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Sample records for 3d dna crystal

  1. Time lapse microscopy of temperature control during self-assembly of 3D DNA crystals

    Science.gov (United States)

    Conn, Fiona W.; Jong, Michael Alexander; Tan, Andre; Tseng, Robert; Park, Eunice; Ohayon, Yoel P.; Sha, Ruojie; Mao, Chengde; Seeman, Nadrian C.

    2017-10-01

    DNA nanostructures are created by exploiting the high fidelity base-pairing interactions of double-stranded branched DNA molecules. These structures present a convenient medium for the self-assembly of macroscopic 3D crystals. In some self-assemblies in this system, crystals can be formed by lowering the temperature, and they can be dissolved by raising it. The ability to monitor the formation and melting of these crystals yields information that can be used to monitor crystal formation and growth. Here, we describe the development of an inexpensive tool that enables direct observation of the crystal growth process as a function of both time and temperature. Using the hanging-drop crystallization of the well-characterized 2-turn DNA tensegrity triangle motif for our model system, its response to temperature has been characterized visually.

  2. A device that operates within a self-assembled 3D DNA crystal

    Science.gov (United States)

    Hao, Yudong; Kristiansen, Martin; Sha, Ruojie; Birktoft, Jens J.; Hernandez, Carina; Mao, Chengde; Seeman, Nadrian C.

    2017-08-01

    Structural DNA nanotechnology finds applications in numerous areas, but the construction of objects, 2D and 3D crystalline lattices and devices is prominent among them. Each of these components has been developed individually, and most of them have been combined in pairs. However, to date there are no reports of independent devices contained within 3D crystals. Here we report a three-state 3D device whereby we change the colour of the crystals by diffusing strands that contain dyes in or out of the crystals through the mother-liquor component of the system. Each colouring strand is designed to pair with an extended triangle strand by Watson-Crick base pairing. The arm that contains the dyes is quite flexible, but it is possible to establish the presence of the duplex proximal to the triangle by X-ray crystallography. We modelled the transition between the red and blue states through a simple kinetic model.

  3. Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, Chad R.; Zhang, Fei; MacCulloch, Tara; Fahmi, Noureddine; Stephanopoulos, Nicholas; Liu, Yan; Seeman, Nadrian C. [Department; Yan, Hao

    2017-08-02

    The foundational goal of structural DNA nanotechnology—the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems—was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest–DNA conjugates with a specified crystalline hand.

  4. From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, J.; Birktoft, J; Yi, C; Tong, W; Ruojie, S; Constantinou, P; Ginell, S; Chenge, M; Seeman, N

    2009-01-01

    We live in a macroscopic three-dimensional (3D) world, but our best description of the structure of matter is at the atomic and molecular scale. Understanding the relationship between the two scales requires a bridge from the molecular world to the macroscopic world. Connecting these two domains with atomic precision is a central goal of the natural sciences, but it requires high spatial control of the 3D structure of matter1. The simplest practical route to producing precisely designed 3D macroscopic objects is to form a crystalline arrangement by self-assembly, because such a periodic array has only conceptually simple requirements: a motif that has a robust 3D structure, dominant affinity interactions between parts of the motif when it self-associates, and predictable structures for these affinity interactions. Fulfilling these three criteria to produce a 3D periodic system is not easy, but should readily be achieved with well-structured branched DNA motifs tailed by sticky ends2. Complementary sticky ends associate with each other preferentially and assume the well-known B-DNA structure when they do so3; the helically repeating nature of DNA facilitates the construction of a periodic array. It is essential that the directions of propagation associated with the sticky ends do not share the same plane, but extend to form a 3D arrangement of matter. Here we report the crystal structure at 4?Angstroms resolution of a designed, self-assembled, 3D crystal based on the DNA tensegrity triangle4. The data demonstrate clearly that it is possible to design and self-assemble a well-ordered macromolecular 3D crystalline lattice with precise control.

  5. DNA biosensing with 3D printing technology.

    Science.gov (United States)

    Loo, Adeline Huiling; Chua, Chun Kiang; Pumera, Martin

    2017-01-16

    3D printing, an upcoming technology, has vast potential to transform conventional fabrication processes due to the numerous improvements it can offer to the current methods. To date, the employment of 3D printing technology has been examined for applications in the fields of engineering, manufacturing and biological sciences. In this study, we examined the potential of adopting 3D printing technology for a novel application, electrochemical DNA biosensing. Metal 3D printing was utilized to construct helical-shaped stainless steel electrodes which functioned as a transducing platform for the detection of DNA hybridization. The ability of electroactive methylene blue to intercalate into the double helix structure of double-stranded DNA was then exploited to monitor the DNA hybridization process, with its inherent reduction peak serving as an analytical signal. The designed biosensing approach was found to demonstrate superior selectivity against a non-complementary DNA target, with a detection range of 1-1000 nM.

  6. DNA origami design of 3D nanostructures

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth; Nielsen, Morten Muhlig

    2009-01-01

    , several dedicated 3D editors for computer-aided design of DNA structures have been developed [4-7]. However, many of these tools are not efficient for designing DNA origami structures that requires the design of more than 200 unique DNA strands to be folded along a scaffold strand into a defined 3D shape......Structural DNA nanotechnology has been heavily dependent on the development of dedicated software tools for the design of unique helical junctions, to define unique sticky-ends for tile assembly, and for predicting the products of the self-assembly reaction of multiple DNA strands [1-3]. Recently...... [8]. We have recently developed a semi-automated DNA origami software package [9] that uses a 2D sequence editor in conjunction with several automated tools to facilitate the design process. Here we extend the use of the program for designing DNA origami structures in 3D and show the application...

  7. DNA Assembly in 3D Printed Fluidics.

    Directory of Open Access Journals (Sweden)

    William G Patrick

    Full Text Available The process of connecting genetic parts-DNA assembly-is a foundational technology for synthetic biology. Microfluidics present an attractive solution for minimizing use of costly reagents, enabling multiplexed reactions, and automating protocols by integrating multiple protocol steps. However, microfluidics fabrication and operation can be expensive and requires expertise, limiting access to the technology. With advances in commodity digital fabrication tools, it is now possible to directly print fluidic devices and supporting hardware. 3D printed micro- and millifluidic devices are inexpensive, easy to make and quick to produce. We demonstrate Golden Gate DNA assembly in 3D-printed fluidics with reaction volumes as small as 490 nL, channel widths as fine as 220 microns, and per unit part costs ranging from $0.61 to $5.71. A 3D-printed syringe pump with an accompanying programmable software interface was designed and fabricated to operate the devices. Quick turnaround and inexpensive materials allowed for rapid exploration of device parameters, demonstrating a manufacturing paradigm for designing and fabricating hardware for synthetic biology.

  8. Optical experiments on 3D photonic crystals

    NARCIS (Netherlands)

    Koenderink, F.; Vos, W.

    2003-01-01

    Photonic crystals are optical materials that have an intricate structure with length scales of the order of the wavelength of light. The flow of photons is controlled in a manner analogous to how electrons propagate through semiconductor crystals, i.e., by Bragg diffraction and the formation of band

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

    Science.gov (United States)

    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.

  10. DNA origami design of 3D nanostructures

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth; Nielsen, Morten Muhlig

    2009-01-01

    Structural DNA nanotechnology has been heavily dependent on the development of dedicated software tools for the design of unique helical junctions, to define unique sticky-ends for tile assembly, and for predicting the products of the self-assembly reaction of multiple DNA strands [1-3]. Recently...

  11. 3D-DART: a DNA structure modelling server

    NARCIS (Netherlands)

    van Dijk, M.; Bonvin, A.M.J.J.

    2009-01-01

    There is a growing interest in structural studies of DNA by both experimental and computational approaches. Often, 3D-structural models of DNA are required, for instance, to serve as templates for homology modeling, as starting structures for macro-molecular docking or as scaffold for NMR structure

  12. 3D Framework DNA Origami with Layered Crossovers.

    Science.gov (United States)

    Hong, Fan; Jiang, Shuoxing; Wang, Tong; Liu, Yan; Yan, Hao

    2016-10-04

    Designer DNA architectures with nanoscale geometric controls provide a programmable molecular toolbox for engineering complex nanodevices. Scaffolded DNA origami has dramatically improved our ability to design and construct DNA nanostructures with finite size and spatial addressability. Here we report a novel design strategy to engineer multilayered wireframe DNA structures by introducing crossover pairs that connect neighboring layers of DNA double helices. These layered crossovers (LX) allow the scaffold or helper strands to travel through different layers and can control the relative orientation of DNA helices in neighboring layers. Using this design strategy, we successfully constructed four versions of two-layer parallelogram structures with well-defined interlayer angles, a three-layer structure with triangular cavities, and a 9- and 15-layer square lattices. This strategy provides a general route to engineer 3D framework DNA nanostructures with controlled cavities and opportunities to design host-guest networks analogs to those produced with metal organic frameworks.

  13. Functionalizing Designer DNA Crystals

    Science.gov (United States)

    Chandrasekaran, Arun Richard

    Three-dimensional crystals have been self-assembled from a DNA tensegrity triangle via sticky end interaction. The tensegrity triangle is a rigid DNA motif containing three double helical edges connected pair-wise by three four-arm junctions. The symmetric triangle contains 3 unique strands combined in a 3:3:1 ratio: 3 crossover, 3 helical and 1 central. The length of the sticky end reported previously was two nucleotides (nt) (GA:TC) and the motif with 2-helical turns of DNA per edge diffracted to 4.9 A at beam line NSLS-X25 and to 4 A at beam line ID19 at APS. The purpose of these self-assembled DNA crystals is that they can be used as a framework for hosting external guests for use in crystallographic structure solving or the periodic positioning of molecules for nanoelectronics. This thesis describes strategies to improve the resolution and to incorporate guests into the 3D lattice. The first chapter describes the effect of varying sticky end lengths and the influence of 5'-phosphate addition on crystal formation and resolution. X-ray diffraction data from beam line NSLS-X25 revealed that the crystal resolution for 1-nt (G:C) sticky end was 3.4 A. Motifs with every possible combination of 1-nt and 2-nt sticky-ended phosphorylated strands were crystallized and X-ray data were collected. The position of the 5'-phosphate on either the crossover (strand 1), helical (strand 2), or central strand (3) had an impact on the resolution of the self-assembled crystals with the 1-nt 1P-2-3 system diffracting to 2.62 A at APS and 3.1 A at NSLS-X25. The second chapter describes the sequence-specific recognition of DNA motifs with triplex-forming oligonucleotides (TFOs). This study examined the feasibility of using TFOs to bind to specific locations within a 3-turn DNA tensegrity triangle motif. The TFO 5'-TTCTTTCTTCTCT was used to target the tensegrity motif containing an appropriately embedded oligopurine.oligopyrimidine binding site. As triplex formation involving cytidine

  14. Large Area Printing of 3D Photonic Crystals

    Science.gov (United States)

    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.

  15. 3D electron tomography of biological photonic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Butz, Benjamin; Winter, Benjamin; Vieweg, Benito; Knoke, Isabel; Spallek, Stefanie; Spiecker, Erdmann [CENEM, Universitaet Erlangen-Nuernberg (Germany); Schroeder-Turk, Gerd; Mecke, Klaus [Theoretische Physik I, Universitaet Erlangen-Nuernberg (Germany)

    2011-07-01

    Photonic crystals, i.e. periodical nanostructures of materials with different dielectric constants, are highly interesting for applications in optics, optoelectronics, and sensing. By tailoring the geometrical parameters radically different and improved optical properties (e.g., optical band-gap structure, extreme refractive indices, or high anisotropy) can be achieved. Naturally occurring photonic crystals, like butterfly scales, exoskeletons of insects (chitin), or seashells (nacre), can serve as model systems for understanding the relationship between structure and optical properties. Butterfly scales are studied by TEM using a FEI Titan{sup 3} 80-300 instrument. An optimized FIB technique or ultramicrotome sectioning were used to prepare the sensitive specimens with desired thickness. Since the periodical structures have dimensions on the sub-{mu}m scale, HAADF-STEM tomography was employed for obtaining extended tilt series under conditions of atomic-number sensitive imaging. Since the solid crystal consists of chemically homogeneous chitin while the pores are unfilled, the distinct contrast in the images can easily be interpreted in terms of the local projected mass density allowing to reconstruct the chitin distribution within the optical unit cell of the scales with high 3D resolution.

  16. Optical properties of 3d-ions in crystals spectroscopy and crystal field analysis

    CERN Document Server

    Brik, Mikhail

    2013-01-01

    "Optical Properties of 3d-Ions in Crystals: Spectroscopy and Crystal Field Analysis" discusses spectral, vibronic and magnetic properties of 3d-ions in a wide range of crystals, used as active media for solid state lasers and potential candidates for this role. Crystal field calculations (including first-principles calculations of energy levels and absorption spectra) and their comparison with experimental spectra, the Jahn-Teller effect, analysis of vibronic spectra, materials science applications are systematically presented. The book is intended for researchers and graduate students in crystal spectroscopy, materials science and optical applications. Dr. N.M. Avram is an Emeritus Professor at the Physics Department, West University of Timisoara, Romania; Dr. M.G. Brik is a Professor at the Institute of Physics, University of Tartu, Estonia.

  17. Programmatic conversion of crystal structures into 3D printable files using Jmol

    OpenAIRE

    Scalfani, Vincent F.; Williams, Antony J.; Tkachenko, Valery; Karapetyan, Karen; Pshenichnov, Alexey; Hanson, Robert M; Liddie, Jahred M.; Bara, Jason E.

    2016-01-01

    Background Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files. Results A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from...

  18. Flexible Holographic Fabrication of 3D Photonic Crystal Templates with Polarization Control through a 3D Printed Reflective Optical Element

    Directory of Open Access Journals (Sweden)

    David Lowell

    2016-07-01

    Full Text Available In this paper, we have systematically studied the holographic fabrication of three-dimensional (3D structures using a single 3D printed reflective optical element (ROE, taking advantage of the ease of design and 3D printing of the ROE. The reflective surface was setup at non-Brewster angles to reflect both s- and p-polarized beams for the interference. The wide selection of reflective surface materials and interference angles allow control of the ratio of s- and p-polarizations, and intensity ratio of side-beam to central beam for interference lithography. Photonic bandgap simulations have also indicated that both s and p-polarized waves are sometimes needed in the reflected side beams for maximum photonic bandgap size and certain filling fractions of dielectric inside the photonic crystals. The flexibility of single ROE and single exposure based holographic fabrication of 3D structures was demonstrated with reflective surfaces of ROEs at non-Brewster angles, highlighting the capability of the ROE technique of producing umbrella configurations of side beams with arbitrary angles and polarizations and paving the way for the rapid throughput of various photonic crystal templates.

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

    Science.gov (United States)

    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…

  20. 3D Printed Fluidic Hardware for DNA Assembly

    Science.gov (United States)

    2015-04-10

    printed parts. The 3D printed parts were designed in SolidWorks and printed using the Makerbot Replicator 2X. The printed parts are modular, enabling...this study had multiple years of experience working with SolidWorks . Many biologists interested in designing fluidics will likely not have similar...Methods Designing & 3D printing fluidics All fluidic devices were designed using SolidWorks . STL files were generated in SolidWorks . For 3D printing

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

    Science.gov (United States)

    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.

  2. IR Sensor Synchronizing Active Shutter Glasses for 3D HDTV with Flexible Liquid Crystal Lenses

    Directory of Open Access Journals (Sweden)

    Jeong In Han

    2013-12-01

    Full Text Available IR sensor synchronizing active shutter glasses for three-dimensional high definition television (3D HDTV were developed using a flexible liquid crystal (FLC lens. The FLC lens was made on a polycarbonate (PC substrate using conventional liquid crystal display (LCD processes. The flexible liquid crystal lens displayed a maximum transmission of 32% and total response time of 2.56 ms. The transmittance, the contrast ratio and the response time of the flexible liquid crystal lens were superior to those of glass liquid crystal lenses. Microcontroller unit and drivers were developed as part of a reception module with power supply for the IR sensor synchronizing active shutter glasses with the flexible liquid crystal lens prototypes. IR sensor synchronizing active shutter glasses for 3D HDTV with flexible liquid crystal lenses produced excellent 3D images viewing characteristics.

  3. Serum induced degradation of 3D DNA box origami observed by high speed atomic force microscope

    DEFF Research Database (Denmark)

    Jiang, Zaixing; Zhang, Shuai; Yang, Chuanxu;

    2015-01-01

    3D DNA origami holds tremendous potential to encapsulate and selectively release therapeutic drugs. Observations of real-time performance of 3D DNA origami structures in physiological environment will contribute much to its further applications. Here, we investigate the degradation kinetics of 3D...... DNA box origami in serum using high-speed atomic force microscope optimized for imaging 3D DNA origami in real time. The time resolution allows characterizing the stages of serum effects on individual 3D DNA box origami with nanometer resolution. Our results indicate that the whole digest process...... is a combination of a rapid collapse phase and a slow degradation phase. The damages of box origami mainly happen in the collapse phase. Thus, the structure stability of 3D DNA box origami should be further improved, especially in the collapse phase, before clinical applications...

  4. IR Sensor Synchronizing Active Shutter Glasses for 3D HDTV with Flexible Liquid Crystal Lenses

    OpenAIRE

    Jeong In Han

    2013-01-01

    IR sensor synchronizing active shutter glasses for three-dimensional high definition television (3D HDTV) were developed using a flexible liquid crystal (FLC) lens. The FLC lens was made on a polycarbonate (PC) substrate using conventional liquid crystal display (LCD) processes. The flexible liquid crystal lens displayed a maximum transmission of 32% and total response time of 2.56 ms. The transmittance, the contrast ratio and the response time of the flexible liquid crystal lens were superio...

  5. 3-D Crystal Tectonics of Red Coral (Corallium Rubrum)

    Science.gov (United States)

    Vielzeuf, D.; Garrabou, J.; Baronnet, A.; Grauby, O.; Marschal, C.

    2007-12-01

    A combination of analytical techniques (petrographic microscopy, SEM, TEM, and EMP) has been used to characterize the internal physico-chemical structure of the red coral (corallium rubrum) skeleton. A section normal to the skeleton axis shows an inner medullar zone with a bulbous-tip cross shape, surrounded by a large circular domain composed of concentric rings (width of each ring ca 150 microns). Growth rings are revealed by the cyclic variation of concentration of the organic matter (OM) and oscillations of the Mg/Ca ratio. Experiments carried out in natural environment show that the detected growth rings are annual. Thus, both oscillations of concentration of OM and Mg/Ca ratio can be used to determine the age of the red coral colonies, some of which can be as old as a few tens (or even a few hundreds) of years. Concentric ring are riddled and display a succession of wavelets (wavelength ca 300 microns). The internal structure of each wavelet is complex, both physically and chemically: it is formed by the accumulation of strata with locally tortuous interfaces due to the presence of micro protuberances (ca 30 microns). This interlocked structure confers an exceptional stiffness on the red coral skeleton. Interfaces between strata sometimes display sharp discontinuities indicating interruption of the mineralizing process. This fact has important consequences on the ability of the whole structure to register external forcings with accuracy. SEM and TEM studies show that each stratum is made of submicron crystalline units (ca 200 nm) organized or not in polycrystalline fibers or blades (ca 1 to 10 microns). Porosity can be observed at all scales between the various structural units. HRTEM studies show that in spite of displaying single crystal scattering behavior, the submicron crystalline units are made of 2-5 nm nanodomains with intercalated nanopores. We interpret the nanodomains as nanograins aggregated by a mechanism of oriented attachment. The red coral

  6. Proteopedia: 3D Visualization and Annotation of Transcription Factor-DNA Readout Modes

    Science.gov (United States)

    Dantas Machado, Ana Carolina; Saleebyan, Skyler B.; Holmes, Bailey T.; Karelina, Maria; Tam, Julia; Kim, Sharon Y.; Kim, Keziah H.; Dror, Iris; Hodis, Eran; Martz, Eric; Compeau, Patricia A.; Rohs, Remo

    2012-01-01

    3D visualization assists in identifying diverse mechanisms of protein-DNA recognition that can be observed for transcription factors and other DNA binding proteins. We used Proteopedia to illustrate transcription factor-DNA readout modes with a focus on DNA shape, which can be a function of either nucleotide sequence (Hox proteins) or base pairing…

  7. Optical parametric oscillators in isotropic photonic crystals and cavities: 3D time domain analysis

    OpenAIRE

    Conti, Claudio; Di Falco, Andrea; Assanto, Gaetano

    2004-01-01

    We investigate optical parametric oscillations through four-wave mixing in resonant cavities and photonic crystals. The theoretical analysis underlines the relevant features of the phenomenon and the role of the density of states. Using fully vectorial 3D time-domain simulations, including both dispersion and nonlinear polarization, for the first time we address this process in a face centered cubic lattice and in a photonic crystal slab. The results lead the way to the development of novel p...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  10. Ultralow-loss 3-dB photonic crystal waveguide splitter

    DEFF Research Database (Denmark)

    Frandsen, Lars Hagedorn; Borel, Peter Ingo; Zhuang, Yanxin;

    2004-01-01

    A photonic crystal waveguide splitter that exhibits ultralow-loss 3-dB splitting for TE-polarized light is fabricated in silicon-on-insulator material by use of deep UV lithography. The high performance is achieved by use of a Y junction, which is designed to ensure single-mode operation, and low...

  11. Resource-saving application of FDTD technique in 3D photonic crystal waveguide calculations

    DEFF Research Database (Denmark)

    Lavrinenko, Andrei; Tromborg, Bjarne

    2002-01-01

    This paper presents an algorithm based on the well-known FDTD numerical method which is adapted for 3D problems of transmission and reflection of photonic crystal waveguides, and which effectively saves memory and computing resources. Specific examples showing its validity and effectiveness...

  12. Bulk crystal growth and electronic characterization of the 3D Dirac semimetal Na3Bi

    Directory of Open Access Journals (Sweden)

    Satya K. Kushwaha

    2015-04-01

    Full Text Available High quality hexagon plate-like Na3Bi 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 Na3Bi. In transport measurements on Na3Bi crystals, the linear magnetoresistance and Shubnikov-de Haas quantum oscillations are observed for the first time.

  13. Reflectivity calculated for a 3D silicon photonic band gap crystal with finite support

    CERN Document Server

    Devashish, D; van der Vegt, J J W; Vos, Willem L

    2016-01-01

    We study numerically the reflectivity of three-dimensional (3D) photonic crystals with a complete 3D photonic band gap, with the aim to interpret recent experiments. We employ the finite element method to study crystals with the cubic diamond-like inverse woodpile structure. The high-index backbone has a dielectric function similar to silicon. We study crystals with a range of thicknesses up to ten unit cells ($L \\leq 10 c$). The crystals are surrounded by vacuum, and have a finite support as in experiments. The polarization-resolved reflectivity spectra reveal Fabry-P{\\'e}rot fringes related to standing waves in the finite crystal, as well as broad stop bands with nearly $100~\\%$ reflectivity, even for thin crystals. From the strong reflectivity peaks, it is inferred that the maximum reflectivity observed in experiments is not limited by finite size. The frequency ranges of the stop bands are in excellent agreement with stop gaps in the photonic band structure, that pertain to infinite and perfect crystals. ...

  14. Construction of a 4 Zeptoliters Switchable 3D DNA Box Origami

    DEFF Research Database (Denmark)

    Zadegan, Reza Mohammad; Jepsen, Mette DE; Thomsen, Karen E

    2012-01-01

    The DNA origami technique is a recently developed self-assembly method that allows construction of 3D objects at the nanoscale for various applications. In the current study we report the production of a 18 × 18 × 24 nm3 hollow DNA box origami structure with a switchable lid. The structure was ef...

  15. Rigorous analysis of an electric-field-driven liquid crystal lens for 3D displays

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Bong-Sik; Lee, Seung-Chul; Park, Woo-Sang [Inha University, Incheon (Korea, Republic of)

    2014-08-15

    We numerically analyzed the optical performance of an electric field driven liquid crystal (ELC) lens adopted for 3-dimensional liquid crystal displays (3D-LCDs) through rigorous ray tracing. For the calculation, we first obtain the director distribution profile of the liquid crystals by using the Erickson-Leslie motional equation; then, we calculate the transmission of light through the ELC lens by using the extended Jones matrix method. The simulation was carried out for a 9 view 3D-LCD with a diagonal of 17.1 inches, where the ELC lens was slanted to achieve natural stereoscopic images. The results show that each view exists separately according to the viewing position at an optimum viewing distance of 80 cm. In addition, our simulation results provide a quantitative explanation for the ghost or blurred images between views observed from a 3D-LCD with an ELC lens. The numerical simulations are also shown to be in good agreement with the experimental results. The present simulation method is expected to provide optimum design conditions for obtaining natural 3D images by rigorously analyzing the optical functionalities of an ELC lens.

  16. Crystallization of Mefenamic Acid from Dimethylformamide Microemulsions: Obtaining Thermodynamic Control through 3D Nanoconfinement

    Directory of Open Access Journals (Sweden)

    Catherine E. Nicholson

    2011-09-01

    Full Text Available Recently we showed how crystallization in microemulsions could lead directly to the most stable polymorph, thereby leapfrogging Ostwald’s rule of stages. Here we consider in more details the crystallization of mefenamic acid from dimethylformamide microemulsions. Crystallization of mefenamic acid from bulk DMF has previously been shown to produce only the metastable Form II irrespective of the supersaturation or temperature. In contrast, we show that stable Form I can be produced from DMF microemulsions provided the lowest supersaturations that can achieve crystallization are used; these correspond to initial supersaturations that are significantly higher than those commonly used in bulk solution crystallizations, owing to the large decrease in supersaturation that occurs when a nuclei grows in a 3D-nanoconfined droplet. Increasing the supersaturation above the minimum required for crystallization leads to increasing proportions of metastable Form II crystals. In compositions crystallizing a mixture of Form I and Form II crystals, the Form I crystals can nevertheless be obtained exclusively by slowly heating the microemulsions.

  17. Modeling and experimental verification of an ultra-wide bandgap in 3D phononic crystal

    Science.gov (United States)

    D'Alessandro, L.; Belloni, E.; Ardito, R.; Corigliano, A.; Braghin, F.

    2016-11-01

    This paper reports a comprehensive modeling and experimental characterization of a three-dimensional phononic crystal composed of a single material, endowed with an ultra-wide complete bandgap. The phononic band structure shows a gap-mid gap ratio of 132% that is by far the greatest full 3D bandgap in literature for any kind of phononic crystals. A prototype of the finite crystal structure has been manufactured in polyamide by means of additive manufacturing technology and tested to assess the transmission spectrum of the crystal. The transmission spectrum has been numerically calculated taking into account a frequency-dependent elastic modulus and a Rayleigh model for damping. The measured and numerical transmission spectra are in good agreement and present up to 75 dB of attenuation for a three-layer crystal.

  18. Predicting DNA-binding sites of proteins based on sequential and 3D structural information.

    Science.gov (United States)

    Li, Bi-Qing; Feng, Kai-Yan; Ding, Juan; Cai, Yu-Dong

    2014-06-01

    Protein-DNA interactions play important roles in many biological processes. To understand the molecular mechanisms of protein-DNA interaction, it is necessary to identify the DNA-binding sites in DNA-binding proteins. In the last decade, computational approaches have been developed to predict protein-DNA-binding sites based solely on protein sequences. In this study, we developed a novel predictor based on support vector machine algorithm coupled with the maximum relevance minimum redundancy method followed by incremental feature selection. We incorporated not only features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure, solvent accessibility, but also five three-dimensional (3D) structural features calculated from PDB data to predict the protein-DNA interaction sites. Feature analysis showed that 3D structural features indeed contributed to the prediction of DNA-binding site and it was demonstrated that the prediction performance was better with 3D structural features than without them. It was also shown via analysis of features from each site that the features of DNA-binding site itself contribute the most to the prediction. Our prediction method may become a useful tool for identifying the DNA-binding sites and the feature analysis described in this paper may provide useful insights for in-depth investigations into the mechanisms of protein-DNA interaction.

  19. A 3D-DNA Molecule Made of PlayMais

    Science.gov (United States)

    Caine, Massimo; Horié, Ninon; Zuchuat, Sandrine; Weber, Aurélia; Ducret, Verena; Linder, Patrick; Perron, Karl

    2015-01-01

    More than 60 years have passed since the work of Rosalind Franklin, James Watson, and Francis Crick led to the discovery of the 3D-DNA double-helix structure. Nowadays, due to the simple and elegant architecture of its double helix, the structure of DNA is widely known. The biological role of the DNA molecule (e.g., genetic information), however,…

  20. Confocal 3D DNA Cytometry: Assessment of Required Coefficient of Variation by Computer Simulation

    Directory of Open Access Journals (Sweden)

    Lennert S. Ploeger

    2004-01-01

    Full Text Available Background: Confocal Laser Scanning Microscopy (CLSM provides the opportunity to perform 3D DNA content measurements on intact cells in thick histological sections. So far, sample size has been limited by the time consuming nature of the technology. Since the power of DNA histograms to resolve different stemlines depends on both the sample size and the coefficient of variation (CV of histogram peaks, interpretation of 3D CLSM DNA histograms might be hampered by both a small sample size and a large CV. The aim of this study was to analyze the required CV for 3D CLSM DNA histograms given a realistic sample size. Methods: By computer simulation, virtual histograms were composed for sample sizes of 20000, 10000, 5000, 1000, and 273 cells and CVs of 30, 25, 20, 15, 10 and 5%. By visual inspection, the histogram quality with respect to resolution of G0/1 and G2/M peaks of a diploid stemline was assessed. Results: As expected, the interpretability of DNA histograms deteriorated with decreasing sample sizes and higher CVs. For CVs of 15% and lower, a clearly bimodal peak pattern with well distinguishable G0/1 and G2/M peaks were still seen at a sample size of 273 cells, which is our current average sample size with 3D CLSM DNA cytometry. Conclusions: For unambiguous interpretation of DNA histograms obtained using 3D CLSM, a CV of at most 15% is tolerable at currently achievable sample sizes. To resolve smaller near diploid stemlines, a CV of 10% or better should be aimed at. With currently available 3D imaging technology, this CV is achievable.

  1. ADN-Viewer: a 3D approach for bioinformatic analyses of large DNA sequences.

    Science.gov (United States)

    Hérisson, Joan; Ferey, Nicolas; Gros, Pierre-Emmanuel; Gherbi, Rachid

    2007-01-20

    Most of biologists work on textual DNA sequences that are limited to the linear representation of DNA. In this paper, we address the potential offered by Virtual Reality for 3D modeling and immersive visualization of large genomic sequences. The representation of the 3D structure of naked DNA allows biologists to observe and analyze genomes in an interactive way at different levels. We developed a powerful software platform that provides a new point of view for sequences analysis: ADNViewer. Nevertheless, a classical eukaryotic chromosome of 40 million base pairs requires about 6 Gbytes of 3D data. In order to manage these huge amounts of data in real-time, we designed various scene management algorithms and immersive human-computer interaction for user-friendly data exploration. In addition, one bioinformatics study scenario is proposed.

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

    Science.gov (United States)

    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

  3. Maximum-likelihood Estimation of 3D Event Position in Monolithic Scintillation Crystals: Experimental Results

    OpenAIRE

    Moore, S K; Hunter, W C J; Furenlid, L.R.; Barrett, H. H.

    2007-01-01

    We present a simple 3D event position-estimation method using raw list-mode acquisition and maximum-likelihood estimation in a modular gamma camera with a thick (25mm) monolithic scintillation crystal. This method involves measuring 2D calibration scans with a well-collimated 511 keV source and fitting each point to a simple depth-dependent light distribution model. Preliminary results show that angled collimated beams appear properly reconstructed.

  4. 3D position determination in monolithic crystals coupled to SiPMs for PET.

    Science.gov (United States)

    Etxebeste, Ane; Barrio, John; Muñoz, Enrique; Oliver, Josep F; Solaz, Carles; Llosá, Gabriela

    2016-05-21

    The interest in using continuous monolithic crystals in positron emission tomography (PET) has grown in the last years. Coupled to silicon photomultipliers (SiPMs), the detector can combine high sensitivity and high resolution, the two main factors to be maximized in a positron emission tomograph. In this work, the position determination capability of a detector comprised of a [Formula: see text] mm(3) LYSO crystal coupled to an [Formula: see text]-pixel array of SiPMs is evaluated. The 3D interaction position of γ-rays is estimated using an analytical model of the light distribution including reflections on the facets of the crystal. Monte Carlo simulations have been performed to evaluate different crystal reflectors and geometries. The method has been characterized and applied to different cases. Intrinsic resolution obtained with the position estimation method used in this work, applied to experimental data, achieves sub-millimetre resolution values. Average resolution over the detector surface for 5 mm thick crystal is  ∼0.9 mm FWHM and  ∼1.2 mm FWHM for 10 mm thick crystal. Depth of interaction resolution is close to 2 mm FWHM in both cases, while the FWTM is  ∼5.3 mm for 5 mm thick crystal and  ∼9.6 mm for 10 mm thick crystal.

  5. Confined Growth of Metal Nanoparticles Within 3D DNA Origami Molds.

    Science.gov (United States)

    Sun, Wei; Shen, Jie

    2017-01-01

    Manufacturing prescribed shaped metal nanoparticles promises emerging applications in plasmonics, energy, and disease diagnosis. The key to the shape-controllable synthesis is generating local environments encoded with prescribed geometrical information. Here, we describe a general strategy that uses 3D self-assembled DNA origami as mold to confine the casting growth of metal nanoparticle. By transferring the shape information from DNA cavities to metal nanoparticles, metal nanoparticles with prescribed shapes, dimensions, and surface binding features could be rationally designed and synthesized.

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

    Science.gov (United States)

    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.

  7. Phase singularities in 3D plasmonic crystal metamaterials for ultra-sensitive biosensing

    Science.gov (United States)

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

    2017-02-01

    Plasmonic biosensors form the core label-free technology for studies of biomolecular interactions, but they still need a drastic improvement of sensitivity and novel nano-architectural implementations to match modern trends of nanobiotechnology. Here, we consider the generation of resonances in light reflected from 3D woodpile plasmonic crystal metamaterials fabricated by Direct Laser Writing by Multi-Photon Polymerization, followed by silver electroless plating. We show that the generation of these resonances is accompanied by the appearance of singularities of phase of reflected light and examine the response of phase characteristics to refractive index variations inside the metamaterial matrix. The recorded phase sensitivity (3*104 deg. of phase shift per RIU change) outperforms most plasmonic counterparts and is attributed to particular conditions of plasmon excitation in 3D plasmonic crystal geometry. Combined with a large surface for biomolecular immobilizations offered by the 3D woodpile matrix, the proposed sensor architecture promises a new important landmark in the advancement of plasmonic biosensing technology.

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

    Science.gov (United States)

    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.

  9. Simulating 3D $Z_2$ Topological Nodes in Nonsymmorphic Photonic Crystals

    CERN Document Server

    Wang, Hai-Xiao; Hang, Zhi Hong; Chen, Huanyang; Kee, Hae-Young; Jiang, Jian-Hua

    2016-01-01

    We propose an all-dielectric, space-time reversal symmetric photonics-crystal architecture that possess 3D Dirac points and line-nodes with nontrivial $Z_2$ topological charge, which can be realized at infrared and microwave frequencies. The protected degeneracy of bands is achieved via nonsymmorphic symmetries despite the lack of Kramers degeneracy in photonic crystal systems. Two orthogonal screw axes lead to 3D $Z_2$ Dirac points on high symmetry Brillouin zone (BZ) boundary line. On the other hand, twofold $Z_2$ line-nodes appear around the $\\Gamma$-point due to a combination of nonsymmorphic and point-group symmetries. The lowest line-node is deterministic because of degeneracy partner switching between Bloch states with opposite parities. A pair of Fermi arcs associated with $Z_2$ topological charge is emerged below light-line and protected by total internal reflection on certain photonic-crystal-air interfaces. These robust surface states offer an unique opportunity to realize "open cavity" with strong...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  12. Monitoring the Activation of the DNA Damage Response Pathway in a 3D Spheroid Model.

    Science.gov (United States)

    Mondesert, Odile; Frongia, Céline; Clayton, Olivia; Boizeau, Marie-Laure; Lobjois, Valérie; Ducommun, Bernard

    2015-01-01

    Monitoring the DNA-Damage Response (DDR) activated pathway in multicellular tumor spheroid models is an important challenge as these 3D models have demonstrated their major relevance in pharmacological evaluation. Herein we present DDR-Act-FP, a fluorescent biosensor that allows detection of DDR activation through monitoring of the p21 promoter p53-dependent activation. We show that cells expressing the DDR-Act-FP biosensor efficiently report activation of the DDR pathway after DNA damage and its pharmacological manipulation using ATM kinase inhibitors. We also report the successful use of this assay to screen a small compound library in order to identify activators of the DDR response. Finally, using multicellular spheroids expressing the DDR-Act-FP we demonstrate that DDR activation and its pharmacological manipulation with inhibitory and activatory compounds can be efficiently monitored in live 3D spheroid model. This study paves the way for the development of innovative screening and preclinical evaluation assays.

  13. 3D photon impact determination in monolithic crystals based on autocorrelation filters and RTP methods

    Energy Technology Data Exchange (ETDEWEB)

    Conde, Pablo; Gonzalez, Antonio [Institute for Instrumentation in Molecular Imaging, I3M-CSIC, Valencia (Spain); Bettiol, Marco; Fabbri, Andrea; Pani, Roberto [Department of Molecular Medicine, Sapienza University of Rome (Italy); Benlloch Baviera, José María; Talens Aguilar, Albert; Hernandez, Liczandro; Sanchez, Filomeno [Institute for Instrumentation in Molecular Imaging, I3M-CSIC, Valencia (Spain)

    2015-05-18

    In PET detectors based on monolithic scintillators, the photon impact position can be estimated from the light intensity distribution (LD) on the photodetector pixels. Typically, there is a poor estimation of the interaction positions towards the edges when linear algorithms such as Center of Gravity (CoG) are used. We present a novel method to determine the interaction coordinates in thick monolithic crystals filtering the digitized LDs from each gamma-event by means of an autocorrelation filter and the raise to power (RTP) positioning algorithm to reduce the border effects. The experimental setup was based on two detector blocks based on monolithic LYSO scintillator crystals (50x50x20 mm{sup 3}). Each crystal is coupled to a SiPMs array as 12x12 photosensors and an electronic readout that outputs information of each SiPM row and column. Between the detector blocks, a collimated array of 9x9 {sup 22}Na sources, separated 5 mm each other, was placed. The optimum power to use in the RTP positioning algorithm was determined using the third order intercept point (IP3) from plots of the measured coordinates versus known positions. After applying the autocorrelation and RTP fifth to the data, we found an improvement of the spatial resolution from 2.5 mm when CoG is used, to 1.2 mm in the crystal center region. In this work we show how to accurately resolve 3D photon impact coordinates in thick monolithic crystals using autocorrelation filters merged with RTP methods. After applying the new approach it is possible to accurately resolve impacts close to the entrance of 20 mm thick LYSO scintillators. The reached spatial resolution at any photon depth of interaction is comparable with state-of-the-art crystal array approaches with the advantage of the proposed work to also provide continuous depth of interaction information.

  14. Implementation of Accurate and Fast DNA Cytometry by Confocal Microscopy in 3D

    Directory of Open Access Journals (Sweden)

    Lennert S. Ploeger

    2005-01-01

    Full Text Available Background: DNA cytometry is a powerful method for measuring genomic instability. Standard approaches that measure DNA content of isolated cells may induce selection bias and do not allow interpretation of genomic instability in the context of the tissue. Confocal Laser Scanning Microscopy (CLSM provides the opportunity to perform 3D DNA content measurements on intact cells in thick histological sections. Because the technique is technically challenging and time consuming, only a small number of usually manually selected nuclei were analyzed in different studies, not allowing wide clinical evaluation. The aim of this study was to describe the conditions for accurate and fast 3D CLSM cytometry with a minimum of user interaction to arrive at sufficient throughput for pilot clinical applications. Methods: Nuclear DNA was stained in 14 μm thick tissue sections of normal liver and adrenal stained with either YOYO-1 iodide or TO-PRO-3 iodide. Different pre-treatment strategies were evaluated: boiling in citrate buffer (pH 6.0 followed by RNase application for 1 or 18 hours, or hydrolysis. The image stacks obtained with CLSM at microscope magnifications of ×40 or ×100 were analyzed off-line using in-house developed software for semi-automated 3D fluorescence quantitation. To avoid sectioned nuclei, the top and bottom of the stacks were identified from ZX and YZ projections. As a measure of histogram quality, the coefficient of variation (CV of the diploid peak was assessed. Results: The lowest CV (10.3% was achieved with a protocol without boiling, with 1 hour RNase treatment and TO-PRO-3 iodide staining, and a final image recording at ×60 or ×100 magnifications. A sample size of 300 nuclei was generally achievable. By filtering the set of automatically segmented nuclei based on volume, size and shape, followed by interactive removal of the few remaining faulty objects, a single measurement was completely analyzed in approximately 3 hours

  15. Synthesis of 3D ordered macroporous indium tin oxide using polymer colloidal crystal template

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Xue'ao; MAN; Yahui; WANG; Jianfang; LIU; Changli; WU; Wenjian

    2006-01-01

    Three-dimensional (3D) ordered macroporous indium tin oxide (ITO) is prepared using a polymer colloidal crystal template that is formed by self-assembly of the monodisperse poly(methyl methacrylate) (PMMA) microspheres. The morphologies and BET surface area of the macroporous material is examined by scanning electron microscope, transmission electron microscopy and N2 adsorption/desorption. Results indicate that the macroporous material has highly ordered arrays of the uniform pores replicated from the PMMA colloidal crystal template when the polymer colloidal crystal template is removed by calcinations at 500℃. The pore diameter (about 450 nm) of macroporous ITO slightly shrank to the PMMA microspheres. The BET surface area and pore volume of the macroporous material are 389 m2·g-1 and 0.36 cm3·g-1, respectively. Moreover, the macroporous ITO, containing 5 mol% Sn and after annealing under vacuum, shows the minimum resistivity of ρ= 8.2×10-3 Ω· cm. The conductive mechanism of macroporous ITO is discussed, and it is believed that the oxygen vacancies are the major factor for excellent electrical properties.

  16. Serum-induced degradation of 3D DNA box origami observed with high-speed atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    Zaixing Jiang[1,2,3; Shuai Zhang[2,3; Chuanxu Yang[2; Jorgen Kjems[2; Yudong Huang[1; Flemming Besenbacher[2; Mingdong Dong[2

    2015-01-01

    3D DNA origami holds tremendous potential for the encapsulation and selective release of therapeutic drugs. Observations of the real-time performance of these structures in physiological environments will contribute to the development of future applications. We investigated the degradation kinetics of 3D DNA box origami in serum by using high-speed atomic force microscope optimized for imaging 3D DNA origami in real time. The time resolution allowed to characterize the stages of serum effects on individual 3D DNA boxes origami with nanometer resolution. Our results indicate that the digestion process is a combination of rapid collapse and slow degradation phases. Damage to box origami occurs mainly in the collapse phase. Thus, the structural stability of 3D DNA box origami should be improved, especially in the collapse phase, before these structures are used in clinical applications.

  17. Percolation lithography: Tuning and freezing disorder in 3D photonic crystals using partial wetting and drying

    CERN Document Server

    Burgess, Ian B; Kay, Theresa M; Shneidman, Anna V; Cranshaw, Derek J; Loncar, Marko; Aizenberg, Joanna

    2015-01-01

    Although complex, hierarchical nanoscale geometries with tailored degrees of disorder are commonly found in biological systems, few simple self-assembly routes to fabricating synthetic analogues have been identified. We present two techniques that exploit basic capillary phenomena to finely control disorder in porous 3D photonic crystals, leading to complex and hierarchical geometries. In the first, we exposed the structures to mixtures of ethanol and water that partially wet their pores, where small adjustments to the ethanol content controlled the degree of partial wetting. In the second, we infiltrated the structures with thin films of volatile alkanes and observed a sequence of partial infiltration patterns as the liquid evaporated. In both cases, macroscopic symmetry breaking was driven by subtle sub-wavelength variations in the pore geometry that directed site-selective infiltration of liquids. The resulting patterns, well described by percolation theory, had significant effects on the photonic structur...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  3. CCDC 1025419: Experimental Crystal Structure Determination : bisthieno[3,2-b:2',3'-d]thiophene

    KAUST Repository

    Castañeda, Raúl

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  4. Guidelines to develop interactive tutorials on 3D biomolecules: the case of DNA repair by photolyase

    Directory of Open Access Journals (Sweden)

    Larissa Assis Barony Valadares Fonseca

    2016-11-01

    Full Text Available INTRODUCTION: This work presents the following guidelines for developing interactive learning objects on the 3D biomolecules: i- identify a relevant educational need; ii-select an appropriate subject; iii- employ interactive 3D molecular structures; iv- simultaneously display animation with related textual information or 2D diagrams; v- integrating different modes of representation of chemical phenomena. Based on these, was constructed the "Photolyase Tutorial". Photolyase is an enzyme that repairs DNA. It recognizes the cyclobutane pyrimidine dimer lesion (CPD caused by exposure to ultraviolet light. Understanding the repair mechanism requires understanding the structure-activity relationships of the molecules involved. Therefore, this topic is a convenient subject for teaching key aspects of the structure of protein and nucleic acids. There are few interactive 3D DNA repair tutorials available and most of these are in english, therefore not acessible for students that do not domain this language. Besides, these tutorials generally focus only on displaying structural features without make foster correlations between the structure and chemical aspects of repair mechanisms. OBJECTIVES: In order to construct a interactive tutorial that fills these gaps, the 3D structures of a DNA molecule, a DNA with CPD lesion and the photolyase enzyme were manipulated focusing on structural and chemical explanation. MATERIALS AND METHODS: These structures were obtained from PDB (http://www.rcsb.org/pdb/home/home.do and manipulated to show biochemical and chemical concepts by using the resources from the LABIQ Platform (http://labiq.is.usp.br. DISCUSSION AND RESULTS: Several concepts are covered, i.e., H-bonding, active site, co-factors etc. The tutorial is organized in small conceptual blocks presenting, in a stepwise fashion, how the enzyme recognizes the DNA lesion and proceeds to repair. Each block comprises a trigger button that controls the interactive

  5. Fabrication of 3-D Reconstituted Organoid Arrays by DNA-Programmed Assembly of Cells (DPAC).

    Science.gov (United States)

    Todhunter, Michael E; Weber, Robert J; Farlow, Justin; Jee, Noel Y; Cerchiari, Alec E; Gartner, Zev J

    2016-09-13

    Tissues are the organizational units of function in metazoan organisms. Tissues comprise an assortment of cellular building blocks, soluble factors, and extracellular matrix (ECM) composed into specific three-dimensional (3-D) structures. The capacity to reconstitute tissues in vitro with the structural complexity observed in vivo is key to understanding processes such as morphogenesis, homeostasis, and disease. In this article, we describe DNA-programmed assembly of cells (DPAC), a method to fabricate viable, functional arrays of organoid-like tissues within 3-D ECM gels. In DPAC, dissociated cells are chemically functionalized with degradable oligonucleotide "Velcro," allowing rapid, specific, and reversible cell adhesion to a two-dimensional (2-D) template patterned with complementary DNA. An iterative assembly process builds up organoids, layer-by-layer, from this initial 2-D template and into the third dimension. Cleavage of the DNA releases the completed array of tissues that are captured and fully embedded in ECM gels for culture and observation. DPAC controls the size, shape, composition, and spatial heterogeneity of organoids and permits positioning of constituent cells with single-cell resolution even within cultures several centimeters long. © 2016 by John Wiley & Sons, Inc.

  6. Synthesis, Crystal Structure and Anticancer Activities of Tetrahydropyrido[4,3-d]dihydropyrimidine-2-thiones

    Institute of Scientific and Technical Information of China (English)

    丁丽; 薛思佳; 李静; 肖笛; 王晶; 郝志兵; 庞春成

    2012-01-01

    A new series of tetrahydropyrido[4,3-d]dihydropyrimidine-2-thiones (3a-3x) were designed and synthesized. Their structures were confirmed by 1H NMR, IR, MS and elemental analysis, and the conformation of compound 3j was confirmed by X-ray diffraction. Preliminary bioassays indicated that most of the target compounds presented good antiproliferative activities against leukemic K562 cells, ovarian cancer HO-8910 cells and liver cancer SMMC-7721 cells in vitro. Among them the compounds 3i and 3m afford the best activity, the IC50 of them were 3.22 and 3.65 μg/mL against leukemic K562 cells, respectively, which were lower than the anticancer drug of clini- cal practice 5-FU (IC50 = 8.56μg/mL). Preliminary mechanism of action studies revealed that compound 3i caused DNA fragmentation and activated caspase-3/7 in leukemic K562 cells.

  7. Crystalline Hybrid Polyphenylene Macromolecules from Octaalkynylsilsesquioxanes, Crystal Structures, and a Potential Route to 3-D Graphenes

    Energy Technology Data Exchange (ETDEWEB)

    Roll, Mark F; Kampf, Jeffrey W.; Laine, Richard M

    2011-05-10

    We report here the Diels–Alder reaction of octa(diphenylacetylene)silsesquioxane [DPA₈OS] with tetraphenylcyclopentadienone or tetra(p-tolyl)cyclopentadienone to form octa(hexaphenylbenzene)octasilsesquioxane, (Ph₆C₆)₈OS, or octa(tetratolyldiphenylbenzene)octasilsesquioxane, (p-Tolyl₄Ph₂C₆)₈OS. Likewise, tetra(p-tolyl)cyclopentadienone reacts with octa(p-tolylethynylphenyl)OS to form octa(pentatolylphenylbenzene)octasilsesquioxane (p-Tolyl₅PhC₆)₈OS. These compounds, with molecular weights of 4685–5245 Da, were isolated and characterized using a variety of analytical methods. The crystal structure of DPA₈OS offers a 3 nm³ unit cell with Z = 1. The crystal structure of (Ph₆C₆)₈OS was determined to have a triclinic unit cell of 11 nm³ with Z = 1. The latter structure is believed to be the largest discrete molecular structure reported with 330 carbons. Efforts to dehydrogenatively cyclize (Scholl reaction) the hexaarylbenzene groups to form 3-D octgraphene compounds are described.

  8. Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT.

    Science.gov (United States)

    Iinuma, Ryosuke; Ke, Yonggang; Jungmann, Ralf; Schlichthaerle, Thomas; Woehrstein, Johannes B; Yin, Peng

    2014-04-01

    DNA self-assembly has produced diverse synthetic three-dimensional polyhedra. These structures typically have a molecular weight no greater than 5 megadaltons. We report a simple, general strategy for one-step self-assembly of wireframe DNA polyhedra that are more massive than most previous structures. A stiff three-arm-junction DNA origami tile motif with precisely controlled angles and arm lengths was used for hierarchical assembly of polyhedra. We experimentally constructed a tetrahedron (20 megadaltons), a triangular prism (30 megadaltons), a cube (40 megadaltons), a pentagonal prism (50 megadaltons), and a hexagonal prism (60 megadaltons) with edge widths of 100 nanometers. The structures were visualized by means of transmission electron microscopy and three-dimensional DNA-PAINT super-resolution fluorescent microscopy of single molecules in solution.

