Formation of bulk refractive index structures

DOEpatents

Potter, Jr., Barrett George; Potter, Kelly Simmons; Wheeler, David R.; Jamison, Gregory M.

2003-07-15

A method of making a stacked three-dimensional refractive index structure in photosensitive materials using photo-patterning where first determined is the wavelength at which a photosensitive material film exhibits a change in refractive index upon exposure to optical radiation, a portion of the surfaces of the photosensitive material film is optically irradiated, the film is marked to produce a registry mark. Multiple films are produced and aligned using the registry marks to form a stacked three-dimensional refractive index structure.

Three-dimensional shape transformations of hydrogel sheets induced by small-scale modulation of internal stresses

NASA Astrophysics Data System (ADS)

Wu, Zi Liang; Moshe, Michael; Greener, Jesse; Therien-Aubin, Heloise; Nie, Zhihong; Sharon, Eran; Kumacheva, Eugenia

2013-03-01

Although Nature has always been a common source of inspiration in the development of artificial materials, only recently has the ability of man-made materials to produce complex three-dimensional (3D) structures from two-dimensional sheets been explored. Here we present a new approach to the self-shaping of soft matter that mimics fibrous plant tissues by exploiting small-scale variations in the internal stresses to form three-dimensional morphologies. We design single-layer hydrogel sheets with chemically distinct, fibre-like regions that exhibit differential shrinkage and elastic moduli under the application of external stimulus. Using a planar-to-helical three-dimensional shape transformation as an example, we explore the relation between the internal architecture of the sheets and their transition to cylindrical and conical helices with specific structural characteristics. The ability to engineer multiple three-dimensional shape transformations determined by small-scale patterns in a hydrogel sheet represents a promising step in the development of programmable soft matter.

Optimum Particle Size for Gold-Catalyzed CO Oxidation

PubMed Central

2018-01-01

The structure sensitivity of gold-catalyzed CO oxidation is presented by analyzing in detail the dependence of CO oxidation rate on particle size. Clusters with less than 14 gold atoms adopt a planar structure, whereas larger ones adopt a three-dimensional structure. The CO and O2 adsorption properties depend strongly on particle structure and size. All of the reaction barriers relevant to CO oxidation display linear scaling relationships with CO and O2 binding strengths as main reactivity descriptors. Planar and three-dimensional gold clusters exhibit different linear scaling relationship due to different surface topologies and different coordination numbers of the surface atoms. On the basis of these linear scaling relationships, first-principles microkinetics simulations were conducted to determine CO oxidation rates and possible rate-determining step of Au particles. Planar Au9 and three-dimensional Au79 clusters present the highest CO oxidation rates for planar and three-dimensional clusters, respectively. The planar Au9 cluster is much more active than the optimum Au79 cluster. A common feature of optimum CO oxidation performance is the intermediate binding strengths of CO and O2, resulting in intermediate coverages of CO, O2, and O. Both these optimum particles present lower performance than maximum Sabatier performance, indicating that there is sufficient room for improvement of gold catalysts for CO oxidation. PMID:29707098

Electron tomography and computer visualisation of a three-dimensional 'photonic' crystal in a butterfly wing-scale.

PubMed

Argyros, A; Manos, S; Large, M C J; McKenzie, D R; Cox, G C; Dwarte, D M

2002-01-01

A combination of transmission electron tomography and computer modelling has been used to determine the three-dimensional structure of the photonic crystals found in the wing-scales of the Kaiser-I-Hind butterfly (Teinopalpus imperialis). These scales presented challenges for electron microscopy because the periodicity of the structure was comparable to the thickness of a section and because of the complex connectivity of the object. The structure obtained has been confirmed by taking slices of the three-dimensional computer model constructed from the tomography and comparing these with transmission electron microscope (TEM) images of microtomed sections of the actual scale. The crystal was found to have chiral tetrahedral repeating units packed in a triclinic lattice.

Three-Dimensional Geometry of Collagenous Tissues by Second Harmonic Polarimetry.

PubMed

Reiser, Karen; Stoller, Patrick; Knoesen, André

2017-06-01

Collagen is a biological macromolecule capable of second harmonic generation, allowing label-free detection in tissues; in addition, molecular orientation can be determined from the polarization dependence of the second harmonic signal. Previously we reported that in-plane orientation of collagen fibrils could be determined by modulating the polarization angle of the laser during scanning. We have now extended this method so that out-of-plane orientation angles can be determined at the same time, allowing visualization of the 3-dimensional structure of collagenous tissues. This approach offers advantages compared with other methods for determining out-of-plane orientation. First, the orientation angles are directly calculated from the polarimetry data obtained in a single scan, while other reported methods require data from multiple scans, use of iterative optimization methods, application of fitting algorithms, or extensive post-optical processing. Second, our method does not require highly specialized instrumentation, and thus can be adapted for use in almost any nonlinear optical microscopy setup. It is suitable for both basic and clinical applications. We present three-dimensional images of structurally complex collagenous tissues that illustrate the power of such 3-dimensional analyses to reveal the architecture of biological structures.

Three-Dimensional Geometry of Collagenous Tissues by Second Harmonic Polarimetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reiser, Karen; Stoller, Patrick; Knoesen, André

Collagen is a biological macromolecule capable of second harmonic generation, allowing label-free detection in tissues; in addition, molecular orientation can be determined from the polarization dependence of the second harmonic signal. Previously we reported that in-plane orientation of collagen fibrils could be determined by modulating the polarization angle of the laser during scanning. We have now extended this method so that out-of-plane orientation angles can be determined at the same time, allowing visualization of the 3-dimensional structure of collagenous tissues. This approach offers advantages compared with other methods for determining out-of-plane orientation. First, the orientation angles are directly calculated frommore » the polarimetry data obtained in a single scan, while other reported methods require data from multiple scans, use of iterative optimization methods, application of fitting algorithms, or extensive post-optical processing. Second, our method does not require highly specialized instrumentation, and thus can be adapted for use in almost any nonlinear optical microscopy setup. It is suitable for both basic and clinical applications. We present three-dimensional images of structurally complex collagenous tissues that illustrate the power of such 3-dimensional analyses to reveal the architecture of biological structures.« less

Three-Dimensional Geometry of Collagenous Tissues by Second Harmonic Polarimetry

DOE PAGES

Reiser, Karen; Stoller, Patrick; Knoesen, André

2017-06-01

Collagen is a biological macromolecule capable of second harmonic generation, allowing label-free detection in tissues; in addition, molecular orientation can be determined from the polarization dependence of the second harmonic signal. Previously we reported that in-plane orientation of collagen fibrils could be determined by modulating the polarization angle of the laser during scanning. We have now extended this method so that out-of-plane orientation angles can be determined at the same time, allowing visualization of the 3-dimensional structure of collagenous tissues. This approach offers advantages compared with other methods for determining out-of-plane orientation. First, the orientation angles are directly calculated frommore » the polarimetry data obtained in a single scan, while other reported methods require data from multiple scans, use of iterative optimization methods, application of fitting algorithms, or extensive post-optical processing. Second, our method does not require highly specialized instrumentation, and thus can be adapted for use in almost any nonlinear optical microscopy setup. It is suitable for both basic and clinical applications. We present three-dimensional images of structurally complex collagenous tissues that illustrate the power of such 3-dimensional analyses to reveal the architecture of biological structures.« less

Three Dimensional Modeling of the Attenuation Structure in the Part of the Kumaon Himalaya, India Using Strong Motion Data

NASA Astrophysics Data System (ADS)

Joshi, A.; LAL, S.

2017-12-01

Attenuation property of the medium determines the amplitude of seismic waves at different locations during an earthquake. Attenuation can be defined by the inverse of the parameter known as quality factor `Q' (Knopoff, 1964). It has been observed that the peak ground acceleration in the strong motion accelerogram is associated with arrival of S-waves which is controlled mainly by the shear wave attenuation characteristics of the medium. In the present work attenuation structure is obtained using the modified inversion algorithm given by Joshi et al. (2010). The modified inversion algorithm is designed to provide three dimensional attenuation structure of the region at different frequencies. A strong motion network is installed in the Kumaon Himalaya by the Department of Earth Sciences, Indian Institute of Technology Roorkee under a major research project sponsored by the Ministry of Earth Sciences, Government of India. In this work the detailed three dimensional shear wave quality factor has been determined for the Kumaon Himalaya using strong motion data obtained from this network. In the present work 164 records from 26 events recorded at 15 stations located in an area of 129 km x 62 km has been used. The shear wave attenuation structure for the Kumaon Himalaya has been calculated by dividing the study region into 108 three dimensional rectangular blocks of size 22 km x 11 km x 5 km. The input to the inversion algorithm is the acceleration spectra of S wave identified from each record. A total of 164 spectra from equal number of accelerograms with sampling frequency of .024 Hz is used as an input to the algorithms. A total of 2048 three dimensional attenuation structure is obtained upto frequency of 50 Hz. The obtained structure at various frequencies is compared with the existing geological models in the region and it is seen that the obtained model correlated well with the geological model of the region. References: Joshi, A., Mohanty, M., Bansal, A. R., Dimri, V. P. and Chadha, R. K., 2010, Use of spectral acceleration data for determination of three dimensional attenuation structure in the Pithoragarh region of Kumaon Himalaya, J Seismol., 14, 247-272. Knopoff, L., 1964, Q, Reviews of Geophysics, 2, 625-660.

Helical structures in vertically aligned dust particle chains in a complex plasma

NASA Astrophysics Data System (ADS)

Hyde, Truell W.; Kong, Jie; Matthews, Lorin S.

2013-05-01

Self-assembly of structures from vertically aligned, charged dust particle bundles within a glass box placed on the lower, powered electrode of a Gaseous Electronics Conference rf reference cell were produced and examined experimentally. Self-organized formation of one-dimensional vertical chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from a one-dimensional chain structure, through a zigzag transition to a two-dimensional, spindlelike structure, and then to various three-dimensional, helical structures exhibiting multiple symmetries. Stable configurations are found to be dependent upon the system confinement, γ2=ω0h/ω0v2 (where ω0h,v are the horizontal and vertical dust resonance frequencies), the total number of particles within a bundle, and the rf power. For clusters having fixed numbers of particles, the rf power at which structural phase transitions occur is repeatable and exhibits no observable hysteresis. The critical conditions for these structural phase transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop are in good agreement with the theoretically predicted configurations of minimum energy determined employing molecular dynamics simulations for charged dust particles confined in a prolate, spheroidal potential as presented theoretically by Kamimura and Ishihara [Kamimura and Ishihara, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.85.016406 85, 016406 (2012)].

Two-Dimensional Nuclear Magnetic Resonance Structure Determination Module for Introductory Biochemistry: Synthesis and Structural Characterization of Lyso-Glycerophospholipids

ERIC Educational Resources Information Center

Garrett, Teresa A.; Rose, Rebecca L.; Bell, Sidney M.

2013-01-01

In this laboratory module, introductory biochemistry students are exposed to two-dimensional [superscript 1]H-nuclear magnetic resonance of glycerophospholipids (GPLs). Working in groups of three, students enzymatically synthesized and purified a variety of 2-acyl lyso GPLs. The structure of the 2-acyl lyso GPL was verified using [superscript…

Accessibility of selenomethionine proteins by total chemical synthesis: structural studies of human herpesvirus-8 MIP-II.

PubMed

Shao, W; Fernandez, E; Wilken, J; Thompson, D A; Siani, M A; West, J; Lolis, E; Schweitzer, B I

1998-12-11

The determination of high resolution three-dimensional structures by X-ray crystallography or nuclear magnetic resonance (NMR) is a time-consuming process. Here we describe an approach to circumvent the cloning and expression of a recombinant protein as well as screening for heavy atom derivatives. The selenomethionine-modified chemokine macrophage inflammatory protein-II (MIP-II) from human herpesvirus-8 has been produced by total chemical synthesis, crystallized, and characterized by NMR. The protein has a secondary structure typical of other chemokines and forms a monomer in solution. These results indicate that total chemical synthesis can be used to accelerate the determination of three-dimensional structures of new proteins identified in genome programs.

Method of fabricating free-form, high-aspect ratio components for high-current, high-speed microelectrics

DOEpatents

Maxwell, James L; Rose, Chris R; Black, Marcie R; Springer, Robert W

2014-03-11

Microelectronic structures and devices, and method of fabricating a three-dimensional microelectronic structure is provided, comprising passing a first precursor material for a selected three-dimensional microelectronic structure into a reaction chamber at temperatures sufficient to maintain said precursor material in a predominantly gaseous state; maintaining said reaction chamber under sufficient pressures to enhance formation of a first portion of said three-dimensional microelectronic structure; applying an electric field between an electrode and said microelectronic structure at a desired point under conditions whereat said first portion of a selected three-dimensional microelectronic structure is formed from said first precursor material; positionally adjusting either said formed three-dimensional microelectronic structure or said electrode whereby further controlled growth of said three-dimensional microelectronic structure occurs; passing a second precursor material for a selected three-dimensional microelectronic structure into a reaction chamber at temperatures sufficient to maintain said precursor material in a predominantly gaseous state; maintaining said reaction chamber under sufficient pressures whereby a second portion of said three-dimensional microelectronic structure formation is enhanced; applying an electric field between an electrode and said microelectronic structure at a desired point under conditions whereat said second portion of a selected three-dimensional microelectronic structure is formed from said second precursor material; and, positionally adjusting either said formed three-dimensional microelectronic structure or said electrode whereby further controlled growth of said three-dimensional microelectronic structure occurs.

Effects of lung disease on the three-dimensional structure and air flow pattern in the human airway tree

NASA Astrophysics Data System (ADS)

van de Moortele, Tristan; Nemes, Andras; Wendt, Christine; Coletti, Filippo

2016-11-01

The morphological features of the airway tree directly affect the air flow features during breathing, which determines the gas exchange and inhaled particle transport. Lung disease, Chronic Obstructive Pulmonary Disease (COPD) in this study, affects the structural features of the lungs, which in turn negatively affects the air flow through the airways. Here bronchial tree air volume geometries are segmented from Computed Tomography (CT) scans of healthy and diseased subjects. Geometrical analysis of the airway centerlines and corresponding cross-sectional areas provide insight into the specific effects of COPD on the airway structure. These geometries are also used to 3D print anatomically accurate, patient specific flow models. Three-component, three-dimensional velocity fields within these models are acquired using Magnetic Resonance Imaging (MRI). The three-dimensional flow fields provide insight into the change in flow patterns and features. Additionally, particle trajectories are determined using the velocity fields, to identify the fate of therapeutic and harmful inhaled aerosols. Correlation between disease-specific and patient-specific anatomical features with dysfunctional airflow patterns can be achieved by combining geometrical and flow analysis.

Binary Colloidal Alloy Test-5: Three-Dimensional Melt

NASA Technical Reports Server (NTRS)

Yodh, Arjun G.

2008-01-01

Binary Colloidal Alloy Test - 5: Three-Dimensional Melt (BCAT-5-3DMelt) photographs initially randomized colloidal samples in microgravity to determine their resulting structure over time. BCAT-5-3D-Melt will allow the scientists to capture the kinetics (evolution) of their samples, as well as the final equilibrium state of each sample. BCAT-5-3D-Melt will look at the mechanisms of melting using three-dimensional temperature sensitive colloidal crystals. Results will help scientists develop fundamental physics concepts previously shadowed by the effects of gravity.

The three-dimensional genome organization of Drosophila melanogaster through data integration.

PubMed

Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, Frank

2017-07-31

Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments. Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this data deconvolution framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our three-dimensional genome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of different chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data. Our approach allows systematic integration of Hi-C and lamina-DamID data for complete three-dimensional genome structure calculation, while also explicitly considering genome structural variability.

Fast computational methods for predicting protein structure from primary amino acid sequence

DOEpatents

Agarwal, Pratul Kumar [Knoxville, TN

2011-07-19

The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.

Effects of three-dimensional velocity structure on the seismicity of the 1984 Morgan Hill, California, aftershock sequence

USGS Publications Warehouse

Michael, A.J.

1988-01-01

A three-dimensional velocity model for the area surrounding the 24 April 1984 Morgan Hill earthquake has been developed by simultaneously inverting local earthquake and refraction arrival-time data. This velocity model corresponds well to the surface geology of the region, predominantly showing a low-velocity region associated with the sedimentary sequence to the south-west of the Madrone Springs fault. The focal mechanisms were also determined for 946 earthquakes using both the one-dimensional and three-dimensional earth models. Both earth models yield similar focal mechanisms for these earthquakes. -from Author

Three-dimensional structure determination protocol for noncrystalline biomolecules using x-ray free-electron laser diffraction imaging.

PubMed

Oroguchi, Tomotaka; Nakasako, Masayoshi

2013-02-01

Coherent and intense x-ray pulses generated by x-ray free-electron laser (XFEL) sources are paving the way for structural determination of noncrystalline biomolecules. However, due to the small scattering cross section of electrons for x rays, the available incident x-ray intensity of XFEL sources, which is currently in the range of 10(12)-10(13) photons/μm(2)/pulse, is lower than that necessary to perform single-molecule diffraction experiments for noncrystalline biomolecules even with the molecular masses of megadalton and submicrometer dimensions. Here, we propose an experimental protocol and analysis method for visualizing the structure of those biomolecules by the combined application of coherent x-ray diffraction imaging and three-dimensional reconstruction methods. To compensate the small scattering cross section of biomolecules, in our protocol, a thin vitreous ice plate containing several hundred biomolecules/μm(2) is used as sample, a setup similar to that utilized by single-molecule cryoelectron microscopy. The scattering cross section of such an ice plate is far larger than that of a single particle. The images of biomolecules contained within irradiated areas are then retrieved from each diffraction pattern, and finally provide the three-dimensional electron density model. A realistic atomic simulation using large-scale computations proposed that the three-dimensional structure determination of the 50S ribosomal subunit embedded in a vitreous ice plate is possible at a resolution of 0.8 nm when an x-ray beam of 10(16) photons/500×500 nm(2)/pulse is available.

A2TiF 5· nH 2O ( A=K, Rb, or Cs; n=0 or 1): Synthesis, structure, characterization, and calculations of three new uni-dimensional titanium fluorides

NASA Astrophysics Data System (ADS)

Jo, Vinna; Woo Lee, Dong; Koo, Hyun-Joo; Ok, Kang Min

2011-04-01

Three new uni-dimensional alkali metal titanium fluoride materials, A2TiF 5· nH 2O ( A=K, Rb, or Cs; n=0 or 1) have been synthesized by hydrothermal reactions. The structures of A2TiF 5· nH 2O have been determined by single-crystal X-ray diffraction. The Ti 4+ cations have been reduced to Ti 3+ during the synthesis reactions. All three A2TiF 5· nH 2O materials contain novel 1-D chain structures that are composed of the slightly distorted Ti 3+F 6 corner-sharing octahedra attributable to the Jahn-Teller distortion. The coordination environment of the alkali metal cations plays an important role to determine the degree of turning in the chain structures. Complete structural analyses, Infrared and UV-vis diffuse reflectance spectra, and thermal analyses are presented, as are electronic structure calculations.

Three-dimensional structure of phosphoribosyl pyrophosphate synthetase from E. coli at 2.71 Å resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Timofeev, V. I., E-mail: inna@ns.crys.ras.ru, E-mail: tostars@mail.ru, E-mail: ugama@yandex.ru; Abramchik, Yu. A.; Zhukhlistova, N. E.

2016-01-15

Phosphoribosyl pyrophosphate synthetase from Escherichia coli was cloned, purified, and crystallized. Single crystals of the enzyme were grown under microgravity. The X-ray diffraction data set was collected at the Spring-8 synchrotron facility and used to determine the three-dimensional structure of the enzyme by the molecular-replacement method at 2.71 Å resolution. The active and regulatory sites in the molecule of E. coli phosphoribosyl pyrophosphate synthetase were revealed by comparison with the homologous protein from Bacillus subtilis, the structure of which was determined in a complex with functional ligands. The conformations of polypeptide-chain fragments surrounding and composing the active and regulatory sitesmore » were shown to be identical in both proteins.« less

Three-dimensional distribution of polymorphs and magnesium in a calcified underwater attachment system by diffraction tomography

PubMed Central

Leemreize, Hanna; Almer, Jonathan D.; Stock, Stuart R.; Birkedal, Henrik

2013-01-01

Biological materials display complicated three-dimensional hierarchical structures. Determining these structures is essential in understanding the link between material design and properties. Herein, we show how diffraction tomography can be used to determine the relative placement of the calcium carbonate polymorphs calcite and aragonite in the highly mineralized holdfast system of the bivalve Anomia simplex. In addition to high fidelity and non-destructive mapping of polymorphs, we use detailed analysis of X-ray diffraction peak positions in reconstructed powder diffraction data to determine the local degree of Mg substitution in the calcite phase. These data show how diffraction tomography can provide detailed multi-length scale information on complex materials in general and of biomineralized tissues in particular. PMID:23804437

GIXSGUI : a MATLAB toolbox for grazing-incidence X-ray scattering data visualization and reduction, and indexing of buried three-dimensional periodic nanostructured films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Zhang

GIXSGUIis a MATLAB toolbox that offers both a graphical user interface and script-based access to visualize and process grazing-incidence X-ray scattering data from nanostructures on surfaces and in thin films. It provides routine surface scattering data reduction methods such as geometric correction, one-dimensional intensity linecut, two-dimensional intensity reshapingetc. Three-dimensional indexing is also implemented to determine the space group and lattice parameters of buried organized nanoscopic structures in supported thin films.

Determination of the three-dimensional structure of oligosaccharides in the solid state from experimental 13C NMR data and ab initio chemical shift surfaces.

PubMed

Sergeyev, Ivan; Moyna, Guillermo

2005-05-02

A novel method for the determination of the three-dimensional (3D) structure of oligosaccharides in the solid state using experimental 13C NMR data is presented. The approach employs this information, combined with 13C chemical shift surfaces (CSSs) for the glycosidic bond carbons in the generation of NMR pseudopotential energy functions suitable for use as constraints in molecular modeling simulations. Application of the method to trehalose, cellobiose, and cellotetraose produces 3D models that agree remarkably well with the reported X-ray structures, with phi and psi dihedral angles that are within 10 degrees from the ones observed in the crystals. The usefulness of the approach is further demonstrated in the determination of the 3D structure of the cellohexaose, an hexasaccharide for which no X-ray data has been reported, as well as in the generation of accurate structural models for cellulose II and amylose V6.

A discrete search algorithm for finding the structure of protein backbones and side chains.

PubMed

Sallaume, Silas; Martins, Simone de Lima; Ochi, Luiz Satoru; Da Silva, Warley Gramacho; Lavor, Carlile; Liberti, Leo

2013-01-01

Some information about protein structure can be obtained by using Nuclear Magnetic Resonance (NMR) techniques, but they provide only a sparse set of distances between atoms in a protein. The Molecular Distance Geometry Problem (MDGP) consists in determining the three-dimensional structure of a molecule using a set of known distances between some atoms. Recently, a Branch and Prune (BP) algorithm was proposed to calculate the backbone of a protein, based on a discrete formulation for the MDGP. We present an extension of the BP algorithm that can calculate not only the protein backbone, but the whole three-dimensional structure of proteins.

Determination of the real structure of artificial and natural opals on the basis of three-dimensional reconstructions of reciprocal space

NASA Astrophysics Data System (ADS)

Eliseev, A. A.; Gorozhankin, D. F.; Napolskii, K. S.; Petukhov, A. V.; Sapoletova, N. A.; Vasilieva, A. V.; Grigoryeva, N. A.; Mistonov, A. A.; Byelov, D. V.; Bouwman, W. G.; Kvashnina, K. O.; Chernyshov, D. Yu.; Bosak, A. A.; Grigoriev, S. V.

2009-10-01

The distribution of the scattering intensity in the reciprocal space for natural and artificial opals has been reconstructed from a set of small-angle X-ray diffraction patterns. The resulting three-dimensional intensity maps are used to analyze the defect structure of opals. The structure of artificial opals can be satisfactorily described in the Wilson probability model with the prevalence of layers in the fcc environment. The diffraction patterns observed for a natural opal confirm the presence of sufficiently long unequally occupied fcc domains.

Quantifying forest vertical structure to determine bird habitat quality in the Greenbelt Corridor, Denton, TX

NASA Astrophysics Data System (ADS)

Matsubayashi, Shiho

This study presents the integration of light detection and range (LiDAR) and hyperspectral remote sensing to create a three-dimensional bird habitat map in the Greenbelt Corridor of the Elm Fork of the Trinity River. This map permits to examine the relationship between forest stand structure, landscape heterogeneity, and bird community composition. A biannual bird census was conducted at this site during the breeding seasons of 2009 and 2010. Census data combined with the three-dimensional map suggest that local breeding bird abundance, community structure, and spatial distribution patterns are highly influenced by vertical heterogeneity of vegetation surface. For local breeding birds, vertical heterogeneity of canopy surface within stands, connectivity to adjacent forest patches, largest forest patch index, and habitat (vegetation) types proved to be the most influential factors to determine bird community assemblages. Results also highlight the critical role of secondary forests to increase functional connectivity of forest patches. Overall, three-dimensional habitat descriptions derived from integrated LiDAR and hyperspectral data serve as a powerful bird conservation tool that shows how the distribution of bird species relates to forest composition and structure at various scales.

Insights into Head-Tailed Viruses Infecting Extremely Halophilic Archaea

PubMed Central

Pietilä, Maija K.; Laurinmäki, Pasi; Russell, Daniel A.; Ko, Ching-Chung; Jacobs-Sera, Deborah; Butcher, Sarah J.

2013-01-01

Extremophilic archaea, both hyperthermophiles and halophiles, dominate in habitats where rather harsh conditions are encountered. Like all other organisms, archaeal cells are susceptible to viral infections, and to date, about 100 archaeal viruses have been described. Among them, there are extraordinary virion morphologies as well as the common head-tailed viruses. Although approximately half of the isolated archaeal viruses belong to the latter group, no three-dimensional virion structures of these head-tailed viruses are available. Thus, rigorous comparisons with bacteriophages are not yet warranted. In the present study, we determined the genome sequences of two of such viruses of halophiles and solved their capsid structures by cryo-electron microscopy and three-dimensional image reconstruction. We show that these viruses are inactivated, yet remain intact, at low salinity and that their infectivity is regained when high salinity is restored. This enabled us to determine their three-dimensional capsid structures at low salinity to a ∼10-Å resolution. The genetic and structural data showed that both viruses belong to the same T-number class, but one of them has enlarged its capsid to accommodate a larger genome than typically associated with a T=7 capsid by inserting an additional protein into the capsid lattice. PMID:23283946

Micrometer-scale fabrication of complex three dimensional lattice + basis structures in silicon

DOE PAGES

Burckel, D. Bruce; Resnick, Paul J.; Finnegan, Patrick S.; ...

2015-01-01

A complementary metal oxide semiconductor (CMOS) compatible version of membrane projection lithography (MPL) for fabrication of micrometer-scale three-dimensional structures is presented. The approach uses all inorganic materials and standard CMOS processing equipment. In a single layer, MPL is capable of creating all 5 2D-Bravais lattices. Furthermore, standard semiconductor processing steps can be used in a layer-by-layer approach to create fully three dimensional structures with any of the 14 3D-Bravais lattices. The unit cell basis is determined by the projection of the membrane pattern, with many degrees of freedom for defining functional inclusions. Here we demonstrate several unique structural motifs, andmore » characterize 2D arrays of unit cells with split ring resonators in a silicon matrix. The structures exhibit strong polarization dependent resonances and, for properly oriented split ring resonators (SRRs), coupling to the magnetic field of a normally incident transverse electromagnetic wave, a response unique to 3D inclusions.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pease, J.H.

The three dimensional structures of several small peptides were determined using a combination of {sup 1}H nuclear magnetic resonance (NMR) and distance geometry calculations. These techniques were found to be particularly helpful for analyzing structural differences between related peptides since all of the peptides' {sup 1}H NMR spectra are very similar. The structures of peptides from two separate classes are presented. Peptides in the first class are related to apamin, an 18 amino acid peptide toxin from honey bee venom. The {sup 1}H NMR assignments and secondary structure determination of apamin were done previously. Quantitative NMR measurements and distance geometrymore » calculations were done to calculate apamin's three dimensional structure. Peptides in the second class are 48 amino acid toxins from the sea anemone Radianthus paumotensis. The {sup 1}H NMR assignments of toxin II were done previously. The {sup 1}H NMR assignments of toxin III and the distance geometry calculations for both peptides are presented.« less

A rudimentary database for three-dimensional objects using structural representation

NASA Technical Reports Server (NTRS)

Sowers, James P.

1987-01-01

A database which enables users to store and share the description of three-dimensional objects in a research environment is presented. The main objective of the design is to make it a compact structure that holds sufficient information to reconstruct the object. The database design is based on an object representation scheme which is information preserving, reasonably efficient, and yet economical in terms of the storage requirement. The determination of the needed data for the reconstruction process is guided by the belief that it is faster to do simple computations to generate needed data/information for construction than to retrieve everything from memory. Some recent techniques of three-dimensional representation that influenced the design of the database are discussed. The schema for the database and the structural definition used to define an object are given. The user manual for the software developed to create and maintain the contents of the database is included.

Coarse-grained mechanics of viral shells

NASA Astrophysics Data System (ADS)

Klug, William S.; Gibbons, Melissa M.

2008-03-01

We present an approach for creating three-dimensional finite element models of viral capsids from atomic-level structural data (X-ray or cryo-EM). The models capture heterogeneous geometric features and are used in conjunction with three-dimensional nonlinear continuum elasticity to simulate nanoindentation experiments as performed using atomic force microscopy. The method is extremely flexible; able to capture varying levels of detail in the three-dimensional structure. Nanoindentation simulations are presented for several viruses: Hepatitis B, CCMV, HK97, and φ29. In addition to purely continuum elastic models a multiscale technique is developed that combines finite-element kinematics with MD energetics such that large-scale deformations are facilitated by a reduction in degrees of freedom. Simulations of these capsid deformation experiments provide a testing ground for the techniques, as well as insight into the strength-determining mechanisms of capsid deformation. These methods can be extended as a framework for modeling other proteins and macromolecular structures in cell biology.

The mesangial matrix in the normal and sclerotic glomerulus.

PubMed

Rosenblum, N D

1994-02-01

Mesangial sclerosis is a final common pathway to glomerular destruction in a variety of glomerular diseases. The expression of several classes of extracellular matrix (ECM) molecules has been defined in the normal and diseased mesangial matrix (MM). However, the manner in which these ECM components determine the three dimensional structure and function of the MM remains to be defined. Structural studies of the MM suggest that its constituent molecules are regionally organized into subcompartments with different three dimensional structures. The diversity of matrix molecules expressed within the MM as well as the organization of these components in nonrenal ECM's, such as the cornea, provides further support for this organizational model. The study of the cornea has also revealed that novel short chain collagenous proteins partially determine the three dimensional structure of the matrix. Recently, a novel collagen, type VIII collagen, has been described in mesangial cells and in the intact glomerulus. It is hypothesized that type VIII collagen is expressed both as a polymer and as a monomer within the glomerulus, and depending on its conformation, may serve unique functions. In the chronically diseased MM, normal MM components are overexpressed and fibrillar collagens are expressed de novo in a delayed fashion. Enhanced proteoglycan expression, observed early in disease, may determine increased volume of the mesangium. This, in turn, may stimulate the production of fibrillar collagens by mesangial cells resulting in a fibrillar noncompliant mesangial matrix.

Dimensional Effects on the Charge Density Waves in Ultrathin Films of TiSe 2

DOE PAGES

Chen, P.; Chan, Y. -H.; Wong, M. -H.; ...

2016-09-20

Charge density wave (CDW) formation in solids is a critical phenomenon involving the collective reorganization of the electrons and atoms in the system into a wave structure, and it is expected to be sensitive to the geometric constraint of the system at the nanoscale. Here, we study the CDW transition in TiSe 2, a quasi-two-dimensional layered material, to determine the effects of quantum confinement and changing dimensions in films ranging from a single layer to multilayers. Of key interest is the characteristic length scale for the transformation from a two-dimensional case to the three-dimensional limit. Angle-resolved photoemission (ARPES) measurements ofmore » films with thicknesses up to six layers reveal substantial variations in the energy structure of discrete quantum well states; however, the temperature-dependent band-gap renormalization converges at just three layers. The results indicate a layer-dependent mixture of two transition temperatures and a very-short-range CDW interaction within a three-dimensional framework.« less

REX3DV1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holm, Elizabeth A.

2002-03-28

This code is a FORTRAN code for three-dimensional Monte Carol Potts Model (MCPM) Recrystallization and grain growth. A continuum grain structure is mapped onto a three-dimensional lattice. The mapping procedure is analogous to color bitmapping the grain structure; grains are clusters of pixels (sites) of the same color (spin). The total system energy is given by the Pott Hamiltonian and the kinetics of grain growth are determined through a Monte Carlo technique with a nonconserved order parameter (Glauber dynamics). The code can be compiled and run on UNIX/Linux platforms.

Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

NASA Astrophysics Data System (ADS)

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; Zhang, Meng; Tong, Huimin; Zhang, Xing; Lu, Zhuoyang; Liu, Jiankang; Alivisatos, A. Paul; Ren, Gang

2016-03-01

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ~2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.

My daily constitutional in martinsried.

PubMed

Allen, James P

2004-01-01

The three-dimensional structures of bacterial reaction centers have served as the framework for much of our understanding of anoxygenic photosynthesis. A key step in the determination of the structure of the reaction center from Rhodobacter sphaeroides was the use the molecular replacement technique. For this technique, we made use of two sets of data. First, X-ray diffraction data had been measured from crystals of the reaction center from R. sphaeroides by our research group in California, led by George Feher and Douglas Rees. The second data set consisted of the coordinates of the three-dimensional structure of the reaction center from Rhodopseudomonas (now Blastochloris) viridis, which had been solved in the pioneering efforts of a group in Martinsried, led by Johann Deisenhofer, Robert Huber and Hartmut Michel. The collaborative efforts of these two groups to determine the structure of the reaction center from R. sphaeroides is described.

Dual wing, swept forward swept rearward wing, and single wing design optimization for high performance business airplanes

NASA Technical Reports Server (NTRS)

Rhodes, M. D.; Selberg, B. P.

1982-01-01

An investigation was performed to compare closely coupled dual wing and swept forward swept rearward wing aircraft to corresponding single wing 'baseline' designs to judge the advantages offered by aircraft designed with multiple wing systems. The optimum multiple wing geometry used on the multiple wing designs was determined in an analytic study which investigated the two- and three-dimensional aerodynamic behavior of a wide range of multiple wing configurations in order to find the wing geometry that created the minimum cruise drag. This analysis used a multi-element inviscid vortex panel program coupled to a momentum integral boundary layer analysis program to account for the aerodynamic coupling between the wings and to provide the two-dimensional aerodynamic data, which was then used as input for a three-dimensional vortex lattice program, which calculated the three-dimensional aerodynamic data. The low drag of the multiple wing configurations is due to a combination of two dimensional drag reductions, tailoring the three dimensional drag for the swept forward swept rearward design, and the structural advantages of the two wings that because of the structural connections permitted higher aspect ratios.

The structure of a cholesterol-trapping protein

Science.gov Websites

Date February 28, 2003 Date Berkeley Lab Science Beat Berkeley Lab Science Beat The structure of a Institute researchers determined the three-dimensional structure of a protein that controls cholesterol level in the bloodstream. Knowing the structure of the protein, a cellular receptor that ensnares

Three-dimensional structure of E. Coli purine nucleoside phosphorylase at 0.99 Å resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Timofeev, V. I., E-mail: tostars@mail.ru; Abramchik, Yu. A., E-mail: ugama@yandex.ru; Zhukhlistova, N. E., E-mail: inna@ns.crys.ras.ru

2016-03-15

Purine nucleoside phosphorylases (PNPs) catalyze the reversible phosphorolysis of nucleosides and are key enzymes involved in nucleotide metabolism. They are essential for normal cell function and can catalyze the transglycosylation. Crystals of E. coli PNP were grown in microgravity by the capillary counterdiffusion method through a gel layer. The three-dimensional structure of the enzyme was determined by the molecular-replacement method at 0.99 Å resolution. The structural features are considered, and the structure of E. coli PNP is compared with the structures of the free enzyme and its complexes with purine base derivatives established earlier. A comparison of the environment ofmore » the purine base in the complex of PNP with formycin A and of the pyrimidine base in the complex of uridine phosphorylase with thymidine revealed the main structural features of the base-binding sites. Coordinates of the atomic model determined with high accuracy were deposited in the Protein Data Bank (PDB-ID: 4RJ2).« less

Analytical Methodology for Predicting the Onset of Widespread Fatigue Damage in Fuselage Structure

NASA Technical Reports Server (NTRS)

Harris, Charles E.; Newman, James C., Jr.; Piascik, Robert S.; Starnes, James H., Jr.

1996-01-01

NASA has developed a comprehensive analytical methodology for predicting the onset of widespread fatigue damage in fuselage structure. The determination of the number of flights and operational hours of aircraft service life that are related to the onset of widespread fatigue damage includes analyses for crack initiation, fatigue crack growth, and residual strength. Therefore, the computational capability required to predict analytically the onset of widespread fatigue damage must be able to represent a wide range of crack sizes from the material (microscale) level to the global structural-scale level. NASA studies indicate that the fatigue crack behavior in aircraft structure can be represented conveniently by the following three analysis scales: small three-dimensional cracks at the microscale level, through-the-thickness two-dimensional cracks at the local structural level, and long cracks at the global structural level. The computational requirements for each of these three analysis scales are described in this paper.

Observation of the magnetic flux and three-dimensional structure of skyrmion lattices by electron holography.

PubMed

Park, Hyun Soon; Yu, Xiuzhen; Aizawa, Shinji; Tanigaki, Toshiaki; Akashi, Tetsuya; Takahashi, Yoshio; Matsuda, Tsuyoshi; Kanazawa, Naoya; Onose, Yoshinori; Shindo, Daisuke; Tonomura, Akira; Tokura, Yoshinori

2014-05-01

Skyrmions are nanoscale spin textures that are viewed as promising candidates as information carriers in future spintronic devices. Skyrmions have been observed using neutron scattering and microscopy techniques. Real-space imaging using electrons is a straightforward way to interpret spin configurations by detecting the phase shifts due to electromagnetic fields. Here, we report the first observation by electron holography of the magnetic flux and the three-dimensional spin configuration of a skyrmion lattice in Fe(0.5)Co(0.5)Si thin samples. The magnetic flux inside and outside a skyrmion was directly visualized and the handedness of the magnetic flux flow was found to be dependent on the direction of the applied magnetic field. The electron phase shifts φ in the helical and skyrmion phases were determined using samples with a stepped thickness t (from 55 nm to 510 nm), revealing a linear relationship (φ = 0.00173 t). The phase measurements were used to estimate the three-dimensional structures of both the helical and skyrmion phases, demonstrating that electron holography is a useful tool for studying complex magnetic structures and for three-dimensional, real-space mapping of magnetic fields.

Synthesis, structure and photoluminescence properties of amine-templated open-framework bismuth sulfates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marri, Subba R.; Behera, J.N., E-mail: jnbehera@niser.ac.in

2014-02-15

Two organically-templated bismuth sulfates of the compositions, [C{sub 6}N{sub 2}H{sub 14}] [Bi(SO{sub 4}){sub 2}(NO{sub 3})], (1) and [C{sub 4}N{sub 2}H{sub 12}]{sub 4}[Bi{sub 4}(SO{sub 4}){sub 10}(H{sub 2}O){sub 4}], (2), with open architecture have been synthesized and their structures determined by single crystal X-ray diffraction. 1 has a corrugated layered structure with 8-membered aperture wherein the SO{sub 4} tetrahedra and the BiO{sub 8} polyhedra join together to form (4, 4) net sheets of the metal centers while 2 has a three-dimensional structure possessing 8- and 12-membered channels. Both the compounds show good fluorescence properties exhibiting blue luminescence. Time-resolved fluorescence behavior of 1more » and 2 shows mean fluorescence life time of 0.9 and 1.0 ns, respectively. - Graphical abstract: Two open-framework bismuth sulfates with the layered and three-dimensional structures have been synthesized and characterized. Both the compounds show good fluorescence properties exhibiting blue luminescence. Display Omitted - Highlights: • Two organically-templated bismuth sulfates with open architecture have been synthesized and characterized. • One has a corrugated layered structure while the other one has a three-dimensional structure possessing channels. • They are novel in that open-framework three-dimensional main group metal sulfates are first to be reported. • They show good fluorescence properties exhibiting blue luminescence.« less

Camps 2.0: exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins.

PubMed

Neumann, Sindy; Hartmann, Holger; Martin-Galiano, Antonio J; Fuchs, Angelika; Frishman, Dmitrij

2012-03-01

Structural bioinformatics of membrane proteins is still in its infancy, and the picture of their fold space is only beginning to emerge. Because only a handful of three-dimensional structures are available, sequence comparison and structure prediction remain the main tools for investigating sequence-structure relationships in membrane protein families. Here we present a comprehensive analysis of the structural families corresponding to α-helical membrane proteins with at least three transmembrane helices. The new version of our CAMPS database (CAMPS 2.0) covers nearly 1300 eukaryotic, prokaryotic, and viral genomes. Using an advanced classification procedure, which is based on high-order hidden Markov models and considers both sequence similarity as well as the number of transmembrane helices and loop lengths, we identified 1353 structurally homogeneous clusters roughly corresponding to membrane protein folds. Only 53 clusters are associated with experimentally determined three-dimensional structures, and for these clusters CAMPS is in reasonable agreement with structure-based classification approaches such as SCOP and CATH. We therefore estimate that ∼1300 structures would need to be determined to provide a sufficient structural coverage of polytopic membrane proteins. CAMPS 2.0 is available at http://webclu.bio.wzw.tum.de/CAMPS2.0/. Copyright © 2011 Wiley Periodicals, Inc.

Mathematical geophysics: A survey of recent developments in seismology and geodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlaar, N.J.

1988-01-01

This survey deals with modern methods for the determination of the structure of the Earth and for the analysis and modeling of the dynamic processes in the Earth's interior. Seismology and the three-dimensional structure of the Earth are covered in chapters devoted to waves in the three-dimensional Earth and large-scale inversion, while the discussion of convection and lithospheric processes focuses on geomagnetism, mantle convection, post-glacial rebound, and thermomechanical processes in the lithosphere. The emphasis of the work is theoretical, but the reader will find a discussion of the pertinent observational evidence.

Supervised Machine-Learning-Based Determination of Three-Dimensional Structure of Metallic Nanoparticles

DOE PAGES

Timoshenko, Janis; Lu, Deyu; Lin, Yuewei; ...

2017-09-29

Tracking the structure of heterogeneous catalysts under operando conditions remains a challenge due to the paucity of experimental techniques that can provide atomic-level information for catalytic metal species. Here we report on the use of X-ray absorption near edge structure (XANES) spectroscopy and supervised machine learning (SML) for refining the three-dimensional geometry of metal catalysts. SML is used to unravel the hidden relationship between the XANES features and catalyst geometry. To train our SML method, we rely on ab-initio XANES simulations. Our approach allows one to solve the structure of a metal catalyst from its experimental XANES, as demonstrated heremore » by reconstructing the average size, shape and morphology of well-defined platinum nanoparticles. This method is applicable to the determination of the nanoparticle structure in operando studies and can be generalized to other nanoscale systems. In conclusion, it also allows on-the-fly XANES analysis, and is a promising approach for high-throughput and time-dependent studies.« less

Supervised Machine-Learning-Based Determination of Three-Dimensional Structure of Metallic Nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Timoshenko, Janis; Lu, Deyu; Lin, Yuewei

Tracking the structure of heterogeneous catalysts under operando conditions remains a challenge due to the paucity of experimental techniques that can provide atomic-level information for catalytic metal species. Here we report on the use of X-ray absorption near edge structure (XANES) spectroscopy and supervised machine learning (SML) for refining the three-dimensional geometry of metal catalysts. SML is used to unravel the hidden relationship between the XANES features and catalyst geometry. To train our SML method, we rely on ab-initio XANES simulations. Our approach allows one to solve the structure of a metal catalyst from its experimental XANES, as demonstrated heremore » by reconstructing the average size, shape and morphology of well-defined platinum nanoparticles. This method is applicable to the determination of the nanoparticle structure in operando studies and can be generalized to other nanoscale systems. In conclusion, it also allows on-the-fly XANES analysis, and is a promising approach for high-throughput and time-dependent studies.« less

3-D photo-patterning of refractive index structures in photosensitive thin film materials

DOEpatents

Potter, Jr., Barrett George; Potter, Kelly Simmons

2002-01-01

A method of making a three-dimensional refractive index structure in a photosensitive material using photo-patterning. The wavelengths at which a photosensitive material exhibits a change in refractive index upon exposure to optical radiation is first determined and then a portion of the surface of the photosensitive material is optically irradiated at a wavelength at which the photosensitive material exhibits a change in refractive index using a designed illumination system to produce a three-dimensional refractive index structure. The illumination system can be a micro-lenslet array, a macroscopic refractive lens array, or a binary optic phase mask. The method is a single-step, direct-write procedure to produce a designed refractive index structure.

Johann Deisenhofer, Crystallography, and Proteins

Science.gov Websites

research using X-ray crystallography to elucidate for the first time the three-dimensional structure of a large membrane-bound protein molecule. This structure helped explain the process of photosynthesis, by a protein structure determination that relied on complementary features of two different beam lines

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system.

PubMed

Ikeya, Teppei; Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune; Güntert, Peter

2009-08-01

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly 13C/15N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional "through-bond" spectrum (and 2D HSQC spectra) in addition to the 13C-edited and 15N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods.

Forced free-shear layer measurements

NASA Technical Reports Server (NTRS)

Leboeuf, Richard L.

1994-01-01

Detailed three-dimensional three-component phase averaged measurements of the spanwise and streamwise vorticity formation and evolution in acoustically forced plane free-shear flows have been obtained. For the first time, phase-averaged measurements of all three velocity components have been obtained in both a mixing layer and a wake on three-dimensional grids, yielding the spanwise and streamwise vorticity distributions without invoking Taylor's hypothesis. Initially, two-frequency forcing was used to phase-lock the roll-up and first pairing of the spanwise vortical structures in a plane mixing layer. The objective of this study was to measure the near-field vortical structure morphology in a mixing layer with 'natural' laminar initial boundary layers. For the second experiment the second and third subharmonics of the fundamental roll-up frequency were added to the previous two-frequency forcing in order to phase-lock the roll-up and first three pairings of the spanwise rollers in the mixing layer. The objective of this study was to determine the details of spanwise scale changes observed in previous time-averaged measurements and flow visualization of unforced mixing layers. For the final experiment, single-frequency forcing was used to phase-lock the Karman vortex street in a plane wake developing from nominally two-dimensional laminar initial boundary layers. The objective of this study was to compare measurements of the three-dimensional structure in a wake developing from 'natural' initial boundary layers to existing models of wake vortical structure.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.

PubMed

Bhardwaj, Anshul; Casjens, Sherwood R; Cingolani, Gino

2014-02-01

Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

DOE PAGES

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; ...

2016-03-30

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtainmore » 14 density maps at ~ 2-nm resolution . Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.« less

Three-Dimensional Molecular Modeling of a Diverse Range of SC Clan Serine Proteases

PubMed Central

Laskar, Aparna; Chatterjee, Aniruddha; Chatterjee, Somnath; Rodger, Euan J.

2012-01-01

Serine proteases are involved in a variety of biological processes and are classified into clans sharing structural homology. Although various three-dimensional structures of SC clan proteases have been experimentally determined, they are mostly bacterial and animal proteases, with some from archaea, plants, and fungi, and as yet no structures have been determined for protozoa. To bridge this gap, we have used molecular modeling techniques to investigate the structural properties of different SC clan serine proteases from a diverse range of taxa. Either SWISS-MODEL was used for homology-based structure prediction or the LOOPP server was used for threading-based structure prediction. The predicted models were refined using Insight II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential patterns between species. Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on SC clan serine proteases. PMID:23213528

Modeling drying of three-dimensional pulp molded structures. Part I, Experimental program

Treesearch

Heike Nyist; John F. Hunt; Margit Tamasy-Bano

1998-01-01

Researchers at the USDA Forest Products Laboratory have developed a new three-dimensional structural panel, called FPL Spaceboard. This panel is formed using a U.S. patented three-dimensional mold capable of using a variety of fibrous materials with either the wet- or dry-forming process. Structurally, the panel departs from the traditional two-dimensional panel by...

Impact of genetic variation on three dimensional structure and function of proteins

PubMed Central

Bhattacharya, Roshni; Rose, Peter W.; Burley, Stephen K.

2017-01-01

The Protein Data Bank (PDB; http://wwpdb.org) was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings. The global PDB archive now contains more than 126,000 experimentally determined atomic level three-dimensional (3D) structures of biological macromolecules (proteins, DNA, RNA), all of which are freely accessible via the Internet. Knowledge of the 3D structure of the gene product can help in understanding its function and role in disease. Of particular interest in the PDB archive are proteins for which 3D structures of genetic variant proteins have been determined, thus revealing atomic-level structural differences caused by the variation at the DNA level. Herein, we present a systematic and qualitative analysis of such cases. We observe a wide range of structural and functional changes caused by single amino acid differences, including changes in enzyme activity, aggregation propensity, structural stability, binding, and dissociation, some in the context of large assemblies. Structural comparison of wild type and mutated proteins, when both are available, provide insights into atomic-level structural differences caused by the genetic variation. PMID:28296894

DNA origami nanopillars as standards for three-dimensional superresolution microscopy.

PubMed

Schmied, Jürgen J; Forthmann, Carsten; Pibiri, Enrico; Lalkens, Birka; Nickels, Philipp; Liedl, Tim; Tinnefeld, Philip

2013-02-13

Nanopillars are promising nanostructures composed of various materials that bring new functionalities for applications ranging from photovoltaics to analytics. We developed DNA nanopillars with a height of 220 nm and a diameter of ~14 nm using the DNA origami technique. Modifying the base of the nanopillars with biotins allowed selective, upright, and rigid immobilization on solid substrates. With the help of site-selective dye labels, we visualized the structure and determined the orientation of the nanopillars by three-dimensional fluorescence superresolution microscopy. Because of their rigidity and nanometer-precise addressability, DNA origami nanopillars qualify as scaffold for the assembly of plasmonic devices as well as for three-dimensional superresolution standards.

Attenuation Tomography Based on Strong Motion Data: Case Study of Central Honshu Region, Japan

NASA Astrophysics Data System (ADS)

Kumar, Parveen; Joshi, A.; Verma, O. P.

2013-12-01

Three-dimensional frequency dependent S-wave quality factor (Qβ(f)) value for the central Honshu region of Japan has been determined in this paper using an algorithm based on inversion of strong motion data. The method of inversion for determination of three-dimensional attenuation coefficients is proposed by H ashida and S himazaki (J Phys Earth. 32, 299-316, 1984) and has been used and modified by J oshi (Curr Sci. 90, 581-585, 2006; Nat Hazards. 43, 129-146, 2007) and J oshi et al. (J. Seismol. 14, 247-272, 2010). Twenty-one earthquakes digitally recorded on strong motion stations of Kik-net network have been used in this work. The magnitude of these earthquake ranges from 3.1 to 4.2 and depth ranging from 5 to 20 km, respectively. The borehole data having high signal to noise ratio and minimum site effect is used in the present work. The attenuation structure is determined by dividing the entire area into twenty-five three-dimensional blocks of uniform thickness having different frequency-dependent shear wave quality factor. Shear wave quality factor values have been determined at frequencies of 2.5, 7.0 and 10 Hz from record in a rectangular grid defined by 35.4°N to 36.4°N and 137.2°E to 138.2°E. The obtained attenuation structure is compared with the available geological features in the region and comparison shows that the obtained structure is capable of resolving important tectonic features present in the area. The proposed attenuation structure is compared with the probabilistic seismic hazard map of the region and shows that it bears some remarkable similarity in the patterns seen in seismic hazard map.

Three-dimensional structure of dominant instabilities in turbulent flow over smooth and rough boundaries

NASA Astrophysics Data System (ADS)

Grass, A. J.; Stuart, R. J.; Mansour-Tehrani, M.

1991-01-01

The current status of knowledge regarding coherent vortical structures in turbulent boundary layers and their role in turbulence generation are reviewed. The investigations reported in the study concentrate attention on rough-wall flows prevailing in the geophysical environment and include an experiment determining the three-dimensional form of the turbulence structures linked to the ejection and inrush events observed over rough walls and an experiment concerned with measuring the actual spanwise scale of the near-wall structures for boundary conditions ranging from hydrodynamically smooth to fully rough. It is demonstrated that horseshoe vortical structures are present and play an important role in rough-wall flows and they increase in scale with increasing wall distance, while a dominant spanwise wavelength occurs in the instantaneous cross-flow distribution of streamwise velocity close to the rough wall.

Three-dimensional structure of Escherichia coli initiator tRNA/f//Met/

NASA Technical Reports Server (NTRS)

Woo, N. H.; Rich, A.; Roe, B. A.

1980-01-01

The crystal structure of Escherichia coli tRNA(f)(Met), an initiator transfer RNA, has been determined. While grossly similar to that of the chain-elongating yeast tRNA(Phe), there are three major differences. One involves the folding of the anticodon loop; in particular, the position of the constant uridine, U33. This difference was unexpected and may be of functional significance.

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

PubMed Central

Marti-Renom, Marc A.; Mirny, Leonid A.

2011-01-01

Over the last decade, and especially after the advent of fluorescent in situ hybridization imaging and chromosome conformation capture methods, the availability of experimental data on genome three-dimensional organization has dramatically increased. We now have access to unprecedented details of how genomes organize within the interphase nucleus. Development of new computational approaches to leverage this data has already resulted in the first three-dimensional structures of genomic domains and genomes. Such approaches expand our knowledge of the chromatin folding principles, which has been classically studied using polymer physics and molecular simulations. Our outlook describes computational approaches for integrating experimental data with polymer physics, thereby bridging the resolution gap for structural determination of genomes and genomic domains. PMID:21779160

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rohrbaugh, Wayne Joseph

Results are reported from an investigation of correlations between molecular structural parameters of selected organophosphorus insecticides and their corresponding toxic effectiveness. The crystal and molecular structures of azinphos-methyl, emidithion, and tetrachlorvinphos were determined via three-dimensional x-ray analysis. Acetylcholinesterase (AChE) in nerve cells was identified as the target for organophosphorus insecticides.

Microgravity

NASA Image and Video Library

2004-04-15

A semiconductor's usefulness is determined by how atoms are ordered within the crystal's underlying three-dimensional structure. While this mercury telluride and cadmium telluride alloy sample mixes completely in Earth -based laboratories, convective flows prevent them from mixing uniformly.

In silico analysis of the three-dimensional structures of the homodimer of uridine phosphorylase from Yersinia Pseudotuberculosis in the ligand-free state and in a complex with 5-fluorouracil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lashkov, A. A., E-mail: alashkov83@gmail.com; Sotnichenko, S. E.; Mikhailov, A. M.

2013-03-15

Pseudotuberculosis is an acute infectious disease characterized by a lesion of the gastrointestinal tract. A positive therapeutic effect can be achieved by selectively suppressing the activity of uridine phosphorylase from the causative agent of the disease Yersinia pseudotuberculosis. The synergistic effect of a combination of the chemotherapeutic agent 5-fluorouracil and antimicrobial drugs, which block the synthesis of pyrimidine bases, on the cells of pathogenic protozoa and bacteria is described in the literature. The three-dimensional structures of uridine phosphorylase from Yersinia pseudotuberculosis (YptUPh) both in the ligand-free state and in complexes with pharmacological agents are unknown, which hinders the search formore » and design of selective inhibitors of YptUPh. The three-dimensional structure of the ligand-free homodimer of YptUPh was determined by homology-based molecular modeling. The three-dimensional structure of the subunit of the YptUPh molecule belongs to {alpha}/{beta} proteins, and its topology is a three-layer {alpha}/{beta}/{alpha} sandwich. The subunit monomer of the YptUPh molecule consists of 38% helices and 24% {beta} strands. A model of the homodimer structure of YptUPh in a complex with 5-FU was obtained by the molecular docking. The position of 5-FU in the active site of the molecule is very consistent with the known data on the X-ray diffraction structures of other bacterial uridine phosphorylases (the complex of uridine phosphorylase from Salmonella typhimurium (StUPh) with 5-FU, ID PDB: 4E1V and the complex of uridine phosphorylase from Escherichia coli (EcUPh) with 5-FU and ribose 1-phosphate, ID PDB: 1RXC).« less

In silico analysis of the three-dimensional structures of the homodimer of uridine phosphorylase from Yersinia Pseudotuberculosis in the ligand-free state and in a complex with 5-fluorouracil

NASA Astrophysics Data System (ADS)

Lashkov, A. A.; Sotnichenko, S. E.; Mikhailov, A. M.

2013-03-01

Pseudotuberculosis is an acute infectious disease characterized by a lesion of the gastrointestinal tract. A positive therapeutic effect can be achieved by selectively suppressing the activity of uridine phosphorylase from the causative agent of the disease Yersinia pseudotuberculosis. The synergistic effect of a combination of the chemotherapeutic agent 5-fluorouracil and antimicrobial drugs, which block the synthesis of pyrimidine bases, on the cells of pathogenic protozoa and bacteria is described in the literature. The three-dimensional structures of uridine phosphorylase from Yersinia pseudotuberculosis ( YptUPh) both in the ligand-free state and in complexes with pharmacological agents are unknown, which hinders the search for and design of selective inhibitors of YptUPh. The three-dimensional structure of the ligand-free homodimer of YptUPh was determined by homology-based molecular modeling. The three-dimensional structure of the subunit of the YptUPh molecule belongs to α/β proteins, and its topology is a three-layer α/β/α sandwich. The subunit monomer of the YptUPh molecule consists of 38% helices and 24% β strands. A model of the homodimer structure of YptUPh in a complex with 5-FU was obtained by the molecular docking. The position of 5-FU in the active site of the molecule is very consistent with the known data on the X-ray diffraction structures of other bacterial uridine phosphorylases (the complex of uridine phosphorylase from Salmonella typhimurium ( StUPh) with 5-FU, ID PDB: 4E1V and the complex of uridine phosphorylase from Escherichia coli ( EcUPh) with 5-FU and ribose 1-phosphate, ID PDB: 1RXC).

Mobile three-dimensional visualisation technologies for clinician-led fall prevention assessments.

PubMed

Hamm, Julian; Money, Arthur G; Atwal, Anita; Ghinea, Gheorghita

2017-08-01

The assistive equipment provision process is routinely carried out with patients to mitigate fall risk factors via the fitment of assistive equipment within the home. However, currently, over 50% of assistive equipment is abandoned by the patients due to poor fit between the patient and the assistive equipment. This paper explores clinician perceptions of an early stage three-dimensional measurement aid prototype, which provides enhanced assistive equipment provision process guidance to clinicians. Ten occupational therapists trialled the three-dimensional measurement aid prototype application; think-aloud and semi-structured interview data was collected. Usability was measured with the System Usability Scale. Participants scored three-dimensional measurement aid prototype as 'excellent' and agreed strongly with items relating to the usability and learnability of the application. The qualitative analysis identified opportunities for improving existing practice, including, improved interpretation/recording measurements; enhanced collaborative practice within the assistive equipment provision process. Future research is needed to determine the clinical utility of this application compared with two-dimensional counterpart paper-based guidance leaflets.

