HRTEM study of {alpha}-AlMnSi crystals including non-crystallographic projection axes

Energy Technology Data Exchange (ETDEWEB)

Song, G.L.; Bursill, L.A.

1997-06-01

The structure of {alpha}-AlMnSi is examined by atomic resolution high-resolution transmission electron microscopy (HRTEM) and computer-based image matching techniques. Six distinct zone axes are examined; including both normal crystallographic and non-crystallographic zones axes of the structural motifs, which have m3-bar 5 icosahedral symmetry. The results provide a sound basis for understanding HRTEM images of the quasicrystalline alloy i-AlMnSi; thus it was examined to what extent the requirements for obtaining so-called structure images of complex alloy structures may be met experimentally and define when the images may be reliably interpreted on the basis of computer simulation and image-matching at about 0.17nm resolution. Most difficulty was experienced in obtaining the experimental images, especially for the non-crystallographic zones, which are very sensitive to slight changes in orientation off the desired zone axis or projection, the rate at which the crystal thickness is increasing (wedge-angle) and the orientation of the surfaces of the specimen. Surface amorphous layers due to oxidation and/or electron-induced irradiation damage also limit the efficiency of the HRTEM analysis. For the thin specimens used for HRTEM, both the electron diffraction patterns and the HRTEM images are characteristic of Im3-bar space group symmetry. It is suggested that this Im3-bar symmetry may be an example of a statistical symmetry, where the local symmetry is close to Pm3-bar but the average symmetry is Im3-bar. The transition from Pm3-bar to Im3-bar may be understood in terms of an analysis of small changes in the outer shells of the large icosahedral structural elements which are located at the corners and body-centers of the cubic unit cell. 21 refs., 3 tabs., 10 figs.

The structure of allophycocyanin from Thermosynechococcus elongatus at 3.5 Å resolution

Energy Technology Data Exchange (ETDEWEB)

Murray, James William; Maghlaoui, Karim; Barber, James, E-mail: j.barber@imperial.ac.uk [Division of Molecular Biosciences, Imperial College, Exhibition Road, London SW7 2AZ (United Kingdom)

2007-12-01

The crystal structure of a light-harvesting protein that interacts with photosystem II is reported. Cyanobacteria and red algae use light-harvesting pigments bound by proteins to capture solar radiation and to channel excitation energy into their reaction centres. In most cyanobacteria, a multi-megadalton soluble structure known as the phycobilisome is a major light-harvesting system. Allophycocyanin is the main component of the phycobilisome core, forming a link between the rest of the phycobilisome and the reaction-centre core. The crystal structure of allophycocyanin from Thermosynechococcus elongatus (TeAPC) has been determined and refined at 3.5 Å resolution to a crystallographic R value of 26.0% (R{sub free} = 28.5%). The structure was solved by molecular replacement using the allophycocyanin structure from Spirulina platensis as the search model. The asymmetric unit contains an (αβ) monomer which is expanded by symmetry to a crystallographic trimer.

High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method.

Science.gov (United States)

Higashiura, Akifumi; Ohta, Kazunori; Masaki, Mika; Sato, Masaru; Inaka, Koji; Tanaka, Hiroaki; Nakagawa, Atsushi

2013-11-01

Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method.

Structural studies of metal oxides related to High-Tc superconductors

International Nuclear Information System (INIS)

Hjorth, M.

1990-02-01

The project was started in order to investigate metal oxide structures related in some way to high-T c superconductors, using the crystallographic methods available; and in order to be able to use crystallographic methods in ways that go beyond routine applications in order to contribute to the crystallographic knowledge concerning these oxides. The project goes a step outside the boarders normally defined by using the term ''high-T c superconductors'', thus studying metal oxides from a more general crystallographic viewpoint. The methods used are the expansions of the spherical atom model, and of the thermal probability density function, and combination of X-ray work with high resolution electron microscopy. The use of the expanded diffraction models presents problems such as bad convergence in least squares refinement, physical unreasonable parameters, problems with interpretation of the results and difficulties due to missing or insufficient computer programs. The use of these models is discussed. Dynamical theory is applied when considering electron diffraction results. The theory is presented, focusing on the modifications of the standard theory used for some of the structures considered in the thesis, and in overview on other theoretical topics is given. A presentation is given of the structures which have been considered and of earlier work on related compounds, of the problems and solutions applied to the compound discussed and of the results obtained. The results are discussed. The appendices describe published papers and the work not directly connected to the main topics, e.g. implementation and development of computer programs. (AB) 172 refs

Automating crystallographic structure solution and refinement of protein–ligand complexes

International Nuclear Information System (INIS)

Echols, Nathaniel; Moriarty, Nigel W.; Klei, Herbert E.; Afonine, Pavel V.; Bunkóczi, Gábor; Headd, Jeffrey J.; McCoy, Airlie J.; Oeffner, Robert D.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

2013-01-01

A software system for automated protein–ligand crystallography has been implemented in the Phenix suite. This significantly reduces the manual effort required in high-throughput crystallographic studies. High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation

High-resolution x-ray imaging using a structured scintillator

Energy Technology Data Exchange (ETDEWEB)

Hormozan, Yashar, E-mail: hormozan@kth.se; Sychugov, Ilya; Linnros, Jan [Materials and Nano Physics, School of Information and Communication Technology, KTH Royal Institute of Technology, Electrum 229, Kista, Stockholm SE-16440 (Sweden)

2016-02-15

Purpose: In this study, the authors introduce a new generation of finely structured scintillators with a very high spatial resolution (a few micrometers) compared to conventional scintillators, yet maintaining a thick absorbing layer for improved detectivity. Methods: Their concept is based on a 2D array of high aspect ratio pores which are fabricated by ICP etching, with spacings (pitches) of a few micrometers, on silicon and oxidation of the pore walls. The pores were subsequently filled by melting of powdered CsI(Tl), as the scintillating agent. In order to couple the secondary emitted photons of the back of the scintillator array to a CCD device, having a larger pixel size than the pore pitch, an open optical microscope with adjustable magnification was designed and implemented. By imaging a sharp edge, the authors were able to calculate the modulation transfer function (MTF) of this finely structured scintillator. Results: The x-ray images of individually resolved pores suggest that they have been almost uniformly filled, and the MTF measurements show the feasibility of a few microns spatial resolution imaging, as set by the scintillator pore size. Compared to existing techniques utilizing CsI needles as a structured scintillator, their results imply an almost sevenfold improvement in resolution. Finally, high resolution images, taken by their detector, are presented. Conclusions: The presented work successfully shows the functionality of their detector concept for high resolution imaging and further fabrication developments are most likely to result in higher quantum efficiencies.

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.

Science.gov (United States)

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-09-01

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

Crystallographic Structure of Xanthorhodopsin, the Light-Driven Proton Pump With a Dual Chromophore

International Nuclear Information System (INIS)

Luecke, H.; Schobert, B.; Stagno, J.; Imasheva, E.S.; Wang, J.M.; Balashov, S.P.; Lanyi, J.K

2008-01-01

Homologous to bacteriorhodopsin and even more to proteorhodopsin, xanthorhodopsin is a light-driven proton pump that, in addition to retinal, contains a noncovalently bound carotenoid with a function of a light-harvesting antenna. We determined the structure of this eubacterial membrane protein-carotenoid complex by X-ray diffraction, to 1.9-(angstrom) resolution. Although it contains 7 transmembrane helices like bacteriorhodopsin and archaerhodopsin, the structure of xanthorhodopsin is considerably different from the 2 archaeal proteins. The crystallographic model for this rhodopsin introduces structural motifs for proton transfer during the reaction cycle, particularly for proton release, that are dramatically different from those in other retinal-based transmembrane pumps. Further, it contains a histidine-aspartate complex for regulating the pK a of the primary proton acceptor not present in archaeal pumps but apparently conserved in eubacterial pumps. In addition to aiding elucidation of a more general proton transfer mechanism for light-driven energy transducers, the structure defines also the geometry of the carotenoid and the retinal. The close approach of the 2 polyenes at their ring ends explains why the efficiency of the excited-state energy transfer is as high as ∼45%, and the 46 o angle between them suggests that the chromophore location is a compromise between optimal capture of light of all polarization angles and excited-state energy transfer

High Resolution Powder Diffraction and Structure Determination

International Nuclear Information System (INIS)

Cox, D. E.

1999-01-01

It is clear that high-resolution synchrotrons X-ray powder diffraction is a very powerful and convenient tool for material characterization and structure determination. Most investigations to date have been carried out under ambient conditions and have focused on structure solution and refinement. The application of high-resolution techniques to increasingly complex structures will certainly represent an important part of future studies, and it has been seen how ab initio solution of structures with perhaps 100 atoms in the asymmetric unit is within the realms of possibility. However, the ease with which temperature-dependence measurements can be made combined with improvements in the technology of position-sensitive detectors will undoubtedly stimulate precise in situ structural studies of phase transitions and related phenomena. One challenge in this area will be to develop high-resolution techniques for ultra-high pressure investigations in diamond anvil cells. This will require highly focused beams and very precise collimation in front of the cell down to dimensions of 50 (micro)m or less. Anomalous scattering offers many interesting possibilities as well. As a means of enhancing scattering contrast it has applications not only to the determination of cation distribution in mixed systems such as the superconducting oxides discussed in Section 9.5.3, but also to the location of specific cations in partially occupied sites, such as the extra-framework positions in zeolites, for example. Another possible application is to provide phasing information for ab initio structure solution. Finally, the precise determination of f as a function of energy through an absorption edge can provide useful information about cation oxidation states, particularly in conjunction with XANES data. In contrast to many experiments at a synchrotron facility, powder diffraction is a relatively simple and user-friendly technique, and most of the procedures and software for data analysis

Surface crystallographic structures of cellulose nanofiber films and overlayers of pentacene

Science.gov (United States)

Nakayama, Yasuo; Mori, Toshiaki; Tsuruta, Ryohei; Yamanaka, Soichiro; Yoshida, Koki; Imai, Kento; Koganezawa, Tomoyuki; Hosokai, Takuya

2018-03-01

Cellulose nanofibers or nanocellulose is a promising recently developed biomass and biodegradable material used for various applications. In order to utilize this material as a substrate in organic electronic devices, thorough understanding of the crystallographic structures of the surfaces of the nanocellulose composites and of their interfaces with organic semiconductor molecules is essential. In this work, surface crystallographic structures of nanocellulose films (NCFs) and overlayers of pentacene were investigated by two-dimensional grazing-incidence X-ray diffraction. The NCFs are found to crystallize on solid surfaces with the crystal lattice preserving the same structure of the known bulk phase, whereas distortion of interchain packing toward the surface normal direction is suggested. The pentacene overlayers on the NCFs are found to form the thin-film phase with an in-plane mean crystallite size of over 10 nm.

Structure Identification in High-Resolution Transmission Electron Microscopic Images

DEFF Research Database (Denmark)

Vestergaard, Jacob Schack; Kling, Jens; Dahl, Anders Bjorholm

2014-01-01

A connection between microscopic structure and macroscopic properties is expected for almost all material systems. High-resolution transmission electron microscopy is a technique offering insight into the atomic structure, but the analysis of large image series can be time consuming. The present ...