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

    Science.gov (United States)

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

    2014-05-01

    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.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

  10. Electrochemiluminescence at Bare and DNA-Coated Graphite Electrodes in 3D-Printed Fluidic Devices.

    Science.gov (United States)

    Bishop, Gregory W; Satterwhite-Warden, Jennifer E; Bist, Itti; Chen, Eric; Rusling, James F

    Clear plastic fluidic devices with ports for incorporating electrodes to enable electrochemiluminescence (ECL) measurements were prepared using a low-cost, desktop three-dimensional (3D) printer based on stereolithography. Electrodes consisted of 0.5 mm pencil graphite rods and 0.5 mm silver wires inserted into commercially available 1/4 in.-28 threaded fittings. A bioimaging system equipped with a CCD camera was used to measure ECL generated at electrodes and small arrays using 0.2 M phosphate buffer solutions containing tris(2,2'-bipyridyl)dichlororuthenium(II) hexahydrate ([Ru(bpy)3](2+)) with 100 mM tri-n-propylamine (TPA) as the coreactant. ECL signals produced at pencil graphite working electrodes were linear with respect to [Ru(bpy)3](2+) concentration for 9-900 μM [Ru(bpy)3](2+). The detection limit was found to be 7 μM using the CCD camera with exposure time set at 10 s. Electrode-to-electrode ECL signals varied by ±7.5%. Device performance was further evaluated using pencil graphite electrodes coated with multilayer poly(diallyldimethylammonium chloride) (PDDA)/DNA films. In these experiments, ECL resulted from the reaction of [Ru(bpy)3](3+) with guanines of DNA. ECL produced at these thin-film electrodes was linear with respect to [Ru(bpy)3](2+) concentration from 180 to 800 μM. These studies provide the first demonstration of ECL measurements obtained using a 3D-printed closed-channel fluidic device platform. The affordable, high-resolution 3D printer used in these studies enables easy, fast, and adaptable prototyping of fluidic devices capable of incorporating electrodes for measuring ECL.

  11. Effect of process parameters and crystal orientation on 3D anisotropic stress during CZ and FZ growth of silicon

    Science.gov (United States)

    Drikis, Ivars; Plate, Matiss; Sennikovs, Juris; Virbulis, Janis

    2017-09-01

    Simulations of 3D anisotropic stress are carried out in and oriented Si crystals grown by FZ and CZ processes for different diameters, growth rates and process stages. Temperature dependent elastic constants and thermal expansion coefficients are used in the FE simulations. The von Mises stress at the triple point line is 5-11% higher in crystals compared to crystals. The process parameters have a larger effect on the von Mises stress than the crystal orientation. Generally, the crystal has a higher azimuthal variation of stress along the triple point line ( 8%) than the crystal ( 2%). The presence of a crystal ridge increases the stress beside the ridge and decreases it on the ridge compared with the round crystal.

  12. Pressure-Induced Oriented Attachment Growth of Large-Size Crystals for Constructing 3D Ordered Superstructures.

    Science.gov (United States)

    Wang, Jun; Lian, Gang; Si, Haibin; Wang, Qilong; Cui, Deliang; Wong, Ching-Ping

    2016-01-26

    Oriented attachment (OA), a nonclassical crystal growth mechanism, provides a powerful bottom-up approach to obtain ordered superstructures, which also demonstrate exciting charge transmission characteristic. However, there is little work observably pronouncing the achievement of 3D OA growth of crystallites with large size (e.g., submicrometer crystals). Here, we report that SnO2 3D ordered superstructures can be synthesized by means of a self-limited assembly assisted by OA in a designed high-pressure solvothermal system. The size of primary building blocks is 200-250 nm, which is significantly larger than that in previous results (normally pressure plays the key role in the formation of 3D configuration and fusion of adjacent crystals. Furthermore, this high-pressure strategy can be readily expanded to additional materials. We anticipate that the welded structures will constitute an ideal system with relevance to applications in optical responses, lithium ion battery, solar cells, and chemical sensing.

  13. Confined Etching within 2D and 3D Colloidal Crystals for Tunable Nanostructured Templates: Local Environment Matters.

    Science.gov (United States)

    Wendisch, Fedja J; Oberreiter, Richard; Salihovic, Miralem; Elsaesser, Michael S; Bourret, Gilles R

    2017-02-01

    We report the isotropic etching of 2D and 3D polystyrene (PS) nanosphere hcp arrays using a benchtop O2 radio frequency plasma cleaner. Unexpectedly, this slow isotropic etching allows tuning of both particle diameter and shape. Due to a suppressed etching rate at the point of contact between the PS particles originating from their arrangement in 2D and 3D crystals, the spherical PS templates are converted into polyhedral structures with well-defined hexagonal cross sections in directions parallel and normal to the crystal c-axis. Additionally, we found that particles located at the edge (surface) of the hcp 2D (3D) crystals showed increased etch rates compared to those of the particles within the crystals. This indicates that 2D and 3D order affect how nanostructures chemically interact with their surroundings. This work also shows that the morphology of nanostructures periodically arranged in 2D and 3D supercrystals can be modified via gas-phase etching and programmed by the superlattice symmetry. To show the potential applications of this approach, we demonstrate the lithographic transfer of the PS template hexagonal cross section into Si substrates to generate Si nanowires with well-defined hexagonal cross sections using a combination of nanosphere lithography and metal-assisted chemical etching.

  14. Percolation and lasing in real 3D crystals with inhomogeneous distributed random pores

    Energy Technology Data Exchange (ETDEWEB)

    Burlak, Gennadiy, E-mail: gburlak@uaem.mx; Calderón-Segura, Yessica

    2014-11-15

    We systematically study the percolation phase transition in real 3D crystals where not only the state of pores but also their radius r and displacement s are random valued numbers. The mean values R=〈r〉 and S=〈s〉 emerge as additional spatial scales in such an extended network. This leads to variations of the threshold (critical) percolation probability p{sub C} and the percolation order parameter P that become to be the intricate functions of R and S. Our numerical simulations have shown that in such extended system the incipient spanning cluster can arise even for situations where for simple periodical system the percolation does not exist. We analyzed the validity of the nearest neighbor's approximation and found that such approximation is not valid for materials with large dispersivity of pores. The lasing of nanoemitters incorporated in such percolating spanning cluster is studied too. This effect can open interesting perspectives in modern nano- and micro-information technologies.

  15. Selecting 3D Chaotic Flow States for Accelerated DNA Replication in Micro Scale Convective PCR

    CERN Document Server

    Priye, Aashish; Hassan, Yassin; Ugaz, Victor

    2016-01-01

    Micro-scale flow in cylindrical geometries can harness chaotic advection to perform complex thermally activated biochemical reactions such as the polymerase chain reaction (PCR). We have applied a 3D computational fluid dynamics model to resolve the complex flow patterns in such geometries. The resulting 3D flow trajectories are then used as input to a kinetic model to resolve the time evolution of DNA replication process. A simple mass action kinetic model was developed to couple these biochemical reactions with the intricate flow. Residence time analysis of virtual particles in the flow revealed that the flow has a strong chaotic component in wider geometries in comparison with taller geometries (quasi periodic motion). This work shows, for the first time that the chaotic aspect of the flow field plays a key role in determining the strength of the coupling between the reactions and the flow. Our model can quantify the doubling times of these reactions capturing the lag, exponential and plateau phases of PCR...

  16. Electrical conduction mechanisms in PbSe and PbS nano crystals 3D matrix layer

    Directory of Open Access Journals (Sweden)

    Matan Arbell

    2016-02-01

    Full Text Available A simulation study and measurements of the electrical conductance in a PbSe and PbS spherical Nano-crystal 3D matrix layer was carried out focusing on its dependences of Nano-crystal size distribution and size gradient along the layer thickness (z-direction. The study suggests a new concept of conductance enhancement by utilizing a size gradient along the layer thickness from mono-layer to the next mono-layer of the Nano-crystals, in order to create a gradient of the energy levels and thus improve directional conductance in this direction. A Monte Carlo simulation of the charge carriers path along the layer thickness of the Nano-crystals 3D matrix using the Miller-Abrahams hopping model was performed. We then compared the conductance characteristics of the gradual size 3D matrix layer to a constant-sized 3D matrix layer that was used as a reference in the simulation. The numerical calculations provided us with insights into the actual conductance mechanism of the PbSe and PbS Nano-crystals 3D matrix and explained the discrepancies in actual conductance and the variability in measured mobilities published in the literature. It is found that the mobility and thus conductance are dependent on a critical electrical field generated between two adjacent nano-crystals. Our model explains the conductance dependents on the: Cathode-Anode distance, the distance between the adjacent nano-crystals in the 3D matrix layer and the size distribution along the current direction. Part of the model (current-voltage dependence was validated using a current-voltage measurements taken on a constant size normal distribution nano-crystals PbS layer (330nm thick compared with the predicted I-V curves. It is shown that under a threshold bias, the current is very low, while after above a threshold bias the conductance is significantly increased due to increase of hopping probability. Once reaching the maximum probability the current tend to level-off reaching the maximal

  17. 2D and 3D crystallization of a bacterial homologue of human vitamin C membrane transport proteins.

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kushwaha, Satya K.; Krizan, Jason W.; Cava, R. J., E-mail: rcava@princeton.edu [Department of Chemistry, Princeton University, Princeton, New Jersey 08542 (United States); 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. [Department of Physics, Princeton University, Princeton, New Jersey 08542 (United States)

    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.

  19. Ice crystallization in porous building materials: assessing damage using real-time 3D monitoring

    Science.gov (United States)

    Deprez, Maxim; De Kock, Tim; De Schutter, Geert; Cnudde, Veerle

    2017-04-01

    Frost action is one of the main causes of deterioration of porous building materials in regions at middle to high latitudes. Damage will occur when the internal stresses due to ice formation become larger than the strength of the material. Hence, the sensitivity of the material to frost damage is partly defined by the structure of the solid body. On the other hand, the size, shape and interconnection of pores manages the water distribution in the building material and, therefore, the characteristics of the pore space control potential to form ice crystals (Ruedrich et al., 2011). In order to assess the damage to building materials by ice crystallization, lot of effort was put into identifying the mechanisms behind the stress build up. First of all, volumetric expansion of 9% (Hirschwald, 1908) during the transition of water to ice should be mentioned. Under natural circumstances, however, water saturation degrees within natural rocks or concrete cannot reach a damaging value. Therefore, linear growth pressure (Scherer, 1999), as well as several mechanisms triggered by water redistribution during freezing (Powers and Helmuth, 1953; Everett, 1961) are more likely responsible for damage due to freezing. Nevertheless, these theories are based on indirect observations and models and, thus, direct evidence that reveals the exact damage mechanism under certain conditions is still lacking. To obtain this proof, in-situ information needs to be acquired while a freezing process is performed. X-ray computed tomography has proven to be of great value in material research. Recent advances at the Ghent University Centre for Tomography (UGCT) have already allowed to dynamically 3D image crack growth in natural rock during freeze-thaw cycles (De Kock et al., 2015). A great potential to evaluate the different stress build-up mechanisms can be found in this imaging technique consequently. It is required to cover a range of materials with different petrophysical properties to achieve

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

    Energy Technology Data Exchange (ETDEWEB)

    Liu Yifei; Manjubala, Inderchand; Fratzl, Peter [Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam (Germany); Roschger, Paul [4th Medical Department, Ludwig Boltzmann Institute of Osteology at Hanusch Hospital of WGKK and AUVA Trauma Centre Meidling, 1140 Vienna (Austria); Schell, Hanna; Duda, Georg N, E-mail: fratzl@mpikg.mpg.d [Julius Wolff Institut and Center for Musculoskeletal Surgery, Charite- University Medicine Berlin, Augustenburger Platz 1, 13353 Berlin (Germany)

    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. Design and development of three-dimensional DNA crystals utilizing CGAA parallel base paired motifs

    Science.gov (United States)

    Muser, Stephanie Elizabeth

    Three-dimensional (3D) DNA crystals hold great potential for various applications such as the development of molecular scaffolds for use in protein structure determination by x-ray crystallography. The programmability and predictability of DNA make it a powerful tool for self-assembly but it is hindered by the linearity of the duplex structure. Predictable noncanonical base pairs and motifs have the potential to connect linear double-helical DNA segments into complex 3D structures. The sequence d(GCGAAAGCT) has been observed to form 3D crystals containing both noncanonical parallel pairs and canonical Watson-Crick pairs. This provided a template structure that we used in expanding the design and development of 3D DNA crystals along with exploring the use of predictable noncanonical motifs. The structures we determined contained all but one or two of the designed secondary structure interactions, depending on pH.

  2. 1D to 3D diffusion-reaction kinetics of defects in crystals

    DEFF Research Database (Denmark)

    Trinkaus, H.; Heinisch, H.L.; Barashev, A.V.

    2002-01-01

    Microstructural features evolving in crystalline solids from diffusion-reaction kinetics of mobile components depend crucially on the dimension of the underlying diffusion process which is commonly assumed to be three-dimensional (3D). In metals, irradiation-induced displacement cascades produce ...... and 3D limiting cases. The analytical result is fully confirmed by kinetic Monte Carlo simulations.......Microstructural features evolving in crystalline solids from diffusion-reaction kinetics of mobile components depend crucially on the dimension of the underlying diffusion process which is commonly assumed to be three-dimensional (3D). In metals, irradiation-induced displacement cascades produce...

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

    Science.gov (United States)

    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.

  4. 3D-Printed High-Density Droplet Array Chip for Miniaturized Protein Crystallization Screening under Vapor Diffusion Mode.

    Science.gov (United States)

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

    2017-04-05

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  6. Fabrication of holographic 3-D polymeric photonic crystals in near-Infrared band and study of Its optical property

    Institute of Scientific and Technical Information of China (English)

    ZHANG Sa-sa; WANG Qing-pu; ZHANG Xing-yu; CHEN Jia-qi; WANG Li

    2008-01-01

    A three-sidewalls-prism holographic method has been provided for the fabrication of 3-D fcc-type polymeric photonic crystal using negative photoresist.Special fabrication treatment has been introduced to ensure the stability of the fabricated nanostructures.The scanning electronic microscopy (SEM) and the diffraction results testified the good dependability of the fabricared structures.The simulation of the partial band structure is in good agreement with the transmission and reflection spectra obtained by Fouricr transform infrared spectroscopy.

  7. Multiple Scattering of Waves in 3D Crystals (Natural or Photonic) Formed by Anisotropically Scattering Centers

    CERN Document Server

    Baryshevsky, V G

    2013-01-01

    This paper considers the refraction and diffraction of waves in three-dimensional crystals formed by anisotropically scattering centers. The partial wave expansion method is used to consider the effect of multiple rescattering of waves by centers composing a crystal. The expression for the refractive index of a crystal is derived. It is shown that instead of the diagonal elements of the scattering matrix $\\mathbf{T}$, appearing in the expression for the refractive index of a chaotic medium, the derived expression includes the diagonal elements of the reaction matrix $\\mathbf{K}$. This fact is taken into account in writing the equations describing the dynamical diffraction of waves in a crystal. The results can be of interest for research into, e.g., diffraction of cold neutrons and photons in crystals, nanocrystalline materials, as well as for the description of parametric and diffraction radiation in electromagnetic crystals formed by anisotropically scattering centers.

  8. Design of a 3D photonic band gap cavity in a diamond-like inverse woodpile photonic crystal

    CERN Document Server

    Woldering, Léon A; Vos, Willem L

    2014-01-01

    We theoretically investigate the design of cavities in a three-dimensional (3D) inverse woodpile photonic crystal. This class of cubic diamond-like crystals has a very broad photonic band gap and consists of two perpendicular arrays of pores with a rectangular structure. The point defect that acts as a cavity is centred on the intersection of two intersecting perpendicular pores with a radius that differs from the ones in the bulk of the crystal. We have performed supercell bandstructure calculations with up to $5 \\times 5 \\times 5$ unit cells. We find that up to five isolated and dispersionless bands appear within the 3D photonic band gap. For each isolated band, the electric-field energy is localized in a volume centred on the point defect, hence the point defect acts as a 3D photonic band gap cavity. The mode volume of the cavities resonances is as small as 0.8 $\\lambda^{3}$ (resonance wavelength cubed), indicating a strong confinement of the light. By varying the radius of the defect pores we found that o...

  9. Observation of wavelength-dependent Brewster angle shift in 3D photonic crystals

    CERN Document Server

    Priya,

    2016-01-01

    The interaction of polarized light with photonic crystals exhibit unique features due to its sub-wavelength nature on the surface and the periodic variation of refractive index in the depth of the crystals. Here, we present a detailed study of polarization anisotropy in light scattering associated with three-dimensional photonic crystals with face centered cubic symmetry over a broad wavelength and angular range. The polarization anisotropy leads to a shift in the conventional Brewster angle defined for a planar interface with certain refractive index. The observed shift in Brewster angle strongly depends on the index contrast and lattice constant. Polarization-dependent stop gap measurements are performed on photonic crystals with different index contrast and lattice constants. These measurements indicate unique stop gap branching at high-symmetry points in the Brillouin zone of the photonic crystals. The inherited stop gap branching is observed for TE polarization whereas that is suppressed for TM polarizat...

  10. A Microfluidic DNA Sensor Based on Three-Dimensional (3D Hierarchical MoS2/Carbon Nanotube Nanocomposites

    Directory of Open Access Journals (Sweden)

    Dahou Yang

    2016-11-01

    Full Text Available In this work, we present a novel microfluidic biosensor for sensitive fluorescence detection of DNA based on 3D architectural MoS2/multi-walled carbon nanotube (MWCNT nanocomposites. The proposed platform exhibits a high sensitivity, selectivity, and stability with a visible manner and operation simplicity. The excellent fluorescence quenching stability of a MoS2/MWCNT aqueous solution coupled with microfluidics will greatly simplify experimental steps and reduce time for large-scale DNA detection.

  11. Lattice Boltzmann Simulation of 3D Nematic Liquid Crystal near Phase Transition

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jun; TAO Rui-Bao

    2002-01-01

    Phase transition between nematic and isotropic liquid crystal is a very weak first order phase transition.We avoid to use the normal Landau-de Gennes's free energy that reduces a strong first order transition, and set up adata base of free energy calculated by means of Tao-Sheng Lin's extended molecular field theory that can explain theexperiments of the equilibrium properties of nematic liquid crystal very well. Then we use the free energy method oflattice Boltzmann developed by Oxford group to study the phase decomposition, pattern formation in the flow of theliquid crystal near transition temperature.

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

    Directory of Open Access Journals (Sweden)

    Kyung-Il Joo

    2016-10-01

    Full Text Available 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.

  13. Delaunay algorithm and principal component analysis for 3D visualization of mitochondrial DNA nucleoids by Biplane FPALM/dSTORM.

    Science.gov (United States)

    Alán, Lukáš; Špaček, Tomáš; Ježek, Petr

    2016-07-01

    Data segmentation and object rendering is required for localization super-resolution microscopy, fluorescent photoactivation localization microscopy (FPALM), and direct stochastic optical reconstruction microscopy (dSTORM). We developed and validated methods for segmenting objects based on Delaunay triangulation in 3D space, followed by facet culling. We applied them to visualize mitochondrial nucleoids, which confine DNA in complexes with mitochondrial (mt) transcription factor A (TFAM) and gene expression machinery proteins, such as mt single-stranded-DNA-binding protein (mtSSB). Eos2-conjugated TFAM visualized nucleoids in HepG2 cells, which was compared with dSTORM 3D-immunocytochemistry of TFAM, mtSSB, or DNA. The localized fluorophores of FPALM/dSTORM data were segmented using Delaunay triangulation into polyhedron models and by principal component analysis (PCA) into general PCA ellipsoids. The PCA ellipsoids were normalized to the smoothed volume of polyhedrons or by the net unsmoothed Delaunay volume and remodeled into rotational ellipsoids to obtain models, termed DVRE. The most frequent size of ellipsoid nucleoid model imaged via TFAM was 35 × 45 × 95 nm; or 35 × 45 × 75 nm for mtDNA cores; and 25 × 45 × 100 nm for nucleoids imaged via mtSSB. Nucleoids encompassed different point density and wide size ranges, speculatively due to different activity stemming from different TFAM/mtDNA stoichiometry/density. Considering twofold lower axial vs. lateral resolution, only bulky DVRE models with an aspect ratio >3 and tilted toward the xy-plane were considered as two proximal nucleoids, suspicious occurring after division following mtDNA replication. The existence of proximal nucleoids in mtDNA-dSTORM 3D images of mtDNA "doubling"-supported possible direct observations of mt nucleoid division after mtDNA replication.

  14. Strategies for the crystallization of viruses: using phase diagrams and gels to produce 3D crystals of Grapevine fanleaf virus.

    Science.gov (United States)

    Schellenberger, Pascale; Demangeat, Gérard; Lemaire, Olivier; Ritzenthaler, Christophe; Bergdoll, Marc; Oliéric, Vincent; Sauter, Claude; Lorber, Bernard

    2011-05-01

    The small icosahedral plant RNA nepovirus Grapevine fanleaf virus (GFLV) is specifically transmitted by a nematode and causes major damage to vineyards worldwide. To elucidate the molecular mechanisms underlying the recognition between the surface of its protein capsid and cellular components of its vector, host and viral proteins synthesized upon infection, the wild type GFLV strain F13 and a natural mutant (GFLV-TD) carrying a Gly₂₉₇Asp mutation were purified, characterized and crystallized. Subsequently, the geometry and volume of their crystals was optimized by establishing phase diagrams. GFLV-TD was twice as soluble as the parent virus in the crystallization solution and its crystals diffracted X-rays to a resolution of 2.7 Å. The diffraction limit of GFLV-F13 crystals was extended from 5.5 to 3 Å by growth in agarose gel. Preliminary crystallographic analyses indicate that both types of crystals are suitable for structure determination. Keys for the successful production of GFLV crystals include the rigorous quality control of virus preparations, crystal quality improvement using phase diagrams, and crystal lattice reinforcement by growth in agarose gel. These strategies are applicable to the production of well-diffracting crystals of other viruses and macromolecular assemblies.

  15. Modeling induction heating and 3-D heat transfer for growth of rectangular crystals using FIDAP

    Science.gov (United States)

    Atherton, L. J.; Martin, R. W.

    1988-09-01

    We are developing a process to grow large rectangular crystals for use as solid state lasers by a Bridgman-like method. The process is based on induction heating of two graphite susceptors which transfer energy to an ampoule containing the melt and crystal. The induction heating version of FIDAP developed by Gresho and Derby is applied to this system to determine the power deposition profile in electrically conducting regions. The calculated power is subsequently used as a source term in the heat equation to calculate the temperature profile. Results are presented which examine the sensitivity of the system to electrical and thermal conductivities, and design modifications are illustrated which could improve the temperature field for crystal growth applications.

  16. Synthesis, Crystal Structure and Magnetic Properties of a New 3D Cobalt Vanadate

    Institute of Scientific and Technical Information of China (English)

    WANG,Lei(王磊); ZHANG,Hong(张宏); ZHANG,Jing-Ping(张景萍); NIU,Ben(牛犇); CUI,Shu-Xin(崔术新)

    2004-01-01

    A new cobalt vanadate compound 1 [CoⅡ(H2O)2 Vv2 O6] has been hydrothermally synthesized and characterized by the elemental analyses and the single crystal X-ray diffraction analysis. Compound 1 crystallizes in the orthorhombic system, space group Pmna, with a=0.55646, b= 1.06900, c= 1.18452 nm, and Z=4. The magnetic susceptibility of the cobalt vanadate has been measured and indicates possible antiferromagnetic coupling between adjacent cobalt (Ⅱ) (0.5432-0.5697 nm) through bond or space.

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

    Science.gov (United States)

    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.

  18. 3D study of the structure of primary crystals in a rheocast Al-Cu alloy

    Energy Technology Data Exchange (ETDEWEB)

    Niroumand, B.; Xia, K. [Melbourne Univ., Parkville, Vic. (Australia). Dept. of Mech. and Manuf. Eng.

    2000-05-15

    An Al-10.25 wt.% Cu alloy was mechanically stirred at 1000 rpm while being cooled to and isothermally held at 619 C for various times before casting. The microstructure of as-cast materials consists of pseudo-particles and pseudo-clusters in two-dimensional (2D) views. Serial sectioning was performed and it was found that pseudo-particles belonging to a pseudo-cluster were connected in three dimensions and a pseudo-cluster was actually a single primary particle. A three dimensional (3-D) model of such a primary particle was constructed from 2D sections which showed the complexity of its structure. It is suggested that the theories based on agglomeration and disagglomeration of particles during rheocasting be re-examined in light of the experimental results. (orig.)

  19. 2D and 3D photonic crystal materials for photocatalysis and electrochemical energy storage and conversion.

    Science.gov (United States)

    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.

  20. Crystal structures and magnetic properties of cyano-bridged 4f-3d complexes

    Institute of Scientific and Technical Information of China (English)

    闫冰; 陈志达

    2001-01-01

    The most recent research progress in the fields of the crystal structure and magnetochemistry for rare earth-transition metal cyano-bridged complexes is reviewed in detail. The emphasis is put on the introduction to the research achievements of our group in this field, including all the types of complexes with different crystal structures in these systems such as dinuclear, trinuclear, one-dimensional chain and hydrogen-bonded network ion-pairs. At the same time a few examples of rare earth-transition metal molecular-based magnets have been found to exhibit excellent magnetochemical properties, such as the long-range magnetic ordering, the higher critical temperature Tc and the stronger coercive force. These results will be expected to promote the research development in this field.

  1. The dominant role of chalcogen bonding in the crystal packing of 2D/3D aromatics.

    Science.gov (United States)

    Fanfrlík, Jindřich; Přáda, Adam; Padělková, Zdeňka; Pecina, Adam; Macháček, Jan; Lepšík, Martin; Holub, Josef; Růžička, Aleš; Hnyk, Drahomír; Hobza, Pavel

    2014-09-15

    The chalcogen bond is a nonclassical σ-hole-based noncovalent interaction with emerging applications in medicinal chemistry and material science. It is found in organic compounds, including 2D aromatics, but has so far never been observed in 3D aromatic inorganic boron hydrides. Thiaboranes, harboring a sulfur heteroatom in the icosahedral cage, are candidates for the formation of chalcogen bonds. The phenyl-substituted thiaborane, synthesized and crystalized in this study, forms sulfur⋅⋅⋅π type chalcogen bonds. Quantum chemical analysis revealed that these interactions are considerably stronger than both in their organic counterparts and in the known halogen bond. The reason is the existence of a highly positive σ-hole on the positively charged sulfur atom. This discovery expands the possibilities of applying substituted boron clusters in crystal engineering and drug design.

  2. Purification and assembly of thermostable Cy5 labeled γ-PNAs into a 3D DNA nanocage.

    Science.gov (United States)

    Flory, Justin D; Johnson, Trey; Simmons, Chad D; Lin, Su; Ghirlanda, Giovanna; Fromme, Petra

    2014-12-15

    PNA is hybrid molecule ideally suited for bridging the functional landscape of polypeptides with the structural diversity that can be engineered with DNA nanostructures. However, PNA can be more challenging to work with in aqueous solvents due to its hydrophobic nature. A solution phase method using strain promoted, copper free click chemistry was developed to conjugate the fluorescent dye Cy5 to 2 bifunctional PNA strands as a first step toward building cyclic PNA-polypeptides that can be arranged within 3D DNA nanoscaffolds. A 3D DNA nanocage was designed with binding sites for the 2 fluorescently labeled PNA strands in close proximity to mimic protein active sites. Denaturing polyacrylamide gel electrophoresis (PAGE) is introduced as an efficient method for purifying charged, dye-labeled NA conjugates from large excesses of unreacted dye and unreacted, neutral PNA. Elution from the gel in water was monitored by fluorescence and found to be more efficient for the more soluble PNA strand. Native PAGE shows that both PNA strands hybridize to their intended binding sites within the DNA nanocage. Förster resonance energy transfer (FRET) with a Cy3 labeled DNA nanocage was used to determine the dissociation temperature of one PNA-Cy5 conjugate to be near 50C. Steady-state and time resolved fluorescence was used to investigate the dye orientation and interactions within the various complexes. Bifunctional, thermostable PNA molecules are intriguing candidates for controlling the assembly and orientation of peptides within small DNA nanocages for mimicking protein catalytic sites.

  3. A 3D MOF showing unprecedented solvent-induced single-crystal-to-single-crystal transformation and excellent CO2 adsorption selectivity at room temperature.

    Science.gov (United States)

    Qin, Tao; Gong, Jun; Ma, Junhan; Wang, Xin; Wang, Yonghua; Xu, Yan; Shen, Xuan; Zhu, Dunru

    2014-12-28

    A water stable porous 3D metal-organic framework, [Cu3L2(μ3-OH)2(μ2-H2O)]·2DMA (1, mother crystal, H2L = 2,2'-dinitrobiphenyl-4,4'-dicarboxylic acid, DMA = N,N-dimethylacetamide), shows unprecedented irreversible solvent-induced substitutions of bridging aqua ligands and guest-exchanges in single-crystal-to-single-crystal (SCSC) transformations at room temperature (RT), producing quantitatively three daughter crystals, [Cu3L2(μ3-OH)2]·2S (2: 2A, S = acetone; 2B, S = 2-propanol; 2C, S = 2-butanol), which exhibit reversible interconversion by guest-exchanges at RT in SCSC transformations. MOF 1 shows excellent separation selectivity (128) of CO2/N2 at RT and is a better sorbent of micro-solid-phase extraction (μ-SPE) than currently known benchmark ZIF-8.

  4. 3D modeling of doping from the atmosphere in floating zone silicon crystal growth

    Science.gov (United States)

    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.

  5. Slow to superluminal light waves in thin 3D photonic crystals.

    Science.gov (United States)

    Galisteo-López, J F; Galli, M; Balestreri, A; Patrini, M; Andreani, L C; López, C

    2007-11-12

    Phase measurements on self-assembled three-dimensional photonic crystals show that the group velocity of light can flip from small positive (slow) to negative (superluminal) values in samples of a few mum size. This phenomenon takes place in a narrow spectral range around the second-order stop band and follows from coupling to weakly dispersive photonic bands associated with multiple Bragg diffraction. The observations are well accounted for by theoretical calculations of the phase delay and of photonic states in the finite-sized systems.

  6. Crystallization of DNA-coated colloids.

    Science.gov (United States)

    Wang, Yu; Wang, Yufeng; Zheng, Xiaolong; Ducrot, Étienne; Yodh, Jeremy S; Weck, Marcus; Pine, David J

    2015-06-16

    DNA-coated colloids hold great promise for self-assembly of programmed heterogeneous microstructures, provided they not only bind when cooled below their melting temperature, but also rearrange so that aggregated particles can anneal into the structure that minimizes the free energy. Unfortunately, DNA-coated colloids generally collide and stick forming kinetically arrested random aggregates when the thickness of the DNA coating is much smaller than the particles. Here we report DNA-coated colloids that can rearrange and anneal, thus enabling the growth of large colloidal crystals from a wide range of micrometre-sized DNA-coated colloids for the first time. The kinetics of aggregation, crystallization and defect formation are followed in real time. The crystallization rate exhibits the familiar maximum for intermediate temperature quenches observed in metallic alloys, but over a temperature range smaller by two orders of magnitude, owing to the highly temperature-sensitive diffusion between aggregated DNA-coated colloids.

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

    Science.gov (United States)

    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.

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

    CERN Document Server

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

    2016-01-01

    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 ...

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

    Science.gov (United States)

    2008-01-28

    configurations will be considered in the designs:    Gold  nanoshell   3D  photonic  crystal:  core  (silica)  diameter  =  418nm,  gold  shell  thickness...into  the  frontier.  Some  metamaterials of new and novel  features  will be designed and synthesized.      PAY‐OFF: To further develop the existing...designs can  be expected. With the to‐be‐developed algorithms, some new and novel  features  of the metamaterials  will be achieved and found.     6

  10. Broadband Transmission Loss Using the Overlap of Resonances in 3D Sonic Crystals

    Directory of Open Access Journals (Sweden)

    Alexandre Lardeau

    2016-05-01

    Full Text Available The acoustic properties of a three-dimensional sonic crystal made of square-rod rigid scatterers incorporating a periodic arrangement of quarter wavelength resonators are theoretically and experimentally reported in this work. The periodicity of the system produces Bragg band gaps that can be tuned in frequency by modifying the orientation of the square-rod scatterers with respect to the incident wave. In addition, the quarter wavelength resonators introduce resonant band gaps that can be tuned by coupling the neighbor resonators. Bragg and resonant band gaps can overlap allowing the wave propagation control inside the periodic resonant medium. In particular, we show theoretically and experimentally that this system can produce a broad frequency band gap exceeding two and a half octaves (from 590 Hz to 3220 Hz with transmission lower than 3%. Finite element methods were used to calculate the dispersion relation of the locally resonant system. The visco-thermal losses were accounted for in the quarter wavelength resonators to simulate the wave propagation in the semi-infinite structures and to compare the numerical results with the experiments performed in an echo-free chamber. The simulations and the experimental results are in good agreement. This work motivates interesting applications of this system as acoustic audible filters.

  11. 3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression.

    Science.gov (United States)

    Löb, D; Lengert, N; Chagin, V O; Reinhart, M; Casas-Delucchi, C S; Cardoso, M C; Drossel, B

    2016-04-07

    DNA replication dynamics in cells from higher eukaryotes follows very complex but highly efficient mechanisms. However, the principles behind initiation of potential replication origins and emergence of typical patterns of nuclear replication sites remain unclear. Here, we propose a comprehensive model of DNA replication in human cells that is based on stochastic, proximity-induced replication initiation. Critical model features are: spontaneous stochastic firing of individual origins in euchromatin and facultative heterochromatin, inhibition of firing at distances below the size of chromatin loops and a domino-like effect by which replication forks induce firing of nearby origins. The model reproduces the empirical temporal and chromatin-related properties of DNA replication in human cells. We advance the one-dimensional DNA replication model to a spatial model by taking into account chromatin folding in the nucleus, and we are able to reproduce the spatial and temporal characteristics of the replication foci distribution throughout S-phase.

  12. CCDC 1004905: Experimental Crystal Structure Determination : 5,11-Dimesitylindeno[2,1-b]indeno[1',2':4,5]thieno[2,3-d]thiophene

    KAUST Repository

    Shi, Xueliang

    2014-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  13. 3D ToF-SIMS Analysis of Peptide Incorporation into MALDI Matrix Crystals with Sub-micrometer Resolution

    Science.gov (United States)

    Körsgen, Martin; Pelster, Andreas; Dreisewerd, Klaus; Arlinghaus, Heinrich F.

    2016-02-01

    The analytical sensitivity in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is largely affected by the specific analyte-matrix interaction, in particular by the possible incorporation of the analytes into crystalline MALDI matrices. Here we used time-of-flight secondary ion mass spectrometry (ToF-SIMS) to visualize the incorporation of three peptides with different hydrophobicities, bradykinin, Substance P, and vasopressin, into two classic MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (HCCA). For depth profiling, an Ar cluster ion beam was used to gradually sputter through the matrix crystals without causing significant degradation of matrix or biomolecules. A pulsed Bi3 ion cluster beam was used to image the lateral analyte distribution in the center of the sputter crater. Using this dual beam technique, the 3D distribution of the analytes and spatial segregation effects within the matrix crystals were imaged with sub-μm resolution. The technique could in the future enable matrix-enhanced (ME)-ToF-SIMS imaging of peptides in tissue slices at ultra-high resolution.

  14. Nanoscale rotary apparatus formed from tight-fitting 3D DNA components

    Science.gov (United States)

    Ketterer, Philip; Willner, Elena M.; Dietz, Hendrik

    2016-01-01

    We report a nanoscale rotary mechanism that reproduces some of the dynamic properties of biological rotary motors in the absence of an energy source, such as random walks on a circle with dwells at docking sites. Our mechanism is built modularly from tight-fitting components that were self-assembled using multilayer DNA origami. The apparatus has greater structural complexity than previous mechanically interlocked objects and features a well-defined angular degree of freedom without restricting the range of rotation. We studied the dynamics of our mechanism using single-particle experiments analogous to those performed previously with actin-labeled adenosine triphosphate synthases. In our mechanism, rotor mobility, the number of docking sites, and the dwell times at these sites may be controlled through rational design. Our prototype thus realizes a working platform toward creating synthetic nanoscale rotary motors. Our methods will support creating other complex nanoscale mechanisms based on tightly fitting, sterically constrained, but mobile, DNA components. PMID:26989778

  15. Molecular docking and 3D-QSAR studies on inhibitors of DNA damage signaling enzyme human PARP-1.

    Science.gov (United States)

    Fatima, Sabiha; Bathini, Raju; Sivan, Sree Kanth; Manga, Vijjulatha

    2012-08-01

    Poly (ADP-ribose) polymerase-1 (PARP-1) operates in a DNA damage signaling network. Molecular docking and three dimensional-quantitative structure activity relationship (3D-QSAR) studies were performed on human PARP-1 inhibitors. Docked conformation obtained for each molecule was used as such for 3D-QSAR analysis. Molecules were divided into a training set and a test set randomly in four different ways, partial least square analysis was performed to obtain QSAR models using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Derived models showed good statistical reliability that is evident from their r², q²(loo) and r²(pred) values. To obtain a consensus for predictive ability from all the models, average regression coefficient r²(avg) was calculated. CoMFA and CoMSIA models showed a value of 0.930 and 0.936, respectively. Information obtained from the best 3D-QSAR model was applied for optimization of lead molecule and design of novel potential inhibitors.

  16. Singular value decomposition of 3-D DNA melting curves reveals complexity in the melting process.

    Science.gov (United States)

    Haq, I; Chowdhry, B Z; Chaires, J B

    1997-01-01

    The thermal denaturation of synthetic deoxypolynucleotides of defined sequence was studied by a three dimensional melting technique in which complete UV absorbance spectra were recorded as a function of temperature. The results of such an experiment defined a surface bounded by absorbance, wavelength, and temperature. A matrix of the experimental data was built, and analyzed by the method of singular value decomposition (SVD). SVD provides a rigorous, model-free analytical tool for evaluating the number of significant spectral species required to account for the changes in UV absorbance accompanying the duplex--to--single strand transition. For all of the polynucleotides studied (Poly dA-Poly dT; [Poly (dAdT)]2; Poly dG-Poly dC; [Poly(dGdC)]2), SVD indicated the existence of at least 4-5 significant spectral species. The DNA melting transition for even these simple repeating sequences cannot, therefore, be a simple two-state process. The basis spectra obtained by SVD analysis were found to be unique for each polynucleotide studied. Differential scanning calorimetry was used to obtain model free estimates for the enthalpy of melting for the polynucleotides studied, with results in good agreement with previously published values.

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

    Science.gov (United States)

    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).

  18. Relationship between DNA damage response, initiated by camptothecin or oxidative stress, and DNA replication, analyzed by quantitative 3D image analysis.

    Science.gov (United States)

    Berniak, K; Rybak, P; Bernas, T; Zarębski, M; Biela, E; Zhao, H; Darzynkiewicz, Z; Dobrucki, J W

    2013-10-01

    A method of quantitative analysis of spatial (3D) relationship between discrete nuclear events detected by confocal microscopy is described and applied in analysis of a dependence between sites of DNA damage signaling (γH2AX foci) and DNA replication (EdU incorporation) in cells subjected to treatments with camptothecin (Cpt) or hydrogen peroxide (H2O2). Cpt induces γH2AX foci, likely reporting formation of DNA double-strand breaks (DSBs), almost exclusively at sites of DNA replication. This finding is consistent with the known mechanism of induction of DSBs by DNA topoisomerase I (topo1) inhibitors at the sites of collisions of the moving replication forks with topo1-DNA "cleavable complexes" stabilized by Cpt. Whereas an increased level of H2AX histone phosphorylation is seen in S-phase of cells subjected to H2O2, only a minor proportion of γH2AX foci coincide with DNA replication sites. Thus, the increased level of H2AX phosphorylation induced by H2O2 is not a direct consequence of formation of DNA lesions at the sites of moving DNA replication forks. These data suggest that oxidative stress induced by H2O2 and formation of the primary H2O2-induced lesions (8-oxo-7,8-dihydroguanosine) inhibits replication globally and triggers formation of γH2AX at various distances from replication forks. Quantitative analysis of a frequency of DNA replication sites and γH2AX foci suggests also that stalling of replicating forks by Cpt leads to activation of new DNA replication origins. © 2013 International Society for Advancement of Cytometry.

  19. Crystal structure of a DNA catalyst.

    Science.gov (United States)

    Ponce-Salvatierra, Almudena; Wawrzyniak-Turek, Katarzyna; Steuerwald, Ulrich; Höbartner, Claudia; Pena, Vladimir

    2016-01-14

    Catalysis in biology is restricted to RNA (ribozymes) and protein enzymes, but synthetic biomolecular catalysts can also be made of DNA (deoxyribozymes) or synthetic genetic polymers. In vitro selection from synthetic random DNA libraries identified DNA catalysts for various chemical reactions beyond RNA backbone cleavage. DNA-catalysed reactions include RNA and DNA ligation in various topologies, hydrolytic cleavage and photorepair of DNA, as well as reactions of peptides and small molecules. In spite of comprehensive biochemical studies of DNA catalysts for two decades, fundamental mechanistic understanding of their function is lacking in the absence of three-dimensional models at atomic resolution. Early attempts to solve the crystal structure of an RNA-cleaving deoxyribozyme resulted in a catalytically irrelevant nucleic acid fold. Here we report the crystal structure of the RNA-ligating deoxyribozyme 9DB1 (ref. 14) at 2.8 Å resolution. The structure captures the ligation reaction in the post-catalytic state, revealing a compact folding unit stabilized by numerous tertiary interactions, and an unanticipated organization of the catalytic centre. Structure-guided mutagenesis provided insights into the basis for regioselectivity of the ligation reaction and allowed remarkable manipulation of substrate recognition and reaction rate. Moreover, the structure highlights how the specific properties of deoxyribose are reflected in the backbone conformation of the DNA catalyst, in support of its intricate three-dimensional organization. The structural principles underlying the catalytic ability of DNA elucidate differences and similarities in DNA versus RNA catalysts, which is relevant for comprehending the privileged position of folded RNA in the prebiotic world and in current organisms.

  20. Large Area 2D and 3D Colloidal Photonic Crystals Fabricated by a Roll-to-Roll Langmuir-Blodgett Method.

    Science.gov (United States)

    Parchine, Mikhail; McGrath, Joe; Bardosova, Maria; Pemble, Martyn E

    2016-06-14

    We present our results on the fabrication of large area colloidal photonic crystals on flexible poly(ethylene terephthalate) (PET) film using a roll-to-roll Langmuir-Blodgett technique. Two-dimensional (2D) and three-dimensional (3D) colloidal photonic crystals from silica nanospheres (250 and 550 nm diameter) with a total area of up to 340 cm(2) have been fabricated in a continuous manner compatible with high volume manufacturing. In addition, the antireflective properties and structural integrity of the films have been enhanced via the use of a second roll-to-roll process, employing a slot-die coating of an optical adhesive over the photonic crystal films. Scanning electron microscopy images, atomic force microscopy images, and UV-vis optical transmission and reflection spectra of the fabricated photonic crystals are analyzed. This analysis confirms the high quality of the 2D and 3D photonic crystals fabricated by the roll-to-roll LB technique. Potential device applications of the large area 2D and 3D colloidal photonic crystals on flexible PET film are briefly reviewed.

  1. Perfectly matched layer stability in 3-D finite-difference time-domain simulation of electroacoustic wave propagation in piezoelectric crystals with different symmetry class.

    Science.gov (United States)

    Nova, Omar; Peña, Néstor; Ney, Michel

    2015-03-01

    Perfectly matched layer stability in 3-D finite-difference time-domain simulations is demonstrated for two piezoelectric crystals: barium sodium niobate and bismuth germanate. Stability is achieved by adapting the discretization grid to meet a central-difference scheme. Stability is demonstrated by showing that the total energy of the piezoelectric system remains constant in the steady state.

  2. Development and evaluation of a LOR-based image reconstruction with 3D system response modeling for a PET insert with dual-layer offset crystal design

    Science.gov (United States)

    Zhang, Xuezhu; Stortz, Greg; Sossi, Vesna; Thompson, Christopher J.; Retière, Fabrice; Kozlowski, Piotr; Thiessen, Jonathan D.; Goertzen, Andrew L.

    2013-12-01

    In this study we present a method of 3D system response calculation for analytical computer simulation and statistical image reconstruction for a magnetic resonance imaging (MRI) compatible positron emission tomography (PET) insert system that uses a dual-layer offset (DLO) crystal design. The general analytical system response functions (SRFs) for detector geometric and inter-crystal penetration of coincident crystal pairs are derived first. We implemented a 3D ray-tracing algorithm with 4π sampling for calculating the SRFs of coincident pairs of individual DLO crystals. The determination of which detector blocks are intersected by a gamma ray is made by calculating the intersection of the ray with virtual cylinders with radii just inside the inner surface and just outside the outer-edge of each crystal layer of the detector ring. For efficient ray-tracing computation, the detector block and ray to be traced are then rotated so that the crystals are aligned along the X-axis, facilitating calculation of ray/crystal boundary intersection points. This algorithm can be applied to any system geometry using either single-layer (SL) or multi-layer array design with or without offset crystals. For effective data organization, a direct lines of response (LOR)-based indexed histogram-mode method is also presented in this work. SRF calculation is performed on-the-fly in both forward and back projection procedures during each iteration of image reconstruction, with acceleration through use of eight-fold geometric symmetry and multi-threaded parallel computation. To validate the proposed methods, we performed a series of analytical and Monte Carlo computer simulations for different system geometry and detector designs. The full-width-at-half-maximum of the numerical SRFs in both radial and tangential directions are calculated and compared for various system designs. By inspecting the sinograms obtained for different detector geometries, it can be seen that the DLO crystal

  3. Chrysotile effects on human lung cell carcinoma in culture: 3-D reconstruction and DNA quantification by image analysis

    Directory of Open Access Journals (Sweden)

    Machado-Santelli Glaucia M

    2008-06-01

    Full Text Available Abstract Background Chrysotile is considered less harmful to human health than other types of asbestos fibers. Its clearance from the lung is faster and, in comparison to amphibole forms of asbestos, chrysotile asbestos fail to accumulate in the lung tissue due to a mechanism involving fibers fragmentation in short pieces. Short exposure to chrysotile has not been associated with any histopathological alteration of lung tissue. Methods The present work focuses on the association of small chrysotile fibers with interphasic and mitotic human lung cancer cells in culture, using for analyses confocal laser scanning microscopy and 3D reconstructions. The main goal was to perform the analysis of abnormalities in mitosis of fibers-containing cells as well as to quantify nuclear DNA content of treated cells during their recovery in fiber-free culture medium. Results HK2 cells treated with chrysotile for 48 h and recovered in additional periods of 24, 48 and 72 h in normal medium showed increased frequency of multinucleated and apoptotic cells. DNA ploidy of the cells submitted to the same chrysotile treatment schedules showed enhanced aneuploidy values. The results were consistent with the high frequency of multipolar spindles observed and with the presence of fibers in the intercellular bridge during cytokinesis. Conclusion The present data show that 48 h chrysotile exposure can cause centrosome amplification, apoptosis and aneuploid cell formation even when long periods of recovery were provided. Internalized fibers seem to interact with the chromatin during mitosis, and they could also interfere in cytokinesis, leading to cytokinesis failure which forms aneuploid or multinucleated cells with centrosome amplification.

  4. 3D Micro-topography of Transferred Laboratory and Natural Ice Crystal Surfaces Imaged by Cryo and Environmental Scanning Electron Microscopy

    Science.gov (United States)

    Magee, N. B.; Boaggio, K.; Bancroft, L.; Bandamede, M.

    2015-12-01

    Recent work has highlighted micro-scale roughness on the surfaces of ice crystals grown and imaged in-situ within the chambers of environmental scanning electron microscopes (ESEM). These observations appear to align with theoretical and satellite observations that suggest a prevalence of rough ice in cirrus clouds. However, the atmospheric application of the lab observations are indeterminate because the observations have been based only on crystals grown on substrates and in pure-water vapor environments. In this work, we present details and results from the development of a transfer technique which allows natural and lab-grown ice and snow crystals to be captured, preserved, and transferred into the ESEM for 3D imaging. Ice crystals were gathered from 1) natural snow, 2) a balloon-borne cirrus particle capture device, and 3) lab-grown ice crystals from a diffusion chamber. Ice crystals were captured in a pre-conditioned small-volume (~1 cm3) cryo-containment cell. The cell was then sealed closed and transferred to a specially-designed cryogenic dewer (filled with liquid nitrogen or crushed dry ice) for transport to a new Hitachi Field Emission, Variable Pressure SEM (SU-5000). The cryo-cell was then removed from the dewer and quickly placed onto the pre-conditioned cryo transfer stage attached to the ESEM (Quorum 3010T). Quantitative 3D topographical digital elevation models of ice surfaces are reported from SEM for the first time, including a variety of objective measures of statistical surface roughness. The surfaces of the transported crystals clearly exhibit signatures of mesoscopic roughening that are similar to examples of roughness seen in ESEM-grown crystals. For most transported crystals, the habits and crystal edges are more intricate that those observed for ice grown directly on substrates within the ESEM chamber. Portions of some crystals do appear smooth even at magnification greater than 1000x, a rare observation in our ESEM-grown crystals. The

  5. Synthesis, characterization and magnetic property of 3D flower-like nickel sulphide nanocrystals through decomposing bis(thiourea) nickel(II) chloride crystals

    Indian Academy of Sciences (India)

    Peng-Fei Yin; Li-Li Sun; Chao Zhou; Yu-Heng Sun; Xiang-Yu Han; Cheng-Rong Deng

    2015-02-01

    Three-dimensional (3D) flower-like cubic Ni3S4 nanoplates with single crystalline nature were successfully prepared through decomposing bis(thiourea) nickel(II) chloride crystals (BTNC). The samples were characterized by X-ray diffraction, scanning electron microscope, transmission electron microscope, selected area electron diffraction and Raman spectroscopy. Results show that the as-prepared products are pure cubic Ni3S4 and stable in range of 180–220°C with single crystal nature providing high surface areas, and higher reaction temperature leads to lower surface areas. Typical Raman peaks of the as-synthesized 3D flower-like cubic Ni3S4 at 200°C are located at 239, 286, 337, 379, 423, 478 and 630 cm-1. Magnetization measurement indicates that single crystalline Ni3S4 nanoplates prepared at 200°C displays antiferromagnetic behaviour.

  6. A SiPM-based isotropic-3D PET detector X'tal cube with a three-dimensional array of 1 mm(3) crystals.

    Science.gov (United States)

    Yamaya, Taiga; Mitsuhashi, Takayuki; Matsumoto, Takahiro; Inadama, Naoko; Nishikido, Fumihiko; Yoshida, Eiji; Murayama, Hideo; Kawai, Hideyuki; Suga, Mikio; Watanabe, Mitsuo

    2011-11-07

    We are developing a novel, general purpose isotropic-3D PET detector X'tal cube which has high spatial resolution in all three dimensions. The research challenge for this detector is implementing effective detection of scintillation photons by covering six faces of a segmented crystal block with silicon photomultipliers (SiPMs). In this paper, we developed the second prototype of the X'tal cube for a proof-of-concept. We aimed at realizing an ultimate detector with 1.0 mm(3) cubic crystals, in contrast to our previous development using 3.0 mm(3) cubic crystals. The crystal block was composed of a 16 × 16 × 16 array of lutetium gadolinium oxyorthosilicate (LGSO) crystals 0.993 × 0.993 × 0.993 mm(3) in size. The crystals were optically glued together without inserting any reflector inside and 96 multi-pixel photon counters (MPPCs, S10931-50P, i.e. six faces each with a 4 × 4 array of MPPCs), each having a sensitive area of 3.0 × 3.0 mm(2), were optically coupled to the surfaces of the crystal block. Almost all 4096 crystals were identified through Anger-type calculation due to the finely adjusted reflector sheets inserted between the crystal block and light guides. The reflector sheets, which formed a belt of 0.5 mm width, were placed to cover half of the crystals of the second rows from the edges in order to improve identification performance of the crystals near the edges. Energy resolution of 12.7% was obtained at 511 keV with almost uniform light output for all crystal segments thanks to the effective detection of the scintillation photons.

