R; Christie, Cole H; Costanzo, Luigi Di; Duarte, Jose M; Dutta, Shuchismita; Feng, Zukang; Green, Rachel Kramer; Goodsell, David S; Hudson, Brian; Kalro, Tara; Lowe, Robert; Peisach, Ezra; Randle, Christopher; Rose, Alexander S; Shao, Chenghua; Tao, Yi-Ping; Valasatava, Yana; Voigt, Maria; Westbrook, John D; Woo, Jesse; Yang, Huangwang; Young, Jasmine Y; Zardecki, Christine; Berman, Helen M; Burley, Stephen K

    2017-01-04

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.

  4. Strategies for the structural analysis of multi-protein complexes: lessons from the 3D-Repertoire project.

    PubMed

    Collinet, B; Friberg, A; Brooks, M A; van den Elzen, T; Henriot, V; Dziembowski, A; Graille, M; Durand, D; Leulliot, N; Saint André, C; Lazar, N; Sattler, M; Séraphin, B; van Tilbeurgh, H

    2011-08-01

    Structural studies of multi-protein complexes, whether by X-ray diffraction, scattering, NMR spectroscopy or electron microscopy, require stringent quality control of the component samples. The inability to produce 'keystone' subunits in a soluble and correctly folded form is a serious impediment to the reconstitution of the complexes. Co-expression of the components offers a valuable alternative to the expression of single proteins as a route to obtain sufficient amounts of the sample of interest. Even in cases where milligram-scale quantities of purified complex of interest become available, there is still no guarantee that good quality crystals can be obtained. At this step, protein engineering of one or more components of the complex is frequently required to improve solubility, yield or the ability to crystallize the sample. Subsequent characterization of these constructs may be performed by solution techniques such as Small Angle X-ray Scattering and Nuclear Magnetic Resonance to identify 'well behaved' complexes. Herein, we recount our experiences gained at protein production and complex assembly during the European 3D Repertoire project (3DR). The goal of this consortium was to obtain structural information on multi-protein complexes from yeast by combining crystallography, electron microscopy, NMR and in silico modeling methods. We present here representative set case studies of complexes that were produced and analyzed within the 3DR project. Our experience provides useful insight into strategies that are more generally applicable for structural analysis of protein complexes.

  5. 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

  6. 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.

  7. 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.

  8. PACS-based interface for 3D anatomical structure visualization and surgical planning

    NASA Astrophysics Data System (ADS)

    Koehl, Christophe; Soler, Luc; Marescaux, Jacques

    2002-05-01

    The interpretation of radiological image is routine but it remains a rather difficult task for physicians. It requires complex mental processes, that permit translation from 2D slices into 3D localization and volume determination of visible diseases. An easier and more extensive visualization and exploitation of medical images can be reached through the use of computer-based systems that provide real help from patient admission to post-operative followup. In this way, we have developed a 3D visualization interface linked to a PACS database that allows manipulation and interaction on virtual organs delineated from CT-scan or MRI. This software provides the 3D real-time surface rendering of anatomical structures, an accurate evaluation of volumes and distances and the improvement of radiological image analysis and exam annotation through a negatoscope tool. It also provides a tool for surgical planning allowing the positioning of an interactive laparoscopic instrument and the organ resection. The software system could revolutionize the field of computerized imaging technology. Indeed, it provides a handy and portable tool for pre-operative and intra-operative analysis of anatomy and pathology in various medical fields. This constitutes the first step of the future development of augmented reality and surgical simulation systems.

  9. 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.

  10. 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.

  11. Molecular docking and 3D-quantitative structure activity relationship analyses of peptidyl vinyl sulfones: Plasmodium Falciparum cysteine proteases inhibitors

    NASA Astrophysics Data System (ADS)