Structure analysis of OmpC, one of the major proteins in the outer membrane of E. coli, by high resolution electron microscopy

International Nuclear Information System (INIS)

Chang, C.F.

1983-07-01

This dissertation is concerned with the structure analysis of a pore-forming membrane protein, OmpC, which is one of the major proteins in the outer membrane of Escherichia coli. In order to obtain structural information it was necessary to develop a suitable technique for preparing two-dimensional crystalline arrays of this membrane protein in an unfixed, unstained and hydrated condition. Electron micrographs were recorded at exposures of less than 5 electrons/A 2 in order to avoid severe radiation damage. The resulting images were crystallographically averaged, in order to overcome the statistical limitations associated with the low electron exposures. The resulting images, which extend to a resolution of approx. 13.5 A, lend themselves to a natural interpretation that is consistent with the mass density of protein, water and lipid, prior data from 2-D and 3-D structure studies of negatively stained specimens at approx. = 20 A resolution, and published spectroscopic data on the peptide chain secondary structure

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank.

Science.gov (United States)

Joosten, Robbie P; Joosten, Krista; Cohen, Serge X; Vriend, Gert; Perrakis, Anastassis

2011-12-15

Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystallography on to a wide base of non-crystallographer structure users. We developed new algorithms to allow automatic rebuilding and remodeling of main chain peptide bonds and side chains in crystallographic electron density maps, and incorporated these and further enhancements in the PDB_REDO procedure. Applying the updated PDB_REDO to the oldest, but also to some of the newest models in the PDB, corrects existing modeling errors and brings these models to a higher quality, as judged by standard validation methods. The PDB_REDO database and links to all software are available at http://www.cmbi.ru.nl/pdb_redo. r.joosten@nki.nl; a.perrakis@nki.nl Supplementary data are available at Bioinformatics online.

Oxide nanoparticles in an Al-alloyed oxide dispersion strengthened steel: crystallographic structure and interface with ferrite matrix

Science.gov (United States)

Zhang, Zhenbo; Pantleon, Wolfgang

2017-07-01

Oxide nanoparticles are quintessential for ensuring the extraordinary properties of oxide dispersion strengthened (ODS) steels. In this study, the crystallographic structure of oxide nanoparticles, and their interface with the ferritic steel matrix in an Al-alloyed ODS steel, i.e. PM2000, were systematically investigated by high-resolution transmission electron microscopy. The majority of oxide nanoparticles were identified to be orthorhombic YAlO3. During hot consolidation and extrusion, they develop a coherent interface and a near cuboid-on-cube orientation relationship with the ferrite matrix in the material. After annealing at 1200 °C for 1 h, however, the orientation relationship between the oxide nanoparticles and the matrix becomes arbitrary, and their interface mostly incoherent. Annealing at 1300 °C leads to considerable coarsening of oxide nanoparticles, and a new orientation relationship of pseudo-cube-on-cube between oxide nanoparticles and ferrite matrix develops. The reason for the developing interfaces and orientation relationships between oxide nanoparticles and ferrite matrix under different conditions is discussed.

Crystallographic contribution to the formation of the columnar grain structure in cobalt films

International Nuclear Information System (INIS)

Hara, K.; Itoh, K.; Okamoto, K.; Hashimoto, T.

1996-01-01

In order to clarify the crystallographic contribution to the formation of the columnar grain structure, the geometric and crystallographic alignments of columnar grains in cobalt films were investigated on the basis of magnetic and optical measurements. The films were deposited by sputtering at an incidence angle of 45 on glass substrates heated at 332 K. The film thickness ranged from 20 to 850 nm. Above 50 nm the columnar grains align in the direction parallel to the incidence plane and form a two-degree crystallographic orientation. The packing density of columnar grains decreases with increasing thickness when the thickness exceeds 50 nm. From these results we conclude that the crystal habit appearing on column tops induces the two-degree orientation through geometric selection and aligns the selected columnar grains in the parallel direction. (orig.)

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

International Nuclear Information System (INIS)

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-01-01

A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

Energy Technology Data Exchange (ETDEWEB)

McGreevy, Ryan; Singharoy, Abhishek [University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); Li, Qufei [The University of Chicago, Chicago, IL 60637 (United States); Zhang, Jingfen; Xu, Dong [University of Missouri, Columbia, MO 65211 (United States); Perozo, Eduardo [The University of Chicago, Chicago, IL 60637 (United States); Schulten, Klaus, E-mail: kschulte@ks.uiuc.edu [University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States)

2014-09-01

A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

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

Science.gov (United States)

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

2017-06-01

Hydrogels are widely used as matrices for cell growth due to the their tuneable chemical and physical properties, which mimic the extracellular matrix of natural tissue. The microfabrication of hydrogels into arbitrarily complex 3D structures is becoming essential for numerous biological applications, and in particular for investigating the correlation between cell shape and cell function in a 3D environment. Micrometric and sub-micrometric resolution hydrogel scaffolds are required to deeply investigate molecular mechanisms behind cell-matrix interaction and downstream cellular processes. We report the design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking. Hydrated structures of lateral linewidth down to 0.5µm, lateral and axial resolution down to a few µm are demonstrated. According to the processing parameters, different degrees of polymerization are obtained, resulting in hydrated scaffolds of variable swelling and deformation. The 3D hydrogels are biocompatible and promote cell adhesion and migration. Interestingly, according to the polymerization degree, 3D hydrogel woodpile structures show variable extent of cell adhesion and invasion. Human BJ cell lines show capability of deforming 3D micrometric resolved hydrogel structures. The design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking is reported. Significantly, topological and mechanical conditions of polymerized gelatin structures were suitable for cell accommodation in the volume of the woodpiles, leading to a cell density per unit area comparable to the bare substrate. The fabricated structures, presenting micrometric features of high resolution, are actively deformed by cells, both in terms of cell invasion within rods and of cell attachment in-between contiguous woodpiles. Possible biological targets for this 3D approach are customized 3D tissue models, or studies of cell adhesion

High-Resolution Reciprocal Space Mapping for Characterizing Deformation Structures

DEFF Research Database (Denmark)

Pantleon, Wolfgang; Wejdemann, Christian; Jakobsen, Bo

2014-01-01

With high-angular resolution three-dimensional X-ray diffraction (3DXRD), quantitative information is gained about dislocation structures in individual grains in the bulk of a macroscopic specimen by acquiring reciprocal space maps. In high-resolution 3D reciprocal space maps of tensile......-deformed copper, individual, almost dislocation-free subgrains are identified from high-intensity peaks and distinguished by their unique combination of orientation and elastic strain; dislocation walls manifest themselves as a smooth cloud of lower intensity. The elastic strain shows only minor variations within...... dynamics is followed in situ during varying loading conditions by reciprocal space mapping: during uninterrupted tensile deformation, formation of subgrains is observed concurrently with broadening of Bragg reflections shortly after the onset of plastic deformation. When the traction is terminated, stress...

High-resolution EELS investigation of the electronic structure of ilmenites

NARCIS (Netherlands)

Radtke, G.; Lazar, S.; Botton, G.A.

2006-01-01

The electronic structure of a series of compounds belonging to the ilmenite family is investigated using high resolution electron energy loss spectroscopy (EELS). The energy loss near edge structure (ELNES) of the O-K, Ti-L23 and transition metal L23 edges have been recorded in MnTiO3, FeTiO3,

Can Morphing Methods Predict Intermediate Structures?

Science.gov (United States)

Weiss, Dahlia R.; Levitt, Michael

2009-01-01

Movement is crucial to the biological function of many proteins, yet crystallographic structures of proteins can give us only a static snapshot. The protein dynamics that are important to biological function often happen on a timescale that is unattainable through detailed simulation methods such as molecular dynamics as they often involve crossing high-energy barriers. To address this coarse-grained motion, several methods have been implemented as web servers in which a set of coordinates is usually linearly interpolated from an initial crystallographic structure to a final crystallographic structure. We present a new morphing method that does not extrapolate linearly and can therefore go around high-energy barriers and which can produce different trajectories between the same two starting points. In this work, we evaluate our method and other established coarse-grained methods according to an objective measure: how close a coarse-grained dynamics method comes to a crystallographically determined intermediate structure when calculating a trajectory between the initial and final crystal protein structure. We test this with a set of five proteins with at least three crystallographically determined on-pathway high-resolution intermediate structures from the Protein Data Bank. For simple hinging motions involving a small conformational change, segmentation of the protein into two rigid sections outperforms other more computationally involved methods. However, large-scale conformational change is best addressed using a nonlinear approach and we suggest that there is merit in further developing such methods. PMID:18996395

Crystallographic Analysis of Nucleation at Hardness Indentations in High-Purity Aluminum

DEFF Research Database (Denmark)

Xu, Chaoling; Zhang, Yubin; Lin, Fengxiang

2016-01-01

Nucleation at Vickers hardness indentations has been studied in high-purity aluminum cold-rolled 12 pct. Electron channeling contrast was used to measure the size of the indentations and to detect nuclei, while electron backscattering diffraction was used to determine crystallographic orientations....... It is found that indentations are preferential nucleation sites. The crystallographic orientations of the deformed grains affect the hardness and the nucleation potentials at the indentations. Higher hardness gives increased nucleation probabilities. Orientation relationships between nuclei developed...... they form. Finally, possible nucleation mechanisms are briefly discussed....

A preliminary neutron crystallographic study of proteinase K at pD 6.5

Energy Technology Data Exchange (ETDEWEB)

Gardberg, Anna S [ORNL; Blakeley, Matthew P. [Institut Laue-Langevin (ILL); Myles, Dean A A [ORNL

2009-01-01

AbstractA preliminary neutron crystallographic study of the proteolytic enzyme proteinase K is presented. Large hydrogenated crystals were prepared in deuterated crystallization buffer using the vapour-diffusion method. Data were collected to a resolution of 2.3 on the LADI-III diffractometer at the Institut Laue Langevin (ILL) in 2.5 days. The results demonstrate the feasibility of a full neutron crystallographic analysis of this structure aimed at providing relevant information on the location of H atoms, particularly at the active site. This information will contribute to further understanding of the molecular mechanisms underlying proteinase K's catalytic activity and to an enriched understanding of the subtilisin clan of serine proteases.

1.55 Å resolution X-ray crystal structure of Rv3902c from Mycobacterium tuberculosis

Energy Technology Data Exchange (ETDEWEB)

Reddy, Bharat G.; Moates, Derek B. [University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35233 (United States); Kim, Heung-Bok [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Green, Todd J. [University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35233 (United States); Kim, Chang-Yub; Terwilliger, Thomas C. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); DeLucas, Lawrence J., E-mail: duke2@uab.edu [University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35233 (United States)

2014-03-25

The 1.55 Å resolution X-ray crystal structure of Rv3902c from M. tuberculosis reveals a novel fold. The crystallographic structure of the Mycobacterium tuberculosis (TB) protein Rv3902c (176 residues; molecular mass of 19.8 kDa) was determined at 1.55 Å resolution. The function of Rv3902c is unknown, although several TB genes involved in bacterial pathogenesis are expressed from the operon containing the Rv3902c gene. The unique structural fold of Rv3902c contains two domains, each consisting of antiparallel β-sheets and α-helices, creating a hand-like binding motif with a small binding pocket in the palm. Structural homology searches reveal that Rv3902c has an overall structure similar to that of the Salmonella virulence-factor chaperone InvB, with an r.m.s.d. for main-chain atoms of 2.3 Å along an aligned domain.