  7. New Synthetic and Assembly Methodology for Guiding Nanomaterial Assembly with High Fidelity into 1D Clusters and 3D Crystals Using Biomimetic Interactions

    Science.gov (United States)

    2015-03-26

    AFRL-OSR-VA-TR-2015-0105 NEW SYNTHETIC AND ASSEMBLY METHODOLOGY FOR GUIDING NANOMATERIAL ASSEMBLY WITH HI Mathew Maye SYRACUSE UNIVERSITY Final...2010 - 12/31/2014 New Synthetic and Assembly Methodology for Guiding Nanomaterial Assembly with High Fidelity into ID cluster and 3D Crystals Using...1) Principle Investigator Name: Mathew M. Maye (2) Grant/Contract Title: PECASE: New Synthetic and Assembly Methodology for Guiding Nanomaterial

  8. 3D global analysis of CZ-Si growth in a transverse magnetic field with rotating crucible and crystal

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Lijun; Kakimoto, Koichi [Research Institute for Applied Mechanics, Kyushu University, 6-1, Kasuga-Koen, Kasuga 816-8580 (Japan)

    2005-04-01

    Three-dimensional global simulations were carried out for a small Czochralski furnace for silicon crystal growth with a recently developed global model. The furnace is placed in a transverse magnetic field with rotating crucible and crystal. The convective, conductive and radiative heat transfers in the entire furnace were solved in a three-dimensionally conjugated way. Three-dimensional distributions of temperature and velocity were analyzed. The melt-crystal interface was found to have nearly rotational symmetry, and the azimuthal non-uniformity of temperature is much weaker on the crystal and crucible sidewalls in the case of high rotation rates of crucible and crystal than in the case of non-rotating crucible and crystal. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  9. Extended depth-of-field 3D endoscopy with synthetic aperture integral imaging using an electrically tunable focal-length liquid-crystal lens.

    Science.gov (United States)

    Wang, Yu-Jen; Shen, Xin; Lin, Yi-Hsin; Javidi, Bahram

    2015-08-01

    Conventional synthetic-aperture integral imaging uses a lens array to sense the three-dimensional (3D) object or scene that can then be reconstructed digitally or optically. However, integral imaging generally suffers from a fixed and limited range of depth of field (DOF). In this Letter, we experimentally demonstrate a 3D integral-imaging endoscopy with tunable DOF by using a single large-aperture focal-length-tunable liquid crystal (LC) lens. The proposed system can provide high spatial resolution and an extended DOF in synthetic-aperture integral imaging 3D endoscope. In our experiments, the image plane in the integral imaging pickup process can be tuned from 18 to 38 mm continuously using a large-aperture LC lens, and the total DOF is extended from 12 to 51 mm. To the best of our knowledge, this is the first report on synthetic aperture integral imaging 3D endoscopy with a large-aperture LC lens that can provide high spatial resolution 3D imaging with an extend DOF.

  10. Crystal-field spectra of 3d super n impurities in II-VI and III-V compound semiconductors.

    Science.gov (United States)

    Allen, J. W.; Baranowski, J. M.; Pearson, G. L.

    1967-01-01

    Impurity crystal-field spectra in II-VI and III- V compound semiconductors used to predict unexplored systems spectra impurity crystal-field spectra in II-VI and III-V compound semiconductors used to predict unexplored systems spectra

  11. 3D investigation on polystyrene colloidal crystals by floatage self-assembly with mixed solvent via synchrotron radiation x-ray phase-contrast computed tomography

    Science.gov (United States)

    Fu, Yanan; Xie, Honglan; Deng, Biao; Du, Guohao; Xiao, Tiqiao

    2017-06-01

    The floatage self-assembly method was introduced with mixed solvent as the medium of polystyrene sphere suspension to fabricate the colloidal crystal. The three dimensional (3D) void system of the colloidal crystal was noninvasively characterized by synchrotron radiation phase-contrast computed tomography, and the quantitative image analysis was implemented aiming to the polystyrene sphere colloidal crystal. Comparing with gravity sedimentation method, the three samples fabricated from floatage self-assembly with mixed solvents have the lowest porosity, and when ethylene glycol and water were mixed with ratio of 1:1, the lowest porosity of 27.49% could be achieved, that has been very close to the minimum porosity of ordered 3D monodisperse sphere array (26%). In single slices, the porosities and fractal dimension for the voids were calculated. The results showed that two factors would significantly influence the porosity of the whole colloidal crystal: the first deposited sphere layer's orderliness and the sedimentation speed of the spheres. The floatage self-assembly could induce a stable close-packing process, resulted from the powerful nucleation force-lateral capillary force coupled with the mixed solvent to regulate the floating upward speed for purpose of matching the assembly rate.

  12. Crystal fields of porphyrins and phthalocyanines from polarization-dependent 2p-to-3d multiplets

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Phillip S.; Boukahil, Idris; Himpsel, F. J., E-mail: fhimpsel@wisc.edu [Department of Physics, University of Wisconsin-Madison, 1150 University Ave., Madison, Wisconsin 53706 (United States); García-Lastra, J. M. [Department of Energy Conversion and Storage, Technical University of Denmark, 4000 Roskilde (Denmark); Kennedy, Colton K.; Jersett, Nathan J.; Cook, Peter L. [Natural Sciences Department, University of Wisconsin-Superior, Belknap and Catlin, Superior, Wisconsin 54880 (United States)

    2014-03-21

    Polarization-dependent X-ray absorption spectroscopy is combined with density functional calculations and atomic multiplet calculations to determine the crystal field parameters 10Dq, Ds, and Dt of transition metal phthalocyanines and octaethylporphyrins (Mn, Fe, Co, Ni). The polarization dependence facilitates the assignment of the multiplets in terms of in-plane and out-of-plane orbitals and avoids ambiguities. Crystal field values from density functional calculations provide starting values close to the optimum fit of the data. The resulting systematics of the crystal field can be used for optimizing electron-hole separation in dye-sensitized solar cells.

  13. Crystal fields of porphyrins and phthalocyanines from polarization-dependent 2p-to-3d multiplets

    Science.gov (United States)

    Johnson, Phillip S.; García-Lastra, J. M.; Kennedy, Colton K.; Jersett, Nathan J.; Boukahil, Idris; Himpsel, F. J.; Cook, Peter L.

    2014-03-01

    Polarization-dependent X-ray absorption spectroscopy is combined with density functional calculations and atomic multiplet calculations to determine the crystal field parameters 10Dq, Ds, and Dt of transition metal phthalocyanines and octaethylporphyrins (Mn, Fe, Co, Ni). The polarization dependence facilitates the assignment of the multiplets in terms of in-plane and out-of-plane orbitals and avoids ambiguities. Crystal field values from density functional calculations provide starting values close to the optimum fit of the data. The resulting systematics of the crystal field can be used for optimizing electron-hole separation in dye-sensitized solar cells.

  14. Polymorphic crystal structures of an all-AT DNA dodecamer.

    Science.gov (United States)

    Acosta-Reyes, Francisco J; Subirana, Juan A; Pous, Joan; Sánchez-Giraldo, Raquel; Condom, Núria; Baldini, Roberto; Malinina, Lucy; Campos, J Lourdes

    2015-03-01

    In this work, we explore the influence of different solvents and ions on the crystallization behavior of an all-AT dodecamer d(AATAAATTTATT)2 In all cases, the oligonucleotides are found as continuous columns of stacked duplexes. The spatial organization of such columns is variable; consequently we have obtained seven different crystal forms. The duplexes can be made to crystallize in either parallel or crossed columns. Such versatility in the formation of a variety of crystal forms is characteristic for this sequence. It had not been previously reported for any other sequence. In all cases, the oligonucleotide duplexes have been found to crystallize in the B form. The crystallization conditions determine the organization of the crystal, although no clear local interactions have been detected. Mg(2+) and Ni(2+) can be used in order to obtain compact crossed structures. DNA-DNA interactions in the crystals of our all-AT duplexes present crossovers which are different from those previously reported for mixed sequence oligonucleotides. Our results demonstrate that changes in the ionic atmosphere and the crystallization solvent have a strong influence on the DNA-DNA interactions. Similar ionic changes will certainly influence the biological activity of DNA. Modulation of the crystal structure by ions should also be explored in DNA crystal engineering. Liquid crystals with a peculiar macroscopic shape have also been observed.

  15. Crystal fields of porphyrins and phthalocyanines from polarization-dependent 2p-to-3d multiplets

    OpenAIRE

    Johnson, Phillip S.; García Lastra, Juan Maria; Kennedy, Colton K.; Jersett, Nathan J.; Boukahil, Idris; Himpsel, F. J.; Cook, Peter L.

    2014-01-01

    Polarization-dependent X-ray absorption spectroscopy is combined with density functional calculations and atomic multiplet calculations to determine the crystal field parameters 10Dq, Ds, and Dt of transition metal phthalocyanines and octaethylporphyrins (Mn, Fe, Co, Ni). The polarization dependence facilitates the assignment of the multiplets in terms of in-plane and out-of-plane orbitals and avoids ambiguities. Crystal field values from density functional calculations provide starting value...

  16. Shape optimization of solid-air porous phononic crystal slabs with widest full 3D bandgap for in-plane acoustic waves

    Science.gov (United States)

    D'Alessandro, Luca; Bahr, Bichoy; Daniel, Luca; Weinstein, Dana; Ardito, Raffaele

    2017-09-01

    The use of Phononic Crystals (PnCs) as smart materials in structures and microstructures is growing due to their tunable dynamical properties and to the wide range of possible applications. PnCs are periodic structures that exhibit elastic wave scattering for a certain band of frequencies (called bandgap), depending on the geometric and material properties of the fundamental unit cell of the crystal. PnCs slabs can be represented by plane-extruded structures composed of a single material with periodic perforations. Such a configuration is very interesting, especially in Micro Electro-Mechanical Systems industry, due to the easy fabrication procedure. A lot of topologies can be found in the literature for PnCs with square-symmetric unit cell that exhibit complete 2D bandgaps; however, due to the application demand, it is desirable to find the best topologies in order to guarantee full bandgaps referred to in-plane wave propagation in the complete 3D structure. In this work, by means of a novel and fast implementation of the Bidirectional Evolutionary Structural Optimization technique, shape optimization is conducted on the hole shape obtaining several topologies, also with non-square-symmetric unit cell, endowed with complete 3D full bandgaps for in-plane waves. Model order reduction technique is adopted to reduce the computational time in the wave dispersion analysis. The 3D features of the PnC unit cell endowed with the widest full bandgap are then completely analyzed, paying attention to engineering design issues.

  17. Tris(bipyridineMetal(II-Templated Assemblies of 3D Alkali-Ruthenium Oxalate Coordination Frameworks: Crystal Structures, Characterization and Photocatalytic Activity in Water Reduction

    Directory of Open Access Journals (Sweden)

    Alla Dikhtiarenko

    2016-02-01

    Full Text Available A series of 3D oxalate-bridged ruthenium-based coordination polymers with the formula of {[ZII(bpy3][MIRu(C2O43]}n (ZII = Zn2+ (1, Cu2+ (3, 4, Ru2+ (5, 6, Os2+ (7, 8; MI = Li+, Na+; bpy = 2,2’-bipyridine and {[ZnII(bpy3](H2O[LiRu(C2O43]}n (2 has been synthesized at room temperature through a self-assembly reaction in aqueous media and characterized by single-crystal and powder X-ray diffraction, elemental analysis, infrared and diffuse reflectance UV–Vis spectroscopy and thermogravimetric analysis. The crystal structures of all compounds comprise chiral 3D honeycomb-like polymeric nets of the srs-type, which possess triangular anionic cages where [ZII(bpy3]2+ cationic templates are selectively embedded. Structural analysis reveals that the electronic configuration of the cationic guests is affected by electrostatic interaction with the anionic framework. Moreover, the MLCT bands gaps values for 1–8 can be tuned in a rational way by judicious choice of [ZII(bpy3]2+ guests. The 3D host-guest polymeric architectures can be used as self-supported heterogeneous photocatalysts for the reductive splitting of water, exhibiting photocatalytic activity for the evolution of H2 under UV light irradiation.

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

    Science.gov (United States)

    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.

  19. Final LDRD report : enhanced spontaneous emission rate in visible III-nitride LEDs using 3D photonic crystal cavities.

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Arthur Joseph; Subramania, Ganapathi S.; Coley, Anthony J.; Lee, Yun-Ju; Li, Qiming; Wang, George T.; Luk, Ting Shan; Koleske, Daniel David; Fullmer, Kristine Wanta

    2009-09-01

    The fundamental spontaneous emission rate for a photon source can be modified by placing the emitter inside a periodic dielectric structure allowing the emission to be dramatically enhanced or suppressed depending on the intended application. We have investigated the relatively unexplored realm of interaction between semiconductor emitters and three dimensional photonic crystals in the visible spectrum. Although this interaction has been investigated at longer wavelengths, very little work has been done in the visible spectrum. During the course of this LDRD, we have fabricated TiO{sub 2} logpile photonic crystal structures with the shortest wavelength band gap ever demonstrated. A variety of different emitters with emission between 365 nm and 700 nm were incorporated into photonic crystal structures. Time-integrated and time-resolved photoluminescence measurements were performed to measure changes to the spontaneous emission rate. Both enhanced and suppressed emission were demonstrated and attributed to changes to the photonic density of states.

  20. Circular Dichroism in the 3d and 4d Core Photoabsorption for Ferromagnetic Ce Compounds —Interplay of Hybridization, Spin Orbit Interaction and Crystal Field—

    Science.gov (United States)

    Jo, Takeo; Imada, Shin

    1990-04-01

    The Ce 3d- and 4d-core photoabsorption spectra (3d XAS and 4d XAS) of ferromagnetic mixed valent Ce compounds are calculated on the basis of the impurity Anderson model. The model takes into account the Coulomb interaction producing multiplet structures, the spin-orbit interaction, the crystal field effect and the molecular field acting on the 4f spin. The calculation shows a strong circular dichroism even for the Ce magnetic moment of ˜0.5 μB. The dichroism is furthermore shown to be a powerful method to measure the spin and orbital contributions to the 4f moment. On the basis of the calculation, the 4f magnetic state of the ferromagnet CeRh3B2 is discussed.

  1. Crystal fields of porphyrins and phthalocyanines from polarization-dependent 2p-to-3d multiplets

    DEFF Research Database (Denmark)

    Johnson, Phillip S.; García Lastra, Juan Maria; Kennedy, Colton K.;

    2014-01-01

    Polarization-dependent X-ray absorption spectroscopy is combined with density functional calculations and atomic multiplet calculations to determine the crystal field parameters 10Dq, Ds, and Dt of transition metal phthalocyanines and octaethylporphyrins (Mn, Fe, Co, Ni). The polarization...

  2. Magnetotransport properties of ferromagnetic LaMnO{sub 3+d}elta nano-sized crystals

    Energy Technology Data Exchange (ETDEWEB)

    Markovich, V., E-mail: markoviv@bgu.ac.i [Department of Physics, Ben-Gurion University of the Negev, 84105 Beer-Sheva (Israel); Jung, G. [Department of Physics, Ben-Gurion University of the Negev, 84105 Beer-Sheva (Israel); Fita, I. [Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw (Poland); Donetsk Institute for Physics and Technology, National Academy of Sciences, 83114 Donetsk (Ukraine); Mogilyansky, D. [Materials Engineering Department, Ben-Gurion University of the Negev, 84105 Beer-Sheva (Israel); Wu, X. [Department of Physics, Ben-Gurion University of the Negev, 84105 Beer-Sheva (Israel); Department of Materials Engineering, Monash University, Clayton 3800 (Australia); Wisniewski, A.; Puzniak, R. [Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw (Poland); Titelman, L.; Vradman, L.; Herskowitz, M. [Blechner Center for Industrial Catalysis and Process Development, Department of Chemical Engineering, Ben-Gurion University of the Negev, 84105 Beer-Sheva (Israel); Gorodetsky, G. [Department of Physics, Ben-Gurion University of the Negev, 84105 Beer-Sheva (Israel)

    2010-05-15

    Transport and magnetic properties of LaMnO{sub 3+d}elta nanoparticles with average size of 18 nm have been investigated. The ensemble of nanoparticles exhibits a paramagnetic to ferromagnetic (FM) transition at T{sub C}approx246 K, while the spontaneous magnetization disappears at Tapprox270 K. It was found that the blocking temperature lies slightly below T{sub C}. The temperature dependence of the resistivity shows a metal-insulator transition at Tapprox192 K and low-temperature upturn at T<50 K. The transport at low temperatures is controlled by the charging energy and spin-dependent tunnelling through grain boundaries. The low temperature I-V characteristics are well described by indirect tunnelling model while at higher temperatures both direct and resonant tunnelling dominates.

  3. Synthesis and Crystal and Band Structures of YbCu_6In_6 with 3D Framework

    Institute of Scientific and Technical Information of China (English)

    LEI Xiao-Wu; YUE Cheng-Yang

    2012-01-01

    A new intermetallic compound,YbCu6In6,has been synthesized by solid-state reaction of the corresponding pure elements in a welded tantalum tube at high temperature.Its crystal structure was established by single-crystal X-ray diffraction.YbCu6In6 crystallizes in tetragonal space group I4/mmm with a = 9.2283(5),c = 5.4015(4),V = 460.00(5) 3,Z = 2,Mr = 1243.20,Dc = 8.976 g/cm3,μ = 38.243 mm-1,F(000) = 1076,and the final R = 0.0258 and wR = 0.0602 for 173 observed reflections with I 〉 2σ(I).The structure of YbCu6In6 belongs to the ThMn12 type.It is isostructural with RECu6In6(RE = Y,Ce,Pr,Nd,Gd,Tb,Dy),containing one-dimensional(1D) [Cu10In6] cluster chain along the c axis,which is interconnected via sharing the Cu(1) atoms to form a three-dimensional(3D) [Cu6In6] framework with Yb atoms encapsulated in the 1D tunnels along the c axis.Band structure calculations based on Density Functional Theory(DFT) method indicate that YbCu6In6 is metallic.

  4. DNA-mediated nanoparticle crystallization into Wulff polyhedra.

    Science.gov (United States)

    Auyeung, Evelyn; Li, Ting I N G; Senesi, Andrew J; Schmucker, Abrin L; Pals, Bridget C; de la Cruz, Monica Olvera; Mirkin, Chad A

    2014-01-02

    Crystallization is a fundamental and ubiquitous process much studied over the centuries. But although the crystallization of atoms is fairly well understood, it remains challenging to predict reliably the outcome of molecular crystallization processes that are complicated by various molecular interactions and solvent involvement. This difficulty also applies to nanoparticles: high-quality three-dimensional crystals are mostly produced using drying and sedimentation techniques that are often impossible to rationalize and control to give a desired crystal symmetry, lattice spacing and habit (crystal shape). In principle, DNA-mediated assembly of nanoparticles offers an ideal opportunity for studying nanoparticle crystallization: a well-defined set of rules have been developed to target desired lattice symmetries and lattice constants, and the occurrence of features such as grain boundaries and twinning in DNA superlattices and traditional crystals comprised of molecular or atomic building blocks suggests that similar principles govern their crystallization. But the presence of charged biomolecules, interparticle spacings of tens of nanometres, and the realization so far of only polycrystalline DNA-interconnected nanoparticle superlattices, all suggest that DNA-guided crystallization may differ from traditional crystal growth. Here we show that very slow cooling, over several days, of solutions of complementary-DNA-modified nanoparticles through the melting temperature of the system gives the thermodynamic product with a specific and uniform crystal habit. We find that our nanoparticle assemblies have the Wulff equilibrium crystal structure that is predicted from theoretical considerations and molecular dynamics simulations, thus establishing that DNA hybridization can direct nanoparticle assembly along a pathway that mimics atomic crystallization.

  5. Mapping the 3D distribution of CdSe nanocrystals in highly oriented and nanostructured hybrid P3HT-CdSe films grown by directional epitaxial crystallization.

    Science.gov (United States)

    Roiban, L; Hartmann, L; Fiore, A; Djurado, D; Chandezon, F; Reiss, P; Legrand, J-F; Doyle, S; Brinkmann, M; Ersen, O

    2012-11-21

    Highly oriented and nanostructured hybrid thin films made of regioregular poly(3-hexylthiophene) and colloidal CdSe nanocrystals are prepared by a zone melting method using epitaxial growth on 1,3,5-trichlorobenzene oriented crystals. The structure of the films has been analyzed by X-ray diffraction using synchrotron radiation, electron diffraction and 3D electron tomography to afford a multi-scale structural and morphological description of the highly structured hybrid films. A quantitative analysis of the reconstructed volumes based on electron tomography is used to establish a 3D map of the distribution of the CdSe nanocrystals in the bulk of the films. In particular, the influence of the P3HT-CdSe ratio on the 3D structure of the hybrid layers has been analyzed. In all cases, a bi-layer structure was observed. It is made of a first layer of pure oriented semi-crystalline P3HT grown epitaxially on the TCB substrate and a second P3HT layer containing CdSe nanocrystals uniformly distributed in the amorphous interlamellar zones of the polymer. The thickness of the P3HT layer containing CdSe nanoparticles increases gradually with increasing content of NCs in the films. A growth model is proposed to explain this original transversal organization of CdSe NCs in the oriented matrix of P3HT.

  6. Synthesis and crystal structure study of 2′-Se-adenosine-derivatized DNA

    Institute of Scientific and Technical Information of China (English)

    SALON; Jozef

    2010-01-01

    The selenium derivatization of nucleic acids is a novel and promising strategy for 3D structure determination of nucleic acids.Selenium can serve as an excellent anomalous scattering center to solve the phase problem,which is one of the two major bottlenecks in macromolecule X-ray crystallography.The other major bottleneck is crystallization.It has been demonstrated that the incorporated selenium functionality at the 2′-positions of the nucleosides and nucleotides is stable and does not cause significant structure perturbation.Furthermore,it was observed that the 2′-Se-derivatization could facilitate crystallization of oligonucleotides with fast crystal growth and high diffraction quality.Herein,we describe a convenient synthesis of the 2′-Se-adenosine phosphoramidite,and report the first synthesis and X-ray crystal structure determination of the DNA containing the 2′-Se-A derivatization.The 3D structure of 2′-Se-A-DNA decamer 5′-GTACGCGT(2′-Se-A)C-3′2 was determined at 1.75 ? resolution,the 2′-Se-functionality points to the minor groove,and the Se-modified and native structures are virtually identical.Moreover,we have observed that the 2′-Se-A modification can greatly facilitate the crystal growth with high diffraction quality.In conjunction with the crystallization facilitation by the 2′-Se-U and 2′-Se-T,this novel observation on the 2′-Se-A functionality suggests that the 2′-Se moiety is sole responsible for the crystallization facilitation and the identity of nucleobases does not influence the crystal growth significantly.

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

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Huai-Xia, E-mail: yanghuaixia886@163.com [Pharmacy College, Henan University of Traditional Chinese Medicine, Zhengzhou 450008 (China); Liang, Zhen; Hao, Bao-Lian [Pharmacy College, Henan University of Traditional Chinese Medicine, Zhengzhou 450008 (China); Meng, Xiang-Ru, E-mail: mxr@zzu.edu.cn [The College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001 (China)

    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.

  8. Effect of anchor positioning on binding and diffusion of elongated 3D DNA nanostructures on lipid membranes

    Science.gov (United States)

    Khmelinskaia, Alena; Franquelim, Henri G.; Petrov, Eugene P.; Schwille, Petra

    2016-05-01

    DNA origami is a state-of-the-art technology that enables the fabrication of nano-objects with defined shapes, to which functional moieties, such as lipophilic anchors, can be attached with a nanometre scale precision. Although binding of DNA origami to lipid membranes has been extensively demonstrated, the specific requirements necessary for membrane attachment are greatly overlooked. Here, we designed a set of amphipathic rectangular-shaped DNA origami structures with varying placement and number of chol-TEG anchors used for membrane attachment. Single- and multiple-cholesteryl-modified origami nanostructures were produced and studied in terms of their membrane localization, density and dynamics. We show that the positioning of at least two chol-TEG moieties near the corners is essential to ensure efficient membrane binding of large DNA nanostructures. Quantitative fluorescence correlation spectroscopy data further confirm that increasing the number of corner-positioned chol-TEG anchors lowers the dynamics of flat DNA origami structures on freestanding membranes. Taken together, our approach provides the first evidence of the importance of the location in addition to the number of hydrophobic moieties when rationally designing minimal DNA nanostructures with controlled membrane binding.

  9. Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes.

    Science.gov (United States)

    Pujato, Mario; Kieken, Fabien; Skiles, Amanda A; Tapinos, Nikos; Fiser, Andras

    2014-12-16

    Proper cell functioning depends on the precise spatio-temporal expression of its genetic material. Gene expression is controlled to a great extent by sequence-specific transcription factors (TFs). Our current knowledge on where and how TFs bind and associate to regulate gene expression is incomplete. A structure-based computational algorithm (TF2DNA) is developed to identify binding specificities of TFs. The method constructs homology models of TFs bound to DNA and assesses the relative binding affinity for all possible DNA sequences using a knowledge-based potential, after optimization in a molecular mechanics force field. TF2DNA predictions were benchmarked against experimentally determined binding motifs. Success rates range from 45% to 81% and primarily depend on the sequence identity of aligned target sequences and template structures, TF2DNA was used to predict 1321 motifs for 1825 putative human TF proteins, facilitating the reconstruction of most of the human gene regulatory network. As an illustration, the predicted DNA binding site for the poorly characterized T-cell leukemia homeobox 3 (TLX3) TF was confirmed with gel shift assay experiments. TLX3 motif searches in human promoter regions identified a group of genes enriched in functions relating to hematopoiesis, tissue morphology, endocrine system and connective tissue development and function. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Evaluation of the effects of 3D diffusion, crystal geometry, and initial conditions on retrieved time-scales from Fe-Mg zoning in natural oriented orthopyroxene crystals

    Science.gov (United States)

    Krimer, Daniel; Costa, Fidel

    2017-01-01

    Volcano petrologists and geochemists increasingly use time-scale determinations of magmatic processes from modeling the chemical zoning patterns in crystals. Most determinations are done using one-dimensional traverses across a two-dimensional crystal section. However, crystals are three-dimensional objects with complex shapes, and diffusion and re-equilibration occurs in multiple dimensions. Given that we can mainly study the crystals in two-dimensional petrographic thin sections, the determined time-scales could be in error if multiple dimensional and geometrical effects are not identified and accounted for. Here we report the results of a numerical study where we investigate the role of multiple dimensions, geometry, and initial conditions of Fe-Mg diffusion in an orthopyroxene crystal with the view towards proper determinations of time scales from modeling natural crystals. We found that merging diffusion fronts (i.e. diffusion from multiple directions) causes 'additional' diffusion that has the greatest influence close to the crystal's corners (i.e. where two crystal faces meet), and with longer times the affected area widens. We also found that the one-dimensional traverses that can lead to the most accurate calculated time-scales from natural crystals are along the b- crystallographic axis on the ab-plane when model inputs (concentration and zoning geometry) are taken as measured (rather than inferred from other observations). More specifically, accurate time-scales are obtained if the compositional traverses are highly symmetrical and contain a concentration plateau measured through the crystal center. On the other hand, for two-dimensional models the ab- and ac-planes are better suited if the initial (pre-diffusion) concentration and zoning geometry inputs are known or can be estimated, although these are a priory unknown, and thus, may be difficult to use in practical terms. We also found that under certain conditions, a combined one-dimensional and two

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qingfu, E-mail: zhangqingfu@lcu.edu.cn; 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.

  12. Study of 3-D stress development in parent and twin pairs of a hexagonal close-packed polycrystal: Part II - Crystal plasticity finite element modeling

    DEFF Research Database (Denmark)

    Abdolvand, Hamidreza; Majkut, Marta; Oddershede, Jette

    2015-01-01

    -of-mass positions and volumes as measured by three-dimensional X-ray diffraction (3DXRD) microscopy. The constructed microstructure is meshed with different element densities and for different numbers of grains. Then a selected group of twin and parent pairs are studied. It is shown that the measured average stress...... each grain, stresses in the parent and twin are quite different if they are plotted in the global coordinate system. However, if the stress tensor is rotated into the local coordinate system of the twin habit plane, all the stress components averaged over the presented population are close, except......Stress heterogeneity within each individual grain of polycrystalline Zircaloy-2 is studied using a crystal plasticity finite element (CPFE) model. For this purpose, the weighted Voronoi tessellation method is used to construct 3D geometries of more than 2600 grains based on their center...

  13. Synthesis, crystal structure and photo luminescent property of a 3D metal-organic hybrid of Cd(II) constructed by two different bridging carboxylate

    Indian Academy of Sciences (India)

    Biswajit Bhattacharya; Rajdip Dey; Debajyoti Ghoshal

    2013-05-01

    A solvothermal reaction of cadmium (II) nitrate with succinic acid and isonicotinic acid creates a novel 3D metal-organic framework, [Cd3(isonicotinate)2(suc)2] (1). Single crystal X-ray structure determination reveals that complex 1 posses two crystallographically independent Cd(II) centres. The succinate anion acts here as a heptadented ligand and binds five Cd(II) centre simultaneously. The heptacoordinated Cd(II) centres are oxo-bridged by succinate moiety and the hexacoordinated metal centres are terminally connected through four different succinate moiety to make the overall 2D sheet arrangement. In unit cell, the ratio of hexadented Cd(II) and heptadented Cd(II) is 1:2. The new compound was also characterized by luminescence spectra and compared with the luminescence spectra of the pure isonicotinic acid.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2017-05-01

    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.

  16. CCDC 1004906: Experimental Crystal Structure Determination : 5,11-bis(4-t-Butylphenyl)indeno[2,1-b]indeno[1',2':4,5]thieno[2,3-d]thiophene

    KAUST Repository

    Shi, Xueliang

    2014-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  17. CCDC 1024868: Experimental Crystal Structure Determination : tris(mu-3,4,5,6-tetrafluorobenzene-1,2-diyl)-tri-mercury bisthieno[3,2-b:2',3'-d]thiophene 1,2-dichloroethane solvate

    KAUST Repository

    Castañeda, Raúl

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  18. CCDC 1024867: Experimental Crystal Structure Determination : tris(mu-3,4,5,6-tetrafluorobenzene-1,2-diyl)-tri-mercury bisthieno[3,2-b:2',3'-d]thiophene dichloromethane solvate

    KAUST Repository

    Castañeda, Raúl

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  19. CCDC 1004907: Experimental Crystal Structure Determination : (bisindeno[1',2':4,5]thieno[3,2-b:2',3'-d]thiene-5,8-diyldiethyne-2,1-diyl)bis(tri-isopropylsilane)

    KAUST Repository

    Shi, Xueliang

    2014-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  20. CCDC 1004904: Experimental Crystal Structure Determination : (Indeno[2,1-b]indeno[1',2':4,5]thieno[2,3-d]thiene-5,11-diyldiethyne-2,1-diyl)bis(tri-isopropylsilane)

    KAUST Repository

    Shi, Xueliang

    2014-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  1. Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies

    Directory of Open Access Journals (Sweden)

    Stegmaier Philip

    2010-05-01

    Full Text Available Abstract Background Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription factors in the literature, however, for many of them the corresponding DNA-binding motifs remain uncharacterized. Results The position weight matrices (PWMs of transcription factors from different structural classes have been determined using a knowledge-based statistical potential. The scoring function calibrated against crystallographic data on protein-DNA contacts recovered PWMs of various members of widely studied transcription factor families such as p53 and NF-κB. Where it was possible, extensive comparison to experimental binding affinity data and other physical models was made. Although the p50p50, p50RelB, and p50p65 dimers belong to the same family, particular differences in their PWMs were detected, thereby suggesting possibly different in vivo binding modes. The PWMs of p63 and p73 were computed on the basis of homology modeling and their performance was studied using upstream sequences of 85 p53/p73-regulated human genes. Interestingly, about half of the p63 and p73 hits reported by the Match algorithm in the altogether 126 promoters lay more than 2 kb upstream of the corresponding transcription start sites, which deviates from the common assumption that most regulatory sites are located more proximal to the TSS. The fact that in most of the cases the binding sites of p63 and p73 did not overlap with the p53 sites suggests that p63 and p73 could influence the p53 transcriptional activity cooperatively. The newly computed p50p50 PWM recovered 5 more experimental binding sites than the corresponding TRANSFAC matrix, while both PWMs showed comparable receiver operator characteristics. Conclusions A novel algorithm was developed to calculate position weight matrices from protein-DNA complex structures. The proposed algorithm was extensively validated

  2. Confirming the 3D Solution Structure of a Short Double-Stranded DNA Sequence Using NMR Spectroscopy

    Science.gov (United States)

    Ruhayel, Rasha A.; Berners-Price, Susan J.

    2010-01-01

    2D [superscript 1]H NOESY NMR spectroscopy is routinely used to give information on the closeness of hydrogen atoms through space. This work is based on a 2D [superscript 1]H NOESY NMR spectrum of a 12 base-pair DNA duplex. This 6-h laboratory workshop aims to provide advanced-level chemistry students with a basic, yet solid, understanding of how…

  3. Confirming the 3D Solution Structure of a Short Double-Stranded DNA Sequence Using NMR Spectroscopy

    Science.gov (United States)

    Ruhayel, Rasha A.; Berners-Price, Susan J.

    2010-01-01

    2D [superscript 1]H NOESY NMR spectroscopy is routinely used to give information on the closeness of hydrogen atoms through space. This work is based on a 2D [superscript 1]H NOESY NMR spectrum of a 12 base-pair DNA duplex. This 6-h laboratory workshop aims to provide advanced-level chemistry students with a basic, yet solid, understanding of how…

  4. Novel substituted benzothiophene and thienothiophene carboxanilides and quinolones: synthesis, photochemical synthesis, DNA-binding properties, antitumor evaluation and 3D-derived QSAR analysis.

    Science.gov (United States)

    Aleksić, Maja; Bertoša, Branimir; Nhili, Raja; Uzelac, Lidija; Jarak, Ivana; Depauw, Sabine; David-Cordonnier, Marie-Hélène; Kralj, Marijeta; Tomić, Sanja; Karminski-Zamola, Grace

    2012-06-14

    A series of new N,N-dimethylaminopropyl- and 2-imidazolinyl-substituted derivatives of benzo[b]thienyl- and thieno[2,3-b]thienylcarboxanilides and benzo[b]thieno[2,3-c]- and thieno[3',2':4,5]thieno[2,3-c]quinolones were prepared. Quinolones were prepared by the reaction of photochemical dehydrohalogenation of corresponding anilides. Carboxanilides and quinolones were tested for the antiproliferative activity. 2-Imidazolinyl-substituted derivatives showed very prominent activity. By use of the experimentally obtained antitumor measurements, 3D-derived QSAR analysis was performed for the set of compounds. Highly predictive 3D-derived QSAR models were obtained, and molecular properties that have the highest impact on antitumor activity were identified. Carboxanilides 6a-c and quinolones 9a-c and 11a were evaluated for DNA binding propensities and topoisomerases I and II inhibition as part of their mechanism of action assessment. The evaluated differences in the mode of action nicely correlate with the results of the 3D-QSAR analysis. Taken together, the results indicate which modifications of the compounds from the series should further improve their anticancer properties.

  5. Defining multiple, distinct, and shared spatiotemporal patterns of DNA replication and endoreduplication from 3D image analysis of developing maize (Zea mays L.) root tip nuclei.

    Science.gov (United States)

    Bass, Hank W; Hoffman, Gregg G; Lee, Tae-Jin; Wear, Emily E; Joseph, Stacey R; Allen, George C; Hanley-Bowdoin, Linda; Thompson, William F

    2015-11-01

    Spatiotemporal patterns of DNA replication have been described for yeast and many types of cultured animal cells, frequently after cell cycle arrest to aid in synchronization. However, patterns of DNA replication in nuclei from plants or naturally developing organs remain largely uncharacterized. Here we report findings from 3D quantitative analysis of DNA replication and endoreduplication in nuclei from pulse-labeled developing maize root tips. In both early and middle S phase nuclei, flow-sorted on the basis of DNA content, replicative labeling was widely distributed across euchromatic regions of the nucleoplasm. We did not observe the perinuclear or perinucleolar replicative labeling patterns characteristic of middle S phase in mammals. Instead, the early versus middle S phase patterns in maize could be distinguished cytologically by correlating two quantitative, continuous variables, replicative labeling and DAPI staining. Early S nuclei exhibited widely distributed euchromatic labeling preferentially localized to regions with weak DAPI signals. Middle S nuclei also exhibited widely distributed euchromatic labeling, but the label was preferentially localized to regions with strong DAPI signals. Highly condensed heterochromatin, including knobs, replicated during late S phase as previously reported. Similar spatiotemporal replication patterns were observed for both mitotic and endocycling maize nuclei. These results revealed that maize euchromatin exists as an intermingled mixture of two components distinguished by their condensation state and replication timing. These different patterns might reflect a previously described genome organization pattern, with "gene islands" mostly replicating during early S phase followed by most of the intergenic repetitive regions replicating during middle S phase.

  6. Photoinitiation and Inhibition under Monochromatic Green Light for Storage of Colored 3D Images in Holographic Polymer-Dispersed Liquid Crystals.

    Science.gov (United States)

    Chen, Guannan; Ni, Mingli; Peng, Haiyan; Huang, Feihong; Liao, Yonggui; Wang, Mingkui; Zhu, Jintao; Roy, V A L; Xie, Xiaolin

    2017-01-18

    Holographic photopolymer composites have garnered a great deal of interest in recent decades, not only because of their advantageous light sensitivity but also due to their attractive capabilities of realizing high capacity three-dimensional (3D) data storage that is long-term stable within two-dimensional (2D) thin films. For achieving high performance holographic photopolymer composites, it is of critical importance to implement precisely spatiotemporal control over the photopolymerization kinetics and gelation during holographic recording. Though a monochromatic blue light photoinitibitor has been demonstrated to be useful for improving the holographic performance, it is impractical to be employed for constructing holograms under green light due to the severe restriction of the First Law of Photochemistry, while holography under green light is highly desirable considering the relatively low cost of laser source and high tolerance to ambient vibration for image reconstruction. Herein, we disclose the concurrent photoinitiation and inhibition functions of the rose bengal (RB)/N-phenylglycine (NPG) system upon green light illumination, which result in significant enhancement of the diffraction efficiency of holographic polymer-dispersed liquid crystal (HPDLC) gratings from zero up to 87.6 ± 1.3%, with an augmentation of the RB concentration from 0.06 × 10(-3) to 9.41 × 10(-3) mol L(-1). Interestingly, no detectable variation of the ϕ(1/2)kp/kt(1/2), which reflects the initiation efficiency and kinetic constants, is given when increasing the RB concentration. The radical inhibition by RBH(•) is believed to account for the greatly improved phase separation and enhanced diffraction efficiency, through shortening the weight-average polymer chain length and subsequently delaying the photopolymerization gelation. The reconstructed colored 3D images that are easily identifiable to the naked eye under white light demonstrate great potential to be applied for advanced

  7. Crystal engineered acid–base complexes with 2D and 3D hydrogen bonding systems using p-hydroxybenzoic acid as the building block

    Directory of Open Access Journals (Sweden)

    PU SU ZHAO

    2010-04-01

    Full Text Available p-Hydroxybenzoic acid (p-HOBA was selected as the building block for self-assembly with five bases, i.e., diethylamine, tert-butylamine, cyclohexylamine, imidazole and piperazine, and generation of the corresponding acid–base complexes 1–5. Crystal structure analyses suggest that proton-transfer from the carboxyl hydrogen to the nitrogen atom of the bases can be observed in 1–4, while only in 5 does a solvent water molecule co-exist with p--HOBA and piperazine. With the presence of O–H···O hydrogen bonds in 1–4, the deprotonated p-hydroxybenzoate anions (p-HOBAA– are simply connected each other in a head-to-tail motif to form one-dimensional (1D arrays, which are further extended to distinct two-dimensional (2D (for 1 and 4 and three-dimensional (3D (for 2 and 3 networks via N–H···O interactions. While in 5, neutral acid and base are combined pair-wise by O–H···N and N–H···O bonds to form a 1D tape and then the 1D tapes are sequentially combined by water molecules to create a 3D network. Some interlayer or intralayer C–H···O, C–H···p and p×××p interactions help to stabilize the supramolecular buildings. Melting point determination analyses indicate that the five acid–base complexes are not the ordinary superposition of the reactants and they are more stable than the original reactants.

  8. Pseudo single crystal, direct-band-gap Ge{sub 0.89}Sn{sub 0.11} on amorphous dielectric layers towards monolithic 3D photonic integration

    Energy Technology Data Exchange (ETDEWEB)

    Li, Haofeng; Brouillet, Jeremy; Wang, Xiaoxin; Liu, Jifeng, E-mail: Jifeng.Liu@dartmouth.edu [Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755 (United States)

    2014-11-17

    We demonstrate pseudo single crystal, direct-band-gap Ge{sub 0.89}Sn{sub 0.11} crystallized on amorphous layers at <450 °C towards 3D Si photonic integration. We developed two approaches to seed the lateral single crystal growth: (1) utilize the Gibbs-Thomson eutectic temperature depression at the tip of an amorphous GeSn nanotaper for selective nucleation; (2) laser-induced nucleation at one end of a GeSn strip. Either way, the crystallized Ge{sub 0.89}Sn{sub 0.11} is dominated by a single grain >18 μm long that forms optoelectronically benign twin boundaries with others grains. These pseudo single crystal, direct-band-gap Ge{sub 0.89}Sn{sub 0.11} patterns are suitable for monolithic 3D integration of active photonic devices on Si.

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

    Science.gov (United States)

    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.

  10. Ga, Ca, and 3d transition element (Cr through Zn) partitioning among spinel-lherzolite phases from the Lanzo massif, Italy: Analytical results and crystal chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Wogelius, R.A. [Argonne National Lab., IL (United States); Fraser, D.G. [Oxford Univ. (United Kingdom). Dept. of Earth Sciences

    1994-06-01

    Ultramafic rocks exposed in Lanzo massif, Italy is a record of mantle geochemistry, melting, sub-solidus re-equilibration. Plagioclase(+ spinel)-lherzolite samples were analyzed by Scanning Proton Microscopy, other techniques. Previous work postulated partial melting events and a two-stage sub-solidus cooling history; this paper notes Ga enrichment on spinel-clinopyroxene grain boundaries, high Ga and transition element content of spinel, and pyroxene zonation in Ca and Al. Trace element levels in olivine and orthopyroxene are also presented. Zoning trends are interpreted as due to diffusion during cooling. Olivine-clinopyroxene Cr and Ca exchange as well as clinopyroxene and spinel zonation trends indicate that the massif experienced at least two sub-solidus cooling episodes, one at 20 kbar to 1000 C and one at 8 kbar <750C. Ga levels in cores of Lanzo high-Cr spinels are high (82-66 ppM) relative to other mantle spinels (66-40 ppM), indicating enrichment. Ga content of ultramafic spinels apparently increases with Cr content; this may be due to: increased Ga solubility stemming from crystal chemical effects and/or higher Ga activities in associated silicate melts. Thus, during melting, high-Cr residual spinel may tend to buffer solid-phase Ga level. These spinels are not only rich in Ga and Cr (max 26.37 el. wt %), but also in Fe (max 21.07 el. wt %), Mn (max 3400 ppM), and Zn (max 2430 ppM). These enrichments are again due to melt extraction and partitioning into spinel structure. Low Ni (min 1050 ppM) levels are due to unsuccessful competition of Ni with Cr for octahedral structural sites caused by crystal field. Comparisons of change in partitioning vs Cr content among several 3d transition elements for spinels from Lanzo, other localities allow us to separate crystal field effects from bulk chemical effects and to show that in typical assemblages, inversion of olivine-spinel partition coefficient for Ni from <1 to >1 should occur at 11% el. wt. Cr in spinel.

  11. 3D video

    CERN Document Server

    Lucas, Laurent; Loscos, Céline

    2013-01-01

    While 3D vision has existed for many years, the use of 3D cameras and video-based modeling by the film industry has induced an explosion of interest for 3D acquisition technology, 3D content and 3D displays. As such, 3D video has become one of the new technology trends of this century.The chapters in this book cover a large spectrum of areas connected to 3D video, which are presented both theoretically and technologically, while taking into account both physiological and perceptual aspects. Stepping away from traditional 3D vision, the authors, all currently involved in these areas, provide th

  12. 3D Animation Essentials

    CERN Document Server

    Beane, Andy

    2012-01-01

    The essential fundamentals of 3D animation for aspiring 3D artists 3D is everywhere--video games, movie and television special effects, mobile devices, etc. Many aspiring artists and animators have grown up with 3D and computers, and naturally gravitate to this field as their area of interest. Bringing a blend of studio and classroom experience to offer you thorough coverage of the 3D animation industry, this must-have book shows you what it takes to create compelling and realistic 3D imagery. Serves as the first step to understanding the language of 3D and computer graphics (CG)Covers 3D anim

  13. 3D origami electrochemical device for sensitive Pb(2+) testing based on DNA functionalized iron-porphyrinic metal-organic framework.

    Science.gov (United States)

    Wang, Xiu; Yang, Chunlei; Zhu, Shaojun; Yan, Mei; Ge, Shenguang; Yu, Jinghua

    2017-01-15

    A highly sensitive electrochemical (EC) biosensor combined with a 3D origami device for detection of Pb(2+)was developed based on novel Au nanoparticles modified paper working electrode (Au-PWE) as sensor platform and DNA functionalized iron-porphyrinic metal-organic framework ((Fe-P)n-MOF-Au-GR) hybrids as signal probes. In the presence of Pb(2+), GR could be specifically cleaved at the ribonucleotide (rA) site, which produced the short (Fe-P)n-MOF-linked oligonucleotide fragment to hybridize with hairpin DNA immobilized on the surface of Au-PWE. Because of the mimic peroxidase property of (Fe-P)n-MOF, enzymatically amplified electrochemical signal was obtained to offer the sensitive detection of Pb(2+). In addition, benefiting from the Pb(2+) dependent GR, the proposed assay could selectively detect Pb(2+) in the presence of other metal ions. This method showed a good linear relationship between the current response and the Pb(2+) concentration ranging from 0.03 to 1000nmolL(-1) with a detection limit of 0.02nmolL(-1). The Au-PWE based electrochemical sensor along with the (Fe-P)n-MOF-Au-GR probe exhibited the advantages of low-cost, simple fabrication, high sensitivity and selectivity, providing potential application of real-time Pb(2+) detection both in environmental and biological samples.

  14. 3D terahertz beam profiling

    DEFF Research Database (Denmark)

    Pedersen, Pernille Klarskov; Strikwerda, Andrew; Wang, Tianwu

    2013-01-01

    We present a characterization of THz beams generated in both a two-color air plasma and in a LiNbO3 crystal. Using a commercial THz camera, we record intensity images as a function of distance through the beam waist, from which we extract 2D beam profiles and visualize our measurements into 3D beam...

  15. Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis

    Energy Technology Data Exchange (ETDEWEB)

    Tajbakhsh, Jian, E-mail: tajbakhshj@cshs.org [Chromatin Biology Laboratory, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Stefanovski, Darko [Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19348 (United States); Tang, George [Chromatin Biology Laboratory, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Wawrowsky, Kolja [Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 (United States); Liu, Naiyou; Fair, Jeffrey H. [Department of Surgery and UF Health Comprehensive Transplant Center, University of Florida College of Medicine, Gainesville, FL 32608 (United States)

    2015-03-15

    Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. In summary: 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC{sup +}/5mC{sup −}, 5hmC{sup +}/5mC{sup +}, and 5hmC{sup −}/5mC{sup +} cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC{sup +}/5mC{sup +} cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably

  16. 3D discrete dislocation dynamics study of creep behavior in Ni-base single crystal superalloys by a combined dislocation climb and vacancy diffusion model

    Science.gov (United States)

    Gao, Siwen; Fivel, Marc; Ma, Anxin; Hartmaier, Alexander

    2017-05-01

    A three-dimensional (3D) discrete dislocation dynamics (DDD) creep model is developed to investigate creep behavior under uniaxial tensile stress along the crystallographic [001] direction in Ni-base single crystal superalloys, which takes explicitly account of dislocation glide, climb and vacancy diffusion, but neglects phase transformation like rafting of γ‧ precipitates. The vacancy diffusion model takes internal stresses by dislocations and mismatch strains into account and it is coupled to the dislocation dynamics model in a numerically efficient way. This model is helpful for understanding the fundamental creep mechanisms in superalloys and clarifying the effects of dislocation glide and climb on creep deformation. In cases where the precipitate cutting rarely occurs, e.g. due to the high anti-phase boundary energy and the lack of superdislocations, the dislocation glide in the γ matrix and the dislocation climb along the γ/γ‧ interface dominate plastic deformation. The simulation results show that a high temperature or a high stress both promote dislocation motion and multiplication, so as to cause a large creep strain. Dislocation climb accelerated by high temperature only produces a small plastic strain, but relaxes the hardening caused by the filling γ channels and lets dislocations further glide and multiply. The strongest variation of vacancy concentration occurs in the horizontal channels, where more mixed dislocations exit and tend to climb. The increasing internal stresses due to the increasing dislocation density are easily overcome by dislocations under a high external stress that leads to a long-term dislocation glide accompanied by multiplication.

  17. Synthetic Strategies Toward DNA-Coated Colloids that Crystallize.

    Science.gov (United States)

    Wang, Yufeng; Wang, Yu; Zheng, Xiaolong; Ducrot, Étienne; Lee, Myung-Goo; Yi, Gi-Ra; Weck, Marcus; Pine, David J

    2015-08-26

    We report on synthetic strategies to fabricate DNA-coated micrometer-sized colloids that, upon thermal annealing, self-assemble into various crystal structures. Colloids of a wide range of chemical compositions, including poly(styrene), poly(methyl methacrylate), titania, silica, and a silica-methacrylate hybrid material, are fabricated with smooth particle surfaces and a dense layer of surface functional anchors. Single-stranded oligonucleotides with a short sticky end are covalently grafted onto particle surfaces employing a strain-promoted alkyne-azide cycloaddition reaction resulting in DNA coatings with areal densities an order of magnitude higher than previously reported. Our approach allows the DNA-coated colloids not only to aggregate upon cooling but also to anneal and rearrange while still bound together, leading to the formation of colloidal crystal compounds when particles of different sizes or different materials are combined.

  18. A liquid-crystal-based DNA biosensor for pathogen detection

    Science.gov (United States)

    Khan, Mashooq; Khan, Abdur Rahim; Shin, Jae-Ho; Park, Soo-Young

    2016-03-01

    A liquid-crystal (LC)-filled transmission electron microscopy (TEM) grid cell coated with the cationic surfactant dodecyltrimethylammonium bromide (DTAB), to which a single-stranded deoxyribonucleic acid probe (ssDNAprobe) was adsorbed at the LC/aqueous interface (TEMDTAB/DNA), was applied for the highly specific detection of target DNA molecules. The DTAB-coated E7 (used LC mixture) in the TEM grid (TEMDTAB) exhibited a homeotropic orientation, and changed to a planar orientation upon adsorption of the ssDNAprobe. The TEMDTAB/DNA was then exposed to complementary (target) ssDNA, which resulted in a planar-to-homeotropic configurational change of E7 that could be observed through a polarized optical microscope under crossed polarizers. The optimum adsorption density (2 μM) of ssDNAprobe enabled the detection of ≥0.05 nM complementary ssDNA. This TEMDTAB/DNA biosensor could differentiate complementary ssDNA from mismatched ssDNA as well as double-stranded DNA. It also successfully detected the genomic DNAs of the bacterium Erwinia carotovora and the fungi Rhazictonia solani. Owe to the high specificity, sensitivity, and label-free detection, this biosensor may broaden the applications of LC-based biosensors to pathogen detection.