Device and nondestructive method to determine subsurface micro-structure in dense materials

DOEpatents

Sun, Jiangang [Westmont, IL

2006-05-09

A method and a device to detect subsurface three-dimensional micro-structure in a sample by illuminating the sample with light of a given polarization and detecting light emanating from the sample that has a different direction of polarization by means of a confocal optical system.

Viewing Angle Classification of Cryo-Electron Microscopy Images Using Eigenvectors

PubMed Central

Singer, A.; Zhao, Z.; Shkolnisky, Y.; Hadani, R.

2012-01-01

The cryo-electron microscopy (cryo-EM) reconstruction problem is to find the three-dimensional structure of a macromolecule given noisy versions of its two-dimensional projection images at unknown random directions. We introduce a new algorithm for identifying noisy cryo-EM images of nearby viewing angles. This identification is an important first step in three-dimensional structure determination of macromolecules from cryo-EM, because once identified, these images can be rotationally aligned and averaged to produce “class averages” of better quality. The main advantage of our algorithm is its extreme robustness to noise. The algorithm is also very efficient in terms of running time and memory requirements, because it is based on the computation of the top few eigenvectors of a specially designed sparse Hermitian matrix. These advantages are demonstrated in numerous numerical experiments. PMID:22506089

Integrated Aeromechanics with Three-Dimensional Solid-Multibody Structures

NASA Technical Reports Server (NTRS)

Datta, Anubhav; Johnson, Wayne

2014-01-01

A full three-dimensional finite element-multibody structural dynamic solver is coupled to a three-dimensional Reynolds-averaged Navier-Stokes solver for the prediction of integrated aeromechanical stresses and strains on a rotor blade in forward flight. The objective is to lay the foundations of all major pieces of an integrated three-dimensional rotor dynamic analysis - from model construction to aeromechanical solution to stress/strain calculation. The primary focus is on the aeromechanical solution. Two types of three-dimensional CFD/CSD interfaces are constructed for this purpose with an emphasis on resolving errors from geometry mis-match so that initial-stage approximate structural geometries can also be effectively analyzed. A three-dimensional structural model is constructed as an approximation to a UH-60A-like fully articulated rotor. The aerodynamic model is identical to the UH-60A rotor. For preliminary validation measurements from a UH-60A high speed flight is used where CFD coupling is essential to capture the advancing side tip transonic effects. The key conclusion is that an integrated aeromechanical analysis is indeed possible with three-dimensional structural dynamics but requires a careful description of its geometry and discretization of its parts.

Defect propagation in one-, two-, and three-dimensional compounds doped by magnetic atoms

DOE PAGES

Furrer, A.; Podlesnyak, A.; Krämer, K. W.; ...

2014-10-29

Inelastic neutron scattering experiments were performed to study manganese(II) dimer excitations in the diluted one-, two-, and three-dimensional compounds CsMn xMg 1-xBr 3, K 2Mn xZn 1-xF 4, and KMn xZn 1-xF 3 (x≤0.10), respectively. The transitions from the ground-state singlet to the excited triplet, split into a doublet and a singlet due to the single-ion anisotropy, exhibit remarkable fine structures. These unusual features are attributed to local structural inhomogeneities induced by the dopant Mn atoms which act like lattice defects. Statistical models support the theoretically predicted decay of atomic displacements according to 1/r 2, 1/r, and constant (for three-,more » two-, and one-dimensional compounds, respectively) where r denotes the distance of the displaced atoms from the defect. In conclusion, the observed fine structures allow a direct determination of the local exchange interactions J, and the local intradimer distances R can be derived through the linear law dJ/dR.« less

Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs

PubMed Central

Baker, T. S.; Olson, N. H.; Fuller, S. D.

1999-01-01

Viruses are cellular parasites. The linkage between viral and host functions makes the study of a viral life cycle an important key to cellular functions. A deeper understanding of many aspects of viral life cycles has emerged from coordinated molecular and structural studies carried out with a wide range of viral pathogens. Structural studies of viruses by means of cryo-electron microscopy and three-dimensional image reconstruction methods have grown explosively in the last decade. Here we review the use of cryo-electron microscopy for the determination of the structures of a number of icosahedral viruses. These studies span more than 20 virus families. Representative examples illustrate the use of moderate- to low-resolution (7- to 35-Å) structural analyses to illuminate functional aspects of viral life cycles including host recognition, viral attachment, entry, genome release, viral transcription, translation, proassembly, maturation, release, and transmission, as well as mechanisms of host defense. The success of cryo-electron microscopy in combination with three-dimensional image reconstruction for icosahedral viruses provides a firm foundation for future explorations of more-complex viral pathogens, including the vast number that are nonspherical or nonsymmetrical. PMID:10585969

Identification, Characterization, and Three-Dimensional Structure of the Novel Circular Bacteriocin, Enterocin NKR-5-3B, from Enterococcus faecium.

PubMed

Himeno, Kohei; Rosengren, K Johan; Inoue, Tomoko; Perez, Rodney H; Colgrave, Michelle L; Lee, Han Siean; Chan, Lai Y; Henriques, Sónia Troeira; Fujita, Koji; Ishibashi, Naoki; Zendo, Takeshi; Wilaipun, Pongtep; Nakayama, Jiro; Leelawatcharamas, Vichien; Jikuya, Hiroyuki; Craik, David J; Sonomoto, Kenji

2015-08-11

Enterocin NKR-5-3B, one of the multiple bacteriocins produced by Enterococcus faecium NKR-5-3, is a 64-amino acid novel circular bacteriocin that displays broad-spectrum antimicrobial activity. Here we report the identification, characterization, and three-dimensional nuclear magnetic resonance solution structure determination of enterocin NKR-5-3B. Enterocin NKR-5-3B is characterized by four helical segments that enclose a compact hydrophobic core, which together with its circular backbone impart high stability and structural integrity. We also report the corresponding structural gene, enkB, that encodes an 87-amino acid precursor peptide that undergoes a yet to be described enzymatic processing that involves adjacent cleavage and ligation of Leu(24) and Trp(87) to yield the mature (circular) enterocin NKR-5-3B.

Three-dimensional P-wave velocity structure of Mt. Etna, Italy

USGS Publications Warehouse

Villasenor, A.; Benz, H.M.; Filippi, L.; De Luca, G.; Scarpa, R.; Patane, G.; Vinciguerra, S.

1998-01-01

The three-dimensional P-wave velocity structure of Mt. Etna is determined to depths of 15 km by tomographic inversion of first arrival times from local earthquakes recorded by a network of 29 permanent and temporary seismographs. Results show a near-vertical low-velocity zone that extends from beneath the central craters to a depth of 10 km. This low-velocity region is coincident with a band of steeply-dipping seismicity, suggesting a magmatic conduit that feeds the summit eruptions. The most prominent structure is an approximately 8-km-diameter high-velocity body located between 2 and 12 km depth below the southeast flank of the volcano. This high-velocity body is interpreted as a remnant mafic intrusion that is an important structural feature influencing both volcanism and east flank slope stability and faulting.

Crystal structure of the HA3 subcomponent of Clostridium botulinum type C progenitor toxin.

PubMed

Nakamura, Toshio; Kotani, Mao; Tonozuka, Takashi; Ide, Azusa; Oguma, Keiji; Nishikawa, Atsushi

2009-01-30

The Clostridium botulinum type C 16S progenitor toxin contains a neurotoxin and several nontoxic components, designated nontoxic nonhemagglutinin (HA), HA1 (HA-33), HA2 (HA-17), HA3a (HA-22-23), and HA3b (HA-53). The HA3b subcomponent seems to play an important role cooperatively with HA1 in the internalization of the toxin by gastrointestinal epithelial cells via binding of these subcomponents to specific oligosaccharides. In this study, we investigated the sugar-binding specificity of the HA3b subcomponent using recombinant protein fused to glutathione S-transferase and determined the three-dimensional structure of the HA3a-HA3b complex based on X-ray crystallography. The crystal structure was determined at a resolution of 2.6 A. HA3b contains three domains, domains I to III, and the structure of domain I resembles HA3a. In crystal packing, three HA3a-HA3b molecules are assembled to form a three-leaved propeller-like structure. The three HA3b domain I and three HA3a alternate, forming a trimer of dimers. In a database search, no proteins with high structural homology to any of the domains (Z score >10) were found. Especially, HA3a and HA3b domain I, mainly composed of beta-sheets, reveal a unique fold. In binding assays, HA3b bound sialic acid with high affinity, but did not bind galactose, N-acetylgalactosamine, or N-acetylglucosamine. The electron density of liganded N-acetylneuraminic acid was determined by crystal soaking. In the sugar-complex structure, the N-acetylneuraminic acid-binding site was located in the cleft formed between domains II and III of HA3b. This report provides the first determination of the three-dimensional structure of the HA3a-HA3b complex and its sialic acid binding site. Our results will provide useful information for elucidating the mechanism of assembly of the C16S toxin and for understanding the interactions with oligosaccharides on epithelial cells and internalization of the botulinum toxin complex.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal.

PubMed

Clabbers, M T B; van Genderen, E; Wan, W; Wiegers, E L; Gruene, T; Abrahams, J P

2017-09-01

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm 3 , i.e. no more than 6 × 10 5 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

PubMed Central

Clabbers, M. T. B.; van Genderen, E.; Wiegers, E. L.; Gruene, T.; Abrahams, J. P.

2017-01-01

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm3, i.e. no more than 6 × 105 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures. PMID:28876237

Structural properties of matrix metalloproteinases.

PubMed

Bode, W; Fernandez-Catalan, C; Tschesche, H; Grams, F; Nagase, H; Maskos, K

1999-04-01

Matrix metalloproteinases (MMPs) are involved in extracellular matrix degradation. Their proteolytic activity must be precisely regulated by their endogenous protein inhibitors, the tissue inhibitors of metalloproteinases (TIMPs). Disruption of this balance results in serious diseases such as arthritis, tumour growth and metastasis. Knowledge of the tertiary structures of the proteins involved is crucial for understanding their functional properties and interference with associated dysfunctions. Within the last few years, several three-dimensional MMP and MMP-TIMP structures became available, showing the domain organization, polypeptide fold and main specificity determinants. Complexes of the catalytic MMP domains with various synthetic inhibitors enabled the structure-based design and improvement of high-affinity ligands, which might be elaborated into drugs. A multitude of reviews surveying work done on all aspects of MMPs have appeared in recent years, but none of them has focused on the three-dimensional structures. This review was written to close the gap.

Construction and validation of the midsagittal reference plane based on the skull base symmetry for three-dimensional cephalometric craniofacial analysis.

PubMed

Kim, Hak-Jin; Kim, Bong Chul; Kim, Jin-Geun; Zhengguo, Piao; Kang, Sang Hoon; Lee, Sang-Hwy

2014-03-01

The objective of this study was to determine the reliable midsagittal (MS) reference plane in practical ways for the three-dimensional craniofacial analysis on three-dimensional computed tomography images. Five normal human dry skulls and 20 normal subjects without any dysmorphoses or asymmetries were used. The accuracies and stability on repeated plane construction for almost every possible candidate MS plane based on the skull base structures were examined by comparing the discrepancies in distances and orientations from the reference points and planes of the skull base and facial bones on three-dimensional computed tomography images. The following reference points of these planes were stable, and their distribution was balanced: nasion and foramen cecum at the anterior part of the skull base, sella at the middle part, and basion and opisthion at the posterior part. The candidate reference planes constructed using the aforementioned reference points were thought to be reliable for use as an MS reference plane for the three-dimensional analysis of maxillofacial dysmorphosis.

Three-dimensional six-connecting organic building blocks based on polychlorotriphenylmethyl units--synthesis, self-assembly, and magnetic properties.

PubMed

Roques, Nans; Maspoch, Daniel; Wurst, Klaus; Ruiz-Molina, Daniel; Rovira, Concepció; Veciana, Jaume

2006-12-13

The synthesis of a three-dimensional, six-connecting, organic building block based on a robust, rigid, and open-shell polychlorotriphenylmethyl (PTM) unit (radical 1) is reported, and its self-assembly properties are described in detail. The tendencies of this highly polar molecule and its hydrogenated precursor, compound 4, to form hydrogen bonds with oxygenated solvents ([1THF(6)] and [4THF(6)]) were reduced by replacing THF with diethyl ether in the crystallization process to yield two-dimensional (2D) hydrogen-bonded structures ([1(Et(2)O)(3)] and [4(Et(2)O)(3)]). The presence of direct hydrogen bonds between the radicals in the latter phase of 1 gives rise to very weak ferromagnetic intermolecular interactions at low temperatures, whereas when the radicals are isolated by THF molecules these interactions are antiferromagnetic and very weak. The role played by the carboxylic groups not only in the self-assembly properties but also in the transmission of the magnetic interactions has been illustrated by determination of the crystal structure and measurement of the magnetic properties of the corresponding hexaester radical 6, in which the close packing of molecular units gives rise to weak antiferromagnetic intermolecular interactions. Attempts to avoid solvation of the molecules in the solid state and to increase the structural and magnetic dimensionality were pursued by recrystallization of both compounds 1 and 4 from concentrated nitric acid, affording two three-dimensional (3D) robust hydrogen-bonded structures. While the structure obtained with compound 4 is characterized by the presence of polar channels and boxes containing water guest molecules along the c axis, radical 1 was oxidized to the corresponding fuchsone 10, which presented a completely different close-packed, guest-free structure.

Antibacterial peptides from plants: what they are and how they probably work.

PubMed

Barbosa Pelegrini, Patrícia; Del Sarto, Rafael Perseghini; Silva, Osmar Nascimento; Franco, Octávio Luiz; Grossi-de-Sa, Maria Fátima

2011-01-01

Plant antibacterial peptides have been isolated from a wide variety of species. They consist of several protein groups with different features, such as the overall charge of the molecule, the content of disulphide bonds, and structural stability under environmental stress. Although the three-dimensional structures of several classes of plant peptides are well determined, the mechanism of action of some of these molecules is still not well defined. However, further studies may provide new evidences for their function on bacterial cell wall. Therefore, this paper focuses on plant peptides that show activity against plant-pathogenic and human-pathogenic bacteria. Furthermore, we describe the folding of several peptides and similarities among their three-dimensional structures. Some hypotheses for their mechanisms of action and attack on the bacterial membrane surface are also proposed.

Three-dimensional structure of porcine pancreatic carboxypeptidase B with an acetate ion and two zinc atoms in the active site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akparov, V. Kh., E-mail: valery@akparov.ru; Timofeev, V. I., E-mail: tostars@mail.ru; Maghsoudi, N. N., E-mail: maghsudi@yahoo.com

2017-03-15

Crystals of porcine pancreatic carboxypeptidase B (CPB) were grown by the capillary counter-diffusion method in the presence of polyethylene glycol and zinc acetate. The three-dimensional structure of CPB was determined at 1.40 Å resolution using the X-ray diffraction data set collected from the crystals of the enzyme at the SPring 8 synchrotron facility and was refined to R{sub fact} = 17.19%, R{sub free} = 19.78%. The structure contains five zinc atoms, two of which are present in the active site of the enzyme, and an acetate ion. The arrangement of an additional zinc atom in the active site and themore » acetate ion is different from that reported by Yoshimoto et al.« less

Three-dimensional structure of photosystem II from Thermosynechococcus elongates in complex with terbutryn

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gabdulkhakov, A. G., E-mail: azat@vega.protes.ru; Dontsova, M. V.; Saenger, W.

Photosystem II is a key component of the photosynthetic pathway producing oxygen at the thylakoid membrane of cyanobacteria, green algae, and plants. The three-dimensional structure of photosystem II from the cyanobacterium Thermosynechococcus elongates in a complex with herbicide terbutryn (a photosynthesis inhibitor) was determined for the first time by X-ray diffraction and refined at 3.2 Angstrom-Sign resolution (R{sub factor} = 26.9%, R{sub free} = 29.9%, rmsd for bond lengths is 0.013 Angstrom-Sign , and rmsd for bond angles is 2.2 Degree-Sign ). The terbutryn molecule was located in the binding pocket of the mobile plastoquinone. The atomic coordinates of themore » refined structure of photosystem II in a complex with terbutryn were deposited in the Protein Data Bank.« less

Large-angle illumination STEM: Toward three-dimensional atom-by-atom imaging

DOE PAGES

Ishikawa, Ryo; Lupini, Andrew R.; Hinuma, Yoyo; ...

2014-11-26

To completely understand and control materials and their properties, it is of critical importance to determine their atomic structures in all three dimensions. Recent revolutionary advances in electron optics – the inventions of geometric and chromatic aberration correctors as well as electron source monochromators – have provided fertile ground for performing optical depth sectioning at atomic-scale dimensions. In this study we theoretically demonstrate the imaging of top/sub-surface atomic structures and identify the depth of single dopants, single vacancies and the other point defects within materials by large-angle illumination scanning transmission electron microscopy (LAI-STEM). The proposed method also allows us tomore » measure specimen properties such as thickness or three-dimensional surface morphology using observations from a single crystallographic orientation.« less

Application of an inverse method for calculating three-dimensional fault geometries and clip vectors, Nun River Field, Nigeria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerr, H.G.; White, N.

A general, automatic method for determining the three-dimensional geometry of a normal fault of any shape and size is applied to a three-dimensional seismic reflection data set from the Nun River field, Nigeria. In addition to calculating fault geometry, the method also automatically retrieves the extension direction without requiring any previous information about either the fault shape or the extension direction. Solutions are found by minimizing the misfit between sets of faults that are calculated from the observed geometries of two or more hanging-wall beds. In the example discussed here, the predicted fault surface is in excellent agreement with themore » shape of the seismically imaged fault. Although the calculated extension direction is oblique to the average strike of the fault, the value of this parameter is not well resolved. Our approach differs markedly from standard section-balancing models in two important ways. First, we do not assume that the extension direction is known, and second, the use of inverse theory ensures that formal confidence bounds can be determined for calculated fault geometries. This ability has important implications for a range of geological problems encountered at both exploration and production scales. In particular, once the three-dimensional displacement field has been constrained, the difficult but important problem of three-dimensional palinspastic restoration of hanging-wall structures becomes tractable.« less

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhardwaj, Anshul; Casjens, Sherwood R.; Cingolani, Gino, E-mail: gino.cingolani@jefferson.edu

2014-02-01

This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identifiedmore » in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.« less

The Effect of Three-Dimensional Simulations on the Understanding of Chemical Structures and Their Properties

ERIC Educational Resources Information Center

Urhahne, Detlef; Nick, Sabine; Schanze, Sascha

2009-01-01

In a series of three experimental studies, the effectiveness of three-dimensional computer simulations to aid the understanding of chemical structures and their properties was investigated. Arguments for the usefulness of three-dimensional simulations were derived from Mayer's generative theory of multimedia learning. Simulations might lead to a…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wismer, Robert Kingsley

The crystal structure of trans-dicyano triethylene-tetramine cobalt (III) perchlorate (monoclinic, P2 1/n, a = 9.85, b= 22.35, c=6.68 A, β = 100.9°, z = 4, MoKα radiation) has been determined by three-dimensional x-ray analysis.

Fabrication and characterization of graphene hydrogel via hydrothermal approach as a scaffold for preliminary study of cell growth

PubMed Central

Lim, HN; Huang, NM; Lim, SS; Harrison, I; Chia, CH

2011-01-01

Background Three-dimensional assembly of graphene hydrogel is rapidly attracting the interest of researchers because of its wide range of applications in energy storage, electronics, electrochemistry, and waste water treatment. Information on the use of graphene hydrogel for biological purposes is lacking, so we conducted a preliminary study to determine the suitability of graphene hydrogel as a substrate for cell growth, which could potentially be used as building blocks for biomolecules and tissue engineering applications. Methods A three-dimensional structure of graphene hydrogel was prepared via a simple hydrothermal method using two-dimensional large-area graphene oxide nanosheets as a precursor. Results The concentration and lateral size of the graphene oxide nanosheets influenced the structure of the hydrogel. With larger-area graphene oxide nanosheets, the graphene hydrogel could be formed at a lower concentration. X-ray diffraction patterns revealed that the oxide functional groups on the graphene oxide nanosheets were reduced after hydrothermal treatment. The three-dimensional graphene hydrogel matrix was used as a scaffold for proliferation of a MG63 cell line. Conclusion Guided filopodia protrusions of MG63 on the hydrogel were observed on the third day of cell culture, demonstrating compatibility of the graphene hydrogel structure for bioapplications. PMID:21931479

Atomic structure and chemistry of human serum albumin

NASA Technical Reports Server (NTRS)

He, Xiao M.; Carter, Daniel C.

1992-01-01

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 A. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and ILIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

Atomic structure and chemistry of human serum albumin

NASA Astrophysics Data System (ADS)

He, Xiao Min; Carter, Daniel C.

1992-07-01

The three-dimensional structure of human serum albumin has been determined crystallographically to a resolution of 2.8 Å. It comprises three homologous domains that assemble to form a heart-shaped molecule. Each domain is a product of two subdomains that possess common structural motifs. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and IIIA, which exhibit similar chemistry. The structure explains numerous physical phenomena and should provide insight into future pharmacokinetic and genetically engineered therapeutic applications of serum albumin.

Recent advances in electron tomography: TEM and HAADF-STEM tomography for materials science and semiconductor applications.

PubMed

Kübel, Christian; Voigt, Andreas; Schoenmakers, Remco; Otten, Max; Su, David; Lee, Tan-Chen; Carlsson, Anna; Bradley, John

2005-10-01

Electron tomography is a well-established technique for three-dimensional structure determination of (almost) amorphous specimens in life sciences applications. With the recent advances in nanotechnology and the semiconductor industry, there is also an increasing need for high-resolution three-dimensional (3D) structural information in physical sciences. In this article, we evaluate the capabilities and limitations of transmission electron microscopy (TEM) and high-angle-annular-dark-field scanning transmission electron microscopy (HAADF-STEM) tomography for the 3D structural characterization of partially crystalline to highly crystalline materials. Our analysis of catalysts, a hydrogen storage material, and different semiconductor devices shows that features with a diameter as small as 1-2 nm can be resolved in three dimensions by electron tomography. For partially crystalline materials with small single crystalline domains, bright-field TEM tomography provides reliable 3D structural information. HAADF-STEM tomography is more versatile and can also be used for high-resolution 3D imaging of highly crystalline materials such as semiconductor devices.

From Two- to Three-Dimensional Structures of a Supertetrahedral Boran Using Density Functional Calculations.

PubMed

Getmanskii, Iliya V; Minyaev, Ruslan M; Steglenko, Dmitrii V; Koval, Vitaliy V; Zaitsev, Stanislav A; Minkin, Vladimir I

2017-08-14

With help of the DFT calculations and imposing of periodic boundary conditions the geometrical and electronic structures were investigated of two- and three-dimensional boron systems designed on the basis of graphane and diamond lattices in which carbons were replaced with boron tetrahedrons. The consequent studies of two- and three-layer systems resulted in the construction of a three-dimensional supertetrahedral borane crystal structure. The two-dimensional supertetrahedral borane structures with less than seven layers are dynamically unstable. At the same time the three-dimensional superborane systems were found to be dynamically stable. Lack of the forbidden electronic zone for the studied boron systems testifies that these structures can behave as good conductors. The low density of the supertetrahedral borane crystal structures (0.9 g cm -3 ) is close to that of water, which offers the perspective for their application as aerospace and cosmic materials. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Three-dimensional video imaging of drainage and imbibition processes in model porous medium

NASA Astrophysics Data System (ADS)

Sharma, Prerna; Aswathi, P.; Sane, Anit; Ghosh, Shankar; Bhattacharya, Sabyasachi

2011-03-01

We report experimental results where we have performed three dimensional video imaging of the displacement of an oil phase by an aqueous phase and vice versa in a model porous medium. The stability of the oil water interface was studied as a function of their viscosity ratios, the wettability of the porous medium and the variation in the pore size distribution. Our experiments captures the pore scale information of the displacement process and its role in determining the long time structure of the interface.

On equations of motion of a nonlinear hydroelastic structure

NASA Astrophysics Data System (ADS)

Plotnikov, P. I.; Kuznetsov, I. V.

2008-07-01

Formal derivation of equations of a nonlinear hydroelastic structure, which is a volume of an ideal incompressible fluid covered by a shell, is proposed. The study is based on two assumptions. The first assumption implies that the energy stored in the shell is completely determined by the mean curvature and by the elementary area. In a three-dimensional case, the energy stored in the shell is chosen in the form of the Willmore functional. In a two-dimensional case, a more generic form of the functional can be considered. The second assumption implies that the equations of motionhave a Hamiltonian structure and can be obtained from the Lagrangian variational principle. In a two-dimensional case, a condition for the hydroelastic structure is derived, which relates the external pressure and the curvature of the elastic shell.

AELAS: Automatic ELAStic property derivations via high-throughput first-principles computation

NASA Astrophysics Data System (ADS)

Zhang, S. H.; Zhang, R. F.

2017-11-01

The elastic properties are fundamental and important for crystalline materials as they relate to other mechanical properties, various thermodynamic qualities as well as some critical physical properties. However, a complete set of experimentally determined elastic properties is only available for a small subset of known materials, and an automatic scheme for the derivations of elastic properties that is adapted to high-throughput computation is much demanding. In this paper, we present the AELAS code, an automated program for calculating second-order elastic constants of both two-dimensional and three-dimensional single crystal materials with any symmetry, which is designed mainly for high-throughput first-principles computation. Other derivations of general elastic properties such as Young's, bulk and shear moduli as well as Poisson's ratio of polycrystal materials, Pugh ratio, Cauchy pressure, elastic anisotropy and elastic stability criterion, are also implemented in this code. The implementation of the code has been critically validated by a lot of evaluations and tests on a broad class of materials including two-dimensional and three-dimensional materials, providing its efficiency and capability for high-throughput screening of specific materials with targeted mechanical properties. Program Files doi:http://dx.doi.org/10.17632/f8fwg4j9tw.1 Licensing provisions: BSD 3-Clause Programming language: Fortran Nature of problem: To automate the calculations of second-order elastic constants and the derivations of other elastic properties for two-dimensional and three-dimensional materials with any symmetry via high-throughput first-principles computation. Solution method: The space-group number is firstly determined by the SPGLIB code [1] and the structure is then redefined to unit cell with IEEE-format [2]. Secondly, based on the determined space group number, a set of distortion modes is automatically specified and the distorted structure files are generated. Afterwards, the total energy for each distorted structure is calculated by the first-principles codes, e.g. VASP [3]. Finally, the second-order elastic constants are determined from the quadratic coefficients of the polynomial fitting of the energies vs strain relationships and other elastic properties are accordingly derived. References [1] http://atztogo.github.io/spglib/. [2] A. Meitzler, H.F. Tiersten, A.W. Warner, D. Berlincourt, G.A. Couqin, F.S. Welsh III, IEEE standard on piezoelectricity, Society, 1988. [3] G. Kresse, J. Furthmüller, Phys. Rev. B 54 (1996) 11169.

Development of a direct three-dimensional biomicrofabrication concept based on electrospraying a custom made siloxane sol.

PubMed

Sullivan, Alice C; Jayasinghe, Suwan N

2007-07-19

We demonstrate here the discovery of a unique and direct three-dimensional biomicrofabrication concept possessing the ability to revolutionize the jet-based fabrication arena. Previous work carried out on similar jet-based approaches have been successful in fabricating only vertical wallpillar-structures by the controlled deposition of stacked droplets. However, these advanced jet-techniques have not been able to directly fabricate self-supporting archeslinks (without molds or reaction methods) between adjacent structures (walls or pillars). Our work reported here gives birth to a unique type of jet determined by high intensity electric fields, which is derived from a specially formulated siloxane sol. The sol studied here has been chosen for its attractive properties (such as an excellent cross-linking nature as well as the ability to polymerize via polycondensation on deposition to its biocompatability), which promotes direct forming of biostructures with nanometer (<50 nm) sized droplets in three dimensions. We foresee that this direct three-dimensional biomicrofabrication jet technique coupled with a variety of formulated sols having focused and enhanced functionality will be explored throughout the physical and life sciences.

Two-dimensional and three-dimensional evaluation of the deformation relief

NASA Astrophysics Data System (ADS)

Alfyorova, E. A.; Lychagin, D. V.

2017-12-01

This work presents the experimental results concerning the research of the morphology of the face-centered cubic single crystal surface after compression deformation. Our aim is to identify the method of forming a quasiperiodic profile of single crystals with different crystal geometrical orientation and quantitative description of deformation structures. A set of modern methods such as optical and confocal microscopy is applied to determine the morphology of surface parameters. The results show that octahedral slip is an integral part of the formation of the quasiperiodic profile surface starting with initial strain. The similarity of the formation process of the surface profile at different scale levels is given. The size of consistent deformation regions is found. This is 45 µm for slip lines ([001]-single crystal) and 30 µm for mesobands ([110]-single crystal). The possibility of using two- and three-dimensional roughness parameters to describe the deformation structures was shown.

A holistic approach to determine tree structural complexity based on laser scanning data and fractal analysis.

PubMed

Seidel, Dominik

2018-01-01

The three-dimensional forest structure affects many ecosystem functions and services provided by forests. As forests are made of trees it seems reasonable to approach their structure by investigating individual tree structure. Based on three-dimensional point clouds from laser scanning, a newly developed holistic approach is presented that enables to calculate the box dimension as a measure of structural complexity of individual trees using fractal analysis. It was found that the box dimension of trees was significantly different among the tested species, among trees belonging to the same species but exposed to different growing conditions (at gap vs. forest interior) or to different kinds of competition (intraspecific vs. interspecific). Furthermore, it was shown that the box dimension is positively related to the trees' growth rate. The box dimension was identified as an easy to calculate measure that integrates the effect of several external drivers of tree structure, such as competition strength and type, while simultaneously providing information on structure-related properties, like tree growth.

Softly-confined water cluster between freestanding graphene sheets

NASA Astrophysics Data System (ADS)

Agustian, Rifan; Akaishi, Akira; Nakamura, Jun

2018-01-01

Confined water could adopt new forms not seen in the open air, such as a two-dimensional (2D) square ice trapped between two graphene sheets [Algara-Siller et al., Nature 519, 443-445 (2015)]. In this study, in order to investigate how the flexibility of graphene affects the confined structure of water molecules, we employed classical molecular dynamics simulations with Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential to produce a soft-confining property of graphene. We discovered various solid-like structures of water molecules ranging from two-dimensional to three-dimensional structure encapsulated between two freestanding graphene sheets even at room temperature (300K). A small amount of water encapsulation leads to a layered two-dimensional form with triangular structure. On the other hand, large amounts of water molecules take a three-dimensional flying-saucer-like form with the square ice intra-layer structure. There is also a metastable state where both two-dimensional and three-dimensional structures coexist.

Hamiltonian structure of three-dimensional gravity in Vielbein formalism

NASA Astrophysics Data System (ADS)

Hajihashemi, Mahdi; Shirzad, Ahmad

2018-01-01

Considering Chern-Simons like gravity theories in three dimensions as first order systems, we analyze the Hamiltonian structure of three theories Topological massive gravity, New massive gravity, and Zwei-Dreibein Gravity. We show that these systems demonstrate a new feature of the constrained systems in which a new kind of constraints emerge due to factorization of determinant of the matrix of Poisson brackets of constraints. We find the desired number of degrees of freedom as well as the generating functional of local Lorentz transformations and diffeomorphism through canonical structure of the system. We also compare the Hamiltonian structure of linearized version of the considered models with the original ones.

Fast determination of three-dimensional fibril orientation of type-I collagen via macroscopic chirality

NASA Astrophysics Data System (ADS)

Zhuo, Guan-Yu; Chen, Mei-Yu; Yeh, Chao-Yuan; Guo, Chin-Lin; Kao, Fu-Jen

2017-01-01

Polarization-resolved second harmonic generation (SHG) microscopy is appealing for studying structural proteins and well-organized biophotonic nanostructures, due to its highly sensitized structural specificity. In recent years, it has been used to investigate the chiroptical effect, particularly SHG circular dichroism (SHG-CD) in biological tissues. Although SHG-CD attributed to macromolecular structures has been demonstrated, the corresponding quantitative analysis and interpretation on how SHG correlates with second-order susceptibility χ(2) under circularly polarized excitations remains unclear. In this study, we demonstrate a method based on macroscopic chirality to elucidate the correlation between SHG-CD and the orientation angle of the molecular structure. By exploiting this approach, three-dimensional (3D) molecular orientation of type-I collagen is revealed with only two cross polarized SHG images (i.e., interactions of left and right circular polarizations) without acquiring an image stack of varying polarization.

Electron crystallography of PhoE porin, an outer membrane, channel- forming protein from E. coli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walian, P.J.

1989-11-01

One approach to studying the structure of membrane proteins is the use of electron crystallography. Dr. Bing Jap has crystallized PhoE pore-forming protein (porin) from the outer membrane of escherichia coli (E. coli) into monolayer crystals. The findings of this research and those of Jap (1988, 1989) have determined these crystals to be highly ordered, yielding structural information to a resolution of better than 2.8 angstroms. The task of this thesis has been to collect and process the electron diffraction patterns necessary to generate a complete three-dimensional set of high resolution structure factor amplitudes of PhoE porin. Fourier processing ofmore » these amplitudes when combined with the corresponding phase data is expected to yield the three-dimensional structure of PhoE porin at better than 3.5 angstroms resolution. 92 refs., 33 figs., 3 tabs. (CBS)« less

High-resolution structure of viruses from random diffraction snapshots

PubMed Central

Hosseinizadeh, A.; Schwander, P.; Dashti, A.; Fung, R.; D'Souza, R. M.; Ourmazd, A.

2014-01-01

The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. Algorithmic means must then be used to determine the snapshot orientations and thence the three-dimensional structure of the object. Existing Bayesian approaches are limited in reconstruction resolution typically to 1/10 of the object diameter, with the computational expense increasing as the eighth power of the ratio of diameter to resolution. We present an approach capable of exploiting object symmetries to recover three-dimensional structure to high resolution, and thus reconstruct the structure of the satellite tobacco necrosis virus to atomic level. Our approach offers the highest reconstruction resolution for XFEL snapshots to date and provides a potentially powerful alternative route for analysis of data from crystalline and nano-crystalline objects. PMID:24914154

High-resolution structure of viruses from random diffraction snapshots.

PubMed

Hosseinizadeh, A; Schwander, P; Dashti, A; Fung, R; D'Souza, R M; Ourmazd, A

2014-07-17

The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. Algorithmic means must then be used to determine the snapshot orientations and thence the three-dimensional structure of the object. Existing Bayesian approaches are limited in reconstruction resolution typically to 1/10 of the object diameter, with the computational expense increasing as the eighth power of the ratio of diameter to resolution. We present an approach capable of exploiting object symmetries to recover three-dimensional structure to high resolution, and thus reconstruct the structure of the satellite tobacco necrosis virus to atomic level. Our approach offers the highest reconstruction resolution for XFEL snapshots to date and provides a potentially powerful alternative route for analysis of data from crystalline and nano-crystalline objects.

Three Dimensional Flow and Pressure Patterns in a Single Pocket of a Hydrostatic Journal Bearing

NASA Technical Reports Server (NTRS)

Braun, M. Jack; Dzodzo, Milorad B.

1996-01-01

The flow in a hydrostatic pocket is described by a mathematical model that uses the three dimensional Navier-Stokes equations written in terms of the primary variables, u, v, w, and p. Using a conservative formulation, a finite volume multi-block method is applied through a collocated, body fitted grid. The flow is simulated in a shallow pocket with a depth/length ratio of 0.02. The flow structures obtained and described by the authors in their previous two dimensional models are made visible in their three dimensional aspect for the Couette flow. It has been found that the flow regimes formed central and secondary vortical cells with three dimensional corkscrew-like structures that lead the fluid on an outward bound path in the axial direction of the pocket. The position of the central vortical cell center is at the exit region of the capillary restrictor feedline. It has also been determined that a fluid turn around zone occupies all the upstream space between the floor of the pocket and the runner, thus preventing any flow exit through the upstream port. The corresponding pressure distribution under the shaft presented as well. It was clearly established that for the Couette dominated case the pressure varies significantly in the pocket in the circumferential direction, while its variation is less pronounced axially.

Building the Peanut: Simulations and Observations of Peanut-shaped Structures and Ansae in Face-on Disk Galaxies

NASA Astrophysics Data System (ADS)

Saha, Kanak; Graham, Alister W.; Rodríguez-Herranz, Isabel

2018-01-01

Peanut/x-shaped features observed in a significant fraction of disk galaxies are thought to have formed from vertically buckled bars. Despite being three-dimensional structures, they are preferentially detected in near edge-on projection. Only a few galaxies are found to have displayed such structures when their disks are relatively face-on—suggesting that either they are generally weak in face-on projection or many may be hidden by the light of their galaxy’s face-on disk. Here, we report on three (collisionless) simulated galaxies displaying peanut-shaped structures when their disks are seen both face-on and edge-on—resembling a three-dimensional peanut or dumbbell. Furthermore, these structures are accompanied by ansae and an outer ring at the end of the bar—as seen in real galaxies such as IC 5240. The same set of quantitative parameters used to measure peanut structures in real galaxies has been determined for the simulated galaxies, and a broad agreement is found. In addition, the peanut length grows in tandem with the bar, and is a maximum at half the length of the bar. Beyond the cutoff of these peanut structures, toward the end of the bar, we discover a new positive/negative feature in the B 6 radial profile associated with the isophotes of the ansae/ring. Our simulated, self-gravitating, three-dimensional peanut structures display cylindrical rotation even in the near-face-on disk projection. In addition, we report on a kinematic pinch in the velocity map along the bar minor axis, matching that seen in the surface density map.

Silver(I) coordination polymers assembled from flexible cyclotriphosphazene ligand: structures, topologies and investigation of the counteranion effects.

PubMed

Davarcı, Derya; Gür, Rüştü; Beşli, Serap; Şenkuytu, Elif; Zorlu, Yunus

2016-06-01

The reactions of a flexible ligand hexakis(3-pyridyloxy)cyclotriphosphazene (HPCP) with a variety of silver(I) salts (AgX; X = NO3(-), PF6(-), ClO4(-), CH3PhSO3(-), BF4(-) and CF3SO3(-)) afforded six silver(I) coordination polymers, namely {[Ag2(HPCP)]·(NO3)2·H2O}n (1), {[Ag2(HPCP)(CH3CN)]·(PF6)2}n (2), {[Ag2(HPCP)(CH3CN)]·(ClO4)2}n (3), [Ag3(HPCP)(CH3PhSO3)3]n (4), [Ag2(HPCP)(CH3CN)(BF4)2]n (5) and {[Ag(HPCP)]·(CF3SO3)}n (6). All of the isolated crystalline compounds were structurally determined by X-ray crystallography. Changing the counteranions in the reactions, which were conducted under similar conditions of M/L ratio (1:1), temperature and solvent, resulted in structures with different types of topologies. In complexes (1)-(6), the ligand HPCP shows different coordination modes with Ag(I) ions giving two-dimensional layered structures and three-dimensional frameworks with different topologies. Complex (1) displays a new three-dimensional framework adopting a (3,3,6)-connected 3-nodal net with point symbol {4.6(2)}2{4(2).6(10).8(3)}. Complexes (2) and (3) are isomorphous and have a two-dimensional layered structure showing the same 3,6L60 topology with point symbol {4.2(6)}2{4(8).6(6).8}. Complex (4) is a two-dimensional structure incorporating short Ag...Ag argentophilic interactions and has a uninodal 4-connected sql/Shubnikov tetragonal plane net with {4(4).6(2)} topology. Complex (5) exhibits a novel three-dimensional framework and more suprisingly contains twofold interpenetrated honeycomb-like networks, in which the single net has a trinodal (2,3,5)-connected 3-nodal net with point symbol {6(3).8(6).12}{6(3)}{8}. Complex (6) crystallizes in a trigonal crystal system with the space group R\\bar 3 and possesses a three-dimensional polymeric structure showing a binodal (4,6)-connected fsh net with the point symbol (4(3).6(3))2.(4(6).6(6).8(3)). The effect of the counteranions on the formation of coordination polymers is discussed in this study.

Experiments on an unsteady, three-dimensional separation

NASA Technical Reports Server (NTRS)

Henk, R. W.; Reynolds, W. C.; Reed, H. L.

1992-01-01

Unsteady, three-dimensional flow separation occurs in a variety of technical situations including turbomachinery and low-speed aircraft. An experimental program at Stanford in unsteady, three-dimensional, pressure-driven laminar separation has investigated the structure and time-scaling of these flows; of particular interest is the development, washout, and control of flow separation. Results reveal that a two-dimensional, laminar boundary layer passes through several stages on its way to a quasi-steady three-dimensional separation. The quasi-steady state of the separation embodies a complex, unsteady, vortical structure.

Review of beetle forewing structures and their biomimetic applications in China: (I) On the structural colors and the vertical and horizontal cross-sectional structures.

PubMed

Chen, Jinxiang; Xie, Juan; Wu, Zhishen; Elbashiry, Elsafi Mohamed Adam; Lu, Yun

2015-10-01

This paper discusses the progress made in China in terms of the structural colors, microstructure and mechanical properties of the beetle forewing. 1) The forewing microstructures can be classified into six phases, the first three of which are characterized by sandwich, multilayer and fiber layer structures, respectively. The fracture behaviors resulting from these three phases suggest that different scale microstructures or coupled adjacent scale microstructures can determine the macroscopic mechanical behavior of the forewing. 2) The forewing colors are derived from three features: regulation of the structural parameters of the internal optical structures, i.e., a sculpted multilayer composite two-dimensional nanopillar structure grating system; scattering on the three-dimensional surface of the bowl-shaped structure; and reversible color changes due to changes in the physical microstructure of fluffs. Their formation mechanisms were clarified, and fibers with ecological biomimetic structural colors have been developed. 3) Beetles exhibit a lightweight sectional frame structure with a trabecular core structure. Both of the joints on the left and right are concave-convex butt-joint structures with burrs, which provide an efficient docking mechanism with high intensity. The forewing of dichotoma exhibits a non-equiangular layered structure, which results in anisotropy in its tensile strength. Finally, the authors propose potential new research directions for the next 20 years. Copyright © 2015 Elsevier B.V. All rights reserved.

In Situ Three-Dimensional Reciprocal-Space Mapping of Diffuse Scattering Intensity Distribution and Data Analysis for Precursor Phenomenon in Shape-Memory Alloy

NASA Astrophysics Data System (ADS)

Cheng, Tian-Le; Ma, Fengde D.; Zhou, Jie E.; Jennings, Guy; Ren, Yang; Jin, Yongmei M.; Wang, Yu U.

2012-01-01

Diffuse scattering contains rich information on various structural disorders, thus providing a useful means to study the nanoscale structural deviations from the average crystal structures determined by Bragg peak analysis. Extraction of maximal information from diffuse scattering requires concerted efforts in high-quality three-dimensional (3D) data measurement, quantitative data analysis and visualization, theoretical interpretation, and computer simulations. Such an endeavor is undertaken to study the correlated dynamic atomic position fluctuations caused by thermal vibrations (phonons) in precursor state of shape-memory alloys. High-quality 3D diffuse scattering intensity data around representative Bragg peaks are collected by using in situ high-energy synchrotron x-ray diffraction and two-dimensional digital x-ray detector (image plate). Computational algorithms and codes are developed to construct the 3D reciprocal-space map of diffuse scattering intensity distribution from the measured data, which are further visualized and quantitatively analyzed to reveal in situ physical behaviors. Diffuse scattering intensity distribution is explicitly formulated in terms of atomic position fluctuations to interpret the experimental observations and identify the most relevant physical mechanisms, which help set up reduced structural models with minimal parameters to be efficiently determined by computer simulations. Such combined procedures are demonstrated by a study of phonon softening phenomenon in precursor state and premartensitic transformation of Ni-Mn-Ga shape-memory alloy.

The three-dimensional structures of bacterial reaction centers.

PubMed

Olson, T L; Williams, J C; Allen, J P

2014-05-01

This review presents a broad overview of the research that enabled the structure determination of the bacterial reaction centers from Blastochloris viridis and Rhodobacter sphaeroides, with a focus on the contributions from Duysens, Clayton, and Feher. Early experiments performed in the laboratory of Duysens and others demonstrated the utility of spectroscopic techniques and the presence of photosynthetic complexes in both oxygenic and anoxygenic photosynthesis. The laboratories of Clayton and Feher led efforts to isolate and characterize the bacterial reaction centers. The availability of well-characterized preparations of pure and stable reaction centers allowed the crystallization and subsequent determination of the structures using X-ray diffraction. The three-dimensional structures of reaction centers revealed an overall arrangement of two symmetrical branches of cofactors surrounded by transmembrane helices from the L and M subunits, which also are related by the same twofold symmetry axis. The structure has served as a framework to address several issues concerning bacterial photosynthesis, including the directionality of electron transfer, the properties of the reaction center-cytochrome c 2 complex, and the coupling of proton and electron transfer. Together, these research efforts laid the foundation for ongoing efforts to address an outstanding question in oxygenic photosynthesis, namely the molecular mechanism of water oxidation.

Two-dimensional nuclear magnetic resonance structure determination module for introductory biochemistry: synthesis and structural characterization of lyso-glycerophospholipids.

PubMed

Garrett, Teresa A; Rose, Rebecca L; Bell, Sidney M

2013-01-01

In this laboratory module, introductory biochemistry students are exposed to two-dimensional (1) H-nuclear magnetic resonance of glycerophospholipids (GPLs). Working in groups of three, students enzymatically synthesized and purified a variety of 2-acyl lyso GPLs. The structure of the 2-acyl lyso GPL was verified using (1) H-correlation spectroscopy. Students scored significantly higher on an assessment of NMR knowledge after having participated in this lab module and in comparison to a similar cohort who did not participate. Inaddition, student confidence in their NMR knowledge and abilities increased 62% following the module and correlated with their ability to apply their NMR knowledge. Based on these results, the laboratory module was very effective at providing students with a more extensive understanding of the underlying concepts of NMR as a tool for structural determination. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

Hexadecameric structure of an invertebrate gap junction channel.

PubMed

Oshima, Atsunori; Matsuzawa, Tomohiro; Murata, Kazuyoshi; Tani, Kazutoshi; Fujiyoshi, Yoshinori

2016-03-27

Innexins are invertebrate-specific gap junction proteins with four transmembrane helices. These proteins oligomerize to constitute intercellular channels that allow for the passage of small signaling molecules associated with neural and muscular electrical activity. In contrast to the large number of structural and functional studies of connexin gap junction channels, few structural studies of recombinant innexin channels are reported. Here we show the three-dimensional structure of two-dimensionally crystallized Caenorhabditis elegans innexin-6 (INX-6) gap junction channels. The N-terminal deleted INX-6 proteins are crystallized in lipid bilayers. The three-dimensional reconstruction determined by cryo-electron crystallography reveals that a single INX-6 gap junction channel comprises 16 subunits, a hexadecamer, in contrast to chordate connexin channels, which comprise 12 subunits. The channel pore diameters at the cytoplasmic entrance and extracellular gap region are larger than those of connexin26. Two bulb densities are observed in each hemichannel, one in the pore and the other at the cytoplasmic side of the hemichannel in the channel pore pathway. These findings imply a structural diversity of gap junction channels among multicellular organisms. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

In situ synchrotron X-ray diffraction study on epitaxial-growth dynamics of III–V semiconductors

NASA Astrophysics Data System (ADS)

Takahasi, Masamitu

2018-05-01

The application of in situ synchrotron X-ray diffraction (XRD) to the molecular-beam epitaxial (MBE) growth of III–V semiconductors is overviewed along with backgrounds of the diffraction theory and instrumentation. X-rays are sensitive not only to the surface of growing films but also to buried interfacial structures because of their large penetration depth. Moreover, a spatial coherence length up to µm order makes X-rays widely applicable to the characterization of low-dimensional structures, such as quantum dots and wires. In situ XRD studies during growth were performed using an X-ray diffractometer, which was combined with an MBE chamber. X-ray reciprocal space mapping at a speed matching a typical growth rate was achieved using intense X-rays available from a synchrotron light source and an area detector. The importance of measuring the three-dimensional distribution of XRD intensity in a reciprocal space map is demonstrated for the MBE growth of two-, one-, and zero-dimensional structures. A large amount of information about the growth process of two-dimensional InGaAs/GaAs(001) epitaxial films has been provided by three-dimensional X-ray reciprocal mappings, including the anisotropic strain relaxation, the compositional inhomogeneity, and the evolution of surface and interfacial roughness. For one-dimensional GaAs nanowires grown in a Au-catalyzed vapor-liquid–solid mode, the relationship between the diameter of the nanowires and the formation of polytypes has been suggested on the basis of in situ XRD measurements. In situ three-dimensional X-ray reciprocal space mapping is also shown to be useful for determining the lateral and vertical sizes of self-assembled InAs/GaAs(001) quantum dots as well as their internal strain distributions during growth.

Structural consequences of metallothionein dimerization: solution structure of the isolated Cd4-alpha-domain and comparison with the holoprotein dimer.

PubMed

Ejnik, John W; Muñoz, Amalia; DeRose, Eugene; Shaw, C Frank; Petering, David H

2003-07-22

The NMR determination of the structure of Cd(7)-metallothionein was done previously using a relatively large protein concentration that favors dimer formation. The reactivity of the protein is also affected under this condition. To examine the influence of protein concentration on metallothionein conformation, the isolated Cd(4)-alpha-domain was prepared from rabbit metallothionein-2 (MT 2), and its three-dimensional structure was determined by heteronuclear, (1)H-(111)Cd, and homonuclear, (1)H-(1)H NMR, correlation experiments. The three-dimensional structure was refined using distance and angle constraints derived from these two-dimensional NMR data sets and a distance geometry/simulated annealing protocol. The backbone superposition of the alpha-domain from rabbit holoprotein Cd(7)-MT 2 and the isolated rabbit Cd(4)-alpha was measured at a RMSD of 2.0 A. Nevertheless, the conformations of the two Cd-thiolate clusters were distinctly different at two of the cadmium centers. In addition, solvent access to the sulfhydryl ligands of the isolated Cd(4)-alpha cluster was 130% larger due to this small change in cluster geometry. To probe whether these differences were an artifact of the structure calculation, the Cd(4)-alpha-domain structure in rabbit Cd(7)-MT 2 was redetermined, using the previously defined set of NOEs and the present calculation protocol. All calculations employed the same ionic radius for Cd(2+) and same cadmium-thiolate bond distance. The newly calculated structure matched the original with an RMSD of 1.24 A. It is hypothesized that differences in the two alpha-domain structures result from a perturbation of the holoprotein structure because of head-to-tail dimerization under the conditions of the NMR experiments.

Genetic algorithm-based multi-objective optimal absorber system for three-dimensional seismic structures

NASA Astrophysics Data System (ADS)

Ren, Wenjie; Li, Hongnan; Song, Gangbing; Huo, Linsheng

2009-03-01

The problem of optimizing an absorber system for three-dimensional seismic structures is addressed. The objective is to determine the number and position of absorbers to minimize the coupling effects of translation-torsion of structures at minimum cost. A procedure for a multi-objective optimization problem is developed by integrating a dominance-based selection operator and a dominance-based penalty function method. Based on the two-branch tournament genetic algorithm, the selection operator is constructed by evaluating individuals according to their dominance in one run. The technique guarantees the better performing individual winning its competition, provides a slight selection pressure toward individuals and maintains diversity in the population. Moreover, due to the evaluation for individuals in each generation being finished in one run, less computational effort is taken. Penalty function methods are generally used to transform a constrained optimization problem into an unconstrained one. The dominance-based penalty function contains necessary information on non-dominated character and infeasible position of an individual, essential for success in seeking a Pareto optimal set. The proposed approach is used to obtain a set of non-dominated designs for a six-storey three-dimensional building with shape memory alloy dampers subjected to earthquake.

Parallel computation of three-dimensional aeroelastic fluid-structure interaction

NASA Astrophysics Data System (ADS)

Sadeghi, Mani

This dissertation presents a numerical method for the parallel computation of aeroelasticity (ParCAE). A flow solver is coupled to a structural solver by use of a fluid-structure interface method. The integration of the three-dimensional unsteady Navier-Stokes equations is performed in the time domain, simultaneously to the integration of a modal three-dimensional structural model. The flow solution is accelerated by using a multigrid method and a parallel multiblock approach. Fluid-structure coupling is achieved by subiteration. A grid-deformation algorithm is developed to interpolate the deformation of the structural boundaries onto the flow grid. The code is formulated to allow application to general, three-dimensional, complex configurations with multiple independent structures. Computational results are presented for various configurations, such as turbomachinery blade rows and aircraft wings. Investigations are performed on vortex-induced vibrations, effects of cascade mistuning on flutter, and cases of nonlinear cascade and wing flutter.

Determination of CME 3D parameters based on a new full ice-cream cone model

NASA Astrophysics Data System (ADS)

Na, Hyeonock; Moon, Yong-Jae

2017-08-01

In space weather forecast, it is important to determine three-dimensional properties of CMEs. Using 29 limb CMEs, we examine which cone type is close to a CME three-dimensional structure. We find that most CMEs have near full ice-cream cone structure which is a symmetrical circular cone combined with a hemisphere. We develop a full ice-cream cone model based on a new methodology that the full ice-cream cone consists of many flat cones with different heights and angular widths. By applying this model to 12 SOHO/LASCO halo CMEs, we find that 3D parameters from our method are similar to those from other stereoscopic methods (i.e., a triangulation method and a Graduated Cylindrical Shell model). In addition, we derive CME mean density (ρmean=Mtotal/Vcone) based on the full ice-cream cone structure. For several limb events, we determine CME mass by applying the Solarsoft procedure (e.g., cme_mass.pro) to SOHO/LASCO C3 images. CME volumes are estimated from the full ice-cream cone structure. From the power-law relationship between CME mean density and its height, we estimate CME mean densities at 20 solar radii (Rs). We will compare the CME densities at 20 Rs with their corresponding ICME densities.

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.

PubMed

Afanasyev, Pavel; Seer-Linnemayr, Charlotte; Ravelli, Raimond B G; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V; Pannu, Navraj S; Schatz, Michael; van Heel, Marin

2017-09-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

Three-Dimensional Conformation of Folded Polymers in Single Crystals

NASA Astrophysics Data System (ADS)

Hong, You-lee; Yuan, Shichen; Li, Zhen; Ke, Yutian; Nozaki, Koji; Miyoshi, Toshikazu

2015-10-01

The chain-folding mechanism and structure of semicrystalline polymers have long been controversial. Solid-state NMR was applied to determine the chain trajectory of 13C CH3 -labeled isotactic poly(1-butene) (i PB 1 ) in form III chiral single crystals blended with nonlabeled i PB 1 crystallized in dilute solutions under low supercooling. An advanced 13C - 13C double-quantum NMR technique probing the spatial proximity pattern of labeled 13C nuclei revealed that the chains adopt a three-dimensional (3D) conformation in single crystals. The determined results indicate a two-step crystallization process of (i) cluster formation via self-folding in the precrystallization stage and (ii) deposition of the nanoclusters as a building block at the growth front in single crystals.

Structure of catalase determined by MicroED

PubMed Central

Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

2014-01-01

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI: http://dx.doi.org/10.7554/eLife.03600.001 PMID:25303172

Education Catching up with Science: Preparing Students for Three-Dimensional Literacy in Cell Biology

ERIC Educational Resources Information Center

Kramer, IJsbrand M.; Dahmani, Hassen-Reda; Delouche, Pamina; Bidabe, Marissa; Schneeberger, Patricia

2012-01-01

The large number of experimentally determined molecular structures has led to the development of a new semiotic system in the life sciences, with increasing use of accurate molecular representations. To determine how this change impacts students' learning, we incorporated image tests into our introductory cell biology course. Groups of students…

Learning the Cell Structures with Three-Dimensional Models: Students' Achievement by Methods, Type of School and Questions' Cognitive Level

ERIC Educational Resources Information Center

Lazarowitz, Reuven; Naim, Raphael

2014-01-01

The cell topic was taught to 9th-grade students in three modes of instruction: (a) students "hands-on," who constructed three-dimensional cell organelles and macromolecules during the learning process; (b) teacher demonstration of the three-dimensional model of the cell structures; and (c) teaching the cell topic with the regular…

Three Dimensional Immobilization of Beta-Galactosidase on a Silicon Surface (Preprint)

DTIC Science & Technology

2006-12-01

initial activity after 10 days at 24°C. The ability to generate three- dimensional structures with enhanced loading capacity for biosensing molecules...dimensional structures for biosensors (Charles et al. 2004). Silicon samples that had been washed but not activated with APTS did not retain any enzyme...preparation. The use of silica particles to build a 3-dimensional structure not only provides an increased capacity for the immobilization of β

Three-dimensional nanostructure determination from a large diffraction data set recorded using scanning electron nanodiffraction.

PubMed

Meng, Yifei; Zuo, Jian-Min

2016-09-01

A diffraction-based technique is developed for the determination of three-dimensional nanostructures. The technique employs high-resolution and low-dose scanning electron nanodiffraction (SEND) to acquire three-dimensional diffraction patterns, with the help of a special sample holder for large-angle rotation. Grains are identified in three-dimensional space based on crystal orientation and on reconstructed dark-field images from the recorded diffraction patterns. Application to a nanocrystalline TiN thin film shows that the three-dimensional morphology of columnar TiN grains of tens of nanometres in diameter can be reconstructed using an algebraic iterative algorithm under specified prior conditions, together with their crystallographic orientations. The principles can be extended to multiphase nanocrystalline materials as well. Thus, the tomographic SEND technique provides an effective and adaptive way of determining three-dimensional nanostructures.

Direct Numerical Simulation of a Temporally Evolving Incompressible Plane Wake: Effect of Initial Conditions on Evolution and Topology

NASA Technical Reports Server (NTRS)

Sondergaard, R.; Cantwell, B.; Mansour, N.

1997-01-01

Direct numerical simulations have been used to examine the effect of the initial disturbance field on the development of three-dimensionality and the transition to turbulence in the incompressible plane wake. The simulations were performed using a new numerical method for solving the time-dependent, three-dimensional, incompressible Navier-Stokes equations in flows with one infinite and two periodic directions. The method uses standard Fast Fourier Transforms and is applicable to cases where the vorticity field is compact in the infinite direction. Initial disturbances fields examined were combinations of two-dimensional waves and symmetric pairs of 60 deg oblique waves at the fundamental, subharmonic, and sub-subharmonic wavelengths. The results of these simulations indicate that the presence of 60 deg disturbances at the subharmonic streamwise wavelength results in the development of strong coherent three-dimensional structures. The resulting strong three-dimensional rate-of-strain triggers the growth of intense fine scale motions. Wakes initiated with 60 deg disturbances at the fundamental streamwise wavelength develop weak coherent streamwise structures, and do not develop significant fine scale motions, even at high Reynolds numbers. The wakes which develop strong three-dimensional structures exhibit growth rates on par with experimentally observed turbulent plane wakes. Wakes which develop only weak three-dimensional structures exhibit significantly lower late time growth rates. Preliminary studies of wakes initiated with an oblique fundamental and a two-dimensional subharmonic, which develop asymmetric coherent oblique structures at the subharmonic wavelength, indicate that significant fine scale motions only develop if the resulting oblique structures are above an angle of approximately 45 deg.

