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Sample records for 3d dna crystal

  1. Integration of a 3D hydrogel matrix within a hollow core photonic crystal fibre for DNA probe immobilization

    NASA Astrophysics Data System (ADS)

    Rutowska, Monika S.; Garcia Gunning, Fatima C.; Kivlehan, Francine; Moore, Eric; Brennan, Des; Galvin, Paul; Ellis, Andrew D.

    2010-09-01

    In this paper, we demonstrate the integration of a 3D hydrogel matrix within a hollow core photonic crystal fibre (HC-PCF). In addition, we also show the fluorescence of Cy5-labelled DNA molecules immobilized within the hydrogel formed in two different types of HC-PCF. The 3D hydrogel matrix is designed to bind with the amino groups of biomolecules using an appropriate cross-linker, providing higher sensitivity and selectivity than the standard 2D coverage, enabling a greater number of probe molecules to be available per unit area. The HC-PCFs, on the other hand, can be designed to maximize the capture of fluorescence to improve sensitivity and provide longer interaction lengths. This could enable the development of fibre-based point-of-care and remote systems, where the enhanced sensitivity would relax the constraints placed on sources and detectors. In this paper, we will discuss the formation of such polyethylene glycol diacrylate (PEGDA) hydrogels within a HC-PCF, including their optical properties such as light propagation and auto-fluorescence.

  2. Optically rewritable 3D liquid crystal displays.

    PubMed

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

    2014-11-01

    Optically rewritable liquid crystal display (ORWLCD) is a concept based on the optically addressed bi-stable display that does not need any power to hold the image after being uploaded. Recently, the demand for the 3D image display has increased enormously. Several attempts have been made to achieve 3D image on the ORWLCD, but all of them involve high complexity for image processing on both hardware and software levels. In this Letter, we disclose a concept for the 3D-ORWLCD by dividing the given image in three parts with different optic axis. A quarter-wave plate is placed on the top of the ORWLCD to modify the emerging light from different domains of the image in different manner. Thereafter, Polaroid glasses can be used to visualize the 3D image. The 3D image can be refreshed, on the 3D-ORWLCD, in one-step with proper ORWLCD printer and image processing, and therefore, with easy image refreshing and good image quality, such displays can be applied for many applications viz. 3D bi-stable display, security elements, etc. PMID:25361316

  3. DNA Assembly in 3D Printed Fluidics

    PubMed Central

    Patrick, William G.; Nielsen, Alec A. K.; Keating, Steven J.; Levy, Taylor J.; Wang, Che-Wei; Rivera, Jaime J.; Mondragón-Palomino, Octavio; Carr, Peter A.; Voigt, Christopher A.; Oxman, Neri; Kong, David S.

    2015-01-01

    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. PMID:26716448

  4. DNA Assembly in 3D Printed Fluidics.

    PubMed

    Patrick, William G; Nielsen, Alec A K; Keating, Steven J; Levy, Taylor J; Wang, Che-Wei; Rivera, Jaime J; Mondragón-Palomino, Octavio; Carr, Peter A; Voigt, Christopher A; Oxman, Neri; Kong, David S

    2015-01-01

    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. PMID:26716448

  5. Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one

    PubMed Central

    Magat Juan, Ella Czarina; Shimizu, Satoru; Ma, Xiao; Kurose, Taizo; Haraguchi, Tsuyoshi; Zhang, Fang; Tsunoda, Masaru; Ohkubo, Akihiro; Sekine, Mitsuo; Shibata, Takayuki; Millington, Christopher L.; Williams, David M.; Takénaka, Akio

    2010-01-01

    The incorporation of the bicyclic cytosine analogue 7,8-dihydropyrido[2,3-d]pyrimidin-2-one (X) into DNA duplexes results in a significant enhancement of their stability (3–4 K per modification). To establish the effects of X on the local hydrogen-bonding and base stacking interactions and the overall DNA conformation, and to obtain insights into the correlation between the structure and stability of X-containing DNA duplexes, the crystal structures of [d(CGCGAATT-X-GCG)]2 and [d(CGCGAAT-X-CGCG)]2 have been determined at 1.9–2.9 Å resolutions. In all of the structures, the analogue X base pairs with the purine bases on the opposite strands through Watson–Crick and/or wobble type hydrogen bonds. The additional ring of the X base is stacked on the thymine bases at the 5′-side and overall exhibits greatly enhanced stacking interactions suggesting that this is a major contribution to duplex stabilization. PMID:20554855

  6. Understanding Crystal Populations; Looking Towards 3D Quantitative Analysis

    NASA Astrophysics Data System (ADS)

    Jerram, D. A.; Morgan, D. J.

    2010-12-01

    In order to understand volcanic systems, the potential record held within crystal populations needs to be revealed. It is becoming increasingly clear, however, that the crystal populations that arrive at the surface in volcanic eruptions are commonly mixtures of crystals, which may be representative of simple crystallization, recycling of crystals and incorporation of alien crystals. If we can quantify the true 3D population within a sample then we will be able to separate crystals with different histories and begin to interrogate the true and complex plumbing within the volcanic system. Modeling crystal populations is one area where we can investigate the best methodologies to use when dealing with sections through 3D populations. By producing known 3D shapes and sizes with virtual textures and looking at the statistics of shape and size when such populations are sectioned, we are able to gain confidence about what our 2D information is telling us about the population. We can also use this approach to test the size of population we need to analyze. 3D imaging through serial sectioning or x-ray CT, provides a complete 3D quantification of a rocks texture. Individual phases can be identified and in principle the true 3D statistics of the population can be interrogated. In practice we need to develop strategies (as with 2D-3D transformations), that enable a true characterization of the 3D data, and an understanding of the errors and pitfalls that exist. Ultimately, the reproduction of true 3D textures and the wealth of information they hold, is now within our reach.

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

    PubMed Central

    Yang, Lina; Yang, Nuo; Li, Baowen

    2013-01-01

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

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

    PubMed

    Yang, Lina; Yang, Nuo; Li, Baowen

    2013-01-01

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

  9. Registration of 3-D holograms of diamond crystals (Abstract Only)

    NASA Astrophysics Data System (ADS)

    Marchenko, S. N.; Smirnova, S. N.

    1991-02-01

    Registration of 3D ho1orarns broadens the possibility of using single-crystal tool for imagining and investigating inner inhomogeneities and dynamic stresses in top area of gem diamond, study of which by other techniques,e.g. polarization optics, is difficult or impossible. The difficulty is that the diamond with significant refractive index of 2.42 has comparatively small angle of total internal reflection of 24°50. As a result, with random illumination of the tops of octahedron diamond crystals, both smooth- faceted and with polycentric facets, illuminating light is successively reflected from different farets and absorbed in the crystal or comes out of it in a spot and direction that are difficult to calculate. Optimal schemes of illuminating crystals for recording 3D holograms of smooth faceted octahedron diamonds are given. Analysis of illumination of the crystal with polycentric facets shows that correction of light in the diamond is determined by directivity diagram the width of which depends in inhomogeneity size of the diamond. 3D holograms of diamonds with different reflectivity were produced. For the first time the possibility is shown for registration of holograms for studying stresses in diamond top using single-crystal tool.

  10. 3D plasmonic crystal metamaterials for ultra-sensitive biosensing.

    PubMed

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

    2016-01-01

    We explore the excitation of plasmons in 3D plasmon crystal metamaterials and report the observation of a delocalized plasmon mode, which provides extremely high spectral sensitivity (>2600 nm per refractive index unit (RIU) change), outperforming all plasmonic counterparts excited in 2D nanoscale geometries, as well as a prominent phase-sensitive response (>3*10(4) deg. of phase per RIU). Combined with a large surface for bioimmobilization provided by the 3D matrix, the proposed sensor architecture promises a new important landmark in the advancement of plasmonic biosensing technology. PMID:27151104

  11. 3D plasmonic crystal metamaterials for ultra-sensitive biosensing

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  12. 3D plasmonic crystal metamaterials for ultra-sensitive biosensing

    PubMed Central

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

    2016-01-01

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

  13. 3D-dynamic representation of DNA sequences.

    PubMed

    Wąż, Piotr; Bielińska-Wąż, Dorota

    2014-03-01

    A new 3D graphical representation of DNA sequences is introduced. This representation is called 3D-dynamic representation. It is a generalization of the 2D-dynamic dynamic representation. The sequences are represented by sets of "material points" in the 3D space. The resulting 3D-dynamic graphs are treated as rigid bodies. The descriptors characterizing the graphs are analogous to the ones used in the classical dynamics. The classification diagrams derived from this representation are presented and discussed. Due to the third dimension, "the history of the graph" can be recognized graphically because the 3D-dynamic graph does not overlap with itself. Specific parts of the graphs correspond to specific parts of the sequence. This feature is essential for graphical comparisons of the sequences. Numerically, both 2D and 3D approaches are of high quality. In particular, a difference in a single base between two sequences can be identified and correctly described (one can identify which base) by both 2D and 3D methods. PMID:24567158

  14. Robust 3D DNA FISH using directly labeled probes.

    PubMed

    Bolland, Daniel J; King, Michelle R; Reik, Wolf; Corcoran, Anne E; Krueger, Christel

    2013-01-01

    3D DNA FISH has become a major tool for analyzing three-dimensional organization of the nucleus, and several variations of the technique have been published. In this article we describe a protocol which has been optimized for robustness, reproducibility, and ease of use. Brightly fluorescent directly labeled probes are generated by nick-translation with amino-allyldUTP followed by chemical coupling of the dye. 3D DNA FISH is performed using a freeze-thaw step for cell permeabilization and a heating step for simultaneous denaturation of probe and nuclear DNA. The protocol is applicable to a range of cell types and a variety of probes (BACs, plasmids, fosmids, or Whole Chromosome Paints) and allows for high-throughput automated imaging. With this method we routinely investigate nuclear localization of up to three chromosomal regions. PMID:23978815

  15. Robust 3D DNA FISH Using Directly Labeled Probes

    PubMed Central

    Bolland, Daniel J.; King, Michelle R.; Reik, Wolf; Corcoran, Anne E.; Krueger, Christel

    2013-01-01

    3D DNA FISH has become a major tool for analyzing three-dimensional organization of the nucleus, and several variations of the technique have been published. In this article we describe a protocol which has been optimized for robustness, reproducibility, and ease of use. Brightly fluorescent directly labeled probes are generated by nick-translation with amino-allyldUTP followed by chemical coupling of the dye. 3D DNA FISH is performed using a freeze-thaw step for cell permeabilization and a heating step for simultaneous denaturation of probe and nuclear DNA. The protocol is applicable to a range of cell types and a variety of probes (BACs, plasmids, fosmids, or Whole Chromosome Paints) and allows for high-throughput automated imaging. With this method we routinely investigate nuclear localization of up to three chromosomal regions. PMID:23978815

  16. 3D holographic polymer photonic crystal for superprism application

    NASA Astrophysics Data System (ADS)

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

    2007-02-01

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

  17. Melting of Temperature-Sensitive 3D Colloidal Crystals

    NASA Astrophysics Data System (ADS)

    Alsayed, Ahmed; Han, Yilong; Yodh, Arjun

    2006-03-01

    We employ thermally responsive monodisperse microgel colloidal spheres to study the melting mechanisms of colloidal crystals [1]. The particle diameter decreases with increasing temperature and leads to volume fraction changes that drive phase-transitions. We will describe observations of a variety of phenomena. Premelting, the localized loss of crystalline order near defects (e.g. grain boundaries) at volume fractions above the bulk melting transition, is directly observed by video microscopy, and is characterized by monitoring the first peak position of the particle pair correlation function. We find the position of the first peak shifts toward smaller particle separations at the onset of premelting. After Delaunay triangulation, mean square rotational and translational fluctuations of bonds were measured close to and away from defects. The behavior of all such quantities exhibits increased disorder near the defects. By locally heating the material within a crystal domain, we also studied the superheating and melting of a perfect 3D crystal. Finally, the introduction of weak attractions between spheres reveals free-floating 3D crystal `blobs' which can be made to melt and recrystallize by tuning the temperature. [1] A. M. Alsayed, M. F. Islam, J. Zhang, P. J. Collings, A. G. Yodh, Science 309, 1207 (2005). This work was supported by grants from NSF (DMR-0505048 and MRSEC DMR05-20020) and NASA (NAG8-2172).

  18. Large Area Printing of 3D Photonic Crystals

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  19. Hexagonal liquid crystal lens array for 3D endoscopy.

    PubMed

    Hassanfiroozi, Amir; Huang, Yi-Pai; Javidi, Bahram; Shieh, Han-Ping D

    2015-01-26

    A liquid crystal lens array with a hexagonal arrangement is investigated experimentally. The uniqueness of this study exists in the fact that using convex-ring electrode provides a smooth and controllable applied potential profile across the aperture to manage the phase profile. We observed considerable differences between flat electrode and convex-ring electrode; in particular the lens focal length is variable in a wider range from 2.5cm to infinity. This study presents several noteworthy characteristics such as low driving voltage; 30 μm cell gap and the lens is electrically switchable between 2D/3D modes. We demonstrate a hexagonal LC-lens array for capturing 3D images by using single sensor using integral imaging. PMID:25835856

  20. Functionalizing Designer DNA Crystals

    NASA Astrophysics Data System (ADS)

    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

  1. 3D crack tip fields for FCC single crystals

    SciTech Connect

    Cuitino, A.M.; Ortiz, M.

    1995-12-31

    Cracks in single crystals are of concern in a number of structural and non-structural applications, ranging form single-crystal turbine blades and rotors to metal interconnect lines in microcircuits. In this paper we present 3D numerical simulations of the crack-tip fields of a Cu single crystal, including stress, strain and slip activity patterns. The orientation of the crack tip is along the crystallographic orientation (101), while the crack plane is (010). A material model based on dislocation mechanics is used in these simulations. This model correctly predicts the observed behavior of Cu, including the basic hardening characteristics of single crystals, orientation dependence and stage I-II-III structure of the stress-strain curves, the observed levels of latent hardening and their variation with orientation and deformation in the primary system and slip activities and dislocation densities. We use the FEM within the context of finite deformation plasticity. In the figure below, we show the finite element mesh composed by 12-noded tetrahedrons with 6-noded triangular faces. The model simulates half of a beam, which is subjected to a concentrated load at 1/8 of total length from the support. Detailed results of the stress, deformation and slip activity are presented at different radii from crack tip and at different depths from the surface. In general, the results show a strong difference in the slip activity pattern form the interior to the exterior, while smaller differences are encountered in the stress and strain fields.

  2. 3-D simulation of nanopore structure for DNA sequencing.

    PubMed

    Park, Jun-Mo; Pak, Y Eugene; Chun, Honggu; Lee, Jong-Ho

    2012-07-01

    In this paper, we propose a method for simulating nanopore structure by using conventional 3-D simulation tool to mimic the I-V behavior of the nanopore structure. In the simulation, we use lightly doped silicon for ionic solution where some parameters like electron affinity and dielectric constant are fitted to consider the ionic solution. By using this method, we can simulate the I-V behavior of nanopore structure depending on the location and the size of the sphere shaped silicon oxide which is considered to be an indicator of a DNA base. In addition, we simulate an Ionic Field Effect Transistor (IFET) which has basically the nanopore structure, and show that the simulated curves follow sufficiently the I-V behavior of the measurement data. Therefore, we think it is reasonable to apply parameter modeling mentioned above to simulate nanopore structure. The key idea is to modify electron affinity of silicon which is used to mimic the KCl solution to avoid band bending and depletion inside the nanopore. We could efficiently utilize conventional 3-D simulation tool to simulate the I-V behavior of nanopore structures. PMID:22966538

  3. Enhancing DNA Crystal Durability through Chemical Crosslinking.

    PubMed

    Zhang, Diana; Paukstelis, Paul J

    2016-06-16

    Three-dimensional (3D) DNA crystals have been envisioned as a powerful tool for the positional control of biological and non-biological arrays on the nanoscale. However, most DNA crystals contain short duplex regions that can result in low thermal stability. Additionally, because DNA is a polyanion, DNA crystals often require high cation concentrations to maintain their integrity. Here, we demonstrate that a DNA alkylating mustard, bis(2-chloroethyl)amine, can form interstrand crosslinks within a model 3D DNA crystal. The crosslinking procedure did not alter crystal X-ray diffraction properties, but it did significantly improve the overall stability of the crystals under a variety of conditions. Crosslinked crystals showed enhanced stability at elevated temperature and were stable at Mg(2+) concentrations as low as 1 mm. Remarkably, the crosslinked crystals showed significant resistance to DNase I treatment, while also having improved longevity in tissue culture mediums. Characterization of the crosslinked species suggest that there are multiple crosslinking sites, but that the most prevalent interstrand crosslink involves an unpaired 3'-terminal guanosine residue. The improved stability of these DNA crystals suggests that simple treatment with alkylating reagents might be sufficient to stabilize crystals and other DNA constructs for improved functionality in biological and non-biological applications. PMID:27108768

  4. Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization

    PubMed Central

    Chaumeil, Julie; Micsinai, Mariann; Skok, Jane A.

    2013-01-01

    Fluorescent in situ hybridization using DNA probes on 3-dimensionally preserved nuclei followed by 3D confocal microscopy (3D DNA FISH) represents the most direct way to visualize the location of gene loci, chromosomal sub-regions or entire territories in individual cells. This type of analysis provides insight into the global architecture of the nucleus as well as the behavior of specific genomic loci and regions within the nuclear space. Immunofluorescence, on the other hand, permits the detection of nuclear proteins (modified histones, histone variants and modifiers, transcription machinery and factors, nuclear sub-compartments, etc). The major challenge in combining immunofluorescence and 3D DNA FISH is, on the one hand to preserve the epitope detected by the antibody as well as the 3D architecture of the nucleus, and on the other hand, to allow the penetration of the DNA probe to detect gene loci or chromosome territories 1-5. Here we provide a protocol that combines visualization of chromatin modifications with genomic loci in 3D preserved nuclei. PMID:23407477

  5. Functionalizing Designer DNA Crystals

    NASA Astrophysics Data System (ADS)

    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

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

    ERIC Educational Resources Information Center

    Casas, Lluís; Estop, Euge`nia

    2015-01-01

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

  7. Template-Directed Directionally Solidified 3D Mesostructured AgCl-KCl Eutectic Photonic Crystals.

    PubMed

    Kim, Jinwoo; Aagesen, Larry K; Choi, Jun Hee; Choi, Jaewon; Kim, Ha Seong; Liu, Jinyun; Cho, Chae-Ryong; Kang, Jin Gu; Ramazani, Ali; Thornton, Katsuyo; Braun, Paul V

    2015-08-19

    3D mesostructured AgCl-KCl photonic crystals emerge from colloidal templating of eutectic solidification. Solvent removal of the KCl phase results in a mesostructured AgCl inverse opal. The 3D-template-induced confinement leads to the emergence of a complex microstructure. The 3D mesostructured eutectic photonic crystals have a large stop band ranging from the near-infrared to the visible tuned by the processing. PMID:26177830

  8. Self assembly of inorganic nanocrystals in 3D supra crystals: Intrinsic properties

    NASA Astrophysics Data System (ADS)

    Pileni, M. P.

    2009-06-01

    Here we describe how arrangements of nanocrystals can self-organize in 3D arrays called supra crystals. The 3D arrays can fall into the familiar categories of face centered cubic (fcc), hexagonal compact packing (hcp) crystals, and body centered (bcc) crystals. Intrinsic collective properties of these 3D arrangements are different from the properties of individual nanoparticles and from particles in bulk. We demonstrate by two various processes and with two types of nanocrystals (silver and cobalt) that when nanocrystals are self ordered in 3D superlattices, they exhibit a coherent breathing mode vibration of the supra crystal, analogous to a breathing mode vibration of atoms in a nanocrystal. Comparison between the approaches to saturation of the magnetic curve for supra crystals and disordered aggregates produced from the same batch of nanocrystals is similar to that observed with films or nanoparticles either highly crystallized or amorphous.

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

    NASA Technical Reports Server (NTRS)

    Brodkey, Robert S.; Russ, Keith M.

    1991-01-01

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

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

    ERIC Educational Resources Information Center

    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…

  11. UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation

    PubMed Central

    Zhu, Jinhao; Wei, Bryan; Yuan, Yuan; Mi, Yongli

    2009-01-01

    A user-friendly software system, UNIQUIMER 3D, was developed to design DNA structures for nanotechnology applications. It consists of 3D visualization, internal energy minimization, sequence generation and construction of motif array simulations (2D tiles and 3D lattices) functionalities. The system can be used to check structural deformation and design errors under scaled-up conditions. UNIQUIMER 3D has been tested on the design of both existing motifs (holiday junction, 4 × 4 tile, double crossover, DNA tetrahedron, DNA cube, etc.) and nonexisting motifs (soccer ball). The results demonstrated UNIQUIMER 3D's capability in designing large complex structures. We also designed a de novo sequence generation algorithm. UNIQUIMER 3D was developed for the Windows environment and is provided free of charge to the nonprofit research institutions. PMID:19228709

  12. C3d enhanced DNA vaccination induced humoral immune response to glycoprotein C of pseudorabies virus

    SciTech Connect

    Tong Tiezhu; Fan Huiying; Tan Yadi; Xiao Shaobo; Ling Jieyu; Chen Huanchun; Guo Aizhen . E-mail: aizhen@mail.hzau.edu.cn

    2006-09-08

    Murine C3d were utilized to enhance immunogenicity of pseudorabies virus (PrV) gC DNA vaccination. Three copies of C3d and four copies of CR2-binding domain M28{sub 4} were fused, respectively, to truncated gC gene encoding soluble glycoprotein C (sgC) in pcDNA3.1. BALB/c mice were, respectively, immunized with recombinant plasmids, blank vector, and inactivated vaccine. The antibody ELISA titer for sgC-C3d{sub 3} DNA was 49-fold more than that for sgC DNA, and the neutralizing antibody obtained 8-fold rise. Protection of mice from death after lethal PrV (316 LD{sub 5}) challenge was augmented from 25% to 100%. Furthermore, C3d fusion increased Th2-biased immune response by inducing IL-4 production. The IL-4 level for sgC-C3d{sub 3} DNA immunization approached that for the inactivated vaccine. Compared to C3d, M28 enhanced sgC DNA immunogenicity to a lesser extent. In conclusion, we demonstrated that murine C3d fusion significantly enhanced gC DNA immunity by directing Th1-biased to a balanced and more effective Th1/Th2 response.

  13. A 3D Model of Double-Helical DNA Showing Variable Chemical Details

    ERIC Educational Resources Information Center

    Cady, Susan G.

    2005-01-01

    Since the first DNA model was created approximately 50 years ago using molecular models, students and teachers have been building simplified DNA models from various practical materials. A 3D double-helical DNA model, made by placing beads on a wire and stringing beads through holes in plastic canvas, is described. Suggestions are given to enhance…

  14. 3D view of chromosomes, DNA damage, and translocations.

    PubMed

    Schwartz, Michal; Hakim, Ofir

    2014-04-01

    The cell nucleus is a busy and organized organelle. In this megalopolis made of billions of nucleotides, protein factors find their target loci to exert nuclear functions such as transcription and replication. Remarkably, despite the lack of internal membrane barrier, the interlinked and tightly regulated nuclear processes occur in spatially organized fashion. These processes can lead to double-strand breaks (DSBs) that compromise the integrity of the genome. Moreover, in some cells like lymphocytes, DNA damage is also targeted within the context of immunoglobulin gene recombination. If not repaired correctly, DSBs can cause chromosomal rearrangements, including translocations which are etiological in numerous tumors. Therefore, the chromosomal locations of DSBs, as well as their spatial positioning, are important contributors to formation of chromosomal translocations at specific genomic loci. To obtain a mechanistic understanding of chromosomal translocations these parameters should be accounted for in a global and integrative fashion. In this review we will discuss recent findings addressing how genome architecture, DNA damage, and repair contribute to the genesis of chromosomal translocations. PMID:24632298

  15. Towards true 3D textural analysis; using your crystal mush wisely.

    NASA Astrophysics Data System (ADS)

    Jerram, D. A.; Morgan, D. J.; Pankhurst, M. J.