    Teixeira, Cátia; Gomes, José R. B.; Couesnon, Thierry; Gomes, Paula

    2011-08-01

    Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) based on three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were conducted on a series (39 molecules) of peptidyl vinyl sulfone derivatives as potential Plasmodium Falciparum cysteine proteases inhibitors. Two different methods of alignment were employed: (i) a receptor-docked alignment derived from the structure-based docking algorithm GOLD and (ii) a ligand-based alignment using the structure of one of the ligands derived from a crystal structure from the PDB databank. The best predictions were obtained for the receptor-docked alignment with a CoMFA standard model ( q 2 = 0.696 and r 2 = 0.980) and with CoMSIA combined electrostatic, and hydrophobic fields ( q 2 = 0.711 and r 2 = 0.992). Both models were validated by a test set of nine compounds and gave satisfactory predictive r 2 pred values of 0.76 and 0.74, respectively. CoMFA and CoMSIA contour maps were used to identify critical regions where any change in the steric, electrostatic, and hydrophobic fields may affect the inhibitory activity, and to highlight the key structural features required for biological activity. Moreover, the results obtained from 3D-QSAR analyses were superimposed on the Plasmodium Falciparum cysteine proteases active site and the main interactions were studied. The present work provides extremely useful guidelines for future structural modifications of this class of compounds towards the development of superior antimalarials.

  12. Proof of Concept of Integrated Load Measurement in 3D Printed Structures

    PubMed Central

    Hinderdael, Michaël; Jardon, Zoé; Lison, Margot; De Baere, Dieter; Devesse, Wim; Strantza, Maria; Guillaume, Patrick

    2017-01-01

    Currently, research on structural health monitoring systems is focused on direct integration of the system into a component or structure. The latter results in a so-called smart structure. One example of a smart structure is a component with integrated strain sensing for continuous load monitoring. Additive manufacturing, or 3D printing, now also enables such integration of functions inside components. As a proof-of-concept, the Fused Deposition Modeling (FDM) technique was used to integrate a strain sensing element inside polymer (ABS) tensile test samples. The strain sensing element consisted of a closed capillary filled with a fluid and connected to an externally mounted pressure sensor. The volumetric deformation of the integrated capillary resulted in pressure changes in the fluid. The obtained pressure measurements during tensile testing are reported in this paper and compared to state-of-the-art extensometer measurements. The sensitivity of the 3D printed pressure-based strain sensor is primarily a function of the compressibility of the capillary fluid. Air- and watertightness are of critical importance for the proper functioning of the 3D printed pressure-based strain sensor. Therefore, the best after-treatment procedure was selected on basis of a comparative analysis. The obtained pressure measurements are linear with respect to the extensometer readings, and the uncertainty on the strain measurement of a capillary filled with water (incompressible fluid) is ±3.1 µstrain, which is approximately three times less sensitive than conventional strain gauges (±1 µstrain), but 32 times more sensitive than the same sensor based on air (compressible fluid) (±101 µstrain). PMID:28208779

  13. Proof of Concept of Integrated Load Measurement in 3D Printed Structures.

    PubMed

    Hinderdael, Michaël; Jardon, Zoé; Lison, Margot; De Baere, Dieter; Devesse, Wim; Strantza, Maria; Guillaume, Patrick

    2017-02-09

    Currently, research on structural health monitoring systems is focused on direct integration of the system into a component or structure. The latter results in a so-called smart structure. One example of a smart structure is a component with integrated strain sensing for continuous load monitoring. Additive manufacturing, or 3D printing, now also enables such integration of functions inside components. As a proof-of-concept, the Fused Deposition Modeling (FDM) technique was used to integrate a strain sensing element inside polymer (ABS) tensile test samples. The strain sensing element consisted of a closed capillary filled with a fluid and connected to an externally mounted pressure sensor. The volumetric deformation of the integrated capillary resulted in pressure changes in the fluid. The obtained pressure measurements during tensile testing are reported in this paper and compared to state-of-the-art extensometer measurements. The sensitivity of the 3D printed pressure-based strain sensor is primarily a function of the compressibility of the capillary fluid. Air- and watertightness are of critical importance for the proper functioning of the 3D printed pressure-based strain sensor. Therefore, the best after-treatment procedure was selected on basis of a comparative analysis. The obtained pressure measurements are linear with respect to the extensometer readings, and the uncertainty on the strain measurement of a capillary filled with water (incompressible fluid) is ±3.1 µstrain, which is approximately three times less sensitive than conventional strain gauges (±1 µstrain), but 32 times more sensitive than the same sensor based on air (compressible fluid) (±101 µstrain).