Coherent structures and flow topology of transitional separated-reattached flow over two and three dimensional geometrical shapes

NASA Astrophysics Data System (ADS)

Diabil, Hayder Azeez; Li, Xin Kai; Abdalla, Ibrahim Elrayah

2017-09-01

Large-scale organized motions (commonly referred to coherent structures) and flow topology of a transitional separated-reattached flow have been visualised and investigated using flow visualisation techniques. Two geometrical shapes including two-dimensional flat plate with rectangular leading edge and three-dimensional square cylinder are chosen to shed a light on the flow topology and present coherent structures of the flow over these shapes. For both geometries and in the early stage of the transition, two-dimensional Kelvin-Helmholtz rolls are formed downstream of the leading edge. They are observed to be twisting around the square cylinder while they stay flat in the case of the two-dimensional flat plate. For both geometrical shapes, the two-dimensional Kelvin-Helmholtz rolls move downstream of the leading edge and they are subjected to distortion to form three-dimensional hairpin structures. The flow topology in the flat plate is different from that in the square cylinder. For the flat plate, there is a merging process by a pairing of the Kelvin-Helmholtz rolls to form a large structure that breaks down directly into many hairpin structures. For the squire cylinder case, the Kelvin-Helmholtz roll evolves topologically to form a hairpin structure. In the squire cylinder case, the reattachment length is much shorter and a forming of the three-dimensional structures is closer to the leading edge than that in the flat plate case.

Three-Dimensional Structure Analysis and Percolation Properties of a Barrier Marine Coating

PubMed Central

Chen, Bo; Guizar-Sicairos, Manuel; Xiong, Gang; Shemilt, Laura; Diaz, Ana; Nutter, John; Burdet, Nicolas; Huo, Suguo; Mancuso, Joel; Monteith, Alexander; Vergeer, Frank; Burgess, Andrew; Robinson, Ian

2013-01-01

Artificially structured coatings are widely employed to minimize materials deterioration and corrosion, the annual direct cost of which is over 3% of the gross domestic product (GDP) for industrial countries. Manufacturing higher performance anticorrosive coatings is one of the most efficient approaches to reduce this loss. However, three-dimensional (3D) structure of coatings, which determines their performance, has not been investigated in detail. Here we present a quantitative nano-scale analysis of the 3D spatial structure of an anticorrosive aluminium epoxy barrier marine coating obtained by serial block-face scanning electron microscopy (SBFSEM) and ptychographic X-ray computed tomography (PXCT). We then use finite element simulations to demonstrate how percolation through this actual 3D structure impedes ion diffusion in the composite materials. We found the aluminium flakes align within 15° of the coating surface in the material, causing the perpendicular diffusion resistance of the coating to be substantially higher than the pure epoxy. PMID:23378910

Structure of a Clostridium botulinum C143S thiaminase I/thiamin complex reveals active site architecture .

PubMed

Sikowitz, Megan D; Shome, Brateen; Zhang, Yang; Begley, Tadhg P; Ealick, Steven E

2013-11-05

Thiaminases are responsible for the degradation of thiamin and its metabolites. Two classes of thiaminases have been identified based on their three-dimensional structures and their requirements for a nucleophilic second substrate. Although the reactions of several thiaminases have been characterized, the physiological role of thiamin degradation is not fully understood. We have determined the three-dimensional X-ray structure of an inactive C143S mutant of Clostridium botulinum (Cb) thiaminase I with bound thiamin at 2.2 Å resolution. The C143S/thiamin complex provides atomic level details of the orientation of thiamin upon binding to Cb-thiaminase I and the identity of active site residues involved in substrate binding and catalysis. The specific roles of active site residues were probed by using site directed mutagenesis and kinetic analyses, leading to a detailed mechanism for Cb-thiaminase I. The structure of Cb-thiaminase I is also compared to the functionally similar but structurally distinct thiaminase II.

Ion current in a magnetic neutral region - Generation of an incipient magnetopause

NASA Technical Reports Server (NTRS)

Whipple, E. C.; Silevitch, M. B.

1982-01-01

The current contributed by ions trapped in the vicinity of a magnetic X line is calculated. The three dimensional configuration of the neutral region is found to be critical in determining the current in that the escape mechanism and trapping times depend on the three-dimensional aspects. A trapping criterion is defined. In the neutral region the ions can gain substantial kinetic energy, and the current will change the X line configuration in such a way that there will be a positive feedback effect, rapidly forming an extended magnetopauselike structure for even very small incident plasma densities.

A Computational and Experimental Investigation of a Three-Dimensional Hypersonic Scramjet Inlet Flow Field. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Holland, Scott Douglas

1991-01-01

A combined computational and experimental parametric study of the internal aerodynamics of a generic three dimensional sidewall compression scramjet inlet configuration was performed. The study was designed to demonstrate the utility of computational fluid dynamics as a design tool in hypersonic inlet flow fields, to provide a detailed account of the nature and structure of the internal flow interactions, and to provide a comprehensive surface property and flow field database to determine the effects of contraction ratio, cowl position, and Reynolds number on the performance of a hypersonic scramjet inlet configuration.

Evaluation of oriented lysozyme immobilized with monoclonal antibody

NASA Astrophysics Data System (ADS)

Aoyagi, Satoka; Okada, Keigo; Shigyo, Ayako; Man, Naoki; Karen, Akiya

2008-12-01

The orientation of a lysozyme immobilized with a monoclonal antibody was evaluated based on determination of the uppermost surface structure using time-of-flight secondary ion mass spectrometry (TOF-SIMS). Specific peaks of the oriented lysozyme immobilized with monoclonal anti-lysozyme antibody were obtained in comparison with reference samples, non-oriented immobilized lysozyme and immobilized anti-lysozyme antibody. All samples were freeze-dried before TOF-SIMS measurement, and then each sample was measured using TOF-SIMS with a bismuth cluster ion source. TOF-SIMS spectra were analyzed to select peaks specific to the oriented immobilized lysozyme as well as to identify their chemical formula and ensemble of amino acids. The possible chemical formulae of the lysozyme fragments were then investigated with an element matching program and a residue matching program. The results from TOF-SIMS spectra analysis were compared to the amino acid sequence of the lysozyme and its three-dimensional structure registered in the protein data bank. Finally, the fragment-ion-generating regions of the oriented immobilized lysozyme were determined based on the suggested residues and the three-dimensional structure.

Vfold: a web server for RNA structure and folding thermodynamics prediction.

PubMed

Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2014-01-01

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

Three-scale analysis of the permeability of a natural shale

NASA Astrophysics Data System (ADS)

Davy, C. A.; Adler, P. M.

2017-12-01

The macroscopic permeability of a natural shale is determined by using structural measurements on three different scales. Transmission electron microscopy yields two-dimensional (2D) images with pixels smaller than 1 nm; these images are used to reconstruct 3D nanostructures. Three-dimensional focused ion beam-scanning electron microscopy (5.95- to 8.48-nm voxel size) provides 3D mesoscale pores of limited relative volume (1.71-5.9%). Micro-computed tomography (700-nm voxel size) provides information on the mineralogy of the shale, including the pores on this scale which do not percolate; synthetic 3D media are derived on the macroscopic scale by a training image technique. Permeability of the nanoscale, of the mesoscale structures and of their superposition is determined by solving the Stokes equation and this enables us to estimate the permeabilities of the 700-nm voxels located within the clay matrix. Finally, the Darcy equation is solved on synthetic 3D macroscale media to obtain the macroscopic permeability which is found in good agreement with experimental results obtained on the centimetric scale.

Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement.

PubMed

Potrzebowski, Wojciech; André, Ingemar

2015-07-01

For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology modeling and protein-protein docking. The generated models explain the experimental data to the same degree as deposited reference structures but with improved structural quality. We also developed a cross-validation method for model selection. The results highlight the power of fiber diffraction data as structural constraints.

Framework to model neutral particle flux in convex high aspect ratio structures using one-dimensional radiosity

NASA Astrophysics Data System (ADS)

Manstetten, Paul; Filipovic, Lado; Hössinger, Andreas; Weinbub, Josef; Selberherr, Siegfried

2017-02-01

We present a computationally efficient framework to compute the neutral flux in high aspect ratio structures during three-dimensional plasma etching simulations. The framework is based on a one-dimensional radiosity approach and is applicable to simulations of convex rotationally symmetric holes and convex symmetric trenches with a constant cross-section. The framework is intended to replace the full three-dimensional simulation step required to calculate the neutral flux during plasma etching simulations. Especially for high aspect ratio structures, the computational effort, required to perform the full three-dimensional simulation of the neutral flux at the desired spatial resolution, conflicts with practical simulation time constraints. Our results are in agreement with those obtained by three-dimensional Monte Carlo based ray tracing simulations for various aspect ratios and convex geometries. With this framework we present a comprehensive analysis of the influence of the geometrical properties of high aspect ratio structures as well as of the particle sticking probability on the neutral particle flux.

Cochlear implant-related three-dimensional characteristics determined by micro-computed tomography reconstruction.

PubMed

Ni, Yusu; Dai, Peidong; Dai, Chunfu; Li, Huawei

2017-01-01

To explore the structural characteristics of the cochlea in three-dimensional (3D) detail using 3D micro-computed tomography (mCT) image reconstruction of the osseous labyrinth, with the aim of improving the structural design of electrodes, the selection of stimulation sites, and the effectiveness of cochlear implantation. Three temporal bones were selected from among adult donors' temporal bone specimens. A micro-CT apparatus (GE eXplore) was used to scan three specimens with a voxel resolution of 45 μm. We obtained about 460 slices/specimen, which produced abundant data. The osseous labyrinth images of three specimens were reconstructed from mCT. The cochlea and its spiral characteristics were measured precisely using Able Software 3D-DOCTOR. The 3D images of the osseous labyrinth, including the cochlea, vestibule, and semicircular canals, were reconstructed. The 3D models of the cochlea showed the spatial relationships and surface structural characteristics. Quantitative data concerning the cochlea and its spiral structural characteristics were analyzed with regard to cochlear implantation. The 3D reconstruction of mCT images clearly displayed the detailed spiral structural characteristics of the osseous labyrinth. Quantitative data regarding the cochlea and its spiral structural characteristics could help to improve electrode structural design, signal processing, and the effectiveness of cochlear implantation. Clin. Anat. 30:39-43, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Functionally Graded Metal-Metal Composite Structures

NASA Technical Reports Server (NTRS)

Brice, Craig A. (Inventor)

2017-01-01

Methods and devices are disclosed for creating a multiple alloy composite structure by forming a three-dimensional arrangement of a first alloy composition in which the three-dimensional arrangement has a substantially open and continuous porosity. The three-dimensional arrangement of the first alloy composition is infused with at least a second alloy composition, where the second alloy composition comprises a shape memory alloy. The three-dimensional arrangement is consolidated into a fully dense solid structure, and the original shape of the second alloy composition is set for reversible transformation. Strain is applied to the fully dense solid structure, which is treated with heat so that the shape memory alloy composition becomes memory activated to recover the original shape. An interwoven composite of the first alloy composition and the memory-activated second alloy composition is thereby formed in the multiple alloy composite structure.

Three-dimensional biofilm structure quantification.

PubMed

Beyenal, Haluk; Donovan, Conrad; Lewandowski, Zbigniew; Harkin, Gary

2004-12-01

Quantitative parameters describing biofilm physical structure have been extracted from three-dimensional confocal laser scanning microscopy images and used to compare biofilm structures, monitor biofilm development, and quantify environmental factors affecting biofilm structure. Researchers have previously used biovolume, volume to surface ratio, roughness coefficient, and mean and maximum thicknesses to compare biofilm structures. The selection of these parameters is dependent on the availability of software to perform calculations. We believe it is necessary to develop more comprehensive parameters to describe heterogeneous biofilm morphology in three dimensions. This research presents parameters describing three-dimensional biofilm heterogeneity, size, and morphology of biomass calculated from confocal laser scanning microscopy images. This study extends previous work which extracted quantitative parameters regarding morphological features from two-dimensional biofilm images to three-dimensional biofilm images. We describe two types of parameters: (1) textural parameters showing microscale heterogeneity of biofilms and (2) volumetric parameters describing size and morphology of biomass. The three-dimensional features presented are average (ADD) and maximum diffusion distances (MDD), fractal dimension, average run lengths (in X, Y and Z directions), aspect ratio, textural entropy, energy and homogeneity. We discuss the meaning of each parameter and present the calculations in detail. The developed algorithms, including automatic thresholding, are implemented in software as MATLAB programs which will be available at site prior to publication of the paper.

One-dimensional, two-dimensional, and three-dimensional photonic crystals fabricated with interferometric techniques on ultrafine-grain silver halide emulsions

NASA Astrophysics Data System (ADS)

Ulibarrena, Manuel; Carretero, Luis; Acebal, Pablo; Madrigal, Roque; Blaya, Salvador; Fimia, Antonio

2004-09-01

Holographic techniques have been used for manufacturing multiple band one-dimensional, two-dimensional, and three-dimensional photonic crystals with different configurations, by multiplexing reflection and transmission setups on a single layer of holographic material. The recording material used for storage is an ultra fine grain silver halide emulsion, with an average grain size around 20 nm. The results are a set of photonic crystals with the one-dimensional, two-dimensional, and three-dimensional index modulation structure consisting of silver halide particles embedded in the gelatin layer of the emulsion. The characterisation of the fabricated photonic crystals by measuring their transmission band structures has been done and compared with theoretical calculations.

Computer system for definition of the quantitative geometry of musculature from CT images.

PubMed

Daniel, Matej; Iglic, Ales; Kralj-Iglic, Veronika; Konvicková, Svatava

2005-02-01

The computer system for quantitative determination of musculoskeletal geometry from computer tomography (CT) images has been developed. The computer system processes series of CT images to obtain three-dimensional (3D) model of bony structures where the effective muscle fibres can be interactively defined. Presented computer system has flexible modular structure and is suitable also for educational purposes.

Fabrication of 3D nano-structures using reverse imprint lithography

NASA Astrophysics Data System (ADS)

Han, Kang-Soo; Hong, Sung-Hoon; Kim, Kang-In; Cho, Joong-Yeon; Choi, Kyung-woo; Lee, Heon

2013-02-01

In spite of the fact that the fabrication process of three-dimensional nano-structures is complicated and expensive, it can be applied to a range of devices to increase their efficiency and sensitivity. Simple and inexpensive fabrication of three-dimensional nano-structures is necessary. In this study, reverse imprint lithography (RIL) with UV-curable benzylmethacrylate, methacryloxypropyl terminated poly-dimethylsiloxane (M-PDMS) resin and ZnO-nano-particle-dispersed resin was used to fabricate three-dimensional nano-structures. UV-curable resins were placed between a silicon stamp and a PVA transfer template, followed by a UV curing process. Then, the silicon stamp was detached and a 2D pattern layer was transferred to the substrate using diluted UV-curable glue. Consequently, three-dimensional nano-structures were formed by stacking the two-dimensional nano-patterned layers. RIL was applied to a light-emitting diode (LED) to evaluate the optical effects of a nano-patterned layer. As a result, the light extraction of the patterned LED was increased by about 12% compared to an unpatterned LED.

Fabrication of 3D nano-structures using reverse imprint lithography.

PubMed

Han, Kang-Soo; Hong, Sung-Hoon; Kim, Kang-In; Cho, Joong-Yeon; Choi, Kyung-Woo; Lee, Heon

2013-02-01

In spite of the fact that the fabrication process of three-dimensional nano-structures is complicated and expensive, it can be applied to a range of devices to increase their efficiency and sensitivity. Simple and inexpensive fabrication of three-dimensional nano-structures is necessary. In this study, reverse imprint lithography (RIL) with UV-curable benzylmethacrylate, methacryloxypropyl terminated poly-dimethylsiloxane (M-PDMS) resin and ZnO-nano-particle-dispersed resin was used to fabricate three-dimensional nano-structures.UV-curable resins were placed between a silicon stamp and a PVA transfer template, followed by a UV curing process. Then, the silicon stamp was detached and a 2D pattern layer was transferred to the substrate using diluted UV-curable glue. Consequently, three-dimensional nano-structures were formed by stacking the two-dimensional nano-patterned layers. RIL was applied to a light-emitting diode (LED) to evaluate the optical effects of a nano-patterned layer. As a result, the light extraction of the patterned LED was increased by about 12% compared to an unpatterned LED.

More About The Farley Three-Dimensional Braider

NASA Technical Reports Server (NTRS)

Farley, Gary L.

1993-01-01

Farley three-dimensional braider, undergoing development, is machine for automatic fabrication of three-dimensional braided structures. Incorporates yarns into structure at arbitrary braid angles to produce complicated shape. Braiding surface includes movable braiding segments containing pivot points, along which yarn carriers travel during braiding process. Yarn carrier travels along sequence of pivot points as braiding segments move. Combined motions position yarns for braiding onto preform. Intended for use in making fiber preforms for fiber/matrix composite parts, such as multiblade propellers. Machine also described in "Farley Three-Dimensional Braiding Machine" (LAR-13911).

The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation.

PubMed

Weyand, Simone; Kefala, Georgia; Svergun, Dmitri I; Weiss, Manfred S

2009-09-01

The three-dimensional structure of the enzyme diaminopimelate decarboxylase from Mycobacterium tuberculosis has been determined in a new crystal form and refined to a resolution of 2.33 A. The monoclinic crystals contain one tetramer exhibiting D(2)-symmetry in the asymmetric unit. The tetramer exhibits a donut-like structure with a hollow interior. All four active sites are accessible only from the interior of the tetrameric assembly. Small-angle X-ray scattering indicates that in solution the predominant oligomeric species of the protein is a dimer, but also that higher oligomers exist at higher protein concentrations. The observed scattering data are best explained by assuming a dimer-tetramer equilibrium with about 7% tetramers present in solution. Consequently, at the elevated protein concentrations in the crowded environment inside the cell the observed tetramer may constitute the biologically relevant functional unit of the enzyme.

Three-dimensional nanostructure determination from a large diffraction data set recorded using scanning electron nanodiffraction

DOE PAGES

Meng, Yifei; Zuo, Jian -Min

2016-07-04

A diffraction-based technique is developed for the determination of three-dimensional nanostructures. The technique employs high-resolution and low-dose scanning electron nanodiffraction (SEND) to acquire three-dimensional diffraction patterns, with the help of a special sample holder for large-angle rotation. Grains are identified in three-dimensional space based on crystal orientation and on reconstructed dark-field images from the recorded diffraction patterns. Application to a nanocrystalline TiN thin film shows that the three-dimensional morphology of columnar TiN grains of tens of nanometres in diameter can be reconstructed using an algebraic iterative algorithm under specified prior conditions, together with their crystallographic orientations. The principles can bemore » extended to multiphase nanocrystalline materials as well. Furthermore, the tomographic SEND technique provides an effective and adaptive way of determining three-dimensional nanostructures.« less

Development of a direct three-dimensional biomicrofabrication concept based on electrospraying a custom made siloxane sol

PubMed Central

Sullivan, Alice C.; Jayasinghe, Suwan N.

2007-01-01

We demonstrate here the discovery of a unique and direct three-dimensional biomicrofabrication concept possessing the ability to revolutionize the jet-based fabrication arena. Previous work carried out on similar jet-based approaches have been successful in fabricating only vertical wall∕pillar-structures by the controlled deposition of stacked droplets. However, these advanced jet-techniques have not been able to directly fabricate self-supporting arches∕links (without molds or reaction methods) between adjacent structures (walls or pillars). Our work reported here gives birth to a unique type of jet determined by high intensity electric fields, which is derived from a specially formulated siloxane sol. The sol studied here has been chosen for its attractive properties (such as an excellent cross-linking nature as well as the ability to polymerize via polycondensation on deposition to its biocompatability), which promotes direct forming of biostructures with nanometer (<50 nm) sized droplets in three dimensions. We foresee that this direct three-dimensional biomicrofabrication jet technique coupled with a variety of formulated sols having focused and enhanced functionality will be explored throughout the physical and life sciences. PMID:19693359

Generation of three-dimensional multiple spheroid model of olfactory ensheathing cells using floating liquid marbles

PubMed Central

Vadivelu, Raja K.; Ooi, Chin H.; Yao, Rebecca-Qing; Tello Velasquez, Johana; Pastrana, Erika; Diaz-Nido, Javier; Lim, Filip; Ekberg, Jenny A. K.; Nguyen, Nam-Trung; St John, James A.

2015-01-01

We describe a novel protocol for three-dimensional culturing of olfactory ensheathing cells (OECs), which can be used to understand how OECs interact with other cells in three dimensions. Transplantation of OECs is being trialled for repair of the paralysed spinal cord, with promising but variable results and thus the therapy needs improving. To date, studies of OEC behaviour in a multicellular environment have been hampered by the lack of suitable three-dimensional cell culture models. Here, we exploit the floating liquid marble, a liquid droplet coated with hydrophobic powder and placed on a liquid bath. The presence of the liquid bath increases the humidity and minimises the effect of evaporation. Floating liquid marbles allow the OECs to freely associate and interact to produce OEC spheroids with uniform shapes and sizes. In contrast, a sessile liquid marble on a solid surface suffers from evaporation and the cells aggregate with irregular shapes. We used floating liquid marbles to co-culture OECs with Schwann cells and astrocytes which formed natural structures without the confines of gels or bounding layers. This protocol can be used to determine how OECs and other cell types associate and interact while forming complex cell structures. PMID:26462469

Generation of three-dimensional multiple spheroid model of olfactory ensheathing cells using floating liquid marbles

NASA Astrophysics Data System (ADS)

Vadivelu, Raja K.; Ooi, Chin H.; Yao, Rebecca-Qing; Tello Velasquez, Johana; Pastrana, Erika; Diaz-Nido, Javier; Lim, Filip; Ekberg, Jenny A. K.; Nguyen, Nam-Trung; St John, James A.

2015-10-01

We describe a novel protocol for three-dimensional culturing of olfactory ensheathing cells (OECs), which can be used to understand how OECs interact with other cells in three dimensions. Transplantation of OECs is being trialled for repair of the paralysed spinal cord, with promising but variable results and thus the therapy needs improving. To date, studies of OEC behaviour in a multicellular environment have been hampered by the lack of suitable three-dimensional cell culture models. Here, we exploit the floating liquid marble, a liquid droplet coated with hydrophobic powder and placed on a liquid bath. The presence of the liquid bath increases the humidity and minimises the effect of evaporation. Floating liquid marbles allow the OECs to freely associate and interact to produce OEC spheroids with uniform shapes and sizes. In contrast, a sessile liquid marble on a solid surface suffers from evaporation and the cells aggregate with irregular shapes. We used floating liquid marbles to co-culture OECs with Schwann cells and astrocytes which formed natural structures without the confines of gels or bounding layers. This protocol can be used to determine how OECs and other cell types associate and interact while forming complex cell structures.

Application of a laser scanner to three dimensional visual sensing tasks

NASA Technical Reports Server (NTRS)

Ryan, Arthur M.

1992-01-01

The issues are described which are associated with using a laser scanner for visual sensing and the methods developed by the author to address them. A laser scanner is a device that controls the direction of a laser beam by deflecting it through a pair of orthogonal mirrors, the orientations of which are specified by a computer. If a calibrated laser scanner is combined with a calibrated camera, it is possible to perform three dimensional sensing by directing the laser at objects within the field of view of the camera. There are several issues associated with using a laser scanner for three dimensional visual sensing that must be addressed in order to use the laser scanner effectively. First, methods are needed to calibrate the laser scanner and estimate three dimensional points. Second, methods to estimate three dimensional points using a calibrated camera and laser scanner are required. Third, methods are required for locating the laser spot in a cluttered image. Fourth, mathematical models that predict the laser scanner's performance and provide structure for three dimensional data points are necessary. Several methods were developed to address each of these and has evaluated them to determine how and when they should be applied. The theoretical development, implementation, and results when used in a dual arm eighteen degree of freedom robotic system for space assembly is described.

Construction of a three-dimensional finite element model of maxillary first molar and it's supporting structures

PubMed Central

Begum, M. Sameena; Dinesh, M. R.; Tan, Kenneth F. H.; Jairaj, Vani; Md Khalid, K.; Singh, Varun Pratap

2015-01-01

The finite element method (FEM) is a powerful computational tool for solving stress-strain problems; its ability to handle material inhomogeneity and complex shapes makes the FEM, the most suitable method for the analysis of internal stress levels in the tooth, periodontium, and alveolar bone. This article intends to explain the steps involved in the generation of a three-dimensional finite element model of tooth, periodontal ligament (PDL) and alveolar bone, as the procedure of modeling is most important because the result is based on the nature of the modeling systems. Finite element analysis offers a means of determining strain-stress levels in the tooth, ligament, and bone structures for a broad range of orthodontic loading scenarios without producing tissue damage. PMID:26538895

Microgravity

NASA Image and Video Library

2004-04-15

A semiconductor's usefulness is determined by how atoms are ordered within the crystal's underlying three-dimensional structure. While this mercury telluride and cadmium telluride alloy sample mixes completely in Earth -based laboratories, convective flows prevent them from mixing uniformly. In space, the ingredients mix more homogenously, resulting in a superior product.

ASTROP2 Users Manual: A Program for Aeroelastic Stability Analysis of Propfans

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Lucero, John M.

1996-01-01

This manual describes the input data required for using the second version of the ASTROP2 (Aeroelastic STability and Response Of Propulsion systems - 2 dimensional analysis) computer code. In ASTROP2, version 2.0, the program is divided into two modules: 2DSTRIP, which calculates the structural dynamic information; and 2DASTROP, which calculates the unsteady aerodynamic force coefficients from which the aeroelastic stability can be determined. In the original version of ASTROP2, these two aspects were performed in a single program. The improvements to version 2.0 include an option to account for counter rotation, improved numerical integration, accommodation for non-uniform inflow distribution, and an iterative scheme to flutter frequency convergence. ASTROP2 can be used for flutter analysis of multi-bladed structures such as those found in compressors, turbines, counter rotating propellers or propfans. The analysis combines a two-dimensional, unsteady cascade aerodynamics model and a three dimensional, normal mode structural model using strip theory. The flutter analysis is formulated in the frequency domain resulting in an eigenvalue determinant. The flutter frequency and damping can be inferred from the eigenvalues.

Three-dimensional structural analysis using interactive graphics

NASA Technical Reports Server (NTRS)

Biffle, J.; Sumlin, H. A.

1975-01-01

The application of computer interactive graphics to three-dimensional structural analysis was described, with emphasis on the following aspects: (1) structural analysis, and (2) generation and checking of input data and examination of the large volume of output data (stresses, displacements, velocities, accelerations). Handling of three-dimensional input processing with a special MESH3D computer program was explained. Similarly, a special code PLTZ may be used to perform all the needed tasks for output processing from a finite element code. Examples were illustrated.

Three-Dimensional Mapping of Atmospheric Boundary Layer Structure and Winds with a High Performance Lidar

DTIC Science & Technology

1991-04-01

convective plumes which originate from the surface through solar heating. Unlike tower, sodar, and airplane measurements, lidar can provide essentially...average spacing between these bands is given by Xmax. The determination of Xma is complicated by the fact that the two-dimensional spectral power...eddy which results depends critically on the choice of the indicator function (Marht and Frank, 1988). This is due to the fact that the measurement

Two- and Three-Dimensional Probes of Parity in Primordial Gravity Waves.

PubMed

Masui, Kiyoshi Wesley; Pen, Ue-Li; Turok, Neil

2017-06-02

We show that three-dimensional information is critical to discerning the effects of parity violation in the primordial gravity-wave background. If present, helical gravity waves induce parity-violating correlations in the cosmic microwave background (CMB) between parity-odd polarization B modes and parity-even temperature anisotropies (T) or polarization E modes. Unfortunately, EB correlations are much weaker than would be naively expected, which we show is due to an approximate symmetry resulting from the two-dimensional nature of the CMB. The detectability of parity-violating correlations is exacerbated by the fact that the handedness of individual modes cannot be discerned in the two-dimensional CMB, leading to a noise contribution from scalar matter perturbations. In contrast, the tidal imprints of primordial gravity waves fossilized into the large-scale structure of the Universe are a three-dimensional probe of parity violation. Using such fossils the handedness of gravity waves may be determined on a mode-by-mode basis, permitting future surveys to probe helicity at the percent level if the amplitude of primordial gravity waves is near current observational upper limits.

Highly cytocompatible and flexible three-dimensional graphene/polydimethylsiloxane composite for culture and electrochemical detection of L929 fibroblast cells.

PubMed

Waiwijit, Uraiwan; Maturos, Thitima; Pakapongpan, Saithip; Phokharatkul, Ditsayut; Wisitsoraat, Anurat; Tuantranont, Adisorn

2016-08-01

Recently, three-dimensional graphene interconnected network has attracted great interest as a scaffold structure for tissue engineering due to its high biocompatibility, high electrical conductivity, high specific surface area and high porosity. However, free-standing three-dimensional graphene exhibits poor flexibility and stability due to ease of disintegration during processing. In this work, three-dimensional graphene is composited with polydimethylsiloxane to improve the structural flexibility and stability by a new simple two-step process comprising dip coating of polydimethylsiloxane on chemical vapor deposited graphene/Ni foam and wet etching of nickel foam. Structural characterizations confirmed an interconnected three-dimensional multi-layer graphene structure with thin polydimethylsiloxane scaffold. The composite was employed as a substrate for culture of L929 fibroblast cells and its cytocompatibility was evaluated by cell viability (Alamar blue assay), reactive oxygen species production and vinculin immunofluorescence imaging. The result revealed that cell viability on three-dimensional graphene/polydimethylsiloxane composite increased with increasing culture time and was slightly different from a polystyrene substrate (control). Moreover, cells cultured on three-dimensional graphene/polydimethylsiloxane composite generated less ROS than the control at culture times of 3-6 h. The results of immunofluorescence staining demonstrated that fibroblast cells expressed adhesion protein (vinculin) and adhered well on three-dimensional graphene/polydimethylsiloxane surface. Good cell adhesion could be attributed to suitable surface properties of three-dimensional graphene/polydimethylsiloxane with moderate contact angle and small negative zeta potential in culture solution. The results of electrochemical study by cyclic voltammetry showed that an oxidation current signal with no apparent peak was induced by fibroblast cells and the oxidation current at an oxidation potential of +0.9 V increased linearly with increasing cell number. Therefore, the three-dimensional graphene/polydimethylsiloxane composite exhibits high cytocompatibility and can potentially be used as a conductive substrate for cell-based electrochemical sensing. © The Author(s) 2016.

Spitting cobras: fluid jets in nature as models for technical applications

NASA Astrophysics Data System (ADS)

Balmert, Alexander; Hess, David; Brücker, Christoph; Bleckmann, Horst; Westhoff, Guido

2011-04-01

Spitting cobras defend themselves by ejecting rapid jets of venom through their fangs towards the face of an offender. To generate these jets, the venom delivery system of spitting cobras has some unique adaptations, such as prominent ridges on the surface of the venom channel. We examined the fluid acceleration mechanisms in three spitting cobra species of the genus Naja. To investigate the liquid-flow through the venom channel we built a three-dimensional 60:1 scale model. First we determined the three-dimensional structure of the channel by using microcomputer tomography. With help of the micro computer tomographical data we then created a negative form out of wax. Finally, silicon was casted around the wax form and the wax removed, resulting in a completely transparent model of the cobrás venom channel. The physical-chemical properties of the cobra venom were measured by micro rheometry and tensiometry. Thereafter, an artificial fluid with similar properties was generated. Particle image velocimetry (PIV) was performed to visualize the flow of the artificial liquid in the three-dimensional model. Our experiments show how the surface structure of the venom channel determines the liquid flow through the channel and ultimately the form of the liquid jet. Understanding the biological mechanisms of venom ejection helps to enhance industrial processes such as water jet cutting and cleaning as well as injection methods in technical and medical sectors, e.g. liquid microjet dissection in microsurgery.

Relationships between convective storms and their environment in AVE IV determined from a three-dimensional subsynoptic-scale, trajectory model

NASA Technical Reports Server (NTRS)

Wilson, G. S.

1977-01-01

The paper describes interrelationships between synoptic-scale and convective-scale systems obtained by following individual air parcels as they traveled within the convective storm environment of AVE IV. (NASA's fourth Atmospheric Variability Experiment, AVE IV, was a 36-hour study in April 1975 of the atmospheric variability and structure in regions of convective storms.) A three-dimensional trajectory model was used to calculate parcel paths, and manually digitized radar was employed to locate convective activity of various intensities and to determine those trajectories that traversed the storm environment. Spatial and temporal interrelationships are demonstrated by reference to selected time periods of AVE IV which contain the development and movement of the squall line in which the Neosho tornado was created.

A new antibacterial silver(I) complex incorporating 2,5-dimethylpyrazine and the anti-inflammatory diclofenac.

PubMed

Hamamci Alisir, Sevim; Dege, Necmi

2016-12-01

Ag I -containing coordination complexes have attracted attention because of their photoluminescence properties and antimicrobial activities and, in principle, these properties depend on the nature of the structural topologies. A novel two-dimensional silver(I) complex with the anti-inflammatory diclofenac molecule, namely bis{μ-2-[2-(2,6-dichloroanilino)phenyl]acetato-κ 3 O,O':O}bis(μ-2,5-dimethylpyrazine-κ 2 N:N')silver(I), [Ag 2 (C 14 H 10 Cl 2 NO 2 ) 2 (C 6 H 8 N 2 )] n , (I), has been synthesized and characterized by single-crystal X-ray diffraction, revealing that the Ag I ions are chelated by the carboxylate groups of the anionic 2-[2-(2,6-dichloroanilino)phenyl]acetate (dicl) ligand in a μ 3 -η 1 :η 2 coordination mode. Each dicl ligand links three Ag I atoms to generate a one-dimensional infinite chain. Adjacent chains are connected through 2,5-dimethylpyrazine (dmpyz) ligands to form a two-dimensional layer structure parallel to the crystallographic bc plane. The layers are further connected by C-H...π interactions to generate a three-dimensional supramolecular structure. Additionally, the most striking feature is that the structure contains an intramolecular C-H ...Ag anagostic interaction. Furthermore, the title complex has been tested for its in vitro antibacterial activity and is determined to be highly effective on the studied microorganisms.

Label-free imaging of the dynamics of cell-to-cell string-like structure bridging in the free-space by low-coherent quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Yamauchi, Toyohiko; Iwai, Hidenao; Yamashita, Yutaka

2013-03-01

We succeeded in utilizing our low-coherent quantitative phase microscopy (LC-QPM) to achieve label-free and three-dimensional imaging of string-like structures bridging the free-space between live cells. In past studies, three dimensional morphology of the string-like structures between cells had been investigated by electron microscopies and fluorescence microscopies and these structures were called "membrane nanotubes" or "tunneling nanotubes." However, use of electron microscopy inevitably kills these cells and fluorescence microscopy is itself a potentially invasive method. To achieve noninvasive imaging of live cells, we applied our LC-QPM which is a reflection-type, phase resolved and full-field interference microscope employing a low-coherent light source. LC-QPM is able to visualize the three-dimensional morphology of live cells without labeling by means of low-coherence interferometry. The lateral (diffraction limit) and longitudinal (coherence-length) spatial resolution of LC-QPM were respectively 0.49 and 0.93 micrometers and the repeatability of the phase measurement was 0.02 radians (1.0 nm). We successfully obtained three-dimensional morphology of live cultured epithelial cells (cell type: HeLa, derived from cervix cancer) and were able to clearly observe the individual string-like structures interconnecting the cells. When we performed volumetric imaging, a 80 micrometer by 60 micrometer by 6.5 micrometer volume was scanned every 5.67 seconds and 70 frames of a three-dimensional movie were recorded for a duration of 397 seconds. Moreover, the optical phase images gave us detailed information about the three-dimensional morphology of the string-like structure at sub-wavelength resolution. We believe that our LC-QPM will be a useful tool for the study of three-dimensional morphology of live cells.

Advances in high-resolution imaging--techniques for three-dimensional imaging of cellular structures.

PubMed

Lidke, Diane S; Lidke, Keith A

2012-06-01

A fundamental goal in biology is to determine how cellular organization is coupled to function. To achieve this goal, a better understanding of organelle composition and structure is needed. Although visualization of cellular organelles using fluorescence or electron microscopy (EM) has become a common tool for the cell biologist, recent advances are providing a clearer picture of the cell than ever before. In particular, advanced light-microscopy techniques are achieving resolutions below the diffraction limit and EM tomography provides high-resolution three-dimensional (3D) images of cellular structures. The ability to perform both fluorescence and electron microscopy on the same sample (correlative light and electron microscopy, CLEM) makes it possible to identify where a fluorescently labeled protein is located with respect to organelle structures visualized by EM. Here, we review the current state of the art in 3D biological imaging techniques with a focus on recent advances in electron microscopy and fluorescence super-resolution techniques.

Life in the fast lane for protein crystallization and X-ray crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2005-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high-rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today's high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Life in the Fast Lane for Protein Crystallization and X-Ray Crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Liu, Zhi-Jie; Tempel, Wolfram; Praissman, Jeremy; Lin, Dawei; Wang, Bi-Cheng; Gavira, Jose A.; Ng, Joseph D.

2004-01-01

The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained easily are studied. Consequently, an astonishing number of genomic proteins remain unexamined. In the era of high-throughput processes, traditional methods in molecular biology, protein chemistry and crystallization are eclipsed by automation and pipeline practices. The necessity for high rate production of protein crystals and structures has prevented the usage of more intellectual strategies and creative approaches in experimental executions. Fundamental principles and personal experiences in protein chemistry and crystallization are minimally exploited only to obtain "low-hanging fruit" protein structures. We review the practical aspects of today s high-throughput manipulations and discuss the challenges in fast pace protein crystallization and tools for crystallography. Structural genomic pipelines can be improved with information gained from low-throughput tactics that may help us reach the higher-bearing fruits. Examples of recent developments in this area are reported from the efforts of the Southeast Collaboratory for Structural Genomics (SECSG).

Three-dimensional structure of an antibody-antigen complex.

PubMed

Sheriff, S; Silverton, E W; Padlan, E A; Cohen, G H; Smith-Gill, S J; Finzel, B C; Davies, D R

1987-11-01

We have determined the three-dimensional structure of two crystal forms of an antilysozyme Fab-lysozyme complex by x-ray crystallography. The epitope on lysozyme consists of three sequentially separated subsites, including one long, nearly continuous, site from Gln-41 through Tyr-53 and one from Gly-67 through Pro-70. Antibody residues interacting with lysozyme occur in each of the six complementarity-determining regions and also include one framework residue. Arg-45 and Arg-68 form a ridge on the surface of lysozyme, which binds in a groove on the antibody surface. Otherwise the surface of interaction between the two proteins is relatively flat, although it curls at the edges. The surface of interaction is approximately 26 X 19 A. No water molecules are found in the interface. The positive charge on the two arginines is complemented by the negative charge of Glu-35 and Glu-50 from the heavy chain of the antibody. The backbone structure of the antigen, lysozyme, is mostly unperturbed, although there are some changes in the epitope region, most notably Pro-70. One side chain not in the epitope, Trp-63, undergoes a rotation of approximately 180 degrees about the C beta--C gamma bond. The Fab elbow bends in the two crystal forms differ by 7 degrees.

Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.

PubMed

Nannenga, Brent L; Iadanza, Matthew G; Vollmar, Breanna S; Gonen, Tamir

2013-01-01

Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

Three-dimensional structure-activity relationship modeling of cocaine binding to two monoclonal antibodies by comparative molecular field analysis.

PubMed

Paula, Stefan; Tabet, Michael R; Keenan, Susan M; Welsh, William J; Ball, W James

2003-01-17

Successful immunotherapy of cocaine addiction and overdoses requires cocaine-binding antibodies with specific properties, such as high affinity and selectivity for cocaine. We have determined the affinities of two cocaine-binding murine monoclonal antibodies (mAb: clones 3P1A6 and MM0240PA) for cocaine and its metabolites by [3H]-radioligand binding assays. mAb 3P1A6 (K(d) = 0.22 nM) displayed a 50-fold higher affinity for cocaine than mAb MM0240PA (K(d) = 11 nM) and also had a greater specificity for cocaine. For the systematic exploration of both antibodies' binding specificities, we used a set of approximately 35 cocaine analogues as structural probes by determining their relative binding affinities (RBAs) using an enzyme-linked immunosorbent competition assay. Three-dimensional quantitative structure-activity relationship (3D-QSAR) models on the basis of comparative molecular field analysis (CoMFA) techniques correlated the binding data with structural features of the ligands. The analysis indicated that despite the mAbs' differing specificities for cocaine, the relative contributions of the steric (approximately 80%) and electrostatic (approximately 20%) field interactions to ligand-binding were similar. Generated three-dimensional CoMFA contour plots then located the specific regions about cocaine where the ligand/receptor interactions occurred. While the overall binding patterns of the two mAbs had many features in common, distinct differences were observed about the phenyl ring and the methylester group of cocaine. Furthermore, using previously published data, a 3D-QSAR model was developed for cocaine binding to the dopamine reuptake transporter (DAT) that was compared to the mAb models. Although the relative steric and electrostatic field contributions were similar to those of the mAbs, the DAT cocaine-binding site showed a preference for negatively charged ligands. Besides establishing molecular level insight into the interactions that govern cocaine binding specificity by biopolymers, the three-dimensional images obtained reflect the properties of the mAbs binding pockets and provide the initial information needed for the possible design of novel antibodies with properties optimized for immunotherapy. Copyright 2003 Elsevier Science Ltd.

Ameba-like diffusion in two-dimensional polymer melts: how critical exponents determine the structural relaxation

NASA Astrophysics Data System (ADS)

Kreer, Torsten; Meyer, Hendrik; Baschnagel, Joerg

2008-03-01

By means of numerical investigations we demonstrate that the structural relaxation of linear polymers in two dimensional (space-filling) melts is characterized by ameba-like diffusion, where the chains relax via frictional dissipation at their interfacial contact lines. The perimeter length of the contact line determines a new length scale, which does not exist in three dimensions. We show how this length scale follows from the critical exponents, which hence characterize not only the static but also the dynamic properties of the melt. Our data is in agreement with recent theoretical predictions, concerning the time-dependence of single-monomer mean-square displacements and the scaling of concomitant relaxation times with the degree of polymerization. For the latter we demonstrate a density crossover-scaling as an additional test for ameba-like relaxation. We compare our results to the conceptually different Rouse model, which predicts numerically close exponents. Our data can clearly rule out the classical picture as the relevant relaxation mechanism in two-dimensional polymer melts.

Development of a thermal and structural analysis procedure for cooled radial turbines

NASA Technical Reports Server (NTRS)

Kumar, Ganesh N.; Deanna, Russell G.

1988-01-01

A procedure for computing the rotor temperature and stress distributions in a cooled radial turbine are considered. Existing codes for modeling the external mainstream flow and the internal cooling flow are used to compute boundary conditions for the heat transfer and stress analysis. The inviscid, quasi three dimensional code computes the external free stream velocity. The external velocity is then used in a boundary layer analysis to compute the external heat transfer coefficients. Coolant temperatures are computed by a viscous three dimensional internal flow cade for the momentum and energy equation. These boundary conditions are input to a three dimensional heat conduction code for the calculation of rotor temperatures. The rotor stress distribution may be determined for the given thermal, pressure and centrifugal loading. The procedure is applied to a cooled radial turbine which will be tested at the NASA Lewis Research Center. Representative results are given.

Gain in three-dimensional metamaterials utilizing semiconductor quantum structures

NASA Astrophysics Data System (ADS)

Schwaiger, Stephan; Klingbeil, Matthias; Kerbst, Jochen; Rottler, Andreas; Costa, Ricardo; Koitmäe, Aune; Bröll, Markus; Heyn, Christian; Stark, Yuliya; Heitmann, Detlef; Mendach, Stefan

2011-10-01

We demonstrate gain in a three-dimensional metal/semiconductor metamaterial by the integration of optically active semiconductor quantum structures. The rolling-up of a metallic structure on top of strained semiconductor layers containing a quantum well allows us to achieve a tightly bent superlattice consisting of alternating layers of lossy metallic and amplifying gain material. We show that the transmission through the superlattice can be enhanced by exciting the quantum well optically under both pulsed or continuous wave excitation. This points out that our structures can be used as a starting point for arbitrary three-dimensional metamaterials including gain.

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

PubMed

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2013-10-01

Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. Copyright © 2013 Elsevier Inc. All rights reserved.

The Structure Lacuna

PubMed Central

Boeyens, Jan C.A.; Levendis, Demetrius C.

2012-01-01

Molecular symmetry is intimately connected with the classical concept of three-dimensional molecular structure. In a non-classical theory of wave-like interaction in four-dimensional space-time, both of these concepts and traditional quantum mechanics lose their operational meaning, unless suitably modified. A required reformulation should emphasize the importance of four-dimensional effects like spin and the symmetry effects of space-time curvature that could lead to a fundamentally different understanding of molecular symmetry and structure in terms of elementary number theory. Isolated single molecules have no characteristic shape and macro-biomolecules only develop robust three-dimensional structure in hydrophobic response to aqueous cellular media. PMID:22942753

Measurement of 3-D Vibrational Motion by Dynamic Photogrammetry Using Least-Square Image Matching for Sub-Pixel Targeting to Improve Accuracy.

PubMed

Lee, Hyoseong; Rhee, Huinam; Oh, Jae Hong; Park, Jin Ho

2016-03-11

This paper deals with an improved methodology to measure three-dimensional dynamic displacements of a structure by digital close-range photogrammetry. A series of stereo images of a vibrating structure installed with targets are taken at specified intervals by using two daily-use cameras. A new methodology is proposed to accurately trace the spatial displacement of each target in three-dimensional space. This method combines the correlation and the least-square image matching so that the sub-pixel targeting can be obtained to increase the measurement accuracy. Collinearity and space resection theory are used to determine the interior and exterior orientation parameters. To verify the proposed method, experiments have been performed to measure displacements of a cantilevered beam excited by an electrodynamic shaker, which is vibrating in a complex configuration with mixed bending and torsional motions simultaneously with multiple frequencies. The results by the present method showed good agreement with the measurement by two laser displacement sensors. The proposed methodology only requires inexpensive daily-use cameras, and can remotely detect the dynamic displacement of a structure vibrating in a complex three-dimensional defection shape up to sub-pixel accuracy. It has abundant potential applications to various fields, e.g., remote vibration monitoring of an inaccessible or dangerous facility.

Measurement of 3-D Vibrational Motion by Dynamic Photogrammetry Using Least-Square Image Matching for Sub-Pixel Targeting to Improve Accuracy

PubMed Central

Lee, Hyoseong; Rhee, Huinam; Oh, Jae Hong; Park, Jin Ho

2016-01-01

This paper deals with an improved methodology to measure three-dimensional dynamic displacements of a structure by digital close-range photogrammetry. A series of stereo images of a vibrating structure installed with targets are taken at specified intervals by using two daily-use cameras. A new methodology is proposed to accurately trace the spatial displacement of each target in three-dimensional space. This method combines the correlation and the least-square image matching so that the sub-pixel targeting can be obtained to increase the measurement accuracy. Collinearity and space resection theory are used to determine the interior and exterior orientation parameters. To verify the proposed method, experiments have been performed to measure displacements of a cantilevered beam excited by an electrodynamic shaker, which is vibrating in a complex configuration with mixed bending and torsional motions simultaneously with multiple frequencies. The results by the present method showed good agreement with the measurement by two laser displacement sensors. The proposed methodology only requires inexpensive daily-use cameras, and can remotely detect the dynamic displacement of a structure vibrating in a complex three-dimensional defection shape up to sub-pixel accuracy. It has abundant potential applications to various fields, e.g., remote vibration monitoring of an inaccessible or dangerous facility. PMID:26978366

Atomic structure of unligated laccase from Cerrena maxima at 1.76 A with molecular oxygen and hydrogen peroxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhukova, Yu. N., E-mail: amm@ns.crys.ras.ru; Lyashenko, A. V.; Lashkov, A. A.

2010-05-15

The three-dimensional structure of unligated laccase from Cerrena maxima was established by X-ray diffraction at 1.76-A resolution; R{sub work} = 18.07%, R{sub free} = 21.71%, rmsd of bond lengths, bond angles, and chiral angles are 0.008 A, 1.19{sup o}, and 0.077{sup o}, respectively. The coordinate error for the refined structure estimated from the Luzzati plot is 0.195 A. The maximum average error in the atomic coordinates is 0.047 A. A total of 99.4% of amino-acid residues of the polypeptide chain are in the most favorable, allowable, and accessible regions of the Ramachandran plot. The three-dimensional structures of the complexes ofmore » laccase from C. maxima with molecular oxygen and hydrogen peroxide were determined by the molecular simulation. These data provide insight into the structural aspect of the mechanism of the enzymatic cycle. The structure factors and the refined atomic coordinates were deposited in the Protein Data Bank (PDB-ID code is 3DIV).« less

The relationship between amplitude modulation, coherent structure and critical layers in wall turbulence

NASA Astrophysics Data System (ADS)

McKeon, Beverley

2015-11-01

The importance of critical layers in determining aspects of the structure of wall turbulence is discussed. We have shown (Jacobi & McKeon, 2013) that the amplitude modulation coefficient investigated most recently by Hutchins & Marusic (2007) and co-authors, which describes the correlation between large scales above a (spatial) wavelength filter with the envelope of small scales below the filter, is dominated by very large scale motion (VLSM) at a single wavelength. The resolvent analysis of McKeon & Sharma (2010) gives a suitable model for the three-dimensional, three-component form of the VLSM and energetic structure at other wavelengths. This model is used to identify the three-dimensional spatial variation of instantaneous critical layers in the presence of a mean velocity profile and to relate this to earlier observations of coherent structure in unperturbed flows (both experimental and via the resolvent model, Sharma & McKeon, 2013); to the phase relationships between scales identified by Chung & McKeon (2010, 2014); and to the structure of wall turbulence that has been modified by the addition of single synthetic scales, e.g. Jacobi & McKeon (2011), Duvvuri & McKeon (2015). The support of AFOSR under grant number FA 9550-12-1-0469 is gratefully acknowledged.

Synthesis, structure determination and properties of MIL-53as and MIL-53ht: the first CrIII hybrid inorganic-organic microporous solids: CrIII(OH).(O2C-C6H4-CO2).(HO2C-C6H4-CO2H)x.

PubMed

Millange, Franck; Serre, Christian; Férey, Gérard

2002-04-21

The first three-dimensional chromium(III) dicarboxylate compounds have been isolated and their structures solved from powder X-ray diffraction data; the flexible framework of these materials delimits large pores.

The Juno Mission to Jupiter

NASA Technical Reports Server (NTRS)

Grammier, Richard S.

2006-01-01

Origin: Determine O/H ratio (water abundance) and constrain core mass to decide among alternative theories of origin. Interior: Understand Jupiter's interior structure and dynamical properties by mapping its gravitational and magnetic fields Atmosphere: Map variations in atmospheric composition, temperature, cloud opacity and dynamics to depths greater than 100 bars at all latitudes. Magnetosphere: Characterize and explore the three-dimensional structure of Jupiter's polar magnetosphere and auroras.

Analytical investigation of a three-dimensional FRP-retrofitted reinforced concrete structure's behaviour under earthquake load effect in ANSYS program

NASA Astrophysics Data System (ADS)

Altun, F.; Birdal, F.

2012-12-01

In this study, a 1:3 scaled, three-storey, FRP (Fiber Reinforced Polymer) retrofitted reinforced concrete model structure whose behaviour and crack development were identified experimentally in the laboratory was investigated analytically. Determination of structural behaviour under earthquake load is only possible in a laboratory environment with a specific scale, as carrying out structural experiments is difficult due to the evaluation of increased parameter numbers and because it requires an expensive laboratory setup. In an analytical study, structure was modelled using ANSYS Finite Element Package Program (2007), and its behaviour and crack development were revealed. When experimental difficulties are taken into consideration, analytical investigation of structure behaviour is more economic and much faster. At the end of the study, experimental results of structural behaviour and crack development were compared with analytical data. It was concluded that in a model structure retrofitted with FRP, the behaviour and cracking model can be determined without testing by determining the reasons for the points where analytical results are not converged with experimental data. Better understanding of structural behaviour is analytically enabled with the study.

Mathematical methods for protein science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hart, W.; Istrail, S.; Atkins, J.

1997-12-31

Understanding the structure and function of proteins is a fundamental endeavor in molecular biology. Currently, over 100,000 protein sequences have been determined by experimental methods. The three dimensional structure of the protein determines its function, but there are currently less than 4,000 structures known to atomic resolution. Accordingly, techniques to predict protein structure from sequence have an important role in aiding the understanding of the Genome and the effects of mutations in genetic disease. The authors describe current efforts at Sandia to better understand the structure of proteins through rigorous mathematical analyses of simple lattice models. The efforts have focusedmore » on two aspects of protein science: mathematical structure prediction, and inverse protein folding.« less

Structure and Dynamics of the Solar Corona

NASA Technical Reports Server (NTRS)

Schnack, D. D.

1994-01-01

Advanced computational techniques were used to study solar coronal heating and coronal mass ejections. A three dimensional, time dependent resistive magnetohydrodynamic code was used to study the dynamic response of a model corona to continuous, slow, random magnetic footpoint displacements in the photosphere. Three dimensional numerical simulations of the response of the corona to simple smooth braiding flows in the photosphere were calculated to illustrate and understand the spontaneous formation of current filaments. Two dimensional steady state helmet streamer configurations were obtained by determining the time asymptotic state of the interaction of an initially one dimensinal transponic solar wind with a spherical potential dipole field. The disruption of the steady state helmet streamer configuration was studied as a response to shearing of the magnetic footpoints of the closed field lines under the helmet.

NMR and computational methods applied to the 3- dimensional structure determination of DNA and ligand-DNA complexes in solution

NASA Astrophysics Data System (ADS)

Smith, Jarrod Anson

2D homonuclear 1H NMR methods and restrained molecular dynamics (rMD) calculations have been applied to determining the three-dimensional structures of DNA and minor groove-binding ligand-DNA complexes in solution. The structure of the DNA decamer sequence d(GCGTTAACGC)2 has been solved both with a distance-based rMD protocol and an NOE relaxation matrix backcalculation-based protocol in order to probe the relative merits of the different refinement methods. In addition, three minor groove binding ligand-DNA complexes have been examined. The solution structure of the oligosaccharide moiety of the antitumor DNA scission agent calicheamicin γ1I has been determined in complex with a decamer duplex containing its high affinity 5'-TCCT- 3' binding sequence. The structure of the complex reinforces the belief that the oligosaccharide moiety is responsible for the sequence selective minor-groove binding activity of the agent, and critical intermolecular contacts are revealed. The solution structures of both the (+) and (-) enantiomers of the minor groove binding DNA alkylating agent duocarmycin SA have been determined in covalent complex with the undecamer DNA duplex d(GACTAATTGTC).d(GAC AATTAGTC). The results support the proposal that the alkylation activity of the duocarmycin antitumor antibiotics is catalyzed by a binding-induced conformational change in the ligand which activates the cyclopropyl group for reaction with the DNA. Comparisons between the structures of the two enantiomers covalently bound to the same DNA sequence at the same 5'-AATTA-3 ' site have provided insight into the binding orientation and site selectivity, as well as the relative rates of reactivity of these two agents.

Novel Three-Dimensional Interphase Characterisation of Polymer Nanocomposites Using Nanoscaled Topography.

PubMed

Mousa, Mohanad; Dong, Yu

2018-06-19

Mechanical properties of polymer nanocomposites depend primarily on nanointerphases as transitional zones between nanoparticles and surrounding matrices. Due to the difficulty in the quantitative characterisation of nanointerphases, previous literatures generally deemed such interphases as one-dimensional uniform zones around nanoparticles by assumption for analytical or theoretical modelling. We hereby have demonstrated for the first time direct three-dimensional topography and physical measurement of nanophase mechanical properties between nanodimeter bamboo charcoals (NBCs) and poly (vinyl alcohol) (PVA) in polymer nanocomposites. Topographical features, nanomechanical properties and dimensions of nanointerphases were systematically determined via peak force quantitative nanomechanical tapping mode (PFQNM). Significantly different mechanical properties of nanointerphases were revealed as opposed to those of individual NBCs and PVA matrices. Non-uniform irregular three-dimensional structures and shapes of nanointerphases are manifested around individual NBCs, which can be greatly influenced by nanoparticle size and roughness, and nanoparticle dispersion and distribution. Elastic moduli of nanointerphases were experimentally determined in range from 25.32 ±3.4 to 66.3±3.2 GPa. Additionally, it is clearly shown that the interphase modulus strongly depends on interphase surface area SAInterphase and interphase volume VInterphase. Different NBC distribution patterns from fully to partially embedded nanoparticles are proven to yield a remarkable reduction in elastic moduli of nanointerphases. © 2018 IOP Publishing Ltd.

Structure of the putative 32 kDa myrosinase-binding protein from Arabidopsis (At3g16450.1) determined by SAIL-NMR.

PubMed

Takeda, Mitsuhiro; Sugimori, Nozomi; Torizawa, Takuya; Terauchi, Tsutomu; Ono, Akira M; Yagi, Hirokazu; Yamaguchi, Yoshiki; Kato, Koichi; Ikeya, Teppei; Jee, Jungoo; Güntert, Peter; Aceti, David J; Markley, John L; Kainosho, Masatsune

2008-12-01

The product of gene At3g16450.1 from Arabidopsis thaliana is a 32 kDa, 299-residue protein classified as resembling a myrosinase-binding protein (MyroBP). MyroBPs are found in plants as part of a complex with the glucosinolate-degrading enzyme myrosinase, and are suspected to play a role in myrosinase-dependent defense against pathogens. Many MyroBPs and MyroBP-related proteins are composed of repeated homologous sequences with unknown structure. We report here the three-dimensional structure of the At3g16450.1 protein from Arabidopsis, which consists of two tandem repeats. Because the size of the protein is larger than that amenable to high-throughput analysis by uniform (13)C/(15)N labeling methods, we used stereo-array isotope labeling (SAIL) technology to prepare an optimally (2)H/(13)C/(15)N-labeled sample. NMR data sets collected using the SAIL protein enabled us to assign (1)H, (13)C and (15)N chemical shifts to 95.5% of all atoms, even at a low concentration (0.2 mm) of protein product. We collected additional NOESY data and determined the three-dimensional structure using the cyana software package. The structure, the first for a MyroBP family member, revealed that the At3g16450.1 protein consists of two independent but similar lectin-fold domains, each composed of three beta-sheets.

Slip as the basic mechanism for formation of deformation relief structural elements

NASA Astrophysics Data System (ADS)

Lychagin, D. V.; Alfyorova, E. A.

2017-07-01

The experimental results of investigation of the nickel single crystal surface morphology after compression deformation are presented. The quasi-periodic character of the deformation profile, common for shear deformation of different types of relief structural elements, is found. It is demonstrated that the morphological manifestation of these structural elements is determined by local shear systems along octahedral planes. The regularities of the deformation structure in these regions defining the material extrusion and intrusion regions and the specific features of disorientation accumulation are established. If reorientation of local regions takes part in the relief element formation, along with octahedral slip, much stronger growth of the surface area is observed. The possibility of application of two-dimensional and three-dimensional surface roughness parameters for description of deformation relief is considered.

Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing.

PubMed

Adhikari, Badri; Trieu, Tuan; Cheng, Jianlin

2016-11-07

Reconstructing three-dimensional structures of chromosomes is useful for visualizing their shapes in a cell and interpreting their function. In this work, we reconstruct chromosomal structures from Hi-C data by translating contact counts in Hi-C data into Euclidean distances between chromosomal regions and then satisfying these distances using a structure reconstruction method rigorously tested in the field of protein structure determination. We first evaluate the robustness of the overall reconstruction algorithm on noisy simulated data at various levels of noise by comparing with some of the state-of-the-art reconstruction methods. Then, using simulated data, we validate that Spearman's rank correlation coefficient between pairwise distances in the reconstructed chromosomal structures and the experimental chromosomal contact counts can be used to find optimum conversion rules for transforming interaction frequencies to wish distances. This strategy is then applied to real Hi-C data at chromosome level for optimal transformation of interaction frequencies to wish distances and for ranking and selecting structures. The chromosomal structures reconstructed from a real-world human Hi-C dataset by our method were validated by the known two-compartment feature of the human chromosome organization. We also show that our method is robust with respect to the change of the granularity of Hi-C data, and consistently produces similar structures at different chromosomal resolutions. Chromosome3D is a robust method of reconstructing chromosome three-dimensional models using distance restraints obtained from Hi-C interaction frequency data. It is available as a web application and as an open source tool at http://sysbio.rnet.missouri.edu/chromosome3d/ .