    2014-12-01

    The crystal cargo that is found in volcanic and plutonic rocks contains a wealth of information about magmatic mush processes, crystallisation history, crystal entrainment and recycling. Phenocryst populations predominantly record episodes of growth/nucleation and bulk geochemical changes within an evolving crystal-melt body. Ante- and xeno-crysts provide useful clues to the nature of mush interaction with wall rock and with principal magma(s). Furthermore, crystal evolutions (core to rim) record pathways through pressure, temperature and compositional space. These can often illustrate complex recycling within systems, describing the plumbing architecture. Understanding this architecture underpins our knowledge of how igneous systems can interact with the crust, grow, freeze, re-mobilise and prime for eruption. Initially, 2D studies produced corrected 3D crystal size distributions to help provide information about nucleation and residence times. It immediately became clear that crystal shape is an important factor in determining the confidence placed upon 3D reconstructions of 2D data. Additionally studies utilised serial sections of medium- to coarse-grain-size populations which allowed 3D reconstruction using modelling software to be improved, since size and shape etc. can be directly constrained. Finally the advent of textural studies using X-ray tomography has revolutionised the way in which we can inspect the crystal cargo in mushy systems, allowing us to image in great detail crystal packing arrangements, 3D CSDs, shapes and orientations etc. The latest most innovative studies use X-ray micro-computed tomography to rapidly characterise chemical populations within the crystal cargo, adding a further dimension to this approach, and implies the ability to untangle magmatic chemical components to better understand their individual and combined evolution. In this contribution key examples of the different types of textural analysis techniques in 2D and 3D

  16. 3D unsteady computer modeling of industrial scale Ky and Cz sapphire crystal growth

    NASA Astrophysics Data System (ADS)

    Demina, S. E.; Kalaev, V. V.

    2011-04-01

    In the present work, 3D features of melt convection during sapphire growth of 100 mm diameter Cz and of 200 mm diameter Ky crystals are studied. The approach accounting for radiative heat exchange with absorption and a specular reflection in the crystal, which we applied in 2D modeling [1-3], has been extended to 3D computational domains and coupled to 3D heat transfer in the melt, crystal, and crucible. 3D melt unsteady convection together with crystallization front formation are taken into account within the Direct Numerical Simulation (DNS) approach. Results of 3D modeling are discussed in detail and quantitatively compared to the previously reported data of 2D modeling and experiments [2,3]. It has been found that the features of unsteady melt convection during the "before seeding", "seeding", and "shouldering" growth stages are quite different from each other, which necessitates a flexible control of the radial and vertical temperature gradients in the crucible to provide optimal conditions for stable growth of high quality sapphire crystals.

  17. 3D photonic crystal-based biosensor functionalized with quantum dot-based aptamer for thrombine detection

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

  18. A 3D-DNA Molecule Made of PlayMais

    ERIC Educational Resources Information Center

    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,…

  19. CMOS compatible fabrication of 3D photonic crystals by nanoimprint lithography

    NASA Astrophysics Data System (ADS)

    Eibelhuber, M.; Uhrmann, T.; Glinsner, T.

    2015-03-01

    Nanoimprinting techniques are an attractive solution for next generation lithography methods for several areas including photonic devices. A variety of potential applications have been demonstrated using nanoimprint lithography (NIL) (e.g. SAW devices, vias and contact layers with dual damascene imprinting process, Bragg structures, patterned media) [1,2]. Nanoimprint lithography is considered for bridging the gap from R and D to high volume manufacturing. In addition, it is capable to adapt to the needs of the fragmented and less standardized photonic market easily. In this work UV-NIL has been selected for the fabrication process of 3D-photonic crystals. It has been shown that UVNIL using a multiple layer approach is well suited to fabricate a 3D woodpile photonic crystal. The necessary alignment accuracies below 100nm were achieved using a simple optical method. In order to obtain sufficient alignment of the stacks to each other, a two stage alignment process is performed: at first proximity alignment is done followed by the Moiré alignment in soft contact with the substrate. Multiple steps of imprinting, etching, Si deposition and chemical mechanical polishing were implemented to create high quality 3D photonic crystals with up to 5 layers. This work has proven the applicability of nanoimprint lithography in a CMOS compatible process on 3D photonic crystals with alignment accuracy down to 100nm. Optimizing the processes will allow scaling up these structures on full wafers while still meeting the requirements of the designated devices.

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

    NASA Astrophysics Data System (ADS)

    Kim, Bong-Sik; Lee, Seung-Chul; Park, Woo-Sang

    2014-08-01

    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 9view 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.

  1. Micromorph silicon tandem solar cells with fully integrated 3D photonic crystal intermediate reflectors

    NASA Astrophysics Data System (ADS)

    Üpping, J.; Bielawny, A.; Fahr, S.; Rockstuhl, C.; Lederer, F.; Steidl, L.; Zentel, R.; Beckers, T.; Lambertz, A.; Carius, R.; Wehrspohn, R. B.

    2010-05-01

    A 3D photonic intermediate reflector for textured micromorph silicon tandem solar cells has been investigated. In thin-film silicon tandem solar cells consisting of amorphous and microcrystalline silicon with two junctions of a-Si/c-Si, efficiency enhancements can be achieved by increasing the current density in the a-Si top cell providing an optimized current matching at high current densities. For an ideal photon-management between top and bottom cell, a spectrally-selective intermediate reflective layer (IRL) is necessary. We present the first fully-integrated 3D photonic thin-film IRL device incorporated on a planar substrate. Using a ZnO inverted opal structure the external quantum efficiency of the top cell in the spectral region of interest could be enhanced. As an outlook we present the design and the preparation of a 3D self organized photonic crystal structure in a textured micromorph tandem solar cell.

  2. 3D position determination in monolithic crystals coupled to SiPMs for PET.

    PubMed

    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. PMID:27119737

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    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 12× 12× 10 mm3 LYSO crystal coupled to an 8× 8 -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.

  4. Precision polymers and 3D DNA nanostructures: emergent assemblies from new parameter space.

    PubMed

    Serpell, Christopher J; Edwardson, Thomas G W; Chidchob, Pongphak; Carneiro, Karina M M; Sleiman, Hanadi F

    2014-11-01

    Polymer self-assembly and DNA nanotechnology have both proved to be powerful nanoscale techniques. To date, most attempts to merge the fields have been limited to placing linear DNA segments within a polydisperse block copolymer. Here we show that, by using hydrophobic polymers of a precisely predetermined length conjugated to DNA strands, and addressable 3D DNA prisms, we are able to effect the formation of unprecedented monodisperse quantized superstructures. The structure and properties of larger micelles-of-prisms were probed in depth, revealing their ability to participate in controlled release of their constituent nanostructures, and template light-harvesting energy transfer cascades, mediated through both the addressability of DNA and the controlled aggregation of the polymers. PMID:25325677

  5. Preparation of Complex DNA Probe Sets for 3D FISH with up to Six Different Fluorochromes.

    PubMed

    Müller, Stefan; Neusser, Michaela; Köhler, Daniela; Cremer, Marion

    2007-01-01

    INTRODUCTIONDNA probes for fluorescence in situ hybridization (FISH) can be generated and labeled by various methods. This protocol describes the conjugation of dUTPs with haptens or fluorochromes, as well as the generation and labeling of DNA probes using those modified dUTPs. Sources of probe DNA include genomic DNA, DNA from flow-sorted chromosomes, bacterial artificial chromosomes (BACs), and cosmids. DNA amplification and labeling procedures involving degenerate oligonucleotide-primed PCR (DOP-PCR) and multiple displacement amplification (MDA) are provided. Advice is given for setting up complex probe pools, such as those containing large pools of BAC probes. Also included is a method for probe precipitation and preparation of a hybridization mix ready to be used for 3D fluorescence in situ hybridization (FISH) experiments. PMID:21357075

  6. Mechanisms of DNA damage response to targeted irradiation in organotypic 3D skin cultures.

    PubMed

    Acheva, Anna; Ghita, Mihaela; Patel, Gaurang; Prise, Kevin M; Schettino, Giuseppe

    2014-01-01

    DNA damage (caused by direct cellular exposure and bystander signaling) and the complex pathways involved in its repair are critical events underpinning cellular and tissue response following radiation exposures. There are limited data addressing the dynamics of DNA damage induction and repair in the skin particularly in areas not directly exposed. Here we investigate the mechanisms regulating DNA damage, repair, intracellular signalling and their impact on premature differentiation and development of inflammatory-like response in the irradiated and surrounding areas of a 3D organotypic skin model. Following localized low-LET irradiation (225 kVp X-rays), low levels of 53BP1 foci were observed in the 3D model (3.8±0.28 foci/Gy/cell) with foci persisting and increasing in size up to 48 h post irradiation. In contrast, in cell monolayers 14.2±0.6 foci/Gy/cell and biphasic repair kinetics with repair completed before 24 h was observed. These differences are linked to differences in cellular status with variable level of p21 driving apoptotic signalling in 2D and accelerated differentiation in both the directly irradiated and bystander areas of the 3D model. The signalling pathways utilized by irradiated keratinocytes to induce DNA damage in non-exposed areas of the skin involved the NF-κB transcription factor and its downstream target COX-2. PMID:24505255

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

    PubMed

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

    2016-04-18

    We propose a novel multiplexing technique for increasing the viewing zone of a multi-view based multi-projection 3D display system by employing double refraction in uniaxial crystal. When linearly polarized images from projector pass through the uniaxial crystal, two possible optical paths exist according to the polarization states of image. Therefore, the optical paths of the image could be changed, and the viewing zone is shifted in a lateral direction. The polarization modulation of the image from a single projection unit enables us to generate two viewing zones at different positions. For realizing full-color images at each viewing zone, a polarization-based temporal multiplexing technique is adopted with a conventional polarization switching device of liquid crystal (LC) display. Through experiments, a prototype of a ten-view multi-projection 3D display system presenting full-colored view images is implemented by combining five laser scanning projectors, an optically clear calcite (CaCO3) crystal, and an LC polarization rotator. For each time sequence of temporal multiplexing, the luminance distribution of the proposed system is measured and analyzed. PMID:27137284

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

    PubMed

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

    2014-02-10

    A 2D/3D switchable and rotatable autostereoscopic display using a high-resistance liquid-crystal (Hi-R LC) lens array is investigated in this paper. Using high-resistance layers in an LC cell, a gradient electric-field distribution can be formed, which can provide a better lens-like shape of the refractive-index distribution. The advantages of the Hi-R LC lens array are its 2D/3D switchability, rotatability (in the horizontal and vertical directions), low driving voltage (~2 volts) and fast response (~0.6 second). In addition, the Hi-R LC lens array requires only a very simple fabrication process. PMID:24663563

  9. Bottom-up Fabrication of Multilayer Stacks of 3D Photonic Crystals from Titanium Dioxide.

    PubMed

    Kubrin, Roman; Pasquarelli, Robert M; Waleczek, Martin; Lee, Hooi Sing; Zierold, Robert; do Rosário, Jefferson J; Dyachenko, Pavel N; Montero Moreno, Josep M; Petrov, Alexander Yu; Janssen, Rolf; Eich, Manfred; Nielsch, Kornelius; Schneider, Gerold A

    2016-04-27

    A strategy for stacking multiple ceramic 3D photonic crystals is developed. Periodically structured porous films are produced by vertical convective self-assembly of polystyrene (PS) microspheres. After infiltration of the opaline templates by atomic layer deposition (ALD) of titania and thermal decomposition of the polystyrene matrix, a ceramic 3D photonic crystal is formed. Further layers with different sizes of pores are deposited subsequently by repetition of the process. The influence of process parameters on morphology and photonic properties of double and triple stacks is systematically studied. Prolonged contact of amorphous titania films with warm water during self-assembly of the successive templates is found to result in exaggerated roughness of the surfaces re-exposed to ALD. Random scattering on rough internal surfaces disrupts ballistic transport of incident photons into deeper layers of the multistacks. Substantially smoother interfaces are obtained by calcination of the structure after each infiltration, which converts amorphous titania into the crystalline anatase before resuming the ALD infiltration. High quality triple stacks consisting of anatase inverse opals with different pore sizes are demonstrated for the first time. The elaborated fabrication method shows promise for various applications demanding broadband dielectric reflectors or titania photonic crystals with a long mean free path of photons. PMID:27045887

  10. 3D motion of DNA-Au nanoconjugates in graphene liquid cell electron microscopy.

    PubMed

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

    2013-09-11

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

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

    PubMed

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

    2015-03-17

    Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase. PMID:25730881

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

    PubMed Central

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

    2015-01-01

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

  13. 3D-DIP-Chip: a microarray-based method to measure genomic DNA damage

    PubMed Central

    Powell, James Rees; Bennett, Mark Richard; Evans, Katie Ellen; Yu, Shirong; Webster, Richard Michael; Waters, Raymond; Skinner, Nigel; Reed, Simon Huw

    2015-01-01

    Genotoxins cause DNA damage, which can result in genomic instability. The genetic changes induced have far-reaching consequences, often leading to diseases such as cancer. A wide range of genotoxins exists, including radiations and chemicals found naturally in the environment, and in man-made forms created by human activity across a variety of industries. Genomic technologies offer the possibility of unravelling the mechanisms of genotoxicity, including the repair of genetic damage, enhancing our ability to develop, test and safely use existing and novel materials. We have developed 3D-DIP-Chip, a microarray-based method to measure the prevalence of genomic genotoxin-induced DNA damage. We demonstrate the measurement of both physical and chemical induced DNA damage spectra, integrating the analysis of these with the associated changes in histone acetylation induced in the epigenome. We discuss the application of the method in the context of basic and translational sciences. PMID:25609656

  14. 2D and 3D Histioid Disclination Networks in Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Jiang, Miao; Guo, Yubing; Lavrentovich, Oleg; Wei, Qi-Huo

    Topological defects and disclination lines are of both fundamental interest and practical importance. In this paper, we will show that periodic/non-periodic 2D/3D networks of disclination lines can be created in nematic liquid crystal cells by setting well-designed alignment patterns at the top and bottom substrate surfaces. The desired complex patterns of liquid crystal molecular alignments at the substrates are obtained using a projection photoalignment technique based on plasmonic metamasks. The designs of alignment patterns and their resulting disclination line networks will be presented. These designable topological networks represent a new kind of artificial materials which could be of useful for directing colloidal and molecular assembly. National Science Foundation CMMI-1436565.

  15. Shaping of light beams by 3D direct laser writing on facets of nonlinear crystals.

    PubMed

    Lightman, Shlomi; Gvishi, Raz; Hurvitz, Gilad; Arie, Ady

    2015-10-01

    We demonstrate experimentally spatial-mode conversions of light beams generated in a quadratic nonlinear process by micron-scale structures placed on the facets of nonlinear crystals. These structures were printed on the crystal facets using a three-dimensional (3D) direct laser writing system. The functional structures were designed to modify the phase of the beam at specific wavelengths, thereby enabling conversion of a fundamental Gaussian laser beam into different high-order Hermite-Gaussian modes, Laguerre-Gaussian modes, and zeroth-order Bessel beams of the second harmonic. This facet functionalization opens exciting new opportunities for robust and compact beam shaping in a nonlinear interaction without compromising the conversion efficiency. PMID:26421556

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

    NASA Astrophysics Data System (ADS)

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

    2008-02-01

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

  17. A 3D parallel simulator for crystal growth and solidification in complex alloy systems

    NASA Astrophysics Data System (ADS)

    Nestler, Britta

    2005-02-01

    A 3D parallel simulator is developed to numerically solve the evolution equations of a new non-isothermal phase-field model for crystal growth and solidification in complex alloy systems. The new model and the simulator are capable to simultaneously describe the diffusion processes of multiple components, the phase transitions between multiple phases and the development of the temperature field. Weak and facetted formulations of both, surface energy and kinetic anisotropies are incorporated in the phase-field model. Multicomponent bulk diffusion effects including interdiffusion coefficients as well as diffusion in the interfacial region of phase or grain boundaries are considered. We introduce our parallel simulator that is based on a finite difference discretization including effective adaptive strategies and multigrid methods to reduce computation time and memory usage. The parallelization is realized for distributed as well as shared memory computer architectures using MPI libraries and OpenMP concepts. Applying the new computer model, we present a variety of simulated crystal structures such as dendrites, grains, binary and ternary eutectics in 2D and 3D. The influence of anisotropy on the microstructure evolution shows the formation of facets in preferred crystallographic directions. Phase transformations and solidification processes in a real multi-component alloy can be described by incorporating the physical data (e.g. surface tensions, kinetic coefficients, specific heat, heat and mass diffusion coefficients) and the specific phase diagram (in particular latent heats and melting temperatures) into the diffuse interface model via the free energies.

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

    PubMed

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

    2016-01-01

    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. PMID:27622567

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    PubMed

    Yang, Lina; Yang, Nuo; Li, Baowen

    2014-01-01

    In this work, we propose a nanoscale three-dimensional (3D) Si phononic crystal (PnC) with spherical pores, which can reduce the thermal conductivity of bulk Si by a factor up to 10,000 times at room temperature. Thermal conductivity of Si PnCs depends on the porosity, for example, the thermal conductivity of Si PnCs with porosity 50% is 300 times smaller than that of bulk Si. The phonon participation ratio spectra demonstrate that more phonons are localized as the porosity increases. The thermal conductivity is insensitive to the temperature changes from room temperature to 1100 K. The extreme-low thermal conductivity could lead to a larger value of ZT than unity as the periodic structure affects very little the electric conductivity. PMID:24559126

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

    NASA Technical Reports Server (NTRS)

    Subramaniam, Girija; Blank, Shannon

    2005-01-01

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

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

    PubMed

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

    2010-09-15

    We apply a simple dynamical density functional theory, the phase-field crystal (PFC) model of overdamped conservative dynamics, to address polymorphism, crystal nucleation, and crystal growth in the diffusion-controlled limit. We refine the phase diagram for 3D, and determine the line free energy in 2D and the height of the nucleation barrier in 2D and 3D for homogeneous and heterogeneous nucleation by solving the respective Euler-Lagrange (EL) equations. We demonstrate that, in the PFC model, the body-centered cubic (bcc), the face-centered cubic (fcc), and the hexagonal close-packed structures (hcp) compete, while the simple cubic structure is unstable, and that phase preference can be tuned by changing the model parameters: close to the critical point the bcc structure is stable, while far from the critical point the fcc prevails, with an hcp stability domain in between. We note that with increasing distance from the critical point the equilibrium shapes vary from the sphere to specific faceted shapes: rhombic dodecahedron (bcc), truncated octahedron (fcc), and hexagonal prism (hcp). Solving the equation of motion of the PFC model supplied with conserved noise, solidification starts with the nucleation of an amorphous precursor phase, into which the stable crystalline phase nucleates. The growth rate is found to be time dependent and anisotropic; this anisotropy depends on the driving force. We show that due to the diffusion-controlled growth mechanism, which is especially relevant for crystal aggregation in colloidal systems, dendritic growth structures evolve in large-scale isothermal single-component PFC simulations. An oscillatory effective pair potential resembling those for model glass formers has been evaluated from structural data of the amorphous phase obtained by instantaneous quenching. Finally, we present results for eutectic solidification in a binary PFC model. PMID:21386517

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

    NASA Astrophysics Data System (ADS)

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

    2010-09-01

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

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

    PubMed Central

    Cherry, Simon R.

    2013-01-01

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

  5. The 3D structure of Kaposi sarcoma herpesvirus LANA C-terminal domain bound to DNA

    PubMed Central

    Hellert, Jan; Weidner-Glunde, Magdalena; Krausze, Joern; Lünsdorf, Heinrich; Ritter, Christiane; Schulz, Thomas F.; Lührs, Thorsten

    2015-01-01

    Kaposi sarcoma herpesvirus (KSHV) persists as a latent nuclear episome in dividing host cells. This episome is tethered to host chromatin to ensure proper segregation during mitosis. For duplication of the latent genome, the cellular replication machinery is recruited. Both of these functions rely on the constitutively expressed latency-associated nuclear antigen (LANA) of the virus. Here, we report the crystal structure of the KSHV LANA DNA-binding domain (DBD) in complex with its high-affinity viral target DNA, LANA binding site 1 (LBS1), at 2.9 Å resolution. In contrast to homologous proteins such as Epstein-Barr virus nuclear antigen 1 (EBNA-1) of the related γ-herpesvirus Epstein-Barr virus, specific DNA recognition by LANA is highly asymmetric. In addition to solving the crystal structure, we found that apart from the two known LANA binding sites, LBS1 and LBS2, LANA also binds to a novel site, denoted LBS3. All three sites are located in a region of the KSHV terminal repeat subunit previously recognized as a minimal replicator. Moreover, we show that the LANA DBD can coat DNA of arbitrary sequence by virtue of a characteristic lysine patch, which is absent in EBNA-1 of the Epstein-Barr virus. Likely, these higher-order assemblies involve the self-association of LANA into supermolecular spirals. One such spiral assembly was solved as a crystal structure of 3.7 Å resolution in the absence of DNA. On the basis of our data, we propose a model for the controlled nucleation of higher-order LANA oligomers that might contribute to the characteristic subnuclear KSHV microdomains (“LANA speckles”), a hallmark of KSHV latency. PMID:25947153

  6. Determining the Architecture of a Protein-DNA Complex by Combining FeBABE Cleavage Analyses, 3-D Printed Structures, and the ICM Molsoft Program.

    PubMed

    James, Tamara; Hsieh, Meng-Lun; Knipling, Leslie; Hinton, Deborah

    2015-01-01

    Determining the structure of a protein-DNA complex can be difficult, particularly if the protein does not bind tightly to the DNA, if there are no homologous proteins from which the DNA binding can be inferred, and/or if only portions of the protein can be crystallized. If the protein comprises just a part of a large multi-subunit complex, other complications can arise such as the complex being too large for NMR studies, or it is not possible to obtain the amounts of protein and nucleic acids needed for crystallographic analyses. Here, we describe a technique we used to map the position of an activator protein relative to the DNA within a large transcription complex. We determined the position of the activator on the DNA from data generated using activator proteins that had been conjugated at specific residues with the chemical cleaving reagent, iron bromoacetamidobenzyl-EDTA (FeBABE). These analyses were combined with 3-D models of the available structures of portions of the activator protein and B-form DNA to obtain a 3-D picture of the protein relative to the DNA. Finally, the Molsoft program was used to refine the position, revealing the architecture of the protein-DNA within the transcription complex. PMID:26404142

  7. Switchable 3D liquid crystal grating generated by periodic photo-alignment on both substrates.

    PubMed

    Nys, I; Beeckman, J; Neyts, K

    2015-10-21

    A planar liquid crystal (LC) cell is developed in which two photo-alignment layers have been illuminated with respectively a horizontal and a vertical diffraction pattern of interfering left- and right-handed circularly polarized light. In the bulk of the cell, a complex LC configuration is obtained with periodicity in two dimensions. Remarkably, the period of the structure is larger than the period of the interference pattern, indicating that lowering of the symmetry allows a reduction in the elastic energy. The liquid crystal configuration depends on the periodicity of the alignment but also on the thickness of the cell. By applying a voltage over the electrodes, the power going into the different diffracted orders can be tuned. Finite element (FE) simulations based on Q-tensor theory are used to find the 3D equilibrium director distribution, which is used to simulate the near-field transmission profile based on the Jones calculus. A 2D Fourier transform is performed for both the x- and y-component of the transmitted wave to find the diffraction efficiency. PMID:26313442

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

    SciTech Connect

    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.