1.55 Å resolution X-ray crystal structure of Rv3902c from Mycobacterium tuberculosis

International Nuclear Information System (INIS)

Reddy, Bharat G.; Moates, Derek B.; Kim, Heung-Bok; Green, Todd J.; Kim, Chang-Yub; Terwilliger, Thomas C.; DeLucas, Lawrence J.

2014-01-01

The 1.55 Å resolution X-ray crystal structure of Rv3902c from M. tuberculosis reveals a novel fold. The crystallographic structure of the Mycobacterium tuberculosis (TB) protein Rv3902c (176 residues; molecular mass of 19.8 kDa) was determined at 1.55 Å resolution. The function of Rv3902c is unknown, although several TB genes involved in bacterial pathogenesis are expressed from the operon containing the Rv3902c gene. The unique structural fold of Rv3902c contains two domains, each consisting of antiparallel β-sheets and α-helices, creating a hand-like binding motif with a small binding pocket in the palm. Structural homology searches reveal that Rv3902c has an overall structure similar to that of the Salmonella virulence-factor chaperone InvB, with an r.m.s.d. for main-chain atoms of 2.3 Å along an aligned domain

Integration of High-Resolution Laser Displacement Sensors and 3D Printing for Structural Health Monitoring

Directory of Open Access Journals (Sweden)

Shu-Wei Chang

2017-12-01

Full Text Available This paper presents a novel experimental design for complex structural health monitoring (SHM studies achieved by integrating 3D printing technologies, high-resolution laser displacement sensors, and multiscale entropy SHM theory. A seven-story structure with a variety of composite bracing systems was constructed using a dual-material 3D printer. A wireless Bluetooth vibration speaker was used to excite the ground floor of the structure, and high-resolution laser displacement sensors (1-μm resolution were used to monitor the displacement history on different floors. Our results showed that the multiscale entropy SHM method could detect damage on the 3D-printed structures. The results of this study demonstrate that integrating 3D printing technologies and high-resolution laser displacement sensors enables the design of cheap, fast processing, complex, small-scale civil structures for future SHM studies. The novel experimental design proposed in this study provides a suitable platform for investigating the validity and sensitivity of SHM in different composite structures and damage conditions for real life applications in the future.

Integration of High-Resolution Laser Displacement Sensors and 3D Printing for Structural Health Monitoring.

Science.gov (United States)

Chang, Shu-Wei; Lin, Tzu-Kang; Kuo, Shih-Yu; Huang, Ting-Hsuan

2017-12-22

This paper presents a novel experimental design for complex structural health monitoring (SHM) studies achieved by integrating 3D printing technologies, high-resolution laser displacement sensors, and multiscale entropy SHM theory. A seven-story structure with a variety of composite bracing systems was constructed using a dual-material 3D printer. A wireless Bluetooth vibration speaker was used to excite the ground floor of the structure, and high-resolution laser displacement sensors (1-μm resolution) were used to monitor the displacement history on different floors. Our results showed that the multiscale entropy SHM method could detect damage on the 3D-printed structures. The results of this study demonstrate that integrating 3D printing technologies and high-resolution laser displacement sensors enables the design of cheap, fast processing, complex, small-scale civil structures for future SHM studies. The novel experimental design proposed in this study provides a suitable platform for investigating the validity and sensitivity of SHM in different composite structures and damage conditions for real life applications in the future.

Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus.

Science.gov (United States)

Organtini, Lindsey J; Lee, Hyunwook; Iketani, Sho; Huang, Kai; Ashley, Robert E; Makhov, Alexander M; Conway, James F; Parrish, Colin R; Hafenstein, Susan

2016-11-01

Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM. Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Free radicals. High-resolution spectroscopy and molecular structure

International Nuclear Information System (INIS)

Hirota, E.

1983-01-01

High-resolution, high-sensitivity spectroscopy using CW laser and microwave sources has been applied to free radicals and transient molecules to establish their existence and to explore their properties in detail. The radicals studied were mainly generated by discharge-induced reactions. A few molecules are used as typical examples to illustrate the results so far obtained. The molecular and electronic structures of free radicals, intramolecular motions of large amplitudes in some labile molecules, and metastable electronic states of carbenes are given special emphasis. The significance of the present spectroscopic results in other related fields such as astronomy and atmospheric chemistry is stressed. 4 figures, 3 tables

Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.

Science.gov (United States)

Huschmann, Franziska U; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S; Mueller, Uwe

2016-05-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein-ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin-fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity.

Structures of endothiapepsin–fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library

Science.gov (United States)

Huschmann, Franziska U.; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S.; Mueller, Uwe

2016-01-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein–ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin–fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity. PMID:27139825

Automated Structure Solution with the PHENIX Suite

Energy Technology Data Exchange (ETDEWEB)

Zwart, Peter H.; Zwart, Peter H.; Afonine, Pavel; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei; Ioerger, Tom R.; McCoy, A.J.; McKee, Eric; Moriarty, Nigel; Read, Randy J.; Sacchettini, James C.; Sauter, Nicholas K.; Storoni, L.C.; Terwilliger, Tomas C.; Adams, Paul D.

2008-06-09

Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix.refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

Automated structure solution with the PHENIX suite

Energy Technology Data Exchange (ETDEWEB)

Terwilliger, Thomas C [Los Alamos National Laboratory; Zwart, Peter H [LBNL; Afonine, Pavel V [LBNL; Grosse - Kunstleve, Ralf W [LBNL

2008-01-01

Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution, and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template- and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix. refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

The Crystallographic Information File (CIF

Directory of Open Access Journals (Sweden)

I D Brown

2006-11-01

Full Text Available The Crystallographic Information File (CIF, owned by the International Union of Crystallography, is a file structure based on tag-value ASCII pairs with tags defined in machine-readable dictionaries. The crystallographic community publishes and archives large quantities of numeric information generated by crystal structure determinations, and CIF's acceptance was assured by its adoption as the submission format for Acta Crystallographica and by the obvious needs of the community. CIF's strength lies in its dictionaries, which define most of the concepts of crystallography; its weakness is the difficulty of writing software that exploits its full potential.

Criteria to Extract High-Quality Protein Data Bank Subsets for Structure Users.

Science.gov (United States)

Carugo, Oliviero; Djinović-Carugo, Kristina

2016-01-01

It is often necessary to build subsets of the Protein Data Bank to extract structural trends and average values. For this purpose it is mandatory that the subsets are non-redundant and of high quality. The first problem can be solved relatively easily at the sequence level or at the structural level. The second, on the contrary, needs special attention. It is not sufficient, in fact, to consider the crystallographic resolution and other feature must be taken into account: the absence of strings of residues from the electron density maps and from the files deposited in the Protein Data Bank; the B-factor values; the appropriate validation of the structural models; the quality of the electron density maps, which is not uniform; and the temperature of the diffraction experiments. More stringent criteria produce smaller subsets, which can be enlarged with more tolerant selection criteria. The incessant growth of the Protein Data Bank and especially of the number of high-resolution structures is allowing the use of more stringent selection criteria, with a consequent improvement of the quality of the subsets of the Protein Data Bank.

Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures

Energy Technology Data Exchange (ETDEWEB)

McLean, Larry R.; Zhang, Ying; Degnen, William; Peppard, Jane; Cabel, Dasha; Zou, Chao; Tsay, Joseph T.; Subramaniam, Arun; Vaz, Roy J.; Li, Yi (Sanofi)

2010-10-28

Amino-benzoic acid derivatives 1-4 were found to be inhibitors for DHODH by virtual screening, biochemical, and X-ray crystallographic studies. X-ray structures showed that 1 and 2 bind to DHODH as predicted by virtual screening, but 3 and 4 were found to be structurally different from the corresponding compounds initially identified by virtual screening.

Neutron crystallographic studies of amino acids and nucleic acids

International Nuclear Information System (INIS)

Kashiwagi, Tatsuki

2014-01-01

Neutron crystallographic studies of two representative umami materials were executed utilizing iBLX at MLF/J-PARC. The results of them will be summarized in this report. At first, structure analysis of the alpha form crystal of L-glutamic acid was performed in order to assess the usefulness of neutron crystallography at iBIX to our company's R and D. Neutron crystal structure of it was successfully determined at 0.6 A resolution. All hydrogen atoms were clearly observed. Next, the mixed crystal of disodium Inosine-5'-phosphate (IMP · 2Na) and disodium Guanosine-5'-phosphate (GMP · 2Na) was analyzed by neutron crystallography. Neutron crystal structure of the mixed crystal of IMP and GMP (IM/GMP rate = 1.7) was successfully determined at 0.8 A resolution. In the neutron crystal structure of the mixed crystal, the hydrogen atom bonded to the C2 atom of purine base in IMP and the nitrogen atom bonded to the C2 atom of purine base in GMP were clearly observed in the nuclear density map, structurally demonstrating that this crystal is the mixed crystal. (author)

Evaluation of variability in high-resolution protein structures by global distance scoring

Directory of Open Access Journals (Sweden)

Risa Anzai

2018-01-01

Full Text Available Systematic analysis of the statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of high-resolution structures is important because it can provide mechanistic details behind the functional properties of protein families, enabling rational comparison between families. Most of the current structural comparisons are pairwise-based, which hampers the global analysis of increasing contents in the Protein Data Bank. Additionally, pairing of protein structures introduces uncertainty with respect to reproducibility because it frequently accompanies other settings for superimposition. This study introduces intramolecular distance scoring for the global analysis of proteins, for each of which at least several high-resolution structures are available. As a pilot study, we have tested 300 human proteins and showed that the method is comprehensively used to overview advances in each protein and protein family at the atomic level. This method, together with the interpretation of the model calculations, provide new criteria for understanding specific structural variation in a protein, enabling global comparison of the variability in proteins from different species.

Evaluation of variability in high-resolution protein structures by global distance scoring.

Science.gov (United States)

Anzai, Risa; Asami, Yoshiki; Inoue, Waka; Ueno, Hina; Yamada, Koya; Okada, Tetsuji

2018-01-01

Systematic analysis of the statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of high-resolution structures is important because it can provide mechanistic details behind the functional properties of protein families, enabling rational comparison between families. Most of the current structural comparisons are pairwise-based, which hampers the global analysis of increasing contents in the Protein Data Bank. Additionally, pairing of protein structures introduces uncertainty with respect to reproducibility because it frequently accompanies other settings for superimposition. This study introduces intramolecular distance scoring for the global analysis of proteins, for each of which at least several high-resolution structures are available. As a pilot study, we have tested 300 human proteins and showed that the method is comprehensively used to overview advances in each protein and protein family at the atomic level. This method, together with the interpretation of the model calculations, provide new criteria for understanding specific structural variation in a protein, enabling global comparison of the variability in proteins from different species.

High resolution electron backscatter diffraction (EBSD) data from calcite biominerals in recent gastropod shells.