An initial investigation into methods of computing transonic aerodynamic sensitivity coefficients

NASA Technical Reports Server (NTRS)

Carlson, Leland A.

1994-01-01

The primary accomplishments of the project are as follows: (1) Using the transonic small perturbation equation as a flowfield model, the project demonstrated that the quasi-analytical method could be used to obtain aerodynamic sensitivity coefficients for airfoils at subsonic, transonic, and supersonic conditions for design variables such as Mach number, airfoil thickness, maximum camber, angle of attack, and location of maximum camber. It was established that the quasi-analytical approach was an accurate method for obtaining aerodynamic sensitivity derivatives for airfoils at transonic conditions and usually more efficient than the finite difference approach. (2) The usage of symbolic manipulation software to determine the appropriate expressions and computer coding associated with the quasi-analytical method for sensitivity derivatives was investigated. Using the three dimensional fully conservative full potential flowfield model, it was determined that symbolic manipulation along with a chain rule approach was extremely useful in developing a combined flowfield and quasi-analytical sensitivity derivative code capable of considering a large number of realistic design variables. (3) Using the three dimensional fully conservative full potential flowfield model, the quasi-analytical method was applied to swept wings (i.e. three dimensional) at transonic flow conditions. (4) The incremental iterative technique has been applied to the three dimensional transonic nonlinear small perturbation flowfield formulation, an equivalent plate deflection model, and the associated aerodynamic and structural discipline sensitivity equations; and coupled aeroelastic results for an aspect ratio three wing in transonic flow have been obtained.

Towards Automated Screening of Two-dimensional Crystals

PubMed Central

Cheng, Anchi; Leung, Albert; Fellmann, Denis; Quispe, Joel; Suloway, Christian; Pulokas, James; Carragher, Bridget; Potter, Clinton S.

2007-01-01

Screening trials to determine the presence of two-dimensional (2D) protein crystals suitable for three-dimensional structure determination using electron crystallography is a very labor-intensive process. Methods compatible with fully automated screening have been developed for the process of crystal production by dialysis and for producing negatively stained grids of the resulting trials. Further automation via robotic handling of the EM grids, and semi-automated transmission electron microscopic imaging and evaluation of the trial grids is also possible. We, and others, have developed working prototypes for several of these tools and tested and evaluated them in a simple screen of 24 crystallization conditions. While further development of these tools is certainly required for a turn-key system, the goal of fully automated screening appears to be within reach. PMID:17977016

Rational Protein Engineering Guided by Deep Mutational Scanning

PubMed Central

Shin, HyeonSeok; Cho, Byung-Kwan

2015-01-01

Sequence–function relationship in a protein is commonly determined by the three-dimensional protein structure followed by various biochemical experiments. However, with the explosive increase in the number of genome sequences, facilitated by recent advances in sequencing technology, the gap between protein sequences available and three-dimensional structures is rapidly widening. A recently developed method termed deep mutational scanning explores the functional phenotype of thousands of mutants via massive sequencing. Coupled with a highly efficient screening system, this approach assesses the phenotypic changes made by the substitution of each amino acid sequence that constitutes a protein. Such an informational resource provides the functional role of each amino acid sequence, thereby providing sufficient rationale for selecting target residues for protein engineering. Here, we discuss the current applications of deep mutational scanning and consider experimental design. PMID:26404267

Skeletal Structural Consequences of Reduced Gravity Environments

NASA Technical Reports Server (NTRS)

Ruff, Christropher B.

1999-01-01

The overall goal of this project is to provide structurally meaningful data on bone loss after exposure to reduced gravity environments so that more precise estimates of fracture risk and the effectiveness of countermeasures in reducing fracture risk can be developed. The project has three major components: (1) measure structural changes in the limb bones of rats subjected to complete and partial nonweightbearing, with and without treatment with ibandronate and periodic full weightbearing; (2) measure structural changes in the limb bones of human bedrest subjects, with and without treatment with alendronate and resistive exercise, and Russian cosmonauts flying on the Mir Space Station; and (3) validate and extend the 2-dimensional structural analyses currently possible in the second project component (bedrest and Mir subjects) using 3-dimensional finite element modeling techniques, and determine actual fracture-producing loads on earth and in space.

Suitability of a three-dimensional model to measure empathy and its relationship with social and normative adjustment in Spanish adolescents: a cross-sectional study

PubMed Central

Gómez-Ortiz, Olga; Ortega-Ruiz, Rosario; Jolliffe, Darrick; Romera, Eva M.

2017-01-01

Objectives (1) To examine the psychometric properties of the Basic Empathy Scale (BES) with Spanish adolescents, comparing a two and a three-dimensional structure;(2) To analyse the relationship between the three-dimensional empathy and social and normative adjustment in school. Design Transversal and ex post facto retrospective study. Confirmatory factorial analysis, multifactorial invariance analysis and structural equations models were used. Participants 747 students (51.3% girls) from Cordoba, Spain, aged 12–17 years (M=13.8; SD=1.21). Results The original two-dimensional structure was confirmed (cognitive empathy, affective empathy), but a three-dimensional structure showed better psychometric properties, highlighting the good fit found in confirmatory factorial analysis and adequate internal consistent valued, measured with Cronbach’s alpha and McDonald’s omega. Composite reliability and average variance extracted showed better indices for a three-factor model. The research also showed evidence of measurement invariance across gender. All the factors of the final three-dimensional BES model were direct and significantly associated with social and normative adjustment, being most strongly related to cognitive empathy. Conclusions This research supports the advances in neuroscience, developmental psychology and psychopathology through a three-dimensional version of the BES, which represents an improvement in the original two-factorial model. The organisation of empathy in three factors benefits the understanding of social and normative adjustment in adolescents, in which emotional disengagement favours adjusted peer relationships. Psychoeducational interventions aimed at improving the quality of social life in schools should target these components of empathy. PMID:28951400

In Silico Docking of Small-Molecule Inhibitors to the Escherichia coli Type III Secretion System EscN ATPase

DTIC Science & Technology

2014-07-01

coordinates of the EscN protein (Zarivach et al., 2007) were downloaded in pdb file format from the Research Collaboratory for Structural Biology...catalytic activity. Two structurally related compounds were observed to adopt extended conformations in the active-site cleft and essentially...adopt a very compact conformation that occupied only one side of the cleft. Our goal was to determine the three-dimensional structures of the

A polyhedron made of tRNAs.

PubMed

Severcan, Isil; Geary, Cody; Chworos, Arkadiusz; Voss, Neil; Jacovetty, Erica; Jaeger, Luc

2010-09-01

Supramolecular assembly is a powerful strategy used by nature to build nanoscale architectures with predefined sizes and shapes. With synthetic systems, however, numerous challenges remain to be solved before precise control over the synthesis, folding and assembly of rationally designed three-dimensional nano-objects made of RNA can be achieved. Here, using the transfer RNA molecule as a structural building block, we report the design, efficient synthesis and structural characterization of stable, modular three-dimensional particles adopting the polyhedral geometry of a non-uniform square antiprism. The spatial control within the final architecture allows the precise positioning and encapsulation of proteins. This work demonstrates that a remarkable degree of structural control can be achieved with RNA structural motifs for the construction of thermostable three-dimensional nano-architectures that do not rely on helix bundles or tensegrity. RNA three-dimensional particles could potentially be used as carriers or scaffolds in nanomedicine and synthetic biology.

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

The Structure of the Protonated Serine Octamer.

PubMed

Scutelnic, Valeriu; Perez, Marta A S; Marianski, Mateusz; Warnke, Stephan; Gregor, Aurelien; Rothlisberger, Ursula; Bowers, Michael T; Baldauf, Carsten; von Helden, Gert; Rizzo, Thomas R; Seo, Jongcheol

2018-06-20

The amino acid serine has long been known to form a protonated "magic-number" cluster containing eight monomer units that shows an unusually high abundance in mass spectra and has a remarkable homochiral preference. Despite many experimental and theoretical studies, there is no consensus on a Ser 8 H + structure that is in agreement with all experimental observations. Here, we present the structure of Ser 8 H + determined by a combination of infrared spectroscopy and ab initio molecular dynamics simulations. The three-dimensional structure that we determine is ∼25 kcal mol -1 more stable than the previous most stable published structure and explains both the homochiral preference and the experimentally observed facile replacement of two serine units.

Mathematical modeling of transformation process of structurally unstable magnetic configurations into structurally stable ones in two-dimensional and three-dimensional geometry

NASA Astrophysics Data System (ADS)

Inovenkov, Igor; Echkina, Eugenia; Ponomarenko, Loubov

Magnetic reconnection is a fundamental process in astrophysical, space and laboratory plasma. In essence, it represents a change of topology of the magnetic field caused by readjustment of the structure of the magnetic field lines. This change leads to release of energy accumulated in the field. We consider transformation process of structurally unstable magnetic configurations into the structurally steady ones from the point of view of the Catastrophe theory. Special attention is paid to modeling of evolution of the structurally unstable three-dimensional magnetic fields.

System for generating two-dimensional masks from a three-dimensional model using topological analysis

DOEpatents

Schiek, Richard [Albuquerque, NM

2006-06-20

A method of generating two-dimensional masks from a three-dimensional model comprises providing a three-dimensional model representing a micro-electro-mechanical structure for manufacture and a description of process mask requirements, reducing the three-dimensional model to a topological description of unique cross sections, and selecting candidate masks from the unique cross sections and the cross section topology. The method further can comprise reconciling the candidate masks based on the process mask requirements description to produce two-dimensional process masks.

Three-dimensional structures of unligated uridine phosphorylase from Yersinia pseudotuberculosis at 1.4 Å resolution and its complex with an antibacterial drug

NASA Astrophysics Data System (ADS)

Balaev, V. V.; Lashkov, A. A.; Gabdulkhakov, A. G.; Dontsova, M. V.; Mironov, A. S.; Betzel, C.; Mikhailov, A. M.

2015-07-01

Uridine phosphorylases play an essential role in the cellular metabolism of some antibacterial agents. Acute infectious diseases (bubonic plague, yersiniosis, pseudotuberculosis, etc., caused by bacteria of the genus Yersinia) are treated using both sulfanilamide medicines and antibiotics, including trimethoprim. The action of an antibiotic on a bacterial cell is determined primarily by the character of its interactions with cellular components, including those which are not targets (for example, with pyrimidine phosphorylases). This type of interaction should be taken into account in designing drugs. The three-dimensional structure of uridine phosphorylase from the bacterium Yersinia pseudotuberculosis ( YptUPh) with the free active site was determined for the first time by X-ray crystallography and refined at 1.40 Å resolution (DPI = 0.062 Å; ID PDB: 4OF4). The structure of the complex of YptUPh with the bacteriostatic drug trimethoprim was studied by molecular docking and molecular dynamics methods. The trimethoprim molecule was shown to be buffered by the enzyme YptUPh, resulting in a decrease in the efficiency of the treatment of infectious diseases caused by bacteria of the genus Yersinia with trimethoprim.

Microscopy and Chemical Inversing Techniques to Determine the Photonic Crystal Structure of Iridescent Beetle Scales in the Cerambycidae Family

NASA Astrophysics Data System (ADS)

Richey, Lauren; Gardner, John; Standing, Michael; Jorgensen, Matthew; Bartl, Michael

2010-10-01

Photonic crystals (PCs) are periodic structures that manipulate electromagnetic waves by defining allowed and forbidden frequency bands known as photonic band gaps. Despite production of PC structures operating at infrared wavelengths, visible counterparts are difficult to fabricate because periodicities must satisfy the diffraction criteria. As part of an ongoing search for naturally occurring PCs [1], a three-dimensional array of nanoscopic spheres in the iridescent scales of the Cerambycidae insects A. elegans and G. celestis has been found. Such arrays are similar to opal gemstones and self-assembled colloidal spheres which can be chemically inverted to create a lattice-like PC. Through a chemical replication process [2], scanning electron microscopy analysis, sequential focused ion beam slicing and three-dimensional modeling, we analyzed the structural arrangement of the nanoscopic spheres. The study of naturally occurring structures and their inversing techniques into PCs allows for diversity in optical PC fabrication. [1] J.W. Galusha et al., Phys. Rev. E 77 (2008) 050904. [2] J.W. Galusha et al., J. Mater. Chem. 20 (2010) 1277.

Rational redesign of inhibitors of furin/kexin processing proteases by electrostatic mutations.

PubMed

Cai, Xiao-hui; Zhang, Qing; Ding, Da-fu

2004-12-01

To model the three-dimensional structure and investigate the interaction mechanism of the proprotein convertase furin/kexin and their inhibitors (eglin c mutants). The three-dimensional complex structures of furin/kexin with its inhibitors, eglin c mutants, were generated by modeller program using the newly published X-ray crystallographical structures of mouse furin and yeast kexin as templates. The electrostatic interaction energy of each complex was calculated and the results were compared with the experimentally determined inhibition constants to find the correlation between them. High quality models of furin/kexin-eglin c mutants were obtained and used for calculation of the electrostatic interaction energies between the proteases and their inhibitors. The calculated electrostatic energies of interaction showed a linear correlation to the experimental inhibition constants. The modeled structures give good explanations of the specificity of eglin c mutants to furin/kexin. The electrostatic interactions play important roles in inhibitory activity of eglin c mutants to furin/kexin. The results presented here provided quantitative structural and functional information concerning the role of the charge-charge interactions in the binding of furin/kexin and their inhibitors.

Detecting 3D Vegetation Structure with the Galileo Space Probe: Can a Distant Probe Detect Vegetation Structure on Earth?

PubMed Central

2016-01-01

Sagan et al. (1993) used the Galileo space probe data and first principles to find evidence of life on Earth. Here we ask whether Sagan et al. (1993) could also have detected whether life on Earth had three-dimensional structure, based on the Galileo space probe data. We reanalyse the data from this probe to see if structured vegetation could have been detected in regions with abundant photosynthetic pigments through the anisotropy of reflected shortwave radiation. We compare changing brightness of the Amazon forest (a region where Sagan et al. (1993) noted a red edge in the reflectance spectrum, indicative of photosynthesis) as the planet rotates to a common model of reflectance anisotropy and found measured increase of surface reflectance of 0.019 ± 0.003 versus a 0.007 predicted from only anisotropic effects. We hypothesize the difference was due to minor cloud contamination. However, the Galileo dataset had only a small change in phase angle (sun-satellite position) which reduced the observed anisotropy signal and we demonstrate that theoretically if the probe had a variable phase angle between 0–20°, there would have been a much larger predicted change in surface reflectance of 0.1 and under such a scenario three-dimensional vegetation structure on Earth could possibly have been detected. These results suggest that anisotropic effects may be useful to help determine whether exoplanets have three-dimensional vegetation structure in the future, but that further comparisons between empirical and theoretical results are first necessary. PMID:27973530

Detecting 3D Vegetation Structure with the Galileo Space Probe: Can a Distant Probe Detect Vegetation Structure on Earth?

PubMed

Doughty, Christopher E; Wolf, Adam

2016-01-01

Sagan et al. (1993) used the Galileo space probe data and first principles to find evidence of life on Earth. Here we ask whether Sagan et al. (1993) could also have detected whether life on Earth had three-dimensional structure, based on the Galileo space probe data. We reanalyse the data from this probe to see if structured vegetation could have been detected in regions with abundant photosynthetic pigments through the anisotropy of reflected shortwave radiation. We compare changing brightness of the Amazon forest (a region where Sagan et al. (1993) noted a red edge in the reflectance spectrum, indicative of photosynthesis) as the planet rotates to a common model of reflectance anisotropy and found measured increase of surface reflectance of 0.019 ± 0.003 versus a 0.007 predicted from only anisotropic effects. We hypothesize the difference was due to minor cloud contamination. However, the Galileo dataset had only a small change in phase angle (sun-satellite position) which reduced the observed anisotropy signal and we demonstrate that theoretically if the probe had a variable phase angle between 0-20°, there would have been a much larger predicted change in surface reflectance of 0.1 and under such a scenario three-dimensional vegetation structure on Earth could possibly have been detected. These results suggest that anisotropic effects may be useful to help determine whether exoplanets have three-dimensional vegetation structure in the future, but that further comparisons between empirical and theoretical results are first necessary.

Microreplication of laser-fabricated surface and three-dimensional structures

NASA Astrophysics Data System (ADS)

Koroleva, Anastasia; Schlie, Sabrina; Fadeeva, Elena; Gittard, Shaun D.; Miller, Philip; Ovsianikov, Aleksandr; Koch, Jürgen; Narayan, Roger J.; Chichkov, Boris N.

2010-12-01

The fabrication of defined surface topographies and three-dimensional structures is a challenging process for various applications, e.g. in photonics and biomedicine. Laser-based technologies provide a promising approach for the production of such structures. The advantages of femtosecond laser ablation and two-photon polymerization for microstructuring are well known. However, these methods cannot be applied to all materials and are limited by their high cost and long production time. In this study, biomedical applications of an indirect rapid prototyping, molding microreplication of laser-fabricated two- and three-dimensional structures are examined. We demonstrate that by this method any laser-generated surface topography as well as three-dimensional structures can be replicated in various materials without losing the original geometry. The replication into multiple copies enables fast and perfect reproducibility of original microstructures for investigations of cell-surface interactions. Compared to unstructured materials, we observe that microstructures have strong influence on morphology and localization of fibroblasts, whereas neuroblastoma cells are not negatively affected.

Invasive plants transform the three-dimensional structure of rain forests

PubMed Central

Asner, Gregory P.; Hughes, R. Flint; Vitousek, Peter M.; Knapp, David E.; Kennedy-Bowdoin, Ty; Boardman, Joseph; Martin, Roberta E.; Eastwood, Michael; Green, Robert O.

2008-01-01

Biological invasions contribute to global environmental change, but the dynamics and consequences of most invasions are difficult to assess at regional scales. We deployed an airborne remote sensing system that mapped the location and impacts of five highly invasive plant species across 221,875 ha of Hawaiian ecosystems, identifying four distinct ways that these species transform the three-dimensional (3D) structure of native rain forests. In lowland to montane forests, three invasive tree species replace native midcanopy and understory plants, whereas one understory invader excludes native species at the ground level. A fifth invasive nitrogen-fixing tree, in combination with a midcanopy alien tree, replaces native plants at all canopy levels in lowland forests. We conclude that this diverse array of alien plant species, each representing a different growth form or functional type, is changing the fundamental 3D structure of native Hawaiian rain forests. Our work also demonstrates how an airborne mapping strategy can identify and track the spread of certain invasive plant species, determine ecological consequences of their proliferation, and provide detailed geographic information to conservation and management efforts. PMID:18316720

Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes.

PubMed

Fujimoto, Akihiro; Okada, Yukinori; Boroevich, Keith A; Tsunoda, Tatsuhiko; Taniguchi, Hiroaki; Nakagawa, Hidewaki

2016-05-26

Protein tertiary structure determines molecular function, interaction, and stability of the protein, therefore distribution of mutation in the tertiary structure can facilitate the identification of new driver genes in cancer. To analyze mutation distribution in protein tertiary structures, we applied a novel three dimensional permutation test to the mutation positions. We analyzed somatic mutation datasets of 21 types of cancers obtained from exome sequencing conducted by the TCGA project. Of the 3,622 genes that had ≥3 mutations in the regions with tertiary structure data, 106 genes showed significant skew in mutation distribution. Known tumor suppressors and oncogenes were significantly enriched in these identified cancer gene sets. Physical distances between mutations in known oncogenes were significantly smaller than those of tumor suppressors. Twenty-three genes were detected in multiple cancers. Candidate genes with significant skew of the 3D mutation distribution included kinases (MAPK1, EPHA5, ERBB3, and ERBB4), an apoptosis related gene (APP), an RNA splicing factor (SF1), a miRNA processing factor (DICER1), an E3 ubiquitin ligase (CUL1) and transcription factors (KLF5 and EEF1B2). Our study suggests that systematic analysis of mutation distribution in the tertiary protein structure can help identify cancer driver genes.

Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes

PubMed Central

Fujimoto, Akihiro; Okada, Yukinori; Boroevich, Keith A.; Tsunoda, Tatsuhiko; Taniguchi, Hiroaki; Nakagawa, Hidewaki

2016-01-01

Protein tertiary structure determines molecular function, interaction, and stability of the protein, therefore distribution of mutation in the tertiary structure can facilitate the identification of new driver genes in cancer. To analyze mutation distribution in protein tertiary structures, we applied a novel three dimensional permutation test to the mutation positions. We analyzed somatic mutation datasets of 21 types of cancers obtained from exome sequencing conducted by the TCGA project. Of the 3,622 genes that had ≥3 mutations in the regions with tertiary structure data, 106 genes showed significant skew in mutation distribution. Known tumor suppressors and oncogenes were significantly enriched in these identified cancer gene sets. Physical distances between mutations in known oncogenes were significantly smaller than those of tumor suppressors. Twenty-three genes were detected in multiple cancers. Candidate genes with significant skew of the 3D mutation distribution included kinases (MAPK1, EPHA5, ERBB3, and ERBB4), an apoptosis related gene (APP), an RNA splicing factor (SF1), a miRNA processing factor (DICER1), an E3 ubiquitin ligase (CUL1) and transcription factors (KLF5 and EEF1B2). Our study suggests that systematic analysis of mutation distribution in the tertiary protein structure can help identify cancer driver genes. PMID:27225414

Tubular Crystals and Helical Arrays: Structural Determination of HIV-1 Capsid Assemblies Using Iterative Helical Real-Space Reconstruction

PubMed Central

Zhang, Peijun; Meng, Xin; Zhao, Gongpu

2013-01-01

Helical structures are important in many different life forms and are well-suited for structural studies by cryo-EM. A unique feature of helical objects is that a single projection image contains all the views needed to perform a three-dimensional (3D) crystallographic reconstruction. Here, we use HIV-1 capsid assemblies to illustrate the detailed approaches to obtain 3D density maps from helical objects. Mature HIV-1 particles contain a conical- or tubular-shaped capsid that encloses the viral RNA genome and performs essential functions in the virus life cycle. The capsid is composed of capsid protein (CA) oligomers which are helically arranged on the surface. The N-terminal domain (NTD) of CA is connected to its C-terminal domain (CTD) through a flexible hinge. Structural analysis of two- and three-dimensional crystals provided molecular models of the capsid protein (CA) and its oligomer forms. We determined the 3D density map of helically assembled HIV-1 CA hexamers at 16 Å resolution using an iterative helical real-space reconstruction method. Docking of atomic models of CA-NTD and CA-CTD dimer into the electron density map indicated that the CTD dimer interface is retained in the assembled CA. Furthermore, molecular docking revealed an additional, novel CTD trimer interface. PMID:23132072

Three-dimensional structural damage localization system and method using layered two-dimensional array of capacitance sensors

NASA Technical Reports Server (NTRS)

Curry, Mark A (Inventor); Senibi, Simon D (Inventor); Banks, David L (Inventor)

2010-01-01

A system and method for detecting damage to a structure is provided. The system includes a voltage source and at least one capacitor formed as a layer within the structure and responsive to the voltage source. The system also includes at least one sensor responsive to the capacitor to sense a voltage of the capacitor. A controller responsive to the sensor determines if damage to the structure has occurred based on the variance of the voltage of the capacitor from a known reference value. A method for sensing damage to a structure involves providing a plurality of capacitors and a controller, and coupling the capacitors to at least one surface of the structure. A voltage of the capacitors is sensed using the controller, and the controller calculates a change in the voltage of the capacitors. The method can include signaling a display system if a change in the voltage occurs.

Concept and development of an orthotropic FE model of the proximal femur.

PubMed

Wirtz, Dieter Christian; Pandorf, Thomas; Portheine, Frank; Radermacher, Klaus; Schiffers, Norbert; Prescher, Andreas; Weichert, Dieter; Niethard, Fritz Uwe

2003-02-01

In contrast to many isotropic finite-element (FE) models of the femur in literature, it was the object of our study to develop an orthotropic FE "model femur" to realistically simulate three-dimensional bone remodelling. The three-dimensional geometry of the proximal femur was reconstructed by CT scans of a pair of cadaveric femurs at equal distances of 2mm. These three-dimensional CT models were implemented into an FE simulation tool. Well-known "density-determined" bony material properties (Young's modulus; Poisson's ratio; ultimate strength in pressure, tension and torsion; shear modulus) were assigned to each FE of the same "CT-density-characterized" volumetric group. In order to fix the principal directions of stiffness in FE areas with the same "density characterization", the cadaveric femurs were cut in 2mm slices in frontal (left femur) and sagittal plane (right femur). Each femoral slice was scanned into a computer-based image processing system. On these images, the principal directions of stiffness of cancellous and cortical bone were determined manually using the orientation of the trabecular structures and the Haversian system. Finally, these geometric data were matched with the "CT-density characterized" three-dimensional femur model. In addition, the time and density-dependent adaptive behaviour of bone remodelling was taken into account by implementation of Carter's criterion. In the constructed "model femur", each FE is characterized by the principal directions of the stiffness and the "CT-density-determined" material properties of cortical and cancellous bone. Thus, on the basis of anatomic data a three-dimensional FE simulation reference model of the proximal femur was realized considering orthotropic conditions of bone behaviour. With the orthotropic "model femur", the fundamental basis has been formed to realize realistic simulations of the dynamical processes of bone remodelling under different loading conditions or operative procedures (osteotomies, total hip replacements, etc).

A Numerical Model of Exchange Chromatography Through 3D Lattice Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salloum, Maher; Robinson, David B.

Rapid progress in the development of additive manufacturing technologies is opening new opportunities to fabricate structures that control mass transport in three dimensions across a broad range of length scales. We describe a structure that can be fabricated by newly available commercial 3D printers. It contains an array of regular three-dimensional flow paths that are in intimate contact with a solid phase, and thoroughly shuffle material among the paths. We implement a chemically reacting flow model to study its behavior as an exchange chromatography column, and compare it to an array of one-dimensional flow paths that resemble more traditional honeycombmore » monoliths. A reaction front moves through the columns and then elutes. Here, the front is sharper at all flow rates for the structure with three-dimensional flow paths, and this structure is more robust to channel width defects than the one-dimensional array.« less

A Numerical Model of Exchange Chromatography Through 3D Lattice Structures

DOE PAGES

Salloum, Maher; Robinson, David B.

2018-01-30

Rapid progress in the development of additive manufacturing technologies is opening new opportunities to fabricate structures that control mass transport in three dimensions across a broad range of length scales. We describe a structure that can be fabricated by newly available commercial 3D printers. It contains an array of regular three-dimensional flow paths that are in intimate contact with a solid phase, and thoroughly shuffle material among the paths. We implement a chemically reacting flow model to study its behavior as an exchange chromatography column, and compare it to an array of one-dimensional flow paths that resemble more traditional honeycombmore » monoliths. A reaction front moves through the columns and then elutes. Here, the front is sharper at all flow rates for the structure with three-dimensional flow paths, and this structure is more robust to channel width defects than the one-dimensional array.« less

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 2. Teaching Units that Utilize an Interactive Web-Accessible Subset of the Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2010-01-01

A series of online interactive teaching units have been developed that illustrate the use of experimentally measured three-dimensional (3D) structures to teach fundamental chemistry concepts. The units integrate a 500-structure subset of the Cambridge Structural Database specially chosen for their pedagogical value. The units span a number of key…

Confinement and Structural Changes in Vertically Aligned Dust Structures

NASA Astrophysics Data System (ADS)

Hyde, Truell

2013-10-01

In physics, confinement is known to influence collective system behavior. Examples include coulomb crystal variants such as those formed from ions or dust particles (classical), electrons in quantum dots (quantum) and the structural changes observed in vertically aligned dust particle systems formed within a glass box placed on the lower electrode of a Gaseous Electronics Conference (GEC) rf reference cell. Recent experimental studies have expanded the above to include the biological domain by showing that the stability and dynamics of proteins confined through encapsulation and enzyme molecules placed in inorganic cavities such as those found in biosensors are also directly influenced by their confinement. In this paper, the self-assembly and subsequent collective behavior of structures formed from n, charged dust particles interacting with one another and located within a glass box placed on the lower, powered electrode of a GEC rf reference cell is discussed. Self-organized formation of vertically aligned one-dimensional chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from one-dimensional chain structures, through a zigzag transition to a two-dimensional, spindle like structures, and then to various three-dimensional, helical structures exhibiting various symmetries. Stable configurations are shown to be strongly dependent upon system confinement. The critical conditions for structural transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop will be shown to be in good agreement with molecular dynamics simulations.

Investigation of deformation of elements of three-dimensional reinforced concrete structures located in the soil, interacting with each other through rubber gaskets

NASA Astrophysics Data System (ADS)

Berezhnoi, D. V.; Balafendieva, I. S.; Sachenkov, A. A.; Sekaeva, L. R.

2017-06-01

In work the technique of calculation of elements of three-dimensional reinforced concrete substructures located in a soil, interacting with each other through rubber linings is realized. To describe the interaction of deformable structures with the ground, special “semi-infinite” finite elements are used. A technique has been implemented that allows one to describe the contact interaction of three-dimensional structures by means of a special contact finite element with specific properties. The obtained numerical results are compared with the experimental data, their good agreement is noted.

Magnetic diagnostics for equilibrium reconstructions in the presence of nonaxisymmetric eddy current distributions in tokamaks (invited).

PubMed

Berzak, L; Jones, A D; Kaita, R; Kozub, T; Logan, N; Majeski, R; Menard, J; Zakharov, L

2010-10-01

The lithium tokamak experiment (LTX) is a modest-sized spherical tokamak (R(0)=0.4 m and a=0.26 m) designed to investigate the low-recycling lithium wall operating regime for magnetically confined plasmas. LTX will reach this regime through a lithium-coated shell internal to the vacuum vessel, conformal to the plasma last-closed-flux surface, and heated to 300-400 °C. This structure is highly conductive and not axisymmetric. The three-dimensional nature of the shell causes the eddy currents and magnetic fields to be three-dimensional as well. In order to analyze the plasma equilibrium in the presence of three-dimensional eddy currents, an extensive array of unique magnetic diagnostics has been implemented. Sensors are designed to survive high temperatures and incidental contact with lithium and provide data on toroidal asymmetries as well as full coverage of the poloidal cross-section. The magnetic array has been utilized to determine the effects of nonaxisymmetric eddy currents and to model the start-up phase of LTX. Measurements from the magnetic array, coupled with two-dimensional field component modeling, have allowed a suitable field null and initial plasma current to be produced. For full magnetic reconstructions, a three-dimensional electromagnetic model of the vacuum vessel and shell is under development.

Localization of an NH2-Terminal Disease-Causing Mutation Hotspot to the “Clamp” Region in the Three-Dimensional Structure of the Cardiac Ryanodine Receptor

PubMed Central

Wang, Ruiwu; Chen, Wenqian; Cai, Shitian; Zhang, Jing; Bolstad, Jeff; Wagenknecht, Terence; Liu, Zheng; Chen, S. R. Wayne

2009-01-01

A region between residues 414 and 466 in the cardiac ryanodine receptor (RyR2) harbors more than half of the known NH2-terminal mutations associated with cardiac arrhythmias and sudden death. To gain insight into the structural basis of this NH2-terminal mutation hotspot, we have determined its location in the three-dimensional structure of RyR2. Green fluorescent protein (GFP), used as a structural marker, was inserted into the middle of this mutation hotspot after Ser-437 in the RyR2 sequence. The resultant GFP-RyR2 fusion protein, RyR2S437-GFP, was expressed in HEK293 cells and characterized using Ca2+ release, [3H]ryanodine binding, and single cell Ca2+ imaging studies. These functional analyses revealed that RyR2S437-GFP forms a caffeine-and ryanodine-sensitive Ca2+ release channel that possesses Ca2+- and caffeine-dependence of activation indistinguishable from that of wild type (wt) RyR2. HEK293 cells expressing RyR2S437-GFP displayed a propensity for store-overload induced Ca2+ release similar to that in cells expressing RyR2-wt. The three-dimensional structure of the purified RyR2S437-GFP was reconstructed using cryo-electron microscopy and single particle image processing. Subtraction of the three-dimensional reconstructions of RyR2-wt and RyR2S437-GFP revealed the location of the inserted GFP, and hence the NH2-terminal mutation hotspot, in a region between domains 5 and 9 in the clamp-shaped structure. This location is close to a previously mapped central disease-causing mutation site located in a region between domains 5 and 6. These results, together with findings from previous studies, suggest that the proposed interactions between the NH2-terminal and central regions of RyR2 are likely to take place between domains 5 and 6, and that the clamp-shaped structure, which shows substantial conformational differences between the closed and open states, is highly susceptible to disease-causing mutations. PMID:17452324

Micro-Mirrors for Nanoscale Three-Dimensional Microscopy

PubMed Central

Seale, Kevin; Janetopoulos, Chris; Wikswo, John

2013-01-01

A research-grade optical microscope is capable of resolving fine structures in two-dimensional images. However, three-dimensional resolution, or the ability of the microscope to distinguish between objects lying above or below the focal plane from in-focus objects, is not nearly as good as in-plane resolution. In this issue of ACS Nano, McMahon et al. report the use of mirrored pyramidal wells with a conventional microscope for rapid, 3D localization and tracking of nanoparticles. Mirrors have been used in microscopy before, but recent work with MPWs is unique because it enables the rapid determination of the x-, y-, and z-position of freely diffusing nanoparticles and cellular nanostructures with unprecedented speed and spatial accuracy. As inexpensive tools for 3D visualization, mirrored pyramidal wells may prove to be invaluable aids in nanotechnology and engineering of nanomaterials. PMID:19309167

Resource for structure related information on transmembrane proteins

NASA Astrophysics Data System (ADS)

Tusnády, Gábor E.; Simon, István

Transmembrane proteins are involved in a wide variety of vital biological processes including transport of water-soluble molecules, flow of information and energy production. Despite significant efforts to determine the structures of these proteins, only a few thousand solved structures are known so far. Here, we review the various resources for structure-related information on these types of proteins ranging from the 3D structure to the topology and from the up-to-date databases to the various Internet sites and servers dealing with structure prediction and structure analysis. Abbreviations: 3D, three dimensional; PDB, Protein Data Bank; TMP, transmembrane protein.

The effect of incidence angle on the overall three-dimensional aerodynamic performance of a classical annular airfoil cascade

NASA Technical Reports Server (NTRS)

Bergsten, D. E.; Fleeter, S.

1983-01-01

To be of quantitative value to the designer and analyst, it is necessary to experimentally verify the flow modeling and the numerics inherent in calculation codes being developed to predict the three dimensional flow through turbomachine blade rows. This experimental verification requires that predicted flow fields be correlated with three dimensional data obtained in experiments which model the fundamental phenomena existing in the flow passages of modern turbomachines. The Purdue Annular Cascade Facility was designed specifically to provide these required three dimensional data. The overall three dimensional aerodynamic performance of an instrumented classical airfoil cascade was determined over a range of incidence angle values. This was accomplished utilizing a fully automated exit flow data acquisition and analysis system. The mean wake data, acquired at two downstream axial locations, were analyzed to determine the effect of incidence angle, the three dimensionality of the cascade exit flow field, and the similarity of the wake profiles. The hub, mean, and tip chordwise airfoil surface static pressure distributions determined at each incidence angle are correlated with predictions from the MERIDL and TSONIC computer codes.

Molecular cloning and characterization of an alpha-amylase from Pichia burtonii 15-1.

PubMed

Kato, Saemi; Shimizu-Ibuka, Akiko; Mura, Kiyoshi; Takeuchi, Akiko; Tokue, Chiyoko; Arai, Soichi

2007-12-01

An alpha-amylase secreted by Pichia burtonii 15-1 isolated from a traditional starter murcha of Nepal, named Pichia burtonii alpha-amylase (PBA), was studied. The gene was cloned and its nucleotide sequence was determined. PBA was deduced to consist of 494 amino acid residues. It shared certain degrees of amino acid sequence identity with other homologous proteins: 60% with Schwanniomyces occidentalis alpha-amylase, 58% with Saccharomycopsis sp. alpha-amylase, and 47% with Taka-amylase A from Aspergillus oryzae. A three-dimensional structural model of PBA generated using the known three-dimensional structure of Taka-amylase A as a template suggested high structural similarity between them. Kinetic analysis revealed that the K(m) values of PBA were lower than those of Taka-amylase A for the oligosaccharides. Although the k(cat) values of PBA were lower than those of Taka-amylase A for the oligosaccharide substrates, the k(cat)/K(m) values of PBA were higher.

Experimental Investigation of the Unsteady Flow Structures of Two Interacting Pitching Wings

NASA Astrophysics Data System (ADS)

Kurt, Melike; Moored, Keith

2015-11-01

Birds, insects and fish propel themselves with unsteady motions of their wings and fins. Many of these animals are also found to fly or swim in three-dimensional flocks and schools. Numerous studies have explored the three-dimensional steady flow interactions and the two-dimensional unsteady flow interactions in collectives. Yet, the characterization of the three-dimensional unsteady interactions remains relatively unexplored. This study aims to characterize the flow structures and interactions between two sinusoidally pitching finite-span wings. The arrangement of the wings varies from a tandem to a bi-plane configuration. The vortex structures for these various arrangements are quantified by using particle image velocimetry. The vortex-wing interactions are also characterized as the synchrony between the wings is modified.

Suitability of a three-dimensional model to measure empathy and its relationship with social and normative adjustment in Spanish adolescents: a cross-sectional study.

PubMed

Herrera-López, Mauricio; Gómez-Ortiz, Olga; Ortega-Ruiz, Rosario; Jolliffe, Darrick; Romera, Eva M

2017-09-25

(1) To examine the psychometric properties of the Basic Empathy Scale (BES) with Spanish adolescents, comparing a two and a three-dimensional structure;(2) To analyse the relationship between the three-dimensional empathy and social and normative adjustment in school. Transversal and ex post facto retrospective study. Confirmatory factorial analysis, multifactorial invariance analysis and structural equations models were used. 747 students (51.3% girls) from Cordoba, Spain, aged 12-17 years (M=13.8; SD=1.21). The original two-dimensional structure was confirmed (cognitive empathy, affective empathy), but a three-dimensional structure showed better psychometric properties, highlighting the good fit found in confirmatory factorial analysis and adequate internal consistent valued, measured with Cronbach's alpha and McDonald's omega. Composite reliability and average variance extracted showed better indices for a three-factor model. The research also showed evidence of measurement invariance across gender. All the factors of the final three-dimensional BES model were direct and significantly associated with social and normative adjustment, being most strongly related to cognitive empathy. This research supports the advances in neuroscience, developmental psychology and psychopathology through a three-dimensional version of the BES, which represents an improvement in the original two-factorial model. The organisation of empathy in three factors benefits the understanding of social and normative adjustment in adolescents, in which emotional disengagement favours adjusted peer relationships. Psychoeducational interventions aimed at improving the quality of social life in schools should target these components of empathy. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Determination of the structure of subsurface layers by means of coaxial time-of-flight scattering and recoiling spectrometry (TOF-SARS)

NASA Astrophysics Data System (ADS)

Wang, Y.; Teplov, S. V.; Rabalais, J. W.

1994-05-01

It is demonstrated that both surface and subsurface structural information can be obtained from Si{100}-(2 × 1) and Si{100}-(1 × 1)-H by coupling coaxial time-of-flight scattering and recoiling spectrometry (TOF-SARS) with three-dimensional trajectory simulations. Experimentally, backscattering intensity versus incident α angle scans at a scattering angle of ˜ 180° have been measured for 2 keV He + incident on both the (2 × 1) and (1 × 1)-H surfaces. Computationally, an efficient three-dimensional version of the Monte Carlo computer code RECAD has been developed and applied to simulation of the TOF-SARS results. An R (reliability) factor has been introduced for quantitative evaluation of the agreement between experimental and simulated scans. For the case of 2 keV He + scattering from Si{100}, scattering features can be observed and delineated from as many as 14 atomic layers ( ˜ 18 Å) below the surface. The intradimer spacing D is determined as 2.2 Å from the minimum in the R-factor versus D plot.

Three-dimensional effects on pure tone fan noise due to inflow distortion. [rotor blade noise prediction

NASA Technical Reports Server (NTRS)

Kobayashi, H.

1978-01-01

Two dimensional, quasi three dimensional and three dimensional theories for the prediction of pure tone fan noise due to the interaction of inflow distortion with a subsonic annular blade row were studied with the aid of an unsteady three dimensional lifting surface theory. The effects of compact and noncompact source distributions on pure tone fan noise in an annular cascade were investigated. Numerical results show that the strip theory and quasi three-dimensional theory are reasonably adequate for fan noise prediction. The quasi three-dimensional method is more accurate for acoustic power and model structure prediction with an acoustic power estimation error of about plus or minus 2db.

Hot-Spot Residues to be Mutated Common in G Protein-Coupled Receptors of Class A: Identification of Thermostabilizing Mutations Followed by Determination of Three-Dimensional Structures for Two Example Receptors.

PubMed

Yasuda, Satoshi; Kajiwara, Yuta; Toyoda, Yosuke; Morimoto, Kazushi; Suno, Ryoji; Iwata, So; Kobayashi, Takuya; Murata, Takeshi; Kinoshita, Masahiro

2017-07-06

G protein-coupled receptors (GPCRs), which are indispensable to life and also implicated in a number of diseases, construct important drug targets. For the efficient structure-guided drug design, however, their structural stabilities must be enhanced. An amino-acid mutation is known to possibly lead to the enhancement, but currently available experimental and theoretical methods for identifying stabilizing mutations suffer such drawbacks as the incapability of exploring the whole mutational space with minor effort and the unambiguous physical origin of the enhanced or lowered stability. In general, after the identification is successfully made for a GPCR, the whole procedure must be followed all over again for the identification for another GPCR. Here we report a theoretical strategy by which many different GPCRs can be considered at the same time. The strategy is illustrated for three GPCRs of Class A in the inactive state. We argue that a mutation of the residue at a position of N BW = 3.39 (N BW is the Ballesteros-Weinstein number), a hot-spot residue, leads to substantially higher stability for significantly many GPCRs of Class A in the inactive state. The most stabilizing mutations of the residues with N BW = 3.39 are then identified for two of the three GPCRs, using the improved version of our free-energy function. These identifications are experimentally corroborated, which is followed by the determination of new three-dimensional (3D) structures for the two GPCRs. We expect that on the basis of the strategy, the 3D structures of many GPCRs of Class A can be solved for the first time in succession.

Power-scaling performance of a three-dimensional tritium betavoltaic diode

NASA Astrophysics Data System (ADS)

Liu, Baojun; Chen, Kevin P.; Kherani, Nazir P.; Zukotynski, Stefan

2009-12-01

Three-dimensional diodes fabricated by electrochemical etching are exposed to tritium gas at pressures from 0.05 to 33 atm at room temperature to examine its power scaling performance. It is shown that the three-dimensional microporous structure overcomes the self-absorption limited saturation of beta flux at high tritium pressures. These results are contrasted against the three-dimensional device powered in one instance by tritium absorbed in the near surface region of the three-dimensional microporous network, and in another by a planar scandium tritide foil. These findings suggest that direct tritium occlusion in the near surface of three-dimensional diode can improve the specific power production.

The Reconstruction of Three-Dimensional Morphological and Electrical Paraneters from Two-Dimensional Sections of Neurones

NASA Astrophysics Data System (ADS)

Brawn, A. D.; Wheal, H. V.

1986-07-01

A system is described which can be used to create a three-dimensional model of a neurone from the central nervous system. This model can then be used to obtain quantitative data on the physical and electrical pro, perties of the neurone. Living neurones are either raised in culture, or taken from in vitro preparations of brain tissue and optically sectioned. These two-dimensional sections are digitised, and input to a 68008-based microcomputer. The system reconstructs the three-dimensional structure of the neurone, both geanetrically and electrically. The user can a) View the structure fran any point at any angle b) "Move through" the structure along any given vector c) Nave through" the structure following a neurone process d) Fire the neurone at any point, and "watch" the action potentials propagate e) Vary the parameters of the electrical model of a process element. The system is targeted to a research programme on epilepsy, which makes frequent use of both geometric and electrical neurone modelling. Current techniques which may involve crude histology and two-dimensional drawings have considerable short camings.

Plenoptic Imaging of a Three Dimensional Cold Atom Cloud

NASA Astrophysics Data System (ADS)

Lott, Gordon

2017-04-01

A plenoptic imaging system is capable of sampling the rays of light in a volume, both spatially and angularly, providing information about the three dimensional (3D) volume being imaged. The extraction of the 3D structure of a cold atom cloud is demonstrated, using a single plenoptic camera and a single image. The reconstruction is tested against a reference image and the results discussed along with the capabilities and limitations of the imaging system. This capability is useful when the 3D distribution of the atoms is desired, such as determining the shape of an atom trap, particularly when there is limited optical access. Gratefully acknowledge support from AFRL.

Pancharatnam-Berry phase and kinetic magnetoelectric effect in trigonal tellurium

NASA Astrophysics Data System (ADS)

Şahin, C.; Rou, J.; Ma, J.; Pesin, D. A.

2018-05-01

We study the kinetic magnetoelectric effect (current-induced magnetization including both the orbital and spin contributions) in three-dimensional conductors, specializing to the case of p -doped trigonal tellurium. We include both intrinsic and extrinsic contributions to the effect, which stem from the band structure of the crystal, and from disorder scattering, respectively. Specifically, we determine the dependence of the kinetic magnetoelectric response on the hole doping in tellurium, and show that the intrinsic and extrinsic effects dominate for low and high levels of doping, respectively. The results of this work imply that three-dimensional helical metals are promising for spintronics applications, in particular, they can provide robust control over current-induced magnetic torques.

Finite element analysis of steady and transiently moving/rolling nonlinear viscoelastic structure. II - Shell and three-dimensional simulations

NASA Technical Reports Server (NTRS)

Kennedy, Ronald; Padovan, Joe

1987-01-01

In a three-part series of papers, a generalized finite element solution strategy is developed to handle traveling load problems in rolling, moving and rotating structure. The main thrust of this section consists of the development of three-dimensional and shell type moving elements. In conjunction with this work, a compatible three-dimensional contact strategy is also developed. Based on these modeling capabilities, extensive analytical and experimental benchmarking is presented. Such testing includes traveling loads in rotating structure as well as low- and high-speed rolling contact involving standing wave-type response behavior. These point to the excellent modeling capabilities of moving element strategies.

Three-Dimensional Printing of a Scalable Molecular Model and Orbital Kit for Organic Chemistry Teaching and Learning

ERIC Educational Resources Information Center

Penny, Matthew R.; Cao, Zi Jing; Patel, Bhaven; dos Santos, Bruno Sil; Asquith, Christopher R. M.; Szulc, Blanka R.; Rao, Zenobia X.; Muwaffak, Zaid; Malkinson, John P.; Hilton, Stephen T.

2017-01-01

Three-dimensional (3D) chemical models are a well-established learning tool used to enhance the understanding of chemical structures by converting two-dimensional paper or screen outputs into realistic three-dimensional objects. While commercial atom model kits are readily available, there is a surprising lack of large molecular and orbital models…

The three-dimensional structure of aquaporin-1

NASA Astrophysics Data System (ADS)

Walz, Thomas; Hirai, Teruhisa; Murata, Kazuyoshi; Heymann, J. Bernard; Mitsuoka, Kaoru; Fujiyoshi, Yoshinori; Smith, Barbara L.; Agre, Peter; Engel, Andreas

1997-06-01

The entry and exit of water from cells is a fundamental process of life. Recognition of the high water permeability of red blood cells led to the proposal that specialized water pores exist in the plasma membrane. Expression in Xenopus oocytes and functional studies of an erythrocyte integral membrane protein of relative molecular mass 28,000, identified it as the mercury-sensitive water channel, aquaporin-1 (AQP1). Many related proteins, all belonging to the major intrinsic protein (MIP) family, are found throughout nature. AQP1 is a homotetramer containing four independent aqueous channels. When reconstituted into lipid bilayers, the protein forms two-dimensional lattices with a unit cell containing two tetramers in opposite orientation. Here we present the three-dimensional structure of AQP1 determined at 6Å resolution by cryo-electron microscopy. Each AQP1 monomer has six tilted, bilayer-spanning α-helices which form a right-handed bundle surrounding a central density. These results, together with functional studies, provide a model that identifies the aqueous pore in the AQP1 molecule and indicates the organization of the tetrameric complex in the membrane.

Structure and topology of three-dimensional hydrocarbon polymers.

PubMed

Kondrin, Mikhail V; Lebed, Yulia B; Brazhkin, Vadim V

2016-08-01

A new family of three-dimensional hydrocarbon polymers which are more energetically favorable than benzene is proposed. Although structurally these polymers are closely related to well known diamond and lonsdaleite carbon structures, using topological arguments we demonstrate that they have no known structural analogs. Topological considerations also give some indication of possible methods of synthesis. Taking into account their exceptional optical, structural and mechanical properties these polymers might have interesting applications.

Cell mechanics, structure, and function are regulated by the stiffness of the three-dimensional microenvironment.

PubMed

Chen, J; Irianto, J; Inamdar, S; Pravincumar, P; Lee, D A; Bader, D L; Knight, M M

2012-09-19

This study adopts a combined computational and experimental approach to determine the mechanical, structural, and metabolic properties of isolated chondrocytes cultured within three-dimensional hydrogels. A series of linear elastic and hyperelastic finite-element models demonstrated that chondrocytes cultured for 24 h in gels for which the relaxation modulus is <5 kPa exhibit a cellular Young's modulus of ∼5 kPa. This is notably greater than that reported for isolated chondrocytes in suspension. The increase in cell modulus occurs over a 24-h period and is associated with an increase in the organization of the cortical actin cytoskeleton, which is known to regulate cell mechanics. However, there was a reduction in chromatin condensation, suggesting that changes in the nucleus mechanics may not be involved. Comparison of cells in 1% and 3% agarose showed that cells in the stiffer gels rapidly develop a higher Young's modulus of ∼20 kPa, sixfold greater than that observed in the softer gels. This was associated with higher levels of actin organization and chromatin condensation, but only after 24 h in culture. Further studies revealed that cells in stiffer gels synthesize less extracellular matrix over a 28-day culture period. Hence, this study demonstrates that the properties of the three-dimensional microenvironment regulate the mechanical, structural, and metabolic properties of living cells. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Moiré-reduction method for slanted-lenticular-based quasi-three-dimensional displays

NASA Astrophysics Data System (ADS)

Zhuang, Zhenfeng; Surman, Phil; Zhang, Lei; Rawat, Rahul; Wang, Shizheng; Zheng, Yuanjin; Sun, Xiao Wei

2016-12-01

In this paper we present a method for determining the preferred slanted angle for a lenticular film that minimizes moiré patterns in quasi-three-dimensional (Q3D) displays. We evaluate the preferred slanted angles of the lenticular film for the stripe-type sub-pixel structure liquid crystal display (LCD) panel. Additionally, the sub-pixels mapping algorithm of the specific angle is proposed to assign the images to either the right or left eye channel. A Q3D display prototype is built. Compared with the conventional SLF, this newly implemented Q3D display can not only eliminate moiré patterns but also provide 3D images in both portrait and landscape orientations. It is demonstrated that the developed slanted lenticular film (SLF) provides satisfactory 3D images by employing a compact structure, minimum moiré patterns and stabilized 3D contrast.

Prototyping of Dental Structures Using Laser Milling

NASA Astrophysics Data System (ADS)

Andreev, A. O.; Kosenko, M. S.; Petrovskiy, V. N.; Mironov, V. D.

2016-02-01

The results of experimental studies of the effect of an ytterbium fiber laser radiation parameters on processing efficiency and quality of ZrO2 ceramics widely used in stomatology are presented. Laser operating conditions with optimum characteristics for obtaining high quality final surfaces and rapid material removal of dental structures are determined. The ability of forming thin-walled ceramic structures by laser milling technology (a minimum wall thickness of 50 μm) is demonstrated. The examples of three-dimensional dental structures created in computer 3D-models of human teeth using laser milling are shown.

Three-Dimensional Model of Holographic Formation of Inhomogeneous PPLC Diffraction Structures

NASA Astrophysics Data System (ADS)

Semkin, A. O.; Sharangovich, S. N.

2018-05-01

A three-dimensional theoretical model of holographic formation of inhomogeneous diffraction structures in composite photopolymer - liquid crystal materials is presented considering both the nonlinearity of recording and the amplitude-phase inhomogeneity of the recording light field. Based on the results of numerical simulation, the kinematics of formations of such structures and their spatial profile are investigated.

Solution structure of the DNA-binding domain of the heat shock transcription factor determined by multidimensional heteronuclear magnetic resonance spectroscopy.

PubMed Central

Damberger, F. F.; Pelton, J. G.; Harrison, C. J.; Nelson, H. C.; Wemmer, D. E.

1994-01-01

The solution structure of the 92-residue DNA-binding domain of the heat shock transcription factor from Kluyveromyces lactis has been determined using multidimensional NMR methods. Three-dimensional (3D) triple resonance, 1H-13C-13C-1H total correlation spectroscopy, and 15N-separated total correlation spectroscopy-heteronuclear multiple quantum correlation experiments were used along with various 2D spectra to make nearly complete assignments for the backbone and side-chain 1H, 15N, and 13C resonances. Five-hundred eighty-three NOE constraints identified in 3D 13C- and 15N-separated NOE spectroscopy (NOESY)-heteronuclear multiple quantum correlation spectra and a 4-dimensional 13C/13C-edited NOESY spectrum, along with 35 phi, 9 chi 1, and 30 hydrogen bond constraints, were used to calculate 30 structures by hybrid distance geometry/stimulated annealing protocol, of which 24 were used for structural comparison. The calculations revealed that a 3-helix bundle packs against a small 4-stranded antiparallel beta-sheet. The backbone RMS deviation (RMSD) for the family of structures was 1.03 +/- 0.19 A with respect to the average structure. The topology is analogous to that of the C-terminal domain of the catabolite gene activator protein and appears to be in the helix-turn-helix family of DNA-binding proteins. The overall fold determined by the NMR data is consistent with recent crystallographic work on this domain (Harrison CJ, Bohm AA, Nelson HCM, 1994, Science 263:224) as evidenced by RMSD between backbone atoms in the NMR and X-ray structures of 1.77 +/- 0.20 A. Several differences were identified some of which may be due to protein-protein interactions in the crystal. PMID:7849597

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin

PubMed Central

Seer-Linnemayr, Charlotte; Ravelli, Raimond B. G.; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V.; Pannu, Navraj S.; Schatz, Michael; van Heel, Marin

2017-01-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the ‘Einstein from random noise’ problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous (‘four-dimensional’) cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, ‘random-startup’ three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external ‘starting models’. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive ‘ABC-4D’ pipeline is based on the two-dimensional reference-free ‘alignment by classification’ (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure. PMID:28989723

Multilocality and fusion rules on the generalized structure functions in two-dimensional and three-dimensional Navier-Stokes turbulence.

PubMed

Gkioulekas, Eleftherios

2016-09-01

Using the fusion-rules hypothesis for three-dimensional and two-dimensional Navier-Stokes turbulence, we generalize a previous nonperturbative locality proof to multiple applications of the nonlinear interactions operator on generalized structure functions of velocity differences. We call this generalization of nonperturbative locality to multiple applications of the nonlinear interactions operator "multilocality." The resulting cross terms pose a new challenge requiring a new argument and the introduction of a new fusion rule that takes advantage of rotational symmetry. Our main result is that the fusion-rules hypothesis implies both locality and multilocality in both the IR and UV limits for the downscale energy cascade of three-dimensional Navier-Stokes turbulence and the downscale enstrophy cascade and inverse energy cascade of two-dimensional Navier-Stokes turbulence. We stress that these claims relate to nonperturbative locality of generalized structure functions on all orders and not the term-by-term perturbative locality of diagrammatic theories or closure models that involve only two-point correlation and response functions.

Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames

NASA Astrophysics Data System (ADS)

Tian, Ye; Wang, Tong; Liu, Wenyan; Xin, Huolin L.; Li, Huilin; Ke, Yonggang; Shih, William M.; Gang, Oleg

2015-07-01

Three-dimensional mesoscale clusters that are formed from nanoparticles spatially arranged in pre-determined positions can be thought of as mesoscale analogues of molecules. These nanoparticle architectures could offer tailored properties due to collective effects, but developing a general platform for fabricating such clusters is a significant challenge. Here, we report a strategy for assembling three-dimensional nanoparticle clusters that uses a molecular frame designed with encoded vertices for particle placement. The frame is a DNA origami octahedron and can be used to fabricate clusters with various symmetries and particle compositions. Cryo-electron microscopy is used to uncover the structure of the DNA frame and to reveal that the nanoparticles are spatially coordinated in the prescribed manner. We show that the DNA frame and one set of nanoparticles can be used to create nanoclusters with different chiroptical activities. We also show that the octahedra can serve as programmable interparticle linkers, allowing one- and two-dimensional arrays to be assembled with designed particle arrangements.

Determination of strain fields in porous shape memory alloys using micro-computed tomography

NASA Astrophysics Data System (ADS)

Bormann, Therese; Friess, Sebastian; de Wild, Michael; Schumacher, Ralf; Schulz, Georg; Müller, Bert

2010-09-01

Shape memory alloys (SMAs) belong to 'intelligent' materials since the metal alloy can change its macroscopic shape as the result of the temperature-induced, reversible martensite-austenite phase transition. SMAs are often applied for medical applications such as stents, hinge-less instruments, artificial muscles, and dental braces. Rapid prototyping techniques, including selective laser melting (SLM), allow fabricating complex porous SMA microstructures. In the present study, the macroscopic shape changes of the SMA test structures fabricated by SLM have been investigated by means of micro computed tomography (μCT). For this purpose, the SMA structures are placed into the heating stage of the μCT system SkyScan 1172™ (SkyScan, Kontich, Belgium) to acquire three-dimensional datasets above and below the transition temperature, i.e. at room temperature and at about 80°C, respectively. The two datasets were registered on the basis of an affine registration algorithm with nine independent parameters - three for the translation, three for the rotation and three for the scaling in orthogonal directions. Essentially, the scaling parameters characterize the macroscopic deformation of the SMA structure of interest. Furthermore, applying the non-rigid registration algorithm, the three-dimensional strain field of the SMA structure on the micrometer scale comes to light. The strain fields obtained will serve for the optimization of the SLM-process and, more important, of the design of the complex shaped SMA structures for tissue engineering and medical implants.

Validating two-dimensional leadership models on three-dimensionally structured fish schools

PubMed Central

Nagy, Máté; Holbrook, Robert I.; Biro, Dora; Burt de Perera, Theresa

2017-01-01

Identifying leader–follower interactions is crucial for understanding how a group decides where or when to move, and how this information is transferred between members. Although many animal groups have a three-dimensional structure, previous studies investigating leader–follower interactions have often ignored vertical information. This raises the question of whether commonly used two-dimensional leader–follower analyses can be used justifiably on groups that interact in three dimensions. To address this, we quantified the individual movements of banded tetra fish (Astyanax mexicanus) within shoals by computing the three-dimensional trajectories of all individuals using a stereo-camera technique. We used these data firstly to identify and compare leader–follower interactions in two and three dimensions, and secondly to analyse leadership with respect to an individual's spatial position in three dimensions. We show that for 95% of all pairwise interactions leadership identified through two-dimensional analysis matches that identified through three-dimensional analysis, and we reveal that fish attend to the same shoalmates for vertical information as they do for horizontal information. Our results therefore highlight that three-dimensional analyses are not always required to identify leader–follower relationships in species that move freely in three dimensions. We discuss our results in terms of the importance of taking species' sensory capacities into account when studying interaction networks within groups. PMID:28280582

Engineering the internal surfaces of three-dimensional nanoporous catalysts by surfactant-modified dealloying.