  9. Observation of superconductivity induced by a point contact on 3D Dirac semimetal Cd3As2 crystals.

    PubMed

    Wang, He; Wang, Huichao; Liu, Haiwen; Lu, Hong; Yang, Wuhao; Jia, Shuang; Liu, Xiong-Jun; Xie, X C; Wei, Jian; Wang, Jian

    2016-01-01

    Three-dimensional (3D) Dirac semimetals, which possess 3D linear dispersion in the electronic structure as a bulk analogue of graphene, have lately generated widespread interest in both materials science and condensed matter physics. Recently, crystalline Cd3As2 has been proposed and proved to be a 3D Dirac semimetal that can survive in the atmosphere. Here, by using point contact spectroscopy measurements, we observe exotic superconductivity around the point contact region on the surface of Cd3As2 crystals. The zero-bias conductance peak (ZBCP) and double conductance peaks (DCPs) symmetric around zero bias suggest p-wave-like unconventional superconductivity. Considering the topological properties of 3D Dirac semimetals, our findings may indicate that Cd3As2 crystals under certain conditions could be topological superconductors, which are predicted to support Majorana zero modes or gapless Majorana edge/surface modes in the boundary depending on the dimensionality of the material. PMID:26524129

  10. Competitive interaction of monovalent cations with DNA from 3D-RISM.

    PubMed

    Giambaşu, George M; Gebala, Magdalena K; Panteva, Maria T; Luchko, Tyler; Case, David A; York, Darrin M

    2015-09-30

    The composition of the ion atmosphere surrounding nucleic acids affects their folding, condensation and binding to other molecules. It is thus of fundamental importance to gain predictive insight into the formation of the ion atmosphere and thermodynamic consequences when varying ionic conditions. An early step toward this goal is to benchmark computational models against quantitative experimental measurements. Herein, we test the ability of the three dimensional reference interaction site model (3D-RISM) to reproduce preferential interaction parameters determined from ion counting (IC) experiments for mixed alkali chlorides and dsDNA. Calculations agree well with experiment with slight deviations for salt concentrations >200 mM and capture the observed trend where the extent of cation accumulation around the DNA varies inversely with its ionic size. Ion distributions indicate that the smaller, more competitive cations accumulate to a greater extent near the phosphoryl groups, penetrating deeper into the grooves. In accord with experiment, calculated IC profiles do not vary with sequence, although the predicted ion distributions in the grooves are sequence and ion size dependent. Calculations on other nucleic acid conformations predict that the variation in linear charge density has a minor effect on the extent of cation competition. PMID:26304542

  11. Competitive interaction of monovalent cations with DNA from 3D-RISM

    PubMed Central

    Giambaşu, George M.; Gebala, Magdalena K.; Panteva, Maria T.; Luchko, Tyler; Case, David A.; York, Darrin M.

    2015-01-01

    The composition of the ion atmosphere surrounding nucleic acids affects their folding, condensation and binding to other molecules. It is thus of fundamental importance to gain predictive insight into the formation of the ion atmosphere and thermodynamic consequences when varying ionic conditions. An early step toward this goal is to benchmark computational models against quantitative experimental measurements. Herein, we test the ability of the three dimensional reference interaction site model (3D-RISM) to reproduce preferential interaction parameters determined from ion counting (IC) experiments for mixed alkali chlorides and dsDNA. Calculations agree well with experiment with slight deviations for salt concentrations >200 mM and capture the observed trend where the extent of cation accumulation around the DNA varies inversely with its ionic size. Ion distributions indicate that the smaller, more competitive cations accumulate to a greater extent near the phosphoryl groups, penetrating deeper into the grooves. In accord with experiment, calculated IC profiles do not vary with sequence, although the predicted ion distributions in the grooves are sequence and ion size dependent. Calculations on other nucleic acid conformations predict that the variation in linear charge density has a minor effect on the extent of cation competition. PMID:26304542

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

    PubMed

    Bisoyi, Hari Krishna; Li, Quan

    2014-10-21

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

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

    PubMed

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

    2016-10-14

    We report experimental observation of intrinsic Bloch-mode emission from a 3D tungsten photonic crystal at low thermal excitation. After the successful removal of conventional metallic emission (normal emission), it is possible to make an accurate comparison of the Bloch-mode and the normal emission. For all biases, we found that the emission intensity of the Bloch-mode is higher than that of the normal emission. The Bloch-mode emission also exhibits a slower dependence on [Formula: see text] than that of the normal emission. The observed higher emission intensity and a different T-dependence is attributed to Bloch-mode assisted emission where emitters have been located into a medium having local density of states different than the isotropic case. Furthermore, our finite-difference time-domain (FDTD) simulation shows the presence of localized spots at metal-air boundaries and corners, having intense electric field. The enhanced plasmonic field and local non-equilibrium could induce a strong thermally stimulated emission and may be the cause of our unusual observation. PMID:27606574

  14. Propagation of Electromagnetic Waves in 3D Opal-based Magnetophotonic Crystals

    NASA Astrophysics Data System (ADS)

    Pardavi-Horvath, Martha; Makeeva, Galina S.; Golovanov, Oleg A.; Rinkevich, Anatolii B.

    2013-03-01

    Opals, a class of self-organized 3D nanostructures, are typical representatives of photonic bandgap structures. The voids inside of the opal structure of close packed SiO2 spheres can be infiltrated by a magnetic material, creating magnetically tunable magnetophotonic crystals with interesting and potentially useful properties at GHz and THz frequencies. The propagation of electromagnetic waves at microwave frequencies was investigated numerically in SiO2 opal based magnetic nanostructures, using rigorous mathematical models to solve Maxwell's equations complemented by the Landau-Lifshitz equation with electrodynamic boundary conditions. The numerical approach is based on Galerkin's projection method using the decomposition algorithm on autonomous blocks with Floquet channels. The opal structure consists of SiO2 nanospheres, with inter-sphere voids infiltrated with nanoparticles of Ni-Zn ferrites. Both the opal matrix and the ferrite are assumed to be lossy. A model, taking into account the real structure of the ferrite particles in the opal's voids was developed to simulate the measured FMR lineshape of the ferrite infiltrated opal. The numerical technique shows an excellent agreement when applied to model recent experimental data on similar ferrite opals.

  15. Crystallization and crystal packing analysis of DNA oligonucleotides

    NASA Astrophysics Data System (ADS)

    Wang, Andrew H.-J.; Teng, M.-K.

    1988-07-01

    There are now over 30 DNA oligonucleotides that have been crystallized and their structure determined by X-ray diffraction analysis. From these studies there is a new wealth of information available to us concerning the fine details of the conformation of DNA molecules and their interactions with other ligands such as antitumor drugs and ions. In addition, the intensive efforts in attempting to crystallize many DNA fragments from several laboratories have resulted in a considerable amount of data related to the crystallization conditions for DNA molecules. Various factors such as the types of metal ion, precipitant, buffer and pH all play important roles in obtaining suitable crystals. We have also analyzed the packings of DNA molecules in the crystal lattice and found that they can be arranged into four different general categories. Those four types of packing interactions are: (1) base-base stacking plus intermolecular hydrogen bonds such as in the crystals of Z-DNA, daunomycin/DNA complex, triostin A/DNA complex, etc.; (2) base pair/A-DNA minor groove stacking, as in several DNA oligomer crystals in the A-DNA conformation; (3) guanine-guanine pairing in the minor groove of B-DNA dodecamers; (4) miscellaneous hydrogen bonding and stacking interactions. Many of those intermolecular interactions are examined in details and their possible biological relevance is discussed.

  16. Direct fabrication of complex 3D hierarchical nanostructures by reactive ion etching of hollow sphere colloidal crystals.

    PubMed

    Zhong, Kuo; Li, Jiaqi; Van Cleuvenbergen, Stijn; Clays, Koen

    2016-09-21

    Direct reactive ion etching (RIE) of hollow SiO2 sphere colloidal crystals (HSCCs) is employed as a facile, low-cost method to fabricate complex three-dimensional (3D) hierarchical nanostructures. These multilayered structures are gradually transformed into nanostructures of increasing complexity by controlling the etching time, without complicated procedures (no mask needed). The resulting 3D topologies are unique, and cannot be obtained through traditional approaches. The formation mechanism of these structures is explained in detail by geometrical modeling during the different etching stages, through shadow effects of the higher layers. SEM images confirm the modeled morphological changes. The nanostructures obtained by our approach show very fine features as small as ∼30 nm. Our approach opens new avenues to directly obtain complex 3D nanostructures from colloidal crystals and can find applications in sensing, templating, and catalysis where fine tuning the specific surface might be critical. PMID:27545098

  17. Combined global 2D-local 3D modeling of the industrial Czochralski silicon crystal growth process

    NASA Astrophysics Data System (ADS)

    Jung, T.; Seebeck, J.; Friedrich, J.

    2013-04-01

    A global, axisymmetric thermal model of a Czochralski furnace is coupled to an external, local, 3D, time-dependent flow model of the melt via the inclusion of turbulent heat fluxes, extracted from the 3D melt model, into the 2D furnace model. Boundary conditions of the 3D model are updated using results from the 2D model. In the 3D model the boundary layers are resolved by aggressive mesh refinement towards the walls, and the Large Eddy Simulation approach is used to model the turbulent flow in the melt volume on a relatively coarse mesh to minimize calculation times. It is shown that by using this approach it is possible to reproduce fairly good results from Direct Numerical Simulations obtained on much finer meshes, as well as experimental results for interface shape and oxygen concentration in the case of growth of silicon crystals with 210 mm diameter for photovoltaics by the Czochralski method.

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

    NASA Astrophysics Data System (ADS)

    Arbell, Matan; Hechster, Elad; Sarusi, Gabby

    2016-02-01

    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 conductance

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

    SciTech Connect

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

    2015-04-01

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

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

    PubMed

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

    2013-11-01

    A 3D organic-inorganic hybrid compound, (2-MepyH)3[{Fe(1,10-phen)3}3][{Pr4Sb12O18(OH)Cl(11.5)}(TDC)(4.5)({Pr4Sb12O18(OH)Cl(9.5)} Cl)]·3(2-Mepy)·28H2O (1; 2-Mepy=2-methylpyridine, 1,10-phen=1,10-phenanthroline, H2TDC=thiophene-2,5-dicarboxylic acid), was hydrothermally synthesized and structurally characterized. Unusually, two kinds of high-nuclearity clusters, namely [(Pr4Sb12O18(OH)Cl11)(COO)5](5-) and [(Pr4Sb12O18(OH)Cl9)Cl(COO)5](4-), coexist in the structure of compound 1; two of the latter clusters are doubly bridged by two μ2-Cl(-) moieties to form a new centrosymmetric dimeric cluster. An unprecedented spontaneous and reversible single-crystal-to-single-crystal transformation was observed, which simultaneously involved a notable organic-ligand movement between the metal ions and an alteration of the bridging ion in the dimeric cluster, induced by guest-release/re-adsorption, thereby giving rise to the interconversion between compound 1 and the compound (2-MepyH)3[{Fe(1,10-phen)3}3][{Pr4Sb12O18(OH)Cl(11.5)}(TDC)4({Pr4Sb12O18Cl(10.5)(TDC)(0.5)(H2O)(1.5)}O(0.5))]·25H2O (1'). The mechanism of this transformation has also been discussed in great detail. Photocatalytic H2-evolution activity was observed for compound 1' under UV light with Pt as a co-catalyst and MeOH as a sacrificial electron donor. PMID:24114981

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

    NASA Astrophysics Data System (ADS)

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

    2010-10-01

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

  2. Light-spectrum modification of warm white-light-emitting diodes with 3D colloidal photonic crystals to approximate candlelight.

    PubMed

    Lai, Chun-Feng; Hsieh, Cheng-Liang; Wu, Chia-Jung

    2013-09-15

    This study presents the light-spectrum modification of warm white-light-emitting diodes (w-WLEDs) with 3D colloidal photonic crystals (3D CPhCs) to approximate candlelight. The study measures the angular-resolved transmission properties of the w-WLEDs with CPhCs, which exhibit photonic stop bands based on the CPhC photonic band structures. The w-WLEDs with 3D CPhCs produce a low correlated color temperature of 1963 K, a high color-rendering index of 85, and a luminous flux of 22.8 lm (four times that of a candle). This study presents the successful development of a novel low-cost technique to produce candlelight w-WLEDs for use as an indoor light source. PMID:24104827

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

    PubMed

    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. PMID:26846371

  4. Novel and simple route to fabricate 2D ordered gold nanobowl arrays based on 3D colloidal crystals.

    PubMed

    Rao, Yanying; Tao, Qin; An, Ming; Rong, Chunhui; Dong, Jian; Dai, Yurong; Qian, Weiping

    2011-11-01

    In this study, we present a new method to fabricate large-area two-dimensionally (2D) ordered gold nanobowl arrays based on 3D colloidal crystals by wet chemosynthesis, which combines the advantages of a very simple preparation and an applicability to "real" nanomaterials. By combination of in situ growth of gold nanoshell (GNSs) arrays based on three-dimensional (3D) colloidal silica crystals, a monolayer ordered reversed GNS array (2D ordered GNS array) was conveniently manufactured by an acrylic ester modified biaxial oriented polypropylene (BOPP). 2D ordered gold nanobowl array with adjustable periodic holes, good stability, reproducibility, and repeatability could be obtained when the silica core was etched by HF solution. The surface-enhanced Raman scattering (SERS) enhancement factor (EF) of this 2D ordered gold nanobowl array could reach 1.27 × 10(7), which shows high SERS enhancing activity and can be used as a universal SERS substrate. PMID:21932785

  5. Nanostructured TTT(TCNQ)2 Organic Crystals as Promising Thermoelectric n-Type Materials: 3D Modeling

    NASA Astrophysics Data System (ADS)

    Sanduleac, Ionel; Casian, Anatolie

    2016-03-01

    The thermoelectric properties of quasi-one-dimensional TTT(TCNQ)2 organic crystals have been investigated to assess the prospect of using this type of compound as an n-type thermoelectric material. A three-dimensional (3D) physical model was elaborated. This takes into account two of the most important interactions of conduction electrons with longitudinal acoustic phonons—scattering of the electrons' by neighboring molecular chains and scattering by impurities and defects. Electrical conductivity, thermopower, power factor, electronic thermal conductivity, and thermoelectric figure of merit in the direction along the conducting molecular chains were calculated numerically for different crystal purity. It was shown that in stoichiometric compounds the thermoelectric figure of merit ZT remains small even after an increase of crystal perfection. The thermoelectric properties may be significantly enhanced by simultaneous increases of crystal perfection and electron concentration. The latter can be achieved by additional doping with donors. For less pure crystals, the interaction with impurities dominates the weak interchain interaction and the simpler one-dimensional (1D) physical model is applicable. When the impurity scattering is reduced, the interchain interaction begins to limit carrier mobility and use of the 3D physical model is required. The optimum properties enabling prediction of ZT ˜ 1 were determined.

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  8. 3D Dewetting for Crystal Patterning: Toward Regular Single-Crystalline Belt Arrays and Their Functionality.

    PubMed

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

    2016-03-01

    Arrays of unidirectional dewetting behaviors can be generated by using 3D-wettability-difference micropillars, yielding highly ordered organic single-crystalline belt arrays. These patterned organic belts show an improved mobility record and can be used as flexible pressure sensors with high sensitivity. PMID:26823061

  9. DNA Brick Crystals with Prescribed Depth

    PubMed Central

    Ke, Yonggang; Ong, Luvena L.; Sun, Wei; Song, Jie; Dong, Mingdong; Shih, William M.; Yin, Peng

    2014-01-01

    We describe a general framework for constructing two-dimensional crystals with prescribed depth and sophisticated three-dimensional features. These crystals may serve as scaffolds for the precise spatial arrangements of functional materials for diverse applications. The crystals are self-assembled from single-stranded DNA components called DNA bricks. We demonstrate the experimental construction of DNA brick crystals that can grow to micron-size in the lateral dimensions with precisely controlled depth up to 80 nanometers. They can be designed to display user-specified sophisticated three-dimensional nanoscale features, such as continuous or discontinuous cavities and channels, and to pack DNA helices at parallel and perpendicular angles relative to the plane of the crystals. PMID:25343605

  10. Crystallization of DNA-coated colloids

    PubMed Central

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

    2015-01-01

    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. PMID:26078020

  11. Crystallization of DNA-coated colloids.

    PubMed

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

    2015-01-01

    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. PMID:26078020

  12. Observation of superconductivity induced by a point contact on 3D Dirac semimetal Cd3 As2 crystals

    NASA Astrophysics Data System (ADS)

    Wang, He; Wang, Huichao; Liu, Haiwen; Lu, Hong; Yang, Wuhao; Jia, Shuang; Liu, Xiongjun; Xie, Xincheng; Wei, Jian; Wang, Jian

    The 3D Dirac semimetal state is located at the topological phase boundary and can potentially be driven into other topological phases including topological insulator, topological metal and the long-pursuit topological superconductor states. Crystalline Cd3As2 has been proposed and proved to be one of 3D Dirac semimetals which can survive in atmosphere. By precisely controlled point contact (PC) measurements, we observe the exotic superconductivity in the vicinity of the point contact region on the surface of Cd3As2 crystal, which might be induced by the local pressure in the out-of-plane direction from the metallic tip for PC. The observation of zero bias conductance peak (ZBCP) and double conductance peaks (DCPs) symmetric to zero bias further reveals p-wave like unconventional superconductivity in Cd3As2. Considering the special topological property of the 3D Dirac semimetal, our findings may indicate that the Cd3As2 crystal under certain conditions is a candidate of topological superconductor, which is predicted to support Majorana zero modes or gapless Majorana edge/surface modes on the boundary depending on the dimensionality of the material. This work was financially supported by the National Basic Research Program of China (Greanted Nos. 2012CB927400).

  13. Direct growth of single-crystal Pt nanowires on Sn@CNT Nanocable: 3D electrodes for highly active electrocatalysts.

    PubMed

    Sun, Shuhui; Zhang, Gaixia; Geng, Dongsheng; Chen, Yougui; Banis, Mohammad Norouzi; Li, Ruying; Cai, Mei; Sun, Xueliang

    2010-01-18

    A newly designed and fabricated novel three dimensional (3D) nanocomposite composed of single-crystal Pt nanowires (PtNW) and a coaxial nanocable support consisting of a tin nanowire and a carbon nanotube (Sn@CNT) is reported. This nanocomposite is fabricated by the synthesis of Sn@CNT nanocables by means of a thermal evaporation method, followed by the direct growth with PtNWs through a facile aqueous solution approach at room temperature. Electrochemical measurements demonstrate that the PtNW--Sn@CNT 3D electrode exhibits enhanced electrocatalytic performance in oxygen reduction reaction (ORR) for polymer electrolyte membrane fuel cells (PEMFCs), methanol oxidation (MOR) for direct methanol fuel cells (DMFCs), and CO tolerance compared with commercial ETEK Pt/C catalyst made of Pt nanoparticles. PMID:20024993

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

    PubMed

    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. PMID:21352920

  15. In situ 2D-extraction of DNA wheels by 3D through-solution transport.

    PubMed

    Yonamine, Yusuke; Cervantes-Salguero, Keitel; Nakanishi, Waka; Kawamata, Ibuki; Minami, Kosuke; Komatsu, Hirokazu; Murata, Satoshi; Hill, Jonathan P; Ariga, Katsuhiko

    2015-12-28

    Controlled transfer of DNA nanowheels from a hydrophilic to a hydrophobic surface was achieved by complexation of the nanowheels with a cationic lipid (2C12N(+)). 2D surface-assisted extraction, '2D-extraction', enabled structure-persistent transfer of DNA wheels, which could not be achieved by simple drop-casting. PMID:26583486

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

    SciTech Connect

    El-Azab, A.

    1999-07-01

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

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

    SciTech Connect

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

    1999-01-01

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

  18. Amino substituted benzimidazo[1,2-a]quinolines: Antiproliferative potency, 3D QSAR study and DNA binding properties.

    PubMed

    Perin, Nataša; Nhili, Raja; Cindrić, Maja; Bertoša, Branimir; Vušak, Darko; Martin-Kleiner, Irena; Laine, William; Karminski-Zamola, Grace; Kralj, Marijeta; David-Cordonnier, Marie-Hélène; Hranjec, Marijana

    2016-10-21

    We describe the synthesis, 3D-derived quantitative structure-activity relationship (QSAR), antiproliferative activity and DNA binding properties of a series of 2-amino, 5-amino and 2,5-diamino substituted benzimidazo[1,2-a]quinolines prepared by environmentally friendly uncatalyzed microwave assisted amination. The antiproliferative activities were assessed in vitro against colon, lung and breast carcinoma cell lines; activities ranged from submicromolar to micromolar. The strongest antiproliferative activity was demonstrated by 2-amino-substituted analogues, whereas 5-amino and or 2,5-diamino substituted derivatives resulted in much less activity. Derivatives bearing 4-methyl- or 3,5-dimethyl-1-piperazinyl substituents emerged as the most active. DNA binding properties and the mode of interaction of chosen substituted benzimidazo[1,2-a]quinolines prepared herein were studied using melting temperature studies, a series of spectroscopic studies (UV/Visible, fluorescence, and circular dichroism), and biochemical experiments (topoisomerase I-mediated DNA relaxation and DNase I footprinting experiments). Both compound 36 and its bis-quaternary iodide salt 37 intercalate between adjacent base pairs of the DNA helix while compound 33 presented a very weak topoisomerase I poisoning activity. A 3D-QSAR analysis was performed to identify hydrogen bonding properties, hydrophobicity, molecular flexibility and distribution of hydrophobic regions as these molecular properties had the highest impact on the antiproliferative activity against the three cell lines. PMID:27448912

  19. Construction and Structure Determination of a Three-Dimensional DNA Crystal.

    PubMed

    Simmons, Chad R; Zhang, Fei; Birktoft, Jens J; Qi, Xiaodong; Han, Dongran; Liu, Yan; Sha, Ruojie; Abdallah, Hatem O; Hernandez, Carina; Ohayon, Yoel P; Seeman, Nadrian C; Yan, Hao

    2016-08-10

    Structural DNA nanotechnology combines branched DNA junctions with sticky-ended cohesion to create self-assembling macromolecular architectures. One of the key goals of structural DNA nanotechnology is to construct three-dimensional (3D) crystalline lattices. Here we present a new DNA motif and a strategy that has led to the assembly of a 3D lattice. We have determined the X-ray crystal structures of two related constructs to 3.1 Å resolution using bromine-derivatized crystals. The motif we used employs a five-nucleotide repeating sequence that weaves through a series of two-turn DNA duplexes. The duplexes are tied into a layered structure that is organized and dictated by a concert of four-arm junctions; these in turn assemble into continuous arrays facilitated by sequence-specific sticky-ended cohesion. The 3D X-ray structure of these DNA crystals holds promise for the design of new structural motifs to create programmable 3D DNA lattices with atomic spatial resolution. The two arrays differ by the use of four or six repeats of the five-nucleotide units in the repeating but statistically disordered central strand. In addition, we report a 2D rhombuslike array formed from similar components. PMID:27447429

  20. Application of liquid crystal polymer films for photolithographic fabrication of 3D structures

    NASA Astrophysics Data System (ADS)

    Fox, Anna E.; Fontecchio, Adam K.