Science.gov (United States)

Pérez-Huerta, Alberto; Dauphin, Yannicke; Cuif, Jean Pierre; Cusack, Maggie

2011-04-01

Electron backscatter diffraction (EBSD) is a microscopy technique that reveals in situ crystallographic information. Currently, it is widely used for the characterization of geological materials and in studies of biomineralization. Here, we analyze high resolution EBSD data from biogenic calcite in two mollusk taxa, Concholepas and Haliotis, previously used in the understanding of complex biomineralization and paleoenvironmental studies. Results indicate that Concholepas has less ordered prisms than in Haliotis, and that in Concholepas the level of order is not homogenous in different areas of the shell. Overall, the usefulness of data integration obtained from diffraction intensity and crystallographic orientation maps, and corresponding pole figures, is discussed as well as its application to similar studies. © 2010 Elsevier Ltd. All rights reserved.

Crystallographic changes in lead zirconate titanate due to neutron irradiation

Directory of Open Access Journals (Sweden)

Alexandra Henriques

2014-11-01

Full Text Available Piezoelectric and ferroelectric materials are useful as the active element in non-destructive monitoring devices for high-radiation areas. Here, crystallographic structural refinement (i.e., the Rietveld method is used to quantify the type and extent of structural changes in PbZr0.5Ti0.5O3 after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 1015 neutrons/cm2. The results show a measurable decrease in the occupancy of Pb and O due to irradiation, with O vacancies in the tetragonal phase being created preferentially on one of the two O sites. The results demonstrate a method by which the effects of radiation on crystallographic structure may be investigated.

Crystallographic Topology 2: Overview and Work in Progress

Energy Technology Data Exchange (ETDEWEB)

Johnson, C.K.

1999-08-01

This overview describes an application of contemporary geometric topology and stochastic process concepts to structural crystallography. In this application, crystallographic groups become orbifolds, crystal structures become Morse functions on orbifolds, and vibrating atoms in a crystal become vector valued Gaussian measures with the Radon-Nikodym property. Intended crystallographic benefits include new methods for visualization of space groups and crystal structures, analysis of the thermal motion patterns seen in ORTEP drawings, and a classification scheme for crystal structures based on their Heegaard splitting properties.

Cluster Analysis of Time-Dependent Crystallographic Data: Direct Identification of Time-Independent Structural Intermediates

Science.gov (United States)

Kostov, Konstantin S.; Moffat, Keith

2011-01-01

The initial output of a time-resolved macromolecular crystallography experiment is a time-dependent series of difference electron density maps that displays the time-dependent changes in underlying structure as a reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which these intermediates interconvert; and thereby to elucidate a chemical kinetic mechanism. One strategy toward achieving this goal is to use cluster analysis, a statistical method that groups objects based on their similarity. If the difference electron density at a particular voxel in the time-dependent difference electron density (TDED) maps is sensitive to the presence of one and only one intermediate, then its temporal evolution will exactly parallel the concentration profile of that intermediate with time. The rationale is therefore to cluster voxels with respect to the shapes of their TDEDs, so that each group or cluster of voxels corresponds to one structural intermediate. Clusters of voxels whose TDEDs reflect the presence of two or more specific intermediates can also be identified. From such groupings one can then infer the number of intermediates, obtain their time-independent difference density characteristics, and refine the structure of each intermediate. We review the principles of cluster analysis and clustering algorithms in a crystallographic context, and describe the application of the method to simulated and experimental time-resolved crystallographic data for the photocycle of photoactive yellow protein. PMID:21244840

In-situ investigations of structural changes during cyclic loading by high resolution reciprocal space mapping

DEFF Research Database (Denmark)

Diederichs, Annika M.; Thiel, Felix; Lienert, Ulrich

2017-01-01

dislocation structures can be identified using advanced electron microscopy and synchrotron techniques. A detailed characterization of the microstructure during cyclic loading by in-situ monitoring the internal structure within individual grains with high energy x-rays can help to understand and predict...... the materials behavior during cyclic deformation and to improve the material design. While monitoring macroscopic stress and strain during cyclic loading, reciprocal space maps of diffraction peaks from single grains are obtained with high resolution. High Resolution Reciprocal Space Mapping was applied...

Structural characterization of suppressor lipids by high-resolution mass spectrometry

DEFF Research Database (Denmark)

Rovillos, Mary Joy; Pauling, Josch Konstantin; Hannibal-Bach, Hans Kristian

2016-01-01

RATIONALE: Suppressor lipids were originally identified in 1993 and reported to encompass six lipid classes that enable Saccharomyces cerevisiae to live without sphingolipids. Structural characterization, using non-mass spectrometric approaches, revealed that these suppressor lipids are very long...... chain fatty acid (VLCFA)-containing glycerophospholipids with polar head groups that are typically incorporated into sphingolipids. Here we report, for the first time, the structural characterization of the yeast suppressor lipids using high-resolution mass spectrometry. METHODS: Suppressor lipids were...... isolated by preparative chromatography and subjected to structural characterization using hybrid quadrupole time-of-flight and ion trap-orbitrap mass spectrometry. RESULTS: Our investigation recapitulates the overall structural features of the suppressor lipids and provides an in-depth characterization...

High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1

International Nuclear Information System (INIS)

Jacobsen, Julian O. B.; Allen, Mark D.; Freund, Stefan M. V.; Bycroft, Mark

2016-01-01

In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and the C-terminal RNA-binding domain of S. cerevisiae Tho1 have been determined. THO is a multi-protein complex involved in the formation of messenger ribonuclear particles (mRNPs) by coupling transcription with mRNA processing and export. THO is thought to be formed from five subunits, Tho2p, Hpr1p, Tex1p, Mft1p and Thp2p, and recent work has determined a low-resolution structure of the complex [Poulsen et al. (2014 ▸), PLoS One, 9, e103470]. A number of additional proteins are thought to be involved in the formation of mRNP in yeast, including Tho1, which has been shown to bind RNA in vitro and is recruited to actively transcribed chromatin in vivo in a THO-complex and RNA-dependent manner. Tho1 is known to contain a SAP domain at the N-terminus, but the ability to suppress the expression defects of the hpr1Δ mutant of THO was shown to reside in the RNA-binding C-terminal region. In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and C-terminal RNA-binding domain have been determined

High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1

Energy Technology Data Exchange (ETDEWEB)

Jacobsen, Julian O. B.; Allen, Mark D.; Freund, Stefan M. V.; Bycroft, Mark, E-mail: mxb@mrc-lmb.cam.ac.uk [MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom)

2016-05-23

In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and the C-terminal RNA-binding domain of S. cerevisiae Tho1 have been determined. THO is a multi-protein complex involved in the formation of messenger ribonuclear particles (mRNPs) by coupling transcription with mRNA processing and export. THO is thought to be formed from five subunits, Tho2p, Hpr1p, Tex1p, Mft1p and Thp2p, and recent work has determined a low-resolution structure of the complex [Poulsen et al. (2014 ▸), PLoS One, 9, e103470]. A number of additional proteins are thought to be involved in the formation of mRNP in yeast, including Tho1, which has been shown to bind RNA in vitro and is recruited to actively transcribed chromatin in vivo in a THO-complex and RNA-dependent manner. Tho1 is known to contain a SAP domain at the N-terminus, but the ability to suppress the expression defects of the hpr1Δ mutant of THO was shown to reside in the RNA-binding C-terminal region. In this study, high-resolution structures of both the N-terminal DNA-binding SAP domain and C-terminal RNA-binding domain have been determined.

Homogenization-based topology optimization for high-resolution manufacturable micro-structures

DEFF Research Database (Denmark)

Groen, Jeroen Peter; Sigmund, Ole

2018-01-01

This paper presents a projection method to obtain high-resolution, manufacturable structures from efficient and coarse-scale, homogenization-based topology optimization results. The presented approach bridges coarse and fine scale, such that the complex periodic micro-structures can be represented...... by a smooth and continuous lattice on the fine mesh. A heuristic methodology allows control of the projected topology, such that a minimum length-scale on both solid and void features is ensured in the final result. Numerical examples show excellent behavior of the method, where performances of the projected...

Deriving the ultrastructure of α-crustacyanin using lower-resolution structural and biophysical methods

International Nuclear Information System (INIS)

Rhys, Natasha H.; Wang, Ming-Chuan; Jowitt, Thomas A.; Helliwell, John R.; Grossmann, J. Günter; Baldock, Clair

2011-01-01

The structure of α-crustacyanin has been determined to 30 Å resolution using negative-stain electron microscopy (EM) single-particle averaging and modelling with the β-crustacyanin dimer from the crystal structure (Protein Data Bank code), guided by PISA protein subunit interface calculations, and compared with the protein arrangements observed in the crystal lattice. This α-crustacyanin EM model has been checked against SAXS experimental data, including comparison with rigid-body models calculated from the SAXS data, and finally with analytical ultracentrifugation measurements. The low-resolution structure of α-crustacyanin has been determined to 30 Å resolution using negative-stain electron microscopy (EM) with single-particle averaging. The protein, which is an assembly of eight β-crustacyanin dimers, appears asymmetrical and rather open in layout. A model was built to the EM map using the X-ray crystallographic structure of β-crustacyanin guided by PISA interface analyses. The model has a theoretical sedimentation coefficient that matches well with the experimentally derived value from sedimentation velocity analytical ultracentrifugation. Additionally, the EM model has similarities to models calculated independently by rigid-body modelling to small-angle X-ray scattering (SAXS) data and extracted in silico from the β-crustacyanin crystal lattice. Theoretical X-ray scattering from each of these models is in reasonable agreement with the experimental SAXS data and together suggest an overall design for the α-crustacyanin assembly

Crystallographic Mapping of Guided Nanowires by Second Harmonic Generation Polarimetry.

Science.gov (United States)

Neeman, Lior; Ben-Zvi, Regev; Rechav, Katya; Popovitz-Biro, Ronit; Oron, Dan; Joselevich, Ernesto

2017-02-08

The growth of horizontal nanowires (NWs) guided by epitaxial and graphoepitaxial relations with the substrate is becoming increasingly attractive owing to the possibility of controlling their position, direction, and crystallographic orientation. In guided NWs, as opposed to the extensively characterized vertically grown NWs, there is an increasing need for understanding the relation between structure and properties, specifically the role of the epitaxial relation with the substrate. Furthermore, the uniformity of crystallographic orientation along guided NWs and over the substrate has yet to be checked. Here we perform highly sensitive second harmonic generation (SHG) polarimetry of polar and nonpolar guided ZnO NWs grown on R-plane and M-plane sapphire. We optically map large areas on the substrate in a nondestructive way and find that the crystallographic orientations of the guided NWs are highly selective and specific for each growth direction with respect to the substrate lattice. In addition, we perform SHG polarimetry along individual NWs and find that the crystallographic orientation is preserved along the NW in both polar and nonpolar NWs. While polar NWs show highly uniform SHG along their axis, nonpolar NWs show a significant change in the local nonlinear susceptibility along a few micrometers, reflected in a reduction of 40% in the ratio of the SHG along different crystal axes. We suggest that these differences may be related to strain accumulation along the nonpolar wires. We find SHG polarimetry to be a powerful tool to study both selectivity and uniformity of crystallographic orientations of guided NWs with different epitaxial relations.