PubMed

Wang, Zhili; Liu, Pan; Han, Jiuhui; Cheng, Chun; Ning, Shoucong; Hirata, Akihiko; Fujita, Takeshi; Chen, Mingwei

2017-10-20

Tuning surface structures by bottom-up synthesis has been demonstrated as an effective strategy to improve the catalytic performances of nanoparticle catalysts. Nevertheless, the surface modification of three-dimensional nanoporous metals, fabricated by a top-down dealloying approach, has not been achieved despite great efforts devoted to improving the catalytic performance of three-dimensional nanoporous catalysts. Here we report a surfactant-modified dealloying method to tailor the surface structure of nanoporous gold for amplified electrocatalysis toward methanol oxidation and oxygen reduction reactions. With the assistance of surfactants, {111} or {100} faceted internal surfaces of nanoporous gold can be realized in a controllable manner by optimizing dealloying conditions. The surface modified nanoporous gold exhibits significantly enhanced electrocatalytic activities in comparison with conventional nanoporous gold. This study paves the way to develop high-performance three-dimensional nanoporous catalysts with a tunable surface structure by top-down dealloying for efficient chemical and electrochemical reactions.

X-ray diffraction study of Penicillium Vitale catalase in the complex with aminotriazole

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borovik, A. A.; Grebenko, A. I.; Melik-Adamyan, V. R., E-mail: mawr@ns.crys.ras.ru

2011-07-15

The three-dimensional structure of the enzyme catalase from Penicillium vitale in a complex with the inhibitor aminotriazole was solved and refined by protein X-ray crystallography methods. An analysis of the three-dimensional structure of the complex showed that the inhibition of the enzyme occurs as a result of the covalent binding of aminotriazole to the amino-acid residue His64 in the active site of the enzyme. An investigation of the three-dimensional structure of the complex resulted in the amino-acid residues being more precisely identified. The binding sites of saccharide residues and calcium ions in the protein molecule were found.

Protein Structure Determination from Pseudocontact Shifts Using ROSETTA

PubMed Central

Schmitz, Christophe; Vernon, Robert; Otting, Gottfried; Baker, David; Huber, Thomas

2013-01-01

Paramagnetic metal ions generate pseudocontact shifts (PCSs) in nuclear magnetic resonance spectra that are manifested as easily measurable changes in chemical shifts. Metals can be incorporated into proteins through metal binding tags, and PCS data constitute powerful long-range restraints on the positions of nuclear spins relative to the coordinate system of the magnetic susceptibility anisotropy tensor (Δχ-tensor) of the metal ion. We show that three-dimensional structures of proteins can reliably be determined using PCS data from a single metal binding site combined with backbone chemical shifts. The program PCS-ROSETTA automatically determines the Δχ-tensor and metal position from the PCS data during the structure calculations, without any prior knowledge of the protein structure. The program can determine structures accurately for proteins of up to 150 residues, offering a powerful new approach to protein structure determination that relies exclusively on readily measurable backbone chemical shifts and easily discriminates between correctly and incorrectly folded conformations. PMID:22285518

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Yifei; Zuo, Jian -Min

A diffraction-based technique is developed for the determination of three-dimensional nanostructures. The technique employs high-resolution and low-dose scanning electron nanodiffraction (SEND) to acquire three-dimensional diffraction patterns, with the help of a special sample holder for large-angle rotation. Grains are identified in three-dimensional space based on crystal orientation and on reconstructed dark-field images from the recorded diffraction patterns. Application to a nanocrystalline TiN thin film shows that the three-dimensional morphology of columnar TiN grains of tens of nanometres in diameter can be reconstructed using an algebraic iterative algorithm under specified prior conditions, together with their crystallographic orientations. The principles can bemore » extended to multiphase nanocrystalline materials as well. Furthermore, the tomographic SEND technique provides an effective and adaptive way of determining three-dimensional nanostructures.« less

Challenges in NMR-based structural genomics

NASA Astrophysics Data System (ADS)

Sue, Shih-Che; Chang, Chi-Fon; Huang, Yao-Te; Chou, Ching-Yu; Huang, Tai-huang

2005-05-01

Understanding the functions of the vast number of proteins encoded in many genomes that have been completely sequenced recently is the main challenge for biologists in the post-genomics era. Since the function of a protein is determined by its exact three-dimensional structure it is paramount to determine the 3D structures of all proteins. This need has driven structural biologists to undertake the structural genomics project aimed at determining the structures of all known proteins. Several centers for structural genomics studies have been established throughout the world. Nuclear magnetic resonance (NMR) spectroscopy has played a major role in determining protein structures in atomic details and in a physiologically relevant solution state. Since the number of new genes being discovered daily far exceeds the number of structures determined by both NMR and X-ray crystallography, a high-throughput method for speeding up the process of protein structure determination is essential for the success of the structural genomics effort. In this article we will describe NMR methods currently being employed for protein structure determination. We will also describe methods under development which may drastically increase the throughput, as well as point out areas where opportunities exist for biophysicists to make significant contribution in this important field.

Structures of cage, prism, and book isomers of water hexamer from broadband rotational spectroscopy.

PubMed

Pérez, Cristóbal; Muckle, Matt T; Zaleski, Daniel P; Seifert, Nathan A; Temelso, Berhane; Shields, George C; Kisiel, Zbigniew; Pate, Brooks H

2012-05-18

Theory predicts the water hexamer to be the smallest water cluster with a three-dimensional hydrogen-bonding network as its minimum energy structure. There are several possible low-energy isomers, and calculations with different methods and basis sets assign them different relative stabilities. Previous experimental work has provided evidence for the cage, book, and cyclic isomers, but no experiment has identified multiple coexisting structures. Here, we report that broadband rotational spectroscopy in a pulsed supersonic expansion unambiguously identifies all three isomers; we determined their oxygen framework structures by means of oxygen-18-substituted water (H(2)(18)O). Relative isomer populations at different expansion conditions establish that the cage isomer is the minimum energy structure. Rotational spectra consistent with predicted heptamer and nonamer structures have also been identified.

Modelling the drying of three-dimensional pulp moulded structures. Part II, Drying data obtained from flat panels using virgin and recycled paper fibre

Treesearch

John F. Hunt; Margit Tamasy-Bano; Heike Nyist

1999-01-01

A three-dimensional structural panel, called FPL Spaceboard, was developed at the USDA Forest Products Laboratory. Spaceboard panels have been formed using a variety of fibrous materials using either a wet- or dry-forming process. Geometrically, the panel departs from the traditional two-dimensional flat panel by integrally forming an array of perpendicular ribs and...

Balancing Newtonian gravity and spin to create localized structures

NASA Astrophysics Data System (ADS)

Bush, Michael; Lindner, John

2015-03-01

Using geometry and Newtonian physics, we design localized structures that do not require electromagnetic or other forces to resist implosion or explosion. In two-dimensional Euclidean space, we find an equilibrium configuration of a rotating ring of massive dust whose inward gravity is the centripetal force that spins it. We find similar solutions in three-dimensional Euclidean and hyperbolic spaces, but only in the limit of vanishing mass. Finally, in three-dimensional Euclidean space, we generalize the two-dimensional result by finding an equilibrium configuration of a spherical shell of massive dust that supports itself against gravitational collapse by spinning isoclinically in four dimensions so its three-dimensional acceleration is everywhere inward. These Newtonian ``atoms'' illuminate classical physics and geometry.

Gold nanocrystals with DNA-directed morphologies.

PubMed

Ma, Xingyi; Huh, June; Park, Wounjhang; Lee, Luke P; Kwon, Young Jik; Sim, Sang Jun

2016-09-16

Precise control over the structure of metal nanomaterials is important for developing advanced nanobiotechnology. Assembly methods of nanoparticles into structured blocks have been widely demonstrated recently. However, synthesis of nanocrystals with controlled, three-dimensional structures remains challenging. Here we show a directed crystallization of gold by a single DNA molecular regulator in a sequence-independent manner and its applications in three-dimensional topological controls of crystalline nanostructures. We anchor DNA onto gold nanoseed with various alignments to form gold nanocrystals with defined topologies. Some topologies are asymmetric including pushpin-, star- and biconcave disk-like structures, as well as more complex jellyfish- and flower-like structures. The approach of employing DNA enables the solution-based synthesis of nanocrystals with controlled, three-dimensional structures in a desired direction, and expands the current tools available for designing and synthesizing feature-rich nanomaterials for future translational biotechnology.

Gold nanocrystals with DNA-directed morphologies

NASA Astrophysics Data System (ADS)

Ma, Xingyi; Huh, June; Park, Wounjhang; Lee, Luke P.; Kwon, Young Jik; Sim, Sang Jun

2016-09-01

Precise control over the structure of metal nanomaterials is important for developing advanced nanobiotechnology. Assembly methods of nanoparticles into structured blocks have been widely demonstrated recently. However, synthesis of nanocrystals with controlled, three-dimensional structures remains challenging. Here we show a directed crystallization of gold by a single DNA molecular regulator in a sequence-independent manner and its applications in three-dimensional topological controls of crystalline nanostructures. We anchor DNA onto gold nanoseed with various alignments to form gold nanocrystals with defined topologies. Some topologies are asymmetric including pushpin-, star- and biconcave disk-like structures, as well as more complex jellyfish- and flower-like structures. The approach of employing DNA enables the solution-based synthesis of nanocrystals with controlled, three-dimensional structures in a desired direction, and expands the current tools available for designing and synthesizing feature-rich nanomaterials for future translational biotechnology.

Three-dimensional confocal microscopy of the living cornea and ocular lens

NASA Astrophysics Data System (ADS)

Masters, Barry R.

1991-07-01

The three-dimensional reconstruction of the optic zone of the cornea and the ocular crystalline lens has been accomplished using confocal microscopy and volume rendering computer techniques. A laser scanning confocal microscope was used in the reflected light mode to obtain the two-dimensional images from the cornea and the ocular lens of a freshly enucleated rabbit eye. The light source was an argon ion laser with a 488 nm wavelength. The microscope objective was a Leitz X25, NA 0.6 water immersion lens. The 400 micron thick cornea was optically sectioned into 133 three micron sections. The semi-transparent cornea and the in-situ ocular lens was visualized as high resolution, high contrast two-dimensional images. The structures observed in the cornea include: superficial epithelial cells and their nuclei, basal epithelial cells and their 'beaded' cell borders, basal lamina, nerve plexus, nerve fibers, nuclei of stromal keratocytes, and endothelial cells. The structures observed in the in- situ ocular lens include: lens capsule, lens epithelial cells, and individual lens fibers. The three-dimensional data sets of the cornea and the ocular lens were reconstructed in the computer using volume rendering techniques. Stereo pairs were also created of the two- dimensional ocular images for visualization. The stack of two-dimensional images was reconstructed into a three-dimensional object using volume rendering techniques. This demonstration of the three-dimensional visualization of the intact, enucleated eye provides an important step toward quantitative three-dimensional morphometry of the eye. The important aspects of three-dimensional reconstruction are discussed.

Quasi-three-dimensional particle imaging with digital holography.

PubMed

Kemppinen, Osku; Heinson, Yuli; Berg, Matthew

2017-05-01

In this work, approximate three-dimensional structures of microparticles are generated with digital holography using an automated focus method. This is done by stacking a collection of silhouette-like images of a particle reconstructed from a single in-line hologram. The method enables estimation of the particle size in the longitudinal and transverse dimensions. Using the discrete dipole approximation, the method is tested computationally by simulating holograms for a variety of particles and attempting to reconstruct the known three-dimensional structure. It is found that poor longitudinal resolution strongly perturbs the reconstructed structure, yet the method does provide an approximate sense for the structure's longitudinal dimension. The method is then applied to laboratory measurements of holograms of single microparticles and their scattering patterns.

Preliminary crystallographic studies of four crystal forms of serum albumin

NASA Technical Reports Server (NTRS)

Carter, D. C.; Chang, B.; Ho, J. X.; Keeling, K.; Krishnasami, Z.

1994-01-01

Several crystal forms of serum albumin suitable for three-dimensional structure determination have been grown. These forms include crystals of recombinant and wild-type human serum albumin, baboon serum albumin, and canine serum albumin. The intrinsic limits of X-ray diffraction for these crystals are in the range 0.28-0.22 nm. Two of the crystal forms produced from human and canine albumin include incorporated long-chain fatty acids. Molecular replacement experiments have been successfully conducted on each crystal form using the previously determined atomic coordinates of human serum albumin illustrating the conserved tertiary structure.

Spatial localization of the Ebola virus glycoprotein mucin-like domain determined by cryo-electron tomography.

PubMed

Tran, Erin E H; Simmons, James A; Bartesaghi, Alberto; Shoemaker, Charles J; Nelson, Elizabeth; White, Judith M; Subramaniam, Sriram

2014-09-01

The Ebola virus glycoprotein mucin-like domain (MLD) is implicated in Ebola virus cell entry and immune evasion. Using cryo-electron tomography of Ebola virus-like particles, we determined a three-dimensional structure for the full-length glycoprotein in a near-native state and compared it to that of a glycoprotein lacking the MLD. Our results, which show that the MLD is located at the apex and the sides of each glycoprotein monomer, provide a structural template for analysis of MLD function. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Exact solution of three-dimensional transport problems using one-dimensional models. [in semiconductor devices

NASA Technical Reports Server (NTRS)

Misiakos, K.; Lindholm, F. A.

1986-01-01

Several parameters of certain three-dimensional semiconductor devices including diodes, transistors, and solar cells can be determined without solving the actual boundary-value problem. The recombination current, transit time, and open-circuit voltage of planar diodes are emphasized here. The resulting analytical expressions enable determination of the surface recombination velocity of shallow planar diodes. The method involves introducing corresponding one-dimensional models having the same values of these parameters.

Three-Dimensional, Inelastic Response of Single-Edge Notch Bend Specimens Subjected to Impact Loading

DTIC Science & Technology

1993-08-01

measure the inherent fracture toughness of a material. A thor- ough understanding of the test specimen behavior is a prerequisite to the application of...measured material properties in structural applications . Three- dimensional dynamic analyses are performed for three different specimen configurations...derstanding of the test specimen behavior is a prerequisite to the application of measured ma- terial properties in structural applications . Three

Synthesis, Structure and Thermal Behavior of Oxalato-Bridged Rb+ and H3O+ Extended Frameworks with Different Dimensionalities

PubMed Central

Kherfi, Hamza; Hamadène, Malika; Guehria-Laïdoudi, Achoura; Dahaoui, Slimane; Lecomte, Claude

2010-01-01

Correlative studies of three oxalato-bridged polymers, obtained under hydrothermal conditions for the two isostructural compounds {Rb(HC2O4)(H2C2O4)(H2O)2}∞1, 1, {H3O(HC2O4)(H2C2O4).2H2O}∞1, 2, and by conventional synthetic method for {Rb(HC2O4)}∞3, 3, allowed the identification of H-bond patterns and structural dimensionality. Ferroïc domain structures are confirmed by electric measurements performed on 3. Although 2 resembles one oxalic acid sesquihydrate, its structure determination doesn’t display any kind of disorder and leads to recognition of a supramolecular network identical to hybrid s-block series, where moreover, unusual H3O+ and NH4+ similarity is brought out. Thermal behaviors show that 1D frameworks with extended H-bonds, whether with or without a metal center, have the same stability. Inversely, despite the dimensionalities, the same metallic intermediate and final compounds are obtained for the two Rb+ ferroïc materials.

Flame-Generated Vorticity Production in Premixed Flame-Vortex Interactions

NASA Technical Reports Server (NTRS)

Patnaik, G.; Kailasanath, K.

2003-01-01

In this study, we use detailed time-dependent, multi-dimensional numerical simulations to investigate the relative importance of the processes leading to FGV in flame-vortex interactions in normal gravity and microgravity and to determine if the production of vorticity in flames in gravity is the same as that in zero gravity except for the contribution of the gravity term. The numerical simulations will be performed using the computational model developed at NRL, FLAME3D. FLAME3D is a parallel, multi-dimensional (either two- or three-dimensional) flame model based on FLIC2D, which has been used extensively to study the structure and stability of premixed hydrogen and methane flames.

Development of a thermal and structural analysis procedure for cooled radial turbines

NASA Technical Reports Server (NTRS)

Kumar, Ganesh N.; Deanna, Russell G.

1988-01-01

A procedure for computing the rotor temperature and stress distributions in a cooled radial turbine is considered. Existing codes for modeling the external mainstream flow and the internal cooling flow are used to compute boundary conditions for the heat transfer and stress analyses. An inviscid, quasi three-dimensional code computes the external free stream velocity. The external velocity is then used in a boundary layer analysis to compute the external heat transfer coefficients. Coolant temperatures are computed by a viscous one-dimensional internal flow code for the momentum and energy equation. These boundary conditions are input to a three-dimensional heat conduction code for calculation of rotor temperatures. The rotor stress distribution may be determined for the given thermal, pressure and centrifugal loading. The procedure is applied to a cooled radial turbine which will be tested at the NASA Lewis Research Center. Representative results from this case are included.

Linking a completely three-dimensional nanostrain to a structural transformation eigenstrain.

PubMed

Tirry, Wim; Schryvers, Dominique

2009-09-01

Ni-Ti is one of the most popular shape-memory alloys, a phenomenon resulting from a martensitic transformation. Commercial Ni-Ti-based alloys are often thermally treated to contain Ni(4)Ti(3) precipitates. The presence of these precipitates can introduce an extra transformation step related to the so-called R-phase. It is believed that the strain field surrounding the precipitates, caused by the matrix-precipitate lattice mismatch, lies at the origin of this intermediate transformation step. Atomic-resolution transmission electron microscopy in combination with geometrical phase analysis is used to measure the elastic strain field surrounding these precipitates. By combining measurements from two different crystallographic directions, the three-dimensional strain matrix is determined from two-dimensional measurements. Comparison of the measured strain matrix to the eigenstrain of the R-phase shows that both are very similar and that the introduction of the R-phase might indeed compensate the elastic strain introduced by the precipitate.

Linking a completely three-dimensional nanostrain to a structural transformation eigenstrain

NASA Astrophysics Data System (ADS)

Tirry, Wim; Schryvers, Dominique

2009-09-01

Ni-Ti is one of the most popular shape-memory alloys, a phenomenon resulting from a martensitic transformation. Commercial Ni-Ti-based alloys are often thermally treated to contain Ni4Ti3 precipitates. The presence of these precipitates can introduce an extra transformation step related to the so-called R-phase. It is believed that the strain field surrounding the precipitates, caused by the matrix-precipitate lattice mismatch, lies at the origin of this intermediate transformation step. Atomic-resolution transmission electron microscopy in combination with geometrical phase analysis is used to measure the elastic strain field surrounding these precipitates. By combining measurements from two different crystallographic directions, the three-dimensional strain matrix is determined from two-dimensional measurements. Comparison of the measured strain matrix to the eigenstrain of the R-phase shows that both are very similar and that the introduction of the R-phase might indeed compensate the elastic strain introduced by the precipitate.

NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins.

PubMed

Borguesan, Bruno; Inostroza-Ponta, Mario; Dorn, Márcio

2017-03-01

The exponential growth in the number of experimentally determined three-dimensional protein structures provide a new and relevant knowledge about the conformation of amino acids in proteins. Only a few of probability densities of amino acids are publicly available for use in structure validation and prediction methods. NIAS (Neighbors Influence of Amino acids and Secondary structures) is a web-based tool used to extract information about conformational preferences of amino acid residues and secondary structures in experimental-determined protein templates. This information is useful, for example, to characterize folds and local motifs in proteins, molecular folding, and can help the solution of complex problems such as protein structure prediction, protein design, among others. The NIAS-Server and supplementary data are available at http://sbcb.inf.ufrgs.br/nias .

Ab Initio Structural Modeling of and Experimental Validation for Chlamydia trachomatis Protein CT296 Reveal Structural Similarity to Fe(II) 2-Oxoglutarate-Dependent Enzymes▿

PubMed Central

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott

2011-01-01

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-Å Cα root mean square deviation [RMSD]) the high-resolution (1.8-Å) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur. PMID:21965559

Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott

2012-02-13

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF)more » CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.« less

Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure.

PubMed

Das, Uday; Naskar, Jishu; Mukherjee, Alok Kumar

2015-12-01

A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

Automated integration of lidar into the LANDFIRE product suite

Treesearch

Birgit Peterson; Kurtis J. Nelson; Carl Seielstad; Jason Stoker; W. Matt Jolly; Russell Parsons

2015-01-01

Accurate information about three-dimensional canopy structure and wildland fuel across the landscape is necessary for fire behaviour modelling system predictions. Remotely sensed data are invaluable for assessing these canopy characteristics over large areas; lidar data, in particular, are uniquely suited for quantifying three-dimensional canopy structure. Although...

Two-photon polymerization of a three dimensional structure using beams with orbital angular momentum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Shi-Jie; Li, Yan, E-mail: li@pku.edu.cn; Liu, Zhao-Pei

The focus of a beam with orbital angular momentum exhibits internal structure instead of an elliptical intensity distribution of a Gaussian beam, and the superposition of Gauss-Laguerre beams realized by two-dimensional phase modulation can generate a complex three-dimensional (3D) focus. By taking advantage of the flexibility of this 3D focus tailoring, we have fabricated a 3D microstructure with high resolution by two-photon polymerization with a single exposure. Furthermore, we have polymerized an array of double-helix structures that demonstrates optical chirality.

Quantized vortices and superflow in arbitrary dimensions: structure, energetics and dynamics

NASA Astrophysics Data System (ADS)

Goldbart, Paul M.; Bora, Florin

2009-05-01

The structure and energetics of superflow around quantized vortices, and the motion inherited by these vortices from this superflow, are explored in the general setting of a superfluid in arbitrary dimensions. The vortices may be idealized as objects of codimension 2, such as one-dimensional loops and two-dimensional closed surfaces, respectively, in the cases of three- and four-dimensional superfluidity. By using the analogy between the vortical superflow and Ampère-Maxwell magnetostatics, the equilibrium superflow containing any specified collection of vortices is constructed. The energy of the superflow is found to take on a simple form for vortices that are smooth and asymptotically large, compared with the vortex core size. The motion of vortices is analyzed in general, as well as for the special cases of hyper-spherical and weakly distorted hyper-planar vortices. In all dimensions, vortex motion reflects vortex geometry. In dimension 4 and higher, this includes not only extrinsic but also intrinsic aspects of the vortex shape, which enter via the first and second fundamental forms of classical geometry. For hyper-spherical vortices, which generalize the vortex rings of three-dimensional superfluidity, the energy-momentum relation is determined. Simple scaling arguments recover the essential features of these results, up to numerical and logarithmic factors.

Three-dimensional nanomagnetism

DOE PAGES

Fernandez-Pacheco, Amalio; Streubel, Robert; Fruchart, Olivier; ...

2017-06-09

Magnetic nanostructures are being developed for use in many aspects of our daily life, spanning areas such as data storage, sensing and biomedicine. Whereas patterned nanomagnets are traditionally two-dimensional planar structures, recent work is expanding nanomagnetism into three dimensions; a move triggered by the advance of unconventional synthesis methods and the discovery of new magnetic effects. In three-dimensional nanomagnets more complex magnetic configurations become possible, many with unprecedented properties. Here we review the creation of these structures and their implications for the emergence of new physics, the development of instrumentation and computational methods, and exploitation in numerous applications.

Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap

NASA Astrophysics Data System (ADS)

Spiwok, Vojtěch; Králová, Blanka

2011-12-01

Atomic motions in molecules are not linear. This infers that nonlinear dimensionality reduction methods can outperform linear ones in analysis of collective atomic motions. In addition, nonlinear collective motions can be used as potentially efficient guides for biased simulation techniques. Here we present a simulation with a bias potential acting in the directions of collective motions determined by a nonlinear dimensionality reduction method. Ad hoc generated conformations of trans,trans-1,2,4-trifluorocyclooctane were analyzed by Isomap method to map these 72-dimensional coordinates to three dimensions, as described by Brown and co-workers [J. Chem. Phys. 129, 064118 (2008)]. Metadynamics employing the three-dimensional embeddings as collective variables was applied to explore all relevant conformations of the studied system and to calculate its conformational free energy surface. The method sampled all relevant conformations (boat, boat-chair, and crown) and corresponding transition structures inaccessible by an unbiased simulation. This scheme allows to use essentially any parameter of the system as a collective variable in biased simulations. Moreover, the scheme we used for mapping out-of-sample conformations from the 72D to 3D space can be used as a general purpose mapping for dimensionality reduction, beyond the context of molecular modeling.

Topology of large-scale structure. IV - Topology in two dimensions

NASA Technical Reports Server (NTRS)

Melott, Adrian L.; Cohen, Alexander P.; Hamilton, Andrew J. S.; Gott, J. Richard, III; Weinberg, David H.

1989-01-01

In a recent series of papers, an algorithm was developed for quantitatively measuring the topology of the large-scale structure of the universe and this algorithm was applied to numerical models and to three-dimensional observational data sets. In this paper, it is shown that topological information can be derived from a two-dimensional cross section of a density field, and analytic expressions are given for a Gaussian random field. The application of a two-dimensional numerical algorithm for measuring topology to cross sections of three-dimensional models is demonstrated.

Hydroelastic behaviour of a structure exposed to an underwater explosion

PubMed Central

Colicchio, G.; Greco, M.; Brocchini, M.; Faltinsen, O. M.

2015-01-01

The hydroelastic interaction between an underwater explosion and an elastic plate is investigated num- erically through a domain-decomposition strategy. The three-dimensional features of the problem require a large computational effort, which is reduced through a weak coupling between a one-dimensional radial blast solver, which resolves the blast evolution far from the boundaries, and a three-dimensional compressible flow solver used where the interactions between the compression wave and the boundaries take place and the flow becomes three-dimensional. The three-dimensional flow solver at the boundaries is directly coupled with a modal structural solver that models the response of the solid boundaries like elastic plates. This enables one to simulate the fluid–structure interaction as a strong coupling, in order to capture hydroelastic effects. The method has been applied to the experimental case of Hung et al. (2005 Int. J. Impact Eng. 31, 151–168 (doi:10.1016/j.ijimpeng.2003.10.039)) with explosion and structure sufficiently far from other boundaries and successfully validated in terms of the evolution of the acceleration induced on the plate. It was also used to investigate the interaction of an underwater explosion with the bottom of a close-by ship modelled as an orthotropic plate. In the application, the acoustic phase of the fluid–structure interaction is examined, highlighting the need of the fluid–structure coupling to capture correctly the possible inception of cavitation. PMID:25512585

Zero Launch Mass Three Dimensional Print Head

NASA Technical Reports Server (NTRS)

Mueller, Robert P.; Gelino, Nathan J.; Smith, Jonathan D.; Buckles, Brad C.; Lippitt, Thomas; Schuler, Jason M.; Nick, Andrew J.; Nugent, Matt W.; Townsend, Ivan I.

2018-01-01

NASA's strategic goal is to put humans on Mars in the 2030's. The NASA Human Spaceflight Architecture Team (HAT) and NASA Mars Design Reference Architecture (DRA) 5.0 has determined that in-situ resource utilization (ISRU) is an essential technology to accomplish this mission. Additive construction technology using in-situ materials from planetary surfaces will reduce launch mass, allow structures to be three dimensionally (3D) printed on demand, and will allow building designs to be transmitted digitally from Earth and printed in space. This will ultimately lead to elimination of reliance on structural materials launched from Earth (zero launch mass of construction consumables). The zero launch mass (ZLM) 3D print head project addressed this need by developing a system that 3D prints using a mixture of in-situ regolith and polymer as feedstock, determining the optimum mixture ratio and regolith particle size distribution, developing software to convert g-code into motion instructions for a FANUC robotic arm, printing test samples, performing materials testing, and printing a reduced scale habitable structure concept. This paper will focus on the ZLM 3D Print Head design, materials selection, software development, and lessons learned from operating the system in the NASA KSC Swamp Works Granular Mechanics & Regolith Operations (GMRO) Laboratory.

Hubble space telescope observations and geometric models of compact multipolar planetary nebulae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hsia, Chih-Hao; Chau, Wayne; Zhang, Yong

2014-05-20

We report high angular resolution Hubble Space Telescope observations of 10 compact planetary nebulae (PNs). Many interesting internal structures, including multipolar lobes, arcs, two-dimensional rings, tori, and halos, are revealed for the first time. These results suggest that multipolar structures are common among PNs, and these structures develop early in their evolution. From three-dimensional geometric models, we have determined the intrinsic dimensions of the lobes. Assuming the lobes are the result of interactions between later-developed fast winds and previously ejected asymptotic giant branch winds, the geometric structures of these PNs suggest that there are multiple phases of fast winds separatedmore » by temporal variations and/or directional changes. A scenario of evolution from lobe-dominated to cavity-dominated stages is presented. The results reported here will provide serious constraints on any dynamical models of PNs.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hosseinizadeh, Ahmad; Mashayekhi, Ghoncheh; Copperman, Jeremy

Using a manifold-based analysis of experimental diffraction snapshots from an X-ray free electron laser, we determine the three-dimensional structure and conformational landscape of the PR772 virus to a detector-limited resolution of 9 nm. Our results indicate that a single conformational coordinate controls reorganization of the genome, growth of a tubular structure from a portal vertex and release of the genome. Furthermore, these results demonstrate that single-particle X-ray scattering has the potential to shed light on key biological processes.

Polymorphism in 'L' shaped lipids: structure of N-, O-diacylethanolamines with mixed acyl chains.

PubMed

Tarafdar, Pradip K; Swamy, Musti J

2009-11-01

Although solid state polymorphism in lipids has been established by spectroscopic and calorimetric studies long ago, only in a few cases crystal structures of different polymorphs of the same compound have been reported, possibly due to difficulties in obtaining high quality single crystals of individual polymorphs. Recent studies show that N-, O-diacylethanolamines (DAEs) can be derived by the O-acylation of the stress-related lipids, the N-acylethanolamines under physiological conditions. In this study, two DAEs with mixed acyl chains, namely N-palmitoyl, O-octanoylethanolamine and N-palmitoyl, O-decanoylethanolamine have been synthesized and their three-dimensional structures were determined. Both the compounds were found to adopt 'L' shaped structures and exist in two polymorphic forms, alpha and beta. In the alpha form a mixed-type chain packing has been observed whereas in the beta form the chain packing is symmetric. Similar polymorphic forms are likely to exist in other 'L' shaped lipids such as 1,3-diacylglycerols and ceramides, where polymorphism has been detected earlier, but three-dimensional structures - which can give precise information about the packing at atomic resolution - have not been reported.

Large 3D direct laser written scaffolds for tissue engineering applications

NASA Astrophysics Data System (ADS)

Trautmann, Anika; Rüth, Marieke; Lemke, Horst-Dieter; Walther, Thomas; Hellmann, Ralf

2018-01-01

We report on the fabrication of three-dimensional direct laser written scaffolds for tissue engineering and the seeding of primary fibroblasts on these structures. Scaffolds are realized by two-photon absorption induced polymerization in the inorganic-organic hybrid polymer OrmoComp using a 515 nm femtosecond laser. A nonstop single-line single-pass writing process is implemented in order to produce periodic reproducible large scaled structures with a dimension in the range of several millimeters and reduce process time to less than one hour. This method allows us to determine optimized process parameters for writing stable structures while achieving pore sizes ranging from 5 μm to 90 μm and a scanning speed of up to 5 mm/s. After a multi-stage post-treatment, normal human dermal fibroblasts are applied to the scaffolds to test if these macroscopic structures with large surface and numerous small gaps between the pores provide nontoxic conditions. Furthermore, we study the cell behavior in this environment and observe both cell growth on as well as ingrowth on the three-dimensional structures. In particular, fibroblasts adhere and grow also on the vertical walls of the scaffolds.

Experimental and theoretical investigation of three-dimensional nitrogen-doped aluminum clusters AI 8N - and AI 8N

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Leiming; Huang, Wei; Wang, Lai S.

The structure and electronic properties of the Al 8N - and Al 8N clusters were investigated by combined photoelectron spectroscopy and ab initio studies. Congested photoelectron spectra were observed and experimental evidence was obtained for the presence of multiple isomers for Al 8N - Global minimum searches revealed several structures for Al 8N - with close energies. The calculated vertical detachment energies of the two lowest-lying isomers, which are of C 2v and C s symmetry, respectively, were shown to agree well with the experimental data. Unlike the three-dimensional structures of Al 6N - and Al 7N -, in whichmore » the dopant N atom has a high coordination number of 6,the dopant N atom in the two low-lying isomers of Al 8N - has a lower coordination number of 4 and 5, respectively. The competition between the Al–Al and Al–N interactions are shown to determine the global minimum structures of the doped aluminum clusters and results in the structural diversity for both Al 8N - and Al8N. © 2009 American Institute of Physics« less

Free and ATP-bound structures of Ap4A hydrolase from Aquifex aeolicus V5.

PubMed

Jeyakanthan, Jeyaraman; Kanaujia, Shankar Prasad; Nishida, Yuya; Nakagawa, Noriko; Praveen, Surendran; Shinkai, Akeo; Kuramitsu, Seiki; Yokoyama, Shigeyuki; Sekar, Kanagaraj

2010-02-01

Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 A resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alphabetaalpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.

Three-dimensional structure of thymidine phosphorylase from E. coli in complex with 3'-azido-2'-fluoro-2',3'-dideoxyuridine

NASA Astrophysics Data System (ADS)

Timofeev, V. I.; Abramchik, Yu. A.; Fateev, I. V.; Zhukhlistova, N. E.; Murav'eva, T. I.; Kuranova, I. P.; Esipov, R. S.

2013-11-01

The three-dimensional structures of thymidine phosphorylase from E. coli containing the bound sulfate ion in the phosphate-binding site and of the complex of thymidine phosphorylase with sulfate in the phosphate-binding site and the inhibitor 3'-azido-2'-fluoro-2',3'-dideoxyuridine (N3F-ddU) in the nucleoside-binding site were determined at 1.55 and 1.50 Å resolution, respectively. The amino-acid residues involved in the ligand binding and the hydrogen-bond network in the active site occupied by a large number of bound water molecules are described. A comparison of the structure of thymidine phosphorylase in complex with N3F-ddU with the structure of pyrimidine nucleoside phosphorylase from St. Aureus in complex with the natural substrate thymidine (PDB_ID: 3H5Q) shows that the substrate and the inhibitor in the nucleoside-binding pocket have different orientations. It is suggested that the position of N3F-ddU can be influenced by the presence of the azido group, which prefers a hydrophobic environment. In both structures, the active sites of the subunits are in the open conformation.

A novel camera localization system for extending three-dimensional digital image correlation

NASA Astrophysics Data System (ADS)

Sabato, Alessandro; Reddy, Narasimha; Khan, Sameer; Niezrecki, Christopher

2018-03-01

The monitoring of civil, mechanical, and aerospace structures is important especially as these systems approach or surpass their design life. Often, Structural Health Monitoring (SHM) relies on sensing techniques for condition assessment. Advancements achieved in camera technology and optical sensors have made three-dimensional (3D) Digital Image Correlation (DIC) a valid technique for extracting structural deformations and geometry profiles. Prior to making stereophotogrammetry measurements, a calibration has to be performed to obtain the vision systems' extrinsic and intrinsic parameters. It means that the position of the cameras relative to each other (i.e. separation distance, cameras angle, etc.) must be determined. Typically, cameras are placed on a rigid bar to prevent any relative motion between the cameras. This constraint limits the utility of the 3D-DIC technique, especially as it is applied to monitor large-sized structures and from various fields of view. In this preliminary study, the design of a multi-sensor system is proposed to extend 3D-DIC's capability and allow for easier calibration and measurement. The suggested system relies on a MEMS-based Inertial Measurement Unit (IMU) and a 77 GHz radar sensor for measuring the orientation and relative distance of the stereo cameras. The feasibility of the proposed combined IMU-radar system is evaluated through laboratory tests, demonstrating its ability in determining the cameras position in space for performing accurate 3D-DIC calibration and measurements.

Solution structure of the C-terminal domain of Ole e 9, a major allergen of olive pollen

PubMed Central

Treviño, Miguel Á.; Palomares, Oscar; Castrillo, Inés; Villalba, Mayte; Rodríguez, Rosalía; Rico, Manuel; Santoro, Jorge; Bruix, Marta

2008-01-01

Ole e 9 is an olive pollen allergen belonging to group 2 of pathogenesis-related proteins. The protein is composed of two immunological independent domains: an N-terminal domain (NtD) with 1,3-β-glucanase activity, and a C-terminal domain (CtD) that binds 1,3-β-glucans. We have determined the three-dimensional structure of CtD-Ole e 9 (101 amino acids), which consists of two parallel α-helices forming an angle of ∼55°, a small antiparallel β-sheet with two short strands, and a 3–10 helix turn, all connected by long coil segments, resembling a novel type of folding among allergens. Two regions surrounded by aromatic residues (F49, Y60, F96, Y91 and Y31, H68, Y65, F78) have been localized on the protein surface, and a role for sugar binding is suggested. The epitope mapping of CtD-Ole e 9 shows that B-cell epitopes are mainly located on loops, although some of them are contained in secondary structural elements. Interestingly, the IgG and IgE epitopes are contiguous or overlapped, rather than coincident. The three-dimensional structure of CtD-Ole e 9 might help to understand the underlying mechanism of its biochemical function and to determine possible structure–allergenicity relationships. PMID:18096638

ePlant and the 3D data display initiative: integrative systems biology on the world wide web.

PubMed

Fucile, Geoffrey; Di Biase, David; Nahal, Hardeep; La, Garon; Khodabandeh, Shokoufeh; Chen, Yani; Easley, Kante; Christendat, Dinesh; Kelley, Lawrence; Provart, Nicholas J

2011-01-10

Visualization tools for biological data are often limited in their ability to interactively integrate data at multiple scales. These computational tools are also typically limited by two-dimensional displays and programmatic implementations that require separate configurations for each of the user's computing devices and recompilation for functional expansion. Towards overcoming these limitations we have developed "ePlant" (http://bar.utoronto.ca/eplant) - a suite of open-source world wide web-based tools for the visualization of large-scale data sets from the model organism Arabidopsis thaliana. These tools display data spanning multiple biological scales on interactive three-dimensional models. Currently, ePlant consists of the following modules: a sequence conservation explorer that includes homology relationships and single nucleotide polymorphism data, a protein structure model explorer, a molecular interaction network explorer, a gene product subcellular localization explorer, and a gene expression pattern explorer. The ePlant's protein structure explorer module represents experimentally determined and theoretical structures covering >70% of the Arabidopsis proteome. The ePlant framework is accessed entirely through a web browser, and is therefore platform-independent. It can be applied to any model organism. To facilitate the development of three-dimensional displays of biological data on the world wide web we have established the "3D Data Display Initiative" (http://3ddi.org).

A three-dimensional neural spheroid model for capillary-like network formation.

PubMed

Boutin, Molly E; Kramer, Liana L; Livi, Liane L; Brown, Tyler; Moore, Christopher; Hoffman-Kim, Diane

2018-04-01

In vitro three-dimensional neural spheroid models have an in vivo-like cell density, and have the potential to reduce animal usage and increase experimental throughput. The aim of this study was to establish a spheroid model to study the formation of capillary-like networks in a three-dimensional environment that incorporates both neuronal and glial cell types, and does not require exogenous vasculogenic growth factors. We created self-assembled, scaffold-free cellular spheroids using primary-derived postnatal rodent cortex as a cell source. The interactions between relevant neural cell types, basement membrane proteins, and endothelial cells were characterized by immunohistochemistry. Transmission electron microscopy was used to determine if endothelial network structures had lumens. Endothelial cells within cortical spheroids assembled into capillary-like networks with lumens. Networks were surrounded by basement membrane proteins, including laminin, fibronectin and collagen IV, as well as key neurovascular cell types. Existing in vitro models of the cortical neurovascular environment study monolayers of endothelial cells, either on transwell inserts or coating cellular spheroids. These models are not well suited to study vasculogenesis, a process hallmarked by endothelial cell cord formation and subsequent lumenization. The neural spheroid is a new model to study the formation of endothelial cell capillary-like structures in vitro within a high cell density three-dimensional environment that contains both neuronal and glial populations. This model can be applied to investigate vascular assembly in healthy or disease states, such as stroke, traumatic brain injury, or neurodegenerative disorders. Copyright © 2017 Elsevier B.V. All rights reserved.

Photoelectron diffraction from single oriented molecules: Towards ultrafast structure determination of molecules using x-ray free-electron lasers

NASA Astrophysics Data System (ADS)

Kazama, Misato; Fujikawa, Takashi; Kishimoto, Naoki; Mizuno, Tomoya; Adachi, Jun-ichi; Yagishita, Akira

2013-06-01

We provide a molecular structure determination method, based on multiple-scattering x-ray photoelectron diffraction (XPD) calculations. This method is applied to our XPD data on several molecules having different equilibrium geometries. Then it is confirmed that, by our method, bond lengths and bond angles can be determined with a resolution of less than 0.1 Å and 10∘, respectively. Differently from any other scenario of ultrafast structure determination, we measure the two- or three-dimensional XPD of aligned or oriented molecules in the energy range from 100 to 200 eV with a 4π detection velocity map imaging spectrometer. Thanks to the intense and ultrashort pulse properties of x-ray free-electron lasers, our approach exhibits the most probable method for obtaining ultrafast real-time structural information on small to medium-sized molecules consisting of light elements, i.e., a “molecular movie.”

Nightside Structure of the Venusian Ionosphere

NASA Astrophysics Data System (ADS)

Ledvina, S. A.; Brecht, S. H.

2017-12-01

The Pioneer Venus Orbiter, PVO, was the first mission to detect large-scale structure in the nightside region of Venus. This structure is often referred to as "tail rays." Since this discovery, there has been continuous discussion as to the cause of the structure. There have been theoretical attempts to explain the structure but no definitive determination of the mechanism. Typically, the wavelengths of the structure were not always consistent with the theory. Three-dimensional hybrid simulations are reported that produce structure on the nightside of Venus. The structure seems consistent with the data. This paper will present the results of the simulations as well as a variety of numerical tests that offer some insight into the mechanism driving the development of the structure. The tests reveal that the ambipolar electric fields as produced by the gradient of the electron pressure seems to be the root cause of the structure. It will be shown that different realizations of the neutral wind modify the structure. The hybrid simulations are three dimensional with neutral winds included in the simulations. The resolution of the simulation is 50 km/cell and lower. The spherical grid used in the simulations to handle chemistry and collisions has a resolution of 5 km radially and under 50 km in the angular directions. It is these high resolution simulations that produce the structure to be discussed in this paper.

Analyzing the Magnetopause Internal Structure: New Possibilities Offered by MMS Tested in a Case Study

NASA Astrophysics Data System (ADS)

Rezeau, L.; Belmont, G.; Manuzzo, R.; Aunai, N.; Dargent, J.

2018-01-01

We explore the structure of the magnetopause using a crossing observed by the Magnetospheric Multiscale (MMS) spacecraft on 16 October 2015. Several methods (minimum variance analysis, BV method, and constant velocity analysis) are first applied to compute the normal to the magnetopause considered as a whole. The different results obtained are not identical, and we show that the whole boundary is not stationary and not planar, so that basic assumptions of these methods are not well satisfied. We then analyze more finely the internal structure for investigating the departures from planarity. Using the basic mathematical definition of what is a one-dimensional physical problem, we introduce a new single spacecraft method, called LNA (local normal analysis) for determining the varying normal, and we compare the results so obtained with those coming from the multispacecraft minimum directional derivative (MDD) tool developed by Shi et al. (2005). This last method gives the dimensionality of the magnetic variations from multipoint measurements and also allows estimating the direction of the local normal when the variations are locally 1-D. This study shows that the magnetopause does include approximate one-dimensional substructures but also two- and three-dimensional structures. It also shows that the dimensionality of the magnetic variations can differ from the variations of other fields so that, at some places, the magnetic field can have a 1-D structure although all the plasma variations do not verify the properties of a global one-dimensional problem. A generalization of the MDD tool is proposed.

Analysing the magnetopause internal structure: new possibilities offered by MMS

NASA Astrophysics Data System (ADS)

Belmont, G.; Rezeau, L.; Manuzzo, R.; Aunai, N.; Dargent, J.

2017-12-01

We explore the structure of the magnetopause using a crossing observed by the MMS spacecraft on October 16th, 2015. Several methods (MVA, BV, CVA) are first applied to compute the normal to the magnetopause considered as a whole. The different results obtained are not identical and we show that the whole boundary is not stationary and not planar, so that basic assumptions of these methods are not well satisfied. We then analyse more finely the internal structure for investigating the departures from planarity. Using the basic mathematical definition of what is a one-dimensional physical problem, we introduce a new method, called LNA (Local Normal Analysis) for determining the varying normal, and we compare the results so obtained with those coming from the MDD tool developed by [Shi et al., 2005]. This method gives the dimensionality of the magnetic variations from multi-point measurements and allows estimating the direction of the local normal using the magnetic field. On the other hand, LNA is a single-spacecraft method which gives the local normal from the magnetic field and particle data. This study shows that the magnetopause does include approximate one-dimensional sub-structures but also two and three dimensional intervals. It also shows that the dimensionality of the magnetic variations can differ from the variations of the other fields so that, at some places, the magnetic field can have a 1D structure although all the plasma variations do not verify the properties of a global one-dimensional problem. Finally a generalisation and a systematic application of the MDD method to the physical quantities of interest is shown.

On the construction of a direct numerical simulation of a breaking inertia-gravity wave in the upper mesosphere

NASA Astrophysics Data System (ADS)

Fruman, Mark D.; Remmler, Sebastian; Achatz, Ulrich; Hickel, Stefan

2014-10-01

A systematic approach to the direct numerical simulation (DNS) of breaking upper mesospheric inertia-gravity waves of amplitude close to or above the threshold for static instability is presented. Normal mode or singular vector analysis applied in a frame of reference moving with the phase velocity of the wave (in which the wave is a steady solution) is used to determine the most likely scale and structure of the primary instability and to initialize nonlinear "2.5-D" simulations (with three-dimensional velocity and vorticity fields but depending only on two spatial coordinates). Singular vector analysis is then applied to the time-dependent 2.5-D solution to predict the transition of the breaking event to three-dimensional turbulence and to initialize three-dimensional DNS. The careful choice of the computational domain and the relatively low Reynolds numbers, on the order of 25,000, relevant to breaking waves in the upper mesosphere, makes the three-dimensional DNS tractable with present-day computing clusters. Three test cases are presented: a statically unstable low-frequency inertia-gravity wave, a statically and dynamically stable inertia-gravity wave, and a statically unstable high-frequency gravity wave. The three-dimensional DNS are compared to ensembles of 2.5-D simulations. In general, the decay of the wave and generation of turbulence is faster in three dimensions, but the results are otherwise qualitatively and quantitatively similar, suggesting that results of 2.5-D simulations are meaningful if the domain and initial condition are chosen properly.

A coupled sharp-interface immersed boundary-finite-element method for flow-structure interaction with application to human phonation.

PubMed

Zheng, X; Xue, Q; Mittal, R; Beilamowicz, S

2010-11-01

A new flow-structure interaction method is presented, which couples a sharp-interface immersed boundary method flow solver with a finite-element method based solid dynamics solver. The coupled method provides robust and high-fidelity solution for complex flow-structure interaction (FSI) problems such as those involving three-dimensional flow and viscoelastic solids. The FSI solver is used to simulate flow-induced vibrations of the vocal folds during phonation. Both two- and three-dimensional models have been examined and qualitative, as well as quantitative comparisons, have been made with established results in order to validate the solver. The solver is used to study the onset of phonation in a two-dimensional laryngeal model and the dynamics of the glottal jet in a three-dimensional model and results from these studies are also presented.

Three dimensional contact/impact methodology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kulak, R.F.

1987-01-01

The simulation of three-dimensional interface mechanics between reactor components and structures during static contact or dynamic impact is necessary to realistically evaluate their structural integrity to off-normal loads. In our studies of postulated core energy release events, we have found that significant structure-structure interactions occur in some reactor vessel head closure designs and that fluid-structure interactions occur within the reactor vessel. Other examples in which three-dimensional interface mechanics play an important role are: (1) impact response of shipping casks containing spent fuel, (2) whipping pipe impact on reinforced concrete panels or pipe-to-pipe impact after a pipe break, (3) aircraft crashmore » on secondary containment structures, (4) missiles generated by turbine failures or tornados, and (5) drops of heavy components due to lifting accidents. The above is a partial list of reactor safety problems that require adequate treatment of interface mechanics and are discussed in this paper.« less

Visualization of molecular structures using HoloLens-based augmented reality

PubMed Central

Hoffman, MA; Provance, JB

2017-01-01

Biological molecules and biologically active small molecules are complex three dimensional structures. Current flat screen monitors are limited in their ability to convey the full three dimensional characteristics of these molecules. Augmented reality devices, including the Microsoft HoloLens, offer an immersive platform to change how we interact with molecular visualizations. We describe a process to incorporate the three dimensional structures of small molecules and complex proteins into the Microsoft HoloLens using aspirin and the human leukocyte antigen (HLA) as examples. Small molecular structures can be introduced into the HoloStudio application, which provides native support for rotating, resizing and performing other interactions with these molecules. Larger molecules can be imported through the Unity gaming development platform and then Microsoft Visual Developer. The processes described here can be modified to import a wide variety of molecular structures into augmented reality systems and improve our comprehension of complex structural features. PMID:28815109

Three-Dimensional Temperature Field Simulation for the Rotor of an Asynchronous Motor

ERIC Educational Resources Information Center

Wang, Yanwu; Fan, Chunli; Yang, Li; Sun, Fengrui

2010-01-01

A three-dimensional heat transfer model is built according to the rotor structure of an asynchronous motor, and three-dimensional temperature fields of the rotor under different working conditions, such as the unloaded, rated loaded and that with broken rotor bars, are studied based on the finite element numerical method and experiments. The…

Fabrication of three-dimensional collagen scaffold using an inverse mould-leaching process.

PubMed

Ahn, SeungHyun; Lee, SuYeon; Cho, Youngseok; Chun, Wook; Kim, GeunHyung

2011-09-01

Natural biopolymers, such as collagen or chitosan, are considered ideal for biomedical scaffolds. However, low processability of the materials has hindered the fabrication of designed pore structures controlled by various solid freeform-fabrication methods. A new technique to fabricate a biomedical three-dimensional collagen scaffold, supplemented with a sacrificial poly(ethylene oxide) mould is proposed. The fabricated collagen scaffold shows a highly porous surface and a three-dimensional structure with high porosity as well as mechanically stable structure. To show its feasibility for biomedical applications, fibroblasts/keratinocytes were co-cultured on the scaffold, and the cell proliferation and cell migration of the scaffold was more favorable than that obtained with a spongy-type collagen scaffold.

Fusion proteins as alternate crystallization paths to difficult structure problems

NASA Technical Reports Server (NTRS)

Carter, Daniel C.; Rueker, Florian; Ho, Joseph X.; Lim, Kap; Keeling, Kim; Gilliland, Gary; Ji, Xinhua

1994-01-01

The three-dimensional structure of a peptide fusion product with glutathione transferase from Schistosoma japonicum (SjGST) has been solved by crystallographic methods to 2.5 A resolution. Peptides or proteins can be fused to SjGST and expressed in a plasmid for rapid synthesis in Escherichia coli. Fusion proteins created by this commercial method can be purified rapidly by chromatography on immobilized glutathione. The potential utility of using SjGST fusion proteins as alternate paths to the crystallization and structure determination of proteins is demonstrated.

High Resolution Crystal Structure of the Catalytic Domain of ADAMTS-5 (Aggrecanase-2)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shieh, Huey-Sheng; Mathis, Karl J.; Williams, Jennifer M.

Aggrecanase-2 (a disintegrin and metalloproteinase with thrombospondin motifs-5 (ADAMTS-5)), a member of the ADAMTS protein family, is critically involved in arthritic diseases because of its direct role in cleaving the cartilage component aggrecan. The catalytic domain of aggrecanase-2 has been refolded, purified, and crystallized, and its three-dimensional structure determined to 1.4{angstrom} resolution in the presence of an inhibitor. A high resolution structure of an ADAMTS/aggrecanase protein provides an opportunity for the development of therapeutics to treat osteoarthritis.

SAIL--stereo-array isotope labeling.

PubMed

Kainosho, Masatsune; Güntert, Peter

2009-11-01

Optimal stereospecific and regiospecific labeling of proteins with stable isotopes enhances the nuclear magnetic resonance (NMR) method for the determination of the three-dimensional protein structures in solution. Stereo-array isotope labeling (SAIL) offers sharpened lines, spectral simplification without loss of information and the ability to rapidly collect and automatically evaluate the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as before. This review gives an overview of stable isotope labeling methods for NMR spectroscopy with proteins and provides an in-depth treatment of the SAIL technology.

Three-Dimensional Gene Map of Cancer Cell Types: Structural Entropy Minimisation Principle for Defining Tumour Subtypes

PubMed Central

Li, Angsheng; Yin, Xianchen; Pan, Yicheng

2016-01-01

In this study, we propose a method for constructing cell sample networks from gene expression profiles, and a structural entropy minimisation principle for detecting natural structure of networks and for identifying cancer cell subtypes. Our method establishes a three-dimensional gene map of cancer cell types and subtypes. The identified subtypes are defined by a unique gene expression pattern, and a three-dimensional gene map is established by defining the unique gene expression pattern for each identified subtype for cancers, including acute leukaemia, lymphoma, multi-tissue, lung cancer and healthy tissue. Our three-dimensional gene map demonstrates that a true tumour type may be divided into subtypes, each defined by a unique gene expression pattern. Clinical data analyses demonstrate that most cell samples of an identified subtype share similar survival times, survival indicators and International Prognostic Index (IPI) scores and indicate that distinct subtypes identified by our algorithms exhibit different overall survival times, survival ratios and IPI scores. Our three-dimensional gene map establishes a high-definition, one-to-one map between the biologically and medically meaningful tumour subtypes and the gene expression patterns, and identifies remarkable cells that form singleton submodules. PMID:26842724

Three-dimensional water impact at normal incidence to a blunt structure

PubMed Central

Cooker, M. J.; Korobkin, A. A.

2016-01-01

The three-dimensional water impact onto a blunt structure with a spreading rectangular contact region is studied. The structure is mounted on a flat rigid plane with the impermeable curved surface of the structure perpendicular to the plane. Before impact, the water region is a rectangular domain of finite thickness bounded from below by the rigid plane and above by the flat free surface. The front free surface of the water region is vertical, representing the front of an advancing steep wave. The water region is initially advancing towards the structure at a constant uniform speed. We are concerned with the slamming loads acting on the surface of the structure during the initial stage of water impact. Air, gravity and surface tension are neglected. The problem is analysed by using some ideas of pressure-impulse theory, but including the time-dependence of the wetted area of the structure. The flow caused by the impact is three-dimensional and incompressible. The distribution of the pressure-impulse (the time-integral of pressure) over the surface of the structure is analysed and compared with the distributions provided by strip theories. The total impulse exerted on the structure during the impact stage is evaluated and compared with numerical and experimental predictions. An example calculation is presented of water impact onto a vertical rigid cylinder. Three-dimensional effects on the slamming loads are the main concern in this study. PMID:27616912

A new idea for broad band reflector and tunable multichannel filter of one dimensional symmetric photonic crystal with magnetized cold plasma defects

NASA Astrophysics Data System (ADS)

Kumar, Asish; Singh, Prabal P.; Thapa, Khem B.

2018-05-01

The optical properties of one-dimensional periodic structure composed by SiO2 and dielectric (air) layers with asymmetric and symmetric forms studied. The transmittance for symmetric periodic defective structure analyzed by introducing one, two, three layers of magnetized cold plasma (MCP) in one-dimensional periodic structure. We found better result for symmetric defect of three layer of the MCP compare to the other defective structures. On the basis of our calculated results, we proposed a new idea for broadband reflector at lower frequency range as well as the multichannel filter at higher frequency range.

A Three-dimensional Non-spherical Calculation Of The Rotationally Distorted Shape And Internal Structure Of A Model Of Jupiter With A Polytropic Index Of Unity

NASA Astrophysics Data System (ADS)

Zhang, Keke; Kong, D.; Schubert, G.; Anderson, J.

2012-10-01

An accurate calculation of the rotationally distorted shape and internal structure of Jupiter is required to understand the high-precision gravitational field that will be measured by the Juno spacecraft now on its way to Jupiter. We present a three-dimensional non-spherical numerical calculation of the shape and internal structure of a model of Jupiter with a polytropic index of unity. The calculation is based on a finite element method and accounts for the full effects of rotation. After validating the numerical approach against the asymptotic solution of Chandrasekhar (1933) that is valid only for a slowly rotating gaseous planet, we apply it to a model of Jupiter whose rapid rotation causes a significant departure from spherical geometry. The two-dimensional distribution of the density and the pressure within Jupiter is then determined via a hybrid inverse approach by matching the a priori unknown coefficient in the equation of state to the observed shape of Jupiter. After obtaining the two-dimensional distribution of Jupiter's density, we then compute the zonal gravity coefficients and the total mass from the non-spherical Jupiter model that takes full account of rotation-induced shape changes. Our non-spherical model with a polytrope of unit index is able to produce the known mass and zonal gravitational coefficients of Jupiter. Chandrasekhar, S. 1933, The equilibrium of distorted polytropes, MNRAS 93, 390

Correlation strength, Lifshitz transition, and the emergence of a two-dimensional to three-dimensional crossover in FeSe under pressure

NASA Astrophysics Data System (ADS)

Skornyakov, S. L.; Anisimov, V. I.; Vollhardt, D.; Leonov, I.

2018-03-01

We report a detailed theoretical study of the electronic structure, spectral properties, and lattice parameters of bulk FeSe under pressure using a fully charge self-consistent implementation of the density functional theory plus dynamical mean-field theory method (DFT+DMFT). In particular, we perform a structural optimization and compute the evolution of the lattice parameters (volume, c /a ratio, and the internal z position of Se) and the electronic structure of the tetragonal (space group P 4 /n m m ) unit cell of paramagnetic FeSe. Our results for the lattice parameters obtained by structural optimization using DFT+DMFT are in good quantitative agreement with experiment, implying a crucial importance of electron correlations in determining the correct lattice properties of FeSe. Most importantly, upon compression to 10 GPa our results reveal a topological change in the Fermi surface (Lifshitz transition) which is accompanied by a two- to three-dimensional crossover and a small reduction of the quasiparticle mass renormalization compared to ambient pressure. The behavior of the momentum-resolved magnetic susceptibility χ (q ) shows no topological changes of magnetic correlations under pressure but demonstrates a reduction of the degree of the in-plane (π ,π ) stripe-type nesting. Our results for the electronic structure and lattice parameters of FeSe are in good qualitative agreement with recent experiments on its isoelectronic counterpart FeSe1 -xSx .

Predicting Structural Behavior of Filament Wound Composite Pressure Vessel Using Three Dimensional Shell Analysis

NASA Astrophysics Data System (ADS)

Madhavi, M.; Venkat, R.