    2008-02-01

    In this paper, we demonstrate a silicon etching application of a holographically formed polymer dispersed liquid crystal (H-PDLC) photomask. H-PDLC is a periodically nanostructured material consisting of stratified layers of polymer and liquid crystal. Due to the natural random alignment of the liquid crystal axes with respect to the polymer layers, an index of refraction mismatch exists and a reflection occurs. Application of bias across the film aligns the liquid crystals and eliminates the index mismatch causing the film to become transparent. H-PDLC films have been shown to sufficiently attenuate the UV exposure dose in the photolithographic process when in the unbiased state, and can be electrically controlled to modulate the amount of UV transmission when electric field is applied. We show etch depth profiles of patterns masked on a silicon substrate using the H-PDLC photomask device compared with etch profiles of similar structures patterned with more conventional ink jet printed photomasks and chrome on quartz glass photomasks. We investigate reactive ion etching technique and potassium hydroxide wet etch technique.

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

  2. 3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression

    PubMed Central

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

    2016-01-01

    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. PMID:27052359

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

    PubMed

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

    2014-01-01

    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 PNA 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 50°C. 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. PMID:25760314

  4. Hierarchical self-assembly of hexagonal single-crystal nanosheets into 3D layered superlattices with high conductivity.

    PubMed

    Tao, Yulun; Shen, Yuhua; Yang, Liangbao; Han, Bin; Huang, Fangzhi; Li, Shikuo; Chu, Zhuwang; Xie, Anjian

    2012-06-21

    While the number of man-made nano superstructures realized by self-assembly is growing in recent years, assemblies of conductive polymer nanocrystals, especially for superlattices, are still a significant challenge, not only because of the simplicity of the shape of the nanocrystal building blocks and their interactions, but also because of the poor control over these parameters in the fabrication of more elaborate nanocrystals. Here, we firstly report a facile and general route to a new generation of 3D layered superlattices of polyaniline doped with CSA (PANI-CSA) and show how PANI crystallize and self-assemble, in a suitable single solution environment. In cyclohexane, 1D amorphous nanofibers transformed to 1D nanorods as building blocks, and then to 2D single-crystal nanosheets with a hexagonal phase, and lastly to 3D ordered layered superlattices with the narrowest polydispersity value (M(w)/M(n) = 1.47). Remarkably, all the instructions for the hierarchical self-assembly are encoded in the layered shape in other non-polar solvents (hexane, octane) and their conductivity in the π-π stacking direction is improved to about 50 S cm(-1), which is even higher than that of the highest previously reported value (16 S cm(-1)). The method used in this study is greatly expected to be readily scalable to produce superlattices of conductive polymers with high quality and low cost. PMID:22609947

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

    NASA Astrophysics Data System (ADS)

    Grothe, Rob; Rixon, Greg; Dabiri, Dana

    2007-11-01

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

  6. Self-assembly of 3D prestressed tensegrity structures from DNA

    PubMed Central

    Liedl, Tim; Högberg, Björn; Tytell, Jessica; Ingber, Donald E.; Shih, William M.

    2010-01-01

    Tensegrity or tensional integrity is a property of a structure that relies on a balance between components that are either in pure compression or in pure tension for its stability [1,2]. Tensegrity structures exhibit extremely high strength-to-weight ratios and great resilience, and are therefore widely used in engineering, robotics and architecture [3,4]. Here we report nanoscale, prestressed, three-dimensional tensegrity structures in which rigid bundles of DNA double helices resist compressive forces exerted by segments of single-stranded DNA that act as tension-bearing cables. Our DNA tensegrity structures can self-assemble against forces up to 14 pN, which is twice the stall force of powerful molecular motors such as kinesin or myosin [5,6]. The forces generated by this molecular prestressing mechanism can be employed to bend the DNA bundles or to actuate the entire structure through enzymatic cleavage at specific sites. In addition to being building blocks for nanostructures, tensile structural elements made of single-stranded DNA could be used to study molecular forces, cellular mechanotransduction, and other fundamental biological processes. PMID:20562873

  7. Genome-Wide Identification and 3D Modeling of Proteins involved in DNA Damage Recognition and Repair (Final Report)

    SciTech Connect

    Ruben A. Abagyan, PhD

    2004-04-15

    OAK-B135 DNA Damage Recognition and Repair (DDR and R) proteins play a critical role in cellular responses to low-dose radiation and are associated with cancer. the authors have performed a systematic, genome-wide computational analysis of genomic data for human genes involved in the DDR and R process. The significant achievements of this project include: (1) Construction of the computational pipeline for searching DDR and R genes, building and validation of 3D models of proteins involved in DDR and R; (2) Functional and structural annotation of the 3D models and generation of comprehensive lists of suggested knock-out mutations; (3) Important improvement of macromolecular docking technology and its application to predict the DNA-Protein complex conformation; (4) Development of a new algorithm for improved analysis of high-density oligonucleotide arrays for gene expression profiling; (5) Construction and maintenance of the DNA Damage Recognition and Repair Database; and (6) Producing 14 research papers (10 published and 4 in preparation).

  8. Clusters, molecular layers, and 3D crystals of water on Ni(111)

    SciTech Connect

    Thürmer, Konrad; Nie, Shu; Bartelt, Norman C.; Feibelman, Peter J.

    2014-11-14

    We examined the growth and stability of ice layers on Ni(111) up to ∼7 molecular layers (ML) thick using scanning tunneling microscopy. At low coverage, films were comprised of ∼1 nm wide two-dimensional (2D) clusters. Only above ∼0.5 ML did patches of continuous 2D layers emerge, coexisting with the clusters until the first ML was complete. The structure of the continuous layer is clearly different from that of the 2D clusters. Subsequently, a second molecular layer grew on top of the first. 3D crystallites started to form only after this 2nd ML was complete. 2D clusters re-appeared when thicker films were partially evaporated, implying that these clusters represent the equilibrium configuration at low coverage. Binding energies and image simulations computed with density functional theory suggest that the 2D clusters are partially dissociated and surrounded by H adatoms. The complete 2D layer contains only intact water molecules because of the lack of favorable binding sites for H atoms. We propose molecular structures for the 2D layer that are composed of the same pentagon-heptagon binding motif and water density observed on Pt(111). The similarity of the water structures on Pt and Ni suggests a general prescription for generating low-energy configurations on close-packed metal substrates.

  9. Inverted Yablonovite-like 3D photonic crystals fabricated by laser nanolithography

    NASA Astrophysics Data System (ADS)

    Shishkin, Ivan I.; Samusev, Kirill B.; Rybin, Mikhail V.; Limonov, Mikhail F.; Kivshar, Yuri S.; Gaidukeviciute, Arune; Kiyan, Roman V.; Chichkov, Boris N.

    2012-06-01

    We report on the fabrication of inverted Yablonovite-like three-dimensional photonic crystals by nonlinear optical nanolithography based on two-photon polymerization of a zirconium propoxide hybrid organic-inorganic material with Irgacure 369 as photo-initiator. Advantage of this material is ultra-low shrinkage that guaranty high fabrication fidelity. Images of the fabricated structure are obtained with a scanning electron microscope. The photonic crystal consists of three sets of nearly cylindrical structural elements directed along the three lattice vectors of the fcc lattice and cross each other at certain angles to produce inverted Yablonovite geometry. To investigate photonic properties of the inverted Yablonovite structures, we calculate the photonic band structure for ten lowest-frequency electromagnetic modes. In contrast to the direct Yablonovite structure that has a complete photonic band gap between the second and third bands, we find no complete photonic band gaps in the inverted Yablonovite lattice. This situation is opposite to the case of fcc lattice of close-packed dielectric spheres in air that has a complete photonic band gap only for the inverted geometry.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  11. Functionalizing designer DNA crystals with a triple-helical veneer.

    PubMed

    Rusling, David A; Chandrasekaran, Arun Richard; Ohayon, Yoel P; Brown, Tom; Fox, Keith R; Sha, Ruojie; Mao, Chengde; Seeman, Nadrian C

    2014-04-01

    DNA is a very useful molecule for the programmed self-assembly of 2D and 3D nanoscale objects.1 The design of these structures exploits Watson-Crick hybridization and strand exchange to stitch linear duplexes into finite assemblies.2-4 The dimensions of these complexes can be increased by over five orders of magnitude through self-assembly of cohesive single-stranded segments (sticky ends).5, 6 Methods that exploit the sequence addressability of DNA nanostructures will enable the programmable positioning of components in 2D and 3D space, offering applications such as the organization of nanoelectronics,7 the direction of biological cascades,8 and the structure determination of periodically positioned molecules by X-ray diffraction.9 To this end we present a macroscopic 3D crystal based on the 3-fold rotationally symmetric tensegrity triangle3, 6 that can be functionalized by a triplex-forming oligonucleotide on each of its helical edges. PMID:24615910

  12. Functionalizing Designer DNA Crystals with a Triple-Helical Veneer**

    PubMed Central

    Rusling, David A; Chandrasekaran, Arun Richard; Ohayon, Yoel P; Brown, Tom; Fox, Keith R; Sha, Ruojie; Mao, Chengde; Seeman, Nadrian C

    2014-01-01

    DNA is a very useful molecule for the programmed self-assembly of 2D and 3D nanoscale objects.[1] The design of these structures exploits Watson–Crick hybridization and strand exchange to stitch linear duplexes into finite assemblies.[2–4] The dimensions of these complexes can be increased by over five orders of magnitude through self-assembly of cohesive single-stranded segments (sticky ends).[5,6] Methods that exploit the sequence addressability of DNA nanostructures will enable the programmable positioning of components in 2D and 3D space, offering applications such as the organization of nanoelectronics,[7] the direction of biological cascades,[8] and the structure determination of periodically positioned molecules by X-ray diffraction.[9] To this end we present a macroscopic 3D crystal based on the 3-fold rotationally symmetric tensegrity triangle[3,6] that can be functionalized by a triplex-forming oligonucleotide on each of its helical edges. PMID:24615910

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

    PubMed Central

    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

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

    PubMed

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

    2016-02-01

    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. Genome-Wide Identification and 3D Modeling of Proteins involved in DNA Damage Recognition and Repair (Final Report)

    SciTech Connect

    Abagyan, Ruben; An, Jianghong

    2005-08-12

    DNA Damage Recognition and Repair (DDR&R) proteins play a critical role in cellular responses to low-dose radiation and are associated with cancer. We have performed a systematic, genome-wide computational analysis of genomic data for human genes involved in the DDR&R process. The significant achievements of this project include: 1) Construction of the computational pipeline for searching DDR&R genes, building and validation of 3D models of proteins involved in DDR&R; 2) Functional and structural annotation of the 3D models and generation of comprehensive lists of suggested knock-out mutations; and the development of a method to predict the effects of mutations. Large scale testing of technology to identify novel small binding pockets in protein structures leading to new DDRR inhibitor strategies 3) Improvements of macromolecular docking technology (see the CAPRI 1-3 and 4-5 results) 4) Development of a new algorithm for improved analysis of high-density oligonucleotide arrays for gene expression profiling; 5) Construction and maintenance of the DNA Damage Recognition and Repair Database; 6) Producing 15 research papers (12 published and 3 in preparation).

  16. 3D visualization of XFEL beam focusing properties using LiF crystal X-ray detector

    PubMed Central

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

    2015-01-01

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

  17. 3D visualization of XFEL beam focusing properties using LiF crystal X-ray detector

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  18. 3D visualization of XFEL beam focusing properties using LiF crystal X-ray detector.

    PubMed

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

    2015-01-01

    Here, we report, that by means of direct irradiation of lithium fluoride a (LiF) crystal, in situ 3D visualization of the SACLA XFEL focused beam profile along the propagation direction is realized, including propagation inside photoluminescence solid matter. High sensitivity and large dynamic range of the LiF crystal detector allowed measurements of the intensity distribution of the beam at distances far from the best focus as well as near the best focus and evaluation of XFEL source size and beam quality factor M(2). Our measurements also support the theoretical prediction that for X-ray photons with energies ~10 keV the radius of the generated photoelectron cloud within the LiF crystal reaches about 600 nm before thermalization. The proposed method has a spatial resolution ~0.4-2.0 μm for photons with energies 6-14 keV and potentially could be used in a single shot mode for optimization of different focusing systems developed at XFEL and synchrotron facilities. PMID:26634431

  19. 3D modeling of the molten zone shape created by an asymmetric HF EM field during the FZ crystal growth process

    NASA Astrophysics Data System (ADS)

    Rudevics, A.; Muiznieks, A.; Ratnieks, G.; Riemann, H.

    2005-06-01

    In the modern industrial floating zone (FZ) silicon crystal growth process by the needle-eye technique, the high frequency (HF) electromagnetic (EM) field plays a crucial role. The EM field melts a rotating poly silicon feed rod and maintains the zone of molten silicon, which is held by the rotating single crystal. To model such a system, the 2D axi-symmetric models can be used, however, due to the system's asymmetry (e.g., the asymmetry of the HF inductor) the applicability of such models is restricted. Therefore, the modeling of FZ process in three dimensions (3D) is necessary. This paper describes a new complex 3D mathematical model of the FZ crystal growth and a correspondingly developed software package Shape3D. A 3D calculation example for the realistic FZ system is also presented. Figs 25, Refs 9.

  20. Hierarchical self-assembly of hexagonal single-crystal nanosheets into 3D layered superlattices with high conductivity

    NASA Astrophysics Data System (ADS)

    Tao, Yulun; Shen, Yuhua; Yang, Liangbao; Han, Bin; Huang, Fangzhi; Li, Shikuo; Chu, Zhuwang; Xie, Anjian

    2012-05-01

    While the number of man-made nano superstructures realized by self-assembly is growing in recent years, assemblies of conductive polymer nanocrystals, especially for superlattices, are still a significant challenge, not only because of the simplicity of the shape of the nanocrystal building blocks and their interactions, but also because of the poor control over these parameters in the fabrication of more elaborate nanocrystals. Here, we firstly report a facile and general route to a new generation of 3D layered superlattices of polyaniline doped with CSA (PANI-CSA) and show how PANI crystallize and self-assemble, in a suitable single solution environment. In cyclohexane, 1D amorphous nanofibers transformed to 1D nanorods as building blocks, and then to 2D single-crystal nanosheets with a hexagonal phase, and lastly to 3D ordered layered superlattices with the narrowest polydispersity value (Mw/Mn = 1.47). Remarkably, all the instructions for the hierarchical self-assembly are encoded in the layered shape in other non-polar solvents (hexane, octane) and their conductivity in the π-π stacking direction is improved to about 50 S cm-1, which is even higher than that of the highest previously reported value (16 S cm-1). The method used in this study is greatly expected to be readily scalable to produce superlattices of conductive polymers with high quality and low cost.While the number of man-made nano superstructures realized by self-assembly is growing in recent years, assemblies of conductive polymer nanocrystals, especially for superlattices, are still a significant challenge, not only because of the simplicity of the shape of the nanocrystal building blocks and their interactions, but also because of the poor control over these parameters in the fabrication of more elaborate nanocrystals. Here, we firstly report a facile and general route to a new generation of 3D layered superlattices of polyaniline doped with CSA (PANI-CSA) and show how PANI crystallize and

  1. Modeling the crystal distribution of lead-sulfate in lead-acid batteries with 3D spatial resolution

    NASA Astrophysics Data System (ADS)

    Huck, Moritz; Badeda, Julia; Sauer, Dirk Uwe

    2015-04-01

    For the reliability of lead-acid batteries it is important to have an accurate prediction of its response to load profiles. A model for the lead-sulfate growth is presented, which is embedded in a physical-chemical model with 3D spatial resolution is presented which is used for analyzing the different mechanism influencing the cell response. One import factor is the chemical dissolution and precipitation of lead-sulfate, since its dissolution speed limits the charging reaction and the accumulation of indissolvable of lead-sulfate leads to capacity degradation. The cell performance/behavior is not only determined by the amount of the sulfate but also by the radii and distribution of the crystals. The presented model can be used to for an improved understanding of the interaction of the different mechanisms.

  2. Photolithographic fabrication of 3D Penrose-like quasi-photonic crystal polymeric templates utilizing lab-made phasemask

    NASA Astrophysics Data System (ADS)

    Torres-Lazos, Faraon

    Photonic crystals (PhC) have recently become of great interest because of their potential as replacement of electronics and/or supplement to semiconductors technology. The PhC's capability to make compact integrated optical circuits has already made possible the laboratory manufacture of an array of different types of optical waveguides, cavities and filters. The work presented here aimed to simultaneously fabricate a 3D-PhC templates employing six-beam holographic lithography. The basic procedures included recording gratings using interference field of laser sources in a photoresist coating on a glass substrate. The manufacturing method utilized only one optical element, a phasemask, drastically reducing the complexity of fabrication by eliminating the need multiple mirrors and beam splitters. Using this approach, a template can be created with a single exposure to laser source and just varying exposure times, increasing reproducibility.

  3. Modelling crystal plasticity by 3D dislocation dynamics and the finite element method: The Discrete-Continuous Model revisited

    NASA Astrophysics Data System (ADS)

    Vattré, A.; Devincre, B.; Feyel, F.; Gatti, R.; Groh, S.; Jamond, O.; Roos, A.

    2014-02-01

    A unified model coupling 3D dislocation dynamics (DD) simulations with the finite element (FE) method is revisited. The so-called Discrete-Continuous Model (DCM) aims to predict plastic flow at the (sub-)micron length scale of materials with complex boundary conditions. The evolution of the dislocation microstructure and the short-range dislocation-dislocation interactions are calculated with a DD code. The long-range mechanical fields due to the dislocations are calculated by a FE code, taking into account the boundary conditions. The coupling procedure is based on eigenstrain theory, and the precise manner in which the plastic slip, i.e. the dislocation glide as calculated by the DD code, is transferred to the integration points of the FE mesh is described in full detail. Several test cases are presented, and the DCM is applied to plastic flow in a single-crystal Nickel-based superalloy.

  4. Plasmonic photonic crystals realized through DNA-programmable assembly

    PubMed Central

    Park, Daniel J.; Zhang, Chuan; Ku, Jessie C.; Zhou, Yu; Schatz, George C.; Mirkin, Chad A.

    2015-01-01

    Three-dimensional dielectric photonic crystals have well-established enhanced light–matter interactions via high Q factors. Their plasmonic counterparts based on arrays of nanoparticles, however, have not been experimentally well explored owing to a lack of available synthetic routes for preparing them. However, such structures should facilitate these interactions based on the small mode volumes associated with plasmonic polarization. Herein we report strong light-plasmon interactions within 3D plasmonic photonic crystals that have lattice constants and nanoparticle diameters that can be independently controlled in the deep subwavelength size regime by using a DNA-programmable assembly technique. The strong coupling within such crystals is probed with backscattering spectra, and the mode splitting (0.10 and 0.24 eV) is defined based on dispersion diagrams. Numerical simulations predict that the crystal photonic modes (Fabry–Perot modes) can be enhanced by coating the crystals with a silver layer, achieving moderate Q factors (∼102) over the visible and near-infrared spectrum. PMID:25548175

  5. 3D ToF-SIMS Analysis of Peptide Incorporation into MALDI Matrix Crystals with Sub-micrometer Resolution

    NASA Astrophysics Data System (ADS)

    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.

  6. 3D ToF-SIMS Analysis of Peptide Incorporation into MALDI Matrix Crystals with Sub-micrometer Resolution.

    PubMed

    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. Graphical Abstract ᅟ. PMID:26419771

  7. Electrostatics and depletion determine competition between 2D nematic and 3D bundled phases of rod-like DNA nanotubes.

    PubMed

    Park, Chang-Young; Fygenson, Deborah K; Saleh, Omar A

    2016-06-21

    Rod-like particles form solutions of technological and biological importance. In particular, biofilaments such as actin and microtubules are known to form a variety of phases, both in vivo and in vitro, whose appearance can be controlled by depletion, confinement, and electrostatic interactions. Here, we utilize DNA nanotubes to undertake a comprehensive study of the effects of those interactions on two particular rod-like phases: a 2D nematic phase consisting of aligned rods pressed against a glass surface, and a 3D bundled network phase. We experimentally measure the stability of these two phases over a range of depletant concentrations and ionic strengths, finding that the 2D phase is slightly more stable than the 3D phase. We formulate a quantitative model of phase stability based on consideration of pairwise rod-rod and rod-surface interactions; notably, we include a careful accounting of solution electrostatics interactions using an effective-charge strategy. The model is relatively simple and contains no free parameters, yet predicts phase boundaries in good agreement with the experiment. Our results indicate that electrostatic interactions, rather than depletion, are largely responsible for the enhanced stability of the 2D phase. This work provides insight into the polymorphism of rod-like solutions, indicating why certain phases appear, and providing a means (and a predictive model) for controlling those phases. PMID:27126684

  8. DNA vaccines expressing soluble CD4-envelope proteins fused to C3d elicit cross-reactive neutralizing antibodies to HIV-1

    SciTech Connect

    Bower, Joseph F.; Green, Thomas D.; Ross, Ted M. . E-mail: tmr15@pitt.edu

    2004-10-25

    DNA vaccines expressing the envelope (Env) of the human immunodeficiency virus type 1 (HIV-1) have been relatively ineffective at generating high-titer, long-lasting, neutralizing antibodies in a variety of animal models. In this study, DNA vaccines were constructed to express a fusion protein of the soluble human CD4 (sCD4) and the gp120 subunit of the HIV-1 envelope. To enhance the immunogenicity of the expressed fusion protein, three copies of the murine C3d (mC3d{sub 3}) were added to the carboxyl terminus of the complex. Monoclonal antibodies that recognize CD4-induced epitopes on gp120 efficiently bound to sCD4-gp120 or sCD4-gp120-mC3d{sub 3}. In addition, both sCD4-gp120 and sCD4-gp120-mC3d{sub 3} bound to cells expressing appropriate coreceptors in the absence of cell surface hCD4. Mice (BALB/c) vaccinated with DNA vaccines expressing either gp120-mC3d{sub 3} or sCD4-gp120-mC3d{sub 3} elicited antibodies that neutralized homologous virus infection. However, the use of sCD4-gp120-mC3d{sub 3}-DNA elicited the highest titers of neutralizing antibodies that persisted after depletion of anti-hCD4 antibodies. Interestingly, only mice vaccinated with DNA expressing sCD4-gp120-mC3d{sub 3} had antibodies that elicited cross-protective neutralizing antibodies. The fusion of sCD4 to the HIV-1 envelope exposes neutralizing epitopes that elicit broad protective immunity when the fusion complex is coupled with the molecular adjuvant, C3d.

  9. Crystal structure of a DNA catalyst.

    PubMed

    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. PMID:26735012

  10. Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components

    NASA Astrophysics Data System (ADS)

    Gerling, Thomas; Wagenbauer, Klaus F.; Neuner, Andrea M.; Dietz, Hendrik

    2015-03-01

    We demonstrate that discrete three-dimensional (3D) DNA components can specifically self-assemble in solution on the basis of shape-complementarity and without base pairing. Using this principle, we produced homo- and heteromultimeric objects, including micrometer-scale one- and two-stranded filaments and lattices, as well as reconfigurable devices, including an actuator, a switchable gear, an unfoldable nanobook, and a nanorobot. These multidomain assemblies were stabilized via short-ranged nucleobase stacking bonds that compete against electrostatic repulsion between the components’ interfaces. Using imaging by electron microscopy, ensemble and single-molecule fluorescence resonance energy transfer spectroscopy, and electrophoretic mobility analysis, we show that the balance between attractive and repulsive interactions, and thus the conformation of the assemblies, may be finely controlled by global parameters such as cation concentration or temperature and by an allosteric mechanism based on strand-displacement reactions.