  19. EUROPEANA AND 3D

    Directory of Open Access Journals (Sweden)

    D. Pletinckx

    2012-09-01

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

  20. Anhydrous crystals of DNA bases are wide gap semiconductors.

    Science.gov (United States)

    Maia, F F; Freire, V N; Caetano, E W S; Azevedo, D L; Sales, F A M; Albuquerque, E L

    2011-05-07

    We present the structural, electronic, and optical properties of anhydrous crystals of DNA nucleobases (guanine, adenine, cytosine, and thymine) found after DFT (Density Functional Theory) calculations within the local density approximation, as well as experimental measurements of optical absorption for powders of these crystals. Guanine and cytosine (adenine and thymine) anhydrous crystals are predicted from the DFT simulations to be direct (indirect) band gap semiconductors, with values 2.68 eV and 3.30 eV (2.83 eV and 3.22 eV), respectively, while the experimentally estimated band gaps we have measured are 3.83 eV and 3.84 eV (3.89 eV and 4.07 eV), in the same order. The electronic effective masses we have obtained at band extremes show that, at low temperatures, these crystals behave like wide gap semiconductors for electrons moving along the nucleobases stacking direction, while the hole transport are somewhat limited. Lastly, the calculated electronic dielectric functions of DNA nucleobases crystals in the parallel and perpendicular directions to the stacking planes exhibit a high degree of anisotropy (except cytosine), in agreement with published experimental results.

  1. Crystal structure determination of anti-DNA Fab A52.

    Science.gov (United States)

    Stanfield, Robyn L; Eilat, Dan

    2014-08-01

    A52 is a murine monoclonal antibody isolated from autoimmune New Zealand Black/New Zealand White F1 mice that recognizes single and double stranded DNA. This mouse strain spontaneously develops systemic lupus erythematosus-like symptoms and has served as a model for that disease for many years. The 1.62 Å crystal structure of the A52 Fab fragment reveals an H3 complementarity determining region with four closely spaced arginine residues, creating a positively charged surface to accommodate bound DNA.

  2. Transformations and Reconstructions of DNA-directed colloidal crystals

    Science.gov (United States)

    Crocker, John; Wang, Yifan; Jenkins, Ian; Sinno, Talid

    DNA is a versatile tool for directing the equilibrium self-assembly of nanoscopic and microscopic objects, but also for subsequently transforming them into new structures. In experiment, at high densities of long grafted DNA strands, and temperatures where the binding is reversible, these systems readily form colloidal crystals and colloidal clusters having a range of symmetries. For interactions that favor alloying between two differently-sized colloidal species, our experimental observations compare favorably to a simulation framework that predicts the equilibrium phase behavior, growth kinetics and solid-solid transitions. Overall, we find that this system recapitulates both ionic crystals and noble-metal alloys. We will discuss the crystallography of the alloy structures formed as well as the interesting Martensitic-type transformations and super-lattice reconstructions they undergo.

  3. IZDELAVA TISKALNIKA 3D

    OpenAIRE

    Brdnik, Lovro

    2015-01-01

    Diplomsko delo analizira trenutno stanje 3D tiskalnikov na trgu. Prikazan je razvoj in principi delovanja 3D tiskalnikov. Predstavljeni so tipi 3D tiskalnikov, njihove prednosti in slabosti. Podrobneje je predstavljena zgradba in delovanje koračnih motorjev. Opravljene so meritve koračnih motorjev. Opisana je programska oprema za rokovanje s 3D tiskalniki in komponente, ki jih potrebujemo za izdelavo. Diploma se oklepa vprašanja, ali je izdelava 3D tiskalnika bolj ekonomična kot pa naložba v ...

  4. [A study on the construction, expression and immunosterility of Lagurus laguru zona pellucida 3 DNA vaccine pVAX1-sig-LTB-lZP3-C3d3].

    Science.gov (United States)

    Li, Chen-Chen; Yu, Ji-Yun; Jiang, Min; Tu, Yi-Xian; Ma, Xiao-Lin; Zhang, Fu-Chun

    2011-09-01

    To enhance the immunocontraceptive effect of Lagurus lagurus zona pellucida 3 DNA vaccine, and to achieve the prospect of application through the pVAX1-sig-LTB-lZP3-C3d3 different immunity pathway. Two adjuvant molecules were constructed into the recombinant plasmid pVAX1-sig-LTB-lZP3-C3d3 as DNA vaccine which contains Escherichia coli heat-labile enterotoxin B subunit and the molecular adjuvant 3 copies of C3d. The results of RT-PCR and western blot showed that the DNA vaccine was expressed in mRNA and protein level. The female C57BL/6 mice were immunized by three ways: intramuscular injection, intranasal or oral route.Antibody levels and types were detected by ELISA. ELISA results showed that recombinant plasmid pVAX1-sig-LTB-lZP3-C3d3 immunization induced specific IgG, IgA levels were significantly different comparing with control (Psig-LTB-lZP3-C3d3 can induce the specific immune response efficiently and enhance the immunocontraceptive effects.

  5. Beyond Textbook Illustrations: Hand-Held Models of Ordered DNA and Protein Structures as 3D Supplements to Enhance Student Learning of Helical Biopolymers

    Science.gov (United States)

    Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2010-01-01

    Textbook illustrations of 3D biopolymers on printed paper, regardless of how detailed and colorful, suffer from its two-dimensionality. For beginners, computer screen display of skeletal models of biopolymers and their animation usually does not provide the at-a-glance 3D perception and details, which can be done by good hand-held models. Here, we…

  6. Molecular engineering of chiral colloidal liquid crystals using DNA origami

    Science.gov (United States)

    Siavashpouri, Mahsa; Wachauf, Christian H.; Zakhary, Mark J.; Praetorius, Florian; Dietz, Hendrik; Dogic, Zvonimir

    2017-08-01

    Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust assembly of DNA origami filaments into cholesteric liquid crystals, one-dimensional supramolecular twisted ribbons and two-dimensional colloidal membranes. The exquisite control afforded by the DNA origami technology establishes a quantitative relationship between the microscopic filament structure and the macroscopic cholesteric pitch. Furthermore, it also enables robust assembly of one-dimensional twisted ribbons, which behave as effective supramolecular polymers whose structure and elastic properties can be precisely tuned by controlling the geometry of the elemental building blocks. Our results demonstrate the potential synergy between DNA origami technology and colloidal science, in which the former allows for rapid and robust synthesis of complex particles, and the latter can be used to assemble such particles into bulk materials.

  7. 3D and Education

    Science.gov (United States)

    Meulien Ohlmann, Odile

    2013-02-01

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

  8. TEHNOLOGIJE 3D TISKALNIKOV

    OpenAIRE

    Kolar, Nataša

    2016-01-01

    Diplomsko delo predstavi razvoj tiskanja skozi čas. Podrobneje so opisani 3D tiskalniki, ki uporabljajo različne tehnologije 3D tiskanja. Predstavljene so različne tehnologije 3D tiskanja, njihova uporaba in narejeni prototipi oz. končni izdelki. Diplomsko delo opiše celoten postopek, od zamisli, priprave podatkov in tiskalnika do izdelave prototipa oz. končnega izdelka.

  9. Micro-CT observations of the 3D distribution of calcium oxalate crystals in cotyledons during maturation and germination in Lotus miyakojimae seeds.

    Science.gov (United States)

    Yamauchi, Daisuke; Tamaoki, Daisuke; Hayami, Masato; Takeuchi, Miyuki; Karahara, Ichirou; Sato, Mayuko; Toyooka, Kiminori; Nishioka, Hiroshi; Terada, Yasuko; Uesugi, Kentaro; Takano, Hidekazu; Kagoshima, Yasushi; Mineyuki, Yoshinobu

    2013-06-01

    The cotyledon of legume seeds is a storage organ that provides nutrients for seed germination and seedling growth. The spatial and temporal control of the degradation processes within cotyledons has not been elucidated. Calcium oxalate (CaOx) crystals, a common calcium deposit in plants, have often been reported to be present in legume seeds. In this study, micro-computed tomography (micro-CT) was employed at the SPring-8 facility to examine the three-dimensional distribution of crystals inside cotyledons during seed maturation and germination of Lotus miyakojimae (previously Lotus japonicus accession Miyakojima MG-20). Using this technique, we could detect the outline of the embryo, void spaces in seeds and the cotyledon venation pattern. We found several sites that strongly inhibited X-ray transmission within the cotyledons. Light and polarizing microscopy confirmed that these areas corresponded to CaOx crystals. Three-dimensional observations of dry seeds indicated that the CaOx crystals in the L. miyakojimae cotyledons were distributed along lateral veins; however, their distribution was limited to the abaxial side of the procambium. The CaOx crystals appeared at stage II (seed-filling stage) of seed development, and their number increased in dry seeds. The number of crystals in cotyledons was high during germination, suggesting that CaOx crystals are not degraded for their calcium supply. Evidence for the conservation of CaOx crystals in cotyledons during the L. miyakojimae germination process was also supported by the biochemical measurement of oxalic acid levels.

  10. Imaging a Sustainable Future in 3D

    Science.gov (United States)

    Schuhr, W.; Lee, J. D.; Kanngieser, E.

    2012-07-01

    It is the intention of this paper, to contribute to a sustainable future by providing objective object information based on 3D photography as well as promoting 3D photography not only for scientists, but also for amateurs. Due to the presentation of this article by CIPA Task Group 3 on "3D Photographs in Cultural Heritage", the presented samples are masterpieces of historic as well as of current 3D photography concentrating on cultural heritage. In addition to a report on exemplarily access to international archives of 3D photographs, samples for new 3D photographs taken with modern 3D cameras, as well as by means of a ground based high resolution XLITE staff camera and also 3D photographs taken from a captive balloon and the use of civil drone platforms are dealt with. To advise on optimum suited 3D methodology, as well as to catch new trends in 3D, an updated synoptic overview of the 3D visualization technology, even claiming completeness, has been carried out as a result of a systematic survey. In this respect, e.g., today's lasered crystals might be "early bird" products in 3D, which, due to lack in resolution, contrast and color, remember to the stage of the invention of photography.

  11. 3D virtuel udstilling

    DEFF Research Database (Denmark)

    Tournay, Bruno; Rüdiger, Bjarne

    2006-01-01

    3d digital model af Arkitektskolens gård med virtuel udstilling af afgangsprojekter fra afgangen sommer 2006. 10 s.......3d digital model af Arkitektskolens gård med virtuel udstilling af afgangsprojekter fra afgangen sommer 2006. 10 s....

  12. Enhanced electrophoretic DNA separation in photonic crystal fiber.

    Science.gov (United States)

    Sun, Yi; Nguyen, Nam-Trung; Kwok, Yien Chian

    2009-07-01

    Joule heating generated by the electrical current in capillary electrophoresis leads to a temperature gradient along the separation channel and consequently affects the separation quality. We describe a method of reducing the Joule heating effect by incorporating photonic crystal fiber into a micro capillary electrophoresis chip. The photonic crystal fiber consists of a bundle of extremely narrow hollow channels, which ideally work as separation columns. Electrophoretic separation of DNA fragments was simultaneously but independently carried out in 54 narrow capillaries with a diameter of 3.7 microm each. The capillary bundle offers more efficient heat dissipation owing to the high surface-to-volume ratio. Under the same electrical field strength, notable improvement in resolution was obtained in the capillary bundle chip.

  13. A DNA Crystal Designed to Contain Two Molecules per Asymmetric Unit

    Energy Technology Data Exchange (ETDEWEB)

    T Wang; R Sha; J Birktoft; J Zheng; C Mao; N Seeman

    2011-12-31

    We describe the self-assembly of a DNA crystal that contains two tensegrity triangle molecules per asymmetric unit. We have used X-ray crystallography to determine its crystal structure. In addition, we have demonstrated control over the colors of the crystals by attaching either Cy3 dye (pink) or Cy5 dye (blue-green) to the components of the crystal, yielding crystals of corresponding colors. Attaching the pair of dyes to the pair of molecules yields a purple crystal.

  14. Crystal Growth and Characterization of MT2Si2 Ternary Intermetallics (M = U, RE and T = 3d, 4d, 5d Transition Metals)

    NARCIS (Netherlands)

    Menovsky, A.A.; Moleman, A.C.; Snel, G.E.; Gortenmulder, T.J.; Palstra, T.T.M.

    1986-01-01

    Bulk single crystals of the ternary intermetallic compounds UT2Si2 (T = Ni, Pd, Pt and Ru), LaT2Si2 (T = Pd and Rh) and LuPd2Si2 have been grown from the melt with a modified “tri-arc” Czochralski method. The as-grown crystals were characterized by X-ray, microprobe and chemical analyses. The

  15. Crystal Growth and Characterization of MT2Si2 Ternary Intermetallics (M = U, RE and T = 3d, 4d, 5d Transition Metals)

    NARCIS (Netherlands)

    Menovsky, A.A.; Moleman, A.C.; Snel, G.E.; Gortenmulder, T.J.; Palstra, T.T.M.

    1986-01-01

    Bulk single crystals of the ternary intermetallic compounds UT2Si2 (T = Ni, Pd, Pt and Ru), LaT2Si2 (T = Pd and Rh) and LuPd2Si2 have been grown from the melt with a modified “tri-arc” Czochralski method. The as-grown crystals were characterized by X-ray, microprobe and chemical analyses. The measur

  16. Controlled dehydration of a ruthenium complex-DNA crystal induces reversible DNA kinking.

    Science.gov (United States)

    Hall, James P; Sanchez-Weatherby, Juan; Alberti, Cora; Quimper, Caroline Hurtado; O'Sullivan, Kyra; Brazier, John A; Winter, Graeme; Sorensen, Thomas; Kelly, John M; Cardin, David J; Cardin, Christine J

    2014-12-17

    Hydration-dependent DNA deformation has been known since Rosalind Franklin recognized that the relative humidity of the sample had to be maintained to observe a single conformation in DNA fiber diffraction. We now report for the first time the crystal structure, at the atomic level, of a dehydrated form of a DNA duplex and demonstrate the reversible interconversion to the hydrated form at room temperature. This system, containing d(TCGGCGCCGA) in the presence of Λ-[Ru(TAP)2(dppz)](2+) (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyrido[3,2-a:2',3'-c]phenazine), undergoes a partial transition from an A/B hybrid to the A-DNA conformation, at 84-79% relative humidity. This is accompanied by an increase in kink at the central step from 22° to 51°, with a large movement of the terminal bases forming the intercalation site. This transition is reversible on rehydration. Seven data sets, collected from one crystal at room temperature, show the consequences of dehydration at near-atomic resolution. This result highlights that crystals, traditionally thought of as static systems, are still dynamic and therefore can be the subject of further experimentation.

  17. Self-assembly of two-dimensional DNA crystals

    Institute of Scientific and Technical Information of China (English)

    SONG Cheng; CHEN Yaqing; WEI Shuai; YOU Xiaozeng; XIAO Shoujun

    2004-01-01

    Self-assembly of synthetic oligonucleotides into two-dimensional lattices presents a 'bottom-up' approach to the fabrication of devices on nanometer scale. We report the design and observation of two-dimensional crystalline forms of DNAs that are composed of twenty-one plane oligonucleotides and one phosphate-modified oligonucleotide. These synthetic sequences are designed to self-assemble into four double-crossover (DX) DNA tiles. The 'sticky ends' of these tiles that associate according to Watson-Crick's base pairing are programmed to build up specific periodic patterns upto tens of microns. The patterned crystals are visualized by the transmission electron microscopy.

  18. 3D imaging using X-Ray tomography and SEM combined FIB to study non isothermal creep damage of (111) oriented samples of γ / γ ′ nickel base single crystal superalloy MC2

    KAUST Repository

    Jouiad, Mustapha

    2012-01-01

    An unprecedented investigation consisting of the association of X-Ray tomography and Scanning Electron Microscopy combined with Focus Ion Beam (SEM-FIB) is conducted to perform a 3D reconstruction imaging. These techniques are applied to study the non-isothermal creep behavior of close (111) oriented samples of MC2 nickel base superalloys single crystal. The issue here is to develop a strategy to come out with the 3D rafting of γ\\' particles and its interaction whether with dislocation structures or/and with the preexisting voids. This characterization is uncommonly performed away from the conventional studied orientation [001] in order to feed the viscoplastic modeling leading to its improvement by taking into account the crystal anisotropy. The creep tests were performed at two different conditions: classical isothermal tests at 1050°C under 140 MPa and a non isothermal creep test consisting of one overheating at 1200°C and 30 seconds dwell time during the isothermal creep life. The X-Ray tomography shows a great deformation heterogeneity that is pronounced for the non-isothermal tested samples. This deformation localization seems to be linked to the preexisting voids. Nevertheless, for both tested samples, the voids coalescence is the precursor of the observed damage leading to failure. SEM-FIB investigation by means of slice and view technique gives 3D views of the rafted γ\\' particles and shows that γ corridors evolution seems to be the main creep rate controlling parameter. © 2012 Trans Tech Publications, Switzerland.

  19. The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA

    OpenAIRE

    Lo, Yu-Hua; Tsai, Kuang-Lei; Sun, Yuh-Ju; Chen, Wei-Ti; Huang, Cheng-Yang; Hsiao, Chwan-Deng

    2008-01-01

    DNA helicases are motor proteins that play essential roles in DNA replication, repair and recombination. In the replicative hexameric helicase, the fundamental reaction is the unwinding of duplex DNA; however, our understanding of this function remains vague due to insufficient structural information. Here, we report two crystal structures of the DnaB-family replicative helicase from Geobacillus kaustophilus HTA426 (GkDnaC) in the apo-form and bound to single-stranded DNA (ssDNA). The GkDnaC–...

  20. 3D Printed Bionic Nanodevices.

    Science.gov (United States)

    Kong, Yong Lin; Gupta, Maneesh K; Johnson, Blake N; McAlpine, Michael C

    2016-06-01

    The ability to three-dimensionally interweave biological and functional materials could enable the creation of bionic devices possessing unique and compelling geometries, properties, and functionalities. Indeed, interfacing high performance active devices with biology could impact a variety of fields, including regenerative bioelectronic medicines, smart prosthetics, medical robotics, and human-machine interfaces. Biology, from the molecular scale of DNA and proteins, to the macroscopic scale of tissues and organs, is three-dimensional, often soft and stretchable, and temperature sensitive. This renders most biological platforms incompatible with the fabrication and materials processing methods that have been developed and optimized for functional electronics, which are typically planar, rigid and brittle. A number of strategies have been developed to overcome these dichotomies. One particularly novel approach is the use of extrusion-based multi-material 3D printing, which is an additive manufacturing technology that offers a freeform fabrication strategy. This approach addresses the dichotomies presented above by (1) using 3D printing and imaging for customized, hierarchical, and interwoven device architectures; (2) employing nanotechnology as an enabling route for introducing high performance materials, with the potential for exhibiting properties not found in the bulk; and (3) 3D printing a range of soft and nanoscale materials to enable the integration of a diverse palette of high quality functional nanomaterials with biology. Further, 3D printing is a multi-scale platform, allowing for the incorporation of functional nanoscale inks, the printing of microscale features, and ultimately the creation of macroscale devices. This blending of 3D printing, novel nanomaterial properties, and 'living' platforms may enable next-generation bionic systems. In this review, we highlight this synergistic integration of the unique properties of nanomaterials with the

  1. 3D Printed Bionic Nanodevices

    Science.gov (United States)

    Kong, Yong Lin; Gupta, Maneesh K.; Johnson, Blake N.; McAlpine, Michael C.

    2016-01-01

    Summary The ability to three-dimensionally interweave biological and functional materials could enable the creation of bionic devices possessing unique and compelling geometries, properties, and functionalities. Indeed, interfacing high performance active devices with biology could impact a variety of fields, including regenerative bioelectronic medicines, smart prosthetics, medical robotics, and human-machine interfaces. Biology, from the molecular scale of DNA and proteins, to the macroscopic scale of tissues and organs, is three-dimensional, often soft and stretchable, and temperature sensitive. This renders most biological platforms incompatible with the fabrication and materials processing methods that have been developed and optimized for functional electronics, which are typically planar, rigid and brittle. A number of strategies have been developed to overcome these dichotomies. One particularly novel approach is the use of extrusion-based multi-material 3D printing, which is an additive manufacturing technology that offers a freeform fabrication strategy. This approach addresses the dichotomies presented above by (1) using 3D printing and imaging for customized, hierarchical, and interwoven device architectures; (2) employing nanotechnology as an enabling route for introducing high performance materials, with the potential for exhibiting properties not found in the bulk; and (3) 3D printing a range of soft and nanoscale materials to enable the integration of a diverse palette of high quality functional nanomaterials with biology. Further, 3D printing is a multi-scale platform, allowing for the incorporation of functional nanoscale inks, the printing of microscale features, and ultimately the creation of macroscale devices. This blending of 3D printing, novel nanomaterial properties, and ‘living’ platforms may enable next-generation bionic systems. In this review, we highlight this synergistic integration of the unique properties of nanomaterials with

  2. Blender 3D cookbook

    CERN Document Server

    Valenza, Enrico

    2015-01-01

    This book is aimed at the professionals that already have good 3D CGI experience with commercial packages and have now decided to try the open source Blender and want to experiment with something more complex than the average tutorials on the web. However, it's also aimed at the intermediate Blender users who simply want to go some steps further.It's taken for granted that you already know how to move inside the Blender interface, that you already have 3D modeling knowledge, and also that of basic 3D modeling and rendering concepts, for example, edge-loops, n-gons, or samples. In any case, it'

  3. 基于柱面光栅的液晶三维自由立体显示%3D Autostereoscopic Liquid Crystal Display Based on Lenticular Lens

    Institute of Scientific and Technical Information of China (English)

    王琼华; 陶宇虹; 李大海; 赵仁亮; 赵悟翔

    2008-01-01

    根据双目视差原理和柱面光栅的分光特性研制了液晶三维自由立体显示器.该立体显示器由二维平板液晶显示器和柱面光栅有机耦合而成.采用九个视差图实现了三维静态、动态和视频的显示效果.一个19英寸的立体显示器具有相对应的平面显示器相同的亮度、对比度和色彩,其分辨率在垂直和水平方向都有合理的下降.该立体显示器的观看距离是(1000±500)mm,视角为 90°,可供多人不戴立体眼镜就能自由观看立体图像.%According to binocular parallax and the optical property of lenticular lens, a three-dimension (3D) au-tostereoscopic liquid crystal display was developed. The display is composed of a two-dimension (2D) fiat liquid crystal display and a lenticular lens sheet. Nine views are used to realize the display of 3D static, animation and video images. A 19-inch 3D monitor prototype presents the same brightness, contrast ratio and color as those of the corresponding 2D display. Only the resolution reduces on both the horizontal and vertical direction of the screen reasonably. The viewing distance is (1000±500)mm and viewing angle is 90°. Several viewers without wearing eyeglass can see 3D stereo images on the prototype of the display.

  4. 3D Digital Modelling

    DEFF Research Database (Denmark)

    Hundebøl, Jesper

    wave of new building information modelling tools demands further investigation, not least because of industry representatives' somewhat coarse parlance: Now the word is spreading -3D digital modelling is nothing less than a revolution, a shift of paradigm, a new alphabet... Research qeustions. Based...... on empirical probes (interviews, observations, written inscriptions) within the Danish construction industry this paper explores the organizational and managerial dynamics of 3D Digital Modelling. The paper intends to - Illustrate how the network of (non-)human actors engaged in the promotion (and arrest) of 3......D Modelling (in Denmark) stabilizes - Examine how 3D Modelling manifests itself in the early design phases of a construction project with a view to discuss the effects hereof for i.a. the management of the building process. Structure. The paper introduces a few, basic methodological concepts...

  5. DELTA 3D PRINTER

    Directory of Open Access Journals (Sweden)

    ȘOVĂILĂ Florin

    2016-07-01

    Full Text Available 3D printing is a very used process in industry, the generic name being “rapid prototyping”. The essential advantage of a 3D printer is that it allows the designers to produce a prototype in a very short time, which is tested and quickly remodeled, considerably reducing the required time to get from the prototype phase to the final product. At the same time, through this technique we can achieve components with very precise forms, complex pieces that, through classical methods, could have been accomplished only in a large amount of time. In this paper, there are presented the stages of a 3D model execution, also the physical achievement after of a Delta 3D printer after the model.

  6. Professional Papervision3D

    CERN Document Server

    Lively, Michael

    2010-01-01

    Professional Papervision3D describes how Papervision3D works and how real world applications are built, with a clear look at essential topics such as building websites and games, creating virtual tours, and Adobe's Flash 10. Readers learn important techniques through hands-on applications, and build on those skills as the book progresses. The companion website contains all code examples, video step-by-step explanations, and a collada repository.

  7. AE3D

    Energy Technology Data Exchange (ETDEWEB)

    2016-06-20

    AE3D solves for the shear Alfven eigenmodes and eigenfrequencies in a torodal magnetic fusion confinement device. The configuration can be either 2D (e.g. tokamak, reversed field pinch) or 3D (e.g. stellarator, helical reversed field pinch, tokamak with ripple). The equations solved are based on a reduced MHD model and sound wave coupling effects are not currently included.

  8. The role of boundary layer aerosol particles for the development of deep convective clouds: A high-resolution 3D model with detailed (bin) microphysics applied to CRYSTAL-FACE

    Science.gov (United States)

    Leroy, Delphine; Wobrock, Wolfram; Flossmann, Andrea I.

    2009-01-01

    This paper reproduces aircraft microphysical measurements using a three-dimensional model with bin resolved microphysics and is then used to analyze in particular the role of boundary layer aerosol particles in the anvil and the ice phase. The simulated case is a convective cloud which develops a large anvil of around 10 km height, which was sampled during the Cirrus Regional Study of Tropical Anvils and Cirrus Layers — Florida Area Cirrus Experiment (CRYSTAL-FACE). The model couples the 3D dynamics of a cloud scale model with a detailed mixed phase microphysical code. The microphysical package considers the evolution of the wet aerosol particles, drop and ice crystal spectra on size grids with 39 bins. With this model hereafter called DESCAM 3D, we are able to simulate the cloud with features close to those observed and to provide explanations of the observed phenomena concerning cloud microphysics as well as cloud dynamics. The same CRYSTAL-FACE cloud has already been simulated by other groups using a similar model. They investigated the role of mid-tropospheric aerosol particles versus boundary layer aerosol on the microphysical properties of the anvil. Similar simulations with our DESCAM 3D lead to quite different results. Reducing the number of mid-tropospheric aerosol particles causes only minor changes in the cloud anvil. However, changing the aerosol particle spectrum in the boundary layer from clean to polluted conditions modifies strongly the dynamical evolution of the convective clouds and thus impacts significantly on the microphysical properties of the anvil. Possible reasons for the differences are discussed.

  9. 3D Petrography - Serendipitous Discovery of Magmatic Vapor Deposition of Anhydrite at Mount Pinatubo by SEM Imaging of Outer Crystal Surfaces

    Science.gov (United States)

    Fournelle, J. H.; Jakubowski, R. T.; Welch, S.; Swope, R. J.

    2003-12-01

    A standard petrographic technique focuses upon examination of surfaces or planes cut through rock samples, with one approach studying chemical variations in a core to rim traverse using various microprobes, and more recently, another determining the distribution of crystal sizes to obtain information about nucleation and growth. We show that another mineral domain deserves petrographic attention: the outer surfaces of crystals, which are normally relegated to nearly invisible thin lines in a cut section. In studying anhydrite phenocrysts from the 1991 climactic eruption of Mt. Pinatubo, SEM examination of "raw" pumice fragments showed the existence of a Ca-sulfur-rich phase with hexagonal morphology residing upon plagioclase phenocryst surfaces in vesicles (Fournelle et al,1996, Fig 9). In 1992, Terry Gerlach suggested that the Pinatubo anhydrite phenocrysts should be evaluated with XRD to determine if they were indeed orthorhombic anhydrite (β -CaSO4), and not a lower temperature polymorph (i.e., α or γ ). In 1998, we recommenced this project, mounting several dozen 100-200 micron-size phenocrysts of the proper density fraction on tape (minerals had been separated from the pumices using standard techniques). They were examined by low resolution SEM with EDS to distinguish the anhydrite from apatite, prior to single-crystal XRD. We were surprised to find that many of the anhydrite surfaces were decorated with small mounds, which upon examination by high resolution SEM turned out to be micron and smaller pyramids, with some surfaces bearing hundreds. Single-crystal XRD verified that the phenocrysts were orthorhombic anhydrite, and EBSD verified that the small pyramids were the same. Eventually we found that these surface pyramids are common phenomena in experimental or industrial chemical vapor deposition processes when nucleation overwhelms growth. Textural relations were consistent with these pyramids being deposited in situ, within the Pinatubo magma chamber

  10. Synthesis, Crystal Structure and Biological Activities of 3-[2-(4-Fluoro-phenyl)-ethyl]-5-methyl-4-hydroxyl-4-methyl-7-methylsulfanyl-3,4-dihydro-pyrido[4,3-d]pyrimidine-8-carbonitrile

    Institute of Scientific and Technical Information of China (English)

    MO Wen-Yan; HE Hong-Wu

    2007-01-01

    The title compound, 3-[2-(4-fluoro-phenyl)-ethyl]-5-methyl-4-hydroxyl-4-methyl-7-methylsulfanyl-3,4-dihydro-pyrido[4,3-d]pyrimidine-8-carbonitrile, has been prepared and detemined by single-crystal X-ray diffraction. The crystal belongs to the triclinic system, space group P1- with a = 6.8754(8), b = 10.2617(12), c = 13.3491(16)(A), α = 93.163(2), β = 96.704(2), γ =102.421(2)°, V= 910.35(19) (A)3, Z = 2, Mr = 370.44, Dc = 1.351 g/cm3,μ = 0.203 mm-1, F(000) =388, the final R = 0.0573 and wR = 0.1497. X-ray analysis reveals that the pyridine and pyrimidine rings are almost coplanar.

  11. The Design and Implementation of 3D Visualization System for Crystal Dislocations in Molecular Dynamics%分子动力学中晶体位错的三维可视化系统设计与实现

    Institute of Scientific and Technical Information of China (English)

    宁媛; 张鹏; 介军

    2014-01-01

    在材料科学中,位错线是晶体或晶格内滑移面上已滑动区的边界,位错线的识别对于鉴定晶体的性能有着重要的影响。该文将三维可视化技术应用到分子动力学领域,改进了原有的只能通过计算结果分析数据、通过二维图像简单观察数据的方法,设计了晶体位错可视化系统,使得晶体中各原子之间形成的三维结构易于观察,便于研究晶体位错等重要的材质特性,提高位错线的识别效率。%In the material science, the dislocation lines are the boundary sliding of a crystal or a lattice slip plane,the identification of dislocation lines have a important impact for the property of crystals. The essay using the application of 3D visualization tech-nology to the field of molecular dynamics and improving the conventional research ways, such as analyzing data by calculating re-sults and observing the data by 2D images inconveniently, designing a visualization system for crystal dislocations. This way can make the 3D structure among atoms be observed easily, which is convenient to research the crystal dislocations and other impor-tant material properties, and improve the efficiency of the identification of dislocation lines.

  12. 3D Projection Installations

    DEFF Research Database (Denmark)

    Halskov, Kim; Johansen, Stine Liv; Bach Mikkelsen, Michelle

    2014-01-01

    Three-dimensional projection installations are particular kinds of augmented spaces in which a digital 3-D model is projected onto a physical three-dimensional object, thereby fusing the digital content and the physical object. Based on interaction design research and media studies, this article...... contributes to the understanding of the distinctive characteristics of such a new medium, and identifies three strategies for designing 3-D projection installations: establishing space; interplay between the digital and the physical; and transformation of materiality. The principal empirical case, From...... Fingerplan to Loop City, is a 3-D projection installation presenting the history and future of city planning for the Copenhagen area in Denmark. The installation was presented as part of the 12th Architecture Biennale in Venice in 2010....

  13. 3D Spectroscopic Instrumentation

    CERN Document Server

    Bershady, Matthew A

    2009-01-01

    In this Chapter we review the challenges of, and opportunities for, 3D spectroscopy, and how these have lead to new and different approaches to sampling astronomical information. We describe and categorize existing instruments on 4m and 10m telescopes. Our primary focus is on grating-dispersed spectrographs. We discuss how to optimize dispersive elements, such as VPH gratings, to achieve adequate spectral resolution, high throughput, and efficient data packing to maximize spatial sampling for 3D spectroscopy. We review and compare the various coupling methods that make these spectrographs ``3D,'' including fibers, lenslets, slicers, and filtered multi-slits. We also describe Fabry-Perot and spatial-heterodyne interferometers, pointing out their advantages as field-widened systems relative to conventional, grating-dispersed spectrographs. We explore the parameter space all these instruments sample, highlighting regimes open for exploitation. Present instruments provide a foil for future development. We give an...

  14. Radiochromic 3D Detectors

    Science.gov (United States)

    Oldham, Mark

    2015-01-01

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

  15. Interaktiv 3D design

    DEFF Research Database (Denmark)

    Villaume, René Domine; Ørstrup, Finn Rude

    2002-01-01

    Projektet undersøger potentialet for interaktiv 3D design via Internettet. Arkitekt Jørn Utzons projekt til Espansiva blev udviklet som et byggesystem med det mål, at kunne skabe mangfoldige planmuligheder og mangfoldige facade- og rumudformninger. Systemets bygningskomponenter er digitaliseret som...... 3D elementer og gjort tilgængelige. Via Internettet er det nu muligt at sammenstille og afprøve en uendelig  række bygningstyper som  systemet blev tænkt og udviklet til....

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

    Science.gov (United States)

    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 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.

  17. Specific features of insulator-metal transitions under high pressure in crystals with spin crossovers of 3 d ions in tetrahedral environment

    Science.gov (United States)

    Lobach, K. A.; Ovchinnikov, S. G.; Ovchinnikova, T. M.

    2015-01-01

    For Mott insulators with tetrahedral environment, the effective Hubbard parameter U eff is obtained as a function of pressure. This function is not universal. For crystals with d 5 configuration, the spin crossover suppresses electron correlations, while for d 4 configurations, the parameter U eff increases after a spin crossover. For d 2 and d 7 configurations, U eff increases with pressure in the high-spin (HS) state and is saturated after the spin crossover. Characteristic features of the insulator-metal transition are considered as pressure increases; it is shown that there may exist cascades of several transitions for various configurations.

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

    Science.gov (United States)

    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+.

  19. Neutron diffraction study on hydrogen bond structure in K{sub 3}H(SeO{sub 4}){sub 2} and K{sub 3}D(SeO{sub 4}){sub 2} crystals

    Energy Technology Data Exchange (ETDEWEB)

    Onoda-Yamamuro, N.; Yamamuro, O.; Matsuo, T. [Department of Chemistry, Graduate School of Science, Osaka University, Machikaneyama-cho 1-1, Toyonaka, Osaka (Japan). E-mail: matsuo@chem.sci.osaka-u.ac.jp; Ichikawa, M. [Division of Physics, Graduate School of Science, Hokkaido University, Sapporo (Japan); Ibberson, R.M.; David, W.I.F. [ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire (United Kingdom)

    2000-10-09

    Neutron diffraction experiments on the room- and low-temperature phases of K{sub 3}H(SeO{sub 4}){sub 2} (T{sub trs} = 21 K) and K{sub 3}D(SeO{sub 4}){sub 2} (T{sub trs} = 105 K) have been performed using the time-of-flight high-resolution powder diffractometer HRPD at the ISIS pulsed neutron source. Data were collected at 2 and 30 K for K{sub 3}H(SeO{sub 4}){sub 2} and 2 and 130 K for K{sub 3}D(SeO{sub 4}){sub 2} over the d-spacing range 0.7-2.4 A. The room-temperature phases of the crystals have monoclinic structure belonging to the space group A2/a. Rietveld refinement combined with the published dielectric and calorimetric studies reveals that H/D atoms are disordered over two symmetry-equivalent positions. The hydrogen bonds are non-linear with an O-H/D...O angle of 175(1) deg. The hydrogen bond length is 2.495(1) A in K{sub 3}H(SeO{sub 4}){sub 2} and 2.533(2) A in K{sub 3}D(SeO{sub 4}){sub 2}. The separation between the half occupancy hydrogen positions is 0.32(1) A for K{sub 3}H(SeO{sub 4}){sub 2} and 0.550(4) A for K{sub 3}D(SeO{sub 4}){sub 2}. The relation between these structural parameters and the isotope effect in the transition temperature is discussed. Diffraction patterns of the low-temperature phases indicated that the structure change accompanying the transition is very small. (author)

  20. 3D Wire 2015

    DEFF Research Database (Denmark)

    Jordi, Moréton; F, Escribano; J. L., Farias

    This document is a general report on the implementation of gamification in 3D Wire 2015 event. As the second gamification experience in this event, we have delved deeply in the previous objectives (attracting public areas less frequented exhibition in previous years and enhance networking) and ha......, improves socialization and networking, improves media impact, improves fun factor and improves encouragement of the production team....

  1. Shaping 3-D boxes

    DEFF Research Database (Denmark)

    Stenholt, Rasmus; Madsen, Claus B.

    2011-01-01

    Enabling users to shape 3-D boxes in immersive virtual environments is a non-trivial problem. In this paper, a new family of techniques for creating rectangular boxes of arbitrary position, orientation, and size is presented and evaluated. These new techniques are based solely on position data...

  2. Tangible 3D Modelling

    DEFF Research Database (Denmark)

    Hejlesen, Aske K.; Ovesen, Nis

    2012-01-01

    This paper presents an experimental approach to teaching 3D modelling techniques in an Industrial Design programme. The approach includes the use of tangible free form models as tools for improving the overall learning. The paper is based on lecturer and student experiences obtained through facil...

  3. Microscopic mechanism of the zero-field splitting parameters for 6S(3d5 ) state ions at trigonal symmetry crystal filed%三角对称晶场中6S(3d5)态离子零场分裂参量的微观起源

    Institute of Scientific and Technical Information of China (English)

    杨子元

    2011-01-01

    基于完全对角化方法(complete diagonalization method,CDM),研究了6S(3d5)态离子在三角晶场(包括C3v,D3,D3d点群对称晶场)中零场分裂(zero-field splitting,ZFS)参量D和(a-F)的微观起源.研究中除了考虑研究者通常考虑的SO(spin-orbit)磁相互作用外,同时考虑了SS(spin-spin),SOO(spin-other-orbit),OO(orbit-orbit)磁相互作用.研究表明:在三角对称晶场中,6S(3d5)态离子的ZFS参量在所选晶场的大多部分区域主要起源于SO机理,但SS机理、SOO机理、OO机理对ZFS参量的贡献不能被忽略.此外研究表明:ZFS参量D和(a-f)主要来自纯自旋四重态及自旋二重态与自旋四重态联合作用的贡献,纯自旋二重态对ZFS参量D和(a-F)的贡献为零.我们发现二阶ZFS参量D与四阶ZFS参量(a-f)有不同的微观起源.二阶ZFS参量D主要来自自旋四重态的贡献,而四阶ZFS参量(a-f)主要来自自旋二重态与自旋四重态联合作用的贡献.作为本文理论的应用,研究了掺杂晶体材料Fe3+:Al2O3,理论与实验测量符合很好.%The microscopic mechanism of the zero-field splitting parameters (ZFS) including D and (a - F) for 6S(3d5) state ion in trigonal-symmetry crystal field have been investigated using the complete diagonaliztion method (CDM) by taking into account the spin-spin (SS) , the spin-other-orbit (SOO) and the orbit-orbit (OO) magnetic interactions besides the well-known spin-orbit (SO) magnetic interaction.It was found that the contribution to the ZFS parameters D and (a -F)arising from the spin-orbit (SO) magnetic interaction is the most important in most of the crystal field (CF) ranges, but the contribution to the zero-field splitting (ZFS) parameter D and ( a - F) from the other three mechanisms, including the SS mechanism, SOO mechanism and OO mechanism, can't be ignored.The ZFS parameters D and (a - F) arise from the net spin quartet states as well as the combined effects of the spin doublet states and the spin quartets

  4. 3D photoacoustic imaging

    Science.gov (United States)

    Carson, Jeffrey J. L.; Roumeliotis, Michael; Chaudhary, Govind; Stodilka, Robert Z.; Anastasio, Mark A.

    2010-06-01

    Our group has concentrated on development of a 3D photoacoustic imaging system for biomedical imaging research. The technology employs a sparse parallel detection scheme and specialized reconstruction software to obtain 3D optical images using a single laser pulse. With the technology we have been able to capture 3D movies of translating point targets and rotating line targets. The current limitation of our 3D photoacoustic imaging approach is its inability ability to reconstruct complex objects in the field of view. This is primarily due to the relatively small number of projections used to reconstruct objects. However, in many photoacoustic imaging situations, only a few objects may be present in the field of view and these objects may have very high contrast compared to background. That is, the objects have sparse properties. Therefore, our work had two objectives: (i) to utilize mathematical tools to evaluate 3D photoacoustic imaging performance, and (ii) to test image reconstruction algorithms that prefer sparseness in the reconstructed images. Our approach was to utilize singular value decomposition techniques to study the imaging operator of the system and evaluate the complexity of objects that could potentially be reconstructed. We also compared the performance of two image reconstruction algorithms (algebraic reconstruction and l1-norm techniques) at reconstructing objects of increasing sparseness. We observed that for a 15-element detection scheme, the number of measureable singular vectors representative of the imaging operator was consistent with the demonstrated ability to reconstruct point and line targets in the field of view. We also observed that the l1-norm reconstruction technique, which is known to prefer sparseness in reconstructed images, was superior to the algebraic reconstruction technique. Based on these findings, we concluded (i) that singular value decomposition of the imaging operator provides valuable insight into the capabilities of

  5. Specific features of insulator-metal transitions under high pressure in crystals with spin crossovers of 3d ions in tetrahedral environment

    Energy Technology Data Exchange (ETDEWEB)

    Lobach, K. A., E-mail: ks-ad@yandex.ru; Ovchinnikov, S. G., E-mail: sgo@iph.krasn.ru [Siberian Federal University (Russian Federation); Ovchinnikova, T. M. [Russian Academy of Sciences, Sukachev Institute of Forest, Siberian Branch (Russian Federation)

    2015-01-15

    For Mott insulators with tetrahedral environment, the effective Hubbard parameter U{sub eff} is obtained as a function of pressure. This function is not universal. For crystals with d{sup 5} configuration, the spin crossover suppresses electron correlations, while for d{sup 4} configurations, the parameter U{sub eff} increases after a spin crossover. For d{sup 2} and d{sup 7} configurations, U{sub eff} increases with pressure in the high-spin (HS) state and is saturated after the spin crossover. Characteristic features of the insulator-metal transition are considered as pressure increases; it is shown that there may exist cascades of several transitions for various configurations.

  6. A stand-alone mesoporous crystal structure model from in situ X-ray diffraction: nitrogen adsorption on 3D cagelike mesoporous silica SBA-16.

    Science.gov (United States)

    Miyasaka, Keiichi; Hano, Hiroko; Kubota, Yoshiki; Lin, Yangzheng; Ryoo, Ryong; Takata, Masaki; Kitagawa, Susumu; Neimark, Alexander V; Terasaki, Osamu

    2012-08-13

    We present a modeling scheme to analyze cagelike silica mesoporous crystals based on in situ X-ray diffraction (XRD) data collected during gas adsorption-desorption (physisorption) processes. Nitrogen physisorption on a silica mesoporous crystal of SBA-16 was directly monitored by using synchrotron in situ powder XRD measurements conducted at SPring-8. SBA-16 is a well-ordered mesoporous silica in which three-dimensional interconnected cagelike primary mesopores are located at the body-centered cubic lattice points. In addition, the surrounding silica matrix contains random microporous and mesoporous intrawall porosities that are significantly influential to the diffusion properties, and thus important to be quantified for this media. The in situ XRD data exhibits seven Bragg reflections throughout the measurements, and the present method allows one to obtain the maximal and stand-alone information about the pore structure (for example, the mesopore size, the matrix density, the intrawall porosity, and pore surface roughness) together with the nitrogen film evolution in the primary mesopores and the intrawall pore-filling in the silica matrix. We furthermore observe a macroscopic amount of nitrogen adsorbed assuming the density of the fluid, and confirm that the XRD "isotherm" recalculated from the analysis result is consistent with the conventional nitrogen isotherm on a semi-quantitative level; however, these results suggest that the intrawall pores would have a greater contribution to the adsorption than considered based on the conventional isotherm analyses. The present method is readily extendable to any ordered mesopores wrapped by the wall matrix containing a certain intrawall porosity.

  7. Unoriented 3d TFTs

    CERN Document Server

    Bhardwaj, Lakshya

    2016-01-01

    This paper generalizes two facts about oriented 3d TFTs to the unoriented case. On one hand, it is known that oriented 3d TFTs having a topological boundary condition admit a state-sum construction known as the Turaev-Viro construction. This is related to the string-net construction of fermionic phases of matter. We show how Turaev-Viro construction can be generalized to unoriented 3d TFTs. On the other hand, it is known that the "fermionic" versions of oriented TFTs, known as Spin-TFTs, can be constructed in terms of "shadow" TFTs which are ordinary oriented TFTs with an anomalous Z_2 1-form symmetry. We generalize this correspondence to Pin+ TFTs by showing that they can be constructed in terms of ordinary unoriented TFTs with anomalous Z_2 1-form symmetry having a mixed anomaly with time-reversal symmetry. The corresponding Pin+ TFT does not have any anomaly for time-reversal symmetry however and hence it can be unambiguously defined on a non-orientable manifold. In case a Pin+ TFT admits a topological bou...

  8. Optical spectroscopy and crystal field studies of the Mn{sup 4+} ion (3d{sup 3}) in the double perovskite NaLaMgTeO{sub 6}

    Energy Technology Data Exchange (ETDEWEB)

    Srivastava, Alok M.; Camardello, Samuel J.; Comanzo, Holly A.; Garcia-Santamaria, Florencio [GE Global Research, Niskayuna, NY (United States); Brik, Mikhail G. [Tartu Univ. (Estonia). Inst. of Physics

    2014-02-15

    The spectroscopic properties of the Mn{sup 4+} ion (3d{sup 3}) in the double perovskite NaLaMgTeO{sub 6} are reported in this work. Evidence is presented for the occupation by the Mn{sup 4+} ion of both the six coordinated Mg{sup 2+} and Te{sup 6+} sites in the host structure. The Mn{sup 4+} energy levels are calculated using the exchange charge model of crystal field theory for both occupied sites. The results of our calculations yield the crystal field splitting and Racah parameters of Dq =2008 cm{sup -1}, B =790 cm{sup -1}, C =2881 cm{sup -1}, with C/B = 3.65 (Mg{sup 2+} site) and Dq =2008 cm{sup -1}, B =790 cm{sup -1}, C =2949 cm{sup -1}, with C/B = 3.73 (Te{sup 6+} site). A cross-cutting comparative study of the variations in the crystal field splitting and the Racah parameters of the six-coordinated Mn{sup 4+} ion in a series of materials with the perovskite structure are presented. (orig.)

  9. Single crystal X-ray diffraction studies of DNA and DNA-drug complexes

    CERN Document Server

    Todd, A K

    1999-01-01

    The structure of the brominated oligonucleotide d(ACGTACG(5-BrU)) sub 2 was solved using the multiwavelength anomalous diffraction (MAD) technique. The space group was P4 sub 3 2 sub 1 2, with unit cell a=b=43.60A, c=26.27A. This structure was an A-DNA, isomorphous with many other previously solved octomers. Single crystal X-ray diffraction data were collected from crystals of the intercalation complexes N-[2-(dimethylamino)ethyl] acridine-4-carboxamide (DACA), d(CGTACG) sub 2 and N-[2-(dimethylamino)ethyl] 9-aminoacridine-4-carboxamide (9- aminoDACA) and some of their derivatives. An attempt was made to solve the structure of the DACA derivative N-[2-(dimethylamino)butyl]-acridine-4-carboxamide (DACA4) by molecular replacement, using the crystal structure of the daunomycin d(CGTACG) sub 2 complex as a search model. Attempts were made to position the molecule in the unit cell based on an SIR map, knowledge of the symmetry and unit cell dimensions. The structure of the 9-amino-5-bromo DACA - d(CGT(5-BrU)CG) su...

  10. Crystallization and preliminary studies of the DNA-binding domain Za from ADAR1 complexed to left-handed DNA.

    Science.gov (United States)

    Schwartz, T; Shafer, K; Lowenhaupt, K; Hanlon, E; Herbert, A; Rich, A

    1999-07-01

    The proteolytically defined Z-DNA binding domain Za of human adenosine deaminase type 1 (hADAR1) has been crystallized in complex with the DNA oligomer d(TCGCGCG). The crystals were obtained from a solution containing ammonium sulfate as precipitating agent and belong to the tetragonal space group P4212. A complete diffraction data set has been collected to a resolution of 2.4 A. The unit-cell dimensions are a = b = 85.9, c = 71.3 A. A Raman spectrum of the complex indicates that the DNA in the complex adopts the left-handed Z conformation.

  11. 3D and beyond

    Science.gov (United States)

    Fung, Y. C.

    1995-05-01

    This conference on physiology and function covers a wide range of subjects, including the vasculature and blood flow, the flow of gas, water, and blood in the lung, the neurological structure and function, the modeling, and the motion and mechanics of organs. Many technologies are discussed. I believe that the list would include a robotic photographer, to hold the optical equipment in a precisely controlled way to obtain the images for the user. Why are 3D images needed? They are to achieve certain objectives through measurements of some objects. For example, in order to improve performance in sports or beauty of a person, we measure the form, dimensions, appearance, and movements.

  12. CCDC 1024817: Experimental Crystal Structure Determination : 2-Mesityl-2,4,6,10b-tetrahydro-1H,5aH-indeno[2,1-b][1,2,4]triazolo[4,3-d][1,4]oxazine-1-selenone

    KAUST Repository

    Vummaleti, Sai V. C.

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  13. CCDC 1055932: Experimental Crystal Structure Determination : [(1,9-dimethylphenaleno[2,1-b]phenaleno[1',2':4,5]thieno[2,3-d]thiene-6,15-diyl)di(ethyne-2,1-diyl)]bis[tri(propan-2-yl)silane

    KAUST Repository

    Shi, Xueliang

    2015-01-01

    An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

  14. 3D Surgical Simulation

    Science.gov (United States)

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

    2009-01-01

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

  15. TOWARDS: 3D INTERNET

    Directory of Open Access Journals (Sweden)

    Ms. Swapnali R. Ghadge

    2013-08-01

    Full Text Available In today’s ever-shifting media landscape, it can be a complex task to find effective ways to reach your desired audience. As traditional media such as television continue to lose audience share, one venue in particular stands out for its ability to attract highly motivated audiences and for its tremendous growth potential the 3D Internet. The concept of '3D Internet' has recently come into the spotlight in the R&D arena, catching the attention of many people, and leading to a lot of discussions. Basically, one can look into this matter from a few different perspectives: visualization and representation of information, and creation and transportation of information, among others. All of them still constitute research challenges, as no products or services are yet available or foreseen for the near future. Nevertheless, one can try to envisage the directions that can be taken towards achieving this goal. People who take part in virtual worlds stay online longer with a heightened level of interest. To take advantage of that interest, diverse businesses and organizations have claimed an early stake in this fast-growing market. They include technology leaders such as IBM, Microsoft, and Cisco, companies such as BMW, Toyota, Circuit City, Coca Cola, and Calvin Klein, and scores of universities, including Harvard, Stanford and Penn State.