An Optimized, Grid Independent, Narrow Band Data Structure for High Resolution Level Sets

DEFF Research Database (Denmark)

Nielsen, Michael Bang; Museth, Ken

2004-01-01

enforced by the convex boundaries of an underlying cartesian computational grid. Here we present a novel very memory efficient narrow band data structure, dubbed the Sparse Grid, that enables the representation of grid independent high resolution level sets. The key features our new data structure are...

Crystallographic tilt and in-plane anisotropies of an a-plane InGaN/GaN layered structure grown by MOCVD on r-plane sapphire using a ZnO buffer

International Nuclear Information System (INIS)

Liu, H F; Chi, D Z; Liu, W; Guo, S

2016-01-01

High-resolution x-ray diffraction (HRXRD) was used to investigate the crystallographic tilts and structural anisotropies in epitaxial nonpolar a-plane InGaN/GaN grown by metal–organic chemical vapor deposition on r-plane sapphire using a ZnO buffer. The substrate had an unintentional miscut of 0.14° towards its [–4 2 2 3] axis. However, HRXRD revealed a tilt of 0.26° (0.20°) between the ZnO (GaN) (11-20) and the Al 2 O 3 (1-102) atomic planes, with the (11-20) axis of ZnO (GaN) tilted towards its c-axis, which has a difference of 163° in azimuth from that of the substrate’s miscut. Excess broadenings in the GaN/ZnO (11-20) rocking curves (RCs) were observed along its c-axis. Specific analyses revealed that partial dislocations and anisotropic in-plane strains, rather than surface-related effects, wafer curvature or stacking faults, are the dominant factors for the structural anisotropy. The orientation of the partial dislocations is most likely affected by the miscut of the substrate, e.g. via tilting of the misfit dislocation gliding planes created during island coalescences. Their Burgers vector components in the growth direction, in turn, gave rise to crystallographic tilts in the same direction as that of the excess RC-broadenings. (paper)

Crystallographic tilt and in-plane anisotropies of an a-plane InGaN/GaN layered structure grown by MOCVD on r-plane sapphire using a ZnO buffer

Science.gov (United States)

Liu, H. F.; Liu, W.; Guo, S.; Chi, D. Z.

2016-03-01

High-resolution x-ray diffraction (HRXRD) was used to investigate the crystallographic tilts and structural anisotropies in epitaxial nonpolar a-plane InGaN/GaN grown by metal-organic chemical vapor deposition on r-plane sapphire using a ZnO buffer. The substrate had an unintentional miscut of 0.14° towards its [-4 2 2 3] axis. However, HRXRD revealed a tilt of 0.26° (0.20°) between the ZnO (GaN) (11-20) and the Al2O3 (1-102) atomic planes, with the (11-20) axis of ZnO (GaN) tilted towards its c-axis, which has a difference of 163° in azimuth from that of the substrate’s miscut. Excess broadenings in the GaN/ZnO (11-20) rocking curves (RCs) were observed along its c-axis. Specific analyses revealed that partial dislocations and anisotropic in-plane strains, rather than surface-related effects, wafer curvature or stacking faults, are the dominant factors for the structural anisotropy. The orientation of the partial dislocations is most likely affected by the miscut of the substrate, e.g. via tilting of the misfit dislocation gliding planes created during island coalescences. Their Burgers vector components in the growth direction, in turn, gave rise to crystallographic tilts in the same direction as that of the excess RC-broadenings.

Characterization of Crystallographic Structures Using Bragg-Edge Neutron Imaging at the Spallation Neutron Source

Directory of Open Access Journals (Sweden)

Gian Song

2017-12-01

Full Text Available Over the past decade, wavelength-dependent neutron radiography, also known as Bragg-edge imaging, has been employed as a non-destructive bulk characterization method due to its sensitivity to coherent elastic neutron scattering that is associated with crystalline structures. Several analysis approaches have been developed to quantitatively determine crystalline orientation, lattice strain, and phase distribution. In this study, we report a systematic investigation of the crystal structures of metallic materials (such as selected textureless powder samples and additively manufactured (AM Inconel 718 samples, using Bragg-edge imaging at the Oak Ridge National Laboratory (ORNL Spallation Neutron Source (SNS. Firstly, we have implemented a phenomenological Gaussian-based fitting in a Python-based computer called iBeatles. Secondly, we have developed a model-based approach to analyze Bragg-edge transmission spectra, which allows quantitative determination of the crystallographic attributes. Moreover, neutron diffraction measurements were carried out to validate the Bragg-edge analytical methods. These results demonstrate that the microstructural complexity (in this case, texture plays a key role in determining the crystallographic parameters (lattice constant or interplanar spacing, which implies that the Bragg-edge image analysis methods must be carefully selected based on the material structures.

High-Resolution Structural Monitoring of Ionospheric Absorption Events

Science.gov (United States)

2013-07-01

7 riometry. Incorporation of an outrigger site, to enable treatment of the unknown structure of the celestial background and the effects of...riometry. Incorporation of an outrigger site, to enable treatment of the unknown structure of the celestial background and the effects of confusion...event captured with this system . Note that, even at this fairly coarse resolution, there is discrete structure that changes in position and strength

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

Science.gov (United States)

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.

Characterization of a defective PbWO4 crystal cut along the a-c crystallographic plane: structural assessment and a novel photoelastic stress analysis

Science.gov (United States)

Montalto, L.; Natali, P. P.; Daví, F.; Mengucci., P.; Paone, N.; Rinaldi, D.

2017-12-01

Among scintillators, the PWO is one of the most widely used, for instance in CMS calorimeter at CERN and PANDA project. Crystallographic structure and chemical composition as well as residual stress condition, are indicators of homogeneity and good quality of the crystal. In this paper, structural characterization of a defective PbWO4 (PWO) crystal has been performed by X-ray Diffraction (XRD), Energy Dispersive Spectroscopy (EDS) and Photoelasticity in the unusual (a, c) crystallographic plane. XRD and EDS analysis have been used to investigate crystallographic orientation and chemical composition, while stress distribution, which indicates macroscopic inhomogeneities and defects, has been obtained by photoelastic approaches, in Conoscopic and Sphenoscopic configuration. Since the sample is cut along the (a, c) crystallographic plane, a new method is proposed for the interpretation of the fringe pattern. The structural analysis has detected odds from the nominal lattice dimension, which can be attributed to the strong presence of Pb and W. A strong inhomogeneity over the crystal sample has been revealed by the photoelastic inspection. The results give reliability to the proposed procedure which is exploitable in crystals with other structures.

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy

International Nuclear Information System (INIS)

Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R.; Murshudov, Garib N.; Short, Judith M.; Scheres, Sjors H.W.; Henderson, Richard

2013-01-01

Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy

Energy Technology Data Exchange (ETDEWEB)

Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R.; Murshudov, Garib N.; Short, Judith M.; Scheres, Sjors H.W.; Henderson, Richard, E-mail: rh15@mrc-lmb.cam.ac.uk

2013-12-15

Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an

Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling

International Nuclear Information System (INIS)

Knight, Jennifer L.; Zhou, Zhiyong; Gallicchio, Emilio; Himmel, Daniel M.; Friesner, Richard A.; Arnold, Eddy; Levy, Ronald M.

2008-01-01

Torsion-angle sampling, as implemented in the Protein Local Optimization Program (PLOP), is used to generate multiple structurally variable single-conformer models which are in good agreement with X-ray data. An ensemble-refinement approach to differentiate between positional uncertainty and conformational heterogeneity is proposed. Modeling structural variability is critical for understanding protein function and for modeling reliable targets for in silico docking experiments. Because of the time-intensive nature of manual X-ray crystallographic refinement, automated refinement methods that thoroughly explore conformational space are essential for the systematic construction of structurally variable models. Using five proteins spanning resolutions of 1.0–2.8 Å, it is demonstrated how torsion-angle sampling of backbone and side-chain libraries with filtering against both the chemical energy, using a modern effective potential, and the electron density, coupled with minimization of a reciprocal-space X-ray target function, can generate multiple structurally variable models which fit the X-ray data well. Torsion-angle sampling as implemented in the Protein Local Optimization Program (PLOP) has been used in this work. Models with the lowest R free values are obtained when electrostatic and implicit solvation terms are included in the effective potential. HIV-1 protease, calmodulin and SUMO-conjugating enzyme illustrate how variability in the ensemble of structures captures structural variability that is observed across multiple crystal structures and is linked to functional flexibility at hinge regions and binding interfaces. An ensemble-refinement procedure is proposed to differentiate between variability that is a consequence of physical conformational heterogeneity and that which reflects uncertainty in the atomic coordinates

A grid-enabled web service for low-resolution crystal structure refinement.

Science.gov (United States)

O'Donovan, Daniel J; Stokes-Rees, Ian; Nam, Yunsun; Blacklow, Stephen C; Schröder, Gunnar F; Brunger, Axel T; Sliz, Piotr

2012-03-01

Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low-resolution X-ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.

An application of impediography to the high sensitivity and high resolution identification of structural damage

International Nuclear Information System (INIS)

Zhao, L; Yang, J; Semperlotti, F; Wang, K W

2015-01-01

In this study we explore the use of impediographic techniques to perform damage detection in plate-like metal structures. Impediography relies on the piezo-resistive coupling of the host structure to reconstruct high sensitivity and high resolution maps of the internal electrical conductivity. By exploiting localized strain perturbations generated via focused acoustic waves, the piezo-resistive coupling allows extracting a set of linearly independent boundary voltage data that drastically reduces the ill-conditioning of the inverse problem, therefore increasing the performance. The localized perturbation is achieved by leveraging the concept of frequency selective structure (FSS), that is a dynamically tailored structural element enabling the required acoustic focusing via vibration localization. Based on the FSS approach, the impediographic technique is numerically tested to investigate the performance of the combined approach for structural damage detection. The effects of practical implementation issues, such as limited perturbations and limited boundary data, are also explored. (paper)

Preservation of high resolution protein structure by cryo-electron microscopy of vitreous sections

International Nuclear Information System (INIS)

Sader, Kasim; Studer, Daniel; Zuber, Benoit; Gnaegi, Helmut; Trinick, John

2009-01-01

We have quantitated the degree of structural preservation in cryo-sections of a vitrified biological specimen. Previous studies have used sections of periodic specimens to assess the resolution present, but preservation before sectioning was not assessed and so the damage due particularly to cutting was not clear. In this study large single crystals of lysozyme were vitrified and from these X-ray diffraction patterns extending to better than 2.1 A were obtained. The crystals were high pressure frozen in 30% dextran, and cryo-sectioned using a diamond knife. In the best case, preservation to a resolution of 7.9 A was shown by electron diffraction, the first observation of sub-nanometre structural preservation in a vitreous section.

Identification of some crystallographic features of martensite in steels by microdiffraction

International Nuclear Information System (INIS)

Sarikaya, M.; Rao, B.V.N.; Thomas, G.

1980-03-01

Considerable attention should be paid to the interpretation of electron diffraction, such as the understanding of the extra reflections and other effects in an SAD pattern obtained from lath martensite by making allowances for spatial resolution limitations in the SAD patterns. These difficulties can be overcome by utilizing the convergent beam electron diffraction (CBED) method which permits the use of different probe sizes to obtain crystallographic information from very small regions. Some crystallographic features of lath martensite in low and medium C steels have been identified and some others verified by using CBED

Streptavidin and its biotin complex at atomic resolution

International Nuclear Information System (INIS)

Le Trong, Isolde; Wang, Zhizhi; Hyre, David E.; Lybrand, Terry P.; Stayton, Patrick S.; Stenkamp, Ronald E.