  11. Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components.

    PubMed

    Gerling, Thomas; Wagenbauer, Klaus F; Neuner, Andrea M; Dietz, Hendrik

    2015-03-27

    We demonstrate that discrete three-dimensional (3D) DNA components can specifically self-assemble in solution on the basis of shape-complementarity and without base pairing. Using this principle, we produced homo- and heteromultimeric objects, including micrometer-scale one- and two-stranded filaments and lattices, as well as reconfigurable devices, including an actuator, a switchable gear, an unfoldable nanobook, and a nanorobot. These multidomain assemblies were stabilized via short-ranged nucleobase stacking bonds that compete against electrostatic repulsion between the components' interfaces. Using imaging by electron microscopy, ensemble and single-molecule fluorescence resonance energy transfer spectroscopy, and electrophoretic mobility analysis, we show that the balance between attractive and repulsive interactions, and thus the conformation of the assemblies, may be finely controlled by global parameters such as cation concentration or temperature and by an allosteric mechanism based on strand-displacement reactions. PMID:25814577

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

    PubMed

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

    2016-02-01

    A new 3D Ag(I)-based coordination network, [Ag2(pz)(bdc)·H2O]n (1; pz = pyrazine and H2bdc = benzene-1,3-dicarboxylic acid), was constructed by one-pot assembly and structurally established by single-crystal X-ray diffraction at different temperatures. Upon cooling from 298 to 93 K, 1 undergo an interesting single-crystal to single-crystal phase transition from orthorhombic Ibca (Z = 16) to Pccn (Z = 32) at around 148 K. Both phases show a rare 2-fold-interpenetrated 4-connected lvt network but incorporate different [Ag2(COO)2] dimeric secondary building units. It is worth mentioning that complex 1 shows red- and blue-shifted luminescences in the 290-170 and 140-80 K temperature ranges, respectively. The variable-temperature single-crystal X-ray crystallographic studies suggest that the argentophilic interactions and rigidity of the structure dominated the luminescence chromism trends at the respective temperature ranges. Upon being mechanically ground, 1 exhibits a slight mechanoluminescence red shift from 589 to 604 nm at 298 K. PMID:26828950

  13. 3D mathematical model system for melt hydrodynamics in the silicon single crystal FZ-growth process with rotating magnetic field

    NASA Astrophysics Data System (ADS)

    Lacis, K.; Muiznieks, A.; Ratnieks, G.

    2005-06-01

    A system of three-dimensional numerical models is described to analyse the melt hydrodynamics in the floating zone crystal growth by the needle-eye technique under a rotating magnetic field for the production of high quality silicon single crystals of large diameters big( 100dots 200 mm big). Since the pancake inductor has only one turn, the high frequency (HF) electromagnetic (EM) field and the distribution of heat sources and EM forces on the melt free surface have distinct asymmetric features. This asymmetry together with the displacement of the crystal and feed rod axis and crystal rotation manifests itself as three dimensional hydrodynamic, thermal and dopant concentration fields in the molten zone and causes variations of resistivity in the grown single crystal, which are known as the so-called rotational striations. Additionally, the rotating magnetic field can be used to influence the melt hydrodynamics and to reduce the flow asymmetry. In the present 3D model system, the shape of the molten zone is obtained from symmetric FZ shape calculations. The asymmetric HF EM field is calculated by the 3D boundary element method. The low-frequency rotating magnetic field and a corresponding force density distribution in the melt are calculated by the 3D finite element method. The obtained asymmetric HF field power distribution on the free melt surface, the corresponding HF EM forces and force density of the rotating magnetic field are used for the coupled calculation of 3D steady-state hydrodynamic and temperature fields in the molten zone on a body fitted structured 3D grid by a commercial program package with a control volume approach. Beside the EM forces, also the buoyancy and Marangoni forces are considered. After HD calculations a corresponding 3D dopant concentration field is calculated and used to derive the variations resistivity in the grown crystal. The capability of the system of models is illustrated by a calculation example of a realistic FZ system

  14. Automated Quantification of DNA Demethylation Effects in Cells via 3D Mapping of Nuclear Signatures and Population Homogeneity Assessment1

    PubMed Central

    Gertych, Arkadiusz; Wawrowsky, Kolja A.; Lindsley, Erik; Vishnevsky, Eugene; Farkas, Daniel L.; Tajbakhsh, Jian

    2009-01-01

    Background Today’s advanced microscopic imaging applies to the preclinical stages of drug discovery that employ high-throughput and high-content three-dimensional (3D) analysis of cells to more efficiently screen candidate compounds. Drug efficacy can be assessed by measuring response homogeneity to treatment within a cell population. In this study topologically quantified nuclear patterns of methylated cytosine and global nuclear DNA are utilized as signatures of cellular response to the treatment of cultured cells with the demethylating anti-cancer agents: 5-azacytidine (5-AZA) and octreotide (OCT). Methods Mouse pituitary folliculostellate TtT-GF cells treated with 5-AZA and OCT for 48 hours, and untreated populations, were studied by immunofluorescence with a specific antibody against 5-methylcytosine (MeC), and 4,6-diamidino-2-phenylindole (DAPI) for delineation of methylated sites and global DNA in nuclei (n=163). Cell images were processed utilizing an automated 3D analysis software that we developed by combining seeded watershed segmentation to extract nuclear shells with measurements of Kullback-Leibler’s (K-L) divergence to analyze cell population homogeneity in the relative nuclear distribution patterns of MeC versus DAPI stained sites. Each cell was assigned to one of the four classes: similar, likely similar, unlikely similar and dissimilar. Results Evaluation of the different cell groups revealed a significantly higher number of cells with similar or likely similar MeC/DAPI patterns among untreated cells (~100%), 5-AZA-treated cells (90%), and a lower degree of same type of cells (64%) in the OCT-treated population. The latter group contained (28%) of unlikely similar or dissimilar (7%) cells. Conclusion Our approach was successful in the assessment of cellular behavior relevant to the biological impact of the applied drugs, i.e. the reorganization of MeC/DAPI distribution by demethylation. In a comparison with other metrics, K-L divergence has

  15. Molecular cloning and 3D structure modeling of APEX1, DNA base excision repair enzyme from the Camel, Camelus dromedarius.

    PubMed

    Ataya, Farid Shokry; Fouad, Dalia; Malik, Ajamaluddin; Saeed, Hesham Mahmoud

    2012-01-01

    The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Desert. It is exposed most of its life to both intrinsic and extrinsic genotoxic factors that are known to cause gross DNA alterations in many organisms. Ionic radiation and sunlight are known producers of Reactive Oxygen Species (ROS), one of the causes for DNA lesions. The damaged DNA is repaired by many enzymes, among of them Base Excision Repair enzymes, producing the highly mutagenic apurinic/apyrimidinicsites (AP sites). Therefore, recognition of AP sites is fundamental to cell/organism survival. In the present work, the full coding sequence of a putative cAPEX1 gene was amplified for the first time from C. dromedarius by RT-PCR and cloned (NCBI accession number are HM209828 and ADJ96599 for nucleotides and amino acids, respectively). cDNA sequencing was deduced to be 1041 nucleotides, of which 954 nucleotides encode a protein of 318 amino acids, similar to the coding region of the APEX1 gene and the protein from many other species. The calculated molecular weight and isoelectric point of cAPEX1 using Bioinformatics tools was 35.5 kDa and 8.11, respectively. The relative expressions of cAPEX1 in camel kidney, spleen, lung and testis were examined using qPCR and compared with that of the liver using a 18S ribosomal subunit as endogenous control. The highest level of cAPEX1 transcript was found in the testis; 325% higher than the liver, followed by spleen (87%), kidney (20%) and lung (5%), respectively. The cAPEX1 is 94%-97% similar to their mammalian counterparts. Phylogenetic analysis revealed that cAPEX1 is grouped together with that of S. scrofa. The predicted 3D structure of cAPEX1 has similar folds and topology with the human (hAPEX1). The root-mean-square deviation (rmsd) between cAPEX1 and hAPEX1 was 0.582 and the Q-score was 0.939. PMID:22942721

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

    PubMed

    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. PMID:27218474

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

    NASA Astrophysics Data System (ADS)

    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

  18. 3D Micro-topography of Transferred Laboratory and Natural Ice Crystal Surfaces Imaged by Cryo and Environmental Scanning Electron Microscopy

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    PubMed

    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. PMID:26258358

  20. A SiPM-based isotropic-3D PET detector X'tal cube with a three-dimensional array of 1 mm3 crystals

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

    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 mm3 cubic crystals, in contrast to our previous development using 3.0 mm3 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 mm3 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 mm2, 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.

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

    PubMed

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

    2011-11-01

    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. PMID:21971079

  2. Importance of the DNA "bond" in programmable nanoparticle crystallization.

    PubMed

    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. PMID:25298535

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

    SciTech Connect

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

    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.

  4. Design, Synthesis, and X-ray Crystal Structures of 2,4-Diaminofuro[2,3-d]pyrimidines as Multireceptor Tyrosine Kinase and Dihydrofolate Reductase Inhibitors

    PubMed Central

    Gangjee, Aleem; Li, Wei; Lin, Lu; Zeng, Yibin; Ihnat, Michael; Warnke, Linda A.; Green, Dixy W.; Cody, Vivian; Pace, Jim; Queener, Sherry F.

    2009-01-01

    To optimize dual receptor tyrosine kinase (RTK) and dihydrofolate reductase (DHFR) inhibition, the E- and Z-isomers of 5-[2-(2-methoxyphenyl)prop-1-en-1-yl]furo[2,3-d]pyrimidine-2,4-diamines (1a and 1b) were separated by HPLC and the X-ray crystal structures (2.0 Å and 1.4 Å respectively) with mouse DHFR and NADPH as well as 1b with human DHFR (1.5 Å) were determined. The E- and Z-isomers adopt different binding modes when bound to mouse DHFR. A series of 2,4-diaminofuro[2,3-d]pyrimidines 2–13 were designed and synthesized using the X-ray crystal structures of 1a and 1b with DHFR to increase their DHFR inhibitory activity. Wittig reactions of appropriate 2-methoxyphenyl ketones with 2,4-diamino-6-chloromethyl furo[2,3-d]pyrimidine afforded the C8–C9 unsaturated compounds 2–7 and catalytic reduction gave the saturated 8–13. Homologation of the C9-methyl analog maintains DHFR inhibitory activity. In addition, inhibition of EGFR and PDGFR-β were discovered for saturated C9-homologated analogs 9 and 10 that were absent in the saturated C9-methyl analogs. PMID:19748785

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

    PubMed Central

    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

    2016-01-01

    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. PMID:27097672

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

    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

    2016-01-01

    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. PMID:27097672

  8. Light control in Ge2Sb2Te5-coated opaline photonic crystals mediated by interplay of Wood anomalies and 3D Bragg diffraction

    NASA Astrophysics Data System (ADS)

    Pevtsov, A. B.; Poddubny, A. N.; Yakovlev, S. A.; Kurdyukov, D. A.; Golubev, V. G.

    2013-04-01

    We present experimental and theoretical study of light reflection spectra from hybrid structures formed by Ge2Sb2Te5 chalcogenide film on top of 3D opaline photonic crystal. We demonstrate the presence of diffraction anomalies (Wood anomalies) in the spectra. These anomalies are caused by the light scattering on the hybrid structure surface of hexagonal symmetry. To interpret the experimental results, we develop a qualitative theoretical model, taking into account the dispersion of quasi-waveguide modes supported by the surface layer of the hybrid structure. We consider the conditions for the coupling between the Bragg resonances associated with the diffraction of light on the 3D opal lattice and the resonances due to Wood anomalies.

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

    SciTech Connect

    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.

  10. On-chip concentration of bacteria using a 3D dielectrophoretic chip and subsequent laser-based DNA extraction in the same chip

    NASA Astrophysics Data System (ADS)

    Cho, Yoon-Kyoung; Kim, Tae-hyeong; Lee, Jeong-Gun

    2010-06-01

    We report the on-chip concentration of bacteria using a dielectrophoretic (DEP) chip with 3D electrodes and subsequent laser-based DNA extraction in the same chip. The DEP chip has a set of interdigitated Au post electrodes with 50 µm height to generate a network of non-uniform electric fields for the efficient trapping by DEP. The metal post array was fabricated by photolithography and subsequent Ni and Au electroplating. Three model bacteria samples (Escherichia coli, Staphylococcus epidermidis, Streptococcus mutans) were tested and over 80-fold concentrations were achieved within 2 min. Subsequently, on-chip DNA extraction from the concentrated bacteria in the 3D DEP chip was performed by laser irradiation using the laser-irradiated magnetic bead system (LIMBS) in the same chip. The extracted DNA was analyzed with silicon chip-based real-time polymerase chain reaction (PCR). The total process of on-chip bacteria concentration and the subsequent DNA extraction can be completed within 10 min including the manual operation time.

  11. Size effects in spin-crossover nanoparticles in framework of 2D and 3D Ising-like breathing crystal field model

    NASA Astrophysics Data System (ADS)

    Gudyma, Iu.; Maksymov, A.; Spinu, L.

    2015-10-01

    The spin-crossover nanoparticles of different sizes and stochastic perturbations in external field taking into account the influence of the dimensionality of the lattice was studied. The analytical tools used for the investigation of spin-crossover system are based on an Ising-like model described using of the breathing crystal field concept. The changes of transition temperatures characterizing the systems' bistable properties for 2D and 3D lattices, and their dependence on its size and fluctuations strength were obtained. The state diagrams with hysteretic and non-hysteretic behavior regions have also been determined.

  12. 3D-Modeling of deformed halite hopper crystals: Object based image analysis and support vector machine, a first evaluation

    NASA Astrophysics Data System (ADS)

    Leitner, Christoph; Hofmann, Peter; Marschallinger, Robert

    2014-05-01

    Halite hopper crystals are thought to develop by displacive growth in unconsolidated mud (Gornitz & Schreiber, 1984). The Alpine Haselgebirge, but also e.g. the salt deposits of the Rhine graben (mined at the beginning of the 20th century), comprise hopper crystals with shapes of cuboids, parallelepipeds and rhombohedrons (Görgey, 1912). Obviously, they deformed under oriented stress, which had been tried to reconstruct with respect to the sedimentary layering (Leitner et al., 2013). In the present work, deformed halite hopper crystals embedded in mudrock were automated reconstructed. Object based image analysis (OBIA) has been used successfully in remote sensing for 2D images before. The present study represents the first time that the method was used for reconstruction of three dimensional geological objects. First, manually a reference (gold standard) was created by redrawing contours of the halite crystals on each HRXCT scanning slice. Then, for OBIA, the computer program eCognition was used. For the automated reconstruction a rule set was developed. Thereby, the strength of OBIA was to recognize all objects similar to halite hopper crystals and in particular to eliminate cracks. In a second step, all the objects unsuitable for a structural deformation analysis were dismissed using a support vector machine (SVM) (clusters, polyhalite-coated crystals and spherical halites) The SVM simultaneously drastically reduced the number of halites. From 184 OBIA-objects 67 well shaped remained, which comes close to the number of pre-selected 52 objects. To assess the accuracy of the automated reconstruction, the result before and after SVM was compared to the reference, i.e. the gold standard. State-of the art per-scene statistics were extended to a per-object statistics. Görgey R (1912) Zur Kenntnis der Kalisalzlager von Wittelsheim im Ober-Elsaß. Tschermaks Mineral Petrogr Mitt 31:339-468 Gornitz VM, Schreiber BC (1981) Displacive halite hoppers from the dead sea

  13. Liquid Crystal Ordering of Random DNA Oligomers

    NASA Astrophysics Data System (ADS)

    Bellini, Tommaso; Zanchetta, Giuliano; Fraccia, Tommaso; Cerbino, Roberto; Tsai, Ethan; Moran, Mark; Smith, Gregory; Walba, David; Clark, Noel

    2012-02-01

    Concentrated solutions of DNA oligomers (6 to 20 base pairs) organize into chiral nematic (NEM) and columnar (COL) liquid crystal (LC) phases. When the oligomer duplexes are mixed with single strands, LC phase formation proceeds through macroscopic phase separation, as a consequence of the combination of various self-assembly processes including strand pairing, reversible linear aggregation, demixing and LC ordering. We extended our investigation to the case of LC ordering in oligonucleotides whose sequences are partially or entirely randomly chosen, and we observed LC phases even in entirely random 20mers, corresponding to a family of 4^20 10^12 different sequences. We have tracked the origin of this behaviour: random sequences pair into generally defected duplexes, a large fraction of them terminating with stretches of unpaired bases (overhangs); overhangs promote linear aggregation of duplexes, with a mean strength depending on the overhang length; LC formation is accompanied by a phase separation where the duplexes with longer overhangs aggregate to form COL LC domains that coexist with an isotropic fluid rich in duplexes whose structure cannot aggregate.

  14. Electric transport in 3D photonic crystal intermediate reflectors for micromorph thin-film tandem solar cells

    NASA Astrophysics Data System (ADS)

    Üpping, J.; Bielawny, A.; Lee, S.; Knez, M.; Carius, R.; Wehrspohn, R. B.

    2009-08-01

    The progress of 3D photonic intermediate reflectors for micromorph silicon tandem cells towards a first prototype cell is presented. Intermediate reflectors enhance the absorption of spectrally-selected light in the top cell and decrease the current mismatch between both junctions. A numerical method to predict filter properties for optimal current matching is presented. Our device is an inverted opal structure made of ZnO and fabricated using self-organized nanoparticles and atomic layer deposition for conformal coating. In particular, the influence of ZnO-doping and replicated cracks during drying of the opal is discussed with respect to conductivity and optical properties. A first prototype is compared to a state-of-the-art reference cell.

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

    NASA Astrophysics Data System (ADS)

    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.

  16. Beyond textbook illustrations: Hand-held models of ordered DNA and protein structures as 3D supplements to enhance student learning of helical biopolymers.

    PubMed

    Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2010-11-01

    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 report a study on how our students learned more from using our ordered DNA and protein models assembled from colored computer-printouts on transparency film sheets that have useful structural details. Our models (reported in BAMBED 2009), having certain distinguished features, helped our students to grasp various aspects of these biopolymers that they usually find difficult. Quantitative and qualitative learning data from this study are reported. PMID:21567863

  17. Duality between the dynamics of line-like brushes of point defects in 2D and strings in 3D in liquid crystals.

    PubMed

    Digal, Sanatan; Ray, Rajarshi; Saumia, P S; Srivastava, Ajit M

    2013-10-01

    We analyze the dynamics of dark brushes connecting point vortices of strength ±1 formed in the isotropic-nematic phase transition of a thin layer of nematic liquid crystals, using a crossed polarizer set up. The evolution of the brushes is seen to be remarkably similar to the evolution of line defects in a three-dimensional nematic liquid crystal system. Even phenomena like the intercommutativity of strings are routinely observed in the dynamics of brushes. We test the hypothesis of a duality between the two systems by determining exponents for the coarsening of total brush length with time as well as shrinking of the size of an isolated loop. Our results show scaling behavior for the brush length as well as the loop size with corresponding exponents in good agreement with the 3D case of string defects. PMID:24026004

  18. A study of the impurity structure for 3d 3 (Cr 3+ and Mn 4+) ions doped into rutile TiO 2 crystal

    NASA Astrophysics Data System (ADS)

    Açıkgöz, Muhammed

    2012-02-01

    The local environment around 3d 3 (Cr 3+ and Mn 4+) ions doped into rutile TiO 2 crystals has been investigated using superposition model (SPM) analysis. The zero-field splitting (ZFS) parameters (ZFSPs) D and E are modeled for the Cr 3+ and Mn 4+ ions at both the substitutional Ti sites with local symmetry orthorhombic D2h and the interstitial sites (ISs) with the same symmetry. Several model parameter sets are adopted so as to acquire the best agreement between the calculated ZFSPs and those measured by electron magnetic resonance (EMR). The feasible values of the structural distortions (Δ RY, Δ RXZ and Δ θ) resulting from dopant Cr 3+ and Mn 4+ ions are determined. As a result, it is confirmed that Mn 4+ ions substitute for Ti 4+ sites in rutile TiO 2 crystal; however, it is suggested that Cr 3+ ions may replace at not only Ti 4+ site but also IS.

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    Three new 1D to 3D complexes, namely, {[Ni(btec)(Himb)2(H2O)2]·6H2O}n (1), {[Cd(btec)0.5(imb)(H2O)]·1.5H2O}n (2), and {[Zn(btec)0.5(imb)]·H2O}n (3) (H4btec=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 (53·62·7)(52·64). Complex 3 presents a 3D framework with a point symbol of (4·64·8)(42·62·82). Moreover, their IR spectra, PXRD patterns, thermogravimetric curves, and luminescent emissions were studied at room temperature.

  20. Quantitative 3D Fluorescence Imaging of Single Catalytic Turnovers Reveals Spatiotemporal Gradients in Reactivity of Zeolite H-ZSM-5 Crystals upon Steaming.

    PubMed

    Ristanović, Zoran; Hofmann, Jan P; De Cremer, Gert; Kubarev, Alexey V; Rohnke, Marcus; Meirer, Florian; Hofkens, Johan; Roeffaers, Maarten B J; Weckhuysen, Bert M

    2015-05-27

    Optimizing the number, distribution, and accessibility of Brønsted acid sites in zeolite-based catalysts is of a paramount importance to further improve their catalytic performance. However, it remains challenging to measure real-time changes in reactivity of single zeolite catalyst particles by ensemble-averaging characterization methods. In this work, a detailed 3D single molecule, single turnover sensitive fluorescence microscopy study is presented to quantify the reactivity of Brønsted acid sites in zeolite H-ZSM-5 crystals upon steaming. This approach, in combination with the oligomerization of furfuryl alcohol as a probe reaction, allowed the stochastic behavior of single catalytic turnovers and temporally resolved turnover frequencies of zeolite domains smaller than the diffraction limited resolution to be investigated with great precision. It was found that the single turnover kinetics of the parent zeolite crystal proceeds with significant spatial differences in turnover frequencies on the nanoscale and noncorrelated temporal fluctuations. Mild steaming of zeolite H-ZSM-5 crystals at 500 °C led to an enhanced surface reactivity, with up to 4 times higher local turnover rates than those of the parent H-ZSM-5 crystals, and revealed remarkable heterogeneities in surface reactivity. In strong contrast, severe steaming at 700 °C significantly dealuminated the zeolite H-ZSM-5 material, leading to a 460 times lower turnover rate. The differences in measured turnover activities are explained by changes in the 3D aluminum distribution due to migration of extraframework Al-species and their subsequent effect on pore accessibility, as corroborated by time-of-flight secondary ion mass spectrometry (TOF-SIMS) sputter depth profiling data. PMID:25867455

  1. Quantitative 3D Fluorescence Imaging of Single Catalytic Turnovers Reveals Spatiotemporal Gradients in Reactivity of Zeolite H-ZSM-5 Crystals upon Steaming

    PubMed Central

    2015-01-01

    Optimizing the number, distribution, and accessibility of Brønsted acid sites in zeolite-based catalysts is of a paramount importance to further improve their catalytic performance. However, it remains challenging to measure real-time changes in reactivity of single zeolite catalyst particles by ensemble-averaging characterization methods. In this work, a detailed 3D single molecule, single turnover sensitive fluorescence microscopy study is presented to quantify the reactivity of Brønsted acid sites in zeolite H-ZSM-5 crystals upon steaming. This approach, in combination with the oligomerization of furfuryl alcohol as a probe reaction, allowed the stochastic behavior of single catalytic turnovers and temporally resolved turnover frequencies of zeolite domains smaller than the diffraction limited resolution to be investigated with great precision. It was found that the single turnover kinetics of the parent zeolite crystal proceeds with significant spatial differences in turnover frequencies on the nanoscale and noncorrelated temporal fluctuations. Mild steaming of zeolite H-ZSM-5 crystals at 500 °C led to an enhanced surface reactivity, with up to 4 times higher local turnover rates than those of the parent H-ZSM-5 crystals, and revealed remarkable heterogeneities in surface reactivity. In strong contrast, severe steaming at 700 °C significantly dealuminated the zeolite H-ZSM-5 material, leading to a 460 times lower turnover rate. The differences in measured turnover activities are explained by changes in the 3D aluminum distribution due to migration of extraframework Al-species and their subsequent effect on pore accessibility, as corroborated by time-of-flight secondary ion mass spectrometry (TOF-SIMS) sputter depth profiling data. PMID:25867455

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

    SciTech Connect

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

    2014-10-15

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

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

    SciTech Connect

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

    2010-01-01

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

  4. Spin glass and semiconducting behavior in one-dimensional BaFe2-dSe3 (d~2) crystals

    SciTech Connect

    Saparov, Bayrammurad I; Calder, Stuart A; Sipos, Balazs; Cao, Huibo; Chi, Songxue; Singh, David J; Christianson, Andrew D; Lumsden, Mark D; Sefat, A. S.