  16. Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system

    Energy Technology Data Exchange (ETDEWEB)

    Egli, Martin; Pallan, Pradeep S.; Pattanayek, Rekha; Wilds, Christopher J.; Lubini, Paolo; Minasov, George; Dobler, Max; Leumann, Christian J.; Eschenmoser, Albert (Bern); (Vanderbilt); (Scripps); (NWU); (Biographics Laboratory 3R); (Alta)

    2010-03-05

    An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that are capable of Watson-Crick base pairing and in some cases cross-pairing with the natural nucleic acids. The earliest among the model systems tested to date, (4{prime} {yields} 6{prime})-linked oligo(2{prime},3{prime}-dideoxy-{beta}-d-glucopyranosyl)nucleotides or homo-DNA, shows stable self-pairing, but the pairing rules for the four natural bases are not the same as those in DNA. However, a complete interpretation and understanding of the properties of the hexapyranosyl (4{prime} {yields} 6{prime}) family of nucleic acids has been impeded until now by the lack of detailed 3D-structural data. We have determined the crystal structure of a homo-DNA octamer. It reveals a weakly twisted right-handed duplex with a strong inclination between the hexose-phosphate backbones and base-pair axes, and highly irregular values for helical rise and twist at individual base steps. The structure allows a rationalization of the inability of allo-, altro-, and glucopyranosyl-based oligonucleotides to form stable pairing systems.

  17. Single-strand DNA detection using a planar photonic-crystal-waveguide-based sensor.

    Science.gov (United States)

    Toccafondo, V; García-Rupérez, J; Bañuls, M J; Griol, A; Castelló, J G; Peransi-Llopis, S; Maquieira, A

    2010-11-01

    We report an experimental demonstration of single-strand DNA (ssDNA) detection at room temperature using a photonic-crystal-waveguide-based optical sensor. The sensor surface was previously biofunctionalized with ssDNA probes to be used as specific target receptors. Our experiments showed that it is possible to detect these hybridization events using planar photonic-crystal structures, reaching an estimated detection limit as low as 19.8 nM for the detection of the complementary DNA strand.

  18. 3D-kompositointi

    OpenAIRE

    Piirainen, Jere

    2015-01-01

    Opinnäytetyössä käydään läpi yleisimpiä 3D-kompositointiin liittyviä tekniikoita sekä kompositointiin käytettyjä ohjelmia ja liitännäisiä. Työssä esitellään myös kompositoinnin juuret 1800-luvun lopulta aina nykyaikaiseen digitaaliseen kompositointiin asti. Kompositointi on yksinkertaisimmillaan usean kuvan liittämistä saumattomasti yhdeksi uskottavaksi kokonaisuudeksi. Vaikka prosessi vaatii visuaalista silmää, vaatii se myös paljon teknistä osaamista. Tämän lisäksi perusymmärrys kamera...

  19. Shaping 3-D boxes

    DEFF Research Database (Denmark)

    Stenholt, Rasmus; Madsen, Claus B.

    2011-01-01

    Enabling users to shape 3-D boxes in immersive virtual environments is a non-trivial problem. In this paper, a new family of techniques for creating rectangular boxes of arbitrary position, orientation, and size is presented and evaluated. These new techniques are based solely on position data......, making them different from typical, existing box shaping techniques. The basis of the proposed techniques is a new algorithm for constructing a full box from just three of its corners. The evaluation of the new techniques compares their precision and completion times in a 9 degree-of-freedom (Do......F) docking experiment against an existing technique, which requires the user to perform the rotation and scaling of the box explicitly. The precision of the users' box construction is evaluated by a novel error metric measuring the difference between two boxes. The results of the experiment strongly indicate...

  20. Synthesis and Crystal Structure of 2-(4'-Methylphenoxy)-5,8,9-trimethyl-3-phenyl Thieno[3',2':5,6]pyrido[4,3-d]pyrimidin-4-(3H)-one Hydrochloride

    Institute of Scientific and Technical Information of China (English)

    LIU Jian-Chao; HE Hong-Wu; DING Ming-Wu

    2006-01-01

    The title compound 2-(4′-methylphenoxy)-5,8,9-trimethyl-3-phenyl thieno[3′,2′:5,6]pyrido[4,3-d]pyrimidin-4(3H)-one hydrochloride (C26H23Cl4N3O2S, Mr = 583.33) has been deter- mined by single-crystal X-ray diffraction. The crystal belongs to monoclinic, space group P21/c with a = 14.8442(11), b = 11.5131(8), c = 17.2010(13) (A), β = 113.7250(10)o, V = 2691.3(3) (A)3, Z = 4, Dc = 1.440 g/cm3, S = 1.094, μ = 0.547 mm-1, F(000) = 1200, the final R = 0.0571 and wR = 0.1458. X-ray analysis reveals that the title compound combines with a molecule of dichloromethane by an intramolecular hydrogen bond. The thienopyridine ring is almost coplanar, and the dihedral angle between the thiophene plane and the pyridine plane is 0.6o.

  1. Hydrothermal synthesis and crystal structure study of two novel 3-D mellitates {Nd2[C6(COO)6](H2O)6} and {Ho2[C6(COO)6](H2O)6}

    Institute of Scientific and Technical Information of China (English)

    TANG Xiaoyong; YUE Shantang; LI Ping; WANG Ning; LIU Yingliang

    2008-01-01

    Two novel 3-D coordination compounds, Nd2[C6(COO)6](H2O)6(1)and Ho2[C6(COO)6](H2O)6(2), were hydrothermally synthe-sized from mellitic acid and neodymium perchlorate (or holmium perchlorate) in the alkaline aqueous solution and characterized with ele-mental analysis, TG, IR spectrum, and single crystal X-ray diffraction. The two compounds were isostructural and crystallized in the ortho-rhombic system, space group Pnnm, with a=1.3531 (4) nm, b=0.6687 (2) nm, c=1.0224(3) nm, V=0.92523(5) nm3, Z=4, D=2.630 g/cm3, F(000)=696.0, Goof=1.052. Final R indices [I 2Σ(I)]: R1=0.0195, wR2=0.0382 for 1; a=1.3411(2) nm, b=0.6586(1) nm, c=1.0116(2) nm, V=0.8935(3) nm3, Z=4, D=2.877 g/cm3, F(000)=724.0, Goof=1.061. Final R indices [I 2Σ(I)]: R1=0.0200, wR2=0.0479 for 2. In the two compounds 1 and 2, the mellitic acid ligand, in which all the carboxylate groups were deprotonated, had only one kind of coordination mode to bridge metal ions to form four-connected three-dimensional diamondiod networks.

  2. 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

    Science.gov (United States)

    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.

  3. Selective detection of labeled DNA using an air-clad photonic crystal fiber

    DEFF Research Database (Denmark)

    Jensen, Jesper Bo Damm; Hoiby, P.E.; Pedersen, L.H.

    2004-01-01

    Demonstration of selective detection of fluorophore labeled DNA by hybridization inside the air holes of a photonic crystal fiber A laser exposes the fiber from the side and the emitted fluorescence tunnels into the core.......Demonstration of selective detection of fluorophore labeled DNA by hybridization inside the air holes of a photonic crystal fiber A laser exposes the fiber from the side and the emitted fluorescence tunnels into the core....

  4. Crystallization and preliminary crystallographic analysis of a DNA (cytosine-5)-methyltransferase from Haemophilus aegyptius bound covalently to DNA.

    Science.gov (United States)

    Reinisch, K M; Chen, L; Verdine, G L; Lipscomb, W N

    1994-05-13

    A DNA (cytosine)-5-methyltransferase from Haemophilus aegyptius (M.Hae III), which catalyzes methyl transfer from S-adenosyl-L-methionine to DNA, has been crystallized as a covalent complex with a suicide oligonucleotide substrate. Crystals of the co-complex were grown by vapor diffusion with hanging droplets, using polyethylene glycol 3500 as the precipitant. The crystals belong to the orthorhombic space group P2(1)2(1)2(1); the unit cell parameters are a = 57.6 A, b = 108.0 A, c = 155.8 A with two protein-DNA complexes in the asymmetric unit. Complete sets of native and derivative data have been collected to 2.7 A using a laboratory source.

  5. 3D Printing with Nucleic Acid Adhesives

    Science.gov (United States)

    2015-01-01

    By relying on specific DNA:DNA interactions as a “smart glue”, we have assembled microparticles into a colloidal gel that can hold its shape. This gel can be extruded with a 3D printer to generate centimeter size objects. We show four aspects of this material: (1) The colloidal gel material holds its shape after extrusion. (2) The connectivity among the particles is controlled by the binding behavior between the surface DNA and this mediates some control over the microscale structure. (3) The use of DNA-coated microparticles dramatically reduces the cost of DNA-mediated assembly relative to conventional DNA nanotechnologies and makes this material accessible for macroscale applications. (4) This material can be assembled under biofriendly conditions and can host growing cells within its matrix. The DNA-based control over organization should provide a new means of engineering bioprinted tissues. PMID:25984570

  6. Towards the chemoinformatic-based identification of DNA methyltransferase inhibitors: 2D- and 3D-similarity profile of screening libraries.

    Science.gov (United States)

    Yoo, Jakyung; Medina-Franco, José Luis

    2012-12-01

    DNA methyltransferases (DNMTs) are emerging targets for the treatment of cancer and other diseases. The quinolone-based compound, SGI-1027, is a promising inhibitor of DNMT1 with a distinct mode of action and it is an attractive starting point for further research. Several experimental and computational approaches can be used to further develop novel DNMT1 inhibitors based on SGI-1027. In this work, we used a chemoinformatic-based approach to explore the potential to identify novel inhibitors in large screening collections of natural products and synthetic commercial libraries. Using the principles of similarity searching, the similarity profile to the active reference compound SGI-1027 was computed for four different screening libraries using a total of 22 two- and three- dimensional representations and two similarity metrics. The compound library with the overall highest similarity profile to the probe molecule was identified as the most promising collection for experimental testing. Individual compounds with high similarity to the reference were also selected as suitable candidates for experimental validation. During the course of this work, the 22 two- and three- dimensional representations were compared to each other and classified based on the similarity values computed with the reference compound. This classification is valuable to select structure representations for similarity searching of any other screening library. This work represents a step forward to further advance epigenetic therapies using computational approaches.

  7. Intraoral 3D scanner

    Science.gov (United States)

    Kühmstedt, Peter; Bräuer-Burchardt, Christian; Munkelt, Christoph; Heinze, Matthias; Palme, Martin; Schmidt, Ingo; Hintersehr, Josef; Notni, Gunther

    2007-09-01

    Here a new set-up of a 3D-scanning system for CAD/CAM in dental industry is proposed. The system is designed for direct scanning of the dental preparations within the mouth. The measuring process is based on phase correlation technique in combination with fast fringe projection in a stereo arrangement. The novelty in the approach is characterized by the following features: A phase correlation between the phase values of the images of two cameras is used for the co-ordinate calculation. This works contrary to the usage of only phase values (phasogrammetry) or classical triangulation (phase values and camera image co-ordinate values) for the determination of the co-ordinates. The main advantage of the method is that the absolute value of the phase at each point does not directly determine the coordinate. Thus errors in the determination of the co-ordinates are prevented. Furthermore, using the epipolar geometry of the stereo-like arrangement the phase unwrapping problem of fringe analysis can be solved. The endoscope like measurement system contains one projection and two camera channels for illumination and observation of the object, respectively. The new system has a measurement field of nearly 25mm × 15mm. The user can measure two or three teeth at one time. So the system can by used for scanning of single tooth up to bridges preparations. In the paper the first realization of the intraoral scanner is described.

  8. Martian terrain - 3D

    Science.gov (United States)

    1997-01-01

    This area of terrain near the Sagan Memorial Station was taken on Sol 3 by the Imager for Mars Pathfinder (IMP). 3D glasses are necessary to identify surface detail.The IMP is a stereo imaging system with color capability provided by 24 selectable filters -- twelve filters per 'eye.' It stands 1.8 meters above the Martian surface, and has a resolution of two millimeters at a range of two meters.Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  9. 3D Printing and 3D Bioprinting in Pediatrics.

    Science.gov (United States)

    Vijayavenkataraman, Sanjairaj; Fuh, Jerry Y H; Lu, Wen Feng

    2017-07-13

    Additive manufacturing, commonly referred to as 3D printing, is a technology that builds three-dimensional structures and components layer by layer. Bioprinting is the use of 3D printing technology to fabricate tissue constructs for regenerative medicine from cell-laden bio-inks. 3D printing and bioprinting have huge potential in revolutionizing the field of tissue engineering and regenerative medicine. This paper reviews the application of 3D printing and bioprinting in the field of pediatrics.

  10. DNA hybridization-induced reorientation of liquid crystal anchoring at the nematic liquid crystal/aqueous interface.

    Science.gov (United States)

    Price, Andrew D; Schwartz, Daniel K

    2008-07-01

    Interactions between DNA and an adsorbed cationic surfactant at the nematic liquid crystal (LC)/aqueous interface were investigated using polarized and fluorescence microscopy. The adsorption of octadecyltrimethylammonium bromide (OTAB) surfactant to the LC/aqueous interface resulted in homeotropic (untilted) LC alignment. Subsequent adsorption of single-stranded DNA (ssDNA) to the surfactant-laden interface modified the interfacial structure, resulting in a reorientation of the LC from homeotropic alignment to an intermediate tilt angle. Exposure of the ssDNA/OTAB interfacial complex to its ssDNA complement induced a second change in the interfacial structure characterized by the nucleation, growth, and coalescence of lateral regions that induced homeotropic LC alignment. Fluorescence microscopy showed explicitly that the complement was colocalized in the same regions as the homeotropic domains. Exposure to noncomplementary ssDNA caused no such response, suggesting that the homeotropic regions were due to DNA hybridization. This hybridization occurred in the vicinity of the interface despite the fact that the conditions in bulk solution were such that hybridization did not occur (high stringency), suggesting that the presence of the cationic surfactant neutralized electrostatic repulsion and allowed for hydrogen bonding between DNA complements. This system has potential for label-less and portable DNA detection. Indeed, LC response to ssDNA target was detected with a lower limit of approximately 50 fmol of complement and was sufficiently selective to differentiate a one-base-pair mismatch in a 16-mer target.

  11. 3D printing for dummies

    CERN Document Server

    Hausman, Kalani Kirk

    2014-01-01

    Get started printing out 3D objects quickly and inexpensively! 3D printing is no longer just a figment of your imagination. This remarkable technology is coming to the masses with the growing availability of 3D printers. 3D printers create 3-dimensional layered models and they allow users to create prototypes that use multiple materials and colors.  This friendly-but-straightforward guide examines each type of 3D printing technology available today and gives artists, entrepreneurs, engineers, and hobbyists insight into the amazing things 3D printing has to offer. You'll discover methods for

  12. 3D game environments create professional 3D game worlds

    CERN Document Server

    Ahearn, Luke

    2008-01-01

    The ultimate resource to help you create triple-A quality art for a variety of game worlds; 3D Game Environments offers detailed tutorials on creating 3D models, applying 2D art to 3D models, and clear concise advice on issues of efficiency and optimization for a 3D game engine. Using Photoshop and 3ds Max as his primary tools, Luke Ahearn explains how to create realistic textures from photo source and uses a variety of techniques to portray dynamic and believable game worlds.From a modern city to a steamy jungle, learn about the planning and technological considerations for 3D modelin

  13. Facile synthesis of Graphene Oxide/Double-stranded DNA composite liquid crystals and Hydrogels

    Indian Academy of Sciences (India)

    Rajendra Kurapati; Ashok M Raichur; U Venkateswara Reddy; N Suryaprakash

    2016-03-01

    Investigation of the interactions between graphene oxide (GO) and biomolecules is very crucialfor the development of biomedical applications based on GO. This study reports the first observation of thespontaneous formation of self-assembled liquid crystals and three-dimensional hydrogels of graphene oxidewith double-stranded DNA by simple mixing in an aqueous buffer media without unwinding double-strandedDNA to single-stranded DNA. The GO/dsDNA hydrogels have shown controlled porosity by changing the concentration of the components. The strong binding between dsDNA and graphene is proved by Ramanspectroscopy

  14. 3D Printing an Octohedron

    OpenAIRE

    Aboufadel, Edward F.

    2014-01-01

    The purpose of this short paper is to describe a project to manufacture a regular octohedron on a 3D printer. We assume that the reader is familiar with the basics of 3D printing. In the project, we use fundamental ideas to calculate the vertices and faces of an octohedron. Then, we utilize the OPENSCAD program to create a virtual 3D model and an STereoLithography (.stl) file that can be used by a 3D printer.

  15. Salient Local 3D Features for 3D Shape Retrieval

    CERN Document Server

    Godil, Afzal

    2011-01-01

    In this paper we describe a new formulation for the 3D salient local features based on the voxel grid inspired by the Scale Invariant Feature Transform (SIFT). We use it to identify the salient keypoints (invariant points) on a 3D voxelized model and calculate invariant 3D local feature descriptors at these keypoints. We then use the bag of words approach on the 3D local features to represent the 3D models for shape retrieval. The advantages of the method are that it can be applied to rigid as well as to articulated and deformable 3D models. Finally, this approach is applied for 3D Shape Retrieval on the McGill articulated shape benchmark and then the retrieval results are presented and compared to other methods.

  16. Atomic resolution 3D electron diffraction microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Miao, Jianwei; Ohsuna, Tetsu; Terasaki, Osamu; O' Keefe, Michael A.

    2002-03-01

    Electron lens aberration is the major barrier limiting the resolution of electron microscopy. Here we describe a novel form of electron microscopy to overcome electron lens aberration. By combining coherent electron diffraction with the oversampling phasing method, we show that the 3D structure of a 2 x 2 x 2 unit cell nano-crystal (framework of LTA [Al12Si12O48]8) can be ab initio determined at the resolution of 1 Angstrom from a series of simulated noisy diffraction pattern projections with rotation angles ranging from -70 degrees to +70 degrees in 5 degrees increments along a single rotation axis. This form of microscopy (which we call 3D electron diffraction microscopy) does not require any reference waves, and can image the 3D structure of nanocrystals, as well as non-crystalline biological and materials science samples, with the resolution limited only by the quality of sample diffraction.

  17. Crystal Structure of a Replicative DNA Polymerase Bound to the Oxidized Guanine Lesion Guanidinohydantoin

    Energy Technology Data Exchange (ETDEWEB)

    Aller, Pierre; Ye, Yu; Wallace, Susan S.; Burrows, Cynthia J.; Doubli, Sylvie (Vermont); (Utah)

    2010-04-12

    The oxidation of guanine generates one of the most common DNA lesions, 8-oxo-7,8-dihydroguanine (8-oxoG). The further oxidation of 8-oxoG can produce either guanidinohydantoin (Gh) in duplex DNA or spiroiminodihydantoin (Sp) in nucleosides and ssDNA. Although Gh can be a strong block for replicative DNA polymerases such as RB69 DNA polymerase, this lesion is also mutagenic: DNA polymerases bypass Gh by preferentially incorporating a purine with a slight preference for adenine, which results in G {center_dot} C {yields} T {center_dot} A or G {center_dot} C {yields} C {center_dot} G transversions. The 2.15 {angstrom} crystal structure of the replicative RB69 DNA polymerase in complex with DNA containing Gh reveals that Gh is extrahelical and rotated toward the major groove. In this conformation Gh is no longer in position to serve as a templating base for the incorporation of an incoming nucleotide. This work also constitutes the first crystallographic structure of Gh, which is stabilized in the R configuration in the two polymerase/DNA complexes present in the crystal asymmetric unit. In contrast to 8-oxoG, Gh is found in a high syn conformation in the DNA duplex and therefore presents the same hydrogen bond donor and acceptor pattern as thymine, which explains the propensity of DNA polymerases to incorporate a purine opposite Gh when bypass occurs.

  18. Collaborative annotation of 3D crystallographic models.

    Science.gov (United States)

    Hunter, J; Henderson, M; Khan, I

    2007-01-01

    This paper describes the AnnoCryst system-a tool that was designed to enable authenticated collaborators to share online discussions about 3D crystallographic structures through the asynchronous attachment, storage, and retrieval of annotations. Annotations are personal comments, interpretations, questions, assessments, or references that can be attached to files, data, digital objects, or Web pages. The AnnoCryst system enables annotations to be attached to 3D crystallographic models retrieved from either private local repositories (e.g., Fedora) or public online databases (e.g., Protein Data Bank or Inorganic Crystal Structure Database) via a Web browser. The system uses the Jmol plugin for viewing and manipulating the 3D crystal structures but extends Jmol by providing an additional interface through which annotations can be created, attached, stored, searched, browsed, and retrieved. The annotations are stored on a standardized Web annotation server (Annotea), which has been extended to support 3D macromolecular structures. Finally, the system is embedded within a security framework that is capable of authenticating users and restricting access only to trusted colleagues.

  19. Importance of the DNA “bond” in programmable nanoparticle crystallization

    Energy Technology Data Exchange (ETDEWEB)

    Macfarlane, Robert J.; Thaner, Ryan V.; Brown, Keith A.; Zhang, Jian; Lee, Byeongdu; Nguyen, SonBinh T.; Mirkin, Chad A.

    2014-10-21

    If a solution of DNA-coated nanoparticles is allowed to crystallize, the thermodynamic structure can be predicted by a set of structural design rules analogous to Pauling's rules for ionic crystallization. The details of the crystallization process, however, have proved more difficult to characterize as they depend on a complex interplay of many factors. Here, we report that this crystallization process is dictated by the individual DNA bonds and that the effect of changing structural or environmental conditions can be understood by considering the effect of these parameters on free oligonucleotides. Specifically, we observed the reorganization of nanoparticle superlattices using time-resolved synchrotron small-angle X-ray scattering in systems with different DNA sequences, salt concentrations, and densities of DNA linkers on the surface of the nanoparticles. The agreement between bulk crystallization and the behavior of free oligonucleotides may bear important consequences for constructing novel classes of crystals and incorporating new interparticle bonds in a rational manner.

  20. The Myb domain of LUX ARRHYTHMO in complex with DNA: expression, purification and crystallization.

    Science.gov (United States)

    Silva, Catarina S; Lai, Xuelei; Nanao, Max; Zubieta, Chloe

    2016-05-01

    LUX ARRHYTHMO (LUX) is a Myb-domain transcription factor that plays an important role in regulating the circadian clock. Lux mutations cause severe clock defects and arrhythmia in constant light and dark. In order to examine the molecular mechanisms underlying the function of LUX, the DNA-binding Myb domain was cloned, expressed and purified. The DNA-binding activity of the Myb domain was confirmed using electrophoretic mobility shift assays (EMSAs), demonstrating that the LUX Myb domain is able to bind to DNA with nanomolar affinity. In order to investigate the specificity determinants of protein-DNA interactions, the protein was co-crystallized with a 10-mer cognate DNA. Initial crystallization results for the selenomethionine-derivatized protein and data-set collection statistics are reported. Data collection was performed using the MeshAndCollect workflow available at the ESRF.

  1. Holography of 3d-3d correspondence at Large N

    OpenAIRE

    Gang, Dongmin; Kim, Nakwoo; Lee, Sangmin

    2014-01-01

    We study the physics of multiple M5-branes compactified on a hyperbolic 3-manifold. On the one hand, it leads to the 3d-3d correspondence which maps an N = 2 $$ \\mathcal{N}=2 $$ superconformal field theory to a pure Chern-Simons theory on the 3-manifold. On the other hand, it leads to a warped AdS 4 geometry in M-theory holographically dual to the superconformal field theory. Combining the holographic duality and the 3d-3d correspondence, we propose a conjecture for the large N limit of the p...

  2. Full-color holographic 3D printer

    Science.gov (United States)

    Takano, Masami; Shigeta, Hiroaki; Nishihara, Takashi; Yamaguchi, Masahiro; Takahashi, Susumu; Ohyama, Nagaaki; Kobayashi, Akihiko; Iwata, Fujio

    2003-05-01

    A holographic 3D printer is a system that produces a direct hologram with full-parallax information using the 3-dimensional data of a subject from a computer. In this paper, we present a proposal for the reproduction of full-color images with the holographic 3D printer. In order to realize the 3-dimensional color image, we selected the 3 laser wavelength colors of red (λ=633nm), green (λ=533nm), and blue (λ=442nm), and we built a one-step optical system using a projection system and a liquid crystal display. The 3-dimensional color image is obtained by synthesizing in a 2D array the multiple exposure with these 3 wavelengths made on each 250mm elementary hologram, and moving recording medium on a x-y stage. For the natural color reproduction in the holographic 3D printer, we take the approach of the digital processing technique based on the color management technology. The matching between the input and output colors is performed by investigating first, the relation between the gray level transmittance of the LCD and the diffraction efficiency of the hologram and second, by measuring the color displayed by the hologram to establish a correlation. In our first experimental results a non-linear functional relation for single and multiple exposure of the three components were found. These results are the first step in the realization of a natural color 3D image produced by the holographic color 3D printer.

  3. The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target

    Energy Technology Data Exchange (ETDEWEB)

    Mak, Amanda Nga-Sze; Bradley, Philip; Cernadas, Raul A.; Bogdanove, Adam J.; Stoddard, Barry L. (FHCRC); (Iowa State)

    2012-02-10

    DNA recognition by TAL effectors is mediated by tandem repeats, each 33 to 35 residues in length, that specify nucleotides via unique repeat-variable diresidues (RVDs). The crystal structure of PthXo1 bound to its DNA target was determined by high-throughput computational structure prediction and validated by heavy-atom derivatization. Each repeat forms a left-handed, two-helix bundle that presents an RVD-containing loop to the DNA. The repeats self-associate to form a right-handed superhelix wrapped around the DNA major groove. The first RVD residue forms a stabilizing contact with the protein backbone, while the second makes a base-specific contact to the DNA sense strand. Two degenerate amino-terminal repeats also interact with the DNA. Containing several RVDs and noncanonical associations, the structure illustrates the basis of TAL effector-DNA recognition.

  4. 3D Printed Multimaterial Microfluidic Valve

    Science.gov (United States)

    Patrick, William G.; Sharma, Sunanda; Kong, David S.; Oxman, Neri

    2016-01-01

    We present a novel 3D printed multimaterial microfluidic proportional valve. The microfluidic valve is a fundamental primitive that enables the development of programmable, automated devices for controlling fluids in a precise manner. We discuss valve characterization results, as well as exploratory design variations in channel width, membrane thickness, and membrane stiffness. Compared to previous single material 3D printed valves that are stiff, these printed valves constrain fluidic deformation spatially, through combinations of stiff and flexible materials, to enable intricate geometries in an actuated, functionally graded device. Research presented marks a shift towards 3D printing multi-property programmable fluidic devices in a single step, in which integrated multimaterial valves can be used to control complex fluidic reactions for a variety of applications, including DNA assembly and analysis, continuous sampling and sensing, and soft robotics. PMID:27525809

  5. Time domain topology optimization of 3D nanophotonic devices

    DEFF Research Database (Denmark)

    Elesin, Yuriy; Lazarov, Boyan Stefanov; Jensen, Jakob Søndergaard;

    2014-01-01

    We present an efficient parallel topology optimization framework for design of large scale 3D nanophotonic devices. The code shows excellent scalability and is demonstrated for optimization of broadband frequency splitter, waveguide intersection, photonic crystal-based waveguide and nanowire...

  6. Synthesis and Crystal Structure of 2’-Se-modified guanosine Containing DNA

    Energy Technology Data Exchange (ETDEWEB)

    Salon, J.; Sheng, J; Gan, J; Huang, Z

    2010-01-01

    Selenium modification of nucleic acids is of great importance in X-ray crystal structure determination and functional study of nucleic acids. Herein, we describe a convenient synthesis of a new building block, the 2{prime}-SeMe-modified guanosine (G{sub Se}) phosphoramidite, and report the first incorporation of the 2{prime}-Se-G moiety into DNA. The X-ray crystal structure of the 2{prime}-Se-modified octamer DNA (5{prime}-GTG{sub Se}TACAC-3{prime}) was determined at a resolution of 1.20 {angstrom}. We also found that the 2{prime}-Se modification points to the minor groove and that the modified and native structures are virtually identical. Furthermore, we observed that the 2{prime}-Se-G modification can significantly facilitate the crystal growth with respect to the corresponding native DNA.

  7. 3D Spectroscopy in Astronomy

    Science.gov (United States)

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

    2011-09-01

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

  8. Spherical 3D isotropic wavelets

    Science.gov (United States)

    Lanusse, F.; Rassat, A.; Starck, J.-L.

    2012-04-01

    Context. Future cosmological surveys will provide 3D large scale structure maps with large sky coverage, for which a 3D spherical Fourier-Bessel (SFB) analysis in spherical coordinates is natural. Wavelets are particularly well-suited to the analysis and denoising of cosmological data, but a spherical 3D isotropic wavelet transform does not currently exist to analyse spherical 3D data. Aims: The aim of this paper is to present a new formalism for a spherical 3D isotropic wavelet, i.e. one based on the SFB decomposition of a 3D field and accompany the formalism with a public code to perform wavelet transforms. Methods: We describe a new 3D isotropic spherical wavelet decomposition based on the undecimated wavelet transform (UWT) described in Starck et al. (2006). We also present a new fast discrete spherical Fourier-Bessel transform (DSFBT) based on both a discrete Bessel transform and the HEALPIX angular pixelisation scheme. We test the 3D wavelet transform and as a toy-application, apply a denoising algorithm in wavelet space to the Virgo large box cosmological simulations and find we can successfully remove noise without much loss to the large scale structure. Results: We have described a new spherical 3D isotropic wavelet transform, ideally suited to analyse and denoise future 3D spherical cosmological surveys, which uses a novel DSFBT. We illustrate its potential use for denoising using a toy model. All the algorithms presented in this paper are available for download as a public code called MRS3D at http://jstarck.free.fr/mrs3d.html

  9. 3D IBFV : Hardware-Accelerated 3D Flow Visualization

    NARCIS (Netherlands)

    Telea, Alexandru; Wijk, Jarke J. van

    2003-01-01

    We present a hardware-accelerated method for visualizing 3D flow fields. The method is based on insertion, advection, and decay of dye. To this aim, we extend the texture-based IBFV technique for 2D flow visualization in two main directions. First, we decompose the 3D flow visualization problem in a

  10. 3D Elevation Program—Virtual USA in 3D

    Science.gov (United States)

    Lukas, Vicki; Stoker, J.M.

    2016-04-14

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

  11. A 3-D Contextual Classifier

    DEFF Research Database (Denmark)

    Larsen, Rasmus

    1997-01-01

    . This includes the specification of a Gaussian distribution for the pixel values as well as a prior distribution for the configuration of class variables within the cross that is m ade of a pixel and its four nearest neighbours. We will extend this algorithm to 3-D, i.e. we will specify a simultaneous Gaussian...... distr ibution for a pixel and its 6 nearest 3-D neighbours, and generalise the class variable configuration distribution within the 3-D cross. The algorithm is tested on a synthetic 3-D multivariate dataset....

  12. 3D Bayesian contextual classifiers

    DEFF Research Database (Denmark)

    Larsen, Rasmus

    2000-01-01

    We extend a series of multivariate Bayesian 2-D contextual classifiers to 3-D by specifying a simultaneous Gaussian distribution for the feature vectors as well as a prior distribution of the class variables of a pixel and its 6 nearest 3-D neighbours.......We extend a series of multivariate Bayesian 2-D contextual classifiers to 3-D by specifying a simultaneous Gaussian distribution for the feature vectors as well as a prior distribution of the class variables of a pixel and its 6 nearest 3-D neighbours....

  13. Using 3D in Visualization

    DEFF Research Database (Denmark)

    Wood, Jo; Kirschenbauer, Sabine; Döllner, Jürgen

    2005-01-01

    to display 3D imagery. The extra cartographic degree of freedom offered by using 3D is explored and offered as a motivation for employing 3D in visualization. The use of VR and the construction of virtual environments exploit navigational and behavioral realism, but become most usefil when combined...... with abstracted representations embedded in a 3D space. The interactions between development of geovisualization, the technology used to implement it and the theory surrounding cartographic representation are explored. The dominance of computing technologies, driven particularly by the gaming industry...

  14. Interactive 3D multimedia content

    CERN Document Server

    Cellary, Wojciech

    2012-01-01

    The book describes recent research results in the areas of modelling, creation, management and presentation of interactive 3D multimedia content. The book describes the current state of the art in the field and identifies the most important research and design issues. Consecutive chapters address these issues. These are: database modelling of 3D content, security in 3D environments, describing interactivity of content, searching content, visualization of search results, modelling mixed reality content, and efficient creation of interactive 3D content. Each chapter is illustrated with example a

  15. 3D for Graphic Designers

    CERN Document Server

    Connell, Ellery

    2011-01-01

    Helping graphic designers expand their 2D skills into the 3D space The trend in graphic design is towards 3D, with the demand for motion graphics, animation, photorealism, and interactivity rapidly increasing. And with the meteoric rise of iPads, smartphones, and other interactive devices, the design landscape is changing faster than ever.2D digital artists who need a quick and efficient way to join this brave new world will want 3D for Graphic Designers. Readers get hands-on basic training in working in the 3D space, including product design, industrial design and visualization, modeling, ani

  16. 3-D printers for libraries

    CERN Document Server

    Griffey, Jason

    2014-01-01

    As the maker movement continues to grow and 3-D printers become more affordable, an expanding group of hobbyists is keen to explore this new technology. In the time-honored tradition of introducing new technologies, many libraries are considering purchasing a 3-D printer. Jason Griffey, an early enthusiast of 3-D printing, has researched the marketplace and seen several systems first hand at the Consumer Electronics Show. In this report he introduces readers to the 3-D printing marketplace, covering such topics asHow fused deposition modeling (FDM) printing workBasic terminology such as build

  17. Preparation of 3D Colloidal Crystal Film and Gold-Infiltrated Silica Artificial Opals%3D胶状晶体膜及其渗透金的氧化硅人工蛋白石的制备

    Institute of Scientific and Technical Information of China (English)

    李文江; 谢飞

    2007-01-01

    A free-standing 3D colloidal crystal film (opal) was fabricated at a water-air interface using purified monodispersed SiO2 colloids. The gold/silica opal was obtained through the infiltration of gold nanoparticles by electroplating. The transmission and reflection spectra of the gold/silica composite opal show a red shift with increasing electroplating time.SEM images show that gold nanoparticles can be directly deposited on the surface of silica spheres in the opaline structure. Gold/silica composite opal film could provide a simple way to tune opal properties through controlling the amount of gold in the silica opal.%用纯的单分散氧化硅胶体微球作为基质,在水-空气界面构筑无载体三维有序胶质晶体膜.该高度有序三维周期性结构具有明显的光学衍射现象.利用电沉积的方法将纳米金渗透到这种人工蛋白石的空隙中,构成gold/silica复合蛋白石材料.详细研究了该复合蛋白石的透射光谱和反射光谱,用扫描电镜观察了复合蛋白石结构的形貌特征,并对渗透金后蛋白石的光谱移动进行了分析.

  18. Lac repressor: Crystallization of intact tetramer and its complexes with inducer and operator DNA

    Energy Technology Data Exchange (ETDEWEB)

    Pace, H.C.; Lu, P. (Univ. of Pennsylvania, Philadelphia (USA)); Lewis, M. (Univ. of Pennsylvania, Philadelphia, (USA) Smith Kline and French Labs., King of Prussia, PA (USA))

    1990-03-01

    The intact lac repressor tetramer, which regulates expression of the lac operon in Escherichia coli, has been crystallized in the native form, with an inducer, and in a ternary complex with operator DNA and an anti-inducer. The crystals without DNA diffract to better than 3.5 {angstrom}. They belong to the monoclinic space group C2 and have cell dimensions a = 164.7 {angstrom}, b = 75.6 {angstrom}, and c = 161.2 {angstrom}, with {alpha} = {gamma} = 90{degree} and {beta} = 125.5{degree}. Cocrystals have been obtained with a number of different lac operator-related DNA fragments. The complex with a blunt-ended 16-base-pair strand yielded tetragonal bipyramids that diffract to 6.5 {angstrom}. These protein-DNA cocrystals crack upon exposure to the gratuitous inducer isopropyl {beta}-D-thiogalactoside, suggesting a conformational change in the repressor-operator complex.

  19. Perception of 3D spatial relations for 3D displays

    Science.gov (United States)

    Rosen, Paul; Pizlo, Zygmunt; Hoffmann, Christoph; Popescu, Voicu S.

    2004-05-01

    We test perception of 3D spatial relations in 3D images rendered by a 3D display (Perspecta from Actuality Systems) and compare it to that of a high-resolution flat panel display. 3D images provide the observer with such depth cues as motion parallax and binocular disparity. Our 3D display is a device that renders a 3D image by displaying, in rapid succession, radial slices through the scene on a rotating screen. The image is contained in a glass globe and can be viewed from virtually any direction. In the psychophysical experiment several families of 3D objects are used as stimuli: primitive shapes (cylinders and cuboids), and complex objects (multi-story buildings, cars, and pieces of furniture). Each object has at least one plane of symmetry. On each trial an object or its "distorted" version is shown at an arbitrary orientation. The distortion is produced by stretching an object in a random direction by 40%. This distortion must eliminate the symmetry of an object. The subject's task is to decide whether or not the presented object is distorted under several viewing conditions (monocular/binocular, with/without motion parallax, and near/far). The subject's performance is measured by the discriminability d', which is a conventional dependent variable in signal detection experiments.

  20. 3D Printing for Bricks

    OpenAIRE

    ECT Team, Purdue

    2015-01-01

    Building Bytes, by Brian Peters, is a project that uses desktop 3D printers to print bricks for architecture. Instead of using an expensive custom-made printer, it uses a normal standard 3D printer which is available for everyone and makes it more accessible and also easier for fabrication.

  1. Market study: 3-D eyetracker

    Science.gov (United States)

    1977-01-01

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

  2. Spherical 3D Isotropic Wavelets

    CERN Document Server

    Lanusse, F; Starck, J -L

    2011-01-01

    Future cosmological surveys will provide 3D large scale structure maps with large sky coverage, for which a 3D Spherical Fourier-Bessel (SFB) analysis in is natural. Wavelets are particularly well-suited to the analysis and denoising of cosmological data, but a spherical 3D isotropic wavelet transform does not currently exist to analyse spherical 3D data. The aim of this paper is to present a new formalism for a spherical 3D isotropic wavelet, i.e. one based on the Fourier-Bessel decomposition of a 3D field and accompany the formalism with a public code to perform wavelet transforms. We describe a new 3D isotropic spherical wavelet decomposition based on the undecimated wavelet transform (UWT) described in Starck et al. 2006. We also present a new fast Discrete Spherical Fourier-Bessel Transform (DSFBT) based on both a discrete Bessel Transform and the HEALPIX angular pixelisation scheme. We test the 3D wavelet transform and as a toy-application, apply a denoising algorithm in wavelet space to the Virgo large...

  3. Improvement of 3D Scanner

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The disadvantage remaining in 3D scanning system and its reasons are discussed. A new host-and-slave structure with high speed image acquisition and processing system is proposed to quicken the image processing and improve the performance of 3D scanning system.

  4. Advanced 3-D Ultrasound Imaging

    DEFF Research Database (Denmark)

    Rasmussen, Morten Fischer

    to produce high quality 3-D images. Because of the large matrix transducers with integrated custom electronics, these systems are extremely expensive. The relatively low price of ultrasound scanners is one of the factors for the widespread use of ultrasound imaging. The high price tag on the high quality 3-D......The main purpose of the PhD project was to develop methods that increase the 3-D ultrasound imaging quality available for the medical personnel in the clinic. Acquiring a 3-D volume gives the medical doctor the freedom to investigate the measured anatomy in any slice desirable after the scan has...... been completed. This allows for precise measurements of organs dimensions and makes the scan more operator independent. Real-time 3-D ultrasound imaging is still not as widespread in use in the clinics as 2-D imaging. A limiting factor has traditionally been the low image quality achievable using...

  5. Using 3D in Visualization

    DEFF Research Database (Denmark)

    Wood, Jo; Kirschenbauer, Sabine; Döllner, Jürgen

    2005-01-01

    The notion of three-dimensionality is applied to five stages of the visualization pipeline. While 3D visulization is most often associated with the visual mapping and representation of data, this chapter also identifies its role in the management and assembly of data, and in the media used...... to display 3D imagery. The extra cartographic degree of freedom offered by using 3D is explored and offered as a motivation for employing 3D in visualization. The use of VR and the construction of virtual environments exploit navigational and behavioral realism, but become most usefil when combined...... with abstracted representations embedded in a 3D space. The interactions between development of geovisualization, the technology used to implement it and the theory surrounding cartographic representation are explored. The dominance of computing technologies, driven particularly by the gaming industry...

  6. 3D printing in dentistry.

    Science.gov (United States)

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

    2015-12-01

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

  7. 3D vision system assessment

    Science.gov (United States)

    Pezzaniti, J. Larry; Edmondson, Richard; Vaden, Justin; Hyatt, Bryan; Chenault, David B.; Kingston, David; Geulen, Vanilynmae; Newell, Scott; Pettijohn, Brad

    2009-02-01

    In this paper, we report on the development of a 3D vision system consisting of a flat panel stereoscopic display and auto-converging stereo camera and an assessment of the system's use for robotic driving, manipulation, and surveillance operations. The 3D vision system was integrated onto a Talon Robot and Operator Control Unit (OCU) such that direct comparisons of the performance of a number of test subjects using 2D and 3D vision systems were possible. A number of representative scenarios were developed to determine which tasks benefited most from the added depth perception and to understand when the 3D vision system hindered understanding of the scene. Two tests were conducted at Fort Leonard Wood, MO with noncommissioned officers ranked Staff Sergeant and Sergeant First Class. The scenarios; the test planning, approach and protocols; the data analysis; and the resulting performance assessment of the 3D vision system are reported.

  8. PLOT3D user's manual

    Science.gov (United States)

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

    1990-01-01

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

  9. Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair

    Energy Technology Data Exchange (ETDEWEB)

    Cappadocia, Laurent; Maréchal, Alexandre; Parent, Jean-Sébastien; Lepage, Étienne; Sygusch, Jurgen; Brisson, Normand (Montreal)

    2010-09-07

    DNA double-strand breaks are highly detrimental to all organisms and need to be quickly and accurately repaired. Although several proteins are known to maintain plastid and mitochondrial genome stability in plants, little is known about the mechanisms of DNA repair in these organelles and the roles of specific proteins. Here, using ciprofloxacin as a DNA damaging agent specific to the organelles, we show that plastids and mitochondria can repair DNA double-strand breaks through an error-prone pathway similar to the microhomology-mediated break-induced replication observed in humans, yeast, and bacteria. This pathway is negatively regulated by the single-stranded DNA (ssDNA) binding proteins from the Whirly family, thus indicating that these proteins could contribute to the accurate repair of plant organelle genomes. To understand the role of Whirly proteins in this process, we solved the crystal structures of several Whirly-DNA complexes. These reveal a nonsequence-specific ssDNA binding mechanism in which DNA is stabilized between domains of adjacent subunits and rendered unavailable for duplex formation and/or protein interactions. Our results suggest a model in which the binding of Whirly proteins to ssDNA would favor accurate repair of DNA double-strand breaks over an error-prone microhomology-mediated break-induced replication repair pathway.

  10. Crystal structure of the human NKX2.5 homeodomain in complex with DNA target.

    Science.gov (United States)

    Pradhan, Lagnajeet; Genis, Caroli; Scone, Peyton; Weinberg, Ellen O; Kasahara, Hideko; Nam, Hyun-Joo

    2012-08-14

    NKX2.5 is a homeodomain containing transcription factor regulating cardiac formation and function, and its mutations are linked to congenital heart disease. Here we provide the first report of the crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene. The crystal structure, determined at 1.8 Å resolution, demonstrates that NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves. The two homeodomains show identical conformation despite the differences in the DNA sequences they bind, and no significant bending of the DNA was observed. Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif. This high resolution crystal structure of NKX2.5 protein provides a detailed picture of protein and DNA interactions, which allows us to predict DNA binding of mutants identified in human patients.

  11. Crystal Structure of the Human NKX2.5 Homeodomain in Complex with DNA Target

    Energy Technology Data Exchange (ETDEWEB)

    Pradhan, Lagnajeet; Genis, Caroli; Scone, Peyton; Weinberg, Ellen O.; Kasahara, Hideko; Nam, Hyun-Joo (BU-M); (Florida); (Texas)

    2012-10-16

    NKX2.5 is a homeodomain containing transcription factor regulating cardiac formation and function, and its mutations are linked to congenital heart disease. Here we provide the first report of the crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene. The crystal structure, determined at 1.8 {angstrom} resolution, demonstrates that NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves. The two homeodomains show identical conformation despite the differences in the DNA sequences they bind, and no significant bending of the DNA was observed. Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif. This high resolution crystal structure of NKX2.5 protein provides a detailed picture of protein and DNA interactions, which allows us to predict DNA binding of mutants identified in human patients.

  12. Anilides and quinolones with nitrogen-bearing substituents from benzothiophene and thienothiophene series: synthesis, photochemical synthesis, cytostatic evaluation, 3D-derived QSAR analysis and DNA-binding properties.

    Science.gov (United States)

    Aleksić, Maja; Bertoša, Branimir; Nhili, Raja; Depauw, Sabine; Martin-Kleiner, Irena; David-Cordonnier, Marie-Hélène; Tomić, Sanja; Kralj, Marijeta; Karminski-Zamola, Grace

    2014-01-01

    A series of new anilides (2a-c, 4-7, 17a-c, 18) and quinolones (3a-b, 8a-b, 9a-b, 10-15, 19) with nitrogen-bearing substituents from benzo[b]thiophene and thieno[2,3-c]thiophene series are prepared. Benzo[b]thieno[2,3-c]- and thieno[3',2':4,5]thieno[2,3-c]quinolones (3a-b, 8a-b) are synthesized by the reaction of photochemical dehydrohalogenation from corresponding anilides. Anilides and quinolones were tested for the antiproliferative activity. Fused quinolones bearing protonated aminium group, quaternary ammonium group, N-methylated and protonated aminium group, amino and protonated amino group (8a, 9b, 10-12) showed very prominent anticancer activity, whereby the hydrochloride salt of N',N'-dimethylaminopropyl-substituted quinolone (14) was the most active one, having the IC50 concentration at submicromolar range in accordance with previous QSAR predictions. On the other hand, flexible anilides were among the less active. Chemometric analysis of investigated compounds was performed. 3D-derived QSAR analysis identified solubility, metabolitic stability and the possibility of the compound to be ionized at pH 4-8 as molecular properties that are positively correlated with anticancer activity of investigated compounds, while molecular flexibility, polarizability and sum of hydrophobic surface areas were found to be negatively correlated. Anilides 2a-b, 4-7 and quinolones 3a-b, 8a-b, 9b and 10-14 were evaluated for DNA binding propensities and topoisomerases I/II inhibition as part of their mechanism of action. Among the anilides, only compound 7 presented some DNA binding propensity whereas the quinolones 8b, 9b and 10-14 intercalate in the DNA base pairs, compounds 8b, 9b and 14 being the most efficient ones. The strongest DNA intercalators, compounds 8b, 9b and 14, were clearly distinguished from the other compounds according to their molecular descriptors by the PCA and PLS analysis.

  13. The New Realm of 3-D Vision

    Science.gov (United States)

    2002-01-01

    Dimension Technologies Inc., developed a line of 2-D/3-D Liquid Crystal Display (LCD) screens, including a 15-inch model priced at consumer levels. DTI's family of flat panel LCD displays, called the Virtual Window(TM), provide real-time 3-D images without the use of glasses, head trackers, helmets, or other viewing aids. Most of the company initial 3-D display research was funded through NASA's Small Business Innovation Research (SBIR) program. The images on DTI's displays appear to leap off the screen and hang in space. The display accepts input from computers or stereo video sources, and can be switched from 3-D to full-resolution 2-D viewing with the push of a button. The Virtual Window displays have applications in data visualization, medicine, architecture, business, real estate, entertainment, and other research, design, military, and consumer applications. Displays are currently used for computer games, protein analysis, and surgical imaging. The technology greatly benefits the medical field, as surgical simulators are helping to increase the skills of surgical residents. Virtual Window(TM) is a trademark of Dimension Technologies Inc.

  14. 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).

    Science.gov (United States)

    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.

  15. ADT-3D Tumor Detection Assistant in 3D

    Directory of Open Access Journals (Sweden)

    Jaime Lazcano Bello

    2008-12-01

    Full Text Available The present document describes ADT-3D (Three-Dimensional Tumor Detector Assistant, a prototype application developed to assist doctors diagnose, detect and locate tumors in the brain by using CT scan. The reader may find on this document an introduction to tumor detection; ADT-3D main goals; development details; description of the product; motivation for its development; result’s study; and areas of applicability.

  16. Unassisted 3D camera calibration

    Science.gov (United States)

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

    2012-03-01

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

  17. Bioprinting of 3D hydrogels.

    Science.gov (United States)

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

    2015-08-07

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

  18. Crystal structure of four-stranded Oxytricha telomeric DNA

    Science.gov (United States)

    Kang, C.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A.

    1992-01-01

    The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

  19. Tuotekehitysprojekti: 3D-tulostin

    OpenAIRE

    Pihlajamäki, Janne

    2011-01-01

    Opinnäytetyössä tutustuttiin 3D-tulostamisen teknologiaan. Työssä käytiin läpi 3D-tulostimesta tehty tuotekehitysprojekti. Sen lisäksi esiteltiin yleisellä tasolla tuotekehitysprosessi ja syntyneiden tulosten mahdollisia suojausmenetelmiä. Tavoitteena tässä työssä oli kehittää markkinoilta jo löytyvää kotitulostin-tasoista 3D-laiteteknologiaa lähemmäksi ammattilaistason ratkaisua. Tavoitteeseen pyrittiin keskittymällä parantamaan laitteella saavutettavaa tulostustarkkuutta ja -nopeutt...

  20. Color 3D Reverse Engineering

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    This paper presents a principle and a method of col or 3D laser scanning measurement. Based on the fundamental monochrome 3D measureme nt study, color information capture, color texture mapping, coordinate computati on and other techniques are performed to achieve color 3D measurement. The syste m is designed and composed of a line laser light emitter, one color CCD camera, a motor-driven rotary filter, a circuit card and a computer. Two steps in captu ring object's images in the measurement process: Firs...

  1. Exploration of 3D Printing

    OpenAIRE

    Lin, Zeyu

    2014-01-01

    3D printing technology is introduced and defined in this Thesis. Some methods of 3D printing are illustrated and their principles are explained with pictures. Most of the essential parts are presented with pictures and their effects are explained within the whole system. Problems on Up! Plus 3D printer are solved and a DIY product is made with this machine. The processes of making product are recorded and the items which need to be noticed during the process are the highlight in this th...