2011-01-01

Analysis of atomic resolution crystal structures of wild-type streptavidin (1.03 Å) and its biotin complex (0.95 Å) indicate the range of conformational states taken on by this protein in the solid state. Most of the structural variation is found in the polypeptide loops between the strands in this β-sandwich protein. Atomic resolution crystallographic studies of streptavidin and its biotin complex have been carried out at 1.03 and 0.95 Å, respectively. The wild-type protein crystallized with a tetramer in the asymmetric unit, while the crystals of the biotin complex contained two subunits in the asymmetric unit. Comparison of the six subunits shows the various ways in which the protein accommodates ligand binding and different crystal-packing environments. Conformational variation is found in each of the polypeptide loops connecting the eight strands in the β-sandwich subunit, but the largest differences are found in the flexible binding loop (residues 45–52). In three of the unliganded subunits the loop is in an ‘open’ conformation, while in the two subunits binding biotin, as well as in one of the unliganded subunits, this loop ‘closes’ over the biotin–binding site. The ‘closed’ loop contributes to the protein’s high affinity for biotin. Analysis of the anisotropic displacement parameters included in the crystallographic models is consistent with the variation found in the loop structures and the view that the dynamic nature of the protein structure contributes to the ability of the protein to bind biotin so tightly

A new class of HIV-1 protease inhibitor: the crystallographic structure, inhibition and chemical synthesis of an aminimide peptide isostere.

Science.gov (United States)

Rutenber, E E; McPhee, F; Kaplan, A P; Gallion, S L; Hogan, J C; Craik, C S; Stroud, R M

1996-09-01

The essential role of HIV-1 protease (HIV-1 PR) in the viral life cycle makes it an attractive target for the development of substrate-based inhibitors that may find efficacy as anti-AIDS drugs. However, resistance has arisen to potent peptidomimetic drugs necessitating the further development of novel chemical backbones for diversity based chemistry focused on probing the active site for inhibitor interactions and binding modes that evade protease resistance. AQ148 is a potent inhibitor of HIV-1 PR and represents a new class of transition state analogues incorporating an aminimide peptide isostere. A 3-D crystallographic structure of AQ148, a tetrapeptide isostere, has been determined in complex with its target HIV-1 PR to a resolution of 2.5 A and used to evaluate the specific structural determinants of AQ148 potency and to correlate structure-activity relationships within the class of related compounds. AQ148 is a competitive inhibitor of HIV-1 PR with a Ki value of 137 nM. Twenty-nine derivatives have been synthesized and chemical modifications have been made at the P1, P2, P1', and P2' sites. The atomic resolution structure of AQ148 bound to HIV-1 PR reveals both an inhibitor binding mode that closely resembles that of other peptidomimetic inhibitors and specific protein/inhibitor interactions that correlate with structure-activity relationships. The structure provides the basis for the design, synthesis and evaluation of the next generation of hydroxyethyl aminimide inhibitors. The aminimide peptide isostere is a scaffold with favorable biological properties well suited to both the combinatorial methods of peptidomimesis and the rational design of potent and specific substrate-based analogues.

Oxide nanoparticles in an Al-alloyed oxide dispersion strengthened steel: crystallographic structure and interface with ferrite matrix

DEFF Research Database (Denmark)

Zhang, Zhenbo; Pantleon, Wolfgang

2017-01-01

Oxide nanoparticles are quintessential for ensuring the extraordinary properties of oxide dispersion strengthened (ODS) steels. In this study, the crystallographic structure of oxide nanoparticles, and their interface with the ferritic steel matrix in an Al-alloyed ODS steel, i.e. PM2000, were...

Influence of the crystallographic structure of the electrode surface on the structure of the electrical double layer and adsorption of organic molecules

International Nuclear Information System (INIS)

Kochorovski, Z.; Zagorska, I.; Pruzhkovska-Drakhal, R.; Trasatti, S.

1995-01-01

The results of systematic investigation of influence of crystal structure of Bi-, Sb- and Cd-electrode surfaces on regularities of double electric layer structure in aqueous and nonaqueous solutions of surface-nonactive electrolyte are given. Influence of electrode surface characteristics on adsorptive behaviour of different organic molecules has been studied. General regularities of of chemical nature influence and surface crystallographic structure on the double layer structure and on organic compounds adsorption have been established. 57 refs., 7 figs., 4 tabs

Structure recognition from high resolution images of ceramic composites

Energy Technology Data Exchange (ETDEWEB)

Ushizima, Daniela; Perciano, Talita; Krishnan, Harinarayan; Loring, Burlen; Bale, Hrishikesh; Parkinson, Dilworth; Sethian, James

2015-01-05

Fibers provide exceptional strength-to-weight ratio capabilities when woven into ceramic composites, transforming them into materials with exceptional resistance to high temperature, and high strength combined with improved fracture toughness. Microcracks are inevitable when the material is under strain, which can be imaged using synchrotron X-ray computed micro-tomography (mu-CT) for assessment of material mechanical toughness variation. An important part of this analysis is to recognize fibrillar features. This paper presents algorithms for detecting and quantifying composite cracks and fiber breaks from high-resolution image stacks. First, we propose recognition algorithms to identify the different structures of the composite, including matrix cracks and fibers breaks. Second, we introduce our package F3D for fast filtering of large 3D imagery, implemented in OpenCL to take advantage of graphic cards. Results show that our algorithms automatically identify micro-damage and that the GPU-based implementation introduced here takes minutes, being 17x faster than similar tools on a typical image file.

Some non-linear physics in crystallographic structures

International Nuclear Information System (INIS)

Aubry, S.

1977-10-01

A summary of studies on simple but strongly nonlinear crystallographic models that make use of some methods in stochasticity is presented. Two one-dimensional models are described; one has been studied to understand some aspects of the nonlinear dynamics in crystals when close to the transition temperature, the other is for commensurability and incommensurability problems. Periodic orbits and the dynamics of a one-dimensional coupled double-well chain are considered, along with lattice locking and stochasticity

New approaches to high-resolution mapping of marine vertical structures.

Science.gov (United States)

Robert, Katleen; Huvenne, Veerle A I; Georgiopoulou, Aggeliki; Jones, Daniel O B; Marsh, Leigh; D O Carter, Gareth; Chaumillon, Leo

2017-08-21

Vertical walls in marine environments can harbour high biodiversity and provide natural protection from bottom-trawling activities. However, traditional mapping techniques are usually restricted to down-looking approaches which cannot adequately replicate their 3D structure. We combined sideways-looking multibeam echosounder (MBES) data from an AUV, forward-looking MBES data from ROVs and ROV-acquired videos to examine walls from Rockall Bank and Whittard Canyon, Northeast Atlantic. High-resolution 3D point clouds were extracted from each sonar dataset and structure from motion photogrammetry (SfM) was applied to recreate 3D representations of video transects along the walls. With these reconstructions, it was possible to interact with extensive sections of video footage and precisely position individuals. Terrain variables were derived on scales comparable to those experienced by megabenthic individuals. These were used to show differences in environmental conditions between observed and background locations as well as explain spatial patterns in ecological characteristics. In addition, since the SfM 3D reconstructions retained colours, they were employed to separate and quantify live coral colonies versus dead framework. The combination of these new technologies allows us, for the first time, to map the physical 3D structure of previously inaccessible habitats and demonstrates the complexity and importance of vertical structures.

Three sets of crystallographic sub-planar structures in quartz formed by tectonic deformation

Science.gov (United States)

Derez, Tine; Pennock, Gill; Drury, Martyn; Sintubin, Manuel

2016-05-01

In quartz, multiple sets of fine planar deformation microstructures that have specific crystallographic orientations parallel to planes with low Miller-Bravais indices are commonly considered as shock-induced planar deformation features (PDFs) diagnostic of shock metamorphism. Using polarized light microscopy, we demonstrate that up to three sets of tectonically induced sub-planar fine extinction bands (FEBs), sub-parallel to the basal, γ, ω, and π crystallographic planes, are common in vein quartz in low-grade tectonometamorphic settings. We conclude that the observation of multiple (2-3) sets of fine scale, closely spaced, crystallographically controlled, sub-planar microstructures is not sufficient to unambiguously distinguish PDFs from tectonic FEBs.

Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography.

Science.gov (United States)

Li, Qiong; Gluch, Jürgen; Krüger, Peter; Gall, Martin; Neinhuis, Christoph; Zschech, Ehrenfried

2016-10-14

A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have a direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. Copyright © 2016 Elsevier Inc. All rights reserved.

Structure and Evolution of Hawaii's Loihi Seamount from High-resolution Mapping

Science.gov (United States)

Clague, D. A.; Paduan, J. B.; Moyer, C. L.; Glazer, B. T.; Caress, D. W.; Yoerger, D.; Kaiser, C. L.

2016-12-01

Loihi Seamount has been mapped repeatedly using shipboard multibeam sonars with improving resolution over time. Simrad EM302 data with 25m resolution at the 950m summit and 90m at the 5000m base of the volcano were collected from Schmidt Ocean Institute's R/V Falkor in 2014. A contracted multibeam survey in 1997 employing a deep-towed vehicle has 7m resolution for the summit and upper north and south rift zones, but suffered from poor navigation. Woods Hole Oceanographic Institution's AUV Sentry surveyed most of the summit and low-T hydrothermal vents on the base of the south rift in 2013 and 2014. The 2m resolution of most data is more precise than the navigation. The 6 summit surveys were reprocessed using MB-System to remove abundant bad bottom picks and adjust the navigation to produce a spatially accurate map. The 3 summit pits, including Pele's Pit that formed in 1996, are complex collapse structures and nested inside a larger caldera that was modified by large landslides on the east and west summit flanks. The pits cut low shields that once formed a complex of overlapping summit shields, similar to Kilauea before the current caldera formed 1500 to 1790 CE. An 11m section of ash deposits crops out on the east rim of the summit along a caldera-bounding fault and is analogous to Kilauea where the caldera-bounding faults expose ash erupted as the present caldera formed. Most of the Loihi ash section is 3300 to 5880 yr BP, indicating that the larger caldera structure at Loihi is younger than 3300 yr BP. The landslides on the east and west edges of the summit are therefore younger 3300 yr BP. The uppermost south rift has several small pit craters between cones and pillow ridges, also analogous to Kilauea. Two cones near the deep low-T vents are steep pillow mounds with slopes of talus. High-resolution mapping reveals, for the first time, the many similarities between the structure and evolution of submarine Loihi Seamount and subaerial Kilauea Volcano.

High-Resolution Printing of 3D Structures Using an Electrohydrodynamic Inkjet with Multiple Functional Inks.