    2011-01-01

    We investigate the physical properties and electronic structure of BaFe{sub 1.79(2)}Se{sub 3} crystals, which were grown out of tellurium flux. The crystal structure of the compound, an iron-deficient derivative of the ThCr{sub 2}Si{sub 2}-type, is built upon edge-shared FeSe{sub 4} tetrahedra fused into double chains. The semiconducting BaFe{sub 1.79(2)}Se{sub 3} ({rho}{sub 295K} = 0.18 {Omega} {center_dot} cm and E{sub g} = 0.30 eV) does not order magnetically; however, there is evidence for short-range magnetic correlations of spin glass type (T{sub f} {approx} 50 K) in magnetization, heat capacity, and neutron diffraction results. A one-third substitution of selenium with sulfur leads to a slightly higher electrical conductivity ({rho}{sub 295K } = 0.11 {Omega} {center_dot} cm and E{sub g} = 0.22 eV) and a lower spin glass freezing temperature (T{sub f} {approx} 15 K), corroborating with higher electrical conductivity reported for BaFe{sub 2}S{sub 3}. According to the electronic structure calculations, BaFe{sub 2}Se{sub 3} can be considered as a one-dimensional ladder structure with a weak interchain coupling.

  5. Monitoring the formation of carbide crystal phases during the thermal decomposition of 3d transition metal dicarboxylate complexes

    SciTech Connect

    Huba, ZJ; Carpenter, EE

    2014-06-06

    Single molecule precursors can help to simplify the synthesis of complex alloys by minimizing the amount of necessary starting reagents. However, single molecule precursors are time consuming to prepare with very few being commercially available. In this study, a simple precipitation method is used to prepare Fe, Co, and Ni fumarate and succinate complexes. These complexes were then thermally decomposed in an inert atmosphere to test their efficiency as single molecule precursors for the formation of metal carbide phases. Elevated temperature X-ray diffraction was used to identify the crystal phases produced upon decomposition of the metal dicarboxylate complexes. Thermogravimetric analysis coupled with an infrared detector was used to identify the developed gaseous decomposition products. All complexes tested showed a reduction from the starting M2+ oxidation state to the M oxidation state, upon decomposition. Also, each complex tested showed CO2 and H2O as gaseous decomposition products. Nickel succinate, iron succinate, and iron fumarate complexes were found to form carbide phases upon decomposition. This proves that transition metal dicarboxylate salts can be employed as efficient single molecule precursors for the formation of metal carbide crystal phases.

  6. Dynamic Properties of DNA-Programmable Nanoparticle Crystallization.

    PubMed

    Yu, Qiuyan; Zhang, Xuena; Hu, Yi; Zhang, Zhihao; Wang, Rong

    2016-08-23

    The dynamics of DNA hybridization is very important in DNA-programmable nanoparticle crystallization. Here, coarse-grained molecular dynamics is utilized to explore the structural and dynamic properties of DNA hybridizations for a self-complementary DNA-directed nanoparticle self-assembly system. The hexagonal close-packed (HCP) and close-packed face-centered cubic (FCC) ordered structures are identified for the systems of different grafted DNA chains per nanoparticle, which are in good agreement with the experimental results. Most importantly, the dynamic crystallization processes of DNA hybridizations are elucidated by virtue of the mean square displacement, the percentage of hybridizations, and the lifetime of DNA bonds. The lifetime can be modeled by the DNA dehybridization, which has an exponential form. The lifetime of DNA bonds closely depends on the temperature. A suitable temperature for the DNA-nanoparticle crystallization is obtained in the work. Moreover, a too large volume fraction hinders the self-assembly process due to steric effects. This work provides some essential information for future design of nanomaterials. PMID:27409362

  7. Probing the 3D structure of cornea-like collagen liquid crystals with polarization-resolved SHG microscopy.

    PubMed

    Teulon, Claire; Tidu, Aurélien; Portier, François; Mosser, Gervaise; Schanne-Klein, Marie-Claire

    2016-07-11

    This work aims at characterizing the three-dimensional organization of liquid crystals composed of collagen, in order to determine the physico-chemical conditions leading to highly organized structures found in biological tissues such as cornea. To that end, we use second-harmonic generation (SHG) microscopy, since aligned collagen structures have been shown to exhibit intrinsic SHG signals. We combine polarization-resolved SHG experiments (P-SHG) with the theoretical derivation of the SHG signal of collagen molecules tilted with respect to the focal plane. Our P-SHG images exhibit striated patterns with variable contrast, as expected from our analytical and numerical calculations for plywood-like nematic structures similar to the ones found in the cornea. This study demonstrates the benefits of P-SHG microscopy for in situ characterization of highly organized biopolymers at micrometer scale, and the unique sensitivity of this nonlinear optical technique to the orientation of collagen molecules. PMID:27410876

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

    PubMed

    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. PMID:22620261

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

    ERIC Educational Resources Information Center

    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…

  10. 3D-Trajectories Adopted by Coding and Regulatory DNA Elements: First-Passage Times for Genomic Interactions

    PubMed Central

    Lucas, Joseph S.; Zhang, Yaojun; Dudko, Olga K.; Murre, Cornelis

    2014-01-01

    SUMMARY During B lymphocyte development, immunoglobulin heavy chain variable (VH), diversity (DH) and joining (JH) segments assemble to generate a diverse antigen receptor repertoire. Here we have marked the distal VH and DH-JH-Eμ regions with Tet-operator binding sites and traced their 3D-trajectories in pro-B cells transduced with a retrovirus encoding Tet-repressor-EGFP. We found that these elements displayed fractional Langevin motion (fLm) due to the viscoelastic hindrance from the surrounding network of proteins and chromatin fibers. Using fractional Langevin dynamics modeling, we found that, with high probability, DHJH elements reach a VH element within minutes. Spatial confinement emerged as the dominant parameter that determined the frequency of such encounters. We propose that the viscoelastic nature of the nuclear environment causes coding elements and regulatory elements to bounce back and forth in a spring-like fashion until specific genomic interactions are established and that spatial confinement of topological domains largely controls first-passage times for genomic interactions. PMID:24998931

  11. Investigation the effect of lattice angle on the band gap width in 3D phononic crystals with rhombohedral(I) lattice

    NASA Astrophysics Data System (ADS)

    Salehi, H.; Aryadoust, M.; Shoushtari, M. Zargar

    2014-07-01

    In this paper, the propagation of acoustic waves in the phononic crystal of 3D with rhombohedral(I) lattice is studied theoretically. The crystal composite constituted of nickel spheres embedded in epoxy. The calculations of the band structure and density of states are performed with the plane wave expansion method in the irreducible part of Brillouin zone. In the present work, we have investigated the effect of lattice angle on the band structure and width of the band gap rhombohedral(I) lattice in the irreducible part of the first Brillouin zone and its planes separately. The results show that more than one complete band gape are formed in the four planes of the irreducible part. The most complete band gaps are formed in the (111) plane and the widest complete band gap in (443) with an angle greater than 80. So, if the sound passes through the (111) and (443) planes for the lattice angle close to 90, the crystal phononic displays the excellent insulation behavior. Moreover, in the other planes, the lattice angle does not affect on the width and the number of band gaps. Also, for the filling fraction 5 %, the widest complete band gap is formed. These results are consistent with the effect of symmetry on the band gap width, because the (111) plane has the most symmetry.

  12. Syntheses, crystal structures and properties of two unusual pillared-layer 3d-4f Ln-Cu heterometallic coordination polymers

    SciTech Connect

    Fan Leqing; Wu Jihuai; Huang Yunfang

    2011-09-15

    Two unusual pillared-layer 3d-4f Ln-Cu heterometallic coordination polymers, {l_brace}[Ln{sub 2}Cu{sub 5}Br{sub 4}(IN){sub 7}(H{sub 2}O){sub 6}].H{sub 2}O{r_brace}{sub n} (Ln=Eu (1) and Gd (2), HIN=isonicotinic acid), have been synthesized under hydrothermal conditions, and characterized by elemental analysis, IR, thermal analysis and single-crystal X-ray diffraction. The structure determination reveals that 1 and 2 are isostructural and feature a novel three-dimensional pillared-layer hetrometallic structure built upon the linkages of one-dimensional (1D) linear Ln-carboxylate chains, zero-dimensional (0D) Ln-carboxylate Ln{sub 2}(IN){sub 8} dimers, rare 1D zigzag [Cu{sub 5}Br{sub 4}]{sub n} inorganic chains and IN{sup -} pillars. In both 3D structures, there are Ln-carboxylate layers resulted from the connections of 1D Ln-carboxylate chains and 0D Ln{sub 2}(IN){sub 8} dimers through O-H...O hydrogen bondings. The luminescent properties of 1 have been investigated. The magnetic properties of 1 and 2 have also been studied. - Graphical abstract: Two unusual pillared-layer Eu (Gd)-Cu heterometallic coordination polymers have been hydrothermally synthesized. The luminescent properties of Eu-Cu compound and magnetic properties of both compounds are investigated. Highlights: > Two unusual 3D pillared-layer Eu (Gd)-Cu heterometallic coordination polymers have been synthesized. > 1D and 0D Ln-carboxylate motifs construct layers by O-H...O hydrogen bondings. > In both the structures, there are rare 1D zigzag Cu/Br inorganic chains. > Luminescent properties of Eu-Cu compound and magnetic properties of both the compounds are investigated.

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

    SciTech Connect

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

    2014-04-01

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

  14. Exploring protein-DNA interactions in 3D using in situ construction, manipulation, and visualization of individual DNA-dumbbells with optical traps, microfluidics, and fluorescence microscopy

    PubMed Central

    Forget, Anthony L.; Dombrowski, Christopher C.; Amitani, Ichiro; Kowalczykowski, Stephen C.

    2015-01-01

    In this Protocol, we describe a procedure to generate ‘DNA-dumbbells’ — single molecules of DNA with a microscopic bead attached at each end — and techniques for manipulating individual DNA-dumbbells. We also detail the design and fabrication of a microfluidic device (flow cell) used in conjunction with dual optical trapping to manipulate DNA-dumbbells and to visualize individual protein–DNA complexes by single-molecule epifluorescence microscopy. Our design of the flow cell enables the rapid movement of trapped molecules between laminar flow channels and a flow-free ‘reservoir’. The reservoir provides the means to examine formation of DNA–protein complexes in solution in the absence of external flow forces, while still maintaining a predetermined end-to-end extension of the DNA. These features facilitate examination of the role of three-dimensional DNA conformation and dynamics in protein–DNA interactions. Preparation of flow cells and reagents requires two days each; in situ DNA-dumbbell assembly and imaging of single protein–DNA complexes requires another day. PMID:23411634

  15. 2H and 133Cs nuclear magnetic resonance study of Cs3D(SO4)2 single crystals in laboratory and rotating frames

    NASA Astrophysics Data System (ADS)

    Lim, Ae Ran; Kim, Sun Ha; Jeong, Se-Young

    2013-01-01

    To understand the physical properties of Cs3D(SO4)2 single crystals, in which deuterium replaces hydrogen, the temperature dependence of the NMR spectrum and the spin-lattice relaxation times in the laboratory frame, T1, and in the rotating frame, T1ρ, for 2H and 133Cs are investigated using Fourier transform nuclear magnetic resonance spectrometry. Our results for the 2H and 133Cs relaxation times provide no evidence of a phase transition. The strong temperature dependence of the 2H resonance lines is associated with deformation of the H(SO4)2- tetrahedra. Further, T1 and T1ρ for the 2H and 133Cs nuclei are governed by different mechanisms, which we discuss in terms of fast and slow motion.

  16. Full-vectorial finite element method based eigenvalue algorithm for the analysis of 2D photonic crystals with arbitrary 3D anisotropy.

    PubMed

    Hsu, Sen-Ming; Chang, Hung-Chun

    2007-11-26

    A full-vectorial finite element method based eigenvalue algorithm is developed to analyze the band structures of two-dimensional (2D) photonic crystals (PCs) with arbitray 3D anisotropy for in-planewave propagations, in which the simple transverse-electric (TE) or transverse-magnetic (TM) modes may not be clearly defined. By taking all the field components into consideration simultaneously without decoupling of the wave modes in 2D PCs into TE and TM modes, a full-vectorial matrix eigenvalue equation, with the square of the wavenumber as the eigenvalue, is derived. We examine the convergence behaviors of this algorithm and analyze 2D PCs with arbitrary anisotropy using this algorithm to demonstrate its correctness and usefulness by explaining the numerical results theoretically. PMID:19550864

  17. [Synthesis, crystal structure and spectral properties study of a 3D netlike coordination polymer [Zn(HBIDC) x H2O]n].

    PubMed

    Dong, Yu-Wei; Fan, Rui-Qing; Wang, Ping; Wang, Li-Yuan; Yang, Yu-Lin

    2013-02-01

    The 3D netlike coordination polymer of Zn II with benzimidazole-5,6-dicarboxylic acid (H3BIDC), [Zn(HBIDC) x H2O]n was synthesized by the hydrothermal method through self-assembling. The crystal structure of complex 1 was characterized by single-crystal X-ray diffraction, elemental analysis and IR spectra, and we also studied the fluorescence properties of complex 1 in DMSO and in the solid state with UV-Vis absorption spectra, fluorescence spectra and fluorescence lifetime. Complex 1 has blue luminescence in solutions of DMSO with emission band at 481 nm; and has blue luminescence in the solid state at room temperature with a strong emission band at 493 nm, and these all can be attributed to the pi* --> pi transition based on the benzimidazole-5,6-dicarboxy acid. The experimental results indicate that complex 1 displays higher fluorescence quantum efficiency and can be used as a potential blue luminescence material. PMID:23697137

  18. Electron crystal structure of the transcription factor and DNA repair complex, core TFIIH.

    PubMed

    Chang, W H; Kornberg, R D

    2000-09-01

    Core TFIIH from yeast, made up of five subunits required both for RNA polymerase II transcription and nucleotide excision DNA repair, formed 2D crystals on charged lipid layers. Diffraction from electron micrographs of the crystals in negative stain extended to about 13 angstrom resolution, and 3D reconstruction revealed several discrete densities whose volumes corresponded well with those of individual TFIIH subunits. The structure is based on a ring of three subunits, Tfb1, Tfb2, and Tfb3, to which are appended several functional moieties: Rad3, bridged to Tfb1 by SsI1; SsI2, known to interact with Tfb2; and Kin28, known to interact with Tfb3. PMID:11007479

  19. DNA induced chirality and helical twist in achiral liquid crystals

    NASA Astrophysics Data System (ADS)

    Garvey, Alfred; Basu, Rajratan; Kinnamon, Daniel

    A small quantity of DNA sample (Deoxyribonucleic acid -cellulose double-stranded from calf thymus DNA in lyophilized powder form) was doped in an achiral liquid crystal (LC), and the mixture was found to exhibit a weak degree of chirality. The induced chirality in the LC was probed by means of the electroclinic effect in the LC's smectic-A phase, which showed significant pretransitional behavior on approaching the smectic- A-smectic- C transition temperature from above. The same DNA was doped in an achiral nematic LC and the mixture was found to exhibit an average mechanical twist over macroscopic dimensions. The double-stranded DNA-induced chiral pitch length P was determined by measuring the radius of curvature of reverse twist disclination lines in 90o nematic twist cells. In the LC +DNA mixture, the LC's benzene rings interact with the nucleobases of the DNA through π - π stacking, which induces a molecular conformational deracemization in the LC.

  20. 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.

    PubMed

    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. PMID:26394866

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

    SciTech Connect

    Li, Haofeng; Brouillet, Jeremy; Wang, Xiaoxin; Liu, Jifeng

    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.

  2. Crystal transformation synthesis of a highly stable fluorescent 3D indium-tetranuclear {In4(μ2-OH)3} building block based metal organic framework through a dinuclear complex.

    PubMed

    Wang, Xin-Ming; Fan, Rui-Qing; Qiang, Liang-Sheng; Wang, Ping; Yang, Yu-Lin; Wang, Yu-Lei

    2014-11-21

    A rare 3D tetranuclear {In4(μ2-OH)3} building block based MOF {[In4/3(μ2-OH)(2,6-pydc)(1,4-bda)0.5(H2O)]·2H2O}n (2) was obtained through a crystal transformation from a dimeric complex In3(2,6-pydc)3(1,4-bda)1.5(H2O)6 (1). With a 2D + 3D3D compact structure, 2 retains crystallinity in boiling water and organic solvents, exhibiting exceptional fluorescence quenching behaviour for the DMSO molecule. PMID:25135576

  3. All-atom crystal simulations of DNA and RNA duplexes

    PubMed Central

    Liu, Chunmei; Janowski, Pawel A.; Case, David A.

    2014-01-01

    Background Molecular dynamics simulations can complement experimental measures of structure and dynamics of biomolecules. The quality of such simulations can be tested by comparisons to models refined against experimental crystallographic data. Methods We report simulations of a DNA and RNA duplex in their crystalline environment. The calculations mimic the conditions for PDB entries 1D23 [d(CGATCGATCG)2] and 1RNA [(UUAUAUAUAUAUAA)2], and contain 8 unit cells, each with 4 copies of the Watson-Crick duplex; this yields in aggregate 64 µs of duplex sampling for DNA and 16 µs for RNA. Results The duplex structures conform much more closely to the average structure seen in the crystal than do structures extracted from a solution simulation with the same force field. Sequence-dependent variations in helical parameters, and in groove widths, are largely maintained in the crystal structure, but are smoothed out in solution. However, the integrity of the crystal lattice is slowly degraded in both simulations, with the result that the interfaces between chains become heterogeneous. This problem is more severe for the DNA crystal, which has fewer inter-chain hydrogen bond contacts than does the RNA crystal. Conclusions Crystal simulations using current force fields reproduce many features of observed crystal structures, but suffer from a gradual degradation of the integrity of the crystal lattice. General significance The results offer insights into force-field simulations that tests their ability to preserve weak interactions between chains, which will be of importance also in non-crystalline applications that involve binding and recognition. PMID:25255706

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

    SciTech Connect

    Tajbakhsh, Jian; Stefanovski, Darko; Tang, George; Wawrowsky, Kolja; Liu, Naiyou; Fair, Jeffrey H.

    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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2016-01-01

    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. PMID:26940532

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

    PubMed Central

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

    2016-01-01

    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. PMID:26940532

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

    PubMed

    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. PMID:26192470

  9. Crystal Structure of Pim1 Kinase in Complex with a Pyrido[4,3-D]Pyrimidine Derivative Suggests a Unique Binding Mode

    PubMed Central

    Cho, Jea-Won; Choi, Jang-Sik; Lee, Jaekyoo; Song, Ho-Juhn; Koh, Jong Sung; Lee, Byung Il

    2013-01-01

    Human Pim1 kinase is a serine/threonine protein kinase that plays important biological roles in cell survival, apoptosis, proliferation, and differentiation. Moreover, Pim1 is up-regulated in various hematopoietic malignancies and solid tumors. Thus, Pim1 is an attractive target for cancer therapeutics, and there has been growing interest in developing small molecule inhibitors for Pim1. Here, we describe the crystal structure of Pim1 in complex with a newly developed pyrido[4,3-d]pyrimidine-derivative inhibitor (SKI-O-068). Our inhibitor exhibits a half maximum inhibitory concentration (IC50) of 123 (±14) nM and has an unusual binding mode in complex with Pim1 kinase. The interactions between SKI-O-068 and the Pim1 active site pocket residue are different from those of other scaffold inhibitor-bound structures. The binding mode analysis suggests that the SKI-O-068 inhibitor can be improved by introducing functional groups that facilitate direct interaction with Lys67, which aid in the design of an optimized inhibitor. PMID:23936194

  10. Quantitative analysis of molecular-level DNA crystal growth on a 2D surface

    PubMed Central

    Lee, Junwye; Hamada, Shogo; Hwang, Si Un; Amin, Rashid; Son, Junyoung; Dugasani, Sreekantha Reddy; Murata, Satoshi; Park, Sung Ha

    2013-01-01

    Crystallization is an essential process for understanding a molecule's aggregation behavior. It provides basic information on crystals, including their nucleation and growth processes. Deoxyribonucleic acid (DNA) has become an interesting building material because of its remarkable properties for constructing various shapes of submicron-scale DNA crystals by self-assembly. The recently developed substrate-assisted growth (SAG) method produces fully covered DNA crystals on various substrates using electrostatic interactions and provides an opportunity to observe the overall crystallization process. In this study, we investigated quantitative analysis of molecular-level DNA crystallization using the SAG method. Coverage and crystal size distribution were studied by controlling the external parameters such as monomer concentration, annealing temperature, and annealing time. Rearrangement during crystallization was also discussed. We expect that our study will provide overall picture of the fabrication process of DNA crystals on the charged substrate and promote practical applications of DNA crystals in science and technology. PMID:23817625

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

    SciTech Connect

    Wogelius, R.A.; Fraser, D.G.

    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.

  12. Thermally-induced single-crystal-to-single-crystal transformations from a 2D two-fold interpenetrating square lattice layer to a 3D four-fold interpenetrating diamond framework and its application in dye-sensitized solar cells.

    PubMed

    Gao, Song; Fan, Rui Qing; Wang, Xin Ming; Wei, Li Guo; Song, Yang; Du, Xi; Xing, Kai; Wang, Ping; Yang, Yu Lin

    2016-07-28

    In this work, a rare 2D → 3D single-crystal-to-single-crystal transformation (SCSC) is observed in metal-organic coordination complexes, which is triggered by thermal treatment. The 2D two-fold interpenetrating square lattice layer [Cd(IBA)2]n (1) is irreversibly converted into a 3D four-fold interpenetrating diamond framework {[Cd(IBA)2(H2O)]·2.5H2O}n (2) (HIBA = 4-(1H-imidazol-1-yl)benzoic acid). Consideration is given to these two complexes with different interpenetrating structures and dimensionality, and their influence on photovoltaic properties are studied. Encouraged by the UV-visible absorption and HOMO-LUMO energy states matched for sensitizing TiO2, the two complexes are employed in combination with N719 in dye-sensitized solar cells (DSSCs) to compensate absorption in the ultraviolet and blue-violet region, offset competitive visible light absorption of I3(-) and reducing charge the recombination of injected electrons. After co-sensitization with 1 and 2, the device co-sensitized by 1/N719 and 2/N719 to yield overall efficiencies of 7.82% and 8.39%, which are 19.94% and 28.68% higher than that of the device sensitized only by N719 (6.52%). Consequently, high dimensional interpenetrating complexes could serve as excellent co-sensitizers and have application in DSSCs. PMID:27356177

  13. Mobility of Electron in DNA Crystals by Laser Radiation

    NASA Technical Reports Server (NTRS)

    Zhang, Kaixi; Zhao, Qingxun; Cui, Zhiyun; Zhang, Ping; Dong, Lifang

    1996-01-01

    The mobility of electrons in laser radiated DNA is closed to the energy transfer and energy migration of a biological molecule. Arrhenius has studied the conductivity of the electrons in a biological molecule. But his result is far from the experimental result and meanwhile the relation between some parameters in his theory and the micro-quantities in DNA is not very clear. In this paper, we propose a new phonon model of electron mobility in DNA and use Lippman-Schwinger equation and S-matrix theory to study the mobility of electrons in DNA crystal. The result is relatively close to the experiment result and some parameters in Arrhenius theory are explained in our work.