2014-01-01

Fiber reinforced polymer composite materials with their higher specific strength, moduli and tailorability characteristics will result in reduction of weight of the structure. The composite pressure vessels with integrated end domes develop hoop stresses that are twice longitudinal stresses and when isotropic materials like metals are used for development of the hardware and the material is not fully utilized in the longitudinal/meridional direction resulting in over weight components. The determination of a proper winding angles and thickness is very important to decrease manufacturing difficulties and to increase structural efficiency. In the present study a methodology is developed to understand structural characteristics of filament wound pressure vessels with integrated end domes. Progressive ply wise failure analysis of composite pressure vessel with geodesic end domes is carried out to determine matrix crack failure, burst pressure values at various positions of the shell. A three dimensional finite element analysis is computed to predict the deformations and stresses in the composite pressure vessel. The proposed method could save the time to design filament wound structures, to check whether the ply design is safe for the given input conditions and also can be adapted to non-geodesic structures. The results can be utilized to understand structural characteristics of filament wound pressure vessels with integrated end domes. This approach can be adopted for various applications like solid rocket motor casings, automobile fuel storage tanks and chemical storage tanks. Based on the predictions a composite pressure vessel is designed and developed. Hydraulic test is performed on the composite pressure vessel till the burst pressure.

Mesenchymal Stem Cells Sense Three Dimensional Type I Collagen through Discoidin Domain Receptor 1.

PubMed

Lund, A W; Stegemann, J P; Plopper, G E

2009-01-01

The extracellular matrix provides structural and organizational cues for tissue development and defines and maintains cellular phenotype during cell fate determination. Multipotent mesenchymal stem cells use this matrix to tightly regulate the balance between their differentiation potential and self-renewal in the native niche. When understood, the mechanisms that govern cell-matrix crosstalk during differentiation will allow for efficient engineering of natural and synthetic matrices to specifically direct and maintain stem cell phenotype. This work identifies the discoidin domain receptor 1 (DDR1), a collagen activated receptor tyrosine kinase, as a potential link through which stem cells sense and respond to the 3D organization of their extracellular matrix microenvironment. DDR1 is dependent upon both the structure and proteolytic state of its collagen ligand and is specifically expressed and localized in three dimensional type I collagen culture. Inhibition of DDR1 expression results in decreased osteogenic potential, increased cell spreading, stress fiber formation and ERK1/2 phosphorylation. Additionally, loss of DDR1 activity alters the cell-mediated organization of the naïve type I collagen matrix. Taken together, these results demonstrate a role for DDR1 in the stem cell response to and interaction with three dimensional type I collagen. Dynamic changes in cell shape in 3D culture and the tuning of the local ECM microstructure, directs crosstalk between DDR1 and two dimensional mechanisms of osteogenesis that can alter their traditional roles.

Yttrium oxide based three dimensional metamaterials for visible light cloaking

NASA Astrophysics Data System (ADS)

Rai, Pratyush; Kumar, Prashanth S.; Varadan, Vijay K.; Ruffin, Paul; Brantley, Christina; Edwards, Eugene

2014-04-01

Metamaterial with negative refractive index is the key phenomenon behind the concept of a cloaking device to hide an object from light in visible spectrum. Metamaterials made of two and three dimensional lattices of periodically placed electromagnetic resonant cells can achieve absorption and propagation of incident electromagnetic radiation as confined electromagnetic fields confined to a waveguide as surface plasmon polaritons, which can be used for shielding an object from in-tune electromagnetic radiation. The periodicity and dimensions of resonant cavity determine the frequency, which are very small as compared to the wavelength of incident light. Till now the phenomena have been demonstrated only for lights in near infrared spectrum. Recent advancements in fabrication techniques have made it possible to fabricate array of three dimensional nanostructures with cross-sections as small as 25 nm that are required for negative refractive index for wavelengths in visible light spectrum of 400-700 nm and for wider view angle. Two types of metamaterial designs, three dimensional concentric split ring and fishnet, are considered. Three dimensional structures consisted of metal-dielectric-metal stacks. The metal is silver and dielectric is yttrium oxide, other than conventional materials such as FR4 and Duroid. High κ dielectric and high refractive index as well as large crystal symmetry of Yttrium oxide has been investigated as encapsulating medium. Dependence of refractive index on wavelength and bandwidth of negative refractive index region are analyzed for application towards cloaking from light in visible spectrum.

Glycoproteomics of cerebrospinal fluid in neurodegenerative disease

NASA Astrophysics Data System (ADS)

Sihlbom, Carina; Davidsson, Pia; Emmett, Mark R.; Marshall, Alan G.; Nilsson, Carol L.

2004-05-01

Cerebrospinal fluid (CSF) from individual patients with Alzheimer's disease (AD) was separated by narrow range two-dimensional (2D) gel electrophoresis and analyzed by electrospray FT-ICR MS in this glycoproteomic study. Because several altered proteins in the comparison between AD patients and healthy controls individuals are isoforms of glycoproteins, it is important to determine if the modifying glycans are also altered. FT-ICR MS and fragmentation of glycopeptides with infrared multiphoton dissociation (IRMPD) offers abundant fragment ions through breakage at the glycosidic linkages with excellent mass accuracy, which facilitates the structural determination of the site-specific N-linked glycosylation. We present results from a structural comparison of proteins from three AD patients and three control individuals of different glycosylated isomers of [alpha]-1-antitrypsin, [beta]-trace and apolipoprotein J.

M553 sphere forming experiment: Pure nickel specimen evaluation

NASA Technical Reports Server (NTRS)

Johnson, P. C.; Peters, E. T.

1973-01-01

A region or cap of very fine two-dimensional surface growth structure was observed at the top of three of the six pure nickel flight specimens. Such two-dimensional surface growth structures have been observed both on the ground-based specimens and on other surface areas of the flight specimens. However, the fine structures observed on the three flight samples are at least an order of magnitude finer than those previously observed, and resemble similar localized, fine, two-dimensional surface structures observed in both ground and flight specimens for the nickel alloys. The two-dimensional growth areas consist primarily of fine equiaxed grains, specimen SL-2.6, fine dendrites, specimen SL-2.5, or a core of fine equiaxed grains surrounded by a ring of fine dendrites, specimen SL-1.9.

Computing approximate solutions of the protein structure determination problem using global constraints on discrete crystal lattices.

PubMed

Dal Palù, Alessandro; Dovier, Agostino; Pontelli, Enrico

2010-01-01

Crystal lattices are discrete models of the three-dimensional space that have been effectively employed to facilitate the task of determining proteins' natural conformation. This paper investigates alternative global constraints that can be introduced in a constraint solver over discrete crystal lattices. The objective is to enhance the efficiency of lattice solvers in dealing with the construction of approximate solutions of the protein structure determination problem. Some of them (e.g., self-avoiding-walk) have been explicitly or implicitly already used in previous approaches, while others (e.g., the density constraint) are new. The intrinsic complexities of all of them are studied and preliminary experimental results are discussed.

Three-dimensionally modulated anisotropic structure for diffractive optical elements created by one-step three-beam polarization holographic photoalignment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kawai, Kotaro, E-mail: s135016@stn.nagaokaut.ac.jp; Sakamoto, Moritsugu; Noda, Kohei

2016-03-28

A diffractive optical element with a three-dimensional liquid crystal (LC) alignment structure for advanced control of polarized beams was fabricated by a highly efficient one-step photoalignment method. This study is of great significance because different two-dimensional continuous and complex alignment patterns can be produced on two alignment films by simultaneously irradiating an empty glass cell composed of two unaligned photocrosslinkable polymer LC films with three-beam polarized interference beam. The polarization azimuth, ellipticity, and rotation direction of the diffracted beams from the resultant LC grating widely varied depending on the two-dimensional diffracted position and the polarization states of the incident beams.more » These polarization diffraction properties are well explained by theoretical analysis based on Jones calculus.« less

Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide.

PubMed

Iwaoka, Michio; Suzuki, Toshiki; Shoji, Yuya; Dedachi, Kenichi; Shimosato, Taku; Minezaki, Toshiya; Hojo, Hironobu; Onuki, Hiroyuki; Hirota, Hiroshi

2017-12-01

Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH 2 ). For chignolin, REMC/SAAP3D simulation correctly produced native β-turn structures, whose minimal all-atom root-mean-square deviation value measured from the native NMR structure (except for H) was 1.2 Å, at 300 K in implicit water, along with misfolded β-hairpin structures with unpacked aromatic side chains of Tyr2 and Trp9. Similar results were obtained for chignolin analog [G1Y,G10Y], which folded more tightly to the native β-turn structure than chignolin did. For C-peptide, on the other hand, the α-helix content was larger than the β content on average, suggesting a significant helix-forming propensity. When the imidazole side chain of His12 was protonated (i.e., [His12Hip]), the α content became larger. These observations as well as the representative structures obtained by clustering analysis were in reasonable agreement not only with the structures of C-peptide that were determined in this study by NMR in 30% CD 3 CD in H 2 O at 298 K but also with the experimental and theoretical behaviors having been reported for protonated C-peptide. Thus, accuracy of the SAAP force field was improved by applying three-dimensional main-chain parameters, supporting prominent importance of SAAP for peptide conformations.

Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide

NASA Astrophysics Data System (ADS)

Iwaoka, Michio; Suzuki, Toshiki; Shoji, Yuya; Dedachi, Kenichi; Shimosato, Taku; Minezaki, Toshiya; Hojo, Hironobu; Onuki, Hiroyuki; Hirota, Hiroshi

2017-12-01

Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH2). For chignolin, REMC/SAAP3D simulation correctly produced native β-turn structures, whose minimal all-atom root-mean-square deviation value measured from the native NMR structure (except for H) was 1.2 Å, at 300 K in implicit water, along with misfolded β-hairpin structures with unpacked aromatic side chains of Tyr2 and Trp9. Similar results were obtained for chignolin analog [G1Y,G10Y], which folded more tightly to the native β-turn structure than chignolin did. For C-peptide, on the other hand, the α-helix content was larger than the β content on average, suggesting a significant helix-forming propensity. When the imidazole side chain of His12 was protonated (i.e., [His12Hip]), the α content became larger. These observations as well as the representative structures obtained by clustering analysis were in reasonable agreement not only with the structures of C-peptide that were determined in this study by NMR in 30% CD3CD in H2O at 298 K but also with the experimental and theoretical behaviors having been reported for protonated C-peptide. Thus, accuracy of the SAAP force field was improved by applying three-dimensional main-chain parameters, supporting prominent importance of SAAP for peptide conformations.

The Impact of Stereoscopic Imagery and Motion on Anatomical Structure Recognition and Visual Attention Performance

ERIC Educational Resources Information Center

Remmele, Martin; Schmidt, Elena; Lingenfelder, Melissa; Martens, Andreas

2018-01-01

Gross anatomy is located in a three-dimensional space. Visualizing aspects of structures in gross anatomy education should aim to provide information that best resembles their original spatial proportions. Stereoscopic three-dimensional imagery might offer possibilities to implement this aim, though some research has revealed potential impairments…

Polyimide Aerogels with Three-Dimensional Cross-Linked Structure

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B. (Inventor)

2016-01-01

A method for creating a three dimensional cross-linked polyimide structure includes dissolving a diamine, a dianhydride, and a triamine in a solvent, imidizing a polyamic acid gel by heating the gel, extracting the gel in a second solvent, supercritically drying the gel, and removing the solvent to create a polyimide aerogel.

A light-trapping strategy for nanocrystalline silicon thin-film solar cells using three-dimensionally assembled nanoparticle structures.

PubMed

Ha, Kyungyeon; Jang, Eunseok; Jang, Segeun; Lee, Jong-Kwon; Jang, Min Seok; Choi, Hoseop; Cho, Jun-Sik; Choi, Mansoo

2016-02-05

We report three-dimensionally assembled nanoparticle structures inducing multiple plasmon resonances for broadband light harvesting in nanocrystalline silicon (nc-Si:H) thin-film solar cells. A three-dimensional multiscale (3DM) assembly of nanoparticles generated using a multi-pin spark discharge method has been accomplished over a large area under atmospheric conditions via ion-assisted aerosol lithography. The multiscale features of the sophisticated 3DM structures exhibit surface plasmon resonances at multiple frequencies, which increase light scattering and absorption efficiency over a wide spectral range from 350-1100 nm. The multiple plasmon resonances, together with the antireflection functionality arising from the conformally deposited top surface of the 3D solar cell, lead to a 22% and an 11% improvement in power conversion efficiency of the nc-Si:H thin-film solar cells compared to flat cells and cells employing nanoparticle clusters, respectively. Finite-difference time-domain simulations were also carried out to confirm that the improved device performance mainly originates from the multiple plasmon resonances generated from three-dimensionally assembled nanoparticle structures.

The geometry of structural equilibrium

PubMed Central

2017-01-01

Building on a long tradition from Maxwell, Rankine, Klein and others, this paper puts forward a geometrical description of structural equilibrium which contains a procedure for the graphic analysis of stress resultants within general three-dimensional frames. The method is a natural generalization of Rankine’s reciprocal diagrams for three-dimensional trusses. The vertices and edges of dual abstract 4-polytopes are embedded within dual four-dimensional vector spaces, wherein the oriented area of generalized polygons give all six components (axial and shear forces with torsion and bending moments) of the stress resultants. The relevant quantities may be readily calculated using four-dimensional Clifford algebra. As well as giving access to frame analysis and design, the description resolves a number of long-standing problems with the incompleteness of Rankine’s description of three-dimensional trusses. Examples are given of how the procedure may be applied to structures of engineering interest, including an outline of a two-stage procedure for addressing the equilibrium of loaded gridshell rooves. PMID:28405361

Learning the Cell Structures with Three-Dimensional Models: Students' Achievement by Methods, Type of School and Questions' Cognitive Level

NASA Astrophysics Data System (ADS)

Lazarowitz, Reuven; Naim, Raphael

2013-08-01

The cell topic was taught to 9th-grade students in three modes of instruction: (a) students "hands-on," who constructed three-dimensional cell organelles and macromolecules during the learning process; (b) teacher demonstration of the three-dimensional model of the cell structures; and (c) teaching the cell topic with the regular learning material in an expository mode (which use one- or two-dimensional cell structures as are presented in charts, textbooks and microscopic slides). The sample included 669, 9th-grade students from 25 classes who were taught by 22 Biology teachers. Students were randomly assigned to the three modes of instruction, and two tests in content knowledge in Biology were used. Data were treated with multiple analyses of variance. The results indicate that entry behavior in Biology was equal for all the study groups and types of schools. The "hands-on" learning group who build three-dimensional models through the learning process achieved significantly higher on academic achievements and on the high and low cognitive questions' levels than the other two groups. The study indicates the advantages students may have being actively engaged in the learning process through the "hands-on" mode of instruction/learning.

Imaging and Radiography with Nuclear Resonance Fluorescence and Effective-Z (EZ-3D) Determination; SNM Detection Using Prompt Neutrons from Photon Induced Fission

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bertozzi, William; Hasty, Richard; Klimenko, Alexei

Four new technologies have been developed for use in non-intrusive inspection systems to detect nuclear materials, explosives and contraband. Nuclear Resonance Fluorescence (NRF) provides a three dimensional image of the isotopic content of a container. NRF determines the isotopic composition of a region and specifies the isotopic structure of the neighboring regions, thus providing the detailed isotopic composition of any threat. In transmission mode, NRF provides a two dimensional projection of the isotopic content of a container, much as standard X-ray radiography provides for density. The effective-Z method (EZ-3D) uses electromagnetic scattering processes to yield a three-dimensional map of themore » effective-Z and the density in a container. The EZ-3D method allows for a rapid discrimination based on effective Z and mass of materials such as those with high Z, as well as specifying regions of interest for other contraband. The energy spectrum of prompt neutrons from photon induced fission (PNPF) provides a unique identification of the presence of actinides and SNM. These four new technologies can be used independently or together to automatically determine the presence of hazardous materials or contraband. They can also be combined with other technologies to provide added specificity.« less

Mapping the universe in three dimensions.

PubMed

Haynes, M P

1996-12-10

The determination of the three-dimensional layout of galaxies is critical to our understanding of the evolution of galaxies and the structures in which they lie, to our determination of the fundamental parameters of cosmology, and to our understanding of both the past and future histories of the universe at large. The mapping of the large scale structure in the universe via the determination of galaxy red shifts (Doppler shifts) is a rapidly growing industry thanks to technological developments in detectors and spectrometers at radio and optical wavelengths. First-order application of the red shift-distance relation (Hubble's law) allows the analysis of the large-scale distribution of galaxies on scales of hundreds of megaparsecs. Locally, the large-scale structure is very complex but the overall topology is not yet clear. Comparison of the observed red shifts with ones expected on the basis of other distance estimates allows mapping of the gravitational field and the underlying total density distribution. The next decade holds great promise for our understanding of the character of large-scale structure and its origin.

Predicting Student Performance in Sonographic Scanning Using Spatial Ability as an Ability Determinent of Skill Acquisition

ERIC Educational Resources Information Center

Clem, Douglas Wayne

2012-01-01

Spatial ability refers to an individual's capacity to visualize and mentally manipulate three dimensional objects. Since sonographers manually manipulate 2D and 3D sonographic images to generate multi-viewed, logical, sequential renderings of an anatomical structure, it can be assumed that spatial ability is central to the perception and…

Three-dimensional metamaterials

DOEpatents

Burckel, David Bruce [Albuquerque, NM

2012-06-12

A fabrication method is capable of creating canonical metamaterial structures arrayed in a three-dimensional geometry. The method uses a membrane suspended over a cavity with predefined pattern as a directional evaporation mask. Metallic and/or dielectric material can be evaporated at high vacuum through the patterned membrane to deposit resonator structures on the interior walls of the cavity, thereby providing a unit cell of micron-scale dimension. The method can produce volumetric metamaterial structures comprising layers of such unit cells of resonator structures.

Iterative optimizing quantization method for reconstructing three-dimensional images from a limited number of views

DOEpatents

Lee, Heung-Rae

1997-01-01

A three-dimensional image reconstruction method comprises treating the object of interest as a group of elements with a size that is determined by the resolution of the projection data, e.g., as determined by the size of each pixel. One of the projections is used as a reference projection. A fictitious object is arbitrarily defined that is constrained by such reference projection. The method modifies the known structure of the fictitious object by comparing and optimizing its four projections to those of the unknown structure of the real object and continues to iterate until the optimization is limited by the residual sum of background noise. The method is composed of several sub-processes that acquire four projections from the real data and the fictitious object: generate an arbitrary distribution to define the fictitious object, optimize the four projections, generate a new distribution for the fictitious object, and enhance the reconstructed image. The sub-process for the acquisition of the four projections from the input real data is simply the function of acquiring the four projections from the data of the transmitted intensity. The transmitted intensity represents the density distribution, that is, the distribution of absorption coefficients through the object.

Biomimetic Hierarchical Assembly of Helical Supraparticles from Chiral Nanoparticles

DOE PAGES

Zhou, Yunlong; Marson, Ryan L.; van Anders, Greg; ...

2016-02-22

Chiroptical materials found in butterflies, beetles, stomatopod crustaceans, and other creatures are attributed to biocomposites with helical motifs and multiscale hierarchical organization. These structurally sophisticated materials self-assemble from primitive nanoscale building blocks, a process that is simpler and more energy efficient than many top-down methods currently used to produce similarly sized three-dimensional materials. In this paper, we report that molecular-scale chirality of a CdTe nanoparticle surface can be translated to nanoscale helical assemblies, leading to chiroptical activity in the visible electromagnetic range. Chiral CdTe nanoparticles coated with cysteine self-organize around Te cores to produce helical supraparticles. D-/L-Form of the aminomore » acid determines the dominant left/right helicity of the supraparticles. Coarse-grained molecular dynamics simulations with a helical pair-potential confirm the assembly mechanism and the origin of its enantioselectivity, providing a framework for engineering three-dimensional chiral materials by self-assembly. Finally, the helical supraparticles further self-organize into lamellar crystals with liquid crystalline order, demonstrating the possibility of hierarchical organization and with multiple structural motifs and length scales determined by molecular-scale asymmetry of nanoparticle interactions.« less

Application of ground-penetrating radar imagery for three-dimensional visualisation of near-surface structures in ice-rich permafrost, Barrow, Alaska

USGS Publications Warehouse

Munroe, Jeffrey S.; Doolittle, James A.; Kanevskiy, Mikhail; Hinkel, Kenneth M.; Nelson, Frederick E.; Jones, Benjamin M.; Shur, Yuri; Kimble, John M.

2007-01-01

Three-dimensional ground-penetrating radar (3D GPR) was used to investigate the subsurface structure of ice-wedge polygons and other features of the frozen active layer and near-surface permafrost near Barrow, Alaska. Surveys were conducted at three sites located on landscapes of different geomorphic age. At each site, sediment cores were collected and characterised to aid interpretation of GPR data. At two sites, 3D GPR was able to delineate subsurface ice-wedge networks with high fidelity. Three-dimensional GPR data also revealed a fundamental difference in ice-wedge morphology between these two sites that is consistent with differences in landscape age. At a third site, the combination of two-dimensional and 3D GPR revealed the location of an active frost boil with ataxitic cryostructure. When supplemented by analysis of soil cores, 3D GPR offers considerable potential for imaging, interpreting and 3D mapping of near-surface soil and ice structures in permafrost environments.

Matching experimental and three dimensional numerical models for structural vibration problems with uncertainties

NASA Astrophysics Data System (ADS)

Langer, P.; Sepahvand, K.; Guist, C.; Bär, J.; Peplow, A.; Marburg, S.

2018-03-01

The simulation model which examines the dynamic behavior of real structures needs to address the impact of uncertainty in both geometry and material parameters. This article investigates three-dimensional finite element models for structural dynamics problems with respect to both model and parameter uncertainties. The parameter uncertainties are determined via laboratory measurements on several beam-like samples. The parameters are then considered as random variables to the finite element model for exploring the uncertainty effects on the quality of the model outputs, i.e. natural frequencies. The accuracy of the output predictions from the model is compared with the experimental results. To this end, the non-contact experimental modal analysis is conducted to identify the natural frequency of the samples. The results show a good agreement compared with experimental data. Furthermore, it is demonstrated that geometrical uncertainties have more influence on the natural frequencies compared to material parameters and material uncertainties are about two times higher than geometrical uncertainties. This gives valuable insights for improving the finite element model due to various parameter ranges required in a modeling process involving uncertainty.

Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research

PubMed Central

Zhang, Shaocun; Cao, Xiaocang; Huang, He

2017-01-01

Identifying intestinal microbiota is arguably an important task that is performed to determine the pathogenesis of inflammatory bowel diseases (IBD); thus, it is crucial to collect and analyze intestinally-associated microbiota. Analyzing a single niche to categorize individuals does not enable researchers to comprehensively study the spatial variations of the microbiota. Therefore, characterizing the spatial community structures of the inflammatory bowel disease microbiome is critical for advancing our understanding of the inflammatory landscape of IBD. However, at present there is no universally accepted consensus regarding the use of specific sampling strategies in different biogeographic locations. In this review, we discuss the spatial distribution when screening sample collections in IBD microbiota research. Here, we propose a novel model, a three-dimensional spatial community structure, which encompasses the x-, y-, and z-axis distributions; it can be used in some sampling sites, such as feces, colonoscopic biopsy, the mucus gel layer, and oral cavity. On the basis of this spatial model, this article also summarizes various sampling and processing strategies prior to and after DNA extraction and recommends guidelines for practical application in future research. PMID:28286741

Construction of three-dimensional DNA hydrogels from linear building blocks.

PubMed

Nöll, Tanja; Schönherr, Holger; Wesner, Daniel; Schopferer, Michael; Paululat, Thomas; Nöll, Gilbert

2014-08-04

A three-dimensional DNA hydrogel was generated by self-assembly of short linear double-stranded DNA (dsDNA) building blocks equipped with sticky ends. The resulting DNA hydrogel is thermoresponsive and the length of the supramolecular dsDNA structures varies with temperature. The average diffusion coefficients of the supramolecular dsDNA structures formed by self-assembly were determined by diffusion-ordered NMR spectroscopy (DOSY NMR) for temperatures higher than 60 °C. Temperature-dependent rheological measurements revealed a gel point of 42±1 °C. Below this temperature, the resulting material behaved as a true gel of high viscosity with values for the storage modulus G' being significantly larger than that for the loss modulus G''. Frequency-dependent rheological measurements at 20 °C revealed a mesh size (ξ) of 15 nm. AFM analysis of the diluted hydrogel in the dry state showed densely packed structures of entangled chains, which are also expected to contain multiple interlocked rings and catenanes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three-dimensional analytical solution for the instability of a parallel array of mutually attracting identical simply supported piezoelectric microplates

NASA Astrophysics Data System (ADS)

Liu, Lei; Wang, Xu

2017-12-01

Three-dimensional analytical solutions are derived for the structural instability of a parallel array of mutually attracting identical simply supported orthotropic piezoelectric rectangular microplates by means of a linear perturbation analysis. The two surfaces of each plate can be either insulating or conducting. By considering the fact that the shear stresses and the normal electric displacement (or electric potential) are zero on the two surfaces of each plate, a 2 × 2 transfer matrix for a plate can be obtained directly from the 8 × 8 fundamental piezoelectricity matrix without resolving the original Stroh eigenrelation. The critical interaction coefficient can be determined by solving the resulting generalized eigenvalue problem for the piezoelectric plate array. Also considered in our analysis is the in-plane uniform edge compression acting on the four sides of each piezoelectric plate. Our results indicate that the stabilizing influence of the piezoelectric effect on the structural instability is unignorable; the edge compression always plays a destabilizing role in the structural instability of the plate array with interactions.

Defining an essence of structure determining residue contacts in proteins.

PubMed

Sathyapriya, R; Duarte, Jose M; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

2009-12-01

The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this "structural essence" has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts-such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed "cone-peeling" that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 A Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This "structural essence" opens new avenues in the fields of structure prediction, empirical potentials and docking.

Defining an Essence of Structure Determining Residue Contacts in Proteins

PubMed Central

Sathyapriya, R.; Duarte, Jose M.; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

2009-01-01

The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this “structural essence” has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts—such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed “cone-peeling” that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 Å Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This “structural essence” opens new avenues in the fields of structure prediction, empirical potentials and docking. PMID:19997489

Approximate Analysis for Interlaminar Stresses in Composite Structures with Thickness Discontinuities

NASA Technical Reports Server (NTRS)

Rose, Cheryl A.; Starnes, James H., Jr.

1996-01-01

An efficient, approximate analysis for calculating complete three-dimensional stress fields near regions of geometric discontinuities in laminated composite structures is presented. An approximate three-dimensional local analysis is used to determine the detailed local response due to far-field stresses obtained from a global two-dimensional analysis. The stress results from the global analysis are used as traction boundary conditions for the local analysis. A generalized plane deformation assumption is made in the local analysis to reduce the solution domain to two dimensions. This assumption allows out-of-plane deformation to occur. The local analysis is based on the principle of minimum complementary energy and uses statically admissible stress functions that have an assumed through-the-thickness distribution. Examples are presented to illustrate the accuracy and computational efficiency of the local analysis. Comparisons of the results of the present local analysis with the corresponding results obtained from a finite element analysis and from an elasticity solution are presented. These results indicate that the present local analysis predicts the stress field accurately. Computer execution-times are also presented. The demonstrated accuracy and computational efficiency of the analysis make it well suited for parametric and design studies.

Cornea and ocular lens visualized with three-dimensional confocal microscopy

NASA Astrophysics Data System (ADS)

Masters, Barry R.

1992-08-01

This paper demonstrates the advantages of three-dimensional reconstruction of the cornea and the ocular crystalline lens by confocal microscopy and volume rendering computer techniques. The advantages of noninvasive observation of ocular structures in living, unstained, unfixed tissue include the following: the tissue is in a natural living state without the artifacts of fixation, mechanical sectioning, and staining; the three-dimensional structure can be observed from any view point and quantitatively analyzed; the dynamics of morphological changes can be studied; and the use of confocal microscopic observation results in a reduction of the number of animals required for ocular morphometric studies. The main advantage is that the dynamic morphology of ocular structures can be investigated in living ocular tissue. A laser scanning confocal microscope was used in the reflected light mode to obtain the two- dimensional images from the cornea and the ocular lens of a freshly enucleated rabbit eye. The light source was an argon ion laser with 488 nm wavelength. The microscope objective was a Leitz 25X, NA 0.6 water immersion lens. The 400 micron thick cornea was optically sectioned into 133, three micron sections. The semi-transparent cornea and the in-situ ocular lens was visualized as high resolution, high contrast two-dimensional images. The under sampling resulted in a three-dimensional visualization rendering in which the corneal thickness (z-axis) is compressed. The structures observed in the cornea include: superficial epithelial cells and their nuclei, basal epithelial cells and their `beaded' cell borders, basal lamina, nerve plexus, nerve fibers, free nerve endings in the basal epithelial cells, nuclei of stromal keratocytes, and endothelial cells. The structures observed in the in-situ ocular lens include: lens capsule, lens epithelial cells, and individual lens fibers.

Hydroelastic behaviour of a structure exposed to an underwater explosion.

PubMed

Colicchio, G; Greco, M; Brocchini, M; Faltinsen, O M

2015-01-28

The hydroelastic interaction between an underwater explosion and an elastic plate is investigated num- erically through a domain-decomposition strategy. The three-dimensional features of the problem require a large computational effort, which is reduced through a weak coupling between a one-dimensional radial blast solver, which resolves the blast evolution far from the boundaries, and a three-dimensional compressible flow solver used where the interactions between the compression wave and the boundaries take place and the flow becomes three-dimensional. The three-dimensional flow solver at the boundaries is directly coupled with a modal structural solver that models the response of the solid boundaries like elastic plates. This enables one to simulate the fluid-structure interaction as a strong coupling, in order to capture hydroelastic effects. The method has been applied to the experimental case of Hung et al. (2005 Int. J. Impact Eng. 31, 151-168 (doi:10.1016/j.ijimpeng.2003.10.039)) with explosion and structure sufficiently far from other boundaries and successfully validated in terms of the evolution of the acceleration induced on the plate. It was also used to investigate the interaction of an underwater explosion with the bottom of a close-by ship modelled as an orthotropic plate. In the application, the acoustic phase of the fluid-structure interaction is examined, highlighting the need of the fluid-structure coupling to capture correctly the possible inception of cavitation. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Three-dimensional boron particle loaded thermal neutron detector

DOEpatents

Nikolic, Rebecca J.; Conway, Adam M.; Graff, Robert T.; Kuntz, Joshua D.; Reinhardt, Catherine; Voss, Lars F.; Cheung, Chin Li; Heineck, Daniel

2014-09-09

Three-dimensional boron particle loaded thermal neutron detectors utilize neutron sensitive conversion materials in the form of nano-powders and micro-sized particles, as opposed to thin films, suspensions, paraffin, etc. More specifically, methods to infiltrate, intersperse and embed the neutron nano-powders to form two-dimensional and/or three-dimensional charge sensitive platforms are specified. The use of nano-powders enables conformal contact with the entire charge-collecting structure regardless of its shape or configuration.

Three-dimensional photography for the evaluation of facial profiles in obstructive sleep apnoea.

PubMed

Lin, Shih-Wei; Sutherland, Kate; Liao, Yu-Fang; Cistulli, Peter A; Chuang, Li-Pang; Chou, Yu-Ting; Chang, Chih-Hao; Lee, Chung-Shu; Li, Li-Fu; Chen, Ning-Hung

2018-06-01

Craniofacial structure is an important determinant of obstructive sleep apnoea (OSA) syndrome risk. Three-dimensional stereo-photogrammetry (3dMD) is a novel technique which allows quantification of the craniofacial profile. This study compares the facial images of OSA patients captured by 3dMD to three-dimensional computed tomography (3-D CT) and two-dimensional (2-D) digital photogrammetry. Measurements were correlated with indices of OSA severity. Thirty-eight patients diagnosed with OSA were included, and digital photogrammetry, 3dMD and 3-D CT were performed. Distances, areas, angles and volumes from the images captured by three methods were analysed. Almost all measurements captured by 3dMD showed strong agreement with 3-D CT measurements. Results from 2-D digital photogrammetry showed poor agreement with 3-D CT. Mandibular width, neck perimeter size and maxillary volume measurements correlated well with the severity of OSA using all three imaging methods. Mandibular length, facial width, binocular width, neck width, cranial base triangle area, cranial base area 1 and middle cranial fossa volume correlated well with OSA severity using 3dMD and 3-D CT, but not with 2-D digital photogrammetry. 3dMD provided accurate craniofacial measurements of OSA patients, which were highly concordant with those obtained by CT, while avoiding the radiation associated with CT. © 2018 Asian Pacific Society of Respirology.

Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells

PubMed Central

Rodriguez, Jose A.; Xu, Rui; Chen, Chien-Chun; Huang, Zhifeng; Jiang, Huaidong; Chen, Allan L.; Raines, Kevin S.; Pryor Jr, Alan; Nam, Daewoong; Wiegart, Lutz; Song, Changyong; Madsen, Anders; Chushkin, Yuriy; Zontone, Federico; Bradley, Peter J.; Miao, Jianwei

2015-01-01

A structural understanding of whole cells in three dimensions at high spatial resolution remains a significant challenge and, in the case of X-rays, has been limited by radiation damage. By alleviating this limitation, cryogenic coherent diffractive imaging (cryo-CDI) can in principle be used to bridge the important resolution gap between optical and electron microscopy in bio-imaging. Here, the first experimental demonstration of cryo-CDI for quantitative three-dimensional imaging of whole frozen-hydrated cells using 8 keV X-rays is reported. As a proof of principle, a tilt series of 72 diffraction patterns was collected from a frozen-hydrated Neospora caninum cell and the three-dimensional mass density of the cell was reconstructed and quantified based on its natural contrast. This three-dimensional reconstruction reveals the surface and internal morphology of the cell, including its complex polarized sub-cellular structure. It is believed that this work represents an experimental milestone towards routine quantitative three-dimensional imaging of whole cells in their natural state with spatial resolutions in the tens of nanometres. PMID:26306199

Face and content validation of a novel three-dimensional printed temporal bone for surgical skills development.

PubMed

Da Cruz, M J; Francis, H W

2015-07-01

To assess the face and content validity of a novel synthetic, three-dimensional printed temporal bone for surgical skills development and training. A synthetic temporal bone was printed using composite materials and three-dimensional printing technology. Surgical trainees were asked to complete three structured temporal bone dissection exercises. Attitudes and impressions were then assessed using a semi-structured questionnaire. Previous cadaver and real operating experiences were used as a reference. Trainees' experiences of the synthetic temporal bone were analysed in terms of four domains: anatomical realism, usefulness as a training tool, task-based usefulness and overall reactions. Responses across all domains indicated a high degree of acceptance, suggesting that the three-dimensional printed temporal bone was a useful tool in skills development. A sophisticated three-dimensional printed temporal bone that demonstrates face and content validity was developed. The efficiency in cost savings coupled with low associated biohazards make it likely that the printed temporal bone will be incorporated into traditional temporal bone skills development programmes in the near future.

Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells

DOE PAGES

Rodriguez, Jose A.; Xu, Rui; Chen, Chien -Chun; ...

2015-09-01

Here, a structural understanding of whole cells in three dimensions at high spatial resolution remains a significant challenge and, in the case of X-rays, has been limited by radiation damage. By alleviating this limitation, cryogenic coherent diffractive imaging (cryo-CDI) can in principle be used to bridge the important resolution gap between optical and electron microscopy in bio-imaging. Here, the first experimental demonstration of cryo-CDI for quantitative three-dimensional imaging of whole frozen-hydrated cells using 8 Kev X-rays is reported. As a proof of principle, a tilt series of 72 diffraction patterns was collected from a frozen-hydrated Neospora caninum cell and themore » three-dimensional mass density of the cell was reconstructed and quantified based on its natural contrast. This three-dimensional reconstruction reveals the surface and internal morphology of the cell, including its complex polarized sub-cellular structure. Finally, it is believed that this work represents an experimental milestone towards routine quantitative three-dimensional imaging of whole cells in their natural state with spatial resolutions in the tens of nanometres.« less

Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells.

PubMed

Rodriguez, Jose A; Xu, Rui; Chen, Chien-Chun; Huang, Zhifeng; Jiang, Huaidong; Chen, Allan L; Raines, Kevin S; Pryor, Alan; Nam, Daewoong; Wiegart, Lutz; Song, Changyong; Madsen, Anders; Chushkin, Yuriy; Zontone, Federico; Bradley, Peter J; Miao, Jianwei

2015-09-01

A structural understanding of whole cells in three dimensions at high spatial resolution remains a significant challenge and, in the case of X-rays, has been limited by radiation damage. By alleviating this limitation, cryogenic coherent diffractive imaging (cryo-CDI) can in principle be used to bridge the important resolution gap between optical and electron microscopy in bio-imaging. Here, the first experimental demonstration of cryo-CDI for quantitative three-dimensional imaging of whole frozen-hydrated cells using 8 keV X-rays is reported. As a proof of principle, a tilt series of 72 diffraction patterns was collected from a frozen-hydrated Neospora caninum cell and the three-dimensional mass density of the cell was reconstructed and quantified based on its natural contrast. This three-dimensional reconstruction reveals the surface and internal morphology of the cell, including its complex polarized sub-cellular structure. It is believed that this work represents an experimental milestone towards routine quantitative three-dimensional imaging of whole cells in their natural state with spatial resolutions in the tens of nanometres.

Photodeposition Method For Fabricating A Three-Dimensional, Patterned Polymer Microstructure

DOEpatents

Walt, David R.; Healey, Brian G.

2001-03-13

The present invention is a photodeposition methodology for fabricating a three-dimensional patterned polymer microstructure. A variety of polymeric structures can be fabricated on solid substrates using unitary fiber optic arrays for light delivery. The methodology allows micrometer-scale photopatterning for the fabricated structures using masks substantially larger than the desired dimensions of the microstructure.

Pressure induced metallization with absence of structural transition in layered molybdenum diselenide

PubMed Central

Zhao, Zhao; Zhang, Haijun; Yuan, Hongtao; Wang, Shibing; Lin, Yu; Zeng, Qiaoshi; Xu, Gang; Liu, Zhenxian; Solanki, G. K.; Patel, K. D.; Cui, Yi; Hwang, Harold Y.; Mao, Wendy L.

2015-01-01

Layered transition-metal dichalcogenides have emerged as exciting material systems with atomically thin geometries and unique electronic properties. Pressure is a powerful tool for continuously tuning their crystal and electronic structures away from the pristine states. Here, we systematically investigated the pressurized behavior of MoSe2 up to ∼60 GPa using multiple experimental techniques and ab-initio calculations. MoSe2 evolves from an anisotropic two-dimensional layered network to a three-dimensional structure without a structural transition, which is a complete contrast to MoS2. The role of the chalcogenide anions in stabilizing different layered patterns is underscored by our layer sliding calculations. MoSe2 possesses highly tunable transport properties under pressure, determined by the gradual narrowing of its band-gap followed by metallization. The continuous tuning of its electronic structure and band-gap in the range of visible light to infrared suggest possible energy-variable optoelectronics applications in pressurized transition-metal dichalcogenides. PMID:26088416

Pressure induced metallization with absence of structural transition in layered molybdenum diselenide

DOE PAGES

Zhao, Zhao; Zhang, Haijun; Yuan, Hongtao; ...

2015-06-19

Layered transition-metal dichalcogenides have emerged as exciting material systems with atomically thin geometries and unique electronic properties. Pressure is a powerful tool for continuously tuning their crystal and electronic structures away from the pristine states. Here, we systematically investigated the pressurized behavior of MoSe 2 up to ~60 GPa using multiple experimental techniques and ab-initio calculations. MoSe 2 evolves from an anisotropic two-dimensional layered network to a three-dimensional structure without a structural transition, which is a complete contrast to MoS 2. The role of the chalcogenide anions in stabilizing different layered patterns is underscored by our layer sliding calculations. MoSemore » 2 possesses highly tunable transport properties under pressure, determined by the gradual narrowing of its band-gap followed by metallization. The continuous tuning of its electronic structure and band-gap in the range of visible light to infrared suggest possible energy-variable optoelectronics applications in pressurized transition-metal dichalcogenides.« less

Structure of turbulence in three-dimensional boundary layers

NASA Technical Reports Server (NTRS)

Subramanian, Chelakara S.

1993-01-01

This report provides an overview of the three dimensional turbulent boundary layer concepts and of the currently available experimental information for their turbulence modeling. It is found that more reliable turbulence data, especially of the Reynolds stress transport terms, is needed to improve the existing modeling capabilities. An experiment is proposed to study the three dimensional boundary layer formed by a 'sink flow' in a fully developed two dimensional turbulent boundary layer. Also, the mean and turbulence field measurement procedure using a three component laser Doppler velocimeter is described.

Microfabrication and Test of a Three-Dimensional Polymer Hydro-focusing Unit for Flow Cytometry Applications

NASA Technical Reports Server (NTRS)

Yang, Ren; Feeback, Daniel L.; Wang, Wan-Jun

2005-01-01

This paper details a novel three-dimensional (3D) hydro-focusing micro cell sorter for micro flow cytometry applications. The unit was microfabricated by means of SU-8 3D lithography. The 3D microstructure for coaxial sheathing was designed, microfabricated, and tested. Three-dimensional hydrofocusing capability was demonstrated with an experiment to sort labeled tanned sheep erythrocytes (red blood cells). This polymer hydro-focusing microstructure is easily microfabricated and integrated with other polymer microfluidic structures. Keywords: SU-8, three-dimensional hydro-focusing, microfluidic, microchannel, cytometer

Three-dimensional macro-structures of two-dimensional nanomaterials.

PubMed

Shehzad, Khurram; Xu, Yang; Gao, Chao; Duan, Xiangfeng

2016-10-21

If two-dimensional (2D) nanomaterials are ever to be utilized as components of practical, macroscopic devices on a large scale, there is a complementary need to controllably assemble these 2D building blocks into more sophisticated and hierarchical three-dimensional (3D) architectures. Such a capability is key to design and build complex, functional devices with tailored properties. This review provides a comprehensive overview of the various experimental strategies currently used to fabricate the 3D macro-structures of 2D nanomaterials. Additionally, various approaches for the decoration of the 3D macro-structures with organic molecules, polymers, and inorganic materials are reviewed. Finally, we discuss the applications of 3D macro-structures, especially in the areas of energy, environment, sensing, and electronics, and describe the existing challenges and the outlook for this fast emerging field.

Applications to car bodies - Generalized layout design of three-dimensional shells

NASA Technical Reports Server (NTRS)

Fukushima, Junichi; Suzuki, Katsuyuki; Kikuchi, Noboru

1993-01-01

We shall describe applications of the homogenization method, formulated in Part 1, to design layout of car bodies represented by three-dimensional shell structures based on a multi-loading optimization.

[Three-dimensional finite element study on the change of glossopharyngeum in patient with obstructive sleep apnea hypopnea syndrome during titrated mandible advancement].

PubMed

Yang, Suixing; Feng, Jing; Zhang, Zuo; Qu, Aili; Gong, Miao; Tang, Jie; Fan, Junheng; Li, Songqing; Zhao, Yanling

2013-04-01

To construct a three-dimensional finite element model of the upper airway and adjacent structure of an obstructive sleep apnea hypopnea syndrome (OSAHS) patient for biomechanical analysis. And to study the influence of glossopharyngeum of an OSAHS patient with three-dimensional finite element model during titrated mandible advancement. DICOM format image information of an OSAHS patient's upper airway was obtained by thin-section CT scanning and digital image processing were utilized to construct a three-dimensional finite element model by Mimics 10.0, Imageware 10.0 and Ansys software. The changes and the law of glossopharyngeum were observed by biomechanics and morphology after loading with titrated mandible advancement. A three-dimensional finite element model of the adjacent upper airway structure of OSAHS was established successfully. After loading, the transverse diameter of epiglottis tip of glossopharyngeum increased significantly, although the sagittal diameter decreased correspondingly. The principal stress was mainly distributed in anterior wall of the upper airway. The location of principal stress concentration did not change significantly with the increasing of distance. The stress of glossopharyngeum increased during titrated mandible advancement. A more precise three-dimensional finite model of upper airway and adjacent structure of an OSAHS patient is established and improved efficiency by Mimics, Imageware and Ansys software. The glossopharyngeum of finite element model of OSAHS is analyzed by titrated mandible advancement and can effectively show the relationship between mandible advancement and the glossopharyngeum.

On the three dimensional structure of stratospheric material transport associated with various types of waves

NASA Astrophysics Data System (ADS)

Kinoshita, T.; Sato, K.

2016-12-01

The Transformed Eulerian-Mean (TEM) equations were derived by Andrews and McIntyre (1976, 1978) and have been widely used to examine wave-mean flow interaction in the meridional cross section. According to previous studies, the Brewer-Dobson circulation in the stratosphere is driven by planetary waves, baroclinic waves, and inertia-gravity waves, and that the meridional circulation from the summer hemisphere to the winter hemisphere in the mesosphere is mainly driven by gravity waves (e.g., Garcia and Boville 1994; Plumb and Semeniuk 2003; Watanabe et al. 2008; Okamoto et al. 2011). However, the TEM equations do not provide the three-dimensional view of the transport, so that the three dimensional TEM equations have been formulated (Hoskins et al. 1983, Trenberth 1986, Plumb 1985, 1986, Takaya and Nakamura 1997, 2001, Miyahara 2006, Kinoshita et al. 2010, Noda 2010, Kinoshita and Sato 2013a, b, and Noda 2014). On the other hand, the TEM equations cannot properly treat the lower boundary and unstable waves. The Mass-weighted Isentropic Mean (MIM) equations derived by Iwasaki (1989, 1990) are the equations that overcome those problems and the formulation of three-dimensional MIM equations have been studied. The present study applies the three-dimensional TEM and MIM equations to the ERA-Interim reanalysis data and examines the climatological character of three-dimensional structure of Stratospheric Brewer-Dobson circulation. Next, we will discuss how to treat the flow associated with spatial structure of stationary waves.

Three-dimensional periodic dielectric structures having photonic Dirac points

DOEpatents

Bravo-Abad, Jorge; Joannopoulos, John D.; Soljacic, Marin

2015-06-02

The dielectric, three-dimensional photonic materials disclosed herein feature Dirac-like dispersion in quasi-two-dimensional systems. Embodiments include a face-centered cubic (fcc) structure formed by alternating layers of dielectric rods and dielectric slabs patterned with holes on respective triangular lattices. This fcc structure also includes a defect layer, which may comprise either dielectric rods or a dielectric slab with patterned with holes. This defect layer introduces Dirac cone dispersion into the fcc structure's photonic band structure. Examples of these fcc structures enable enhancement of the spontaneous emission coupling efficiency (the .beta.-factor) over large areas, contrary to the conventional wisdom that the .beta.-factor degrades as the system's size increases. These results enable large-area, low-threshold lasers; single-photon sources; quantum information processing devices; and energy harvesting systems.

Inverse and Direct Energy Cascades in Three-Dimensional Magnetohydrodynamic Turbulence at Low Magnetic Reynolds Number

NASA Astrophysics Data System (ADS)

Baker, Nathaniel T.; Pothérat, Alban; Davoust, Laurent; Debray, François

2018-06-01

This experimental study analyzes the relationship between the dimensionality of turbulence and the upscale or downscale nature of its energy transfers. We do so by forcing low-R m magnetohydrodynamic turbulence in a confined channel, while precisely controlling its dimensionality by means of an externally applied magnetic field. We first identify a specific length scale l^⊥ c that separates smaller 3D structures from larger quasi-2D ones. We then show that an inverse energy cascade of horizontal kinetic energy along horizontal scales is always observable at large scales, and that it extends well into the region of 3D structures. At the same time, a direct energy cascade confined to the smallest and strongly 3D scales is observed. These dynamics therefore appear not to be simply determined by the dimensionality of individual scales, nor by the forcing scale, unlike in other studies. In fact, our findings suggest that the relationship between kinematics and dynamics is not universal and may strongly depend on the forcing and dissipating mechanisms at play.

Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots.

PubMed

Hirata, Yoshito; Oda, Arisa; Ohta, Kunihiro; Aihara, Kazuyuki

2016-10-11

Single-cell analysis of the three-dimensional (3D) chromosome structure can reveal cell-to-cell variability in genome activities. Here, we propose to apply recurrence plots, a mathematical method of nonlinear time series analysis, to reconstruct the 3D chromosome structure of a single cell based on information of chromosomal contacts from genome-wide chromosome conformation capture (Hi-C) data. This recurrence plot-based reconstruction (RPR) method enables rapid reconstruction of a unique structure in single cells, even from incomplete Hi-C information.

Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots

NASA Astrophysics Data System (ADS)

Hirata, Yoshito; Oda, Arisa; Ohta, Kunihiro; Aihara, Kazuyuki

2016-10-01

Single-cell analysis of the three-dimensional (3D) chromosome structure can reveal cell-to-cell variability in genome activities. Here, we propose to apply recurrence plots, a mathematical method of nonlinear time series analysis, to reconstruct the 3D chromosome structure of a single cell based on information of chromosomal contacts from genome-wide chromosome conformation capture (Hi-C) data. This recurrence plot-based reconstruction (RPR) method enables rapid reconstruction of a unique structure in single cells, even from incomplete Hi-C information.

Etched distributed Bragg reflectors as three-dimensional photonic crystals: photonic bands and density of states.

PubMed

Pavarini, E; Andreani, L C

2002-09-01

The photonic band dispersion and density of states (DOS) are calculated for the three-dimensional (3D) hexagonal structure corresponding to a distributed Bragg reflector patterned with a 2D triangular lattice of circular holes. Results for the Si/SiO(2) and GaAs/Al(x)Ga(1-x)As systems determine the optimal parameters for which a gap in the 2D plane occurs and overlaps the 1D gap of the multilayer. The DOS is considerably reduced in correspondence with the overlap of 2D and 1D gaps. Also, the local density of states (i.e., the DOS weighted with the squared electric field at a given point) has strong variations depending on the position. Both results imply substantial changes of spontaneous emission rates and patterns for a local emitter embedded in the structure and make this system attractive for the fabrication of a 3D photonic crystal with controlled radiative properties.

Sandwiched polymer fibre in fibrin matrices for the dictation of endothelial cells undergoing angiogenesis

NASA Astrophysics Data System (ADS)

Sukmana, I.; Djuansjah, J. R. P.

2013-04-01

We present here a three-dimensional (3D) sandwich system made by poly(ethylene terephthalate) (PET) fibre and fibrin extracellular matrix (ECM) for endothelial cell dictation and angiogenesis guidance. In this three-dimensional system, Human Umbilical Vein Endothelial cells (HUVECs) were firstly cultured for 2 (two) days to cover the PET fibre before sandwiched in two layer fibrin gel containing HUVECs. After 4 (four) days of culture, cel-to-cel connection, tube-like structure and multi-cellular lumen formation were then assessed and validated. Phase contrast and fluorescence imaging using an inverted microscope were used to determine cell-to-cell and cell-ECM interactions. Laser scanning confocal microscopy and histological techniques were used to confirm the development of tube-like structure and multi-cellular lumen formation. This study shows that polymer fibres sandwiched in fibrin gel can be used to dictate endothelial cells undergoing angiogenesis with potential application in cancer and cardiovascular study and tissue engineering vascularisation.

The upper mantle shear wave velocity structure of East Africa derived from Rayleigh wave tomography

NASA Astrophysics Data System (ADS)

O'Donnell, J.; Nyblade, A.; Adams, A. N.; Weeraratne, D. S.; Mulibo, G.; Tugume, F.

2012-12-01

An expanded model of the three-dimensional shear wave velocity structure of the upper mantle beneath East Africa has been developed using data from the latest phases of the AfricaArray East African Seismic Experiment in conjunction with data from preceding studies. The combined dataset consists of 331 events recorded on a total of 95 seismic stations spanning Kenya, Uganda, Tanzania, Zambia and Malawi. In this latest study, 149 events were used to determine fundamental mode Rayleigh wave phase velocities at periods ranging from 20 to 182 seconds using the two-plane-wave method. These were subsequently combined with the similarly processed published measurements and inverted for an updated upper mantle three-dimensional shear wave velocity model. Newly imaged features include a substantial fast anomaly in eastern Zambia that may have exerted a controlling influence on the evolution of the Western Rift Branch. Furthermore, there is a suggestion that the Eastern Rift Branch trends southeastward offshore eastern Tanzania.

Three-Dimensional Morphological and Chemical Evolution of Nanoporous Stainless Steel by Liquid Metal Dealloying [3D Morphological and Chemical Evolution of Nanoporous Stainless Steel by Liquid Metal Dealloying

DOE PAGES

Zhao, Chonghang; Wada, Takeshi; De Andrade, Vincent; ...

2017-09-04

Nanoporous materials, especially those fabricated by liquid metal dealloying processes, possess great potential in a wide range of applications due to their high surface area, bicontinuous structure with both open pores for transport and solid phase for conductivity or support, and low material cost. Here, we used X-ray nanotomography and X-ray fluorescence microscopy to reveal the three-dimensional (3D) morphology and elemental distribution within materials. Focusing on nanoporous stainless steel, we evaluated the 3D morphology of the dealloying front and established a quantitative processing-structure-property relationship at a later stage of dealloying. The morphological differences of samples created by liquid metal dealloyingmore » and aqueous dealloying methods were also discussed. Here, we concluded that it is particularly important to consider the dealloying, coarsening, and densification mechanisms in influencing the performance-determining, critical 3D parameters, such as tortuosity, pore size, porosity, curvature, and interfacial shape.« less

Experimental tests of linear and nonlinear three-dimensional equilibrium models in DIII-D

DOE PAGES

King, Josh D.; Strait, Edward J.; Lazerson, Samuel A.; ...

2015-07-01

DIII-D experiments using new detailed magnetic diagnostics show that linear, ideal magnetohydrodynamics (MHD) theory quantitatively describes the magnetic structure (as measured externally) of three-dimensional (3D) equilibria resulting from applied fields with toroidal mode number n = 1, while a nonlinear solution to ideal MHD force balance, using the VMEC code, requires the inclusion of n ≥ 1 to achieve similar agreement. Moreover, these tests are carried out near ITER baseline parameters, providing a validated basis on which to exploit 3D fields for plasma control development. We determine scans of the applied poloidal spectrum and edge safety factors which confirm thatmore » low-pressure, n = 1 non-axisymmetric tokamak equilibria are a single, dominant, stable eigenmode. But, at higher beta, near the ideal kink mode stability limit in the absence of a conducting wall, the qualitative features of the 3D structure are observed to vary in a way that is not captured by ideal MHD.« less

Three-Dimensional Morphological and Chemical Evolution of Nanoporous Stainless Steel by Liquid Metal Dealloying [3D Morphological and Chemical Evolution of Nanoporous Stainless Steel by Liquid Metal Dealloying

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Chonghang; Wada, Takeshi; De Andrade, Vincent

Nanoporous materials, especially those fabricated by liquid metal dealloying processes, possess great potential in a wide range of applications due to their high surface area, bicontinuous structure with both open pores for transport and solid phase for conductivity or support, and low material cost. Here, we used X-ray nanotomography and X-ray fluorescence microscopy to reveal the three-dimensional (3D) morphology and elemental distribution within materials. Focusing on nanoporous stainless steel, we evaluated the 3D morphology of the dealloying front and established a quantitative processing-structure-property relationship at a later stage of dealloying. The morphological differences of samples created by liquid metal dealloyingmore » and aqueous dealloying methods were also discussed. Here, we concluded that it is particularly important to consider the dealloying, coarsening, and densification mechanisms in influencing the performance-determining, critical 3D parameters, such as tortuosity, pore size, porosity, curvature, and interfacial shape.« less

Collimated Outflow Formation via Binary Stars: Three-Dimensional Simulations of Asymptotic Giant Branch Wind and Disk Wind Interactions

NASA Astrophysics Data System (ADS)

García-Arredondo, F.; Frank, Adam

2004-01-01

We present three-dimensional hydrodynamic simulations of the interaction of a slow wind from an asymptotic giant branch (AGB) star and a jet blown by an orbiting companion. The jet or ``collimated fast wind'' is assumed to originate from an accretion disk that forms via Bondi accretion of the AGB wind or Roche lobe overflow. We present two distinct regimes in the wind-jet interaction determined by the ratio of the AGB wind to jet momentum flux. Our results show that when the wind momentum flux overwhelms the flux in the jet, a more disordered outflow results with the jet assuming a corkscrew pattern and multiple shock structures driven into the AGB wind. In the opposite regime, the jet dominates and will drive a highly collimated, narrow-waisted outflow. We compare our results with scenarios described by Soker & Rappaport and extrapolate to the structures observed in planetary nebulae (PNs) and symbiotic stars.

Dorello's Canal for Laymen: A Lego-Like Presentation.

PubMed

Ezer, Haim; Banerjee, Anirban Deep; Thakur, Jai Deep; Nanda, Anil

2012-06-01

Objective Dorello's canal was first described by Gruber in 1859, and later by Dorello. Vail also described the anatomy of Dorello's canal. In the preceding century, Dorello's canal was clinically important, in understanding sixth nerve palsy and nowadays it is mostly important for skull base surgery. The understanding of the three dimensional anatomy, of this canal is very difficult to understand, and there is no simple explanation for its anatomy and its relationship with adjacent structures. We present a simple, Lego-like, presentation of Dorello's canal, in a stepwise manner. Materials and Methods Dorello's canal was dissected in five formalin-fixed cadaver specimens (10 sides). The craniotomy was performed, while preserving the neural and vascular structures associated with the canal. A 3D model was created, to explain the canal's anatomy. Results Using the petrous pyramid, the sixth nerve, the cavernous sinus, the trigeminal ganglion, the petorclival ligament and the posterior clinoid, the three-dimensional structure of Dorello's canal was defined. This simple representation aids in understanding the three dimensional relationship of Dorello's canal to its neighboring structures. Conclusion Dorello's canal with its three dimensional structure and relationship to its neighboring anatomical structures could be reconstructed using a few anatomical building blocks. This method simplifies the understanding of this complex anatomical structure, and could be used for teaching purposes for aspiring neurosurgeons, and anatomy students.