Science.gov (United States)

An, Byeong Wan; Kim, Kukjoo; Lee, Heejoo; Kim, So-Yun; Shim, Yulhui; Lee, Dae-Young; Song, Jun Yeob; Park, Jang-Ung

2015-08-05

Electrohydrodynamic-inkjet-printed high-resolution complex 3D structures with multiple functional inks are demonstrated. Printed 3D structures can have a variety of fine patterns, such as vertical or helix-shaped pillars and straight or rounded walls, with high aspect ratios (greater than ≈50) and narrow diameters (≈0.7 μm). Furthermore, the formation of freestanding, bridge-like Ag wire structures on plastic substrates suggests substantial potentials as high-precision, flexible 3D interconnects. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystallographic Structure of Human β-Hexosaminidase A: Interpretation of Tay-Sachs Mutations and Loss of GM2 Ganglioside Hydrolysis

Science.gov (United States)

Lemieux, M. Joanne; Mark, Brian L.; Cherney, Maia M.; Withers, Stephen G.; Mahuran, Don J.; James, Michael N. G.

2010-01-01

Lysosomal β-hexosaminidase A (Hex A) is essential for the degradation of GM2 gangliosides in the central and peripheral nervous system. Accumulation of GM2 leads to severely debilitating neurodegeneration associated with Tay-Sachs disease (TSD), Sandoff disease (SD) and AB variant. Here, we present the X-ray crystallographic structure of Hex A to 2.8 Å resolution and the structure of Hex A in complex with NAG-thiazoline, (NGT) to 3.25 Å resolution. NGT, a mechanism-based inhibitor, has been shown to act as a chemical chaperone that, to some extent, prevents misfolding of a Hex A mutant associated with adult onset Tay Sachs disease and, as a result, increases the residual activity of Hex A to a level above the critical threshold for disease. The crystal structure of Hex A reveals an αβ heterodimer, with each subunit having a functional active site. Only the α-subunit active site can hydrolyze GM2 gangliosides due to a flexible loop structure that is removed post-translationally from β, and to the presence of αAsn423 and αArg424. The loop structure is involved in binding the GM2 activator protein, while αArg424 is critical for binding the carboxylate group of the N-acetyl-neuraminic acid residue of GM2. The β-subunit lacks these key residues and has βAsp452 and βLeu453 in their place; the β-subunit therefore cleaves only neutral substrates efficiently. Mutations in the α-subunit, associated with TSD, and those in the β-subunit, associated with SD are discussed. The effect of NGT binding in the active site of a mutant Hex A and its effect on protein function is discussed. PMID:16698036

Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases.

Science.gov (United States)

McGregor, Nicholas; Yin, Victor; Tung, Ching-Chieh; Van Petegem, Filip; Brumer, Harry

2017-02-01

The xyloglucan endotransglycosylase/hydrolase (XTH) gene family encodes enzymes of central importance to plant cell wall remodeling. The evolutionary history of plant XTH gene products is incompletely understood vis-à-vis the larger body of bacterial endoglycanases in Glycoside Hydrolase Family 16 (GH16). To provide molecular insight into this issue, high-resolution X-ray crystal structures and detailed enzyme kinetics of an extant transitional plant endoglucanase (EG) were determined. Functionally intermediate between plant XTH gene products and bacterial licheninases of GH16, Vitis vinifera EG16 (VvEG16) effectively catalyzes the hydrolysis of the backbones of two dominant plant cell wall matrix glycans, xyloglucan (XyG) and β(1,3)/β(1,4)-mixed-linkage glucan (MLG). Crystallographic complexes with extended oligosaccharide substrates reveal the structural basis for the accommodation of both unbranched, mixed-linked (MLG) and highly decorated, linear (XyG) polysaccharide chains in a broad, extended active-site cleft. Structural comparison with representative bacterial licheninases, a xyloglucan endotranglycosylase (XET), and a xyloglucan endohydrolase (XEH) outline the functional ramifications of key sequence deletions and insertions across the phylogenetic landscape of GH16. Although the biological role(s) of EG16 orthologs remains to be fully resolved, the present biochemical and tertiary structural characterization provides key insight into plant cell wall enzyme evolution, which will continue to inform genomic analyses and functional studies across species. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Crystallographic features related to a van der Waals coupling in the layered chalcogenide FePS{sub 3}

Energy Technology Data Exchange (ETDEWEB)

Murayama, Chisato; Okabe, Momoko; Fukuda, Koichiro [Department of Materials Science and Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku Nagoya 466-8555 (Japan); Urushihara, Daisuke; Asaka, Toru, E-mail: asaka.toru@nitech.ac.jp [Department of Materials Science and Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku Nagoya 466-8555 (Japan); Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Gokiso-cho, Showa-ku Nagoya 466-8555 (Japan); Isobe, Masahiko [Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart (Germany); Yamamoto, Kazuo [Nanostructures Research Laboratory, Japan Fine Ceramics Center, Nagoya 456-8587 (Japan); Matsushita, Yoshitaka [Research Network and Facility Services Division, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047 (Japan)

2016-10-14

We investigated the crystallographic structure of FePS{sub 3} with a layered structure using transmission electron microscopy and powder X-ray diffraction. We found that FePS{sub 3} forms a rotational twin structure with the common axis along the c*-axis. The high-resolution transmission electron microscopy images revealed that the twin boundaries were positioned at the van der Waals gaps between the layers. The narrow bands of dark contrast were observed in the bright-field transmission electron microscopy images below the antiferromagnetic transition temperature, T{sub N} ≈ 120 K. Low-temperature X-ray diffraction showed a lattice distortion; the a- and b-axes shortened and lengthened, respectively, as the temperature decreased below T{sub N.} We propose that the narrow bands of dark contrast observed in the bright-field transmission electron microscopy images are caused by the directional lattice distortion with respect to each micro-twin variant in the antiferromagnetic phase.

Global crystallographic textures obtained by neutron and synchrotron radiation

International Nuclear Information System (INIS)

Brokmeier, Heinz-Guenter

2006-01-01

Global crystallographic textures belong to the main characteristic parameters of engineering materials. The global crystallographic texture is always the average texture of a well-defined sample volume which is representative to solve practical engineering problems. Thus a beam having a high penetration power is needed available as neutron or high energetic X-ray radiation. Texture type and texture sharpness are of great importance for materials properties such as the deep drawing behaviour, one of the basic techniques in many industries. Advantages and disadvantages of both radiations make them complementary for measuring crystallographic textures in a wide range of materials

Crystal structure of the alkaline proteinase Savinase from Bacillus lentus at 1.4 A resolution.

Science.gov (United States)

Betzel, C; Klupsch, S; Papendorf, G; Hastrup, S; Branner, S; Wilson, K S

1992-01-20

Savinase (EC3.4.21.14) is secreted by the alkalophilic bacterium Bacillus lentus and is a representative of that subgroup of subtilisin enzymes with maximum stability in the pH range 7 to 10 and high activity in the range 8 to 12. It is therefore of major industrial importance for use in detergents. The crystal structure of the native form of Savinase has been refined using X-ray diffraction data to 1.4 A resolution. The starting model was that of subtilisin Carlsberg. A comparison to the structures of the closely related subtilisins Carlsberg and BPN' and to the more distant thermitase and proteinase K is presented. The structure of Savinase is very similar to those of homologous Bacillus subtilisins. There are two calcium ions in the structure, equivalent to the strong and the weak calcium-binding sites in subtilisin Carlsberg and subtilisin BPN', well known for their stabilizing effect on the subtilisins. The structure of Savinase shows novel features that can be related to its stability and activity. The relatively high number of salt bridges in Savinase is likely to contribute to its high thermal stability. The non-conservative substitutions and deletions in the hydrophobic binding pocket S1 result in the most significant structural differences from the other subtilisins. The different composition of the S1 binding loop as well as the more hydrophobic character of the substrate-binding region probably contribute to the alkaline activity profile of the enzyme. The model of Savinase contains 1880 protein atoms, 159 water molecules and two calcium ions. The crystallographic R-factor [formula; see text].

Effects of NMR spectral resolution on protein structure calculation.

Directory of Open Access Journals (Sweden)

Suhas Tikole

Full Text Available Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.

Ultra high resolution tomography

Energy Technology Data Exchange (ETDEWEB)

Haddad, W.S.

1994-11-15

Recent work and results on ultra high resolution three dimensional imaging with soft x-rays will be presented. This work is aimed at determining microscopic three dimensional structure of biological and material specimens. Three dimensional reconstructed images of a microscopic test object will be presented; the reconstruction has a resolution on the order of 1000 A in all three dimensions. Preliminary work with biological samples will also be shown, and the experimental and numerical methods used will be discussed.

High-resolution x-ray spectroscopy of coherent bremsstrahlung fine structure

International Nuclear Information System (INIS)

Lund, M.W.

1989-01-01

The aim of this research was to provide experimental evidence for fine structure due to umklapp by distinct reciprocal lattice vectors in coherent bremsstrahlung spectra. The spontaneous emission of photons by relativistic electrons transversing thin crystals is made possible by recoil of the crystal, which absorbs momentum in multiples of ℎG where G is a reciprocal lattice vector. Previous work in the MeV-GeV beam energy range used detectors whose energy resolution was greater than 10%. By fitting a Johann wavelength dispersive spectrometer to a transmission electron microscope the author obtained coherent bremsstrahlung spectra of very high quality with energy resolution of 1%. Important to this result were also the fine angular collimation, small energy width of the electron beam in the microscope, and the accurate control of crystal orientation possible in a modern goniometer stage. The theory of the design of bent crystal x-ray spectrometers is extended to include effects of defocus and aberrations. The theory for diffraction from a stationary three dimensional grating due to a dipole radiator moving at relativistic speeds is derived as well as several other broadening mechanisms stemming from experimental variables. This dissertation provides the first experimental observations and corresponding theoretical background for the fine structure of coherent bremsstrahlung due to umklapp by different G-vectors in the same reciprocal lattice plane

A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution

International Nuclear Information System (INIS)

Tronrud, Dale E.; Karplus, P. Andrew

2011-01-01

A script was created to allow SHELXL to use the new CDL v.1.2 stereochemical library which defines the target values for main-chain bond lengths and angles as a function of the residue’s ϕ/ψ angles. Test refinements using this script show that the refinement behavior of structures at resolutions even better than 1 Å is substantially enhanced by the use of the new conformation-dependent ideal geometry paradigm. To utilize a new conformation-dependent backbone-geometry library (CDL) in protein refinements at atomic resolution, a script was written that creates a restraint file for the SHELXL refinement program. It was found that the use of this library allows models to be created that have a substantially better fit to main-chain bond angles and lengths without degrading their fit to the X-ray data even at resolutions near 1 Å. For models at much higher resolution (∼0.7 Å), the refined model for parts adopting single well occupied positions is largely independent of the restraints used, but these structures still showed much smaller r.m.s.d. residuals when assessed with the CDL. Examination of the refinement tests across a wide resolution range from 2.4 to 0.65 Å revealed consistent behavior supporting the use of the CDL as a next-generation restraint library to improve refinement. CDL restraints can be generated using the service at http://pgd.science.oregonstate.edu/cdl_shelxl/

Recovery of crystallographic texture in remineralized dental enamel.