  14. Europeana and 3D

    NASA Astrophysics Data System (ADS)

    Pletinckx, D.

    2011-09-01

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

  15. Structural Code for DNA Recognition Revealed in Crystal Structures of Papillomavirus E2-DNA Targets

    NASA Astrophysics Data System (ADS)

    Rozenberg, Haim; Rabinovich, Dov; Frolow, Felix; Hegde, Rashmi S.; Shakked, Zippora

    1998-12-01

    Transcriptional regulation in papillomaviruses depends on sequence-specific binding of the regulatory protein E2 to several sites in the viral genome. Crystal structures of bovine papillomavirus E2 DNA targets reveal a conformational variant of B-DNA characterized by a roll-induced writhe and helical repeat of 10.5 bp per turn. A comparison between the free and the protein-bound DNA demonstrates that the intrinsic structure of the DNA regions contacted directly by the protein and the deformability of the DNA region that is not contacted by the protein are critical for sequence-specific protein/DNA recognition and hence for gene-regulatory signals in the viral system. We show that the selection of dinucleotide or longer segments with appropriate conformational characteristics, when positioned at correct intervals along the DNA helix, can constitute a structural code for DNA recognition by regulatory proteins. This structural code facilitates the formation of a complementary protein-DNA interface that can be further specified by hydrogen bonds and nonpolar interactions between the protein amino acids and the DNA bases.

  16. Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA.

    PubMed

    Burmeister, Wim P; Tarbouriech, Nicolas; Fender, Pascal; Contesto-Richefeu, Céline; Peyrefitte, Christophe N; Iseni, Frédéric

    2015-07-17

    Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase catalytic subunit E9 associated with its heterodimeric co-factor A20·D4 required for processive genome synthesis. Although A20 has no known enzymatic activity, D4 is an active uracil-DNA glycosylase (UNG). The presence of a repair enzyme as a component of the viral replication machinery suggests that, for poxviruses, DNA synthesis and base excision repair is coupled. We present the 2.7 Å crystal structure of the complex formed by D4 and the first 50 amino acids of A20 (D4·A201-50) bound to a 10-mer DNA duplex containing an abasic site resulting from the cleavage of a uracil base. Comparison of the viral complex with its human counterpart revealed major divergences in the contacts between protein and DNA and in the enzyme orientation on the DNA. However, the conformation of the dsDNA within both structures is very similar, suggesting a dominant role of the DNA conformation for UNG function. In contrast to human UNG, D4 appears rigid, and we do not observe a conformational change upon DNA binding. We also studied the interaction of D4·A201-50 with different DNA oligomers by surface plasmon resonance. D4 binds weakly to nonspecific DNA and to uracil-containing substrates but binds abasic sites with a Kd of <1.4 μm. This second DNA complex structure of a family I UNG gives new insight into the role of D4 as a co-factor of vaccinia virus DNA polymerase and allows a better understanding of the structural determinants required for UNG action. PMID:26045555

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

    ERIC Educational Resources Information Center

    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…

  18. Independent and arbitrary generation of spots in the 3D space domain with computer generated holograms written on a phase-only liquid crystal spatial light modulator

    NASA Astrophysics Data System (ADS)

    Wang, Dong; Zhang, Jian; Xia, Yang; Wang, Hao

    2012-10-01

    An improved multiple independent iterative plane algorithm, based on a projection optimization idea, is proposed for the independent and arbitrary generation of one spot or multiple spots in a speckle-suppressed 3D work-area. Details of the mathematical expressions of the algorithm are given to theoretically show how it is improved for 3D spot generation. Both simulations and experiments are conducted to investigate the performance of the algorithm for independent and arbitrary 3D spot generation in several different cases. Simulation results agree well with experimental results, which validates the effectiveness of the algorithm proposed. Several additional experiments are demonstrated for fast and independent generation of four or more spots in the 3D space domain, which confirms the capabilities and practicalities of the algorithm further.

  19. 3d-3d correspondence revisited

    NASA Astrophysics Data System (ADS)

    Chung, Hee-Joong; Dimofte, Tudor; Gukov, Sergei; Sułkowski, Piotr

    2016-04-01

    In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d {N}=2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. We also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  20. DNA-mediated engineering of multicomponent enzyme crystals.

    PubMed

    Brodin, Jeffrey D; Auyeung, Evelyn; Mirkin, Chad A

    2015-04-14

    The ability to predictably control the coassembly of multiple nanoscale building blocks, especially those with disparate chemical and physical properties such as biomolecules and inorganic nanoparticles, has far-reaching implications in catalysis, sensing, and photonics, but a generalizable strategy for engineering specific contacts between these particles is an outstanding challenge. This is especially true in the case of proteins, where the types of possible interparticle interactions are numerous, diverse, and complex. Herein, we explore the concept of trading protein-protein interactions for DNA-DNA interactions to direct the assembly of two nucleic-acid-functionalized proteins with distinct surface chemistries into six unique lattices composed of catalytically active proteins, or of a combination of proteins and DNA-modified gold nanoparticles. The programmable nature of DNA-DNA interactions used in this strategy allows us to control the lattice symmetries and unit cell constants, as well as the compositions and habit, of the resulting crystals. This study provides a potentially generalizable strategy for constructing a unique class of materials that take advantage of the diverse morphologies, surface chemistries, and functionalities of proteins for assembling functional crystalline materials. PMID:25831510

  1. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.

    PubMed Central

    Young, M A; Ravishanker, G; Beveridge, D L; Berman, H M

    1995-01-01

    Sequence-dependent bending of the helical axes in 112 oligonucleotide duplex crystal structures resident in the Nucleic Acid Database have been analyzed and compared with the use of bending dials, a computer graphics tool. Our analysis includes structures of both A and B forms of DNA and considers both uncomplexed forms of the double helix as well as those bound to drugs and proteins. The patterns in bending preferences in the crystal structures are analyzed by base pair steps, and emerging trends are noted. Analysis of the 66 B-form structures in the Nucleic Acid Database indicates that uniform trends within all pyrimidine-purine and purine-pyrimidine steps are not necessarily observed but are found particularly at CG and GC steps of dodecamers. The results support the idea that AA steps are relatively straight and that larger roll bends occur at or near the junctions of these A-tracts with their flanking sequences. The data on 16 available crystal structures of protein-DNA complexes indicate that the majority of the DNA bends induced via protein binding are sharp localized kinks. The analysis of the 30 available A-form DNA structures indicates that these structures are also bent and show a definitive preference for bending into the deep major groove over the shallow minor groove. PMID:7647248

  2. Structural analysis of the diadenylate cyclase reaction of DNA-integrity scanning protein A (DisA) and its inhibition by 3'-dATP.

    PubMed

    Müller, Martina; Deimling, Tobias; Hopfner, Karl-Peter; Witte, Gregor

    2015-08-01

    The identification of the essential bacterial second messenger cyclic-di-AMP (c-di-AMP) synthesized by the DNA-integrity scanning protein A (DisA) has opened up a new and emerging field in bacterial signalling. To further analyse the diadenylate cyclase (DAC) reaction catalysed by the DAC domains of DisA, we crystallized Thermotoga maritima DisA in the presence of different ATP analogues and metal ions to identify the metal-binding site and trap the enzyme in pre- and post-reaction states. Through structural and biochemical assays we identified important residues essential for the reaction in the active site of the DAC domains. Our structures resolve the metal-binding site and thus explain the activation of ATP for the DAC reaction. Moreover, we were able to identify a potent inhibitor of the DAC domain. Based on the available structures and homology to annotated DAC domains we propose a common mechanism for c-di-AMP synthesis by DAC domains in c-di-AMP-producing species and a possible approach for its effective inhibition. PMID:26014055

  3. 3D and Education

    NASA Astrophysics Data System (ADS)

    Meulien Ohlmann, Odile

    2013-02-01

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

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

    SciTech Connect

    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.

  5. Imaging a Sustainable Future in 3D

    NASA Astrophysics Data System (ADS)

    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.

  6. Construction and 3-D computer modeling of connector arrays with tetragonal to decagonal transition induced by pRNA of phi29 DNA-packaging motor.

    PubMed

    Guo, Yin Yin; Blocker, Forrest; Xiao, Feng; Guo, Peixuan

    2005-06-01

    The bottom-up assembly of patterned arrays is an exciting and important area in current nanotechnology. Arrays can be engineered to serve as components in chips for a virtually inexhaustible list of applications ranging from disease diagnosis to ultrahigh-density data storage. In attempting to achieve this goal, a number of methods to facilitate array design and production have been developed. Cloning and expression of the gene coding for the connector of the bacterial virus phi29 DNA-packaging motor, overproduction of the gene products, and the in vitro construction of large-scale carpet-like arrays composed of connector are described in this report. The stability of the arrays under various conditions, including varied pH, temperature and ionic strength, was tested. The addition of packaging RNA (pRNA) into the array caused a dramatic shift in array structure, and resulted in the conversion of tetragonal arrays into larger decagonal structures comprised of both protein and RNA. RNase digestion confirmed that the conformational shift was caused by pRNA, and that RNA was present in the decagons. As has been demonstrated in biomotors, conformational shift of motor components can generate force for motor motion. The conformational shift reported here can be utilized as a potential force-generating mechanism for the construction of nanomachines. Three-dimensional computer models of the constructed arrays were also produced using a variety of connector building blocks with or without the N- or C-terminal sequence, which is absent from the current published crystal structures. Both the connector array and the decagon are ideal candidates to be used as templates to build patterned suprastructures in nanotechnology. PMID:16060143

  7. Photonic Crystal Biosensor with In-Situ Synthesized DNA Probes for Enhanced Sensitivity

    SciTech Connect

    Hu, Shuren; Zhao, Y.; Retterer, Scott T; Kravchenko, Ivan I; Weiss, Sharon

    2013-01-01

    We report on a nearly 8-fold increase in multi-hole defect photonic crystal biosensor response by incorporating in-situ synthesis of DNA probes, as compared to the conventional functionalization method employing pre-synthesized DNA probe immobilization.

  8. Comparison of the solution and crystal conformations of (G + C)-rich fragments of DNA.

    PubMed Central

    Vorlícková, M; Subirana, J A; Chládková, J; Tejralová, I; Huynh-Dinh, T; Arnold, L; Kypr, J

    1996-01-01

    DNA fragments crystallize in an unpredictable manner, and relationships between their crystal and solution conformations still are not known. We have studied, using circular dichroism spectroscopy, solution conformations of (G + C)-rich DNA fragments, the crystal structures of which were solved in the laboratory of one of the present authors. In aqueous trifluorethanol (TFE) solutions, all of the examined oligonucleotides adopted the same type of double helix as in the crystal. Specifically, the dodecamer d(CCCCCGCGGGGG) crystalized as A-DNA and isomerized into A-DNA at high TFE concentrations. On the other hand, the hexamer d(CCGCGG) crystallized in Z-form containing tilted base pairs, and high TFE concentrations cooperatively transformed it into the same Z-form as adopted by the RNA hexamer r(CGCGCG), although d(CCGCGG) could isomerize into Z-DNA in the NaCl + NiCl2) aqueous solution. The fragments crystallizing as B-DNA remained B-DNA, regardless of the solution conditions, unless they denatured or aggregated. Effects on the oligonucleotide conformation of 2-methyl-2,4-pentanediol and other crystallization agents were also studied. 2-Methyl-2,4-pentanediol induced the same conformational transitions as TFE but, in addition, caused an oligonucleotide condensation that was also promoted by the other crystallization agents. The present results indicate that the crystal double helices of DNA are stable in aqueous TFE rather than aqueous solution. PMID:8874026

  9. Growth dynamics for DNA-guided nanoparticle crystallization.

    PubMed

    Dhakal, Subas; Kohlstedt, Kevin L; Schatz, George C; Mirkin, Chad A; Olvera de la Cruz, Monica

    2013-12-23

    Spherical nucleic acid (SNA) nanostructures assemble into a large variety of well-defined crystalline superlattices via DNA-directed hybridization. Crystallities of SNA with various shapes emerge during the assembly process, which coalesce during coarsening, leading to polycrystalline materials. Here, we investigate the growth dynamics of SNAs into body-centered cubic superlattices and the coalescence of SNA aggregates using a colloidal model formulated from the competition of electrostatic core repulsions and localized DNA hybridization attractions. We find that the growth law of isolated SNA crystallities is well-described by the power law t(1/2), in agreement with experimental observations. At later times, coalescence slows the growth dynamics considerably and is dependent on the orientational mismatch (misorientation angle) of the coalescing crystallites. Molecular dynamics simulations show that the misorientation angle decreases continually during the coalescence, which is a signature of the grain rotation induced coalescence mechanism. This mechanism is followed by the coarsening of a "neck" that develops at the boundary between the coalescing crystallites. Remarkably, we find faster coalescence dynamics for larger SNAs compared to smaller SNAs due to their enhanced surface diffusion, which more effectively reduces curvature at the boundary of two superlattices. These findings provide fundamental insight into the relationship between nanoparticle surface chemistry and its crystallite growth and coalescence. PMID:24274629

  10. 3D Imaging.

    ERIC Educational Resources Information Center

    Hastings, S. K.

    2002-01-01

    Discusses 3 D imaging as it relates to digital representations in virtual library collections. Highlights include X-ray computed tomography (X-ray CT); the National Science Foundation (NSF) Digital Library Initiatives; output peripherals; image retrieval systems, including metadata; and applications of 3 D imaging for libraries and museums. (LRW)

  11. DNA-mediated engineering of multicomponent enzyme crystals

    PubMed Central

    Brodin, Jeffrey D.; Auyeung, Evelyn; Mirkin, Chad A.

    2015-01-01

    The ability to predictably control the coassembly of multiple nanoscale building blocks, especially those with disparate chemical and physical properties such as biomolecules and inorganic nanoparticles, has far-reaching implications in catalysis, sensing, and photonics, but a generalizable strategy for engineering specific contacts between these particles is an outstanding challenge. This is especially true in the case of proteins, where the types of possible interparticle interactions are numerous, diverse, and complex. Herein, we explore the concept of trading protein–protein interactions for DNA–DNA interactions to direct the assembly of two nucleic-acid–functionalized proteins with distinct surface chemistries into six unique lattices composed of catalytically active proteins, or of a combination of proteins and DNA-modified gold nanoparticles. The programmable nature of DNA–DNA interactions used in this strategy allows us to control the lattice symmetries and unit cell constants, as well as the compositions and habit, of the resulting crystals. This study provides a potentially generalizable strategy for constructing a unique class of materials that take advantage of the diverse morphologies, surface chemistries, and functionalities of proteins for assembling functional crystalline materials. PMID:25831510

  12. Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule

    SciTech Connect

    Changela, A.; Digate, R.J.; Mondragon, A.

    2010-03-05

    A variety of cellular processes, including DNA replication, transcription, and chromosome condensation, require enzymes that can regulate the ensuing topological changes occurring in DNA. Such enzymes - DNA topoisomerases - alter DNA topology by catalysing the cleavage of single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA), the passage of DNA through the resulting break, and the rejoining of the broken phosphodiester backbone. DNA topoisomerase III from Escherichia coli belongs to the type IA family of DNA topoisomerases, which transiently cleave ssDNA via formation of a covalent 5' phosphotyrosine intermediate. Here we report the crystal structure, at 2.05 {angstrom} resolution, of an inactive mutant of E. coli DNA topoisomerase III in a non-covalent complex with an 8-base ssDNA molecule. The enzyme undergoes a conformational change that allows the oligonucleotide to bind within a groove leading to the active site. We note that the ssDNA molecule adopts a conformation like that of B-DNA while bound to the enzyme. The position of the DNA within the realigned active site provides insight into the role of several highly conserved residues during catalysis. These findings confirm various aspects of the type IA topoisomerase mechanism while suggesting functional implications for other topoisomerases and proteins that perform DNA rearrangements.

  13. TRACE 3-D documentation

    SciTech Connect

    Crandall, K.R.

    1987-08-01

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

  14. Crystallization and X-ray diffraction analysis of the DNA-remodelling protein DnaD from Bacillus subtilis

    SciTech Connect

    Schneider, Sabine; Carneiro, Maria J. V. M.; Ioannou, Charikleia; Soultanas, Panos; Paoli, Max

    2007-02-01

    Crystallization and preliminary X-ray diffraction analysis of the two domains of DnaD from B. subtilis is reported. The DnaD protein is an essential component of the chromosome-replication machinery of the Gram-positive bacterium Bacillus subtilis and is part of the primosomal cascade that ultimately loads the replicative ring helicase DnaC onto DNA. Moreover, DnaD is a global regulator of DNA architecture, as it forms higher order nucleoprotein structures in order to open supercoiled DNA. Here, the crystallization and preliminary X-ray diffraction analysis of the two domains of DnaD from B. subtilis are reported. Crystals of the N-terminal domain are trigonal, with either P3{sub 1}21 or P3{sub 2}21 space-group symmetry, and diffracted X-rays to 2.0 Å resolution; crystals of the C-terminal domain are hexagonal, with space group P6{sub 1} or P6{sub 5}, and diffracted X-rays to 2.9 Å resolution in-house. Determination of the structure of the DnaD domains will provide insight into how remodelling of the nucleoid is associated with priming of replication in the model Gram-positive organism B. subtilis.

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

    SciTech Connect

    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.

  16. Antiproliferative, DNA intercalation and redox cycling activities of dioxonaphtho[2,3-d]imidazolium analogs of YM155: A structure-activity relationship study.

    PubMed

    Ho, Si-Han Sherman; Sim, Mei-Yi; Yee, Wei-Loong Sherman; Yang, Tianming; Yuen, Shyi-Peng John; Go, Mei-Lin

    2015-11-01

    The anticancer agent YM155 is widely investigated as a specific survivin suppressant. More recently, YM155 was found to induce DNA damage and this has raised doubts as to whether survivin is its primary target. In an effort to assess the contribution of DNA damage to the anticancer activity of YM155, several analogs were prepared and evaluated for antiproliferative activity on malignant cells, participation in DNA intercalation and free radical generation by redox cycling. The intact positively charged scaffold was found to be essential for antiproliferative activity and intercalation but was less critical for redox cycling where the minimal requirement was a pared down bicyclic quinone. Side chain requirements at the N(1) and N(3) positions of the scaffold were more alike for redox cycling and intercalation than antiproliferative activity, underscoring yet again, the limited structural overlaps for these activities. Furthermore, antiproliferative activities were poorly correlated to DNA intercalation and redox cycling. Potent antiproliferative activity (IC50 9-23 nM), exceeding that of YM155, was found for a minimally substituted methyl analog AB7. Like YM155 and other dioxonaphthoimidazoliums, AB7 was a modest DNA intercalator but with weak redox cycling activity. Thus, the capacity of this scaffold to inflict direct DNA damage leading to cell death may not be significant and YM155 should not be routinely classified as a DNA damaging agent. PMID:26433618

  17. Crystal Structure of Human Thymine DNA Glycosylase Bound to DNA Elucidates Sequence-Specific Mismatch Recognition

    SciTech Connect

    Maiti, A.; Morgan, M.T.; Pozharski, E.; Drohat, A.C.

    2009-05-19

    Cytosine methylation at CpG dinucleotides produces m{sup 5}CpG, an epigenetic modification that is important for transcriptional regulation and genomic stability in vertebrate cells. However, m{sup 5}C deamination yields mutagenic G{center_dot}T mispairs, which are implicated in genetic disease, cancer, and aging. Human thymine DNA glycosylase (hTDG) removes T from G{center_dot}T mispairs, producing an abasic (or AP) site, and follow-on base excision repair proteins restore the G{center_dot}C pair. hTDG is inactive against normal A{center_dot}T pairs, and is most effective for G{center_dot}T mispairs and other damage located in a CpG context. The molecular basis of these important catalytic properties has remained unknown. Here, we report a crystal structure of hTDG (catalytic domain, hTDG{sup cat}) in complex with abasic DNA, at 2.8 {angstrom} resolution. Surprisingly, the enzyme crystallized in a 2:1 complex with DNA, one subunit bound at the abasic site, as anticipated, and the other at an undamaged (nonspecific) site. Isothermal titration calorimetry and electrophoretic mobility-shift experiments indicate that hTDG and hTDG{sup cat} can bind abasic DNA with 1:1 or 2:1 stoichiometry. Kinetics experiments show that the 1:1 complex is sufficient for full catalytic (base excision) activity, suggesting that the 2:1 complex, if adopted in vivo, might be important for some other activity of hTDG, perhaps binding interactions with other proteins. Our structure reveals interactions that promote the stringent specificity for guanine versus adenine as the pairing partner of the target base and interactions that likely confer CpG sequence specificity. We find striking differences between hTDG and its prokaryotic ortholog (MUG), despite the relatively high (32%) sequence identity.

  18. Metal electrode dependent field effect transistors made of lanthanide ion-doped DNA crystals

    NASA Astrophysics Data System (ADS)

    Reddy Dugasani, Sreekantha; Hwang, Taehyun; Kim, Jang Ah; Gnapareddy, Bramaramba; Kim, Taesung; Park, Sung Ha

    2016-03-01

    We fabricated lanthanide ion (Ln3+, e.g. Dy3+, Er3+, Eu3+, and Gd3+)-doped self-assembled double-crossover (DX) DNA crystals grown on the surface of field effect transistors (FETs) containing either a Cr, Au, or Ni electrode. Here we demonstrate the metal electrode dependent FET characteristics as a function of various Ln3+. The drain-source current (I ds), controlled by the drain-source voltage (V ds) of Ln3+-doped DX DNA crystals with a Cr electrode on an FET, changed significantly under various gate voltages (V g) due to the relative closeness of the work function of Cr to the energy band gap of Ln3+-DNA crystals compared to those of Au and Ni. For Ln3+-DNA crystals on an FET with either a Cr or Ni electrode at a fixed V ds, I ds decreased with increasing V g ranging from  -2 to 0 V and from 0 to  +3 V in the positive and negative regions, respectively. By contrast, I ds for Ln3+-DNA crystals on an FET with Au decreased with increasing V g in only the positive region due to the greater electronegativity of Au. Furthermore, Ln3+-DNA crystals on an FET exhibited behaviour sensitive to V g due to the appreciable charge carriers generated from Ln3+. Finally, we address the resistivity and the mobility of Ln3+-DNA crystals on an FET with different metal electrodes obtained from I ds-V ds and I ds-V g curves. The resistivities of Ln3+-DNA crystals on FETs with Cr and Au electrodes were smaller than those of pristine DNA crystals on an FET, and the mobility of Ln3+-DNA crystals on an FET with Cr was relatively higher than that associated with other electrodes.