  2. Handbook of 3D integration

    CERN Document Server

    Garrou , Philip; Ramm , Peter

    2014-01-01

    Edited by key figures in 3D integration and written by top authors from high-tech companies and renowned research institutions, this book covers the intricate details of 3D process technology.As such, the main focus is on silicon via formation, bonding and debonding, thinning, via reveal and backside processing, both from a technological and a materials science perspective. The last part of the book is concerned with assessing and enhancing the reliability of the 3D integrated devices, which is a prerequisite for the large-scale implementation of this emerging technology. Invaluable reading fo

  3. Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil

    Directory of Open Access Journals (Sweden)

    Masaru Tsunoda

    2010-01-01

    Full Text Available Hydroxyl radicals are potent mutagens that attack DNA to form various base and ribose derivatives. One of the major damaged thymine derivatives is 5-formyluracil (fU, which induces pyrimidine transition during replication. In order to establish the structural basis for such mutagenesis, the crystal structures of two kinds of DNA d(CGCGRATfUCGCG with R = A/G have been determined by X-ray crystallography. The fU residues form a Watson-Crick-type pair with A and two types of pairs (wobble and reversed wobble with G, the latter being a new type of base pair between ionized thymine base and guanine base. In silico structural modeling suggests that the DNA polymerase can accept the reversed wobble pair with G, as well as the Watson-Crick pair with A.

  4. In-Plane Switching Mode for Liquid Crystal Displays Using a DNA Alignment Layer.

    Science.gov (United States)

    Cha, Yun Jeong; Gim, Min-Jun; Oh, Kyunghwan; Yoon, Dong Ki

    2015-06-24

    We successfully fabricated the in-plane switching mode (IPS) LC display (LCD) based on a double stranded DNA (dsDNA) alignment layer. As widely known, the DNA has the right-handed double helical structure that has naturally grown grooves with a very regular period, which can be used as an alignment layer to control the orientation of liquid crystal (LC) molecules. The LC molecules on this topographical layer of DNA material align obliquely at a specific angle with respect to the direction of DNA chains, providing an instant and convenient tool for the fabrication of the IPS display compared to the conventional ways such as rubbing and mechanical shearing methods. The electro-optical performance and response time of this device were also investigated. Our result will be of great use in further exploration of the electro-optical properties of the other biomaterials.

  5. Conducting polymer 3D microelectrodes

    DEFF Research Database (Denmark)

    Sasso, Luigi; Vazquez, Patricia; Vedarethinam, Indumathi

    2010-01-01

    Conducting polymer 3D microelectrodes have been fabricated for possible future neurological applications. A combination of micro-fabrication techniques and chemical polymerization methods has been used to create pillar electrodes in polyaniline and polypyrrole. The thin polymer films obtained...

  6. Accepting the T3D

    Energy Technology Data Exchange (ETDEWEB)

    Rich, D.O.; Pope, S.C.; DeLapp, J.G.

    1994-10-01

    In April, a 128 PE Cray T3D was installed at Los Alamos National Laboratory`s Advanced Computing Laboratory as part of the DOE`s High-Performance Parallel Processor Program (H4P). In conjunction with CRI, the authors implemented a 30 day acceptance test. The test was constructed in part to help them understand the strengths and weaknesses of the T3D. In this paper, they briefly describe the H4P and its goals. They discuss the design and implementation of the T3D acceptance test and detail issues that arose during the test. They conclude with a set of system requirements that must be addressed as the T3D system evolves.

  7. 3-D Vector Flow Imaging

    DEFF Research Database (Denmark)

    Holbek, Simon

    For the last decade, the field of ultrasonic vector flow imaging has gotten an increasingly attention, as the technique offers a variety of new applications for screening and diagnostics of cardiovascular pathologies. The main purpose of this PhD project was therefore to advance the field of 3-D...... ultrasonic vector flow estimation and bring it a step closer to a clinical application. A method for high frame rate 3-D vector flow estimation in a plane using the transverse oscillation method combined with a 1024 channel 2-D matrix array is presented. The proposed method is validated both through phantom......, if this significant reduction in the element count can still provide precise and robust 3-D vector flow estimates in a plane. The study concludes that the RC array is capable of estimating precise 3-D vector flow both in a plane and in a volume, despite the low channel count. However, some inherent new challenges...

  8. 3D Face Apperance Model

    DEFF Research Database (Denmark)

    Lading, Brian; Larsen, Rasmus; Astrom, K

    2006-01-01

    We build a 3D face shape model, including inter- and intra-shape variations, derive the analytical Jacobian of its resulting 2D rendered image, and show example of its fitting performance with light, pose, id, expression and texture variations......We build a 3D face shape model, including inter- and intra-shape variations, derive the analytical Jacobian of its resulting 2D rendered image, and show example of its fitting performance with light, pose, id, expression and texture variations...

  9. 3D Face Appearance Model

    DEFF Research Database (Denmark)

    Lading, Brian; Larsen, Rasmus; Åström, Kalle

    2006-01-01

    We build a 3d face shape model, including inter- and intra-shape variations, derive the analytical jacobian of its resulting 2d rendered image, and show example of its fitting performance with light, pose, id, expression and texture variations.}......We build a 3d face shape model, including inter- and intra-shape variations, derive the analytical jacobian of its resulting 2d rendered image, and show example of its fitting performance with light, pose, id, expression and texture variations.}...

  10. Main: TATCCAYMOTIFOSRAMY3D [PLACE

    Lifescience Database Archive (English)

    Full Text Available TATCCAYMOTIFOSRAMY3D S000256 01-August-2006 (last modified) kehi TATCCAY motif foun...d in rice (O.s.) RAmy3D alpha-amylase gene promoter; Y=T/C; a GATA motif as its antisense sequence; TATCCAY ...motif and G motif (see S000130) are responsible for sugar repression (Toyofuku et al. 1998); GATA; amylase; sugar; repression; rice (Oryza sativa) TATCCAY ...

  11. Crystal structure of yeast DNA polymerase ε catalytic domain.

    Directory of Open Access Journals (Sweden)

    Rinku Jain

    Full Text Available DNA polymerase ε (Polε is a multi-subunit polymerase that contributes to genomic stability via its roles in leading strand replication and the repair of damaged DNA. Here we report the ternary structure of the Polε catalytic subunit (Pol2 bound to a nascent G:C base pair (Pol2G:C. Pol2G:C has a typical B-family polymerase fold and embraces the template-primer duplex with the palm, fingers, thumb and exonuclease domains. The overall arrangement of domains is similar to the structure of Pol2T:A reported recently, but there are notable differences in their polymerase and exonuclease active sites. In particular, we observe Ca2+ ions at both positions A and B in the polymerase active site and also observe a Ca2+ at position B of the exonuclease site. We find that the contacts to the nascent G:C base pair in the Pol2G:C structure are maintained in the Pol2T:A structure and reflect the comparable fidelity of Pol2 for nascent purine-pyrimidine and pyrimidine-purine base pairs. We note that unlike that of Pol3, the shape of the nascent base pair binding pocket in Pol2 is modulated from the major grove side by the presence of Tyr431. Together with Pol2T:A, our results provide a framework for understanding the structural basis of high fidelity DNA synthesis by Pol2.

  12. MPML3D: Scripting Agents for the 3D Internet.

    Science.gov (United States)

    Prendinger, Helmut; Ullrich, Sebastian; Nakasone, Arturo; Ishizuka, Mitsuru

    2011-05-01

    The aim of this paper is two-fold. First, it describes a scripting language for specifying communicative behavior and interaction of computer-controlled agents ("bots") in the popular three-dimensional (3D) multiuser online world of "Second Life" and the emerging "OpenSimulator" project. While tools for designing avatars and in-world objects in Second Life exist, technology for nonprogrammer content creators of scenarios involving scripted agents is currently missing. Therefore, we have implemented new client software that controls bots based on the Multimodal Presentation Markup Language 3D (MPML3D), a highly expressive XML-based scripting language for controlling the verbal and nonverbal behavior of interacting animated agents. Second, the paper compares Second Life and OpenSimulator platforms and discusses the merits and limitations of each from the perspective of agent control. Here, we also conducted a small study that compares the network performance of both platforms.

  13. 3D-mallinnus ja 3D-animaatiot biovoimalaitoksesta

    OpenAIRE

    Hiltula, Tytti

    2014-01-01

    Opinnäytetyössä tehtiin biovoimalaitoksen piirustuksista 3D-mallinnus ja animaatiot. Työn tarkoituksena oli saada valmiiksi Recwell Oy:lle markkinointiin tarkoitetut kuva- ja videomateriaalit. Työssä perehdyttiin 3D-mallintamisen perustietoihin ja lähtökohtiin sekä animaation laatimiseen. Työ laadittiin kokonaisuudessaan AutoCAD-ohjelmalla, ja työn aikana tutustuttiin huolellisesti myös ohjelman käyttöohjeisiin. Piirustusten mitoituksessa huomattiin jo alkuvaiheessa suuria puutteita, ...

  14. From 3D view to 3D print

    Science.gov (United States)

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

    2014-08-01

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

  15. Protein purification in multicompartment electrolyzers for crystal growth of r-DNA products in microgravity

    Science.gov (United States)

    Righetti, Pier Giorgio; Casale, Elena; Carter, Daniel; Snyder, Robert S.; Wenisch, Elisabeth; Faupel, Michel

    1990-01-01

    Recombinant-DNA (deoxyribonucleic acid) (r-DNA) proteins, produced in large quantities for human consumption, are now available in sufficient amounts for crystal growth. Crystallographic analysis is the only method now available for defining the atomic arrangements within complex biological molecules and decoding, e.g., the structure of the active site. Growing protein crystals in microgravity has become an important aspect of biology in space, since crystals that are large enough and of sufficient quality to permit complete structure determinations are usually obtained. However even small amounts of impurities in a protein preparation are anathema for the growth of a regular crystal lattice. A multicompartment electrolyzer with isoelectric, immobiline membranes, able to purify large quantities of r-DNA proteins is described. The electrolyzer consists of a stack of flow cells, delimited by membranes of very precise isoelectric point (pI, consisting of polyacrylamide supported by glass fiber filters containing Immobiline buffers and titrants to uniquely define a pI value) and very high buffering power, able to titrate all proteins tangent or crossing such membranes. By properly selecting the pI values of two membranes delimiting a flow chamber, a single protein can be kept isoelectric in a single flow chamber and thus, be purified to homogeneity (by the most stringent criterion, charge homogeneity).

  16. Crystallization of a self-assembled three-dimensional DNA nanostructure.

    Science.gov (United States)

    Rendek, Kimberly N; Fromme, Raimund; Grotjohann, Ingo; Fromme, Petra

    2013-02-01

    The powerful and specific molecular-recognition system present in the base-pairing of DNA allows for the design of a plethora of nanostructures. In this work, the crystallization of a self-assembling three-dimensional B-DNA nanostructure is described. The DNA nanostructure consists of six single-stranded oligonucleotides that hybridize to form a three-dimensional tetrahedron of 80 kDa in molecular mass and 20 bp on each edge. Crystals of the tetrahedron have been successfully produced and characterized. These crystals may form the basis for an X-ray structure of the tetrahedron in the future. Nucleotide crystallography poses many challenges, leading to the fact that only 1352 X-ray structures of nucleic acids have been solved compared with more than 80,000 protein structures. In this work, the crystallization optimization for three-dimensional tetrahedra is also described, with the eventual goal of producing nanocrystals to overcome the radiation-damage obstacle by the use of free-electron laser technology in the future.

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

    Science.gov (United States)

    Schild, Jonas; Seele, Sven; Masuch, Maic

    2012-03-01

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

  18. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA

    Directory of Open Access Journals (Sweden)

    Yijin Liu

    2015-12-01

    Full Text Available We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction.

  19. Materialedreven 3d digital formgivning

    DEFF Research Database (Denmark)

    Hansen, Flemming Tvede

    2010-01-01

    Formålet med forskningsprojektet er for det første at understøtte keramikeren i at arbejde eksperimenterende med digital formgivning, og for det andet at bidrage til en tværfaglig diskurs om brugen af digital formgivning. Forskningsprojektet fokuserer på 3d formgivning og derved på 3d digital...... formgivning og Rapid Prototyping (RP). RP er en fællesbetegnelse for en række af de teknikker, der muliggør at overføre den digitale form til 3d fysisk form. Forskningsprojektet koncentrerer sig om to overordnede forskningsspørgsmål. Det første handler om, hvordan viden og erfaring indenfor det keramiske...... fagområde kan blive udnyttet i forhold til 3d digital formgivning. Det andet handler om, hvad en sådan tilgang kan bidrage med, og hvordan den kan blive udnyttet i et dynamisk samspil med det keramiske materiale i formgivningen af 3d keramiske artefakter. Materialedreven formgivning er karakteriseret af en...

  20. Novel 3D media technologies

    CERN Document Server

    Dagiuklas, Tasos

    2015-01-01

    This book describes recent innovations in 3D media and technologies, with coverage of 3D media capturing, processing, encoding, and adaptation, networking aspects for 3D Media, and quality of user experience (QoE). The contributions are based on the results of the FP7 European Project ROMEO, which focuses on new methods for the compression and delivery of 3D multi-view video and spatial audio, as well as the optimization of networking and compression jointly across the future Internet. The delivery of 3D media to individual users remains a highly challenging problem due to the large amount of data involved, diverse network characteristics and user terminal requirements, as well as the user’s context such as their preferences and location. As the number of visual views increases, current systems will struggle to meet the demanding requirements in terms of delivery of consistent video quality to fixed and mobile users. ROMEO will present hybrid networking solutions that combine the DVB-T2 and DVB-NGH broadcas...

  1. 3D future internet media

    CERN Document Server

    Dagiuklas, Tasos

    2014-01-01

    This book describes recent innovations in 3D media and technologies, with coverage of 3D media capturing, processing, encoding, and adaptation, networking aspects for 3D Media, and quality of user experience (QoE). The main contributions are based on the results of the FP7 European Projects ROMEO, which focus on new methods for the compression and delivery of 3D multi-view video and spatial audio, as well as the optimization of networking and compression jointly across the Future Internet (www.ict-romeo.eu). The delivery of 3D media to individual users remains a highly challenging problem due to the large amount of data involved, diverse network characteristics and user terminal requirements, as well as the user’s context such as their preferences and location. As the number of visual views increases, current systems will struggle to meet the demanding requirements in terms of delivery of constant video quality to both fixed and mobile users. ROMEO will design and develop hybrid-networking solutions that co...

  2. Speaking Volumes About 3-D

    Science.gov (United States)

    2002-01-01

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

  3. Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

    Science.gov (United States)

    Egli, M.; Usman, N.; Rich, A.

    1993-01-01

    We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

  4. Modification of 3D milling machine to 3D printer

    OpenAIRE

    Halamíček, Lukáš

    2015-01-01

    Tato práce se zabývá přestavbou gravírovací frézky na 3D tiskárnu. V první části se práce zabývá možnými technologiemi 3D tisku a možností jejich využití u přestavby. Dále jsou popsány a vybrány vhodné součásti pro přestavbu. V další části je realizováno řízení ohřevu podložky, trysky a řízení posuvu drátu pomocí softwaru TwinCat od společnosti Beckhoff na průmyslovém počítači. Výsledkem práce by měla být oživená 3D tiskárna. This thesis deals with rebuilding of engraving machine to 3D pri...

  5. Aspects of defects in 3d-3d correspondence

    Energy Technology Data Exchange (ETDEWEB)

    Gang, Dongmin [Kavli Institute for the Physics and Mathematics of the Universe (WPI), University of Tokyo,Chiba 277-8583 (Japan); Kim, Nakwoo [Department of Physics and Research Institute of Basic Science, Kyung Hee University,Seoul 02447 (Korea, Republic of); School of Physics, Korea Institute for Advanced Study,Seoul 02455 (Korea, Republic of); Romo, Mauricio; Yamazaki, Masahito [Kavli Institute for the Physics and Mathematics of the Universe (WPI), University of Tokyo,Chiba 277-8583 (Japan); School of Natural Sciences, Institute for Advanced Study,Princeton, NJ 08540 (United States)

    2016-10-12

    In this paper we study supersymmetric co-dimension 2 and 4 defects in the compactification of the 6d (2,0) theory of type A{sub N−1} on a 3-manifold M. The so-called 3d-3d correspondence is a relation between complexified Chern-Simons theory (with gauge group SL(N,ℂ)) on M and a 3d N=2 theory T{sub N}[M]. We study this correspondence in the presence of supersymmetric defects, which are knots/links inside the 3-manifold. Our study employs a number of different methods: state-integral models for complex Chern-Simons theory, cluster algebra techniques, domain wall theory T[SU(N)], 5d N=2 SYM, and also supergravity analysis through holography. These methods are complementary and we find agreement between them. In some cases the results lead to highly non-trivial predictions on the partition function. Our discussion includes a general expression for the cluster partition function, which can be used to compute in the presence of maximal and certain class of non-maximal punctures when N>2. We also highlight the non-Abelian description of the 3d N=2T{sub N}[M] theory with defect included, when such a description is available. This paper is a companion to our shorter paper http://dx.doi.org/10.1088/1751-8113/49/30/30LT02, which summarizes our main results.

  6. Aspects of defects in 3d-3d correspondence

    Science.gov (United States)

    Gang, Dongmin; Kim, Nakwoo; Romo, Mauricio; Yamazaki, Masahito

    2016-10-01

    In this paper we study supersymmetric co-dimension 2 and 4 defects in the compactification of the 6d (2, 0) theory of type A N -1 on a 3-manifold M . The so-called 3d-3d correspondence is a relation between complexified Chern-Simons theory (with gauge group SL(N,C) ) on M and a 3d N=2 theory T N [ M ]. We study this correspondence in the presence of supersymmetric defects, which are knots/links inside the 3-manifold. Our study employs a number of different methods: state-integral models for complex Chern-Simons theory, cluster algebra techniques, domain wall theory T [SU( N )], 5d N=2 SYM, and also supergravity analysis through holography. These methods are complementary and we find agreement between them. In some cases the results lead to highly non-trivial predictions on the partition function. Our discussion includes a general expression for the cluster partition function, which can be used to compute in the presence of maximal and certain class of non-maximal punctures when N > 2. We also highlight the non-Abelian description of the 3d N=2 T N [ M ] theory with defect included, when such a description is available. This paper is a companion to our shorter paper [1], which summarizes our main results.

  7. Holography of 3d-3d correspondence at large N

    Energy Technology Data Exchange (ETDEWEB)

    Gang, Dongmin [School of Physics, Korea Institute for Advanced Study,85 Hoegiro, Dongdaemun-gu, Seoul, 130-722 (Korea, Republic of); Kim, Nakwoo [Department of Physics and Research Institute of Basic Science, Kyung Hee University,26 Kyungheedaero, Dongdaemun-gu, Seoul, 130-701 (Korea, Republic of); Lee, Sangmin [School of Physics, Korea Institute for Advanced Study,85 Hoegiro, Dongdaemun-gu, Seoul, 130-722 (Korea, Republic of); Center for Theoretical Physics, Department of Physics and Astronomy, College of Liberal Studies,Seoul National University, 1 Gwanakro, Gwanak-gu, Seoul, 151-742 (Korea, Republic of)

    2015-04-20

    We study the physics of multiple M5-branes compactified on a hyperbolic 3-manifold. On the one hand, it leads to the 3d-3d correspondence which maps an N=2 superconformal field theory to a pure Chern-Simons theory on the 3-manifold. On the other hand, it leads to a warped AdS{sub 4} geometry in M-theory holographically dual to the superconformal field theory. Combining the holographic duality and the 3d-3d correspondence, we propose a conjecture for the large N limit of the perturbative free energy of a Chern-Simons theory on hyperbolic 3-manifold. The conjecture claims that the tree, one-loop and two-loop terms all share the same N{sup 3} scaling behavior and are proportional to the volume of the 3-manifold, while the three-loop and higher terms are suppressed at large N. Under mild assumptions, we prove the tree and one-loop parts of the conjecture. For the two-loop part, we test the conjecture numerically in a number of examples and find precise agreement. We also confirm the suppression of higher loop terms in a few examples.

  8. 3D vector flow imaging

    DEFF Research Database (Denmark)

    Pihl, Michael Johannes

    The main purpose of this PhD project is to develop an ultrasonic method for 3D vector flow imaging. The motivation is to advance the field of velocity estimation in ultrasound, which plays an important role in the clinic. The velocity of blood has components in all three spatial dimensions, yet...... conventional methods can estimate only the axial component. Several approaches for 3D vector velocity estimation have been suggested, but none of these methods have so far produced convincing in vivo results nor have they been adopted by commercial manufacturers. The basis for this project is the Transverse...... on the TO fields are suggested. They can be used to optimize the TO method. In the third part, a TO method for 3D vector velocity estimation is proposed. It employs a 2D phased array transducer and decouples the velocity estimation into three velocity components, which are estimated simultaneously based on 5...

  9. Markerless 3D Face Tracking

    DEFF Research Database (Denmark)

    Walder, Christian; Breidt, Martin; Bulthoff, Heinrich

    2009-01-01

    We present a novel algorithm for the markerless tracking of deforming surfaces such as faces. We acquire a sequence of 3D scans along with color images at 40Hz. The data is then represented by implicit surface and color functions, using a novel partition-of-unity type method of efficiently...... combining local regressors using nearest neighbor searches. Both these functions act on the 4D space of 3D plus time, and use temporal information to handle the noise in individual scans. After interactive registration of a template mesh to the first frame, it is then automatically deformed to track...... the scanned surface, using the variation of both shape and color as features in a dynamic energy minimization problem. Our prototype system yields high-quality animated 3D models in correspondence, at a rate of approximately twenty seconds per timestep. Tracking results for faces and other objects...

  10. 3-D Vector Flow Imaging

    DEFF Research Database (Denmark)

    Holbek, Simon

    studies and in vivo. Phantom measurements are compared with their corresponding reference value, whereas the in vivo measurement is validated against the current golden standard for non-invasive blood velocity estimates, based on magnetic resonance imaging (MRI). The study concludes, that a high precision......, if this significant reduction in the element count can still provide precise and robust 3-D vector flow estimates in a plane. The study concludes that the RC array is capable of estimating precise 3-D vector flow both in a plane and in a volume, despite the low channel count. However, some inherent new challenges......For the last decade, the field of ultrasonic vector flow imaging has gotten an increasingly attention, as the technique offers a variety of new applications for screening and diagnostics of cardiovascular pathologies. The main purpose of this PhD project was therefore to advance the field of 3-D...

  11. Microfluidic 3D Helix Mixers

    Directory of Open Access Journals (Sweden)

    Georgette B. Salieb-Beugelaar

    2016-10-01

    Full Text Available Polymeric microfluidic systems are well suited for miniaturized devices with complex functionality, and rapid prototyping methods for 3D microfluidic structures are increasingly used. Mixing at the microscale and performing chemical reactions at the microscale are important applications of such systems and we therefore explored feasibility, mixing characteristics and the ability to control a chemical reaction in helical 3D channels produced by the emerging thread template method. Mixing at the microscale is challenging because channel size reduction for improving solute diffusion comes at the price of a reduced Reynolds number that induces a strictly laminar flow regime and abolishes turbulence that would be desired for improved mixing. Microfluidic 3D helix mixers were rapidly prototyped in polydimethylsiloxane (PDMS using low-surface energy polymeric threads, twisted to form 2-channel and 3-channel helices. Structure and flow characteristics were assessed experimentally by microscopy, hydraulic measurements and chromogenic reaction, and were modeled by computational fluid dynamics. We found that helical 3D microfluidic systems produced by thread templating allow rapid prototyping, can be used for mixing and for controlled chemical reaction with two or three reaction partners at the microscale. Compared to the conventional T-shaped microfluidic system used as a control device, enhanced mixing and faster chemical reaction was found to occur due to the combination of diffusive mixing in small channels and flow folding due to the 3D helix shape. Thus, microfluidic 3D helix mixers can be rapidly prototyped using the thread template method and are an attractive and competitive method for fluid mixing and chemical reactions at the microscale.

  12. Ideal 3D asymmetric concentrator

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Botella, Angel [Departamento Fisica Aplicada a los Recursos Naturales, Universidad Politecnica de Madrid, E.T.S.I. de Montes, Ciudad Universitaria s/n, 28040 Madrid (Spain); Fernandez-Balbuena, Antonio Alvarez; Vazquez, Daniel; Bernabeu, Eusebio [Departamento de Optica, Universidad Complutense de Madrid, Fac. CC. Fisicas, Ciudad Universitaria s/n, 28040 Madrid (Spain)

    2009-01-15

    Nonimaging optics is a field devoted to the design of optical components for applications such as solar concentration or illumination. In this field, many different techniques have been used for producing reflective and refractive optical devices, including reverse engineering techniques. In this paper we apply photometric field theory and elliptic ray bundles method to study 3D asymmetric - without rotational or translational symmetry - concentrators, which can be useful components for nontracking solar applications. We study the one-sheet hyperbolic concentrator and we demonstrate its behaviour as ideal 3D asymmetric concentrator. (author)

  13. 3D digitization of mosaics

    Directory of Open Access Journals (Sweden)

    Anna Maria Manferdini

    2012-11-01

    Full Text Available In this paper we present a methodology developed to access to Cultural Heritage information using digital 3d reality-based models as graphic interfaces. The case studies presented belong to the wide repertoire of mosaics of Ravenna. One of the most peculiar characteristics of mosaics that often limits their digital survey is their multi-scale complexity; nevertheless their models could be used in 3d information systems, for digital exhibitions, for reconstruction aims and to document their conservation conditions in order to conduct restoration interventions in digital environments aiming at speeding and performing more reliable evaluations.

  14. Detection of anthrax lef with DNA-based photonic crystal sensors

    Science.gov (United States)

    Zhang, Bailin; Dallo, Shatha; Peterson, Ralph; Hussain, Syed; Weitao, Tao; Ye, Jing Yong

    2011-12-01

    Bacillus anthracis has posed a threat of becoming biological weapons of mass destruction due to its virulence factors encoded by the plasmid-borne genes, such as lef for lethal factor. We report the development of a fast and sensitive anthrax DNA biosensor based on a photonic crystal structure used in a total-internal-reflection configuration. For the detection of the lef gene, a single-stranded DNA lef probe was biotinylated and immobilized onto the sensor via biotin-streptavidin interactions. A positive control, lef-com, was the complementary strand of the probe, while a negative control was an unrelated single-stranded DNA fragment from the 16S rRNA gene of Acinetobacter baumannii. After addition of the biotinylated lef probe onto the sensor, significant changes in the resonance wavelength of the sensor were observed, resulting from binding of the probe to streptavidin on the sensor. The addition of lef-com led to another significant increase as a result of hybridization between the two DNA strands. The detection sensitivity for the target DNA reached as low as 0.1 nM. In contrast, adding the unrelated DNAs did not cause an obvious shift in the resonant wavelength. These results demonstrate that detection of the anthrax lef by the photonic crystal structure in a total-internal-reflection sensor is highly specific and sensitive.

  15. Detection of anthrax lef with DNA-based photonic crystal sensors.

    Science.gov (United States)

    Zhang, Bailin; Dallo, Shatha; Peterson, Ralph; Hussain, Syed; Weitao, Tao; Ye, Jing Yong

    2011-12-01

    Bacillus anthracis has posed a threat of becoming biological weapons of mass destruction due to its virulence factors encoded by the plasmid-borne genes, such as lef for lethal factor. We report the development of a fast and sensitive anthrax DNA biosensor based on a photonic crystal structure used in a total-internal-reflection configuration. For the detection of the lef gene, a single-stranded DNA lef probe was biotinylated and immobilized onto the sensor via biotin-streptavidin interactions. A positive control, lef-com, was the complementary strand of the probe, while a negative control was an unrelated single-stranded DNA fragment from the 16S rRNA gene of Acinetobacter baumannii. After addition of the biotinylated lef probe onto the sensor, significant changes in the resonance wavelength of the sensor were observed, resulting from binding of the probe to streptavidin on the sensor. The addition of lef-com led to another significant increase as a result of hybridization between the two DNA strands. The detection sensitivity for the target DNA reached as low as 0.1 nM. In contrast, adding the unrelated DNAs did not cause an obvious shift in the resonant wavelength. These results demonstrate that detection of the anthrax lef by the photonic crystal structure in a total-internal-reflection sensor is highly specific and sensitive.

  16. PubChem3D: Biologically relevant 3-D similarity

    Directory of Open Access Journals (Sweden)

    Kim Sunghwan

    2011-07-01

    Full Text Available Abstract Background The use of 3-D similarity techniques in the analysis of biological data and virtual screening is pervasive, but what is a biologically meaningful 3-D similarity value? Can one find statistically significant separation between "active/active" and "active/inactive" spaces? These questions are explored using 734,486 biologically tested chemical structures, 1,389 biological assay data sets, and six different 3-D similarity types utilized by PubChem analysis tools. Results The similarity value distributions of 269.7 billion unique conformer pairs from 734,486 biologically tested compounds (all-against-all from PubChem were utilized to help work towards an answer to the question: what is a biologically meaningful 3-D similarity score? The average and standard deviation for the six similarity measures STST-opt, CTST-opt, ComboTST-opt, STCT-opt, CTCT-opt, and ComboTCT-opt were 0.54 ± 0.10, 0.07 ± 0.05, 0.62 ± 0.13, 0.41 ± 0.11, 0.18 ± 0.06, and 0.59 ± 0.14, respectively. Considering that this random distribution of biologically tested compounds was constructed using a single theoretical conformer per compound (the "default" conformer provided by PubChem, further study may be necessary using multiple diverse conformers per compound; however, given the breadth of the compound set, the single conformer per compound results may still apply to the case of multi-conformer per compound 3-D similarity value distributions. As such, this work is a critical step, covering a very wide corpus of chemical structures and biological assays, creating a statistical framework to build upon. The second part of this study explored the question of whether it was possible to realize a statistically meaningful 3-D similarity value separation between reputed biological assay "inactives" and "actives". Using the terminology of noninactive-noninactive (NN pairs and the noninactive-inactive (NI pairs to represent comparison of the "active/active" and

  17. Crystal structure of the homology domain of the eukaryotic DNA replication proteins Sld3/Treslin.

    Science.gov (United States)

    Itou, Hiroshi; Muramatsu, Sachiko; Shirakihara, Yasuo; Araki, Hiroyuki

    2014-09-02

    The initiation of eukaryotic chromosomal DNA replication requires the formation of an active replicative helicase at the replication origins of chromosomal DNA. Yeast Sld3 and its metazoan counterpart Treslin are the hub proteins mediating protein associations critical for the helicase formation. Here, we show the crystal structure of the central domain of Sld3 that is conserved in Sld3/Treslin family of proteins. The domain consists of two segments with 12 helices and is sufficient to bind to Cdc45, the essential helicase component. The structure model of the Sld3-Cdc45 complex, which is crucial for the formation of the active helicase, is proposed.

  18. 3D visualization of polymer nanostructure

    Energy Technology Data Exchange (ETDEWEB)

    Werner, James H [Los Alamos National Laboratory

    2009-01-01

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

  19. Viewing galaxies in 3D

    CERN Document Server

    Krajnović, Davor

    2016-01-01

    Thanks to a technique that reveals galaxies in 3D, astronomers can now show that many galaxies have been wrongly classified. Davor Krajnovi\\'c argues that the classification scheme proposed 85 years ago by Edwin Hubble now needs to be revised.

  20. 3D Printing: Exploring Capabilities

    Science.gov (United States)

    Samuels, Kyle; Flowers, Jim

    2015-01-01

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

  1. When Art Meets 3D

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The presentation of the vanguard work,My Dream3D,the innovative production by the China Disabled People’s Performing Art Troupe(CDPPAT),directed by Joy Joosang Park,provided the film’s domestic premiere at Beijing’s Olympic Park onApril7.The show provided an intriguing insight not

  2. 3D Printing of Metals

    Directory of Open Access Journals (Sweden)

    Manoj Gupta

    2017-09-01

    Full Text Available The potential benefits that could be derived if the science and technology of 3D printing were to be established have been the crux behind monumental efforts by governments, in most countries, that invest billions of dollars to develop this manufacturing technology.[...

  3. Making Inexpensive 3-D Models

    Science.gov (United States)

    Manos, Harry

    2016-01-01

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

  4. 3D Printing: Exploring Capabilities

    Science.gov (United States)

    Samuels, Kyle; Flowers, Jim

    2015-01-01

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

  5. Nuclear 3D organization and radiosensitivity

    Science.gov (United States)

    Eidelman, Y. A.; Slanina, S. V.; Aleshchenko, A. V.; Sen'ko, O. V.; Kononkova, A. D.; Andreev, S. G.

    2017-01-01

    Current mechanisms of radiation-induced chromosomal aberration (CA) formation suggest misrepair of chromosomal lesions being in spatial proximity. In this case CAs have to depend on pattern of chromosomal contacts and on chromosome spatial organization in a cell nucleus. We were interested in whether variation of nucleus 3D organization results in difference of radiation induced CA formation frequency. Experimental data available do not provide information sufficient for definite conclusions. To have more deep insight in this issue we developed the biophysical modeling technique taking into account different levels of chromosome/nuclear organization and radiation damage of DNA and chromosomes. Computer experiments on gamma irradiation were carried out for two types of cells with different 3D organization of nuclei, preferentially peripheral and internal. CA frequencies were found to depend on spatial positioning of chromosomes within a nucleus which determines a pattern of interchromosomal contacts. For individual chromosomes this effect can be more pronounced than for genome averaged. Since significant part of aberrations, for example dicentrics, results in cell death, the proposed technique is capable of evaluating radiosensitivity of cells, both normal and cancer, with the incorporation of 3D genome information. This predictive technology allows to reduce uncertainties of prognosis of biological effects of radiation compared to phenomenological methods and may have variety of biomedical applications, in particular, in cancer radiation therapy.

  6. Priprava 3D modelov za 3D tisk

    OpenAIRE

    2015-01-01

    Po mnenju nekaterih strokovnjakov bo aditivna proizvodnja (ali 3D tiskanje) spremenila proizvodnjo industrijo, saj si bo vsak posameznik lahko natisnil svoj objekt po želji. V diplomski nalogi so predstavljene nekatere tehnologije aditivne proizvodnje. V nadaljevanju diplomske naloge je predstavljena izdelava makete hiše v merilu 1:100, vse od modeliranja do tiskanja. Poseben poudarek je posvečen predelavi modela, da je primeren za tiskanje, kjer je razvit pristop za hitrejše i...

  7. Post processing of 3D models for 3D printing

    OpenAIRE

    2015-01-01

    According to the opinion of some experts the additive manufacturing or 3D printing will change manufacturing industry, because any individual could print their own model according to his or her wishes. In this graduation thesis some of the additive manufacturing technologies are presented. Furthermore in the production of house scale model in 1:100 is presented, starting from modeling to printing. Special attention is given to postprocessing of the building model elements us...

  8. 3D Printable Graphene Composite.

    Science.gov (United States)

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

    2015-07-08

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

  9. Forensic 3D Scene Reconstruction

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-10-12

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

  10. 3D Printed Robotic Hand

    Science.gov (United States)

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

    2013-01-01

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

  11. Crystal structure of the shrimp proliferating cell nuclear antigen: structural complementarity with WSSV DNA polymerase PIP-box.

    Directory of Open Access Journals (Sweden)

    Jesus S Carrasco-Miranda

    Full Text Available DNA replication requires processivity factors that allow replicative DNA polymerases to extend long stretches of DNA. Some DNA viruses encode their own replicative DNA polymerase, such as the white spot syndrome virus (WSSV that infects decapod crustaceans but still require host replication accessory factors. We have determined by X-ray diffraction the three-dimensional structure of the Pacific white leg shrimp Litopenaeus vannamei Proliferating Cell Nuclear Antigen (LvPCNA. This protein is a member of the sliding clamp family of proteins, that binds DNA replication and DNA repair proteins through a motif called PIP-box (PCNA-Interacting Protein. The crystal structure of LvPCNA was refined to a resolution of 3 Å, and allowed us to determine the trimeric protein assembly and details of the interactions between PCNA and the DNA. To address the possible interaction between LvPCNA and the viral DNA polymerase, we docked a theoretical model of a PIP-box peptide from the WSSV DNA polymerase within LvPCNA crystal structure. The theoretical model depicts a feasible model of interaction between both proteins. The crystal structure of shrimp PCNA allows us to further understand the mechanisms of DNA replication processivity factors in non-model systems.

  12. Medical 3D thermography system

    OpenAIRE

    GRUBIŠIĆ, IVAN

    2011-01-01

    Infrared (IR) thermography determines the surface temperature of an object or human body using thermal IR measurement camera. It is an imaging technology which is contactless and completely non-invasive. These propertiesmake IR thermography a useful method of analysis that is used in various industrial applications to detect, monitor and predict irregularities in many fields from engineering to medical and biological observations. This paper presents a conceptual model of Medical 3D Thermo...

  13. Synthesis, crystal structure and thermal properties of Ca6(C12H14O4)4(CO3)(OH)2(H2O)x – a 3D inorganic hybrid material

    DEFF Research Database (Denmark)

    Nielsen, Renie Birkedal; Norby, Poul; Kongshaug, Kjell Ove

    2012-01-01

    of Ca6(C12H14O4)4(CO3)(OH)2(H2O)14 is tetragonal, space group I41/amd (141) with a = 29.12 Å, c = 15.85 Å, V = 13 440 Å3 and Z = 8. The compound is classified as a 3D inorganic hybrid material with a 3-dimensional inorganic framework consisting of Ca and O, connected to 1,3-adamantanedicarboxylate...

  14. Nitrilotriacetate Bridged 3d-4f Heteronuclear Complex: Synthesis and Crystal Structure of {[GdCu(NTA)(H2O)6Cl]ClO4·H2O}n

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The heteronuclear gadolinium-copper complex was synthesized. Its crystal structure was determined by single-crystal diffraction. The crystal crystallizes in triclinic, space group P-1, a=0.8483(1) nm, b=0.9642(2) nm, c=1.2838(2) nm, α=111.17(1)°, β= 93.52(1)°, γ=100.89(1)°, Z=2, Dc=2.335 g·cm-3. The complex appears as a zigzag 1D chain. Each gadolinium ion is coordinated by three carboxylic oxygen atoms and six oxygen atoms from H2O. Each copper ion is chelated by NTA with its nitrogen atom and three oxygen atoms of three carboxyl groups, and coordinated by a chlorine ion. The ClO4- is located between the chains as a counter ion.

  15. 3D silicon strip detectors

    Energy Technology Data Exchange (ETDEWEB)

    Parzefall, Ulrich [Physikalisches Institut, Universitaet Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg (Germany)], E-mail: ulrich.parzefall@physik.uni-freiburg.de; Bates, Richard [University of Glasgow, Department of Physics and Astronomy, Glasgow G12 8QQ (United Kingdom); Boscardin, Maurizio [FBK-irst, Center for Materials and Microsystems, via Sommarive 18, 38050 Povo di Trento (Italy); Dalla Betta, Gian-Franco [INFN and Universita' di Trento, via Sommarive 14, 38050 Povo di Trento (Italy); Eckert, Simon [Physikalisches Institut, Universitaet Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg (Germany); Eklund, Lars; Fleta, Celeste [University of Glasgow, Department of Physics and Astronomy, Glasgow G12 8QQ (United Kingdom); Jakobs, Karl; Kuehn, Susanne [Physikalisches Institut, Universitaet Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg (Germany); Lozano, Manuel [Instituto de Microelectronica de Barcelona, IMB-CNM, CSIC, Barcelona (Spain); Pahn, Gregor [Physikalisches Institut, Universitaet Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg (Germany); Parkes, Chris [University of Glasgow, Department of Physics and Astronomy, Glasgow G12 8QQ (United Kingdom); Pellegrini, Giulio [Instituto de Microelectronica de Barcelona, IMB-CNM, CSIC, Barcelona (Spain); Pennicard, David [University of Glasgow, Department of Physics and Astronomy, Glasgow G12 8QQ (United Kingdom); Piemonte, Claudio; Ronchin, Sabina [FBK-irst, Center for Materials and Microsystems, via Sommarive 18, 38050 Povo di Trento (Italy); Szumlak, Tomasz [University of Glasgow, Department of Physics and Astronomy, Glasgow G12 8QQ (United Kingdom); Zoboli, Andrea [INFN and Universita' di Trento, via Sommarive 14, 38050 Povo di Trento (Italy); Zorzi, Nicola [FBK-irst, Center for Materials and Microsystems, via Sommarive 18, 38050 Povo di Trento (Italy)

    2009-06-01

    While the Large Hadron Collider (LHC) at CERN has started operation in autumn 2008, plans for a luminosity upgrade to the Super-LHC (sLHC) have already been developed for several years. This projected luminosity increase by an order of magnitude gives rise to a challenging radiation environment for tracking detectors at the LHC experiments. Significant improvements in radiation hardness are required with respect to the LHC. Using a strawman layout for the new tracker of the ATLAS experiment as an example, silicon strip detectors (SSDs) with short strips of 2-3 cm length are foreseen to cover the region from 28 to 60 cm distance to the beam. These SSD will be exposed to radiation levels up to 10{sup 15}N{sub eq}/cm{sup 2}, which makes radiation resistance a major concern for the upgraded ATLAS tracker. Several approaches to increasing the radiation hardness of silicon detectors exist. In this article, it is proposed to combine the radiation hard 3D-design originally conceived for pixel-style applications with the benefits of the established planar technology for strip detectors by using SSDs that have regularly spaced doped columns extending into the silicon bulk under the detector strips. The first 3D SSDs to become available for testing were made in the Single Type Column (STC) design, a technological simplification of the original 3D design. With such 3D SSDs, a small number of prototype sLHC detector modules with LHC-speed front-end electronics as used in the semiconductor tracking systems of present LHC experiments were built. Modules were tested before and after irradiation to fluences of 10{sup 15}N{sub eq}/cm{sup 2}. The tests were performed with three systems: a highly focused IR-laser with 5{mu}m spot size to make position-resolved scans of the charge collection efficiency, an Sr{sup 90}{beta}-source set-up to measure the signal levels for a minimum ionizing particle (MIP), and a beam test with 180 GeV pions at CERN. This article gives a brief overview of

  16. 3D-Printing Crystallographic Unit Cells for Learning Materials Science and Engineering

    Science.gov (United States)

    Rodenbough, Philip P.; Vanti, William B.; Chan, Siu-Wai

    2015-01-01

    Introductory materials science and engineering courses universally include the study of crystal structure and unit cells, which are by their nature highly visual 3D concepts. Traditionally, such topics are explored with 2D drawings or perhaps a limited set of difficult-to-construct 3D models. The rise of 3D printing, coupled with the wealth of…

  17. 3D-Printing Crystallographic Unit Cells for Learning Materials Science and Engineering

    Science.gov (United States)

    Rodenbough, Philip P.; Vanti, William B.; Chan, Siu-Wai

    2015-01-01

    Introductory materials science and engineering courses universally include the study of crystal structure and unit cells, which are by their nature highly visual 3D concepts. Traditionally, such topics are explored with 2D drawings or perhaps a limited set of difficult-to-construct 3D models. The rise of 3D printing, coupled with the wealth of…

  18. In-situ monitoring of potential enhanced DNA related processes using electrochemical quartz crystal microbalance with dissipation (EQCM-D)

    DEFF Research Database (Denmark)

    Quan, Xueling; Heiskanen, Arto; Tenje, Maria

    2014-01-01

    The effect of applied potential pulses on DNA functionalization (thiolated single stranded DNA) and hybridization processes has been monitored in-situ on gold surfaces using electrochemical quartz crystal microbalance with dissipation (EQCM-D). The applied potentials were chosen with respect to t...

  19. Interactive 3D Mars Visualization

    Science.gov (United States)

    Powell, Mark W.

    2012-01-01

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

  20. Wireless 3D Chocolate Printer

    Directory of Open Access Journals (Sweden)

    FROILAN G. DESTREZA

    2014-02-01

    Full Text Available This study is for the BSHRM Students of Batangas State University (BatStateU ARASOF for the researchers believe that the Wireless 3D Chocolate Printer would be helpful in their degree program especially on making creative, artistic, personalized and decorative chocolate designs. The researchers used the Prototyping model as procedural method for the successful development and implementation of the hardware and software. This method has five phases which are the following: quick plan, quick design, prototype construction, delivery and feedback and communication. This study was evaluated by the BSHRM Students and the assessment of the respondents regarding the software and hardware application are all excellent in terms of Accuracy, Effecitveness, Efficiency, Maintainability, Reliability and User-friendliness. Also, the overall level of acceptability of the design project as evaluated by the respondents is excellent. With regard to the observation about the best raw material to use in 3D printing, the chocolate is good to use as the printed material is slightly distorted,durable and very easy to prepare; the icing is also good to use as the printed material is not distorted and is very durable but consumes time to prepare; the flour is not good as the printed material is distorted, not durable but it is easy to prepare. The computation of the economic viability level of 3d printer with reference to ROI is 37.14%. The recommendation of the researchers in the design project are as follows: adding a cooling system so that the raw material will be more durable, development of a more simplified version and improving the extrusion process wherein the user do not need to stop the printing process just to replace the empty syringe with a new one.

  1. Crystal structure of the breakage-reunion domain of DNA gyrase.

    Science.gov (United States)

    Morais Cabral, J H; Jackson, A P; Smith, C V; Shikotra, N; Maxwell, A; Liddington, R C

    1997-08-28

    DNA gyrase is a type II DNA topoisomerase from bacteria that introduces supercoils into DNA. It catalyses the breakage of a DNA duplex (the G segment), the passage of another segment (the T segment) through the break, and then the reunification of the break. This activity involves the opening and dosing of a series of molecular 'gates' which is coupled to ATP hydrolysis. Here we present the crystal structure of the 'breakage-reunion' domain of the gyrase at 2.8 A resolution. Comparison of the structure of this 59K (relative molecular mass, 59,000) domain with that of a 92K fragment of yeast topoisomerase II reveals a very different quaternary organization, and we propose that the two structures represent two principal conformations that participate in the enzymatic pathway. The gyrase structure reveals a new dimer contact with a grooved concave surface for binding the G segment and a cluster of conserved charged residues surrounding the active-site tyrosines. It also shows how breakage of the G segment can occur and, together with the topoisomerase II structure, suggests a pathway by which the T segment can be released through the second gate of the enzyme. Mutations that confer resistance to the quinolone antibacterial agents cluster at the new dimer interface, indicating how these drugs might interact with the gyrase-DNA complex.

  2. Virtual 3-D Facial Reconstruction

    Directory of Open Access Journals (Sweden)

    Martin Paul Evison

    2000-06-01

    Full Text Available Facial reconstructions in archaeology allow empathy with people who lived in the past and enjoy considerable popularity with the public. It is a common misconception that facial reconstruction will produce an exact likeness; a resemblance is the best that can be hoped for. Research at Sheffield University is aimed at the development of a computer system for facial reconstruction that will be accurate, rapid, repeatable, accessible and flexible. This research is described and prototypical 3-D facial reconstructions are presented. Interpolation models simulating obesity, ageing and ethnic affiliation are also described. Some strengths and weaknesses in the models, and their potential for application in archaeology are discussed.

  3. How 3-D Movies Work

    Institute of Scientific and Technical Information of China (English)

    吕铁雄

    2011-01-01

    难度:★★★★☆词数:450 建议阅读时间:8分钟 Most people see out of two eyes. This is a basic fact of humanity,but it’s what makes possible the illusion of depth(纵深幻觉) that 3-D movies create. Human eyes are spaced about two inches apart, meaning that each eye gives the brain a slightly different perspective(透视感)on the same object. The brain then uses this variance to quickly determine an object’s distance.

  4. Positional Awareness Map 3D (PAM3D)

    Science.gov (United States)

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

    2012-01-01

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

  5. 3D Printable Graphene Composite

    Science.gov (United States)

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

    2015-07-01

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

  6. 3D medical thermography device

    Science.gov (United States)

    Moghadam, Peyman

    2015-05-01

    In this paper, a novel handheld 3D medical thermography system is introduced. The proposed system consists of a thermal-infrared camera, a color camera and a depth camera rigidly attached in close proximity and mounted on an ergonomic handle. As a practitioner holding the device smoothly moves it around the human body parts, the proposed system generates and builds up a precise 3D thermogram model by incorporating information from each new measurement in real-time. The data is acquired in motion, thus it provides multiple points of view. When processed, these multiple points of view are adaptively combined by taking into account the reliability of each individual measurement which can vary due to a variety of factors such as angle of incidence, distance between the device and the subject and environmental sensor data or other factors influencing a confidence of the thermal-infrared data when captured. Finally, several case studies are presented to support the usability and performance of the proposed system.

  7. 3D Printed Bionic Ears

    Science.gov (United States)

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

    2013-01-01

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

  8. 3D printed bionic ears.

    Science.gov (United States)

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

    2013-06-12

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

  9. Crystal structure of a four-stranded intercalated DNA: d(C4)

    Science.gov (United States)

    Chen, L.; Cai, L.; Zhang, X.; Rich, A.

    1994-01-01

    The crystal structure of d(C4) solved at 2.3-A resolution reveals a four-stranded molecule composed of two interdigitated or intercalated duplexes. The duplexes are held together by hemiprotonated cytosine-cytosine base pairs and are parallel stranded, but the two duplexes point in opposite directions. The molecule has a slow right-handed twist of 12.4 degrees between covalently linked cytosine base pairs, and the base stacking distance is 3.1 A. This is in general agreement with the NMR studies. A biological role for DNA in this conformation is suggested.

  10. 3D biometrics systems and applications

    CERN Document Server

    Zhang, David

    2013-01-01

    Includes discussions on popular 3D imaging technologies, combines them with biometric applications, and then presents real 3D biometric systems Introduces many efficient 3D feature extraction, matching, and fusion algorithms Techniques presented have been supported by experimental results using various 3D biometric classifications

  11. Conducting Polymer 3D Microelectrodes

    Directory of Open Access Journals (Sweden)

    Jenny Emnéus

    2010-12-01

    Full Text Available Conducting polymer 3D microelectrodes have been fabricated for possible future neurological applications. A combination of micro-fabrication techniques and chemical polymerization methods has been used to create pillar electrodes in polyaniline and polypyrrole. The thin polymer films obtained showed uniformity and good adhesion to both horizontal and vertical surfaces. Electrodes in combination with metal/conducting polymer materials have been characterized by cyclic voltammetry and the presence of the conducting polymer film has shown to increase the electrochemical activity when compared with electrodes coated with only metal. An electrochemical characterization of gold/polypyrrole electrodes showed exceptional electrochemical behavior and activity. PC12 cells were finally cultured on the investigated materials as a preliminary biocompatibility assessment. These results show that the described electrodes are possibly suitable for future in-vitro neurological measurements.

  12. Crystal Structure, Thermal Decomposition Behavior and the Standard Molar Enthalpy of Formation of a Novel 3D Hydrogen Bonded Supramolecular [Co(HnicO)2·(H2O)2

    Institute of Scientific and Technical Information of China (English)

    ZENG,Ming-Hua; WU,Mei-Chun; ZHU,Li-Hong; LIANG,Hong; YANG Xu-Wu

    2007-01-01

    Hydrothermal synthesis and X-ray characterized 3D supramolecular networks were constructed by [Co(HnicO)2·(H2O)2] (HnicOH=2-hydroxynicotinic acid) (1) as building block via abundant dimeric homomeric (N-H…O) and unusually cyclic tetrameric heteromeric (O-H…O) hydrogen-bonds. It is noted that there exist unusually linear metal-water chains comprised of tetrameric units linked by vertexes sharing cobalt centers through hydrogen-bonding. TG-DTG curves illustrated that thermal decomposition was completed by two steps, one is the loss of two terminal water molecules in the range of 156-234 ℃, and the other is the pyrolysis of HnicO ligand in the range of 234-730 ℃. The standard molar enthalpy of formation of the complex was determined to be (-1845.43±2.77) kJ·mol-1 by a rotary-bomb combustion calorimeter.