  14. Modeling the crystal distribution of lead-sulfate in lead-acid batteries with 3D spatial resolution

    NASA Astrophysics Data System (ADS)

    Huck, Moritz; Badeda, Julia; Sauer, Dirk Uwe

    2015-04-01

    For the reliability of lead-acid batteries it is important to have an accurate prediction of its response to load profiles. A model for the lead-sulfate growth is presented, which is embedded in a physical-chemical model with 3D spatial resolution is presented which is used for analyzing the different mechanism influencing the cell response. One import factor is the chemical dissolution and precipitation of lead-sulfate, since its dissolution speed limits the charging reaction and the accumulation of indissolvable of lead-sulfate leads to capacity degradation. The cell performance/behavior is not only determined by the amount of the sulfate but also by the radii and distribution of the crystals. The presented model can be used to for an improved understanding of the interaction of the different mechanisms.

  15. Hierarchical self-assembly of hexagonal single-crystal nanosheets into 3D layered superlattices with high conductivity

    NASA Astrophysics Data System (ADS)

    Tao, Yulun; Shen, Yuhua; Yang, Liangbao; Han, Bin; Huang, Fangzhi; Li, Shikuo; Chu, Zhuwang; Xie, Anjian

    2012-05-01

    While the number of man-made nano superstructures realized by self-assembly is growing in recent years, assemblies of conductive polymer nanocrystals, especially for superlattices, are still a significant challenge, not only because of the simplicity of the shape of the nanocrystal building blocks and their interactions, but also because of the poor control over these parameters in the fabrication of more elaborate nanocrystals. Here, we firstly report a facile and general route to a new generation of 3D layered superlattices of polyaniline doped with CSA (PANI-CSA) and show how PANI crystallize and self-assemble, in a suitable single solution environment. In cyclohexane, 1D amorphous nanofibers transformed to 1D nanorods as building blocks, and then to 2D single-crystal nanosheets with a hexagonal phase, and lastly to 3D ordered layered superlattices with the narrowest polydispersity value (Mw/Mn = 1.47). Remarkably, all the instructions for the hierarchical self-assembly are encoded in the layered shape in other non-polar solvents (hexane, octane) and their conductivity in the π-π stacking direction is improved to about 50 S cm-1, which is even higher than that of the highest previously reported value (16 S cm-1). The method used in this study is greatly expected to be readily scalable to produce superlattices of conductive polymers with high quality and low cost.While the number of man-made nano superstructures realized by self-assembly is growing in recent years, assemblies of conductive polymer nanocrystals, especially for superlattices, are still a significant challenge, not only because of the simplicity of the shape of the nanocrystal building blocks and their interactions, but also because of the poor control over these parameters in the fabrication of more elaborate nanocrystals. Here, we firstly report a facile and general route to a new generation of 3D layered superlattices of polyaniline doped with CSA (PANI-CSA) and show how PANI crystallize and

  16. 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.

  17. 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

  18. 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.

  19. Interactive 3D visualization of structural changes in the brain of a person with corticobasal syndrome.

    PubMed

    Hänel, Claudia; Pieperhoff, Peter; Hentschel, Bernd; Amunts, Katrin; Kuhlen, Torsten

    2014-01-01

    The visualization of the progression of brain tissue loss in neurodegenerative diseases like corticobasal syndrome (CBS) can provide not only information about the localization and distribution of the volume loss, but also helps to understand the course and the causes of this neurodegenerative disorder. The visualization of such medical imaging data is often based on 2D sections, because they show both internal and external structures in one image. Spatial information, however, is lost. 3D visualization of imaging data is capable to solve this problem, but it faces the difficulty that more internally located structures may be occluded by structures near the surface. Here, we present an application with two designs for the 3D visualization of the human brain to address these challenges. In the first design, brain anatomy is displayed semi-transparently; it is supplemented by an anatomical section and cortical areas for spatial orientation, and the volumetric data of volume loss. The second design is guided by the principle of importance-driven volume rendering: A direct line-of-sight to the relevant structures in the deeper parts of the brain is provided by cutting out a frustum-like piece of brain tissue. The application was developed to run in both, standard desktop environments and in immersive virtual reality environments with stereoscopic viewing for improving the depth perception. We conclude, that the presented application facilitates the perception of the extent of brain degeneration with respect to its localization and affected regions.

  20. Sequence co-evolution gives 3D contacts and structures of protein complexes

    PubMed Central

    Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

    2014-01-01

    Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution. DOI: http://dx.doi.org/10.7554/eLife.03430.001 PMID:25255213