Dorello's Canal for Laymen: A Lego-Like Presentation

PubMed Central

Ezer, Haim; Banerjee, Anirban Deep; Thakur, Jai Deep; Nanda, Anil

2012-01-01

Objective Dorello's canal was first described by Gruber in 1859, and later by Dorello. Vail also described the anatomy of Dorello's canal. In the preceding century, Dorello's canal was clinically important, in understanding sixth nerve palsy and nowadays it is mostly important for skull base surgery. The understanding of the three dimensional anatomy, of this canal is very difficult to understand, and there is no simple explanation for its anatomy and its relationship with adjacent structures. We present a simple, Lego-like, presentation of Dorello's canal, in a stepwise manner. Materials and Methods Dorello's canal was dissected in five formalin-fixed cadaver specimens (10 sides). The craniotomy was performed, while preserving the neural and vascular structures associated with the canal. A 3D model was created, to explain the canal's anatomy. Results Using the petrous pyramid, the sixth nerve, the cavernous sinus, the trigeminal ganglion, the petorclival ligament and the posterior clinoid, the three-dimensional structure of Dorello's canal was defined. This simple representation aids in understanding the three dimensional relationship of Dorello's canal to its neighboring structures. Conclusion Dorello's canal with its three dimensional structure and relationship to its neighboring anatomical structures could be reconstructed using a few anatomical building blocks. This method simplifies the understanding of this complex anatomical structure, and could be used for teaching purposes for aspiring neurosurgeons, and anatomy students. PMID:23730547

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

PubMed Central

Cruz, José Almeida; Blanchet, Marc-Frédérick; Boniecki, Michal; Bujnicki, Janusz M.; Chen, Shi-Jie; Cao, Song; Das, Rhiju; Ding, Feng; Dokholyan, Nikolay V.; Flores, Samuel Coulbourn; Huang, Lili; Lavender, Christopher A.; Lisi, Véronique; Major, François; Mikolajczak, Katarzyna; Patel, Dinshaw J.; Philips, Anna; Puton, Tomasz; Santalucia, John; Sijenyi, Fredrick; Hermann, Thomas; Rother, Kristian; Rother, Magdalena; Serganov, Alexander; Skorupski, Marcin; Soltysinski, Tomasz; Sripakdeevong, Parin; Tuszynska, Irina; Weeks, Kevin M.; Waldsich, Christina; Wildauer, Michael; Leontis, Neocles B.; Westhof, Eric

2012-01-01

We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The results should give potential users insight into the suitability of available methods for different applications and facilitate efforts in the RNA structure prediction community in ongoing efforts to improve prediction tools. We also report the creation of an automated evaluation pipeline to facilitate the analysis of future RNA structure prediction exercises. PMID:22361291

Forming three-dimensional closed shapes from two-dimensional soft ribbons by controlled buckling

PubMed Central

Aoki, Michio

2018-01-01

Conventional manufacturing techniques—moulding, machining and casting—exist to produce three-dimensional (3D) shapes. However, these industrial processes are typically geared for mass production and are not directly applicable to residential settings, where inexpensive and versatile tools are desirable. Moreover, those techniques are, in general, not adequate to process soft elastic materials. Here, we introduce a new concept of forming 3D closed hollow shapes from two-dimensional (2D) elastic ribbons by controlled buckling. We numerically and experimentally characterize how the profile and thickness of the ribbon determine its buckled shape. We find a 2D master profile with which various elliptical 3D shapes can be formed. More complex natural and artificial hollow shapes, such as strawberry, hourglass and wheel, can also be achieved via strategic design and pattern engraving on the ribbons. The nonlinear response of the post-buckling regime is rationalized through finite-element analysis, which shows good quantitative agreement with experiments. This robust fabrication should complement conventional techniques and provide a rich arena for future studies on the mechanics and new applications of elastic hollow structures. PMID:29515894

Forming three-dimensional closed shapes from two-dimensional soft ribbons by controlled buckling

NASA Astrophysics Data System (ADS)

Aoki, Michio; Juang, Jia-Yang

2018-02-01

Conventional manufacturing techniques-moulding, machining and casting-exist to produce three-dimensional (3D) shapes. However, these industrial processes are typically geared for mass production and are not directly applicable to residential settings, where inexpensive and versatile tools are desirable. Moreover, those techniques are, in general, not adequate to process soft elastic materials. Here, we introduce a new concept of forming 3D closed hollow shapes from two-dimensional (2D) elastic ribbons by controlled buckling. We numerically and experimentally characterize how the profile and thickness of the ribbon determine its buckled shape. We find a 2D master profile with which various elliptical 3D shapes can be formed. More complex natural and artificial hollow shapes, such as strawberry, hourglass and wheel, can also be achieved via strategic design and pattern engraving on the ribbons. The nonlinear response of the post-buckling regime is rationalized through finite-element analysis, which shows good quantitative agreement with experiments. This robust fabrication should complement conventional techniques and provide a rich arena for future studies on the mechanics and new applications of elastic hollow structures.

Evaluating the effects of modeling errors for isolated finite three-dimensional targets

NASA Astrophysics Data System (ADS)

Henn, Mark-Alexander; Barnes, Bryan M.; Zhou, Hui

2017-10-01

Optical three-dimensional (3-D) nanostructure metrology utilizes a model-based metrology approach to determine critical dimensions (CDs) that are well below the inspection wavelength. Our project at the National Institute of Standards and Technology is evaluating how to attain key CD and shape parameters from engineered in-die capable metrology targets. More specifically, the quantities of interest are determined by varying the input parameters for a physical model until the simulations agree with the actual measurements within acceptable error bounds. As in most applications, establishing a reasonable balance between model accuracy and time efficiency is a complicated task. A well-established simplification is to model the intrinsically finite 3-D nanostructures as either periodic or infinite in one direction, reducing the computationally expensive 3-D simulations to usually less complex two-dimensional (2-D) problems. Systematic errors caused by this simplified model can directly influence the fitting of the model to the measurement data and are expected to become more apparent with decreasing lengths of the structures. We identify these effects using selected simulation results and present experimental setups, e.g., illumination numerical apertures and focal ranges, that can increase the validity of the 2-D approach.

Small-angle x-ray scattering study of polymer structure: Carbosilane dendrimers in hexane solution

NASA Astrophysics Data System (ADS)

Shtykova, E. V.; Feigin, L. A.; Volkov, V. V.; Malakhova, Yu. N.; Streltsov, D. R.; Buzin, A. I.; Chvalun, S. N.; Katarzhanova, E. Yu.; Ignatieva, G. M.; Muzafarov, A. M.

2016-09-01

The three-dimensional organization of monodisperse hyper-branched macromolecules of regular structure—carbosilane dendrimers of zero, third, and sixth generations—has been studied by small-angle X-ray scattering (SAXS) in solution. The use of modern methods of SAXS data interpretation, including ab initio modeling, has made it possible to determine the internal architecture of the dendrimers in dependence of the generation number and the number of cyclosiloxane end groups (forming the shell of dendritic macromolecules) and show dendrimers to be spherical. The structural results give grounds to consider carbosilane dendrimers promising objects for forming crystals with subsequent structural analysis and determining their structure with high resolution, as well as for designing new materials to be used in various dendrimer-based technological applications.

The young person's guide to the PDB.

PubMed

Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120, 000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview.

Three-dimensional spiral CT during arterial portography: comparison of three rendering techniques.

PubMed

Heath, D G; Soyer, P A; Kuszyk, B S; Bliss, D F; Calhoun, P S; Bluemke, D A; Choti, M A; Fishman, E K

1995-07-01

The three most common techniques for three-dimensional reconstruction are surface rendering, maximum-intensity projection (MIP), and volume rendering. Surface-rendering algorithms model objects as collections of geometric primitives that are displayed with surface shading. The MIP algorithm renders an image by selecting the voxel with the maximum intensity signal along a line extended from the viewer's eye through the data volume. Volume-rendering algorithms sum the weighted contributions of all voxels along the line. Each technique has advantages and shortcomings that must be considered during selection of one for a specific clinical problem and during interpretation of the resulting images. With surface rendering, sharp-edged, clear three-dimensional reconstruction can be completed on modest computer systems; however, overlapping structures cannot be visualized and artifacts are a problem. MIP is computationally a fast technique, but it does not allow depiction of overlapping structures, and its images are three-dimensionally ambiguous unless depth cues are provided. Both surface rendering and MIP use less than 10% of the image data. In contrast, volume rendering uses nearly all of the data, allows demonstration of overlapping structures, and engenders few artifacts, but it requires substantially more computer power than the other techniques.

A Score of the Ability of a Three-Dimensional Protein Model to Retrieve Its Own Sequence as a Quantitative Measure of Its Quality and Appropriateness

PubMed Central

Martínez-Castilla, León P.; Rodríguez-Sotres, Rogelio

2010-01-01

Background Despite the remarkable progress of bioinformatics, how the primary structure of a protein leads to a three-dimensional fold, and in turn determines its function remains an elusive question. Alignments of sequences with known function can be used to identify proteins with the same or similar function with high success. However, identification of function-related and structure-related amino acid positions is only possible after a detailed study of every protein. Folding pattern diversity seems to be much narrower than sequence diversity, and the amino acid sequences of natural proteins have evolved under a selective pressure comprising structural and functional requirements acting in parallel. Principal Findings The approach described in this work begins by generating a large number of amino acid sequences using ROSETTA [Dantas G et al. (2003) J Mol Biol 332:449–460], a program with notable robustness in the assignment of amino acids to a known three-dimensional structure. The resulting sequence-sets showed no conservation of amino acids at active sites, or protein-protein interfaces. Hidden Markov models built from the resulting sequence sets were used to search sequence databases. Surprisingly, the models retrieved from the database sequences belonged to proteins with the same or a very similar function. Given an appropriate cutoff, the rate of false positives was zero. According to our results, this protocol, here referred to as Rd.HMM, detects fine structural details on the folding patterns, that seem to be tightly linked to the fitness of a structural framework for a specific biological function. Conclusion Because the sequence of the native protein used to create the Rd.HMM model was always amongst the top hits, the procedure is a reliable tool to score, very accurately, the quality and appropriateness of computer-modeled 3D-structures, without the need for spectroscopy data. However, Rd.HMM is very sensitive to the conformational features of the models' backbone. PMID:20830209

Three-dimensional structure of interleukin 8 in solution.

PubMed

Clore, G M; Appella, E; Yamada, M; Matsushima, K; Gronenborn, A M

1990-02-20

The solution structure of the interleukin 8 (IL-8) dimer has been solved by nuclear magnetic resonance (NMR) spectroscopy and hybrid distance geometry-dynamical simulated annealing calculations. The structure determination is based on a total of 1880 experimental distance restraints (of which 82 are intersubunit) and 362 torsion angle restraints (comprising phi, psi, and chi 1 torsion angles). A total of 30 simulated annealing structures were calculated, and the atomic rms distribution about the mean coordinate positions (excluding residues 1-5 of each subunit) is 0.41 +/- 0.08 A for the backbone atoms and 0.90 +/- 0.08 A for all atoms. The three-dimensional solution structure of the IL-8 dimer reveals a structural motif in which two symmetry-related antiparallel alpha-helices, approximately 24 A long and separated by about 14 A, lie on top of a six-stranded antiparallel beta-sheet platform derived from two three-stranded Greek keys, one from each monomer unit. The general architecture is similar to that of the alpha 1/alpha 2 domains of the human class I histocompatibility antigen HLA-A2. It is suggested that the two alpha-helices form the binding site for the cellular receptor and that the specificity of IL-8, as well as that of a number of related proteins involved in cell-specific chemotaxis, mediation of cell growth, and the inflammatory response, is achieved by the distinct distribution of charged and polar residues at the surface of the helices.

Hydrophobic core malleability of a de novo designed three-helix bundle protein.

PubMed

Walsh, S T; Sukharev, V I; Betz, S F; Vekshin, N L; DeGrado, W F

2001-01-12

De novo protein design provides a tool for testing the principles that stabilize the structures of proteins. Recently, we described the design and structure determination of alpha(3)D, a three-helix bundle protein with a well-packed hydrophobic core. Here, we test the malleability and adaptability of this protein's structure by mutating a small, Ala residue (A60) in its core to larger, hydrophobic side-chains, Leu and Ile. Such changes introduce strain into the structures of natural proteins, and therefore generally destabilize the native state. By contrast, these mutations were slightly stabilizing ( approximately 1.5 kcal mol(-1)) to the tertiary structure of alpha(3)D. The value of DeltaC(p) for unfolding of these mutants was not greatly affected relative to wild-type, indicating that the change in solvent accessibility for unfolding was similar. However, two-dimensional heteronuclear single quantum coherence spectra indicate that the protein adjusts to the introduction of steric bulk in different ways. A60L-alpha(3)D showed serious erosion in the dispersion of both the amide backbone as well as the side-chain methyl chemical shifts. By contrast, A60I-alpha(3)D showed excellent dispersion of the backbone resonances, and selective changes in dispersion of the aliphatic side-chains proximal to the site of mutation. Together, these data suggest that alpha(3)D, although folded into a unique three-dimensional structure, is nevertheless more malleable and flexible than most natural, native proteins. Copyright 2001 Academic Press.

CCR2 and CCR5 receptor-binding properties of herpesvirus-8 vMIP-II based on sequence analysis and its solution structure.

PubMed

Shao, W; Fernandez, E; Sachpatzidis, A; Wilken, J; Thompson, D A; Schweitzer, B I; Lolis, E

2001-05-01

Human herpesvirus-8 (HHV-8) is the infectious agent responsible for Kaposi's sarcoma and encodes a protein, macrophage inflammatory protein-II (vMIP-II), which shows sequence similarity to the human CC chemokines. vMIP-II has broad receptor specificity that crosses chemokine receptor subfamilies, and inhibits HIV-1 viral entry mediated by numerous chemokine receptors. In this study, the solution structure of chemically synthesized vMIP-II was determined by nuclear magnetic resonance. The protein is a monomer and possesses the chemokine fold consisting of a flexible N-terminus, three antiparallel beta strands, and a C-terminal alpha helix. Except for the N-terminal residues (residues 1-13) and the last two C-terminal residues (residues 73-74), the structure of vMIP-II is well-defined, exhibiting average rmsd of 0.35 and 0.90 A for the backbone heavy atoms and all heavy atoms of residues 14-72, respectively. Taking into account the sequence differences between the various CC chemokines and comparing their three-dimensional structures allows us to implicate residues that influence the quaternary structure and receptor binding and activation of these proteins in solution. The analysis of the sequence and three-dimensional structure of vMIP-II indicates the presence of epitopes involved in binding two receptors CCR2 and CCR5. We propose that vMIP-II was initially specific for CCR5 and acquired receptor-binding properties to CCR2 and other chemokine receptors.

Nonlinear geometric scaling of coercivity in a three-dimensional nanoscale analog of spin ice

NASA Astrophysics Data System (ADS)

Shishkin, I. S.; Mistonov, A. A.; Dubitskiy, I. S.; Grigoryeva, N. A.; Menzel, D.; Grigoriev, S. V.

2016-08-01

Magnetization hysteresis loops of a three-dimensional nanoscale analog of spin ice based on the nickel inverse opal-like structure (IOLS) have been studied at room temperature. The samples are produced by filling nickel into the voids of artificial opal-like films. The spin ice behavior is induced by tetrahedral elements within the IOLS, which have the same arrangement of magnetic moments as a spin ice. The thickness of the films vary from a two-dimensional, i.e., single-layered, antidot array to a three-dimensional, i.e., multilayered, structure. The coercive force, the saturation, and the irreversibility field have been measured in dependence of the thickness of the IOLS for in-plane and out-of-plane applied fields. The irreversibility and saturation fields change abruptly from the antidot array to the three-dimensional IOLS and remain constant upon further increase of the number of layers n . The coercive force Hc seems to increase logarithmically with increasing n as Hc=Hc 0+α ln(n +1 ) . The logarithmic law implies the avalanchelike remagnetization of anisotropic structural elements connecting tetrahedral and cubic nodes in the IOLS. We conclude that the "ice rule" is the base of mechanism regulating this process.

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package

PubMed Central

Kumar, Yadhu; Westram, Ralf; Kipfer, Peter; Meier, Harald; Ludwig, Wolfgang

2006-01-01

Background Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. Results Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. Conclusion Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via . PMID:16672074

Bayesian Peak Picking for NMR Spectra

PubMed Central

Cheng, Yichen; Gao, Xin; Liang, Faming

2013-01-01

Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method. PMID:24184964

A Microfluidic Route to Breaking Chiral Symmetry: Theory and Experiment

NASA Astrophysics Data System (ADS)

Ocko, Samuel; Adams, Laura

A robust route for the biased production of single handed chiral structures has been found in generating non-spherical, multi-component double emulsions using glass microfluidic devices. The specific type of handedness is determined by the final packing geometry of four different inner drops inside an ultra-thin sheath of oil. Before the three dimensional chiral structures are formed, the quasi-one dimensional chain of four inner drops re-arranges in two dimensions into either checkerboard or stripe patterns. We derive an analytical model predicting which pattern is more likely and assembles in the least amount of time. Moreover, our model accurately predicts our experimental results and is based on local bending dynamics, rather than global surface energy minimization. We gratefully acknowledge Professors D. Weitz and L. Mahadevan's support.

Reverse Monte Carlo simulation of Se{sub 80}Te{sub 20} and Se{sub 80}Te{sub 15}Sb{sub 5} glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abdel-Baset, A. M.; Rashad, M.; Moharram, A. H.

2013-12-16

Two-dimensional Monte Carlo of the total pair distribution functions g(r) is determined for Se{sub 80}Te{sub 20} and Se{sub 80}Te{sub 15}Sb{sub 5} alloys, and then it used to assemble the three-dimensional atomic configurations using the reverse Monte Carlo simulation. The partial pair distribution functions g{sub ij}(r) indicate that the basic structure unit in the Se{sub 80}Te{sub 15}Sb{sub 5} glass is di-antimony tri-selenide units connected together through Se-Se and Se-Te chain. The structure of Se{sub 80}Te{sub 20} alloys is a chain of Se-Te and Se-Se in addition to some rings of Se atoms.

Three-Dimensional Model of the Scatterer Distribution in Cirrhotic Liver

NASA Astrophysics Data System (ADS)

Yamaguchi, Tadashi; Nakamura, Keigo; Hachiya, Hiroyuki

2003-05-01

Ultrasonic B-mode images are affected by changes in scatterer distribution. It is hard to estimate the relationship between the ultrasonic image and the tissue structure quantitatively because we cannot observe the continuous stages of liver cirrhosis tissue clinically, particularly the beginning stage. In this paper, we propose a three-dimensional modeling method of scatterer distribution for normal and cirrhotic livers to confirm the influence of the change in the form of scatterer distribution on echo information. The algorithm of the method includes parameters which determine the expansion of nodules and fibers. Using the B-mode images which are obtained from these scatterer distributions, we analyze the relationship between the changes in the form of biological tissue and the changes in the B-mode images during progressive liver cirrhosis.

Performance of a non-tapered 3D morphing wing with integrated compliant ribs

NASA Astrophysics Data System (ADS)

Previtali, F.; Ermanni, P.

2012-05-01

Morphing wings have a high potential for improving the performance and reducing the fuel consumption of modern aircraft. Thanks to its simplicity, the compliant belt-rib concept is regarded by the authors as a promising solution. Using the compliant rib designed by Hasse and Campanile as a starting point, a compliant morphing wing made of composite materials is designed. Innovative methods for optimal placing of the actuation and for the quantification of the morphing are used. The performance of the compliant morphing wing in terms of three-dimensional (3D) structural behaviour and aerodynamic properties, both two- and three-dimensional, is presented and discussed. The fundamental importance of considering 3D coupling effects in the determination of the performance of morphing aerofoils is shown.

Three-dimensional vectorial multifocal arrays created by pseudo-period encoding

NASA Astrophysics Data System (ADS)

Zeng, Tingting; Chang, Chenliang; Chen, Zhaozhong; Wang, Hui-Tian; Ding, Jianping

2018-06-01

Multifocal arrays have been attracting considerable attention recently owing to their potential applications in parallel optical tweezers, parallel single-molecule orientation determination, parallel recording and multifocal multiphoton microscopy. However, the generation of vectorial multifocal arrays with a tailorable structure and polarization state remains a great challenge, and reports on multifocal arrays have hitherto been restricted either to scalar focal spots without polarization versatility or to regular arrays with fixed spacing. In this work, we propose a specific pseudo-period encoding technique to create three-dimensional (3D) vectorial multifocal arrays with the ability to manipulate the position, polarization state and intensity of each focal spot. We experimentally validated the flexibility of our approach in the generation of 3D vectorial multiple spots with polarization multiplicity and position tunability.

Three dimensional investigation of the shock train structure in a convergent-divergent nozzle

NASA Astrophysics Data System (ADS)

Mousavi, Seyed Mahmood; Roohi, Ehsan

2014-12-01

Three-dimensional computational fluid dynamics analyses have been employed to study the compressible and turbulent flow of the shock train in a convergent-divergent nozzle. The primary goal is to determine the behavior, location, and number of shocks. In this context, full multi-grid initialization, Reynolds stress turbulence model (RSM), and the grid adaption techniques in the Fluent software are utilized under the 3D investigation. The results showed that RSM solution matches with the experimental data suitably. The effects of applying heat generation sources and changing inlet flow total temperature have been investigated. Our simulations showed that changes in the heat generation rate and total temperature of the intake flow influence on the starting point of shock, shock strength, minimum pressure, as well as the maximum flow Mach number.

Residual Strength Analyses of Monolithic Structures

NASA Technical Reports Server (NTRS)

Forth, Scott (Technical Monitor); Ambur, Damodar R. (Technical Monitor); Seshadri, B. R.; Tiwari, S. N.

2003-01-01

Finite-element fracture simulation methodology predicts the residual strength of damaged aircraft structures. The methodology uses the critical crack-tip-opening-angle (CTOA) fracture criterion to characterize the fracture behavior of the material. The CTOA fracture criterion assumes that stable crack growth occurs when the crack-tip angle reaches a constant critical value. The use of the CTOA criterion requires an elastic- plastic, finite-element analysis. The critical CTOA value is determined by simulating fracture behavior in laboratory specimens, such as a compact specimen, to obtain the angle that best fits the observed test behavior. The critical CTOA value appears to be independent of loading, crack length, and in-plane dimensions. However, it is a function of material thickness and local crack-front constraint. Modeling the local constraint requires either a three-dimensional analysis or a two-dimensional analysis with an approximation to account for the constraint effects. In recent times as the aircraft industry is leaning towards monolithic structures with the intention of reducing part count and manufacturing cost, there has been a consistent effort at NASA Langley to extend critical CTOA based numerical methodology in the analysis of integrally-stiffened panels.In this regard, a series of fracture tests were conducted on both flat and curved aluminum alloy integrally-stiffened panels. These flat panels were subjected to uniaxial tension and during the test, applied load-crack extension, out-of-plane displacements and local deformations around the crack tip region were measured. Compact and middle-crack tension specimens were tested to determine the critical angle (wc) using three-dimensional code (ZIP3D) and the plane-strain core height (hJ using two-dimensional code (STAGS). These values were then used in the STAGS analysis to predict the fracture behavior of the integrally-stiffened panels. The analyses modeled stable tearing, buckling, and crack branching at the integral stiffener using different values of critical CTOA for different material thicknesses and orientation. Comparisons were made between measured and predicted load-crack extension, out-of-plane displacements and local deformations around the crack tip region. Simultaneously, three-dimensional capabilities to model crack branching and to monitor stable crack growth of multiple cracks in a large thick integrally-stiffened flat panels were implemented in three-dimensional finite element code (ZIP3D) and tested by analyzing the integrally-stiffened panels tested at Alcoa. The residual strength of the panels predicted from STAGS and ZP3D code compared very well with experimental data. In recent times, STAGS software has been updated with new features and now one can have combinations of solid and shell elements in the residual strength analysis of integrally-stiffened panels.

Impedance Eduction in Sound Fields With Peripherally Varying Liners and Flow

NASA Technical Reports Server (NTRS)

Watson, W. R.; Jones, M. G.

2015-01-01

A two-dimensional impedance eduction theory is extended to three-dimensional sound fields and peripherally varying duct liners. The approach is to first measure the acoustic pressure field at a series of flush-mounted wall microphones located around the periphery of the flow duct. The numerical solution for the acoustic pressure field at these microphones is also obtained by solving the three-dimensional convected Helmholtz equation using the finite element method. A quadratic objective function based on the difference between the measured and finite element solution is constructed and the unknown impedance function is obtained by minimizing this objective function. Impedance spectra educed for two uniform-structure liners (a wire-mesh and a conventional liner) and a hard-soft-hard peripherally varying liner (for which the soft segment is that of the conventional liner) are presented. Results are presented at three mean flow Mach numbers and fourteen sound source frequencies. The impedance spectra of the uniform-structure liners are also computed using a two-dimensional impedance eduction theory. The primary conclusions of the study are: 1) when measured data is used with the uniform-structure liners, the three-dimensional theory reproduces the same impedance spectra as the two-dimensional theory except for frequencies corresponding to very low or very high liner attenuation; and 2) good agreement between the educed impedance spectra of the uniform structure conventional liner and the soft segment of the peripherally varying liner is obtained.

Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap.

PubMed

Spiwok, Vojtěch; Králová, Blanka

2011-12-14

Atomic motions in molecules are not linear. This infers that nonlinear dimensionality reduction methods can outperform linear ones in analysis of collective atomic motions. In addition, nonlinear collective motions can be used as potentially efficient guides for biased simulation techniques. Here we present a simulation with a bias potential acting in the directions of collective motions determined by a nonlinear dimensionality reduction method. Ad hoc generated conformations of trans,trans-1,2,4-trifluorocyclooctane were analyzed by Isomap method to map these 72-dimensional coordinates to three dimensions, as described by Brown and co-workers [J. Chem. Phys. 129, 064118 (2008)]. Metadynamics employing the three-dimensional embeddings as collective variables was applied to explore all relevant conformations of the studied system and to calculate its conformational free energy surface. The method sampled all relevant conformations (boat, boat-chair, and crown) and corresponding transition structures inaccessible by an unbiased simulation. This scheme allows to use essentially any parameter of the system as a collective variable in biased simulations. Moreover, the scheme we used for mapping out-of-sample conformations from the 72D to 3D space can be used as a general purpose mapping for dimensionality reduction, beyond the context of molecular modeling. © 2011 American Institute of Physics

Bi-directional evolutionary structural optimization for strut-and-tie modelling of three-dimensional structural concrete

NASA Astrophysics Data System (ADS)

Shobeiri, Vahid; Ahmadi-Nedushan, Behrouz

2017-12-01

This article presents a method for the automatic generation of optimal strut-and-tie models in reinforced concrete structures using a bi-directional evolutionary structural optimization method. The methodology presented is developed for compliance minimization relying on the Abaqus finite element software package. The proposed approach deals with the generation of truss-like designs in a three-dimensional environment, addressing the design of corbels and joints as well as bridge piers and pile caps. Several three-dimensional examples are provided to show the capabilities of the proposed framework in finding optimal strut-and-tie models in reinforced concrete structures and verifying its efficiency to cope with torsional actions. Several issues relating to the use of the topology optimization for strut-and-tie modelling of structural concrete, such as chequerboard patterns, mesh-dependency and multiple load cases, are studied. In the last example, a design procedure for detailing and dimensioning of the strut-and-tie models is given according to the American Concrete Institute (ACI) 318-08 provisions.

Kinetics of hexacelsian to celsian phase transformation in SrAl2Si2O8

NASA Technical Reports Server (NTRS)

Bansal, Narottam P.; Drummond, Charles H., III

1992-01-01

The kinetics of hexacelsian to celsian phase transformation in SrAl2Si2O8 have been investigated. Phase pure hexacelsian was prepared by heat treatment of glass flakes at 990 C for 10 h. Bulk hexacelsian was isothermally heat treated at 1026, 1050, 1100, 1152, and 1200 C for various times. The amounts of monoclinic celsian formed were determined using quantitative X-ray diffraction. Values of reaction rate constant, k, at various temperatures were evaluated from the Avrami equation. The Avrami parameter was determined to be 1.1, suggesting a diffusionless, one-dimensional transformation mechanism. From the temperature dependence of k, the activation energy for this reaction was evaluated to be 527 plus or minus 50 kJ/mole (126 plus or minus 12 kcal/mole). This value is consistent with a mechanism involving the transformation of the layered hexacelsian structure to a three-dimensional network celsian structure which necessitates breaking of the strongest bonds, the Si-O bonds.

Kinetics of hexacelsian-to-celsian phase transformation in SrAl2Si2O8

NASA Technical Reports Server (NTRS)

Bansal, Narottam P.; Drummond, Charles H., III

1993-01-01

The kinetics of hexacelsian to celsian phase transformation in SrAl2Si2O8 have been investigated. Phase pure hexacelsian was prepared by heat treatment of glass flakes at 990 C for 10 h. Bulk hexacelsian was isothermally heat treated at 1026, 1050, 1100, 1152, and 1200 C for various times. The amounts of monoclinic celsian formed were determined using quantitative X-ray diffraction. Values of reaction rate constant, k, at various temperatures were evaluated from the Avrami equation. The Avrami parameter was determined to be 1.1, suggesting a diffusionless, one-dimensional transformation mechanism. From the temperature dependence of k, the activation energy for this reaction was evaluated to be 527 plus or minus 50 kJ/mole (126 plus or minus 12 kcal/mole). This value is consistent with a mechanism involving the transformation of the layered hexacelsian structure to a three-dimensional network celsian structure which necessitates breaking of the strongest bonds, the Si-O bonds.

Computer program for assessing the theoretical performance of a three dimensional inlet

NASA Technical Reports Server (NTRS)

Agnone, A. M.; Kung, F.

1972-01-01

A computer program for determining the theoretical performance of a three dimensional inlet is presented. An analysis for determining the capture area, ram force, spillage force, and surface pressure force is presented, along with the necessary computer program. A sample calculation is also included.

Insights into the dissolution and the three-dimensional structure of insensitive munitions formulations.

PubMed

Taylor, Susan; Ringelberg, David B; Dontsova, Katerina; Daghlian, Charles P; Walsh, Marianne E; Walsh, Michael R

2013-11-01

Two compounds, 2,4-dinitroanisole (DNAN) and 3-nitro-1,2,4-triazol-5-one (NTO) are the main ingredients in a suite of explosive formulations that are being, or soon will be, fielded at military training ranges. We aim to understand the dissolution characteristics of DNAN and NTO and three insensitive muntions (IM) formulations that contain them. This information is needed to accurately predict the environmental fate of IM constituents, some of which may be toxic to people and the environment. We used Raman spectroscopy to identify the different constituents in the IM formulations and micro computed tomography to image their three-dimensional structure. These are the first three-dimensional images of detonated explosive particles. For multi-component explosives the solubility of the individual constituents and the fraction of each constituent wetted by water controls the dissolution. We found that the order of magnitude differences in solubility amongst the constituents of these IM formulations quickly produced hole-riddled particles when these were exposed to water. Micro-computed tomography showed that particles resulting from field detonations were fractured, producing conduits by which water could access the interior of the particle. We think that micro-computed tomography can also be used to determine the initial composition of IM particles and to track how their compositions change as the particles dissolve. This information is critical to quantifying dissolution and developing physically based dissolution models. Published by Elsevier Ltd.

Direction-finding measurements of type 3 radio bursts out of the ecliptic plane

NASA Technical Reports Server (NTRS)

Baumback, M. M.; Kurth, W. S.; Gurnett, D. A.

1975-01-01

Direction-finding measurements with the plasma wave experiments on the HAWKEYE 1 and IMP 8 satellites are used to find the source locations of type 3 solar radio bursts in heliocentric latitude and longitude in a frequency range from 31.1 kHz to 500 kHz. Using an empirical model for the emission frequency as a function of radial distance from the sun the three-dimensional trajectory of the type 3 radio source can be determined from direction-finding measurements at different frequencies. Since the electrons which produce these radio emissions follow the magnetic field lines from the sun these measurements provide information on the three-dimensional structure of the magnetic field in the solar wind. The source locations projected into the ecliptic plane follow an Archimedian spiral. Perpendicular to the ecliptic plane the source locations usually follow a constant heliocentric latitude. With direction-finding measurements of this type it is also possible to determine the source size from the modulation factor of the received signals.

Three dimensional unstructured multigrid for the Euler equations

NASA Technical Reports Server (NTRS)

Mavriplis, D. J.

1991-01-01

The three dimensional Euler equations are solved on unstructured tetrahedral meshes using a multigrid strategy. The driving algorithm consists of an explicit vertex-based finite element scheme, which employs an edge-based data structure to assemble the residuals. The multigrid approach employs a sequence of independently generated coarse and fine meshes to accelerate the convergence to steady-state of the fine grid solution. Variables, residuals and corrections are passed back and forth between the various grids of the sequence using linear interpolation. The addresses and weights for interpolation are determined in a preprocessing stage using linear interpolation. The addresses and weights for interpolation are determined in a preprocessing stage using an efficient graph traversal algorithm. The preprocessing operation is shown to require a negligible fraction of the CPU time required by the overall solution procedure, while gains in overall solution efficiencies greater than an order of magnitude are demonstrated on meshes containing up to 350,000 vertices. Solutions using globally regenerated fine meshes as well as adaptively refined meshes are given.

Factors influencing perceived angular velocity.

PubMed

Kaiser, M K; Calderone, J B

1991-11-01

The assumption that humans are able to perceive and process angular kinematics is critical to many structure-from-motion and optical flow models. The current studies investigate this sensitivity, and examine several factors likely to influence angular velocity perception. In particular, three factors are considered: (1) the extent to which perceived angular velocity is determined by edge transitions of surface elements, (2) the extent to which angular velocity estimates are influenced by instantaneous linear velocities of surface elements, and (3) whether element-velocity effects are related to three-dimensional (3-D) tangential velocities or to two-dimensional (2-D) image velocities. Edge-transition rate biased angular velocity estimates only when edges were highly salient. Element velocities influenced perceived angular velocity; this bias was related to 2-D image velocity rather than 3-D tangential velocity. Despite these biases, however, judgments were most strongly determined by the true angular velocity. Sensitivity to this higher order motion parameter was surprisingly good, for rotations both in depth (y-axis) and parallel to the line of sight (z-axis).

New three-dimensional modeling technique for studying porous media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quiblier, J.A.

A great deal of research has been done on the relationships between the structure of porous media on the microscopic level and their overall properties. A short bibliographic survey is attempted, with special attention being paid to the use of models. The limitations of such research are outlined. A three-dimensional simulation process is proposed. On the basis of measurements of characteristics using thin sections of porous media, the aim is to simulate, through a random process, a porous medium which is at the same time geometrically realistic and fully determined (i.e., the coordinates of a point in the medium fullymore » determine whether this point belongs to the matrix or to the pores). Simulation opens the way to further studies of the porous medium, some of which are outlined. It is clear that a good deal of research remains to be done in this field, and some ideas are suggested for this research. 78 references.« less

Syntactic Approach To Geometric Surface Shell Determination

NASA Astrophysics Data System (ADS)

DeGryse, Donald G.; Panton, Dale J.

1980-12-01

Autonomous terminal homing of a smart missile requires a stored reference scene of the target for which the missle is destined. The reference scene is produced from stereo source imagery by deriving a three-dimensional model containing cultural structures such as buildings, towers, bridges, and tanks. This model is obtained by the precise matching of cultural features from one image of the stereo pair to the other. In the past, this stereo matching process has relied heavily on local edge operators and a gray scale matching metric. The processing is performed line by line over the imagery and the amount of geometric control is minimal. As a result, the gross structure of the scene is determined but the derived three-dimensional data is noisy, oscillatory, and at times significantly inaccurate. This paper discusses new concepts that are currently being developed to stabilize this geometric reference preparation process. The new concepts involve the use of a structural syntax which will be used as a geometric constraint on automatic stereo matching. The syntax arises from the stereo configuration of the imaging platforms at the time of exposure and the knowledge of how various cultural structures are constructed. The syntax is used to parse a scene in terms of its cultural surfaces and to dictate to the matching process the allowable relative positions and orientations of surface edges in the image planes. Using the syntax, extensive searches using a gray scale matching metric are reduced.

Depth-enhanced three-dimensional-two-dimensional convertible display based on modified integral imaging.

PubMed

Park, Jae-Hyeung; Kim, Hak-Rin; Kim, Yunhee; Kim, Joohwan; Hong, Jisoo; Lee, Sin-Doo; Lee, Byoungho

2004-12-01

A depth-enhanced three-dimensional-two-dimensional convertible display that uses a polymer-dispersed liquid crystal based on the principle of integral imaging is proposed. In the proposed method, a lens array is located behind a transmission-type display panel to form an array of point-light sources, and a polymer-dispersed liquid crystal is electrically controlled to pass or to scatter light coming from these point-light sources. Therefore, three-dimensional-two-dimensional conversion is accomplished electrically without any mechanical movement. Moreover, the nonimaging structure of the proposed method increases the expressible depth range considerably. We explain the method of operation and present experimental results.

Google Earth Mapping Exercises for Structural Geology Students--A Promising Intervention for Improving Penetrative Visualization Ability

ERIC Educational Resources Information Center

Giorgis, Scott

2015-01-01

Three-dimensional thinking skills are extremely useful for geoscientists, and at the undergraduate level, these skills are often emphasized in structural geology courses. Google Earth is a powerful tool for visualizing the three-dimensional nature of data collected on the surface of Earth. The results of a 5 y pre- and posttest study of the…

Three-dimensional flow visualization and vorticity dynamics in revolving wings

NASA Astrophysics Data System (ADS)

Cheng, Bo; Sane, Sanjay P.; Barbera, Giovanni; Troolin, Daniel R.; Strand, Tyson; Deng, Xinyan

2013-01-01

We investigated the three-dimensional vorticity dynamics of the flows generated by revolving wings using a volumetric 3-component velocimetry system. The three-dimensional velocity and vorticity fields were represented with respect to the base axes of rotating Cartesian reference frames, and the second invariant of the velocity gradient was evaluated and used as a criterion to identify two core vortex structures. The first structure was a composite of leading, trailing, and tip-edge vortices attached to the wing edges, whereas the second structure was a strong tip vortex tilted from leading-edge vortices and shed into the wake together with the vorticity generated at the tip edge. Using the fundamental vorticity equation, we evaluated the convection, stretching, and tilting of vorticity in the rotating wing frame to understand the generation and evolution of vorticity. Based on these data, we propose that the vorticity generated at the leading edge is carried away by strong tangential flow into the wake and travels downwards with the induced downwash. The convection by spanwise flow is comparatively negligible. The three-dimensional flow in the wake also exhibits considerable vortex tilting and stretching. Together these data underscore the complex and interconnected vortical structures and dynamics generated by revolving wings.

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

Three-dimensional cross-linking composite of graphene, carbon nanotubes and Si nanoparticles for lithium ion battery anode

NASA Astrophysics Data System (ADS)

Tian, Suyun; Zhu, Guannan; Tang, Yanping; Xie, Xiaohua; Wang, Qian; Ma, Yufei; Ding, Guqiao; Xie, Xiaoming

2018-03-01

Various graphene-based Si nanocomposites have been reported to improve the performance of active materials in Li-ion batteries. However, these candidates still yield severe capacity fading due to the electrical disconnection and fractures caused by the huge volume changes over extended cycles. Therefore, we have designed a novel three-dimensional cross-linked graphene and single-wall carbon nanotube structure to encapsulate the Si nanoparticles. The synthesized three-dimensional structure is attributed to the excellent self-assembly of carbon nanotubes with graphene oxide as well as a thermal treatment process at 900 °C. This special structure provides sufficient void spaces for the volume expansion of Si nanoparticles and channels for the diffusion of ions and electrons. In addition, the cross-linking of the graphene and single-wall carbon nanotubes also strengthens the stability of the structure. As a result, the volume expansion of the Si nanoparticles is restrained. The specific capacity remains at 1450 mAh g-1 after 100 cycles at 200 mA g-1. This well-defined three-dimensional structure facilitates superior capacity and cycling stability in comparison with bare Si and a mechanically mixed composite electrode of graphene, single-wall carbon nanotubes and silicon nanoparticles.

Method of using triaxial magnetic fields for making particle structures

DOEpatents

Martin, James E.; Anderson, Robert A.; Williamson, Rodney L.

2005-01-18

A method of producing three-dimensional particle structures with enhanced magnetic susceptibility in three dimensions by applying a triaxial energetic field to a magnetic particle suspension and subsequently stabilizing said particle structure. Combinations of direct current and alternating current fields in three dimensions produce particle gel structures, honeycomb structures, and foam-like structures.

Plasma sheath structure surrounding a large powered spacecraft

NASA Technical Reports Server (NTRS)

Mandell, M. J.; Jongeward, G. A.; Katz, I.

1984-01-01

Various factors determining the floating potential of a highly biased (about 4-kV) spacecraft in low earth orbit are discussed. While the common rule of thumb (90 percent negative; 10 percent positive) is usually a good guide, different biasing and grounding patterns can lead to high positive potentials. The NASCAP/LEO code can be used to predict spacecraft floating potential for complex three-dimensional spacecraft.

On the problem of resonance assignments in solid state NMR of uniformly 15N, 13C-labeled proteins

NASA Astrophysics Data System (ADS)

Tycko, Robert

2015-04-01

Determination of accurate resonance assignments from multidimensional chemical shift correlation spectra is one of the major problems in biomolecular solid state NMR, particularly for relative large proteins with less-than-ideal NMR linewidths. This article investigates the difficulty of resonance assignment, using a computational Monte Carlo/simulated annealing (MCSA) algorithm to search for assignments from artificial three-dimensional spectra that are constructed from the reported isotropic 15N and 13C chemical shifts of two proteins whose structures have been determined by solution NMR methods. The results demonstrate how assignment simulations can provide new insights into factors that affect the assignment process, which can then help guide the design of experimental strategies. Specifically, simulations are performed for the catalytic domain of SrtC (147 residues, primarily β-sheet secondary structure) and the N-terminal domain of MLKL (166 residues, primarily α-helical secondary structure). Assuming unambiguous residue-type assignments and four ideal three-dimensional data sets (NCACX, NCOCX, CONCA, and CANCA), uncertainties in chemical shifts must be less than 0.4 ppm for assignments for SrtC to be unique, and less than 0.2 ppm for MLKL. Eliminating CANCA data has no significant effect, but additionally eliminating CONCA data leads to more stringent requirements for chemical shift precision. Introducing moderate ambiguities in residue-type assignments does not have a significant effect.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, J.S.; Technical Research Laboratories, POSCO, Pohang 790-300; Seol, Jae-Bok, E-mail: j.seol@mpie.de

We investigated the microstructural evolution of high strength low alloy steel, Fe–2.0Mn–0.15Si–0.05C (wt.%), by varying the continuous cooling rates from 1 K/s to 50 K/s using three-dimensional electron backscatter diffraction and transmission electron microscopy. Granular bainitic microstructure was prevalent under a slow cooling rate of 1–10 K/s, while lath-type bainite was dominant at a high cooling rate of 50 K/s. The acicular ferrite that was the major microstructure under the intermediate ranges of cooling rates between 10 K/s and 30 K/s was tangled with each other, leading to a three-dimensional interwoven structure with highly misoriented grains. Because of the formationmore » of three-dimensional structures, we propose that the terms “acicular ferrite” and “bainitic ferrite,” which are currently used in steel, be replaced by the terms “interwoven acicular bainite” and “lath bainite,” respectively. Moreover, we also confirmed that the cooling rate is an important factor in determining whether bainitic microstructures occur in the form of granular bainite, interwoven bainite, or lath bainite. - Highlights: • The morphology of bainitic grains was characterized by 3D-EBSD. • The ‘interwoven bainite’ and ‘lath bainite’ were suggested. • Interwoven bainite consisted of lenticular plates that were interlinked in 3D regime. • The packets of lath bainite were aligned in a specific direction.« less

Three-dimensional structure of homodimeric cholesterol esterase-ligand complex at 1.4 Å resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pletnev, V.; Addlagatta, A.; Wawrzak, Z.

2010-03-08

The three-dimensional structure of a Candida cylindracea cholesterol esterase (ChE) homodimer (534 x 2 amino acids) in complex with a ligand of proposed formula C{sub 23}H{sub 48}O{sub 2} has been determined at 1.4 {angstrom} resolution in space group P1 using synchrotron low-temperature data. The structure refined to R = 0.136 and R{sub free} = 0.169 and has revealed new stereochemical details in addition to those detected for the apo- and holo-forms at 1.9 and 2.0 {angstrom} resolution, respectively [Ghosh et al. (1995), Structure, 3, 279-288]. The cholesterol esterase structure is a dimer with four spatially separated interfacial contact areas andmore » two symmetry-related pairs of openings to an internal intradimer cavity. Hydrophobic active-site gorges in each subunit face each other across a central interfacial cavity. The ChE subunits have carbohydrate chains attached to their Asn314 and Asn351 residues, with two ordered N-acetyl-D-glucosoamine moieties visible at each site. The side chains of 14 residues have two alternative conformations with occupancy values of 0.5 {+-} 0.2. For each subunit the electron density in the enzyme active-site gorge is well modeled by a C{sub 23}-chain fatty acid.« less

Structural and Kinetic Basis for Substrate Selectivity in Populus tremuloides Sinapyl Alcohol Dehydrogenase

PubMed Central

Bomati, Erin K.; Noel, Joseph P.

2005-01-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities. PMID:15829607

Structural and kinetic basis for substrate selectivity in Populus tremuloides sinapyl alcohol dehydrogenase.

PubMed

Bomati, Erin K; Noel, Joseph P

2005-05-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities.

Zebrafish Cardiac Muscle Thick Filaments: Isolation Technique and Three-Dimensional Structure

PubMed Central

González-Solá, Maryví; AL-Khayat, Hind A.; Behra, Martine; Kensler, Robert W.

2014-01-01

To understand how mutations in thick filament proteins such as cardiac myosin binding protein-C or titin, cause familial hypertrophic cardiomyopathies, it is important to determine the structure of the cardiac thick filament. Techniques for the genetic manipulation of the zebrafish are well established and it has become a major model for the study of the cardiovascular system. Our goal is to develop zebrafish as an alternative system to the mammalian heart model for the study of the structure of the cardiac thick filaments and the proteins that form it. We have successfully isolated thick filaments from zebrafish cardiac muscle, using a procedure similar to those for mammalian heart, and analyzed their structure by negative-staining and electron microscopy. The isolated filaments appear well ordered with the characteristic 42.9 nm quasi-helical repeat of the myosin heads expected from x-ray diffraction. We have performed single particle image analysis on the collected electron microscopy images for the C-zone region of these filaments and obtained a three-dimensional reconstruction at 3.5 nm resolution. This reconstruction reveals structure similar to the mammalian thick filament, and demonstrates that zebrafish may provide a useful model for the study of the changes in the cardiac thick filament associated with disease processes. PMID:24739166

Graphic kinematics, visual virtual work and elastographics

PubMed Central

Konstantatou, Marina; Athanasopoulos, Georgios; Hannigan, Laura

2017-01-01

In this paper, recent progress in graphic statics is combined with Williot displacement diagrams to create a graphical description of both statics and kinematics for two- and three-dimensional pin-jointed trusses. We begin with reciprocal form and force diagrams. The force diagram is dissected into its component cells which are then translated relative to each other. This defines a displacement diagram which is topologically equivalent to the form diagram (the structure). The various contributions to the overall Virtual Work appear as parallelograms (for two-dimensional trusses) or parallelopipeds (for three-dimensional trusses) that separate the force and the displacement pieces. Structural mechanisms can be identified by translating the force cells such that their shared faces slide across each other without separating. Elastic solutions can be obtained by choosing parallelograms or parallelopipeds of the appropriate aspect ratio. Finally, a new type of ‘elastographic’ diagram—termed a deformed Maxwell–Williot diagram (two-dimensional) or a deformed Rankine–Williot diagram (three-dimensional)—is presented which combines the deflected structure with the forces carried by its members. PMID:28573030

Maxwell Strata and Cut Locus in the Sub-Riemannian Problem on the Engel Group

NASA Astrophysics Data System (ADS)

Ardentov, Andrei A.; Sachkov, Yuri L.

2017-12-01

We consider the nilpotent left-invariant sub-Riemannian structure on the Engel group. This structure gives a fundamental local approximation of a generic rank 2 sub-Riemannian structure on a 4-manifold near a generic point (in particular, of the kinematic models of a car with a trailer). On the other hand, this is the simplest sub-Riemannian structure of step three. We describe the global structure of the cut locus (the set of points where geodesics lose their global optimality), the Maxwell set (the set of points that admit more than one minimizer), and the intersection of the cut locus with the caustic (the set of conjugate points along all geodesics). The group of symmetries of the cut locus is described: it is generated by a one-parameter group of dilations R+ and a discrete group of reflections Z2 × Z2 × Z2. The cut locus admits a stratification with 6 three-dimensional strata, 12 two-dimensional strata, and 2 one-dimensional strata. Three-dimensional strata of the cut locus are Maxwell strata of multiplicity 2 (for each point there are 2 minimizers). Two-dimensional strata of the cut locus consist of conjugate points. Finally, one-dimensional strata are Maxwell strata of infinite multiplicity, they consist of conjugate points as well. Projections of sub-Riemannian geodesics to the 2-dimensional plane of the distribution are Euler elasticae. For each point of the cut locus, we describe the Euler elasticae corresponding to minimizers coming to this point. Finally, we describe the structure of the optimal synthesis, i. e., the set of minimizers for each terminal point in the Engel group.

Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type

NASA Technical Reports Server (NTRS)

He, X. M.; Ruker, F.; Casale, E.; Carter, D. C.

1992-01-01

The three-dimensional structure of a human monoclonal antibody (Fab), which binds specifically to a major epitope of the transmembrane protein gp41 of the human immunodeficiency virus type 1, has been determined by crystallographic methods to a resolution of 2.7 A. It has been previously determined that this antibody recognizes the epitope SGKLICTTAVPWNAS, belongs to the subclass IgG1 (kappa), and exhibits antibody-dependent cellular cytotoxicity. The quaternary structure of the Fab is in an extended conformation with an elbow bend angle between the constant and variable domains of 175 degrees. Structurally, four of the hypervariable loops can be classified according to previously recognized canonical structures. The third hypervariable loops of the heavy (H3) and light chain (L3) are structurally distinct. Hypervariable loop H3, residues 102H-109H, is unusually extended from the surface. The complementarity-determining region forms a hydrophobic binding pocket that is created primarily from hypervariable loops L3, H3, and H2.

Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type 1

NASA Technical Reports Server (NTRS)

He, Xiao M.; Rueker, Florian; Casale, Elena; Carter, Daniel C.

1992-01-01

The three-dimensional structure of a human monoclonal antibody (Fab), which binds specifically to a major epitope of the transmembrane protein gp41 of the human immunodeficiency virus type 1, has been determined by crystallographic methods to a resolution of 2.7 A. It has been previously determined that this antibody recognizes the epitope SGKLICTTAVPWNAS, belongs to the subclass IgG1 (kappa), and exhibits antibody-dependent cellular cytotoxicity. The quaternary structure of the Fab is in an extended conformation with an elbow bend angle between the constant and variable domains of 175 deg. Structurally, four of the hypervariable loops can be classified according to previously recognized canonical structures. The third hypervariable loops of the heavy (H3) and light chain (L3) are structurally distinct. Hypervariable loop H3, residues 102H-109H, is unusually extended from the surface. The complementarity-determining region forms a hydrophobic binding pocket that is created primarily from hypervariable loops L3, H3, and H2.

Localization of PKA Phosphorylation Site, Serine-2030, in the Three-Dimensional Structure of Cardiac Ryanodine Receptor

PubMed Central

Jones, Peter P.; Meng, Xing; Xiao, Bailong; Cai, Shitian; Bolstad, Jeff; Wagenknecht, Terence; Liu, Zheng; Chen, S. R. Wayne

2009-01-01

Protein kinase A (PKA)-dependent phosphorylation of the cardiac Ca2+ release channel/ryanodine receptor (RyR2) is believed to directly dissociate FKBP12.6 from the channel, causing abnormal channel activation and Ca2+ release. To gain insight into the structural basis of the regulation of RyR2 by PKA, we determined the three-dimensional location of the PKA site S2030. Green fluorescent protein (GFP) was inserted into the wild type (wt) RyR2 and RyR2 mutant, A4860G, after T2023. The resultant GFP-RyR2 fusion proteins, RyR2T2023-GFP and RyR2(A4860G)T2023-GFP, were expressed in HEK293 cells and functionally characterized. Ca2+ release assays revealed that both GFP-RyR2 fusion proteins formed caffeine- and ryanodine-sensitive Ca2+ release channels. Further analyses using [3H]ryanodine binding demonstrated that the insertion of GFP into RyR2 wt after T2023 reduced the sensitivity of the channel to activation by Ca2+ or caffeine. RyR2(A4860G)T2023-GFP was found to be structurally more stable than RyR2T2023-GFP and was subsequently used as a basis for three-dimensional reconstruction. Cryo-electron microscopy and single particle image processing of the purified RyR2(A4860G)T2023-GFP protein revealed the location of the inserted GFP, and hence the S2030 PKA site in domain 4, a region that may be involved in signal transduction between the transmembrane and cytoplasmic domains. Like the S2808 PKA site reported previously, the S2030 site is not located close to the FKBP12.6 binding site mapped previously, indicating that neither of these PKA sites is directly involved in FKBP12.6 binding. Based on the three-dimensional localizations of a number of residues or regions, a model for the subunit organization in the structure of RyR2 is proposed. PMID:17967164

A three-dimensional wide-angle BPM for optical waveguide structures.

PubMed

Ma, Changbao; Van Keuren, Edward

2007-01-22

Algorithms for effective modeling of optical propagation in three- dimensional waveguide structures are critical for the design of photonic devices. We present a three-dimensional (3-D) wide-angle beam propagation method (WA-BPM) using Hoekstra's scheme. A sparse matrix algebraic equation is formed and solved using iterative methods. The applicability, accuracy and effectiveness of our method are demonstrated by applying it to simulations of wide-angle beam propagation, along with a technique for shifting the simulation window to reduce the dimension of the numerical equation and a threshold technique to further ensure its convergence. These techniques can ensure the implementation of iterative methods for waveguide structures by relaxing the convergence problem, which will further enable us to develop higher-order 3-D WA-BPMs based on Padé approximant operators.

A three-dimensional wide-angle BPM for optical waveguide structures

NASA Astrophysics Data System (ADS)

Ma, Changbao; van Keuren, Edward

2007-01-01

Algorithms for effective modeling of optical propagation in three- dimensional waveguide structures are critical for the design of photonic devices. We present a three-dimensional (3-D) wide-angle beam propagation method (WA-BPM) using Hoekstra’s scheme. A sparse matrix algebraic equation is formed and solved using iterative methods. The applicability, accuracy and effectiveness of our method are demonstrated by applying it to simulations of wide-angle beam propagation, along with a technique for shifting the simulation window to reduce the dimension of the numerical equation and a threshold technique to further ensure its convergence. These techniques can ensure the implementation of iterative methods for waveguide structures by relaxing the convergence problem, which will further enable us to develop higher-order 3-D WA-BPMs based on Padé approximant operators.

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

PubMed

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

2012-01-01

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

Quantitative molecular characterization of bovine vitreous and lens with non-invasive dynamic light scattering

NASA Technical Reports Server (NTRS)

Ansari, R. R.; Suh, K. I.; Dunker, S.; Kitaya, N.; Sebag, J.

2001-01-01

The non-invasive technique of dynamic light scattering (DLS) was used to quantitatively characterize vitreous and lens structure on a molecular level by measuring the sizes of the predominant particles and mapping the three-dimensional topographic distribution of these structural macromolecules in three spatial dimensions. The results of DLS measurements in five fresh adult bovine eyes were compared to DLS measurements in model solutions of hyaluronan (HA) and collagen (Coll). In the bovine eyes DLS measurements were obtained from excised samples of gel and liquid vitreous and compared to the model solutions. Measurements in whole vitreous were obtained at multiple points posterior to the lens to generate a three-dimensional 'map' of molecular structure. The macromolecule distribution in bovine lens was similarly characterized.In each bovine vitreous (Bo Vit) specimen, DLS predominantly detected two distinct particles, which differed in diffusion properties and hence size. Comparisons with model vitreous solutions demonstrated that these most likely corresponded to the Coll and HA components of vitreous. Three-dimensional mapping of Bo Vit found heterogeneity throughout the vitreous body, with different particle size distributions for Coll and HA at different loci. In contrast, the three-dimensional distribution of lens macromolecules was more homogeneous. Thus, the non-invasive DLS technique can quantitate the average sizes of vitreous and lens macromolecules and map their three-dimensional distribution. This method to assess quantitatively the macromolecular structure of vitreous and lens should be useful for clinical as well as experimental applications in health and disease. Copyright 2001 Academic Press.

Topology of three-dimensional separated flows

NASA Technical Reports Server (NTRS)

Tobak, M.; Peake, D. J.

1981-01-01

Based on the hypothesis that patterns of skin-friction lines and external streamlines reflect the properties of continuous vector fields, topology rules define a small number of singular points (nodes, saddle points, and foci) that characterize the patterns on the surface and on particular projections of the flow (e.g., the crossflow plane). The restricted number of singular points and the rules that they obey are considered as an organizing principle whose finite number of elements can be combined in various ways to connect together the properties common to all steady three dimensional viscous flows. Introduction of a distinction between local and global properties of the flow resolves an ambiguity in the proper definition of a three dimensional separated flow. Adoption of the notions of topological structure, structural stability, and bifurcation provides a framework to describe how three dimensional separated flows originate and succeed each other as the relevant parameters of the problem are varied.

System and method for representing and manipulating three-dimensional objects on massively parallel architectures

DOEpatents

Karasick, Michael S.; Strip, David R.

1996-01-01

A parallel computing system is described that comprises a plurality of uniquely labeled, parallel processors, each processor capable of modelling a three-dimensional object that includes a plurality of vertices, faces and edges. The system comprises a front-end processor for issuing a modelling command to the parallel processors, relating to a three-dimensional object. Each parallel processor, in response to the command and through the use of its own unique label, creates a directed-edge (d-edge) data structure that uniquely relates an edge of the three-dimensional object to one face of the object. Each d-edge data structure at least includes vertex descriptions of the edge and a description of the one face. As a result, each processor, in response to the modelling command, operates upon a small component of the model and generates results, in parallel with all other processors, without the need for processor-to-processor intercommunication.

Observation of three-dimensional internal structure of steel materials by means of serial sectioning with ultrasonic elliptical vibration cutting.

PubMed

Fujisaki, K; Yokota, H; Nakatsuchi, H; Yamagata, Y; Nishikawa, T; Udagawa, T; Makinouchi, A

2010-01-01

A three-dimensional (3D) internal structure observation system based on serial sectioning was developed from an ultrasonic elliptical vibration cutting device and an optical microscope combined with a high-precision positioning device. For bearing steel samples, the cutting device created mirrored surfaces suitable for optical metallography, even for long-cutting distances during serial sectioning of these ferrous materials. Serial sectioning progressed automatically by means of numerical control. The system was used to observe inclusions in steel materials on a scale of several tens of micrometers. Three specimens containing inclusions were prepared from bearing steels. These inclusions could be detected as two-dimensional (2D) sectional images with resolution better than 1 mum. A three-dimensional (3D) model of each inclusion was reconstructed from the 2D serial images. The microscopic 3D models had sharp edges and complicated surfaces.

A comparison of VRML and animation of rotation for teaching 3-dimensional crystal lattice structures

NASA Astrophysics Data System (ADS)

Sauls, Barbara Lynn

Chemistry students often have difficulty visualizing abstract concepts of molecules and atoms, which may lead to misconceptions. The three-dimensionality of these structures presents a challenge to educators. Typical methods of teaching include text with two-dimensional graphics and structural models. Improved methods to allow visualization of 3D structures may improve learning of these concepts. This research compared the use of Virtual Reality Modeling Language (VRML) and animation of rotation for teaching three-dimensional structures. VRML allows full control of objects by altering angle, size, rotation, and provides the ability to zoom into and through objects. Animations may only be stopped, restarted and replayed. A web-based lesson teaching basic concepts of crystals, which requires comprehension of their three-dimensional structure was given to 100 freshmen chemistry students. Students were stratified by gender then randomly to one of two lessons, which were identical except for the multimedia method used to show the lattices and unit cells. One method required exploration of the structures using VRML, the other provided animations of the same structures rotating. The students worked through an examination as the lesson progressed. A Welch t' test was used to compare differences between groups. No significant difference in mean achievement was found between the two methods, between genders, or within gender. There was no significant difference in mean total SAT in the animation and VRML group. Total time on task had no significant difference nor did enjoyment of the lesson. Students, however, spent 14% less time maneuvering VRML structures than viewing the animations of rotation. Neither method proved superior for presenting three-dimensional information. The students spent less time maneuvering the VRML structures with no difference in mean score so the use of VRML may be more efficient. The investigator noted some manipulation difficulties using VRML to rotate structures. Some students had difficulty obtaining the correct angle required to properly interpret spatial relationships. This led to frustration and caused some students to quit trying before they could answer questions fully. Even though there were some difficulties, outcomes were not affected. Higher scores, however, may have been achieved had the students been proficient in VRML maneuvering.