  13. Crystal structure of Cpf1 in complex with guide RNA and target DNA

    Science.gov (United States)

    Yamano, Takashi; Nishimasu, Hiroshi; Zetsche, Bernd; Hirano, Hisato; Slaymaker, Ian M.; Li, Yinqing; Fedorova, Iana; Nakane, Takanori; Makarova, Kira S.; Koonin, Eugene V.; Ishitani, Ryuichiro; Zhang, Feng; Nureki, Osamu

    2016-01-01

    Cpf1 is an RNA-guided endonuclease of a type V CRISPR-Cas system that has been recently harnessed for genome editing. Here, we report the crystal structure of Acidaminococcus sp. Cpf1 (AsCpf1) in complex with the guide RNA and its target DNA, at 2.8 Å resolution. AsCpf1 adopts a bilobed architecture, with the RNA–DNA heteroduplex bound inside the central channel. The structural comparison of AsCpf1 with Cas9, a type II CRISPR-Cas nuclease, reveals both striking similarity and major differences, thereby explaining their distinct functionalities. AsCpf1 contains the RuvC domain and a putative novel nuclease domain, which are responsible for the cleavage of the non-target and target strands, respectively, and jointly generate staggered DNA double-strand breaks. AsCpf1 recognizes the 5′-TTTN-3′ protospacer adjacent motif by base and shape readout mechanisms. Our findings provide mechanistic insights into RNA-guided DNA cleavage by Cpf1, and establish a framework for rational engineering of the CRISPR-Cpf1 toolbox. PMID:27114038

  14. Supernova Remnant in 3-D

    Science.gov (United States)

    2009-01-01

    of the wavelength shift is related to the speed of motion, one can determine how fast the debris are moving in either direction. Because Cas A is the result of an explosion, the stellar debris is expanding radially outwards from the explosion center. Using simple geometry, the scientists were able to construct a 3-D model using all of this information. A program called 3-D Slicer modified for astronomical use by the Astronomical Medicine Project at Harvard University in Cambridge, Mass. was used to display and manipulate the 3-D model. Commercial software was then used to create the 3-D fly-through. The blue filaments defining the blast wave were not mapped using the Doppler effect because they emit a different kind of light synchrotron radiation that does not emit light at discrete wavelengths, but rather in a broad continuum. The blue filaments are only a representation of the actual filaments observed at the blast wave. This visualization shows that there are two main components to this supernova remnant: a spherical component in the outer parts of the remnant and a flattened (disk-like) component in the inner region. The spherical component consists of the outer layer of the star that exploded, probably made of helium and carbon. These layers drove a spherical blast wave into the diffuse gas surrounding the star. The flattened component that astronomers were unable to map into 3-D prior to these Spitzer observations consists of the inner layers of the star. It is made from various heavier elements, not all shown in the visualization, such as oxygen, neon, silicon, sulphur, argon and iron. High-velocity plumes, or jets, of this material are shooting out from the explosion in the plane of the disk-like component mentioned above. Plumes of silicon appear in the northeast and southwest, while those of iron are seen in the southeast and north. These jets were already known and Doppler velocity measurements have been made for these structures, but their orientation and

  15. 3D Printing of Graphene Aerogels.

    Science.gov (United States)

    Zhang, Qiangqiang; Zhang, Feng; Medarametla, Sai Pradeep; Li, Hui; Zhou, Chi; Lin, Dong

    2016-04-01

    3D printing of a graphene aerogel with true 3D overhang structures is highlighted. The aerogel is fabricated by combining drop-on-demand 3D printing and freeze casting. The water-based GO ink is ejected and freeze-cast into designed 3D structures. The lightweight (<10 mg cm(-3) ) 3D printed graphene aerogel presents superelastic and high electrical conduction.

  16. The 3D chromatin structure of the mouse β-haemoglobin gene cluster

    NARCIS (Netherlands)

    M.P.C. van de Corput (Mariëtte); T.A. Knoch (Tobias); E. de Boer (Ernie); W.A. van Cappellen (Gert); M. Lesnussa (Michael); H.J.F.M.M. Eussen (Bert)

    2010-01-01

    textabstractHere we show a 3D DNA-FISH method to visualizes the 3D structure of the β-globin locus. Geometric size and shape measurements of the 3D rendered signals (128Kb) show that the volume of the β-globin locus decreases almost two fold upon gene activation. A decrease in length and a

  17. The 3D chromatin structure of the mouse β-haemoglobin gene cluster

    NARCIS (Netherlands)

    M.P.C. van de Corput (Mariëtte); T.A. Knoch (Tobias); E. de Boer (Ernie); W.A. van Cappellen (Gert); M. Lesnussa (Michael); H.J.F.M.M. Eussen (Bert)

    2010-01-01

    textabstractHere we show a 3D DNA-FISH method to visualizes the 3D structure of the β-globin locus. Geometric size and shape measurements of the 3D rendered signals (128Kb) show that the volume of the β-globin locus decreases almost two fold upon gene activation. A decrease in length and a distinc

  18. 3D similar pattern generation of snow crystals with cellular automata%基于元胞自动化模型的三维雪花晶体近似模式的产生

    Institute of Scientific and Technical Information of China (English)

    李芳佳; 高尚策; 唐政; 石井雅博; 山下和也

    2009-01-01

    Computer simulation of snow crystal growing process has been done for many years. Cellular automaton is a computing model which is made from lattice cells and simple rules. Though it is a very simple model, it gives good results when used to imitate complex processes such as the life phenomenon, crystal growth and the turbulent flow. In this paper, a cellular model for 3Dimensional snow crystallization was proposed by extending the traditional 2-Dimensional cellular model. Simulation results indicated that the proposed model can accurately simulate most 3-Dimensional snow erystaUization processes.%关于雪花生长过程的计算机模拟已经受到了广泛关注.其中,元胞自动化模型是一种基于网格和简单规则的计算方法.尽管这是一种简单的模型,但其在模拟复杂过程(比如:生命现象,晶体生长和湍流)时往往能取得较好的结果.提出了一种由传统的二维模型扩展而来的三维雪花晶体生长方法.计算机模拟结果显示提出的方法能够更精确地模拟出三维雪花的晶体化过程.

  19. The crystal structure of sulfamethoxazole, interaction with DNA, DFT calculation, and molecular docking studies

    Science.gov (United States)

    Das, Dipankar; Sahu, Nilima; Roy, Suman; Dutta, Paramita; Mondal, Sudipa; Torres, Elena L.; Sinha, Chittaranjan

    2015-02-01

    Sulfamethoxazole (SMX) [4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide] is structurally established by single crystal X-ray diffraction measurement. The crystal packing shows H-bonded 2D polymer through N(7)sbnd H(7A)---O(2), N(7)sbnd H(7B)---O(3), N(1)sbnd H(1)---N(2), C(5)sbnd H(5)---O(3)sbnd S(1) and N(7)sbnd (H7A)---O(2)sbnd S(1). Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) computations of optimized structure of SMX determine the electronic structure and has explained the electronic spectral transitions. The interaction of SMX with CT-DNA has been studied by absorption spectroscopy and the binding constant (Kb) is 4.37 × 104 M-1. The in silico test of SMX with DHPS from Escherichia coli and Streptococcus pneumoniae helps to understand drug metabolism and accounts the drug-molecule interactions. The molecular docking of SMX-DNA also helps to predict the interaction feature.

  20. The crystal structure of sulfamethoxazole, interaction with DNA, DFT calculation, and molecular docking studies.

    Science.gov (United States)

    Das, Dipankar; Sahu, Nilima; Roy, Suman; Dutta, Paramita; Mondal, Sudipa; Torres, Elena L; Sinha, Chittaranjan

    2015-02-25

    Sulfamethoxazole (SMX) [4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide] is structurally established by single crystal X-ray diffraction measurement. The crystal packing shows H-bonded 2D polymer through N(7)-H(7A)-O(2), N(7)-H(7B)-O(3), N(1)-H(1)-N(2), C(5)-H(5)-O(3)-S(1) and N(7)-(H7A)-O(2)-S(1). Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) computations of optimized structure of SMX determine the electronic structure and has explained the electronic spectral transitions. The interaction of SMX with CT-DNA has been studied by absorption spectroscopy and the binding constant (Kb) is 4.37×10(4)M(-1). The in silico test of SMX with DHPS from Escherichia coli and Streptococcus pneumoniae helps to understand drug metabolism and accounts the drug-molecule interactions. The molecular docking of SMX-DNA also helps to predict the interaction feature.

  1. 3D multiplexed immunoplasmonics microscopy

    Science.gov (United States)

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

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  2. Filling gaps in cultural heritage documentation by 3D photography

    Science.gov (United States)

    Schuhr, W.; Lee, J. D.

    2015-08-01

    geometry" and to multistage concepts of 3D photographs in Cultural Heritage just started. Furthermore a revised list of the 3D visualization principles, claiming completeness, has been carried out. Beside others in an outlook *It is highly recommended, to list every historical and current stereo view with relevance to Cultural Heritage in a global Monument Information System (MIS), like in google earth. *3D photographs seem to be very suited, to complete and/or at least partly to replace manual archaeological sketches. In this concern the still underestimated 3D effect will be demonstrated, which even allows, e.g., the spatial perception of extremely small scratches etc... *A consequent dealing with 3D Technology even seems to indicate, currently we experience the beginning of a new age of "real 3DPC- screens", which at least could add or even partly replace the conventional 2D screens. Here the spatial visualization is verified without glasses in an all-around vitreous body. In this respect nowadays widespread lasered crystals showing monuments are identified as "Early Bird" 3D products, which, due to low resolution and contrast and due to lack of color, currently might even remember to the status of the invention of photography by Niepce (1827), but seem to promise a great future also in 3D Cultural Heritage documentation. *Last not least 3D printers more and more seem to conquer the IT-market, obviously showing an international competition.

  3. Crystallization and preliminary X-ray analysis of the Plasmodium falciparum apicoplast DNA polymerase

    Science.gov (United States)

    Milton, Morgan E.; Choe, Jun-yong; Honzatko, Richard B.; Nelson, Scott W.

    2015-01-01

    Infection by the parasite Plasmodium falciparum is the leading cause of malaria in humans. The parasite has a unique and essential plastid-like organelle called the apicoplast. The apicoplast contains a genome that undergoes replication and repair through the action of a replicative polymerase (apPOL). apPOL has no direct orthologs in mammalian polymerases and is therefore an attractive antimalarial drug target. No structural information exists for apPOL, and the Klenow fragment of Escherichia coli DNA polymerase I, which is its closest structural homolog, shares only 28% sequence identity. Here, conditions for the crystallization of and preliminary X-ray diffraction data from crystals of P. falciparum apPOL are reported. Data complete to 3.5 Å resolution were collected from a single crystal (2 × 2 × 5 µm) using a 5 µm beam. The space group P6522 (unit-cell parameters a = b = 141.8, c = 149.7 Å, α = β = 90, γ = 120°) was confirmed by molecular replacement. Refinement is in progress. PMID:25760711

  4. DNA- and AC electric field-assisted assembly of two-dimensional colloidal photonic crystals and their controlled defect insertion

    Science.gov (United States)

    Kim, Sejong

    Photonic crystals (PC) are structures in which the refractive index is a periodic function in space. The ability of photonic crystals to localize and manipulate electromagnetic waves has attracted considerable attention from the scientific community. The self-assembly of monodisperse micrometer scale colloidal spheres into hexagonal closed-packed colloidal crystals provides a simple, fast, and cheap materials chemistry approach to PCs. Employing DNA supramolecular recognition, 2-dimensional (2D) photonic crystal monolayer was fabricated with monodisperse polystyrene colloidal microspheres. Amine-terminated DNA oligomers were covalently attached onto carboxy-decorated microspheres and enabled their DNA-functionalization while preserving their colloidal stability and organization properties. Following a capillary-force-assisted organization of DNA-decorated microspheres into close-packed 2D opaline arrays, the first monolayer was immobilized by DNA hybridization. Insertion of vacancies at predetermined sites within the lattice of colloidal crystals is a prerequisite in order to realize high-quality, opaline-based photonic devices. The previously obtained DNA-hybridization type binding of 2D-opaline arrays provides a heat-sensitive "adhesive" between substrate and microspheres within a surrounding aqueous medium that enables tuning the hybridization strength of DNA linker as well as a mechanism to facilitate the removal of unbound microspheres. Focusing a laser beam onto a single microsphere of the opaline array induces localized heating that enables the microsphere to detach, leaving behind vacancies. By repeating this process, line vacancies were successfully obtained. The effects of salt concentration, laser power, light-absorbing dyes, DNA length and refractive index mismatch were investigated and found to correlate with heat-induced DNA dehybridization. In addition, AC (alternating current) electrokinetic force was also utilized to obtain assembly of colloidal

  5. Crowdsourcing Based 3d Modeling

    Science.gov (United States)

    Somogyi, A.; Barsi, A.; Molnar, B.; Lovas, T.

    2016-06-01

    Web-based photo albums that support organizing and viewing the users' images are widely used. These services provide a convenient solution for storing, editing and sharing images. In many cases, the users attach geotags to the images in order to enable using them e.g. in location based applications on social networks. Our paper discusses a procedure that collects open access images from a site frequently visited by tourists. Geotagged pictures showing the image of a sight or tourist attraction are selected and processed in photogrammetric processing software that produces the 3D model of the captured object. For the particular investigation we selected three attractions in Budapest. To assess the geometrical accuracy, we used laser scanner and DSLR as well as smart phone photography to derive reference values to enable verifying the spatial model obtained from the web-album images. The investigation shows how detailed and accurate models could be derived applying photogrammetric processing software, simply by using images of the community, without visiting the site.

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

    Science.gov (United States)

    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.

  7. Syntheses and Crystal Structure of a New 3D Ag(I)—fumaric Acid Framework,[Ag(hmt)(fma)1/2·2H2O]n

    Institute of Scientific and Technical Information of China (English)

    毕文华; 孙道峰; 曹荣; 李星; 时茜; 洪茂椿

    2003-01-01

    A new silver(I) coordination polymer,[Ag(hmt)(fma)1/2·2H2O]n,(hmt=hexamethylenetetramine,fma=furmaric acid),was obtained by self-assembly of hmt,fma and AgNO3 in the mixed solvent of methanol,dichloromethane and water (CH3OH:CH2Cl2:H2O=5:5:1),and characterized by X-ray diffraction analysis.Complex 1 belongs to orthorhombic space group Pbcn with cell parameters a=1.72043(5)nm,b=1.19704(2)nm,c=1.11685(3)nm,V=2.30007(10)nm3,Z=8,CCDC number:194381.In complex 1,each hmt ligand acts as a μ3-bridge to link three Ag(I) atoms and in turn every Ag(I)ion attaches to three hmt ligands to produce a 2D honeycomb network,which is further linked by the bidentate fma ligands to form a 3D noninterpenetrating open framework with one-dimensional channels being filled by guest molecules.

  8. Vrste i tehnike 3D modeliranja

    OpenAIRE

    Bernik, Andrija

    2010-01-01

    Proces stvaranja 3D stvarnih ili imaginarnih objekata naziva se 3D modeliranje. Razvoj računalne tehnologije omogućuje korisniku odabir raznih metoda i tehnika kako bi se postigla optimalna učinkovitost. Odabir je vezan za klasično 3D modeliranje ili 3D skeniranje pomoću specijaliziranih programskih i sklopovskih rješenja. 3D tehnikama modeliranja korisnik može izraditi 3D model na nekoliko načina: koristi poligone, krivulje ili hibrid dviju spomenutih tehnika pod nazivom subdivizijsko modeli...

  9. Kuvaus 3D-tulostamisesta hammastekniikassa

    OpenAIRE

    Munne, Mauri; Mustonen, Tuomas; Vähäjylkkä, Jaakko

    2013-01-01

    3D-tulostaminen kehittyy nopeasti ja yleistyy koko ajan. Tulostimien tarkkuuksien kehittyessä 3D-tulostus on ottamassa myös jalansijaa hammastekniikan alalta. Tämän opinnäytetyön tarkoituksena on kuvata 3D-tulostamisen tilaa hammastekniikassa. 3D-tulostaminen on Suomessa vielä melko harvinaista, joten opinnäytetyön tavoitteena on koota yhteen kaikki mahdollinen tieto liittyen 3D-tulostamiseen hammastekniikassa. Tavoitteena on myös 3D-tulostimen testaaminen käytännössä aina suun skannaami...

  10. Crystal structure of 6-(p-tolylbenzo[b]naphtho[2,3-d]thiophene and of an orthorhombic polymorph of 7-phenylanthra[2,3-b]benzo[d]thiophene

    Directory of Open Access Journals (Sweden)

    S. Gopinath

    2016-09-01

    Full Text Available The title compounds, C23H16S, (I, and C26H16S, (II, are benzothiophene derivatives in which the benzothiophene moiety is fused with a naphthalene ring system in (I, and with an anthracene ring system in (II. In (I, the mean plane of the benzothiophene ring system makes a dihedral angle of 2.28 (6° with the naphthalene ring system, and a dihedral angle of 1.28 (6° with the anthracene ring system in (II, showing that the fused units are essentially planar. In (I, the 4-methylbenzene ring substituent makes a dihedral angle of 71.40 (9° with the naphthalene ring system, while the phenyl ring substituent in (II makes a dihedral angle of 67.08 (12° with the anthracene ring system. In the crystals of both compounds, molecules are linked by C—H...π interactions, leading to the formation of slabs parallel to (001 in (I and to zigzag chains along [001] in (II. There are also offset π–π interactions present within the slabs in (I. In the crystal of (II, they link the chains, forming sheets parallel to (010. The triclinic polymorph of compound (II has been reported [Sivasakthikumaran et al., (2012. J. Org. Chem. 77, 9053–9071].

  11. Preparation, crystallization and preliminary X-ray diffraction analysis of the DNA-binding domain of the Ets transcription factor in complex with target DNA

    Energy Technology Data Exchange (ETDEWEB)

    Suwa, Yoshiaki; Nakamura, Teruya; Toma, Sachiko; Ikemizu, Shinji; Kai, Hirofumi; Yamagata, Yuriko, E-mail: yamagata@gpo.kumamoto-u.ac.jp [Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973 (Japan)

    2008-03-01

    The complex between the Ets domain of Ets2 and its target DNA has been crystallized. The crystals diffracted to 3.0 Å resolution. The Ets2 transcription factor is a member of the Ets transcription-factor family. Ets2 plays a role in the malignancy of cancer and in Down’s syndrome by regulating the transcription of various genes. The DNA-binding domain of Ets2 (Ets domain; ETSD), which contains residues that are highly conserved among Ets transcription-factor family members, was expressed as a GST-fusion protein. The aggregation of ETSD produced after thrombin cleavage could be prevented by treatment with NDSB-195 (nondetergent sulfobetaine 195). ETSD was crystallized in complex with DNA containing the Ets2 target sequence (GGAA) by the hanging-drop vapour-diffusion method. The best crystals were grown using 25% PEG 3350, 80 mM magnesium acetate, 50 mM sodium cacodylate pH 5.0/5.5 as the reservoir at 293 K. The crystals belonged to space group C2, with unit-cell parameters a = 85.89, b = 95.52, c = 71.89 Å, β = 101.7° and a V{sub M} value of 3.56 Å{sup 3} Da{sup −1}. Diffraction data were collected to a resolution of 3.0 Å.

  12. ExpandplusCrystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA

    Energy Technology Data Exchange (ETDEWEB)

    M Langelier; J Planck; S Roy; J Pascal

    2011-12-31

    Poly(ADP-ribose) polymerase-1 (PARP-1) has two homologous zinc finger domains, Zn1 and Zn2, that bind to a variety of DNA structures to stimulate poly(ADP-ribose) synthesis activity and to mediate PARP-1 interaction with chromatin. The structural basis for interaction with DNA is unknown, which limits our understanding of PARP-1 regulation and involvement in DNA repair and transcription. Here, we have determined crystal structures for the individual Zn1 and Zn2 domains in complex with a DNA double strand break, providing the first views of PARP-1 zinc fingers bound to DNA. The Zn1-DNA and Zn2-DNA structures establish a novel, bipartite mode of sequence-independent DNA interaction that engages a continuous region of the phosphodiester backbone and the hydrophobic faces of exposed nucleotide bases. Biochemical and cell biological analysis indicate that the Zn1 and Zn2 domains perform distinct functions. The Zn2 domain exhibits high binding affinity to DNA compared with the Zn1 domain. However, the Zn1 domain is essential for DNA-dependent PARP-1 activity in vitro and in vivo, whereas the Zn2 domain is not strictly required. Structural differences between the Zn1-DNA and Zn2-DNA complexes, combined with mutational and structural analysis, indicate that a specialized region of the Zn1 domain is re-configured through the hydrophobic interaction with exposed nucleotide bases to initiate PARP-1 activation.

  13. Laser-induced defect insertion in DNA-linked 2D colloidal crystal array

    Science.gov (United States)

    Geiss, Erik; Kim, Sejong; Marcus, Harris L.; Papadimitrakopoulos, Fotios

    2009-02-01

    Insertion of vacancies at predetermined sites within the lattice of colloidal crystals is a prerequisite in order to realize high-quality, opaline-based photonic devices. In this contribution, we demonstrate a novel methodology to afford controlled insertion of vacancies within two-dimensional (2D) opaline arrays. These 2D opaline arrays have been substrate-anchored with the help of DNA hybridization. This provides a heat-sensitive ‘adhesive’ between substrate and microspheres within a surrounding aqueous medium that enables tuning the hybridization strength of DNA linker as well as a mechanism to facilitate the removal of unbound microspheres. Focusing a laser beam onto the substrate/microsphere interface induces a localized heating event that detaches the irradiated microspheres, leaving behind vacancies. By repeating this process, line vacancies were successfully obtained. The effects of salt concentration, laser power, light-absorbing dyes, DNA length and refractive-index mismatch were investigated and found to correlate with heat-induced microsphere release.

  14. Zinc(II) complexes of carboxamide derivatives: Crystal structures and interaction with calf thymus DNA

    Indian Academy of Sciences (India)

    Biplab Mondal; Buddhadeb Sen; Ennio Zangrando; Pabitra Chattopadhyay

    2015-10-01

    Two mononuclear zinc(II) complexes of newly designed carboxamide derivatives, formulated as [Zn(L1)3](ClO4)2 (1) and [Zn(L2)3](ClO4)2 (2) [where L1 = -(furan-2-ylmethyl)-2-pyridinecarboxamide and L2 = -(thiophen-2-ylmethyl)-2-pyridine-carboxamide], have been isolated in pure form in the reaction of perchlorate salts of Zn(II) with ligands L1 and L2, respectively. The two complexes were characterized by physicochemical and spectroscopic tools, and by X-ray crystal structures of both ligands and the complex 1. In complex 1, zinc(II) is chelated by three ligands with a distorted octahedral geometry. The DNA-binding properties of zinc complexes 1 and 2 have been investigated by spectroscopic methods and viscosity measurements. The results suggest that both complexes 1 and 2 bind to DNA in an intercalation mode between the uncoordinated furan or thiophene chromophore and the base pairs of DNA.

  15. 3D visualization for research and teaching in geosciences

    Science.gov (United States)

    Manea, Marina; Constantin Manea, Vlad

    2010-05-01

    Today, we are provided with an abundance of visual images from a variety of sources. In doing research, data visualization represents an important part, and sophisticated models require special tools that should enhance the comprehension of modeling results. Also, helping our students gain visualization skills is an important way to foster greater comprehension when studying geosciences. For these reasons we build a 3D stereo-visualization system, or a GeoWall, that permits to explore in depth 3D modeling results and provide for students an attractive way for data visualization. In this study, we present the architecture of such low cost system, and how is used. The system consists of three main parts: a DLP-3D capable display, a high performance workstation and several pairs of wireless liquid crystal shutter eyewear. The system is capable of 3D stereo visualization of Google Earth and/or 3D numeric modeling results. Also, any 2D image or movie can be instantly viewed in 3D stereo. Such flexible-easy-to-use visualization system proved to be an essential research and teaching tool.

  16. Research of 3D display using anamorphic optics

    Science.gov (United States)

    Matsumoto, Kenji; Honda, Toshio

    1997-05-01

    This paper describes the auto-stereoscopic display which can reconstruct more reality and viewer friendly 3-D image by increasing the number of parallaxes and giving motion parallax horizontally. It is difficult to increase number of parallaxes to give motion parallax to the 3-D image without reducing the resolution, because the resolution of display device is insufficient. The magnification and the image formation position can be selected independently in horizontal direction and the vertical direction by projecting between the display device and the 3-D image with the anamorphic optics. The anamorphic optics is an optics system with different magnification in horizontal direction and the vertical direction. It consists of the combination of cylindrical lenses with different focal length. By using this optics, even if we use a dynamic display such as liquid crystal display (LCD), it is possible to display the realistic 3-D image having motion parallax. Motion parallax is obtained by assuming width of the single parallax at the viewing position to be about the same size as the pupil diameter of viewer. In addition, because the focus depth of the 3-D image is deep in this method, conflict of accommodation and convergence is small, and natural 3-D image can be displayed.

  17. Crystallization and preliminary X-ray analysis of the NKX2.5 homeodomain in complex with DNA.

    Science.gov (United States)

    Genis, Caroli; Scone, Peyton; Kasahara, Hideko; Nam, Hyun Joo

    2008-11-01

    As part of an effort to elucidate the molecular basis for the pathogenesis of NKX2.5 mutations in congenital heart disease using X-ray crystallography, the NKX2.5 homeodomain has been crystallized in complex with a specific DNA element, the -242 promoter region of atrial natriuretic factor. Crystals of the homeodomain-DNA complex diffracted X-rays to 1.7 A resolution and belonged to space group P6(5), with unit-cell parameters a = b = 71.5, c = 94.3 A. The asymmetric unit contained two molecules of the NKX2.5 homeodomain and one double-stranded oligonucleotide.

  18. Forward ramp in 3D

    Science.gov (United States)

    1997-01-01

    Mars Pathfinder's forward rover ramp can be seen successfully unfurled in this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. This ramp was not used for the deployment of the microrover Sojourner, which occurred at the end of Sol 2. When this image was taken, Sojourner was still latched to one of the lander's petals, waiting for the command sequence that would execute its descent off of the lander's petal.The image helped Pathfinder scientists determine whether to deploy the rover using the forward or backward ramps and the nature of the first rover traverse. The metallic object at the lower left of the image is the lander's low-gain antenna. The square at the end of the ramp is one of the spacecraft's magnetic targets. Dust that accumulates on the magnetic targets will later be examined by Sojourner's Alpha Proton X-Ray Spectrometer instrument for chemical analysis. At right, a lander petal is visible.The IMP is a stereo imaging system with color capability provided by 24 selectable filters -- twelve filters per 'eye.' It stands 1.8 meters above the Martian surface, and has a resolution of two millimeters at a range of two meters.Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  19. Synthesis and Crystal Structure of a 3-D Hydrogen-bonded Supramolecular Decavanadate Compound [Habo]6[V10O28]·2C3H7OH·2H2O

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A new inorganic-organic hybrid supramolecular compound [Habo]6[V10O28]·solvents and its crystal structure was reported as follows: monoclinic, space group P21/n, a =11.419(9), b = 16.811(16), c = 15.521(12) (A), β= 102.98(2)°, V= 2903(4) (A)3, Z = 4, C15H46N3O19V5,Mr = 827.25, Dc = 1.893 g/cm3, λ(MoKα) = 0.71073 A,μ = 1.636 mm-1, F(000) = 1696, the final R =0.0696 and wR = 0.1361 for 4641 observed reflections with I > 2σ(I). The compound is based on decavanadate clusters [V 1oO28]6-. The hydrogen bonding interactions among Habo+ cations, solvents and decavanadate clusters extend 1 into a three-dimensional supramolecular architecture.

  20. Sliding Adjustment for 3D Video Representation

    Directory of Open Access Journals (Sweden)

    Galpin Franck

    2002-01-01

    Full Text Available This paper deals with video coding of static scenes viewed by a moving camera. We propose an automatic way to encode such video sequences using several 3D models. Contrary to prior art in model-based coding where 3D models have to be known, the 3D models are automatically computed from the original video sequence. We show that several independent 3D models provide the same functionalities as one single 3D model, and avoid some drawbacks of the previous approaches. To achieve this goal we propose a novel algorithm of sliding adjustment, which ensures consistency of successive 3D models. The paper presents a method to automatically extract the set of 3D models and associate camera positions. The obtained representation can be used for reconstructing the original sequence, or virtual ones. It also enables 3D functionalities such as synthetic object insertion, lightning modification, or stereoscopic visualization. Results on real video sequences are presented.

  1. An interactive multiview 3D display system

    Science.gov (United States)

    Zhang, Zhaoxing; Geng, Zheng; Zhang, Mei; Dong, Hui

    2013-03-01

    The progresses in 3D display systems and user interaction technologies will help more effective 3D visualization of 3D information. They yield a realistic representation of 3D objects and simplifies our understanding to the complexity of 3D objects and spatial relationship among them. In this paper, we describe an autostereoscopic multiview 3D display system with capability of real-time user interaction. Design principle of this autostereoscopic multiview 3D display system is presented, together with the details of its hardware/software architecture. A prototype is built and tested based upon multi-projectors and horizontal optical anisotropic display structure. Experimental results illustrate the effectiveness of this novel 3D display and user interaction system.

  2. Will 3D printers manufacture your meals?

    NARCIS (Netherlands)

    Bommel, K.J.C. van

    2013-01-01

    These days, 3D printers are laying down plastics, metals, resins, and other materials in whatever configurations creative people can dream up. But when the next 3D printing revolution comes, you'll be able to eat it.

  3. 3D ultrasound in fetal spina bifida.

    Science.gov (United States)

    Schramm, T; Gloning, K-P; Minderer, S; Tutschek, B

    2008-12-01

    3D ultrasound can be used to study the fetal spine, but skeletal mode can be inconclusive for the diagnosis of fetal spina bifida. We illustrate a diagnostic approach using 2D and 3D ultrasound and indicate possible pitfalls.

  4. 3D Flash LIDAR Space Laser Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Advanced Scientific Concepts, Inc. (ASC) is a small business that has developed 3D Flash LIDAR systems for space and terrestrial applications. 3D Flash LIDAR is...

  5. Eesti 3D jaoks kitsas / Virge Haavasalu

    Index Scriptorium Estoniae

    Haavasalu, Virge

    2009-01-01

    Produktsioonifirma Digitaalne Sputnik: Kaur ja Kaspar Kallas tegelevad filmide produtseerimise ning 3D digitaalkaamerate tootearendusega (Silicon Imaging LLC). Vendade Kallaste 3D-kaamerast. Kommenteerib Eesti Filmi Sihtasutuse direktor Marge Liiske

  6. Will 3D printers manufacture your meals?

    NARCIS (Netherlands)

    Bommel, K.J.C. van

    2013-01-01

    These days, 3D printers are laying down plastics, metals, resins, and other materials in whatever configurations creative people can dream up. But when the next 3D printing revolution comes, you'll be able to eat it.

  7. 3D printing of microscopic bacterial communities

    National Research Council Canada - National Science Library

    Jodi L. Connell; Eric T. Ritschdorff; Marvin Whiteley; Jason B. Shear

    2013-01-01

    .... Here, we describe a microscopic threedimensional (3D) printing strategy that enables multiple populations of bacteria to be organized within essentially any 3D geometry, including adjacent, nested, and free-floating...

  8. 3D Scanning technology for offshore purposes

    DEFF Research Database (Denmark)

    Christoffersen, Morten Thoft

    2005-01-01

    New scanning technology makes for construction of precision 3D models of production plants and offshore production facilities......New scanning technology makes for construction of precision 3D models of production plants and offshore production facilities...

  9. Laser Based 3D Volumetric Display System

    Science.gov (United States)

    1993-03-01

    Literature, Costa Mesa, CA July 1983. 3. "A Real Time Autostereoscopic Multiplanar 3D Display System", Rodney Don Williams, Felix Garcia, Jr., Texas...8217 .- NUMBERS LASER BASED 3D VOLUMETRIC DISPLAY SYSTEM PR: CD13 0. AUTHOR(S) PE: N/AWIU: DN303151 P. Soltan, J. Trias, W. Robinson, W. Dahlke 7...laser generated 3D volumetric images on a rotating double helix, (where the 3D displays are computer controlled for group viewing with the naked eye

  10. 3D-Printed Millimeter Wave Structures

    Science.gov (United States)

    2016-03-14

    demonstrates the resolution of the printer with a 10 micron nozzle. Figure 2: Measured loss tangent of SEBS and SBS samples. 3D - Printed Millimeter... 3D printing of styrene-butadiene-styrene (SBS) and styrene ethylene/butylene-styrene (SEBS) is used to demonstrate the feasibility of 3D - printed ...Additionally, a dielectric lens is printed which improves the antenna gain of an open-ended WR-28 waveguide from 7 to 8.5 dBi. Keywords: 3D printing

  11. Assembly of a New Cyano-bridged 4f-3d Dimer Sm(DMSO)4-(H2O)3Cr(CN)6 and Crystal Structure of [K3(18-crown-6)3-(H2O)4] Cr(CN)6 ·3H2O

    Institute of Scientific and Technical Information of China (English)

    周北川; 王宏根; 等

    2003-01-01

    A new syano-bridged binuclear 4f-3d complex Sm(DMSO)4-(H2O)3Cr(CN)6 was synthesized and characterized by single crystal structure analysis.It crystallizes in monoclinic,space group P21 with a=0.9367(3)°and Z=2,In this binuclear complex,Sm atom is eight coordinated and linked to the Cr atom by a cyano bridge,The molecules packs to form 3D structure due to the hydrogen bonds among them. [K3(18-crown-6)3-(H2O)4] Cr(CN)6 ·3H2O(18-C-6 represents 18-crown-6-ether)that was synthesized as a byproduct in the preparation of a Gd-Cr complex is also structurally characterized.Crystal data:triclinic,space group p-1 with a=1.0496(7)nm,b=1.1567(14)nm,c=1.3530(13)nm,α=94.15(9)°,β=96.04(8)°,γ=95.25(9)° and Z=1, [K3(18-crown-6)3-(H2O)4] Cr(CN)6 ·3H2O consists of ionic [K3(18-crown-6)3-(H2O)4]3+ and [Cr(CN)6]3- pairs,of which the [K3(18-C-6)3(H2O)4]3+ ion is a trinuclear cluster connected by water,and K atome are eight coordinated by eight oxygen atoms of one 18-C-6 and two water molecules.

  12. Crystallization of a member of the recFOR DNA repair pathway, RecO, with and without bound oligonucleotide

    Energy Technology Data Exchange (ETDEWEB)

    Aono, Shelly; Hartsch, Thomas; Schulze-Gahmen, Ursula

    2003-01-22

    RecFOR proteins are important for DNA repair by homologous recombination in bacteria. The RecO protein from Thermus thermophilus was cloned, purified and characterized for its binding to oligonucleotides. The protein was crystallized alone and in complex with a 14-mer oligonucleotide. Both crystal forms grow under different crystallization conditions in the same space group, P3121 or P3221, with almost identical unit cell parameters. Complete data sets were collected to 2.8 Angstrom and 2.5 Angstrom for RecO alone and the RecO-oligonucleotide complex, respectively. Visual comparison of the diffraction patterns between the two crystal forms and calculation of an Rmerge of 33.9 percent on F indicate that one of the crystal forms is indeed a complex of RecO with bound oligonucleotide.

  13. 3D Printing and Its Urologic Applications

    Science.gov (United States)

    Soliman, Youssef; Feibus, Allison H; Baum, Neil

    2015-01-01

    3D printing is the development of 3D objects via an additive process in which successive layers of material are applied under computer control. This article discusses 3D printing, with an emphasis on its historical context and its potential use in the field of urology. PMID:26028997

  14. Beowulf 3D: a case study

    Science.gov (United States)

    Engle, Rob

    2008-02-01

    This paper discusses the creative and technical challenges encountered during the production of "Beowulf 3D," director Robert Zemeckis' adaptation of the Old English epic poem and the first film to be simultaneously released in IMAX 3D and digital 3D formats.

  15. Expanding Geometry Understanding with 3D Printing

    Science.gov (United States)

    Cochran, Jill A.; Cochran, Zane; Laney, Kendra; Dean, Mandi

    2016-01-01

    With the rise of personal desktop 3D printing, a wide spectrum of educational opportunities has become available for educators to leverage this technology in their classrooms. Until recently, the ability to create physical 3D models was well beyond the scope, skill, and budget of many schools. However, since desktop 3D printers have become readily…

  16. 3D Printing and Its Urologic Applications.

    Science.gov (United States)

    Soliman, Youssef; Feibus, Allison H; Baum, Neil

    2015-01-01

    3D printing is the development of 3D objects via an additive process in which successive layers of material are applied under computer control. This article discusses 3D printing, with an emphasis on its historical context and its potential use in the field of urology.

  17. Expanding Geometry Understanding with 3D Printing

    Science.gov (United States)

    Cochran, Jill A.; Cochran, Zane; Laney, Kendra; Dean, Mandi

    2016-01-01

    With the rise of personal desktop 3D printing, a wide spectrum of educational opportunities has become available for educators to leverage this technology in their classrooms. Until recently, the ability to create physical 3D models was well beyond the scope, skill, and budget of many schools. However, since desktop 3D printers have become readily…

  18. 3D immersive and interactive learning

    CERN Document Server

    Cai, Yiyu

    2014-01-01

    This book reviews innovative uses of 3D for immersive and interactive learning, covering gifted programs, normal stream and special needs education. Reports on curriculum-based 3D learning in classrooms, and co-curriculum-based 3D student research projects.

  19. Hydrothermal synthesis of 3D porous architectures

    Institute of Scientific and Technical Information of China (English)

    XIAO Wanyan; GU Xiaojun; XUE Dongfeng

    2009-01-01

    A novel porous lanthanide-organic coordination polymer, [Nd(H2O)(HnicO)(TP)]·2H2O (1) (H2nicO=2-hydroxynieotinic acid, TP= terephthalate), was prepared under hydrothermai condition and characterized by single-crystal X-ray diffraction, thermogravimetrie analysis and infrared spectroscopy. Compound 1 exhibited a flexible coordination geometry of lanthanide ions, which possessed a three-dimensional (3D) open framework with one-dimensional (1D) channels containing lattice water molecules. This framework structure exhibited a high stability up to 330 ℃ after removing free water molecules. A homometallic supramolecular framework (Zn(HnicO)2(H2O)2 (2)) was obtained due to the competitive reaction between organic ligands, Nd3+ and Zn2+ ions. The results showed that on the basis of the soft-hard/acid-base principle the coordination selection between metal ions and organic ligands played an essential role in the smart construc-tion of lanthanide architectures.

  20. Wafer level 3-D ICs process technology

    CERN Document Server

    Tan, Chuan Seng; Reif, L Rafael

    2009-01-01

    This book focuses on foundry-based process technology that enables the fabrication of 3-D ICs. The core of the book discusses the technology platform for pre-packaging wafer lever 3-D ICs. However, this book does not include a detailed discussion of 3-D ICs design and 3-D packaging. This is an edited book based on chapters contributed by various experts in the field of wafer-level 3-D ICs process technology. They are from academia, research labs and industry.

  1. View-based 3-D object retrieval

    CERN Document Server

    Gao, Yue

    2014-01-01

    Content-based 3-D object retrieval has attracted extensive attention recently and has applications in a variety of fields, such as, computer-aided design, tele-medicine,mobile multimedia, virtual reality, and entertainment. The development of efficient and effective content-based 3-D object retrieval techniques has enabled the use of fast 3-D reconstruction and model design. Recent technical progress, such as the development of camera technologies, has made it possible to capture the views of 3-D objects. As a result, view-based 3-D object retrieval has become an essential but challenging res

  2. Investigating Mobile Stereoscopic 3D Touchscreen Interaction

    OpenAIRE

    Colley, Ashley; Hakkila, Jonna; SCHOENING, Johannes; Posti, Maaret

    2013-01-01

    3D output is no longer limited to large screens in cinemas or living rooms. Nowadays more and more mobile devices are equipped with autostereoscopic 3D (S3D) touchscreens. As a consequence interaction with 3D content now also happens whilst users are on the move. In this paper we carried out a user study with 27 participants to assess how mobile interaction, i.e. whilst walking, with mobile S3D devices, differs from interaction with 2D mobile touchscreens. We investigate the difference in tou...

  3. Case study: Beauty and the Beast 3D: benefits of 3D viewing for 2D to 3D conversion

    Science.gov (United States)

    Handy Turner, Tara

    2010-02-01

    From the earliest stages of the Beauty and the Beast 3D conversion project, the advantages of accurate desk-side 3D viewing was evident. While designing and testing the 2D to 3D conversion process, the engineering team at Walt Disney Animation Studios proposed a 3D viewing configuration that not only allowed artists to "compose" stereoscopic 3D but also improved efficiency by allowing artists to instantly detect which image features were essential to the stereoscopic appeal of a shot and which features had minimal or even negative impact. At a time when few commercial 3D monitors were available and few software packages provided 3D desk-side output, the team designed their own prototype devices and collaborated with vendors to create a "3D composing" workstation. This paper outlines the display technologies explored, final choices made for Beauty and the Beast 3D, wish-lists for future development and a few rules of thumb for composing compelling 2D to 3D conversions.

  4. Web-based interactive visualization of 3D video mosaics using X3D standard

    Institute of Scientific and Technical Information of China (English)

    CHON Jaechoon; LEE Yang-Won; SHIBASAKI Ryosuke

    2006-01-01

    We present a method of 3D image mosaicing for real 3D representation of roadside buildings, and implement a Web-based interactive visualization environment for the 3D video mosaics created by 3D image mosaicing. The 3D image mosaicing technique developed in our previous work is a very powerful method for creating textured 3D-GIS data without excessive data processing like the laser or stereo system. For the Web-based open access to the 3D video mosaics, we build an interactive visualization environment using X3D, the emerging standard of Web 3D. We conduct the data preprocessing for 3D video mosaics and the X3D modeling for textured 3D data. The data preprocessing includes the conversion of each frame of 3D video mosaics into concatenated image files that can be hyperlinked on the Web. The X3D modeling handles the representation of concatenated images using necessary X3D nodes. By employing X3D as the data format for 3D image mosaics, the real 3D representation of roadside buildings is extended to the Web and mobile service systems.

  5. DNA, dichotomic classes and frame synchronization: a quasi-crystal framework.

    Science.gov (United States)

    Giannerini, Simone; Gonzalez, Diego Luis; Rosa, Rodolfo

    2012-06-28

    In this article, we show how a new mathematical model of the genetic code can be exploited for investigating the almost periodic properties of DNA and mRNA protein-coding sequences. We present the main mathematical features of the model and highlight its connections with both number theory and group theory. The group theoretic framework presents interesting analogies with the theory of crystals. Moreover, we exploit the information provided by dichotomic classes, binary variables naturally derived from the mathematical model, in order to build statistical classifiers for retrieving and predicting the normal reading frame used by the ribosome in protein synthesis. The results show that coding sequences possess a local informational structure that can be related to frame synchronization processes. The information for retrieving the normal reading frame, which implies the existence of short-range correlations and almost periodic structures related to the organization of codons, offers an interesting analogy with the properties of quasi-crystals. From a theoretical point of view, our results might contribute to clarifying the relation between biological information and shape in nucleic acids and proteins. Also, from the point of view of applications, we present new promising tools for designing efficient algorithms for frame synchronization, which plays a crucial role in faithful synthesis of proteins.

  6. User-centered 3D geovisualisation

    DEFF Research Database (Denmark)

    Nielsen, Anette Hougaard

    2004-01-01

    3D Geovisualisation is a multidisciplinary science mainly utilizing geographically related data, developing software systems for 3D visualisation and producing relevant models. In this paper the connection between geoinformation stored as 3D objects and the end user is of special interest....... In a broader perspective, the overall aim is to develop a language in 3D Geovisualisation gained through usability projects and the development of a theoretical background. A conceptual level of user-centered 3D Geovisualisation is introduced by applying a categorisation originating from Virtual Reality....... The conceptual level is used to structure and organise user-centered 3D Geovisualisation into four categories: representation, rendering, interface and interaction. The categories reflect a process of development of 3D Geovisualisation where objects can be represented verisimilar to the real world...

  7. 3D laptop for defense applications

    Science.gov (United States)

    Edmondson, Richard; Chenault, David

    2012-06-01

    Polaris Sensor Technologies has developed numerous 3D display systems using a US Army patented approach. These displays have been developed as prototypes for handheld controllers for robotic systems and closed hatch driving, and as part of a TALON robot upgrade for 3D vision, providing depth perception for the operator for improved manipulation and hazard avoidance. In this paper we discuss the prototype rugged 3D laptop computer and its applications to defense missions. The prototype 3D laptop combines full temporal and spatial resolution display with the rugged Amrel laptop computer. The display is viewed through protective passive polarized eyewear, and allows combined 2D and 3D content. Uses include robot tele-operation with live 3D video or synthetically rendered scenery, mission planning and rehearsal, enhanced 3D data interpretation, and simulation.

  8. 3D液晶显示模组不均匀分区背光扫描及其设计方法%Shutter glass type of 3D liquid crystal display module non-uniform partition scanning backlight and its design method based on

    Institute of Scientific and Technical Information of China (English)

    吴琦

    2013-01-01

    With the rapid development of liquid crystal display technology, 3D display gradually sought after the market and consumers. In the 3D LCD TV, there is a kind of shutter type 3D display technology. This technique also shot the same object's left and right eyes two pictures by two cameras at certain intervals, and synthetic treatment, on the display screen through time-sharing display out, then match the shutter glasses with the same time frequency, the same object images to the left and the right eyes respectively to watch camera captured. As the two pictures there is disparity is different, the human eye can feel the stereo image, realize 3D display effect. In order to achieve better 3D display effect, generally control the scanning backlight system through mode of backlight.%随着液晶显示技术的快速发展,3D液晶显示逐渐受到市场和消费者的追捧。在3D液晶电视中,有一类快门式3D显示技术。这种技术通过一定间隔的两台摄像机同时拍摄同一个物体的左右眼两幅画面,然后合成处理后,在显示屏上通过分时显示的方式显示出来,然后搭配与分时频率相同的快门式眼镜,使人的左右眼分别观看到摄像机拍摄到的同一物体画面。由于两幅画面存在视差的不同,人眼即可感受到了立体的影像,实现3D效果显示。为了实现更好的3D显示效果,一般通过扫描背光的方式来对背光系统进行控制。

  9. 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.

    Science.gov (United States)

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

    2013-02-01

    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.

  10. Crystal structure of the DNA-binding domain of Myelin-gene Regulatory Factor.

    Science.gov (United States)

    Zhen, Xiangkai; Li, Bowen; Hu, Fen; Yan, Shufeng; Meloni, Gabriele; Li, Huiliang; Shi, Ning

    2017-06-16

    Myelin-gene Regulatory Factor (MyRF) is one of the master transcription factors controlling myelin formation and development in oligodendrocytes which is crucial for the powerful brain functions. The N-terminal of MyRF, which contains a proline-rich region and a DNA binding domain (DBD), is auto-cleaved from the ER membrane, and then enters the nucleus to participate in transcription regulation of the myelin genes. Here we report the crystal structure of MyRF DBD. It shows an Ig-fold like architecture which consists of two antiparallel β-sheets with 7 main strands, packing against each other, forming a β-sandwich. Compared to its homolog, Ndt80, MyRF has a smaller and less complex DBD lacking the helices and the big loops outside the core. Structural alignment reveals that MyRF DBD possess less interaction sites with DNA than Ndt80 and may bind only at the major groove of DNA. Moreover, the structure reveals a trimeric assembly, agreeing with the previous report that MyRF DBD functions as a trimer. The mutant that we designed based on the structure disturbed trimer formation, but didn't affect the auto-cleavage reaction. It demonstrates that the activation of self-cleavage reaction of MyRF is independent of the presence of its N-terminal DBD homotrimer. The structure reported here will help to understand the molecular mechanism underlying the important roles of MyRF in myelin formation and development.

  11. FROM 3D MODEL DATA TO SEMANTICS

    Directory of Open Access Journals (Sweden)

    My Abdellah Kassimi

    2012-01-01

    Full Text Available The semantic-based 3D models retrieval systems have become necessary since the increase of 3D modelsdatabases. In this paper, we propose a new method for the mapping problem between 3D model data andsemantic data involved in semantic based retrieval for 3D models given by polygonal meshes. First, wefocused on extracting invariant descriptors from the 3D models and analyzing them to efficient semanticannotation and to improve the retrieval accuracy. Selected shape descriptors provide a set of termscommonly used to describe visually a set of objects using linguistic terms and are used as semanticconcept to label 3D model. Second, spatial relationship representing directional, topological anddistance relationships are used to derive other high-level semantic features and to avoid the problem ofautomatic 3D model annotation. Based on the resulting semantic annotation and spatial concepts, anontology for 3D model retrieval is constructed and other concepts can be inferred. This ontology is usedto find similar 3D models for a given query model. We adopted the query by semantic example approach,in which the annotation is performed mostly automatically. The proposed method is implemented in our3D search engine (SB3DMR, tested using the Princeton Shape Benchmark Database.

  12. RT3D tutorials for GMS users

    Energy Technology Data Exchange (ETDEWEB)

    Clement, T.P. [Pacific Northwest National Lab., Richland, WA (United States); Jones, N.L. [Brigham Young Univ., Provo, UT (United States)

    1998-02-01

    RT3D (Reactive Transport in 3-Dimensions) is a computer code that solves coupled partial differential equations that describe reactive-flow and transport of multiple mobile and/or immobile species in a three dimensional saturated porous media. RT3D was developed from the single-species transport code, MT3D (DoD-1.5, 1997 version). As with MT3D, RT3D also uses the USGS groundwater flow model MODFLOW for computing spatial and temporal variations in groundwater head distribution. This report presents a set of tutorial problems that are designed to illustrate how RT3D simulations can be performed within the Department of Defense Groundwater Modeling System (GMS). GMS serves as a pre- and post-processing interface for RT3D. GMS can be used to define all the input files needed by RT3D code, and later the code can be launched from within GMS and run as a separate application. Once the RT3D simulation is completed, the solution can be imported to GMS for graphical post-processing. RT3D v1.0 supports several reaction packages that can be used for simulating different types of reactive contaminants. Each of the tutorials, described below, provides training on a different RT3D reaction package. Each reaction package has different input requirements, and the tutorials are designed to describe these differences. Furthermore, the tutorials illustrate the various options available in GMS for graphical post-processing of RT3D results. Users are strongly encouraged to complete the tutorials before attempting to use RT3D and GMS on a routine basis.

  13. 3D change detection - Approaches and applications

    Science.gov (United States)

    Qin, Rongjun; Tian, Jiaojiao; Reinartz, Peter

    2016-12-01

    Due to the unprecedented technology development of sensors, platforms and algorithms for 3D data acquisition and generation, 3D spaceborne, airborne and close-range data, in the form of image based, Light Detection and Ranging (LiDAR) based point clouds, Digital Elevation Models (DEM) and 3D city models, become more accessible than ever before. Change detection (CD) or time-series data analysis in 3D has gained great attention due to its capability of providing volumetric dynamics to facilitate more applications and provide more accurate results. The state-of-the-art CD reviews aim to provide a comprehensive synthesis and to simplify the taxonomy of the traditional remote sensing CD techniques, which mainly sit within the boundary of 2D image/spectrum analysis, largely ignoring the particularities of 3D aspects of the data. The inclusion of 3D data for change detection (termed 3D CD), not only provides a source with different modality for analysis, but also transcends the border of traditional top-view 2D pixel/object-based analysis to highly detailed, oblique view or voxel-based geometric analysis. This paper reviews the recent developments and applications of 3D CD using remote sensing and close-range data, in support of both academia and industry researchers who seek for solutions in detecting and analyzing 3D dynamics of various objects of interest. We first describe the general considerations of 3D CD problems in different processing stages and identify CD types based on the information used, being the geometric comparison and geometric-spectral analysis. We then summarize relevant works and practices in urban, environment, ecology and civil applications, etc. Given the broad spectrum of applications and different types of 3D data, we discuss important issues in 3D CD methods. Finally, we present concluding remarks in algorithmic aspects of 3D CD.