  19. Crystal structure of (E)-9-(4-nitro-benzyl-idene)-8,9-di-hydro-pyrido[2,3-d]pyrrolo-[1,2-a]pyrimidin-5(7H)-one.

    PubMed

    Khodjaniyazov, Khamid U; Ashurov, Jamshid M

    2016-04-01

    The title compound, C17H12N4O3, a pyrido-pyrrolo-pyrimidine derivative, is almost planar. The nitro-benzene ring is inclined to the mean plane of the 8,9-di-hydro-pyrido[2,3-d]pyrrolo-[1,2-a]pyrimidin-5(7H)-one moiety (r.m.s. deviation = 0.023 Å) by 6.8 (1)°. In the crystal, mol-ecules are linked via C-H⋯O and C-H⋯N hydrogen bonds, forming layers parallel to (101). PMID:27375862

  20. 3D Rare earth porous coordination frameworks with formamide generated in situ syntheses: Crystal structure and down- and up-conversion luminescence

    SciTech Connect

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

    2013-05-01

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

  1. Self-assembly of cholesterol DNA at liquid crystal/aqueous interface and its application for DNA detection

    NASA Astrophysics Data System (ADS)

    Lai, Siok Lian; Hartono, Deny; Yang, Kun-Lin

    2009-10-01

    In this letter, we report a strategy of detecting the DNA targets by using a thin layer of self-assembled cholesterol-labeled DNA probes at the liquid crystal (LC)/aqueous interface. When the system is exposed to 51 μg/ml of complementary DNA targets, the optical appearance of LC shows a continuous change from dark to bright under the crossed polars within 15 min. No obvious change can be observed when the system is exposed to one or two base-pair mismatch DNA targets. This system provides a principle for label-free and real-time detection of DNA targets without any fluorescent labeling.

  2. Radiochromic 3D Detectors

    NASA Astrophysics Data System (ADS)

    Oldham, Mark

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

    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

  4. Gold nanoparticle based signal enhancement liquid crystal biosensors for DNA hybridization assays.

    PubMed

    Yang, Shengyuan; Liu, Yanmei; Tan, Hui; Wu, Chao; Wu, Zhaoyang; Shen, Guoli; Yu, Ruqin

    2012-03-18

    A novel signal enhanced liquid crystal biosensor based on using AuNPs for highly sensitive DNA detection has been developed. This biosensor not only significantly decreases the detection limit, but also offers a simple detection process and shows a good selectivity to distinguish perfectly matched target DNA from two-base mismatched DNA. PMID:22302154

  5. Bootstrapping 3D fermions

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  6. Design, synthesis, biological evaluation and X-ray crystal structure of novel classical 6,5,6-tricyclic benzo[4,5]thieno[2,3-d]pyrimidines as dual thymidylate synthase and dihydrofolate reductase inhibitors

    PubMed Central

    Zhang, Xin; Zhou, Xilin; L.Kisliuk, Roy; Piraino, Jennifer; Cody, Vivian

    2011-01-01

    Classical antifolates (4-7) with a tricyclic benzo[4,5]thieno[2,3-d]pyrimidine scaffold and a flexible and rigid benzoylglutamate were synthesized as dual thymidylate synthase (TS) and dihydrofolate reductase (DHFR) inhibitors. Oxidative aromatization of ethyl 2-amino-4-methyl-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxylate (±)-9 to ethyl 2-amino-4-methyl-1-benzothiophene-3-carboxylate 10 with 10% Pd/C was a key synthetic step. Compounds with 2-CH3 substituents inhibited human (h) TS (IC50 = 0.26-0.8 μM), but not hDHFR. Substitution of the 2-CH3 with a 2-NH2 increases hTS inhibition by more than 10-fold and also affords excellent hDHFR inhibition (IC50 = 0.09-0.1 μM). This study shows that the tricyclic benzo[4,5]thieno[2,3-d]pyrimidine scaffold is highly conducive to single hTS or dual hTS-hDHFR inhibition depending on the 2-position substituents. The X-ray crystal structures of 6 and 7 with hDHFR reveal, for the first time, that tricyclics 6 and 7 bind with the benzo[4,5]thieno[2,3-d]pyrimidine ring in the folate binding mode with the thieno S mimicking the 4-amino of methotrexate. PMID:21550809

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

    PubMed

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

    2016-04-27

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

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

    PubMed Central

    2016-01-01

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

  9. Mono- and binuclear Pd(II) complexes with 2-(5,6-dimethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-2-yl)-N-phenylhydrazinecarbothioamide: Synthesis, crystal structure and spectroscopic characterization

    NASA Astrophysics Data System (ADS)

    Repich, Hlib; Orysyk, Svitlana; Bon, Volodymyr; Savytskyi, Pavlo; Pekhnyo, Vasyl

    2015-12-01

    Two novel Pd2+ mononuclear [Pd(HL)PPh3Cl]·nDMF (1) (n = 1, 2) and binuclear [Pd2(L)2(PPh3)2]·SPPh3·3DMF (2) complexes have been synthesized by reaction of [Pd(PPh3)2Cl2] with 2-(5,6-dimethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidin-2-yl)-N-phenylhydrazinecarbothioamide and characterized by single-crystal X-ray diffraction. Complex 1 has been additionally characterized by 1H NMR, IR and UV-Vis spectroscopy. For the complex 1, two crystalline polymorphic modifications have been found: monoclinic (1a) and more stable triclinic (1b) one, which crystal structure differs by different crystal packing and number of lattice solvent molecules. In both polymorphs, the ligand molecules are coordinated as monoanion in thiol tautomeric form with transferring of thiosemicarbazide proton to nitrogen atom of thienopyrimidine moiety. In the case of complex 2, additional deprotonation of thienopyrimidine nitrogen atom leads to coordination of the ligand as dianion. The crystal structure of 2 also contains one molecule of triphenylphosphine sulfide formed by side reaction. In both complexes "soft" phosphorus atoms of triphenylphosphine molecules are coordinated in trans-positions to more "hard" nitrogen atoms.

  10. A DNA crystal designed to contain two molecules per asymmetric unit.

    PubMed

    Wang, Tong; Sha, Ruojie; Birktoft, Jens; Zheng, Jianping; Mao, Chengde; Seeman, Nadrian C

    2010-11-10

    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. PMID:20958065

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

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

    PubMed

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

    2014-06-16

    Six new heterometallic cobalt(II)-lanthanide(III) complexes of formulas [Ln(bta)(H2O)2]2[Co(H2O)6]·10H2O [Ln = Nd(III) (1) and Eu(III) (2)] and [Ln2Co(bta)2(H2O)8]n·6nH2O [Ln = Eu(III) (3), Sm(III) (4), Gd(III) (5), and Tb(III) (6)] (H4bta = 1,2,4,5-benzenetretracaboxylic acid) have been synthesized and characterized via single-crystal X-ray diffraction. 1 and 2 are isostructural compounds with a structure composed of anionic layers of [Ln(bta)(H2O)2]n(n-) sandwiching mononuclear [Co(H2O)6](2+) cations plus crystallization water molecules, which are interlinked by electrostatic forces and hydrogen bonds, leading to a supramolecular three-dimensional network. 3-6 are also isostructural compounds, and their structure consists of neutral layers of formula [Ln2Co(bta)2(H2O)8]n and crystallization water molecules, which are connected through hydrogen bonds to afford a supramolecular three-dimensional network. Heterometallic chains formed by the regular alternation of two nine-coordinate lanthanide(III) polyhedra [Ln(III)O9] and one compressed cobalt(II) octahedron [Co(II)O6] along the crystallographic c-axis are cross-linked by bta ligands within each layer of 3-6. Magnetic susceptibility measurements on polycrystalline samples for 3-6 have been carried out in the temperature range of 2.0-300 K. The magnetic behavior of these types of Ln(III)-Co(II) complexes, which have been modeled by using matrix dagonalization techniques, reveals the lack of magnetic coupling for 3 and 4, and the occurrence of weak antiferromagnetic interactions within the Gd(III)-Gd(III) (5) and Tb(III)-Tb(III) (6) dinuclear units through the exchange pathway provided by the double oxo(carboxylate) and double syn-syn carboxylate bridges. PMID:24901707

  13. Crystal Structure of the Chromodomain Helicase DNA-binding Protein 1 (Chd1) DNA-binding Domain in Complex with DNA

    SciTech Connect

    Sharma A.; Heroux A.; Jenkins K. R.; Bowman G. D.

    2011-12-09

    Chromatin remodelers are ATP-dependent machines that dynamically alter the chromatin packaging of eukaryotic genomes by assembling, sliding, and displacing nucleosomes. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. The structure of the Chd1 DNA-binding domain was recently shown to consist of a SANT and SLIDE domain, analogous to the DNA-binding domain of the ISWI family, yet the details of how Chd1 recognized DNA were not known. Here we present the crystal structure of the Saccharomyces cerevisiae Chd1 DNA-binding domain in complex with a DNA duplex. The bound DNA duplex is straight, consistent with the preference exhibited by the Chd1 DNA-binding domain for extranucleosomal DNA. Comparison of this structure with the recently solved ISW1a DNA-binding domain bound to DNA reveals that DNA lays across each protein at a distinct angle, yet contacts similar surfaces on the SANT and SLIDE domains. In contrast to the minor groove binding seen for Isw1 and predicted for Chd1, the SLIDE domain of the Chd1 DNA-binding domain contacts the DNA major groove. The majority of direct contacts with the phosphate backbone occur only on one DNA strand, suggesting that Chd1 may not strongly discriminate between major and minor grooves.

  14. Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids.

    PubMed

    Aramesh, M; Shimoni, O; Fox, K; Karle, T J; Lohrmann, A; Ostrikov, K; Prawer, S; Cervenka, J

    2015-04-14

    Extracellular nucleic acids freely circulating in blood and other physiologic fluids are important biomarkers for non-invasive diagnostics and early detection of cancer and other diseases, yet difficult to detect because they exist in very low concentrations and large volumes. Here we demonstrate a new broad-range sensor platform for ultrasensitive and selective detection of circulating DNA down to the single-molecule level. The biosensor is based on a chemically functionalized nanoporous diamond-like carbon (DLC) coated alumina membrane. The few nanometer-thick, yet perfect and continuous DLC-coating confers the chemical stability and biocompatibility of the sensor, allowing its direct application in biological conditions. The selective detection is based on complementary hybridization of a fluorescently-tagged circulating cancer oncomarker (a 21-mer nucleic acid) with covalently immobilized DNA on the surface of the membrane. The captured DNAs are detected in the nanoporous structure of the sensor using confocal scanning laser microscopy. The flow-through membrane sensor demonstrates broad-range sensitivity, spanning from 10(15) molecules per cm(2) down to single molecules, which is several orders of magnitude improvement compared to the flat DNA microarrays. Our study suggests that these flow-through type nanoporous sensors represent a new powerful platform for large volume sampling and ultrasensitive detection of different chemical biomarkers. PMID:25744416

  15. Three-Dimensional (3D) Bicontinuous Hierarchically Porous Mn2O3 Single Crystals for High Performance Lithium-Ion Batteries.

    PubMed

    Huang, Shao-Zhuan; Jin, Jun; Cai, Yi; Li, Yu; Deng, Zhao; Zeng, Jun-Yang; Liu, Jing; Wang, Chao; Hasan, Tawfique; Su, Bao-Lian

    2015-01-01

    Bicontinuous hierarchically porous Mn2O3 single crystals (BHP-Mn2O3-SCs) with uniform parallelepiped geometry and tunable sizes have been synthesized and used as anode materials for lithium-ion batteries (LIBs). The monodispersed BHP-Mn2O3-SCs exhibit high specific surface area and three dimensional interconnected bimodal mesoporosity throughout the entire crystal. Such hierarchical interpenetrating porous framework can not only provide a large number of active sites for Li ion insertion, but also good conductivity and short diffusion length for Li ions, leading to a high lithium storage capacity and enhanced rate capability. Furthermore, owing to their specific porosity, these BHP-Mn2O3-SCs as anode materials can accommodate the volume expansion/contraction that occurs with lithium insertion/extraction during discharge/charge processes, resulting in their good cycling performance. Our synthesized BHP-Mn2O3-SCs with a size of ~700 nm display the best electrochemical performance, with a large reversible capacity (845 mA h g(-1) at 100 mA g(-1) after 50 cycles), high coulombic efficiency (>95%), excellent cycling stability and superior rate capability (410 mA h g(-1) at 1 Ag(-1)). These values are among the highest reported for Mn2O3-based bulk solids and nanostructures. Also, electrochemical impedance spectroscopy study demonstrates that the BHP-Mn2O3-SCs are suitable for charge transfer at the electrode/electrolyte interface. PMID:26439102

  16. Three-Dimensional (3D) Bicontinuous Hierarchically Porous Mn2O3 Single Crystals for High Performance Lithium-Ion Batteries

    NASA Astrophysics Data System (ADS)

    Huang, Shao-Zhuan; Jin, Jun; Cai, Yi; Li, Yu; Deng, Zhao; Zeng, Jun-Yang; Liu, Jing; Wang, Chao; Hasan, Tawfique; Su, Bao-Lian

    2015-10-01

    Bicontinuous hierarchically porous Mn2O3 single crystals (BHP-Mn2O3-SCs) with uniform parallelepiped geometry and tunable sizes have been synthesized and used as anode materials for lithium-ion batteries (LIBs). The monodispersed BHP-Mn2O3-SCs exhibit high specific surface area and three dimensional interconnected bimodal mesoporosity throughout the entire crystal. Such hierarchical interpenetrating porous framework can not only provide a large number of active sites for Li ion insertion, but also good conductivity and short diffusion length for Li ions, leading to a high lithium storage capacity and enhanced rate capability. Furthermore, owing to their specific porosity, these BHP-Mn2O3-SCs as anode materials can accommodate the volume expansion/contraction that occurs with lithium insertion/extraction during discharge/charge processes, resulting in their good cycling performance. Our synthesized BHP-Mn2O3-SCs with a size of ~700 nm display the best electrochemical performance, with a large reversible capacity (845 mA h g-1 at 100 mA g-1 after 50 cycles), high coulombic efficiency (>95%), excellent cycling stability and superior rate capability (410 mA h g-1 at 1 Ag-1). These values are among the highest reported for Mn2O3-based bulk solids and nanostructures. Also, electrochemical impedance spectroscopy study demonstrates that the BHP-Mn2O3-SCs are suitable for charge transfer at the electrode/electrolyte interface.

  17. Three-Dimensional (3D) Bicontinuous Hierarchically Porous Mn2O3 Single Crystals for High Performance Lithium-Ion Batteries

    PubMed Central

    Huang, Shao-Zhuan; Jin, Jun; Cai, Yi; Li, Yu; Deng, Zhao; Zeng, Jun-Yang; Liu, Jing; Wang, Chao; Hasan, Tawfique; Su, Bao-Lian

    2015-01-01

    Bicontinuous hierarchically porous Mn2O3 single crystals (BHP-Mn2O3-SCs) with uniform parallelepiped geometry and tunable sizes have been synthesized and used as anode materials for lithium-ion batteries (LIBs). The monodispersed BHP-Mn2O3-SCs exhibit high specific surface area and three dimensional interconnected bimodal mesoporosity throughout the entire crystal. Such hierarchical interpenetrating porous framework can not only provide a large number of active sites for Li ion insertion, but also good conductivity and short diffusion length for Li ions, leading to a high lithium storage capacity and enhanced rate capability. Furthermore, owing to their specific porosity, these BHP-Mn2O3-SCs as anode materials can accommodate the volume expansion/contraction that occurs with lithium insertion/extraction during discharge/charge processes, resulting in their good cycling performance. Our synthesized BHP-Mn2O3-SCs with a size of ~700 nm display the best electrochemical performance, with a large reversible capacity (845 mA h g−1 at 100 mA g−1 after 50 cycles), high coulombic efficiency (>95%), excellent cycling stability and superior rate capability (410 mA h g−1 at 1 Ag−1). These values are among the highest reported for Mn2O3-based bulk solids and nanostructures. Also, electrochemical impedance spectroscopy study demonstrates that the BHP-Mn2O3-SCs are suitable for charge transfer at the electrode/electrolyte interface. PMID:26439102

  18. 3D microscope

    NASA Astrophysics Data System (ADS)

    Iizuka, Keigo

    2008-02-01

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

  19. Recent developments in DFD (depth-fused 3D) display and arc 3D display

    NASA Astrophysics Data System (ADS)

    Suyama, Shiro; Yamamoto, Hirotsugu

    2015-05-01

    We will report our recent developments in DFD (Depth-fused 3D) display and arc 3D display, both of which have smooth movement parallax. Firstly, fatigueless DFD display, composed of only two layered displays with a gap, has continuous perceived depth by changing luminance ratio between two images. Two new methods, called "Edge-based DFD display" and "Deep DFD display", have been proposed in order to solve two severe problems of viewing angle and perceived depth limitations. Edge-based DFD display, layered by original 2D image and its edge part with a gap, can expand the DFD viewing angle limitation both in 2D and 3D perception. Deep DFD display can enlarge the DFD image depth by modulating spatial frequencies of front and rear images. Secondly, Arc 3D display can provide floating 3D images behind or in front of the display by illuminating many arc-shaped directional scattering sources, for example, arcshaped scratches on a flat board. Curved Arc 3D display, composed of many directional scattering sources on a curved surface, can provide a peculiar 3D image, for example, a floating image in the cylindrical bottle. The new active device has been proposed for switching arc 3D images by using the tips of dual-frequency liquid-crystal prisms as directional scattering sources. Directional scattering can be switched on/off by changing liquid-crystal refractive index, resulting in switching of arc 3D image.

  20. Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids

    NASA Astrophysics Data System (ADS)

    Aramesh, M.; Shimoni, O.; Fox, K.; Karle, T. J.; Lohrmann, A.; Ostrikov, K.; Prawer, S.; Cervenka, J.

    2015-03-01

    Extracellular nucleic acids freely circulating in blood and other physiologic fluids are important biomarkers for non-invasive diagnostics and early detection of cancer and other diseases, yet difficult to detect because they exist in very low concentrations and large volumes. Here we demonstrate a new broad-range sensor platform for ultrasensitive and selective detection of circulating DNA down to the single-molecule level. The biosensor is based on a chemically functionalized nanoporous diamond-like carbon (DLC) coated alumina membrane. The few nanometer-thick, yet perfect and continuous DLC-coating confers the chemical stability and biocompatibility of the sensor, allowing its direct application in biological conditions. The selective detection is based on complementary hybridization of a fluorescently-tagged circulating cancer oncomarker (a 21-mer nucleic acid) with covalently immobilized DNA on the surface of the membrane. The captured DNAs are detected in the nanoporous structure of the sensor using confocal scanning laser microscopy. The flow-through membrane sensor demonstrates broad-range sensitivity, spanning from 1015 molecules per cm2 down to single molecules, which is several orders of magnitude improvement compared to the flat DNA microarrays. Our study suggests that these flow-through type nanoporous sensors represent a new powerful platform for large volume sampling and ultrasensitive detection of different chemical biomarkers.Extracellular nucleic acids freely circulating in blood and other physiologic fluids are important biomarkers for non-invasive diagnostics and early detection of cancer and other diseases, yet difficult to detect because they exist in very low concentrations and large volumes. Here we demonstrate a new broad-range sensor platform for ultrasensitive and selective detection of circulating DNA down to the single-molecule level. The biosensor is based on a chemically functionalized nanoporous diamond-like carbon (DLC) coated

  1. Holographic Interferometry based on photorefractive crystal to measure 3D thermo-elastic distortion of composite structures and comparison with finite element models

    NASA Astrophysics Data System (ADS)

    Thizy, C.; Eliot, F.; Ballhause, D.; Olympio, K. R.; Kluge, R.; Shannon, A.; Laduree, G.; Logut, D.; Georges, M. P.

    2013-04-01

    Thermo-elastic distortions of composite structures have been measured by a holographic camera using a BSO photorefractive crystal as the recording medium. The first test campaign (Phase 1) was performed on CFRP struts with titanium end-fittings glued to the tips of the strut. The samples were placed in a vacuum chamber. The holographic camera was located outside the chamber and configured with two illuminations to measure the relative out-of-plane and in-plane (in one direction) displacements. The second test campaign (Phase 2) was performed on a structure composed of a large Silicon Carbide base plate supported by 3 GFRP struts with glued Titanium end-fittings. Thermo-elastic distortions have been measured with the same holographic camera used in phase 1, but four illuminations, instead of two, have been used to provide the three components of displacement. This technique was specially developed and validated during the phase 2 in CSL laboratory. The system has been designed to measure an object size of typically 250x250 mm2; the measurement range is such that the sum of the largest relative displacements in the three measurement directions is maximum 20 μm. The validation of the four-illuminations technique led to measurement uncertainties of 120 nm for the relative in-plane and out-of-plane displacements, 230 nm for the absolute in-plane displacement and 400 nm for the absolute out-of-plane displacement. For both campaigns, the test results have been compared to the predictions obtained by finite element analyses and the correlation of these results was good.

  2. 3D Audio System

    NASA Technical Reports Server (NTRS)

    1992-01-01

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

  3. Multiviewer 3D monitor

    NASA Astrophysics Data System (ADS)

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

    1998-09-01

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

  4. Dynamic Heterogeneity of DNA Methylation and Hydroxymethylation in Embryonic Stem Cell Populations Captured by Single-Cell 3D High-Content Analysis

    PubMed Central

    Tajbakhsh, Jian; Stefanovski, Darko; Tang, George; Wawrowsky, Kolja; Liu, Naiyou; Fair, Jeffrey H.

    2015-01-01

    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 ten-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 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 per day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17:0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, DNA global 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+/5mC−, 5hmC+/5mC+, and 5hmC−/5mC+ 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+/5mC+ 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 delineating chromatin domains in remodeling. We

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

    PubMed

    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. PMID:18528984

  6. 3D Surgical Simulation

    PubMed Central

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

    2009-01-01

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

  7. 3D Printing with Nucleic Acid Adhesives

    PubMed Central

    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

  8. Crystallization of DNA-capped gold nanoparticles in high-concentration, divalent salt environments.

    PubMed

    Tan, Shawn J; Kahn, Jason S; Derrien, Thomas L; Campolongo, Michael J; Zhao, Mervin; Smilgies, Detlef-M; Luo, Dan

    2014-01-27

    The multiparametric nature of nanoparticle self-assembly makes it challenging to circumvent the instabilities that lead to aggregation and achieve crystallization under extreme conditions. By using non-base-pairing DNA as a model ligand instead of the typical base-pairing design for programmability, long-range 2D DNA-gold nanoparticle crystals can be obtained at extremely high salt concentrations and in a divalent salt environment. The interparticle spacings in these 2D nanoparticle crystals can be engineered and further tuned based on an empirical model incorporating the parameters of ligand length and ionic strength. PMID:24459055

  9. Crystal structure of a p53 core tetramer bound to DNA

    SciTech Connect

    Malecka, K.A.; Ho, W.C.; Marmorstein, R.

    2009-09-02

    The tumor suppressor p53 regulates downstream genes in response to many cellular stresses and is frequently mutated in human cancers. Here, we report the use of a crosslinking strategy to trap a tetrameric p53 DNA-binding domain (p53DBD) bound to DNA and the X-ray crystal structure of the protein/DNA complex. The structure reveals that two p53DBD dimers bind to B form DNA with no relative twist and that a p53 tetramer can bind to DNA without introducing significant DNA bending. The numerous dimer-dimer interactions involve several strictly conserved residues, thus suggesting a molecular basis for p53DBD-DNA binding cooperativity. Surface residue conservation of the p53DBD tetramer bound to DNA highlights possible regions of other p53 domain or p53 cofactor interactions.

  10. 'Bonneville' in 3-D!

    NASA Technical Reports Server (NTRS)

    2004-01-01

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