Compact 3D photonic crystals sensing platform with 45 degree angle polished fibers

NASA Astrophysics Data System (ADS)

Guo, Yuqing; Chen, Lu; Zhu, Jiali; Ni, Haibin; Xia, Wei; Wang, Ming

2017-07-01

Three dimensional photonic crystals are a kind of promising sensing materials in biology and chemistry. A compact structure, consists of planner colloidal crystals and 45 degree angle polished fiber, is proposed as a platform for accurate, fast, reliable three dimensional photonic crystals sensing in practice. This structure show advantages in compact size for integration and it is ease for large scale manufacture. Reflectivity of the 45 degree angle polished surface with and without a layer of Ag film are simulated by FDTD simulation. Refractive index sensing properties as well as mode distribution of this structure consists of both polystyrene opal and silica inverse opal film is investigated, and an experimental demonstration of silica inverse opal film is performed, which shows a sensitivity of 733 nm/RIU. Different kinds of three dimensional photonic crystals can also be applied in this structure for particular purpose.

Comparative analysis of three-dimensional structures of homodimers of uridine phosphorylase from Salmonella typhimurium in the unligated state and in a complex with potassium ion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lashkov, A. A.; Zhukhlistova, N. E.; Gabdulkhakov, A. G.

2009-03-15

The spatial organization of the homodimer of unligated uridine phosphorylase from Salmonella typhimurium (St UPh) was determined with high accuracy. The structure was refined at 1.80 A resolution to R{sub work} = 16.1% and R{sub free} = 20.0%. The rms deviations for the bond lengths, bond angles, and chiral angles are 0.006 A, 1.042{sup o}, and 0.071{sup o}, respectively. The coordinate error estimated by the Luzzati plot is 0.166 A. The coordinate error based on the maximum likelihood is 0.199 A. A comparative analysis of the spatial organization of the homodimer in two independently refined structures and the structure ofmore » the homodimer St UPh in the complex with a K{sup +} ion was performed. The substrate-binding sites in the homodimers StUPhs in the unligated state were found to act asynchronously. In the presence of a potassium ion, the three-dimensional structures of the subunits in the homodimer are virtually identical, which is apparently of importance for the synchronous action of both substrate-binding sites. The atomic coordinates of the refined structure of the homodimer and structure factors have been deposited in the Protein Data Bank (PDB ID code 3DPS).« less

Structure of the Bacillus anthracis dTDP- L -rhamnose-biosynthetic enzyme glucose-1-phosphate thymidylyltransferase (RfbA)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baumgartner, Jackson; Lee, Jesi; Halavaty, Andrei S.

L-Rhamnose is a ubiquitous bacterial cell-wall component. The biosynthetic pathway for its precursor dTDP-L-rhamnose is not present in humans, which makes the enzymes of the pathway potential drug targets. In this study, the three-dimensional structure of the first protein of this pathway, glucose-1-phosphate thymidylyltransferase (RfbA), fromBacillus anthraciswas determined. In other organisms this enzyme is referred to as RmlA. RfbA was co-crystallized with the products of the enzymatic reaction, dTDP-α-D-glucose and pyrophosphate, and its structure was determined at 2.3 Å resolution. This is the first reported thymidylyltransferase structure from a Gram-positive bacterium. RfbA shares overall structural characteristics with known RmlA homologs.more » However, RfbA exhibits a shorter sequence at its C-terminus, which results in the absence of three α-helices involved in allosteric site formation. Consequently, RfbA was observed to exhibit a quaternary structure that is unique among currently reported glucose-1-phosphate thymidylyltransferase bacterial homologs. These structural analyses suggest that RfbA may not be allosterically regulated in some organisms and is structurally distinct from other RmlA homologs.« less

[Research progress of three-dimensional digital model for repair and reconstruction of knee joint].

PubMed

Tong, Lu; Li, Yanlin; Hu, Meng

2013-01-01

To review recent advance in the application and research of three-dimensional digital knee model. The recent original articles about three-dimensional digital knee model were extensively reviewed and analyzed. The digital three-dimensional knee model can simulate the knee complex anatomical structure very well. Based on this, there are some developments of new software and techniques, and good clinical results are achieved. With the development of computer techniques and software, the knee repair and reconstruction procedure has been improved, the operation will be more simple and its accuracy will be further improved.

[Advances in the research of application of hydrogels in three-dimensional bioprinting].

PubMed

Yang, J; Zhao, Y; Li, H H; Zhu, S H

2016-08-20

Hydrogels are three-dimensional networks made of hydrophilic polymer crosslinked through covalent bonds or physical intermolecular attractions, which can contain growth media and growth factors to support cell growth. In bioprinting, hydrogels are used to provide accurate control over cellular microenvironment and to dramatically reduce experimental repetition times, meanwhile we can obtain three-dimensional cell images of high quality. Hydrogels in three-dimensional bioprinting have received a considerable interest due to their structural similarities to the natural extracellular matrix and polyporous frameworks which can support the cellular proliferation and survival. Meanwhile, they are accompanied by many challenges.

Three-dimensional behavior of ice crystals and biological cells during freezing of cell suspensions.

PubMed

Ishiguro, H; Koike, K

1998-09-11

Behavior of ice crystals and human red blood cells during extracellular-freezing was investigated in three-dimensions using a confocal laser scanning microscope(CLSM), which noninvasively produces tomograms of biological materials. Physiological saline and physiological saline with 2.4 M glycerol were used for suspension. Various cooling rates for directional solidification were used for distinctive morphology of the ice crystals. Addition of acridine orange as a fluorescent dye into the cell suspension enabled ice crystal, cells and unfrozen solution to be distinguished by different colors. The results indicate that the microscopic structure is three-dimensional for flat, cellular, and dendritic solid-liquid interfaces and that a CLSM is very effective in studying three-dimensional structure during the freezing of cell suspensions.

Magnetic resonance imaging-three-dimensional printing technology fabricates customized scaffolds for brain tissue engineering

PubMed Central

Fu, Feng; Qin, Zhe; Xu, Chao; Chen, Xu-yi; Li, Rui-xin; Wang, Li-na; Peng, Ding-wei; Sun, Hong-tao; Tu, Yue; Chen, Chong; Zhang, Sai; Zhao, Ming-liang; Li, Xiao-hong

2017-01-01

Conventional fabrication methods lack the ability to control both macro- and micro-structures of generated scaffolds. Three-dimensional printing is a solid free-form fabrication method that provides novel ways to create customized scaffolds with high precision and accuracy. In this study, an electrically controlled cortical impactor was used to induce randomized brain tissue defects. The overall shape of scaffolds was designed using rat-specific anatomical data obtained from magnetic resonance imaging, and the internal structure was created by computer-aided design. As the result of limitations arising from insufficient resolution of the manufacturing process, we magnified the size of the cavity model prototype five-fold to successfully fabricate customized collagen-chitosan scaffolds using three-dimensional printing. Results demonstrated that scaffolds have three-dimensional porous structures, high porosity, highly specific surface areas, pore connectivity and good internal characteristics. Neural stem cells co-cultured with scaffolds showed good viability, indicating good biocompatibility and biodegradability. This technique may be a promising new strategy for regenerating complex damaged brain tissues, and helps pave the way toward personalized medicine. PMID:28553343

Toward atomic-scale bright-field electron tomography for the study of fullerene-like nanostructures.

PubMed

Bar Sadan, Maya; Houben, Lothar; Wolf, Sharon G; Enyashin, Andrey; Seifert, Gotthard; Tenne, Reshef; Urban, Knut

2008-03-01

We present the advancement of electron tomography for three-dimensional structure reconstruction of fullerene-like particles toward atomic-scale resolution. The three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is achieved by the combination of low voltage operation of the electron microscope with aberration-corrected phase contrast imaging. The method enables the study of defects and irregularities in the three-dimensional structure of individual fullerene-like particles on the scale of 2-3 A. Control over shape, size, and atomic architecture is a key issue in synthesis and design of functional nanoparticles. Transmission electron microscopy (TEM) is the primary technique to characterize materials down to the atomic level, albeit the images are two-dimensional projections of the studied objects. Recent advancements in aberration-corrected TEM have demonstrated single atom sensitivity for light elements at subångström resolution. Yet, the resolution of tomographic schemes for three-dimensional structure reconstruction has not surpassed 1 nm3, preventing it from becoming a powerful tool for characterization in the physical sciences on the atomic scale. Here we demonstrate that negative spherical aberration imaging at low acceleration voltage enables tomography down to the atomic scale at reduced radiation damage. First experimental data on the three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is presented. The method is applicable to the analysis of the atomic architecture of a wide range of nanostructures where strong electron channeling is absent, in particular to carbon fullerenes and inorganic fullerenes.

Two- and three-dimensional networks of gadolinium(III) with dicarboxylate ligands: synthesis, crystal structure, and magnetic properties.

PubMed

Cañadillas-Delgado, Laura; Pasan, Jorge; Fabelo, Oscar; Hernandez-Molina, María; Lloret, Francesc; Julve, Miguel; Ruiz-Pérez, Catalina

2006-12-25

Four gadolinium(III) complexes with dicarboxylate ligands of formulas [Gd2(mal)3(H2O)5]n.2nH2O (1), [Gd2(mal)3(H2O)6]n (2), [NaGd(mal)(ox)(H2O)3]n (3), and [Gd2(ox)3(H2O)6]n.2.5nH2O (4) (mal = malonate; ox = oxalate) have been prepared, and their magnetic properties have been investigated as a function of the temperature. The structures of 1-3 have been determined by X-ray diffraction methods. The crystal structure of 4 was already known, and it is made of hexagonal layers of Gd atoms that are bridged by bis-bidentate oxalate. Compound 1 is isostructural with the europium(III) malonate complex [Eu2(mal)3(H2O)5]n.2nH2O,1 whose structure was reported elsewhere. The Gd atoms in 1 define a two-dimensional network where a terminal bidentate and bridging bidentate/bis-monodentate and tris-bidentate coordination modes of malonate occur. Compound 2 has a three-dimensional structure with a structural phase transition at 226 K, which involves a change of the space group from I2/a to Ia. Although its structure at room temperature was already known, that below 226 K was not. Pairs of Gd atoms with a double oxo-carboxylate bridge occur in both phases, and the main differences between both structures deal with the Gd environment and the H-bond pattern. 3 is also a three-dimensional compound, and it was obtained by reacting Gd(III) ions with malonic acid in a silica gel medium. Oxalic acid results as an oxidized product of the malonic acid, and single crystals of the heteroleptic complex were produced. The Gd atoms in 3 are connected through bis-bidentate oxalate and carboxylate-malonate bridges in the anti-anti and anti-syn coordination modes. Compounds 1 and 2 exhibit weak but significant ferromagnetic couplings between the Gd(III) ions through the single (1) and double (2) oxo-carboxylate bridges, whereas antiferromagnetic interactions across the bis-bidentate oxalate account for the overall antiferromagnetic behavior observed in 3 and 4.

Tonal Interface to MacroMolecules (TIMMol): A Textual and Tonal Tool for Molecular Visualization

ERIC Educational Resources Information Center

Cordes, Timothy J.; Carlson, C. Britt; Forest, Katrina T.

2008-01-01

We developed the three-dimensional visualization software, Tonal Interface to MacroMolecules or TIMMol, for studying atomic coordinates of protein structures. Key features include audio tones indicating x, y, z location, identification of the cursor location in one-dimensional and three-dimensional space, textual output that can be easily linked…

Analysis of the Three-Dimensional Vector FAÇADE Model Created from Photogrammetric Data

NASA Astrophysics Data System (ADS)

Kamnev, I. S.; Seredovich, V. A.

2017-12-01

The results of the accuracy assessment analysis for creation of a three-dimensional vector model of building façade are described. In the framework of the analysis, analytical comparison of three-dimensional vector façade models created by photogrammetric and terrestrial laser scanning data has been done. The three-dimensional model built from TLS point clouds was taken as the reference one. In the course of the experiment, the three-dimensional model to be analyzed was superimposed on the reference one, the coordinates were measured and deviations between the same model points were determined. The accuracy estimation of the three-dimensional model obtained by using non-metric digital camera images was carried out. Identified façade surface areas with the maximum deviations were revealed.

Creating 3D Physical Models to Probe Student Understanding of Macromolecular Structure

ERIC Educational Resources Information Center

Cooper, A. Kat; Oliver-Hoyo, M. T.

2017-01-01

The high degree of complexity of macromolecular structure is extremely difficult for students to process. Students struggle to translate the simplified two-dimensional representations commonly used in biochemistry instruction to three-dimensional aspects crucial in understanding structure-property relationships. We designed four different physical…

Three-Dimensional Magnetic Resonance Imaging of Velopharyngeal Structures

ERIC Educational Resources Information Center

Bae, Youkyung; Kuehn, David P.; Sutton, Bradley P.; Conway, Charles A.; Perry, Jamie L.

2011-01-01

Purpose: To report the feasibility of using a 3-dimensional (3D) magnetic resonance imaging (MRI) protocol for examining velopharyngeal structures. Using collected 3D MRI data, the authors investigated the effect of sex on the midsagittal velopharyngeal structures and the levator veli palatini (levator) muscle configurations. Method: Ten Caucasian…

Building a Three-Dimensional Nano-Bio Interface for Aptasensing: An Analytical Methodology Based on Steric Hindrance Initiated Signal Amplification Effect.

PubMed

Du, Xiaojiao; Jiang, Ding; Hao, Nan; Qian, Jing; Dai, Liming; Zhou, Lei; Hu, Jianping; Wang, Kun

2016-10-04

The development of novel detection methodologies in electrochemiluminescence (ECL) aptasensor fields with simplicity and ultrasensitivity is essential for constructing biosensing architectures. Herein, a facile, specific, and sensitive methodology was developed unprecedentedly for quantitative detection of microcystin-LR (MC-LR) based on three-dimensional boron and nitrogen codoped graphene hydrogels (BN-GHs) assisted steric hindrance amplifying effect between the aptamer and target analytes. The recognition reaction was monitored by quartz crystal microbalance (QCM) to validate the possible steric hindrance effect. First, the BN-GHs were synthesized via self-assembled hydrothermal method and then applied as the Ru(bpy) 3 2+ immobilization platform for further loading the biomolecule aptamers due to their nanoporous structure and large specific surface area. Interestingly, we discovered for the first time that, without the aid of conventional double-stranded DNA configuration, such three-dimensional nanomaterials can directly amplify the steric hindrance effect between the aptamer and target analytes to a detectable level, and this facile methodology could be for an exquisite assay. With the MC-LR as a model, this novel ECL biosensor showed a high sensitivity and a wide linear range. This strategy supplies a simple and versatile platform for specific and sensitive determination of a wide range of aptamer-related targets, implying that three-dimensional nanomaterials would play a crucial role in engineering and developing novel detection methodologies for ECL aptasensing fields.

Analysis of high-rise constructions with the using of three-dimensional models of rods in the finite element program PRINS

NASA Astrophysics Data System (ADS)

Agapov, Vladimir

2018-03-01

The necessity of new approaches to the modeling of rods in the analysis of high-rise constructions is justified. The possibility of the application of the three-dimensional superelements of rods with rectangular cross section for the static and dynamic calculation of the bar and combined structures is considered. The results of the eighteen-story spatial frame free vibrations analysis using both one-dimensional and three-dimensional models of rods are presented. A comparative analysis of the obtained results is carried out and the conclusions on the possibility of three-dimensional superelements application in static and dynamic analysis of high-rise constructions are given on its basis.

A matrix dependent/algebraic multigrid approach for extruded meshes with applications to ice sheet modeling

DOE PAGES

Tuminaro, Raymond S.; Perego, Mauro; Tezaur, Irina Kalashnikova; ...

2016-10-06

A multigrid method is proposed that combines ideas from matrix dependent multigrid for structured grids and algebraic multigrid for unstructured grids. It targets problems where a three-dimensional mesh can be viewed as an extrusion of a two-dimensional, unstructured mesh in a third dimension. Our motivation comes from the modeling of thin structures via finite elements and, more specifically, the modeling of ice sheets. Extruded meshes are relatively common for thin structures and often give rise to anisotropic problems when the thin direction mesh spacing is much smaller than the broad direction mesh spacing. Within our approach, the first few multigridmore » hierarchy levels are obtained by applying matrix dependent multigrid to semicoarsen in a structured thin direction fashion. After sufficient structured coarsening, the resulting mesh contains only a single layer corresponding to a two-dimensional, unstructured mesh. Algebraic multigrid can then be employed in a standard manner to create further coarse levels, as the anisotropic phenomena is no longer present in the single layer problem. The overall approach remains fully algebraic, with the minor exception that some additional information is needed to determine the extruded direction. Furthermore, this facilitates integration of the solver with a variety of different extruded mesh applications.« less

Sculpting Cells with Play Doh.

ERIC Educational Resources Information Center

Way, Virginia A.

1982-01-01

Suggests using Play Doh to mold models of the nucleus, mitochondria, and inner cellular structures. Students can conceptualize the cell's structures as three-dimensional even though they appear two-dimensional under a microscope. Includes instructions for preparing homemade dough. (Author/JN)

Structure of the extracellular domain of matrix protein 2 of influenza A virus in complex with a protective monoclonal antibody.

PubMed

Cho, Ki Joon; Schepens, Bert; Seok, Jong Hyeon; Kim, Sella; Roose, Kenny; Lee, Ji-Hye; Gallardo, Rodrigo; Van Hamme, Evelien; Schymkowitz, Joost; Rousseau, Frederic; Fiers, Walter; Saelens, Xavier; Kim, Kyung Hyun

2015-04-01

The extracellular domain of influenza A virus matrix protein 2 (M2e) is conserved and is being evaluated as a quasiuniversal influenza A vaccine candidate. We describe the crystal structure at 1.6 Å resolution of M2e in complex with the Fab fragment of an M2e-specific monoclonal antibody that protects against influenza A virus challenge. This antibody binds M2 expressed on the surfaces of cells infected with influenza A virus. Five out of six complementary determining regions interact with M2e, and three highly conserved M2e residues are critical for this interaction. In this complex, M2e adopts a compact U-shaped conformation stabilized in the center by the highly conserved tryptophan residue in M2e. This is the first description of the three-dimensional structure of M2e. M2e of influenza A is under investigation as a universal influenza A vaccine, but its three-dimensional structure is unknown. We describe the structure of M2e stabilized with an M2e-specific monoclonal antibody that recognizes natural M2. We found that the conserved tryptophan is positioned in the center of the U-shaped structure of M2e and stabilizes its conformation. The structure also explains why previously reported in vivo escape viruses, selected with a similar monoclonal antibody, carried proline residue substitutions at position 10 in M2. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Beyond crystallography: Diffractive imaging using coherent x-ray light sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miao, J.; Ishikawa, T.; Robinson, I. K.

X-ray crystallography has been central to the development of many fields of science over the past century. It has now matured to a point that as long as good-quality crystals are available, their atomic structure can be routinely determined in three dimensions. However, many samples in physics, chemistry, materials science, nanoscience, geology, and biology are noncrystalline, and thus their three-dimensional structures are not accessible by traditional x-ray crystallography. Overcoming this hurdle has required the development of new coherent imaging methods to harness new coherent x-ray light sources. Here we review the revolutionary advances that are transforming x-ray sources and imagingmore » in the 21st century.« less

Hydrothermal synthesis of zinc(II)-phosphonate coordination polymers with different dimensionality (0D, 2D, 3D) and dimensionality change in the solid phase (0D→3D) induced by temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fernández-Zapico, Eva; Montejo-Bernardo, Jose; Fernández-González, Alfonso

2015-05-15

Three new zinc(II) coordination polymers, [Zn(HO{sub 3}PCH{sub 2}CH{sub 2}COO)(C{sub 12}H{sub 8}N{sub 2})(H{sub 2}O)] (1), [Zn{sub 3}(O{sub 3}PCH{sub 2}CH{sub 2}COO){sub 2}(C{sub 12}H{sub 8}N{sub 2})](H{sub 2}O){sub 3.40} (2) and [Zn{sub 5}(HO{sub 3}PCH{sub 2}CH{sub 2}COO){sub 2}(O{sub 3}PCH{sub 2}CH{sub 2}COO){sub 2}(C{sub 12}H{sub 8}N{sub 2}){sub 4}](H{sub 2}O){sub 0.32} (3), with different structural dimensionality (0D, 2D and 3D, respectively) have been prepared by hydrothermal synthesis, and their structures were determined by single-crystal X-ray diffraction. Compound 1 crystallizes in the monoclinic system (P2{sub 1}/c) forming discrete dimeric units bonded through H-bonds, while compounds 2 and 3 crystallize in the triclinic (P−1) and the monoclinic (C2/c) systems, respectively.more » Compound 3, showing three different coordination numbers (4, 5 and 6) for the zinc atoms, has also been obtained by thermal treatment of 1 (probed by high-temperature XRPD experiments). The crystalline features of these compounds, related to the coordination environments for the zinc atoms in each structure, provoke the increase of the relative fluorescence for 2 and 3, compared to the free phenanthroline. Thermal analysis (TG and DSC) and XPS studies have been also carried out for all compounds. - Graphical abstract: Three new coordination compounds of zinc with 2-carboxyethylphosphonic acid (H{sub 2}PPA) and phenanthroline have been obtained by hydrothermal synthesis. The crystalline structure depends on the different coordination environments of the zinc atoms (see two comparative Zn{sub 6}-moieties). The influence of the different coordination modes of H{sub 2}PPA with the central atom in all structures have been studied, being found new coordination modes for this ligand. Several compounds show a significant increase in relative fluorescence with respect to the free phenanthroline. - Highlights: • Compounds have been obtained modifying the reaction time and the rate of reagents. • Dimensionality and crystalline structure is a function of the zinc environments. • New coordination modes for 2-carboxyethylphosphonic acid are reported. • 3D-compound presents three different coordination environments for the zinc atoms. • Fluorescence properties are related to the structural dimensionality.« less

Research in Seismology

DTIC Science & Technology

1978-12-31

Koyanagi, Three-dimensional crust and mantle structure of Kilauea Volcano , Hawaii , J. Geophys. Res., 82, 5379-5394, 1977. Engdahl, E.R., J.G. Sindorf, and...Johnson, 1967), in Japan (Zandt, 1975; Hirahara, 1977), at NORSAR (Aki, 1977), in Yellowstone National Park (1yer, 1975; Zandt, 1978), in Hawaii ...1962. Ellsworth, W.L., Three-dimensional structure of the crust and mantle beneath the island of Hawaii , unpublished Ph.D. thesis, Massachusetts

A density functional global optimisation study of neutral 8-atom Cu-Ag and Cu-Au clusters

NASA Astrophysics Data System (ADS)

Heard, Christopher J.; Johnston, Roy L.

2013-02-01

The effect of doping on the energetics and dimensionality of eight atom coinage metal subnanometre particles is fully resolved using a genetic algorithm in tandem with on the fly density functional theory calculations to determine the global minima (GM) for Cu n Ag(8- n) and Cu n Au(8- n) clusters. Comparisons are made to previous ab initio work on mono- and bimetallic clusters, with excellent agreement found. Charge transfer and geometric arguments are considered to rationalise the stability of the particular permutational isomers found. An interesting transition between three dimensional and two dimensional GM structures is observed for copper-gold clusters, which is sharper and appears earlier in the doping series than is known for gold-silver particles.

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

NASA Technical Reports Server (NTRS)

Lim, Kap; Ho, Joseph X.; Keeling, Kim; Gilliland, Gary L.; Ji, Xinhua; Rueker, Florian; Carter, Daniel C.

1994-01-01

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(sub 3)2(sub 1)2 with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

A plasma source driven predator-prey like mechanism as a potential cause of spiraling intermittencies in linear plasma devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reiser, D.; Ohno, N.; Tanaka, H.

2014-03-15

Three-dimensional global drift fluid simulations are carried out to analyze coherent plasma structures appearing in the NAGDIS-II linear device (nagoya divertor plasma Simulator-II). The numerical simulations reproduce several features of the intermittent spiraling structures observed, for instance, statistical properties, rotation frequency, and the frequency of plasma expulsion. The detailed inspection of the three-dimensional plasma dynamics allows to identify the key mechanism behind the formation of these intermittent events. The resistive coupling between electron pressure and parallel electric field in the plasma source region gives rise to a quasilinear predator-prey like dynamics where the axisymmetric mode represents the prey and themore » spiraling structure with low azimuthal mode number represents the predator. This interpretation is confirmed by a reduced one-dimensional quasilinear model derived on the basis of the findings in the full three-dimensional simulations. The dominant dynamics reveals certain similarities to the classical Lotka-Volterra cycle.« less

Two-Dimensional Versus Three-Dimensional Conceptualization in Astronomy Education

NASA Astrophysics Data System (ADS)

Reynolds, Michael David

Numerous science conceptual issues are naturally three-dimensional. Classroom presentations are often two -dimensional or at best multidimensional. Several astronomy topics are of this nature, e. g. mechanics of the phases of the moon. Textbooks present this three-dimensional topic in two-dimensions; such is often the case in the classroom. This study was conducted to examine conceptions exhibited by pairs of like-sex 11th grade standard physics students as they modeled the lunar phases. Student pairs, 13 male and 13 female, were randomly selected and assigned. Pairing comes closer to classroom emulation, minimizes needs for direct probes, and pair discussion is more likely to display variety and depth. Four hypotheses were addressed: (1) Participants who model three-dimensionally will more likely achieve a higher explanation score. (2) Students who experienced more earth or physical science exposure will more likely model three-dimensionally. (3) Pairs that exhibit a strong science or mathematics preference will more likely model three-dimensionally. (4) Males will model in three dimensions more than females. Students provided background information, including science course exposure and subject preference. Each pair laid out a 16-card set representing two complete lunar phase changes. The pair was asked to explain why the phases occur. Materials were provided for use, including disks, spheres, paper and pen, and flashlight. Activities were videotaped for later evaluation. Statistics of choice was a correlation determination between course preference and model type and ANOVA for the other hypotheses. It was determined that pairs who modeled three -dimensionally achieved a higher score on their phases mechanics explanation at p <.05 level. Pairs with earth science or physical science exposure, those who prefer science or mathematics, and male participants were not more likely to model three-dimensionally. Possible reasons for lack of significance was small sample size and in the case of course preferences, small differences in course preference means. Based on this study, instructors should be aware of dimensionality and student misconceptions. Whenever possible, three-dimensional concepts should be modeled as such. Authors and publishers should consider modeling suggestions and three-dimensional ancillaries.

Aromatic carboxylate effect on dimensionality of three bis(benzimidazole)-based cobalt(II) coordination polymers: Syntheses, structures and properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Ju-Wen; Gong, Chun-Hua; Hou, Li-Li

2013-09-15

Three new metal-organic coordination polymers [Co(4-bbc){sub 2}(bbbm)] (1), [Co(3,5-pdc)(bbbm)]·2H{sub 2}O (2) and [Co(1,4-ndc)(bbbm)] (3) (4-Hbbc=4-bromobenzoic acid, 3,5-H{sub 2}pdc=3,5-pyridinedicarboxylic acid, 1,4-H{sub 2}ndc=1,4-naphthalenedicarboxylic acid and bbbm=1,1-(1,4-butanediyl)bis-1H-benzimidazole) were hydrothermally synthesized and structurally characterized. Polymer 1 is a 1D chain formed by the bbbm ligands and Co{sup II} ions. Polymer 2 exhibits a 2D network with a (3·4·5)(3{sup 2}·4·5·6{sup 2}·7{sup 4}) topology. Polymer 3 possesses a 3D three-fold interpenetrating framework. The versatile structures of title polymers indicate that the aromatic carboxylates have an important influence on the dimensionality of 1–3. Moreover, the thermal stability, electrochemical and luminescent properties of 1–3 were investigated. - graphicalmore » abstract: Three bis(benzimidazole)-based cobalt(II) coordination polymers tuned by aromatic carboxylates were hydrothermally synthesized and structurally characterized. The aromatic carboxylates play a key role in the dimensionality of three polymers. The electrochemical and luminescent properties of three polymers were investigated. Display Omitted - Highlights: • Three bis(benzimidazole)-based cobalt(II) coordination polymers tuned by aromatic carboxylates were obtained. • The aromatic carboxylates have an important influence on the dimensionality of three polymers. • The electrochemical and luminescent properties of three polymers were investigated.« less

Structure of the Putative 32 kDa Myrosinase Binding Protein from Arabidopsis (At3g16450.1) Determined by SAIL-NMR

PubMed Central

Takeda, Mitsuhiro; Sugimori, Nozomi; Torizawa, Takuya; Terauchi, Tsutomu; Ono, Akira Mei; Yagi, Hirokazu; Yamaguchi, Yoshiki; Kato, Koichi; Ikeya, Teppei; Jee, JunGoo; Güntert, Peter; Aceti, David J.; Markley, John L.; Kainosho, Masatsune

2009-01-01

The product of gene At3g16450.1 from Arabidopsis thaliana is a 32 kDa, 299-residue protein classified as resembling a myrosinase-binding protein (MyroBP). MyroBPs are found in plants as part of a complex with the glucosinolate-degrading enzyme, myrosinase, and are suspected to play a role in myrosinase-dependent defense against pathogens. Many MyroBPs and MyroBP-related proteins are composed of repeated homologous sequences with unknown structure. We report here the three-dimensional structure of the At3g16450.1 protein from Arabidopsis, which consists of two tandem repeats. Because the size of the protein is larger than that amenable to high-throughput analysis by uniformly 13C/15N labeling methods, we used our stereo-array isotope labeling (SAIL) technology to prepare an optimally 2H/13C/15N-labeled sample. NMR data sets collected with the SAIL-protein enabled us to assign 1H, 13C and 15N chemical shifts to 95.5% of all atoms, even at the low concentration (0.2 mM) of the protein product. We collected additional NOESY data and solved the three-dimensional structure with the CYANA software package. The structure, the first for a MyroBP family member, revealed that the At3g16450.1 protein consists of two independent, but similar, lectin-fold domains composed of three β-sheets. PMID:19021763

Analysis of x-ray tomography data of an extruded low density styrenic foam: an image analysis study

NASA Astrophysics Data System (ADS)

Lin, Jui-Ching; Heeschen, William

2016-10-01

Extruded styrenic foams are low density foams that are widely used for thermal insulation. It is difficult to precisely characterize the structure of the cells in low density foams by traditional cross-section viewing due to the frailty of the walls of the cells. X-ray computed tomography (CT) is a non-destructive, three dimensional structure characterization technique that has great potential for structure characterization of styrenic foams. Unfortunately the intrinsic artifacts of the data and the artifacts generated during image reconstruction are often comparable in size and shape to the thin walls of the foam, making robust and reliable analysis of cell sizes challenging. We explored three different image processing methods to clean up artifacts in the reconstructed images, thus allowing quantitative three dimensional determination of cell size in a low density styrenic foam. Three image processing approaches - an intensity based approach, an intensity variance based approach, and a machine learning based approach - are explored in this study, and the machine learning image feature classification method was shown to be the best. Individual cells are segmented within the images after the images were cleaned up using the three different methods and the cell sizes are measured and compared in the study. Although the collected data with the image analysis methods together did not yield enough measurements for a good statistic of the measurement of cell sizes, the problem can be resolved by measuring multiple samples or increasing imaging field of view.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bena, Iosif; Kraus, Per; Warner, Nicholas P.

We construct the most generic three-charge, three-dipole-charge, BPS black-ring solutions in a Taub-NUT background. These solutions depend on seven charges and six moduli, and interpolate between a four-dimensional black hole and a five-dimensional black ring. They are also instrumental in determining the correct microscopic description of the five-dimensional BPS black rings.

Laboratory-size three-dimensional water-window x-ray microscope with Wolter type I mirror optics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohsuka, Shinji; The Graduate School for the Creation of New Photonics Industries, 1955-1 Kurematsu-cho, Nishi-ku, Hamamatsu-City, 431-1202; Ohba, Akira

2016-01-28

We constructed a laboratory-size three-dimensional water-window x-ray microscope that combines wide-field transmission x-ray microscopy with tomographic reconstruction techniques. It consists of an electron-impact x-ray source emitting oxygen Kα x-rays, Wolter type I grazing incidence mirror optics, and a back-illuminated CCD for x-ray imaging. A spatial resolution limit better than 1.0 line pairs per micrometer was obtained for two-dimensional transmission images, and 1-μm-scale three-dimensional fine structures were resolved.

Anhydrous 1:1 proton-transfer compounds of isonipecotamide with picric acid and 3,5-dinitrosalicylic acid: 4-carbamoylpiperidinium 2,4,6-trinitrophenolate and two polymorphs of 4-carbamoylpiperidinium 2-carboxy-4,6-dinitrophenolate.

PubMed

Smith, Graham; Wermuth, Urs D

2010-12-01

The structures of the anhydrous 1:1 proton-transfer compounds of isonipecotamide (piperidine-4-carboxamide) with picric acid and 3,5-dinitrosalicylic acid, namely 4-carbamoylpiperidinium 2,4,6-trinitrophenolate, C(6)H(13)N(2)O(+)·C(6)H(2)N(3)O(7)(-), (I), and 4-carbamoylpiperidinium 2-carboxy-4,6-dinitrophenolate [two forms of which were found, the monoclinic α-polymorph, (II), and the triclinic β-polymorph, (III)], C(6)H(13)N(2)O(+)·C(7)H(3)N(2)O(7)(-), have been determined at 200 K. All three compounds form hydrogen-bonded structures, viz. one-dimensional in (II), two-dimensional in (I) and three-dimensional in (III). In (I), the cations form centrosymmetric cyclic head-to-tail hydrogen-bonded homodimers [graph set R(2)(2)(14)] through lateral duplex piperidinium-amide N-H...O interactions. These dimers are extended into a two-dimensional network structure through further interactions with phenolate and nitro O-atom acceptors, including a direct symmetric piperidinium-phenol/nitro N-H...O,O cation-anion association [graph set R(1)(2)(6)]. The monoclinic polymorph, (II), has a similar R(1)(2)(6) cation-anion hydrogen-bonding interaction to (I) but with an additional conjoint symmetrical R(1)(2)(4) interaction as well as head-to-tail piperidinium-amide N-H...O,O hydrogen bonds and amide-carboxyl N-H...O hydrogen bonds, giving a network structure which includes large R(4)(3)(20) rings. The hydrogen bonding in the triclinic polymorph, (III), is markedly different from that of monoclinic (II). The asymmetric unit contains two independent cation-anion pairs which associate through cyclic piperidinium-carboxyl N-H...O,O' interactions [graph set R(1)(2)(4)]. The cations also show the zigzag head-to-tail piperidinium-amide N-H...O hydrogen-bonded chain substructures found in (II), but in addition feature amide-nitro and amide-phenolate N-H...O associations. As well, there is a centrosymmetric double-amide N-H...O(carboxyl) bridged bis(cation-anion) ring system [graph set R(4)(2)(8)] in the three-dimensional framework. The structures reported here demonstrate the utility of the isonipecotamide cation as a synthon with previously unrecognized potential for structure assembly applications. Furthermore, the structures of the two polymorphic 3,5-dinitrosalicylic acid salts show an unusual dissimilarity in hydrogen-bonding characteristics, considering that both were obtained from identical solvent systems.

Self-assembly of three-dimensional open structures using patchy colloidal particles.

PubMed

Rocklin, D Zeb; Mao, Xiaoming

2014-10-14

Open structures can display a number of unusual properties, including a negative Poisson's ratio, negative thermal expansion, and holographic elasticity, and have many interesting applications in engineering. However, it is a grand challenge to self-assemble open structures at the colloidal scale, where short-range interactions and low coordination number can leave them mechanically unstable. In this paper we discuss the self-assembly of three-dimensional open structures using triblock Janus particles, which have two large attractive patches that can form multiple bonds, separated by a band with purely hard-sphere repulsion. Such surface patterning leads to open structures that are stabilized by orientational entropy (in an order-by-disorder effect) and selected over close-packed structures by vibrational entropy. For different patch sizes the particles can form into either tetrahedral or octahedral structural motifs which then compose open lattices, including the pyrochlore, the hexagonal tetrastack and the perovskite lattices. Using an analytic theory, we examine the phase diagrams of these possible open and close-packed structures for triblock Janus particles and characterize the mechanical properties of these structures. Our theory leads to rational designs of particles for the self-assembly of three-dimensional colloidal structures that are possible using current experimental techniques.

Three-dimensional magnetophotonic crystals based on artificial opals

NASA Astrophysics Data System (ADS)

Baryshev, A. V.; Kodama, T.; Nishimura, K.; Uchida, H.; Inoue, M.

2004-06-01

We fabricated and experimentally investigated three-dimensional magnetophotonic crystals (3D MPCs) based on artificial opals. Opal samples with three-dimensional dielectric lattices were impregnated with different types of magnetic material. Magnetic and structural properties of 3D MPCs were studied by field emission scanning electron microscopy, x-ray diffraction analysis, and vibrating sample magnetometer. We have shown that magnetic materials synthesized in voids of opal lattices and the composites obtained have typical magnetic properties.

Test of Shi et al. Method to Infer the Magnetic Reconnection Geometry from Spacecraft Data: MHD Simulation with Guide Field and Antiparallel Kinetic Simulation

NASA Technical Reports Server (NTRS)

Denton, R.; Sonnerup, B. U. O.; Swisdak, M.; Birn, J.; Drake, J. F.; Heese, M.

2012-01-01

When analyzing data from an array of spacecraft (such as Cluster or MMS) crossing a site of magnetic reconnection, it is desirable to be able to accurately determine the orientation of the reconnection site. If the reconnection is quasi-two dimensional, there are three key directions, the direction of maximum inhomogeneity (the direction across the reconnection site), the direction of the reconnecting component of the magnetic field, and the direction of rough invariance (the "out of plane" direction). Using simulated spacecraft observations of magnetic reconnection in the geomagnetic tail, we extend our previous tests of the direction-finding method developed by Shi et al. (2005) and the method to determine the structure velocity relative to the spacecraft Vstr. These methods require data from four proximate spacecraft. We add artificial noise and calibration errors to the simulation fields, and then use the perturbed gradient of the magnetic field B and perturbed time derivative dB/dt, as described by Denton et al. (2010). Three new simulations are examined: a weakly three-dimensional, i.e., quasi-two-dimensional, MHD simulation without a guide field, a quasi-two-dimensional MHD simulation with a guide field, and a two-dimensional full dynamics kinetic simulation with inherent noise so that the apparent minimum gradient was not exactly zero, even without added artificial errors. We also examined variations of the spacecraft trajectory for the kinetic simulation. The accuracy of the directions found varied depending on the simulation and spacecraft trajectory, but all the directions could be found within about 10 for all cases. Various aspects of the method were examined, including how to choose averaging intervals and the best intervals for determining the directions and velocity. For the kinetic simulation, we also investigated in detail how the errors in the inferred gradient directions from the unmodified Shi et al. method (using the unperturbed gradient) depended on the amplitude of the calibration errors. For an accuracy of 3 for the maximum gradient direction, the calibration errors could be as large as 3% of reconnection magnetic field, while for the same accuracy for the minimum gradient direction, the calibration errors could only be as large as 0.03% of the reconnection magnetic field. These results suggest that the maximum gradient direction can normally be determined by the unmodified Shi et al. method, while the modified method or some other method must be used to accurately determine the minimum gradient direction. The structure velocity was found with magnitude accurate to 2% and direction accurate to within 5%.

Small-angle scattering from 3D Sierpinski tetrahedron generated using chaos game

NASA Astrophysics Data System (ADS)

Slyamov, Azat

2017-12-01

We approximate a three dimensional version of deterministic Sierpinski gasket (SG), also known as Sierpinski tetrahedron (ST), by using the chaos game representation (CGR). Structural properties of the fractal, generated by both deterministic and CGR algorithms are determined using small-angle scattering (SAS) technique. We calculate the corresponding monodisperse structure factor of ST, using an optimized Debye formula. We show that scattering from CGR of ST recovers basic fractal properties, such as fractal dimension, iteration number, scaling factor, overall size of the system and the number of units composing the fractal.

Conformational landscape of a virus by single-particle X-ray scattering

DOE PAGES

Hosseinizadeh, Ahmad; Mashayekhi, Ghoncheh; Copperman, Jeremy; ...

2017-08-14

Using a manifold-based analysis of experimental diffraction snapshots from an X-ray free electron laser, we determine the three-dimensional structure and conformational landscape of the PR772 virus to a detector-limited resolution of 9 nm. Our results indicate that a single conformational coordinate controls reorganization of the genome, growth of a tubular structure from a portal vertex and release of the genome. Furthermore, these results demonstrate that single-particle X-ray scattering has the potential to shed light on key biological processes.

Effects of front-surface target structures on properties of relativistic laser-plasma electrons.

PubMed

Jiang, S; Krygier, A G; Schumacher, D W; Akli, K U; Freeman, R R

2014-01-01

We report the results of a study of the role of prescribed geometrical structures on the front of a target in determining the energy and spatial distribution of relativistic laser-plasma electrons. Our three-dimensional particle-in-cell simulation studies apply to short-pulse, high-intensity laser pulses, and indicate that a judicious choice of target front-surface geometry provides the realistic possibility of greatly enhancing the yield of high-energy electrons while simultaneously confining the emission to narrow (<5°) angular cones.

Magnetorheological Fluids-Earth Applications Video

NASA Technical Reports Server (NTRS)

1997-01-01

Principal investigator Alice Gast describes magnetorheological (MR) fluids and how they differ from other fluids, such as blood or milk. Gast is the principal investigator for Investigating the structure of Paramagnetic Aggregates from Colloidal Emulsions (InSPACE), which was conducted by the Expedition 6 crew onboard the International Space Station (ISS). The goal of inSPACE is to determine the true three-dimensional (3-D) low energy (equilibrium) structure of the MR fluids in a periodically interrupted magnetic field. Applications for MR fluids could include electrical clutches, brakes, robotic devices, seat suspension systems, and shock absorbers.

Manipulation of fluids in three-dimensional porous photonic structures with patterned surface properties

DOEpatents

Aizenberg, Joanna; Burgess, Ian B.; Mishchenko, Lidiya; Hatton, Benjamin; Loncar, Marko

2016-03-08

A three-dimensional porous photonic structure, whose internal pore surfaces can be provided with desired surface properties in a spatially selective manner with arbitrary patterns, and methods for making the same are described. When exposed to a fluid (e.g., via immersion or wicking), the fluid can selectively penetrate the regions of the structure with compatible surface properties. Broad applications, for example in security, encryption and document authentication, as well as in areas such as simple microfluidics and diagnostics, are anticipated.

An Essential Protein Repair Enzyme: Investigation of the Molecular Recognition Mechanism of Methionine Sulfoxide Reductase A

DTIC Science & Technology

2008-05-01

4 ). The three-dimensional spatial orientation of the atoms for these resolved solution structures (Protein Data Bank accession codes: 2gt3...Crystal structure of the Escherichia coli peptide methionine sulphoxide reductase at 1.9 Å resolution . Struct. Fold. Des. 8: 1167 – 1178. 2 . Brot...sources (8). There is a 67% sequence identity between the E.coli and human MsrA ( 2 ). N-terminus C-terminus Figure 2 . Three-dimensional structure

Manipulation of fluids in three-dimensional porous photonic structures with patterned surface properties

DOEpatents

Aizenberg, Joanna; Burgess, Ian; Mishchenko, Lidiya; Hatton, Benjamin; Loncar, Marko

2017-12-26

A three-dimensional porous photonic structure, whose internal pore surfaces can be provided with desired surface properties in a spatially selective manner with arbitrary patterns, and methods for making the same are described. When exposed to a fluid (e.g., via immersion or wicking), the fluid can selectively penetrate the regions of the structure with compatible surface properties. Broad applications, for example in security, encryption and document authentication, as well as in areas such as simple microfluidics and diagnostics, are anticipated.

Biomotor structures in elite female handball players.

PubMed

Katić, Ratko; Cavala, Marijana; Srhoj, Vatromir

2007-09-01

In order to identify biomotor structures in elite female handball players, factor structures of morphological characteristics and basic motor abilities of elite female handball players (N = 53) were determined first, followed by determination of relations between the morphological-motor space factors obtained and the set of criterion variables evaluating situation motor abilities in handball. Factor analysis of 14 morphological measures produced three morphological factors, i.e. factor of absolute voluminosity (mesoendomorph), factor of longitudinal skeleton dimensionality, and factor of transverse hand dimensionality. Factor analysis of 15 motor variables yielded five basic motor dimensions, i.e. factor of agility, factor of jumping explosive strength, factor of throwing explosive strength, factor of movement frequency rate, and factor of running explosive strength (sprint). Four significant canonic correlations, i.e. linear combinations, explained the correlation between the set of eight latent variables of the morphological and basic motor space and five variables of situation motoricity. First canonic linear combination is based on the positive effect of the factors of agility/coordination on the ability of fast movement without ball. Second linear combination is based on the effect of jumping explosive strength and transverse hand dimensionality on ball manipulation, throw precision, and speed of movement with ball. Third linear combination is based on the running explosive strength determination by the speed of movement with ball, whereas fourth combination is determined by throwing and jumping explosive strength, and agility on ball pass. The results obtained were consistent with the model of selection in female handball proposed (Srhoj et al., 2006), showing the speed of movement without ball and the ability of ball manipulation to be the predominant specific abilities, as indicated by the first and second linear combination.

TOPEX/Poseidon - An international satellite oceanography mission

NASA Technical Reports Server (NTRS)

Townsend, W. F.; Fellous, J.-L.

1986-01-01

The TOPEX/Poseidon mission, a joint NASA-CNES effort, strives to provide highly accurate global ocean topography measurements over a three year period utilizing highly advanced satellite radar altimetry techniques. Scheduled for launch in late 1991, the TOPEX/Poseidon satellite, together with ESA's first European remote sensing satellite and NASA's scatterometer, promises to provide a fundamental breakthrough in the present knowledge of how the oceans work as a global system. As part of the World Ocean Circulation Experiment, TOPEX/Poseidon measurements will aid in the determination of the three-dimensional current structure of the global oceans.

Fabrication of dielectric elastomer stack transducers (DEST) by liquid deposition modeling

NASA Astrophysics Data System (ADS)

Klug, Florian; Solano-Arana, Susana; Mößinger, Holger; Förster-Zügel, Florentine; Schlaak, Helmut F.

2017-04-01

Established fabrication methods for dielectric elastomer stack transducers (DEST) are mostly based on twodimensional thin-film technology. Because of this, DEST are based on simple two-dimensionally structured shapes. For certain applications, like valves or Braille displays, these structures are suited well enough. However, a more flexible fabrication method allows for more complex actuator designs, which would otherwise require extra processing steps. Fabrication methods with the possibility of three-dimensional structuring allow e.g. the integration of electrical connections, cavities, channels, sensor and other structural elements during the fabrication. This opens up new applications, as well as the opportunity for faster prototype production of individually designed DEST for a given application. In this work, a manufacturing system allowing three dimensional structuring is described. It enables the production of multilayer and three-dimensional structured DEST by liquid deposition modelling. The system is based on a custom made dual extruder, connected to a commercial threeaxis positioning system. It allows a computer controlled liquid deposition of two materials. After tuning the manufacturing parameters the production of thin layers with at thickness of less than 50 μm, as well as stacking electrode and dielectric materials is feasible. With this setup a first DEST with dielectric layer thickness less than 50 μm is build successfully and its performance is evaluated.

Condensed-matter research at the Los Alamos pulsed neutron source (WNR)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eckert, J.

1982-01-01

The experimental program at the WNR in condensed matter research at present is aimed principally at utilizing the high epithermal neutron flux available at a spallation neutron source. Interesting new results have been obtained in several areas including hydrogen vibrations in metals, chemical vibrational spectroscopy and the structure of liquids. For example, extensive vibrational spectra were obtained of hydrogen in Nb which could be described in terms of a three-dimensional localized anharmonic oscillator, deuterium substitution methods were used to determine the variation with 0-0 distance of the hydrogen bending mode frequency in extremely short intramolecular hydrogen bonds, and model-independent partialmore » structure factors were determined for liquid water.« less

Crystallization of Macromolecules

PubMed Central

Friedmann, David; Messick, Troy; Marmorstein, Ronen

2014-01-01

X-ray crystallography has evolved into a very powerful tool to determine the three-dimensional structure of macromolecules and macromolecular complexes. The major bottleneck in structure determination by X-ray crystallography is the preparation of suitable crystalline samples. This unit outlines steps for the crystallization of a macromolecule, starting with a purified, homogeneous sample. The first protocols describe preparation of the macromolecular sample (i.e., proteins, nucleic acids, and macromolecular complexes). The preparation and assessment of crystallization trials is then described, along with a protocol for confirming whether the crystals obtained are composed of macromolecule as opposed to a crystallization reagent . Next, the optimization of crystallization conditions is presented. Finally, protocols that facilitate the growth of larger crystals through seeding are described. PMID:22045560

The young person’s guide to the PDB*

PubMed Central

Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2017-01-01

The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120,000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview. PMID:28132477

Life Origination Hydrate Theory (LOH-Theory) and Mitosis and Replication Hydrate Theory (MRH-Theory): three-dimensional PC validation

NASA Astrophysics Data System (ADS)

Kadyshevich, E. A.; Dzyabchenko, A. V.; Ostrovskii, V. E.

2014-04-01

Size compatibility of the CH4-hydrate structure II and multi-component DNA fragments is confirmed by three-dimensional simulation; it is validation of the Life Origination Hydrate Theory (LOH-Theory).

New Computer Automated Holo-Photoelastic Method For Measuring Planar Principal Stress Magnitudes And Orientation

NASA Astrophysics Data System (ADS)

Brown, G. M.; Sullivan, J. L.

1987-09-01

A complete experimental determination of the stress and strain fields in an arbitrary deformed structure is generally unavailable. However, for two dimensional elasticity problems, such determinations are possible since in those cases one needs only to solve for three stresses (two normal and one shear). In fact, such determinations have been conducted quite often. By using isochromatic and isoclinic photoelastic data, the shear difference and numerical iteration techniques (1) and the least squares techniques (2) have been successfully used for complete stress field determinations of two dimensional elasticity problems. Though the shear difference technique can be particularly sensitive to cumulative errors resulting from numerical integration, the least squares technique is not affected by this and appears to yield better accuracy. The methods just cited use both experimental data and one or more mechanics conditions(e.g., the equations of equilibrium) to determine the stress field. However, the stress field can also be obtained from experimental data alone for planar elasticity problems, if there is enough of it to solve for the three stresses. For example, the Moire* technique or the combination of isochromatic, isoclinic, and isopachic data (for transparent models) can be used for such determinations. Further, with the marriage of advanced image processing equipment to computers, such analyses using this type of data can be conveniently conducted. It is even possible that such analyses could be more accurate than those using the combined experimental/numerical techniques cited above. The purposes of this report are two fold: i) to describe a single apparatus for obtaining isochromatic, isopachic, and isoclinic results for complete stress field determinations of two dimensional transparent models, and ii) to compare experimental and theoretical stress field values for an antisymmetrically loaded beam obtained using that apparatus.

Three dimensional fabrication at small size scales

PubMed Central

Leong, Timothy G.; Zarafshar, Aasiyeh M.; Gracias, David H.

2010-01-01

Despite the fact that we live in a three-dimensional (3D) world and macroscale engineering is 3D, conventional sub-mm scale engineering is inherently two-dimensional (2D). New fabrication and patterning strategies are needed to enable truly three-dimensionally-engineered structures at small size scales. Here, we review strategies that have been developed over the last two decades that seek to enable such millimeter to nanoscale 3D fabrication and patterning. A focus of this review is the strategy of self-assembly, specifically in a biologically inspired, more deterministic form known as self-folding. Self-folding methods can leverage the strengths of lithography to enable the construction of precisely patterned 3D structures and “smart” components. This self-assembling approach is compared with other 3D fabrication paradigms, and its advantages and disadvantages are discussed. PMID:20349446

Increasing the structural coverage of tuberculosis drug targets.

PubMed

Baugh, Loren; Phan, Isabelle; Begley, Darren W; Clifton, Matthew C; Armour, Brianna; Dranow, David M; Taylor, Brandy M; Muruthi, Marvin M; Abendroth, Jan; Fairman, James W; Fox, David; Dieterich, Shellie H; Staker, Bart L; Gardberg, Anna S; Choi, Ryan; Hewitt, Stephen N; Napuli, Alberto J; Myers, Janette; Barrett, Lynn K; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W; Stacy, Robin; Stewart, Lance J; Edwards, Thomas E; Van Voorhis, Wesley C; Myler, Peter J

2015-03-01

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. Copyright © 2014 Elsevier Ltd. All rights reserved.

Increasing the Structural Coverage of Tuberculosis Drug Targets

PubMed Central

Baugh, Loren; Phan, Isabelle; Begley, Darren W.; Clifton, Matthew C.; Armour, Brianna; Dranow, David M.; Taylor, Brandy M.; Muruthi, Marvin M.; Abendroth, Jan; Fairman, James W.; Fox, David; Dieterich, Shellie H.; Staker, Bart L.; Gardberg, Anna S.; Choi, Ryan; Hewitt, Stephen N.; Napuli, Alberto J.; Myers, Janette; Barrett, Lynn K.; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W.; Stacy, Robin; Stewart, Lance J.; Edwards, Thomas E.; Van Voorhis, Wesley C.; Myler, Peter J.

2015-01-01

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. PMID:25613812

Three dimensional canonical singularity and five dimensional N = 1 SCFT

NASA Astrophysics Data System (ADS)

Xie, Dan; Yau, Shing-Tung

2017-06-01

We conjecture that every three dimensional canonical singularity defines a five dimensional N = 1 SCFT. Flavor symmetry can be found from singularity structure: non-abelian flavor symmetry is read from the singularity type over one dimensional singular locus. The dimension of Coulomb branch is given by the number of compact crepant divisors from a crepant resolution of singularity. The detailed structure of Coulomb branch is described as follows: a) a chamber of Coulomb branch is described by a crepant resolution, and this chamber is given by its Nef cone and the prepotential is computed from triple intersection numbers; b) Crepant resolution is not unique and different resolutions are related by flops; Nef cones from crepant resolutions form a fan which is claimed to be the full Coulomb branch.

Computer-Aided Design Of Turbine Blades And Vanes

NASA Technical Reports Server (NTRS)

Hsu, Wayne Q.

1988-01-01

Quasi-three-dimensional method for determining aerothermodynamic configuration of turbine uses computer-interactive analysis and design and computer-interactive graphics. Design procedure executed rapidly so designer easily repeats it to arrive at best performance, size, structural integrity, and engine life. Sequence of events in aerothermodynamic analysis and design starts with engine-balance equations and ends with boundary-layer analysis and viscous-flow calculations. Analysis-and-design procedure interactive and iterative throughout.

Dimensional stabilization of southern pines

Treesearch

E.T. Choong; H.M. Barnes

1969-01-01

The effectiveness of five dimensional stabilizing agents and three impregnation methods on southern pine was determined. Four southern pine species were studies in order to determine the effect of wood factors. The best dimensional stability was obtained when the wood was preswollen and the chemical was impregnated by a diffusion process. In general, polyethylene...

Processing, properties and applications of composites using powder-coated epoxy towpreg technology

NASA Technical Reports Server (NTRS)

Bayha, T. D.; Osborne, P. P.; Thrasher, T. P.; Hartness, J. T.; Johnston, N. J.; Marchello, J. M.; Hugh, M. K.

1993-01-01

Composite manufacturing using the current prepregging technology of impregnating liquid resin into three-dimensionally reinforced textile preforms can be a costly and difficult operation. Alternatively, using polymer in the solid form, grinding it into a powder, and then depositing it onto a carbon fiber tow prior to making a textile preform is a viable method for the production of complex textile shapes. The powder-coated towpreg yarn is stable, needs no refrigeration, contains no solvents and is easy to process into various woven and braided preforms for later consolidation into composite structures. NASA's Advanced Composites Technology (ACT) program has provided an avenue for developing the technology by which advanced resins and their powder-coated preforms may be used in aircraft structures. Two-dimensional braiding and weaving studies using powder-coated towpreg have been conducted to determine the effect of resin content, towpreg size and twist on textile composite properties. Studies have been made to customize the towpreg to reduce friction and bulk factor. Processing parameters have been determined for three epoxy resin systems on eight-harness satin fabric, and on more advanced 3-D preform architectures for the downselected resin system. Processing effects and the resultant mechanical properties of these textile composites will be presented and compared.

Iterative optimizing quantization method for reconstructing three-dimensional images from a limited number of views

DOEpatents

Lee, H.R.

1997-11-18

A three-dimensional image reconstruction method comprises treating the object of interest as a group of elements with a size that is determined by the resolution of the projection data, e.g., as determined by the size of each pixel. One of the projections is used as a reference projection. A fictitious object is arbitrarily defined that is constrained by such reference projection. The method modifies the known structure of the fictitious object by comparing and optimizing its four projections to those of the unknown structure of the real object and continues to iterate until the optimization is limited by the residual sum of background noise. The method is composed of several sub-processes that acquire four projections from the real data and the fictitious object: generate an arbitrary distribution to define the fictitious object, optimize the four projections, generate a new distribution for the fictitious object, and enhance the reconstructed image. The sub-process for the acquisition of the four projections from the input real data is simply the function of acquiring the four projections from the data of the transmitted intensity. The transmitted intensity represents the density distribution, that is, the distribution of absorption coefficients through the object. 5 figs.

Three-dimensional vortex wake structure of flapping wings in hovering flight.

PubMed

Cheng, Bo; Roll, Jesse; Liu, Yun; Troolin, Daniel R; Deng, Xinyan

2014-02-06

Flapping wings continuously create and send vortices into their wake, while imparting downward momentum into the surrounding fluid. However, experimental studies concerning the details of the three-dimensional vorticity distribution and evolution in the far wake are limited. In this study, the three-dimensional vortex wake structure in both the near and far field of a dynamically scaled flapping wing was investigated experimentally, using volumetric three-component velocimetry. A single wing, with shape and kinematics similar to those of a fruitfly, was examined. The overall result of the wing action is to create an integrated vortex structure consisting of a tip vortex (TV), trailing-edge shear layer (TESL) and leading-edge vortex. The TESL rolls up into a root vortex (RV) as it is shed from the wing, and together with the TV, contracts radially and stretches tangentially in the downstream wake. The downwash is distributed in an arc-shaped region enclosed by the stretched tangential vorticity of the TVs and the RVs. A closed vortex ring structure is not observed in the current study owing to the lack of well-established starting and stopping vortex structures that smoothly connect the TV and RV. An evaluation of the vorticity transport equation shows that both the TV and the RV undergo vortex stretching while convecting downwards: a three-dimensional phenomenon in rotating flows. It also confirms that convection and secondary tilting and stretching effects dominate the evolution of vorticity.

Electron coherent diffraction tomography of a nanocrystal

NASA Astrophysics Data System (ADS)

Dronyak, Roman; Liang, Keng S.; Tsai, Jin-Sheng; Stetsko, Yuri P.; Lee, Ting-Kuo; Chen, Fu-Rong

2010-05-01

Coherent diffractive imaging (CDI) with electron or x-ray sources is a promising technique for investigating the structure of nanoparticles down to the atomic scale. In electron CDI, a two-dimensional reconstruction is demonstrated using highly coherent illumination from a field-emission gun as a source of electrons. In a three-dimensional (3D) electron CDI, we experimentally determine the morphology of a single MgO nanocrystal using the Bragg diffraction geometry. An iterative algorithm is applied to invert the 3D diffraction pattern about a (200) reflection of the nanoparticle measured at an angular range of 1.8°. The results reveal a 3D image of the sample at ˜8 nm resolution, and agree with a simulation. Our work demonstrates an alternative approach to obtain the 3D structure of nanocrystals with an electron microscope.