  14. Analysis of temporal stability of autostereoscopic 3D displays

    Science.gov (United States)

    Rubiño, Manuel; Salas, Carlos; Pozo, Antonio M.; Castro, J. J.; Pérez-Ocón, Francisco

    2013-11-01

    An analysis has been made of the stability of the images generated by electronic autostereoscopic 3D displays, studying the time course of the photometric and colorimetric parameters. The measurements were made on the basis of the procedure recommended in the European guideline EN 61747-6 for the characterization of electronic liquid-crystal displays (LCD). The study uses 3 different models of autostereoscopic 3D displays of different sizes and numbers of pixels, taking the measurements with a spectroradiometer (model PR-670 SpectraScan of PhotoResearch). For each of the displays, the time course is shown for the tristimulus values and the chromaticity coordinates in the XYZ CIE 1931 system and values from the time periods required to reach stable values of these parameters are presented. For the analysis of how the procedure recommended in the guideline EN 61747-6 for 2D displays influenced the results, and for the adaption of the procedure to the characterization of 3D displays, the experimental conditions of the standard procedure were varied, making the stability analysis in the two ocular channels (RE and LE) of the 3D mode and comparing the results with those corresponding to the 2D. The results of our study show that the stabilization time of a autostereoscopic 3D display with parallax barrier technology depends on the tristimulus value analysed (X, Y, Z) as well as on the presentation mode (2D, 3D); furthermore, it was found that whether the 3D mode is used depends on the ocular channel evaluated (RE, LE).

  15. 3D printing of natural organic materials by photochemistry

    Science.gov (United States)

    Da Silva Gonçalves, Joyce Laura; Valandro, Silvano Rodrigo; Wu, Hsiu-Fen; Lee, Yi-Hsiung; Mettra, Bastien; Monnereau, Cyrille; Schmitt Cavalheiro, Carla Cristina; Pawlicka, Agnieszka; Focsan, Monica; Lin, Chih-Lang; Baldeck, Patrice L.

    2016-03-01

    In previous works, we have used two-photon induced photochemistry to fabricate 3D microstructures based on proteins, anti-bodies, and enzymes for different types of bio-applications. Among them, we can cite collagen lines to guide the movement of living cells, peptide modified GFP biosensing pads to detect Gram positive bacteria, anti-body pads to determine the type of red blood cells, and trypsin columns in a microfluidic channel to obtain a real time biochemical micro-reactor. In this paper, we report for the first time on two-photon 3D microfabrication of DNA material. We also present our preliminary results on using a commercial 3D printer based on a video projector to polymerize slicing layers of gelatine-objects.

  16. 3D Systems” ‘Stuck in the Middle’ of the 3D Printer Boom?

    NARCIS (Netherlands)

    A. Hoffmann (Alan)

    2014-01-01

    textabstract3D Systems, the pioneer of 3D printing, predicted a future where "kids from 8 to 80" could design and print their ideas at home. By 2013, 9 years after the creation of the first working 3D printer, there were more than 30 major 3D printing companies competing for market share. 3DS and it

  17. 3D-Barolo: 3D fitting tool for the kinematics of galaxies

    NARCIS (Netherlands)

    Di Teodoro, E. M.; Fraternali, F.

    3D-Barolo (3D-Based Analysis of Rotating Object via Line Observations) or BBarolo is a tool for fitting 3D tilted-ring models to emission-line datacubes. BBarolo works with 3D FITS files, i.e. image arrays with two spatial and one spectral dimensions. BBarolo recovers the true rotation curve and

  18. 3D Systems” ‘Stuck in the Middle’ of the 3D Printer Boom?

    NARCIS (Netherlands)

    A. Hoffmann (Alan)

    2014-01-01

    textabstract3D Systems, the pioneer of 3D printing, predicted a future where "kids from 8 to 80" could design and print their ideas at home. By 2013, 9 years after the creation of the first working 3D printer, there were more than 30 major 3D printing companies competing for market share. 3DS and

  19. Stability Criteria of 3D Inviscid Shears

    CERN Document Server

    Li, Y Charles

    2009-01-01

    The classical plane Couette flow, plane Poiseuille flow, and pipe Poiseuille flow share some universal 3D steady coherent structure in the form of "streak-roll-critical layer". As the Reynolds number approaches infinity, the steady coherent structure approaches a 3D limiting shear of the form ($U(y,z), 0, 0$) in velocity variables. All such 3D shears are steady states of the 3D Euler equations. This raises the importance of investigating the stability of such inviscid 3D shears in contrast to the classical Rayleigh theory of inviscid 2D shears. Several general criteria of stability for such inviscid 3D shears are derived. In the Appendix, an argument is given to show that a 2D limiting shear can only be the classical laminar shear.

  20. 3D-tulostus : case Printrbot

    OpenAIRE

    Arvekari, Lassi

    2013-01-01

    Opinnäytetyön tavoitteena on selvittää 3D-tulostustekniikan perusteita ja 3D-tulostuksen nykytilannetta. 3D-tulostukseen sopivien mallien luomista tutkitaan ja mallin tekemiseen on etsitty toimivia ohjesääntöjä. Tärkeä osa työtä on tutkia mitä vaiheita 3D-tulostimen hankinnassa kotikäyttöön tulee vastaan. Käytännön kokeita varten opinnäytetyössä on case Printrbot, jossa on tutustuttu edulliseen 3D-tulostuslaitteeseen kokoonpanosta lähtien. Työn kuluessa selvisi että edulliset 3D-tulos...

  1. ERP system for 3D printing industry

    Directory of Open Access Journals (Sweden)

    Deaky Bogdan

    2017-01-01

    Full Text Available GOCREATE is an original cloud-based production management and optimization service which helps 3D printing service providers to use their resources better. The proposed Enterprise Resource Planning system can significantly increase income through improved productivity. With GOCREATE, the 3D printing service providers get a much higher production efficiency at a much lower licensing cost, to increase their competitiveness in the fast growing 3D printing market.

  2. Reconhecimento de faces 3D com Kinect

    OpenAIRE

    Cardia Neto, João Baptista [UNESP

    2014-01-01

    For person identification, facil recognition has several advantages over other biometric traits due mostly to its high universelly, collectability, and acceptability. When dealing with 2D face images several problems arise related to pose, illumination, and facial expressions. To increase the performance of facial recognition, 3D mehtods have been proposed and developedm since working with 3D objects allow us to handle better the aforementioned problems. With 3D object, it is possible to rota...

  3. Ultrasonic Sensor Based 3D Mapping & Localization

    Directory of Open Access Journals (Sweden)

    Shadman Fahim Ahmad

    2016-04-01

    Full Text Available This article provides a basic level introduction to 3D mapping using sonar sensors and localization. It describes the methods used to construct a low-cost autonomous robot along with the hardware and software used as well as an insight to the background of autonomous robotic 3D mapping and localization. We have also given an overview to what the future prospects of the robot may hold in 3D based mapping.

  4. Ekologinen 3D-tulostettava asuste

    OpenAIRE

    Paulasaari, Laura

    2014-01-01

    Tämän opinnäytetyön aiheena oli ekologisuus 3D-tulostuksessa ja sen hyödynnettävyys erityisesti asustesuunnittelussa. Työn tarkoituksena oli selvittää, kuinka 3D-tulostusta voi tehdä ekologisemmin ja mitä vaihtoehtoja kuluttajalle tällä hetkellä on. Työ tehtiin Young skills –osuuskunnalle. 3D-tulostuksella on mahdollisuus antaa todella paljon tulevaisuuden tuotantomenetelmille ja se vapauttaa tuotteiden muotoilua täysin uudella tavalla. 3D-tulostuksen avulla voidaan keskittyä enemmän esim...

  5. Topology Dictionary for 3D Video Understanding

    OpenAIRE

    2012-01-01

    This paper presents a novel approach that achieves 3D video understanding. 3D video consists of a stream of 3D models of subjects in motion. The acquisition of long sequences requires large storage space (2 GB for 1 min). Moreover, it is tedious to browse data sets and extract meaningful information. We propose the topology dictionary to encode and describe 3D video content. The model consists of a topology-based shape descriptor dictionary which can be generated from either extracted pattern...

  6. Perspectives on Materials Science in 3D

    DEFF Research Database (Denmark)

    Juul Jensen, Dorte

    2016-01-01

    Materials characterization in 3D has opened a new era in materials science, which is discussed in this paper. The original motivations and visions behind the development of one of the new 3D techniques, namely the three dimensional x-ray diffraction (3DXRD) method, are presented and the route...... to its implementation is described. The present status of materials science in 3D is illustrated by examples related to recrystallization. Finally, challenges and suggestions for the future success for 3D Materials Science relating to hardware evolution, data analysis, data exchange and modeling...

  7. Virtual Realization using 3D Password

    Directory of Open Access Journals (Sweden)

    A.B.Gadicha

    2012-03-01

    Full Text Available Current authentication systems suffer from many weaknesses. Textual passwords are commonly used; however, users do not follow their requirements. Users tend to choose meaningful words from dictionaries, which make textual passwords easy to break and vulnerable to dictionary or brute force attacks. Many available graphical passwords have a password space that is less than or equal to the textual password space. Smart cards or tokens can be stolen. Many biometric authentications have been proposed; however, users tend to resist using biometrics because of their intrusiveness and the effect on their privacy. Moreover, biometrics cannot be revoked. In this paper, we present and evaluate our contribution, i.e., the 3D password. The 3D password is a multifactor authentication scheme. To be authenticated, we present a 3D virtual environment where the user navigates and interacts with various objects. The sequence of actions and interactions toward the objects inside the 3D environment constructs the user’s 3D password. The 3D password can combine most existing authentication schemes such as textual passwords, graphical passwords, and various types of biometrics into a 3D virtual environment. The design of the 3D virtual environment and the type of objects selected determine the 3D password key space.

  8. Dimensional accuracy of 3D printed vertebra

    Science.gov (United States)

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

    2014-03-01

    3D printer applications in the biomedical sciences and medical imaging are expanding and will have an increasing impact on the practice of medicine. Orthopedic and reconstructive surgery has been an obvious area for development of 3D printer applications as the segmentation of bony anatomy to generate printable models is relatively straightforward. There are important issues that should be addressed when using 3D printed models for applications that may affect patient care; in particular the dimensional accuracy of the printed parts needs to be high to avoid poor decisions being made prior to surgery or therapeutic procedures. In this work, the dimensional accuracy of 3D printed vertebral bodies derived from CT data for a cadaver spine is compared with direct measurements on the ex-vivo vertebra and with measurements made on the 3D rendered vertebra using commercial 3D image processing software. The vertebra was printed on a consumer grade 3D printer using an additive print process using PLA (polylactic acid) filament. Measurements were made for 15 different anatomic features of the vertebral body, including vertebral body height, endplate width and depth, pedicle height and width, and spinal canal width and depth, among others. It is shown that for the segmentation and printing process used, the results of measurements made on the 3D printed vertebral body are substantially the same as those produced by direct measurement on the vertebra and measurements made on the 3D rendered vertebra.

  9. Illustrating Mathematics using 3D Printers

    OpenAIRE

    Knill, Oliver; Slavkovsky, Elizabeth

    2013-01-01

    3D printing technology can help to visualize proofs in mathematics. In this document we aim to illustrate how 3D printing can help to visualize concepts and mathematical proofs. As already known to educators in ancient Greece, models allow to bring mathematics closer to the public. The new 3D printing technology makes the realization of such tools more accessible than ever. This is an updated version of a paper included in book Low-Cost 3D Printing for science, education and Sustainable Devel...

  10. Calibration for 3D Structured Light Measurement

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A calibration procedure was developed for three-dimensional(3D) binocular structured light measurement systems. In virtue of a specially designed pattern, matching points in stereo images are extracted. And then sufficient 3D space points are obtained through pairs of images with the intrinsic and extrinsic parameters of each camera estimated prior and consequently some lights are calibrated by means of multi point fitting. Finally, a mathematical model is applied to interpolate and approximate all dynamic scanning lights based on geometry. The process of calibration method is successfully used in the binocular 3D measurement system based on structured lights and the 3D reconstruction results are satisfying.

  11. Getting started in 3D with Maya

    CERN Document Server

    Watkins, Adam

    2012-01-01

    Deliver professional-level 3D content in no time with this comprehensive guide to 3D animation with Maya. With over 12 years of training experience, plus several award winning students under his belt, author Adam Watkins is the ideal mentor to get you up to speed with 3D in Maya. Using a structured and pragmatic approach Getting Started in 3D with Maya begins with basic theory of fundamental techniques, then builds on this knowledge using practical examples and projects to put your new skills to the test. Prepared so that you can learn in an organic fashion, each chapter builds on the know

  12. FastScript3D - A Companion to Java 3D

    Science.gov (United States)

    Koenig, Patti

    2005-01-01

    FastScript3D is a computer program, written in the Java 3D(TM) programming language, that establishes an alternative language that helps users who lack expertise in Java 3D to use Java 3D for constructing three-dimensional (3D)-appearing graphics. The FastScript3D language provides a set of simple, intuitive, one-line text-string commands for creating, controlling, and animating 3D models. The first word in a string is the name of a command; the rest of the string contains the data arguments for the command. The commands can also be used as an aid to learning Java 3D. Developers can extend the language by adding custom text-string commands. The commands can define new 3D objects or load representations of 3D objects from files in formats compatible with such other software systems as X3D. The text strings can be easily integrated into other languages. FastScript3D facilitates communication between scripting languages [which enable programming of hyper-text markup language (HTML) documents to interact with users] and Java 3D. The FastScript3D language can be extended and customized on both the scripting side and the Java 3D side.

  13. Directing Matter: Toward Atomic-Scale 3D Nanofabrication.

    Science.gov (United States)

    Jesse, Stephen; Borisevich, Albina Y; Fowlkes, Jason D; Lupini, Andrew R; Rack, Philip D; Unocic, Raymond R; Sumpter, Bobby G; Kalinin, Sergei V; Belianinov, Alex; Ovchinnikova, Olga S

    2016-06-28

    Enabling memristive, neuromorphic, and quantum-based computing as well as efficient mainstream energy storage and conversion technologies requires the next generation of materials customized at the atomic scale. This requires full control of atomic arrangement and bonding in three dimensions. The last two decades witnessed substantial industrial, academic, and government research efforts directed toward this goal through various lithographies and scanning-probe-based methods. These technologies emphasize 2D surface structures, with some limited 3D capability. Recently, a range of focused electron- and ion-based methods have demonstrated compelling alternative pathways to achieving atomically precise manufacturing of 3D structures in solids, liquids, and at interfaces. Electron and ion microscopies offer a platform that can simultaneously observe dynamic and static structures at the nano- and atomic scales and also induce structural rearrangements and chemical transformation. The addition of predictive modeling or rapid image analytics and feedback enables guiding these in a controlled manner. Here, we review the recent results that used focused electron and ion beams to create free-standing nanoscale 3D structures, radiolysis, and the fabrication potential with liquid precursors, epitaxial crystallization of amorphous oxides with atomic layer precision, as well as visualization and control of individual dopant motion within a 3D crystal lattice. These works lay the foundation for approaches to directing nanoscale level architectures and offer a potential roadmap to full 3D atomic control in materials. In this paper, we lay out the gaps that currently constrain the processing range of these platforms, reflect on indirect requirements, such as the integration of large-scale data analysis with theory, and discuss future prospects of these technologies.

  14. Crystal Structure of DNA-PKcs Reveals a Large Open-Ring Cradle Comprised of HEAT Repeats

    Science.gov (United States)

    Sibanda, Bancinyane L.; Chirgadze, Dimitri Y.; Blundell, Tom L.

    2009-01-01

    Broken chromosomes arising from DNA double strand breaks result from endogenous events such as the production of reactive oxygen species during cellular metabolism, as well as from exogenous sources such as ionizing radiation1, 2, 3. Left unrepaired or incorrectly repaired they can lead to genomic changes that may result in cell death or cancer. DNA-dependent protein kinase (DNA-PK), a holo-enzyme that comprises DNA-dependent protein kinase catalytic subunit (DNA-PKcs)4, 5 and the heterodimer Ku70/Ku80, plays a major role in non-homologous end joining (NHEJ), the main pathway in mammals used to repair double strand breaks6, 7, 8. DNA-PKcs is a serine/threonine protein kinase comprising a single polypeptide chain of 4128 amino acids and belonging to the phosphotidyl inositol 3-kinase (PI3-K)- related protein family9. DNA-PKcs is involved in the sensing and transmission of DNA damage signals to proteins such as p53, setting off events that lead to cell cycle arrest10, 11. It phosphorylates a wide range of substrates in vitro, including Ku70/Ku80, which is translocated along DNA12. Here we present the crystal structure of human DNA-PKcs at 6.6Å resolution, in which the overall fold is for the first time clearly visible. The many α-helical HEAT repeats (helix-turn-helix motifs) facilitate bending and allow the polypeptide chain to fold into a hollow circular structure. The C-terminal kinase domain is located on top of this structure and a small HEAT repeat domain that likely binds DNA is inside. The structure provides a flexible cradle to promote DNA double-strand-break repair. PMID:20023628

  15. An aerial 3D printing test mission

    Science.gov (United States)

    Hirsch, Michael; McGuire, Thomas; Parsons, Michael; Leake, Skye; Straub, Jeremy

    2016-05-01

    This paper provides an overview of an aerial 3D printing technology, its development and its testing. This technology is potentially useful in its own right. In addition, this work advances the development of a related in-space 3D printing technology. A series of aerial 3D printing test missions, used to test the aerial printing technology, are discussed. Through completing these test missions, the design for an in-space 3D printer may be advanced. The current design for the in-space 3D printer involves focusing thermal energy to heat an extrusion head and allow for the extrusion of molten print material. Plastics can be used as well as composites including metal, allowing for the extrusion of conductive material. A variety of experiments will be used to test this initial 3D printer design. High altitude balloons will be used to test the effects of microgravity on 3D printing, as well as parabolic flight tests. Zero pressure balloons can be used to test the effect of long 3D printing missions subjected to low temperatures. Vacuum chambers will be used to test 3D printing in a vacuum environment. The results will be used to adapt a current prototype of an in-space 3D printer. Then, a small scale prototype can be sent into low-Earth orbit as a 3-U cube satellite. With the ability to 3D print in space demonstrated, future missions can launch production hardware through which the sustainability and durability of structures in space will be greatly improved.

  16. Synthesis, crystal structure and electrochemical and DNA binding studies of oxygen bridged-copper(II) carboxylate

    Science.gov (United States)

    Iqbal, Muhammad; Ali, Saqib; Tahir, Muhammad Nawaz; Muhammad, Niaz; Shah, Naseer Ali; Sohail, Manzar; Pandarinathan, Vedapriya

    2015-08-01

    A new binuclear O-bridged Cu(II) complex with 4-chlorophenyl acetate and 2,2‧-bipyridine has been synthesized and characterized using FT-IR, powder and single crystal XRD and electrochemical solution studies. The results revealed that the two penta-coordinated Cu(II) centers are linked by two carboxylate ligands in end-on bonding fashion. The coordination geometry is slightly distorted square pyramidal (SP) with bridging oxygen atoms occupying the apical position and other ligands lying in the equatorial plane. The striking difference in Cu-O bond distance of the bridging oxygen atom in the complex may be responsible for the SP geometry of Cu(II) ion. The complex gave rise to metal centered irreversible electro-activity where one electron Cu(II)/Cu(III) oxidation process and a single step two electron Cu(II)/Cu(0) reduction process was observed. The redox processes were found predominantly adsorption controlled. The values of diffusion coefficient and heterogeneous rate constant for oxidation process were 6.98 × 10-7 cm2 s-1 and 4.60 × 10-5 cm s-1 while the corresponding values for reduction were 5.30 × 10-8 cm2 s-1 and 5.41 × 10-6 cm s-1, respectively. The formal potential and charge transfer coefficient were also calculated. The DNA-binding ability was explored through cyclic voltammetry and UV-Visible spectroscopy. Diminution in the value of Do for oxidation indicated the binding of the complex with DNA corresponding to Kb = 8.58 × 104 M-1. UV-Visible spectroscopy yielded ε = 49 L mol-1 cm-1 and Kb = 2.96 × 104 M-1. The data of both techniques support each other. The self-induced redox activation of the complex, as indicated by cyclic voltammetry heralds its potential applications in redox catalysis and anticancer activity.

  17. Synthesis and structure of 3D heterometallic (3d-4f) coordination polymers: {[Ln_2Cu(pydc)_4(H_2O)_6]·2H_2O}_n

    Institute of Scientific and Technical Information of China (English)

    MA JingXin; HUANG XiaoFeng; WEI RuiPing; LIU WeiSheng

    2009-01-01

    Two new 3D heterometallic (3d-4f) coordination polymers {[Ln_2Cu(pydc)_4(H_2O)_6]·2H_2O}_n [Ln = Eu (1) and Gd (2)] have been synthesized by hydrothermal reactions and characterized by elemental analysis, X-ray single-crystal analyses, and IR spectroscopy. X-ray crystal structure analyses show that 1 and 2 possess 3D networks and strong intramolecular hydrogen bonding interactions which was confirmed by thermogravimetric (TG) analysis.

  18. The 3D-city model

    DEFF Research Database (Denmark)

    Holmgren, Steen; Rüdiger, Bjarne; Tournay, Bruno

    2001-01-01

    We have worked with the construction and use of 3D city models for about ten years. This work has given us valuable experience concerning model methodology. In addition to this collection of knowledge, our perception of the concept of city models has changed radically. In order to explain...... of 3D city models....

  19. 3D, or Not to Be?

    Science.gov (United States)

    Norbury, Keith

    2012-01-01

    It may be too soon for students to be showing up for class with popcorn and gummy bears, but technology similar to that behind the 3D blockbuster movie "Avatar" is slowly finding its way into college classrooms. 3D classroom projectors are taking students on fantastic voyages inside the human body, to the ruins of ancient Greece--even to faraway…

  20. User-centered 3D geovisualisation

    DEFF Research Database (Denmark)

    Nielsen, Anette Hougaard

    2004-01-01

    . In a broader perspective, the overall aim is to develop a language in 3D Geovisualisation gained through usability projects and the development of a theoretical background. A conceptual level of user-centered 3D Geovisualisation is introduced by applying a categorisation originating from Virtual Reality...

  1. 3D Printing. What's the Harm?

    Science.gov (United States)

    Love, Tyler S.; Roy, Ken

    2016-01-01

    Health concerns from 3D printing were first documented by Stephens, Azimi, Orch, and Ramos (2013), who found that commercially available 3D printers were producing hazardous levels of ultrafine particles (UFPs) and volatile organic compounds (VOCs) when plastic materials were melted through the extruder. UFPs are particles less than 100 nanometers…

  2. 3D Printing of Molecular Models

    Science.gov (United States)

    Gardner, Adam; Olson, Arthur

    2016-01-01

    Physical molecular models have played a valuable role in our understanding of the invisible nano-scale world. We discuss 3D printing and its use in producing models of the molecules of life. Complex biomolecular models, produced from 3D printed parts, can demonstrate characteristics of molecular structure and function, such as viral self-assembly,…

  3. 3D printing of functional structures

    NARCIS (Netherlands)

    Krijnen, Gijsbertus J.M.

    2016-01-01

    The technology colloquial known as ‘3D printing’ has developed in such diversity in printing technologies and application fields that meanwhile it seems anything is possible. However, clearly the ideal 3D Printer, with high resolution, multi-material capability, fast printing, etc. is yet to be deve

  4. 3D printing of functional structures

    NARCIS (Netherlands)

    Krijnen, Gijsbertus J.M.

    The technology colloquial known as ‘3D printing’ has developed in such diversity in printing technologies and application fields that meanwhile it seems anything is possible. However, clearly the ideal 3D Printer, with high resolution, multi-material capability, fast printing, etc. is yet to be

  5. 3D Printed Block Copolymer Nanostructures

    Science.gov (United States)

    Scalfani, Vincent F.; Turner, C. Heath; Rupar, Paul A.; Jenkins, Alexander H.; Bara, Jason E.

    2015-01-01

    The emergence of 3D printing has dramatically advanced the availability of tangible molecular and extended solid models. Interestingly, there are few nanostructure models available both commercially and through other do-it-yourself approaches such as 3D printing. This is unfortunate given the importance of nanotechnology in science today. In this…

  6. 3D elastic control for mobile devices.

    Science.gov (United States)

    Hachet, Martin; Pouderoux, Joachim; Guitton, Pascal

    2008-01-01

    To increase the input space of mobile devices, the authors developed a proof-of-concept 3D elastic controller that easily adapts to mobile devices. This embedded device improves the completion of high-level interaction tasks such as visualization of large documents and navigation in 3D environments. It also opens new directions for tomorrow's mobile applications.

  7. Parametrizable cameras for 3D computational steering

    NARCIS (Netherlands)

    Mulder, J.D.; Wijk, J.J. van

    1997-01-01

    We present a method for the definition of multiple views in 3D interfaces for computational steering. The method uses the concept of a point-based parametrizable camera object. This concept enables a user to create and configure multiple views on his custom 3D interface in an intuitive graphical man

  8. 3D printing of functional structures

    NARCIS (Netherlands)

    Krijnen, G.J.M.

    2016-01-01

    The technology colloquial known as ‘3D printing’ has developed in such diversity in printing technologies and application fields that meanwhile it seems anything is possible. However, clearly the ideal 3D Printer, with high resolution, multi-material capability, fast printing, etc. is yet to be deve

  9. 3D Printed Block Copolymer Nanostructures

    Science.gov (United States)

    Scalfani, Vincent F.; Turner, C. Heath; Rupar, Paul A.; Jenkins, Alexander H.; Bara, Jason E.

    2015-01-01

    The emergence of 3D printing has dramatically advanced the availability of tangible molecular and extended solid models. Interestingly, there are few nanostructure models available both commercially and through other do-it-yourself approaches such as 3D printing. This is unfortunate given the importance of nanotechnology in science today. In this…

  10. 3D Printing of Molecular Models

    Science.gov (United States)

    Gardner, Adam; Olson, Arthur

    2016-01-01

    Physical molecular models have played a valuable role in our understanding of the invisible nano-scale world. We discuss 3D printing and its use in producing models of the molecules of life. Complex biomolecular models, produced from 3D printed parts, can demonstrate characteristics of molecular structure and function, such as viral self-assembly,…

  11. 3D Printing. What's the Harm?

    Science.gov (United States)

    Love, Tyler S.; Roy, Ken

    2016-01-01

    Health concerns from 3D printing were first documented by Stephens, Azimi, Orch, and Ramos (2013), who found that commercially available 3D printers were producing hazardous levels of ultrafine particles (UFPs) and volatile organic compounds (VOCs) when plastic materials were melted through the extruder. UFPs are particles less than 100 nanometers…

  12. 3D background aerodynamics using CFD

    DEFF Research Database (Denmark)

    Sørensen, Niels N.

    2002-01-01

    3D rotor computations for the Greek Geovilogiki (GEO) 44 meter rotor equipped with 19 meters blades are performed. The lift and drag polars are extracted at five spanvise locations r/R= (.37, .55, .71, .82, .93) based on identification of stagnationpoints between 2D and 3D computations. The inner...

  13. Topology dictionary for 3D video understanding.

    Science.gov (United States)

    Tung, Tony; Matsuyama, Takashi

    2012-08-01

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

  14. Integration of real-time 3D image acquisition and multiview 3D display

    Science.gov (United States)

    Zhang, Zhaoxing; Geng, Zheng; Li, Tuotuo; Li, Wei; Wang, Jingyi; Liu, Yongchun

    2014-03-01

    Seamless integration of 3D acquisition and 3D display systems offers enhanced experience in 3D visualization of the real world objects or scenes. The vivid representation of captured 3D objects displayed on a glasses-free 3D display screen could bring the realistic viewing experience to viewers as if they are viewing real-world scene. Although the technologies in 3D acquisition and 3D display have advanced rapidly in recent years, effort is lacking in studying the seamless integration of these two different aspects of 3D technologies. In this paper, we describe our recent progress on integrating a light-field 3D acquisition system and an autostereoscopic multiview 3D display for real-time light field capture and display. This paper focuses on both the architecture design and the implementation of the hardware and the software of this integrated 3D system. A prototype of the integrated 3D system is built to demonstrate the real-time 3D acquisition and 3D display capability of our proposed system.

  15. Limited Feedback for 3D Massive MIMO under 3D-UMa and 3D-UMi Scenarios

    Directory of Open Access Journals (Sweden)

    Zheng Hu

    2015-01-01

    Full Text Available For three-dimensional (3D massive MIMO utilizing the uniform rectangular array (URA in the base station (BS, we propose a limited feedback transmission scheme in which the channel state information (CSI feedback operations for horizontal domain and vertical domain are separate. Compared to the traditional feedback scheme, the scheme can reduce the feedback overhead, code word index search complexity, and storage requirement. Also, based on the zenith of departure angle (ZoD distribution in 3D-Urban Macro Cell (3D-UMa and 3D-Urban Micro Cell (3D-UMi scenarios, we propose the angle quantization codebook for vertical domain, while the codebook of long term evolution-advanced (LTE-Advanced is still adopted in horizontal domain to preserve compatibility with the LTE-Advanced. Based on the angle quantization codebook, the subsampled 3-bit DFT codebook is designed for vertical domain. The system-level simulation results reveal that, to compromise the feedback overhead and system performance, 2-bit codebook for 3D-UMa scenario and 3-bit codebook for 3D-UMi scenario can meet requirements in vertical domain. The feedback period for vertical domain can also be extended appropriately to reduce the feedback overhead.

  16. 6D Interpretation of 3D Gravity

    Science.gov (United States)

    Herfray, Yannick; Krasnov, Kirill; Scarinci, Carlos

    2017-02-01

    We show that 3D gravity, in its pure connection formulation, admits a natural 6D interpretation. The 3D field equations for the connection are equivalent to 6D Hitchin equations for the Chern–Simons 3-form in the total space of the principal bundle over the 3-dimensional base. Turning this construction around one gets an explanation of why the pure connection formulation of 3D gravity exists. More generally, we interpret 3D gravity as the dimensional reduction of the 6D Hitchin theory. To this end, we show that any \\text{SU}(2) invariant closed 3-form in the total space of the principal \\text{SU}(2) bundle can be parametrised by a connection together with a 2-form field on the base. The dimensional reduction of the 6D Hitchin theory then gives rise to 3D gravity coupled to a topological 2-form field.

  17. 6D Interpretation of 3D Gravity

    CERN Document Server

    Herfray, Yannick; Scarinci, Carlos

    2016-01-01

    We show that 3D gravity, in its pure connection formulation, admits a natural 6D interpretation. The 3D field equations for the connection are equivalent to 6D Hitchin equations for the Chern-Simons 3-form in the total space of the principal bundle over the 3-dimensional base. Turning this construction around one gets an explanation of why the pure connection formulation of 3D gravity exists. More generally, we interpret 3D gravity as the dimensional reduction of the 6D Hitchin theory. To this end, we show that any SU(2) invariant closed 3-form in the total space of the principal SU(2) bundle can be parametrised by a connection together with a 2-form field on the base. The dimensional reduction of the 6D Hitchin theory then gives rise to 3D gravity coupled to a topological 2-form field.

  18. 2D/3D switchable displays

    Science.gov (United States)

    Dekker, T.; de Zwart, S. T.; Willemsen, O. H.; Hiddink, M. G. H.; IJzerman, W. L.

    2006-02-01

    A prerequisite for a wide market acceptance of 3D displays is the ability to switch between 3D and full resolution 2D. In this paper we present a robust and cost effective concept for an auto-stereoscopic switchable 2D/3D display. The display is based on an LCD panel, equipped with switchable LC-filled lenticular lenses. We will discuss 3D image quality, with the focus on display uniformity. We show that slanting the lenticulars in combination with a good lens design can minimize non-uniformities in our 20" 2D/3D monitors. Furthermore, we introduce fractional viewing systems as a very robust concept to further improve uniformity in the case slanting the lenticulars and optimizing the lens design are not sufficient. We will discuss measurements and numerical simulations of the key optical characteristics of this display. Finally, we discuss 2D image quality, the switching characteristics and the residual lens effect.

  19. Density-Based 3D Shape Descriptors

    Directory of Open Access Journals (Sweden)

    Schmitt Francis

    2007-01-01

    Full Text Available We propose a novel probabilistic framework for the extraction of density-based 3D shape descriptors using kernel density estimation. Our descriptors are derived from the probability density functions (pdf of local surface features characterizing the 3D object geometry. Assuming that the shape of the 3D object is represented as a mesh consisting of triangles with arbitrary size and shape, we provide efficient means to approximate the moments of geometric features on a triangle basis. Our framework produces a number of 3D shape descriptors that prove to be quite discriminative in retrieval applications. We test our descriptors and compare them with several other histogram-based methods on two 3D model databases, Princeton Shape Benchmark and Sculpteur, which are fundamentally different in semantic content and mesh quality. Experimental results show that our methodology not only improves the performance of existing descriptors, but also provides a rigorous framework to advance and to test new ones.

  20. Fabrication of 3D Silicon Sensors

    Energy Technology Data Exchange (ETDEWEB)

    Kok, A.; Hansen, T.E.; Hansen, T.A.; Lietaer, N.; Summanwar, A.; /SINTEF, Oslo; Kenney, C.; Hasi, J.; /SLAC; Da Via, C.; /Manchester U.; Parker, S.I.; /Hawaii U.

    2012-06-06

    Silicon sensors with a three-dimensional (3-D) architecture, in which the n and p electrodes penetrate through the entire substrate, have many advantages over planar silicon sensors including radiation hardness, fast time response, active edge and dual readout capabilities. The fabrication of 3D sensors is however rather complex. In recent years, there have been worldwide activities on 3D fabrication. SINTEF in collaboration with Stanford Nanofabrication Facility have successfully fabricated the original (single sided double column type) 3D detectors in two prototype runs and the third run is now on-going. This paper reports the status of this fabrication work and the resulted yield. The work of other groups such as the development of double sided 3D detectors is also briefly reported.

  1. Maintaining and troubleshooting your 3D printer

    CERN Document Server

    Bell, Charles

    2014-01-01

    Maintaining and Troubleshooting Your 3D Printer by Charles Bell is your guide to keeping your 3D printer running through preventive maintenance, repair, and diagnosing and solving problems in 3D printing. If you've bought or built a 3D printer such as a MakerBot only to be confounded by jagged edges, corner lift, top layers that aren't solid, or any of a myriad of other problems that plague 3D printer enthusiasts, then here is the book to help you get past all that and recapture the joy of creative fabrication. The book also includes valuable tips for builders and those who want to modify the

  2. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex.

    Science.gov (United States)

    Ellenberger, T E; Brandl, C J; Struhl, K; Harrison, S C

    1992-12-24

    The yeast transcriptional activator GCN4 is 1 of over 30 identified eukaryotic proteins containing the basic region leucine zipper (bZIP) DNA-binding motif. We have determined the crystal structure of the GCN4 bZIP element complexed with DNA at 2.9 A resolution. The bZIP dimer is a pair of continuous alpha helices that form a parallel coiled coil over their carboxy-terminal 30 residues and gradually diverge toward their amino termini to pass through the major groove of the DNA-binding site. The coiled-coil dimerization interface is oriented almost perpendicular to the DNA axis, giving the complex the appearance of the letter T. There are no kinks or sharp bends in either bZIP monomer. Numerous contacts to DNA bases and phosphate oxygens are made by basic region residues that are conserved in the bZIP protein family. The details of the bZIP dimer interaction with DNA can explain recognition of the AP-1 site by the GCN4 protein.

  3. The Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi's Sarcoma-Associated Herpesvirus

    Energy Technology Data Exchange (ETDEWEB)

    Baltz, Jennifer L.; Filman, David J.; Ciustea, Mihai; Silverman, Janice Elaine Y.; Lautenschlager, Catherine L.; Coen, Donald M.; Ricciardi, Robert P.; Hogle, James M.; (UPENN)

    2009-12-01

    Kaposi's sarcoma-associated herpesvirus is an emerging pathogen whose mechanism of replication is poorly understood. PF-8, the presumed processivity factor of Kaposi's sarcoma-associated herpesvirus DNA polymerase, acts in combination with the catalytic subunit, Pol-8, to synthesize viral DNA. We have solved the crystal structure of residues 1 to 304 of PF-8 at a resolution of 2.8 {angstrom}. This structure reveals that each monomer of PF-8 shares a fold common to processivity factors. Like human cytomegalovirus UL44, PF-8 forms a head-to-head dimer in the form of a C clamp, with its concave face containing a number of basic residues that are predicted to be important for DNA binding. However, there are several differences with related proteins, especially in loops that extend from each monomer into the center of the C clamp and in the loops that connect the two subdomains of each protein, which may be important for determining PF-8's mode of binding to DNA and to Pol-8. Using the crystal structures of PF-8, the herpes simplex virus catalytic subunit, and RB69 bacteriophage DNA polymerase in complex with DNA and initial experiments testing the effects of inhibition of PF-8-stimulated DNA synthesis by peptides derived from Pol-8, we suggest a model for how PF-8 might form a ternary complex with Pol-8 and DNA. The structure and the model suggest interesting similarities and differences in how PF-8 functions relative to structurally similar proteins.

  4. 3D Visualization Development of SIUE Campus

    Science.gov (United States)

    Nellutla, Shravya

    Geographic Information Systems (GIS) has progressed from the traditional map-making to the modern technology where the information can be created, edited, managed and analyzed. Like any other models, maps are simplified representations of real world. Hence visualization plays an essential role in the applications of GIS. The use of sophisticated visualization tools and methods, especially three dimensional (3D) modeling, has been rising considerably due to the advancement of technology. There are currently many off-the-shelf technologies available in the market to build 3D GIS models. One of the objectives of this research was to examine the available ArcGIS and its extensions for 3D modeling and visualization and use them to depict a real world scenario. Furthermore, with the advent of the web, a platform for accessing and sharing spatial information on the Internet, it is possible to generate interactive online maps. Integrating Internet capacity with GIS functionality redefines the process of sharing and processing the spatial information. Enabling a 3D map online requires off-the-shelf GIS software, 3D model builders, web server, web applications and client server technologies. Such environments are either complicated or expensive because of the amount of hardware and software involved. Therefore, the second objective of this research was to investigate and develop simpler yet cost-effective 3D modeling approach that uses available ArcGIS suite products and the free 3D computer graphics software for designing 3D world scenes. Both ArcGIS Explorer and ArcGIS Online will be used to demonstrate the way of sharing and distributing 3D geographic information on the Internet. A case study of the development of 3D campus for the Southern Illinois University Edwardsville is demonstrated.

  5. The psychology of the 3D experience

    Science.gov (United States)

    Janicke, Sophie H.; Ellis, Andrew

    2013-03-01

    With 3D televisions expected to reach 50% home saturation as early as 2016, understanding the psychological mechanisms underlying the user response to 3D technology is critical for content providers, educators and academics. Unfortunately, research examining the effects of 3D technology has not kept pace with the technology's rapid adoption, resulting in large-scale use of a technology about which very little is actually known. Recognizing this need for new research, we conducted a series of studies measuring and comparing many of the variables and processes underlying both 2D and 3D media experiences. In our first study, we found narratives within primetime dramas had the power to shift viewer attitudes in both 2D and 3D settings. However, we found no difference in persuasive power between 2D and 3D content. We contend this lack of effect was the result of poor conversion quality and the unique demands of 3D production. In our second study, we found 3D technology significantly increased enjoyment when viewing sports content, yet offered no added enjoyment when viewing a movie trailer. The enhanced enjoyment of the sports content was shown to be the result of heightened emotional arousal and attention in the 3D condition. We believe the lack of effect found for the movie trailer may be genre-related. In our final study, we found 3D technology significantly enhanced enjoyment of two video games from different genres. The added enjoyment was found to be the result of an increased sense of presence.

  6. 3D nano- and micro-patterning of biomaterials for controlled drug delivery.

    Science.gov (United States)

    Curry, Eli J; Henoun, Atta D; Miller, Albert N; Nguyen, Thanh D

    2017-01-01

    Recently, there has been an emerging interest in controlling 3D structures and designing novel 3D shapes for drug carriers at nano- and micro-scales. Certain 3D shapes and structures of drug particles enable transportation of the drugs to desired areas of the body, allow drugs to target specific cells and tissues, and influence release kinetics. Advanced nano- and micro-manufacturing methods including 3D printing, photolithography-based processes, microfluidics and DNA origami have been developed to generate defined 3D shapes and structures for drug carriers. This paper reviews the importance of 3D structures and shapes on controlled drug delivery, and the current state-of-the-art technologies that allow the creation of novel 3D drug carriers at nano- and micro-scales.

  7. Human connexin 32 overexpression for 3D crystallization

    OpenAIRE

    Volkov, Oleksandr

    2014-01-01

    The genome sequencing projects reveal that integral membrane proteins represent up to one third of the predicted proteins of all organisms examined so far. Furthermore, membrane proteins are targets of the large majority of the drugs that are currently in use. About 80% of all cellular responses are thought to occur through the proteins linked to the cell membrane. An ultimate understanding of their function depends on detailed structural data for each class of membrane proteins, such as tran...

  8. The Significance of Multivalent Bonding Motifs and “Bond Order” in DNA-Directed Nanoparticle Crystallization

    Energy Technology Data Exchange (ETDEWEB)

    Thaner, Ryan V.; Eryazici, Ibrahim; Macfarlane, Robert J.; Brown, Keith A.; Lee, Byeongdu; Nguyen, SonBinh T.; Mirkin, Chad A.

    2016-05-18

    Multivalent oligonucleotide-based bonding elements have been synthesized and studied for the assembly and crystallization of gold nanoparticles. Through the use of organic branching points, divalent and trivalent DNA linkers were readily incorporated into the oligonucleotide shells that define DNA-nanoparticles and compared to monovalent linker systems. These multivalent bonding motifs enable the change of "bond strength" between particles and therefore modulate the effective "bond order." In addition, the improved accessibility of strands between neighboring particles, either due to multivalency or modifications to increase strand flexibility, gives rise to superlattices with less strain in the crystallites compared to traditional designs. Furthermore, the increased availability and number of binding modes also provide a new variable that allows previously unobserved crystal structures to be synthesized, as evidenced by the formation of a thorium phosphide superlattice.

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

    Science.gov (United States)

    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. Digital relief generation from 3D models

    Science.gov (United States)

    Wang, Meili; Sun, Yu; Zhang, Hongming; Qian, Kun; Chang, Jian; He, Dongjian

    2016-09-01

    It is difficult to extend image-based relief generation to high-relief generation, as the images contain insufficient height information. To generate reliefs from three-dimensional (3D) models, it is necessary to extract the height fields from the model, but this can only generate bas-reliefs. To overcome this problem, an efficient method is proposed to generate bas-reliefs and high-reliefs directly from 3D meshes. To produce relief features that are visually appropriate, the 3D meshes are first scaled. 3D unsharp masking is used to enhance the visual features in the 3D mesh, and average smoothing and Laplacian smoothing are implemented to achieve better smoothing results. A nonlinear variable scaling scheme is then employed to generate the final bas-reliefs and high-reliefs. Using the proposed method, relief models can be generated from arbitrary viewing positions with different gestures and combinations of multiple 3D models. The generated relief models can be printed by 3D printers. The proposed method provides a means of generating both high-reliefs and bas-reliefs in an efficient and effective way under the appropriate scaling factors.

  11. 3D imaging in forensic odontology.

    Science.gov (United States)

    Evans, Sam; Jones, Carl; Plassmann, Peter

    2010-06-16

    This paper describes the investigation of a new 3D capture method for acquiring and subsequent forensic analysis of bite mark injuries on human skin. When documenting bite marks with standard 2D cameras errors in photographic technique can occur if best practice is not followed. Subsequent forensic analysis of the mark is problematic when a 3D structure is recorded into a 2D space. Although strict guidelines (BAFO) exist, these are time-consuming to follow and, due to their complexity, may produce errors. A 3D image capture and processing system might avoid the problems resulting from the 2D reduction process, simplifying the guidelines and reducing errors. Proposed Solution: a series of experiments are described in this paper to demonstrate that the potential of a 3D system might produce suitable results. The experiments tested precision and accuracy of the traditional 2D and 3D methods. A 3D image capture device minimises the amount of angular distortion, therefore such a system has the potential to create more robust forensic evidence for use in courts. A first set of experiments tested and demonstrated which method of forensic analysis creates the least amount of intra-operator error. A second set tested and demonstrated which method of image capture creates the least amount of inter-operator error and visual distortion. In a third set the effects of angular distortion on 2D and 3D methods of image capture were evaluated.

  12. Medical 3D Printing for the Radiologist.

    Science.gov (United States)

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

    2015-01-01

    While use of advanced visualization in radiology is instrumental in diagnosis and communication with referring clinicians, there is an unmet need to render Digital Imaging and Communications in Medicine (DICOM) images as three-dimensional (3D) printed models capable of providing both tactile feedback and tangible depth information about anatomic and pathologic states. Three-dimensional printed models, already entrenched in the nonmedical sciences, are rapidly being embraced in medicine as well as in the lay community. Incorporating 3D printing from images generated and interpreted by radiologists presents particular challenges, including training, materials and equipment, and guidelines. The overall costs of a 3D printing laboratory must be balanced by the clinical benefits. It is expected that the number of 3D-printed models generated from DICOM images for planning interventions and fabricating implants will grow exponentially. Radiologists should at a minimum be familiar with 3D printing as it relates to their field, including types of 3D printing technologies and materials used to create 3D-printed anatomic models, published applications of models to date, and clinical benefits in radiology. Online supplemental material is available for this article. (©)RSNA, 2015.

  13. 3D Reconstruction Technique for Tomographic PIV

    Institute of Scientific and Technical Information of China (English)

    姜楠; 包全; 杨绍琼

    2015-01-01

    Tomographic particle image velocimetry(Tomo-PIV) is a state-of-the-art experimental technique based on a method of optical tomography to achieve the three-dimensional(3D) reconstruction for three-dimensional three-component(3D-3C) flow velocity measurements. 3D reconstruction for Tomo-PIV is carried out herein. Meanwhile, a 3D simplified tomographic reconstruction model reduced from a 3D volume light inten-sity field with 2D projection images into a 2D Tomo-slice plane with 1D projecting lines, i.e., simplifying this 3D reconstruction into a problem of 2D Tomo-slice plane reconstruction, is applied thereafter. Two kinds of the most well-known algebraic reconstruction techniques, algebraic reconstruction technique(ART) and multiple algebraic reconstruction technique(MART), are compared as well. The principles of the two reconstruction algorithms are discussed in detail, which has been performed by a series of simulation images, yielding the corresponding recon-struction images that show different features between the ART and MART algorithm, and then their advantages and disadvantages are discussed. Further discussions are made for the standard particle image reconstruction when the background noise of the pre-initial particle image has been removed. Results show that the particle image recon-struction has been greatly improved. The MART algorithm is much better than the ART. Furthermore, the computa-tional analyses of two parameters(the particle density and the number of cameras), are performed to study their effects on the reconstruction. Lastly, the 3D volume particle field is reconstructed by using the improved algorithm based on the simplified 3D tomographic reconstruction model, which proves that the algorithm simplification is feasible and it can be applied to the reconstruction of 3D volume particle field in a Tomo-PIV system.

  14. 3D object-oriented image analysis in 3D geophysical modelling

    DEFF Research Database (Denmark)

    Fadel, I.; van der Meijde, M.; Kerle, N.

    2015-01-01

    Non-uniqueness of satellite gravity interpretation has traditionally been reduced by using a priori information from seismic tomography models. This reduction in the non-uniqueness has been based on velocity-density conversion formulas or user interpretation of the 3D subsurface structures (objects......) based on the seismic tomography models and then forward modelling these objects. However, this form of object-based approach has been done without a standardized methodology on how to extract the subsurface structures from the 3D models. In this research, a 3D object-oriented image analysis (3D OOA......) approach was implemented to extract the 3D subsurface structures from geophysical data. The approach was applied on a 3D shear wave seismic tomography model of the central part of the East African Rift System. Subsequently, the extracted 3D objects from the tomography model were reconstructed in the 3D...

  15. The reactor dynamics code DYN3D

    Energy Technology Data Exchange (ETDEWEB)

    Kliem, Soeren; Bilodid, Yuri; Fridman, Emil; Baier, Silvio; Grahn, Alexander; Gommlich, Andre; Nikitin, Evgeny; Rohde, Ulrich [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany)

    2016-05-15

    The article provides an overview on the code DYN3D which is a three-dimensional core model for steady-state, dynamic and depletion calculations in reactor cores with quadratic or hexagonal fuel assembly geometry being developed by the Helmholtz-Zentrum Dresden-Rossendorf for more than 20 years. The current paper gives an overview on the basic DYN3D models and the available code couplings. The verification and validation status is shortly outlined. The paper concludes with the current developments of the DYN3D code. For more detailed information the reader is referred to the publications cited in the corresponding chapters.

  16. Automatic balancing of 3D models

    DEFF Research Database (Denmark)

    Christiansen, Asger Nyman; Schmidt, Ryan; Bærentzen, Jakob Andreas

    2014-01-01

    3D printing technologies allow for more diverse shapes than are possible with molds and the cost of making just one single object is negligible compared to traditional production methods. However, not all shapes are suitable for 3D print. One of the remaining costs is therefore human time spent......, in these cases, we will apply a rotation of the object which only deforms the shape a little near the base. No user input is required but it is possible to specify manufacturing constraints related to specific 3D print technologies. Several models have successfully been balanced and printed using both polyjet...

  17. Participation and 3D Visualization Tools

    DEFF Research Database (Denmark)

    Mullins, Michael; Jensen, Mikkel Holm; Henriksen, Sune

    2004-01-01

    With a departure point in a workshop held at the VR Media Lab at Aalborg University , this paper deals with aspects of public participation and the use of 3D visualisation tools. The workshop grew from a desire to involve a broad collaboration between the many actors in the city through using new...... perceptions of architectural representation in urban design where 3D visualisation techniques are used. It is the authors? general finding that, while 3D visualisation media have the potential to increase understanding of virtual space for the lay public, as well as for professionals, the lay public require...

  18. Computer Modelling of 3D Geological Surface

    CERN Document Server

    Kodge, B G

    2011-01-01

    The geological surveying presently uses methods and tools for the computer modeling of 3D-structures of the geographical subsurface and geotechnical characterization as well as the application of geoinformation systems for management and analysis of spatial data, and their cartographic presentation. The objectives of this paper are to present a 3D geological surface model of Latur district in Maharashtra state of India. This study is undertaken through the several processes which are discussed in this paper to generate and visualize the automated 3D geological surface model of a projected area.

  19. RHOCUBE: 3D density distributions modeling code

    Science.gov (United States)

    Nikutta, Robert; Agliozzo, Claudia

    2016-11-01

    RHOCUBE models 3D density distributions on a discrete Cartesian grid and their integrated 2D maps. It can be used for a range of applications, including modeling the electron number density in LBV shells and computing the emission measure. The RHOCUBE Python package provides several 3D density distributions, including a powerlaw shell, truncated Gaussian shell, constant-density torus, dual cones, and spiralling helical tubes, and can accept additional distributions. RHOCUBE provides convenient methods for shifts and rotations in 3D, and if necessary, an arbitrary number of density distributions can be combined into the same model cube and the integration ∫ dz performed through the joint density field.

  20. A high capacity 3D steganography algorithm.

    Science.gov (United States)

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

    2009-01-01

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