Science.gov (United States)

Siddiqui, Samera; Anderson, Paul; Al-Jawad, Maisoon

2014-01-01

Dental caries is the most prevalent disease encountered by people of all ages around the world. Chemical changes occurring in the oral environment during the caries process alter the crystallography and microstructure of dental enamel resulting in loss of mechanical function. Little is known about the crystallographic effects of demineralization and remineralization. The motivation for this study was to develop understanding of the caries process at the crystallographic level in order to contribute towards a long term solution. In this study synchrotron X-ray diffraction combined with scanning electron microscopy and scanning microradiography have been used to correlate enamel crystallography, microstructure and mineral concentration respectively in enamel affected by natural caries and following artificial demineralization and remineralization regimes. In particular, the extent of destruction and re-formation of this complex structure has been measured. 2D diffraction patterns collected at the European Synchrotron Radiation Facility were used to quantify changes in the preferred orientation (crystallographic texture) and position of the (002) Bragg reflection within selected regions of interest in each tooth slice, and then correlated with the microstructure and local mineral mass. The results revealed that caries and artificial demineralization cause a large reduction in crystallographic texture which is coupled with the loss of mineral mass. Remineralization restores the texture to the original level seen in healthy enamel and restores mineral density. The results also showed that remineralization promotes ordered formation of new crystallites and growth of pre-existing crystallites which match the preferred orientation of healthy enamel. Combining microstructural and crystallographic characterization aids the understanding of caries and erosion processes and assists in the progress towards developing therapeutic treatments to allow affected enamel to regain

Broken symmetry within crystallographic super-spaces: structural and dynamical aspects

International Nuclear Information System (INIS)

Mariette, Celine

2013-01-01

Aperiodic crystals have the property to possess long range order without translational symmetry. These crystals are described within the formalism of super-space crystallography. In this manuscript, we will focus on symmetry breaking which take place in such crystallographic super-space groups, considering the prototype family of n-alkane/urea. Studies performed by X-ray diffraction using synchrotron sources reveal multiple structural solutions implying or not changes of the dimension of the super-space. Once the characterization of the order parameter and of the symmetry breaking is done, we present the critical pre-transitional phenomena associated to phase transitions of group/subgroup types. Coherent neutron scattering and inelastic X-ray scattering allow a dynamical analysis of different kind of excitations in these materials (phonons, phasons). The inclusion compounds with short guest molecules (alkane C n H 2n+2 , n varying from 7 to 13) show at room temperature unidimensional 'liquid-like' phases. The dynamical disorder along the incommensurate direction of these materials generates new structural solutions at low temperature (inter-modulated monoclinic composite, commensurate lock-in). (author) [fr

High-resolution structure of a retroviral protease folded as a monomer

International Nuclear Information System (INIS)

Gilski, Miroslaw; Kazmierczyk, Maciej; Krzywda, Szymon; Zábranská, Helena; Cooper, Seth; Popović, Zoran; Khatib, Firas; DiMaio, Frank; Thompson, James; Baker, David; Pichová, Iva; Jaskolski, Mariusz

2011-01-01

The crystal structure of Mason–Pfizer monkey virus protease folded as a monomer has been solved by molecular replacement using a model generated by players of the online game Foldit. The structure shows at high resolution the details of a retroviral protease folded as a monomer which can guide rational design of protease dimerization inhibitors as retroviral drugs. Mason–Pfizer monkey virus (M-PMV), a D-type retrovirus assembling in the cytoplasm, causes simian acquired immunodeficiency syndrome (SAIDS) in rhesus monkeys. Its pepsin-like aspartic protease (retropepsin) is an integral part of the expressed retroviral polyproteins. As in all retroviral life cycles, release and dimerization of the protease (PR) is strictly required for polyprotein processing and virion maturation. Biophysical and NMR studies have indicated that in the absence of substrates or inhibitors M-PMV PR should fold into a stable monomer, but the crystal structure of this protein could not be solved by molecular replacement despite countless attempts. Ultimately, a solution was obtained in mr-rosetta using a model constructed by players of the online protein-folding game Foldit. The structure indeed shows a monomeric protein, with the N- and C-termini completely disordered. On the other hand, the flap loop, which normally gates access to the active site of homodimeric retropepsins, is clearly traceable in the electron density. The flap has an unusual curled shape and a different orientation from both the open and closed states known from dimeric retropepsins. The overall fold of the protein follows the retropepsin canon, but the C α deviations are large and the active-site ‘DTG’ loop (here NTG) deviates up to 2.7 Å from the standard conformation. This structure of a monomeric retropepsin determined at high resolution (1.6 Å) provides important extra information for the design of dimerization inhibitors that might be developed as drugs for the treatment of retroviral infections

High resolution CT of the chest

Energy Technology Data Exchange (ETDEWEB)

Barneveld Binkhuysen, F H [Eemland Hospital (Netherlands), Dept. of Radiology

1996-12-31

Compared to conventional CT high resolution CT (HRCT) shows several extra anatomical structures which might effect both diagnosis and therapy. The extra anatomical structures were discussed briefly in this article. (18 refs.).

Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins.

Science.gov (United States)

Merlino, Antonello; Vitagliano, Luigi; Howes, Barry D; Verde, Cinzia; di Prisco, Guido; Smulevich, Giulietta; Sica, Filomena; Vergara, Alessandro

2009-12-01

Recent studies have demonstrated that hemoglobins isolated from Antarctic fish undergo peculiar oxidation processes. Here we show, by combining crystallographic and spectroscopic data, that the oxidation pathway of Trematomus bernacchii hemoglobin (HbTb) is distinct from that observed for the major component of Trematomus newnesi (Hb1Tn), despite the high sequence identity of the two proteins and structural similarity of their ferrous and fully oxidized states. Resonance Raman analysis of HbTb autoxidation upon air-exposure reveals the absence of the oxidized pentacoordinated state that was observed for Hb1Tn. The HbTb oxidation pathway is characterized by two ferric species: an aquo hexacoordinated high spin state and a bis-histidyl hexacoordinated low spin form, which appear in the early stages of the oxidation process. The high resolution structure of an intermediate along the oxidation pathway has been determined at 1.4 A resolution. The analysis of the electron density of the heme pocket shows, for both the alpha and the beta iron, the coexistence of multiple binding states. In this partially oxidized form, HbTb exhibits significant deviations from the canonical R state both at the local and global level. The analysis of these modifications highlights the structural correlation between key functional regions of the protein.

A crystallographic perspective on sharing data and knowledge

Science.gov (United States)

Bruno, Ian J.; Groom, Colin R.

2014-10-01

The crystallographic community is in many ways an exemplar of the benefits and practices of sharing data. Since the inception of the technique, virtually every published crystal structure has been made available to others. This has been achieved through the establishment of several specialist data centres, including the Cambridge Crystallographic Data Centre, which produces the Cambridge Structural Database. Containing curated structures of small organic molecules, some containing a metal, the database has been produced for almost 50 years. This has required the development of complex informatics tools and an environment allowing expert human curation. As importantly, a financial model has evolved which has, to date, ensured the sustainability of the resource. However, the opportunities afforded by technological changes and changing attitudes to sharing data make it an opportune moment to review current practices.

The development of high-resolution spectroscopic methods and their use in atomic structure studies

International Nuclear Information System (INIS)

Poulsen, O.

1984-01-01

This thesis discusses work performed during the last nine years in the field of atomic spectroscopy. Several high-resolution techniques, ranging from quantum beats, level crossings, rf-laser double resonances to nonlinear field atom interactions, have been employed. In particular, these methods have been adopted and developed to deal with fast accelerated atomic or ionic beams, allowing studies of problems in atomic-structure theory. Fine- and hyperfine-structure determinations in the He I and Li I isoelectronic sequences, in 51 V I, and in 235 U I, II have permitted a detailed comparison with ab initio calculations, demonstrating the change in problems when going towards heavier elements or higher ionization stage. The last part of the thesis is concerned with the fundamental question of obtaining very high optical resolution in the interaction between a fast accelerated atom or ion beam and a laser field, this problem being the core in the continuing development of atomic spectroscopy necessary to challenge the more precise and sophisticated theories advanced. (Auth.)

Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery.

Science.gov (United States)

Patel, Disha; Bauman, Joseph D; Arnold, Eddy

2014-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this "chemical interrogation" of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. Copyright © 2014. Published by Elsevier Ltd.

Advantages of Crystallographic Fragment Screening: Functional and Mechanistic Insights from a Powerful Platform for Efficient Drug Discovery

Science.gov (United States)

Patel, Disha; Bauman, Joseph D.; Arnold, Eddy

2015-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this “chemical interrogation” of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. PMID:25117499

Synthesis, structure and magnetic properties of crystallographically aligned CuCr_2Se_4 thin films

International Nuclear Information System (INIS)

Esters, Marco; Liebig, Andreas; Ditto, Jeffrey J.; Falmbigl, Matthias; Albrecht, Manfred; Johnson, David C.

2016-01-01

We report the low temperature synthesis of highly textured CuCr_2Se_4 thin films using the modulated elemental reactant (MER) method. The structure of CuCr_2Se_4 is determined for the first time in its thin film form and exhibits cell parameters that are smaller than found in bulk CuCr_2Se_4. X-ray diffraction and precession electron diffraction show a strong degree of crystallographic alignment of the crystallites, where the axis is oriented perpendicular to the substrate surface, while being rotationally disordered within the plane. Temperature and field dependent in-plane and out-of-plane magnetization measurements show that the film is ferromagnetic with a Curie temperature of 406 K CuCr_2Se_4 synthesized utilizing the MER method shows stronger magnetic anisotropy (effective anisotropy: 1.82 × 10"6 erg cm"−"3; shape anisotropy: 1.07 × 10"6 erg cm"−"3), with the easy axis lying out of plane, and a larger magnetic moment (6 μ_B/f.u.) than bulk CuCr_2Se_4. - Highlights: • Crystallographically aligned, phase pure CuCr_2Se_4 were synthesized. • The degree of alignment decreases with annealing time. • The films are ferromagnetic with the easy axis along the direction. • The magnetization is larger than bulk CuCr_2Se_4 or other CuCr_2Se_4 films made to date.

Crystallographic features of lath martensite in low-carbon steel

International Nuclear Information System (INIS)

Kitahara, Hiromoto; Ueji, Rintaro; Tsuji, Nobuhiro; Minamino, Yoritoshi

2006-01-01

Electron backscattering diffraction with field-emission scanning electron microscopy was used to analyze crystallographically the lath martensite structure in a 0.20% carbon steel. The crystallographic features of the lath martensite structure, of the order of the prior austenite grain size or larger, were clarified. Although the orientations of the martensite crystals were scattered around the ideal variant orientations, the martensite in this steel maintained the Kurdjumov-Sachs (K-S) orientation relationship. The procedures of the crystallographic analysis of the martensite (ferrite) phase with the K-S orientation relationship were explained in detail. Variant analysis showed that all 24 possible variants did not necessarily appear within a single prior austenite grain and that all six variants did not necessarily appear within each packet. Specific combinations of two variants appeared within local regions (sub-blocks), indicating a strict rule for variant selection. Prior austenite grain boundaries and most of the packet boundaries were clearly recognized. However, it was difficult to determine the block boundaries within the sub-blocks

The crystallographic growth directions of Sn whiskers

International Nuclear Information System (INIS)

Stein, J.; Welzel, U.; Leineweber, A.; Huegel, W.; Mittemeijer, E.J.

2015-01-01

The growth directions of 55 Sn whiskers, i.e. the crystallographic orientation parallel to the whisker-growth axes, were determined using (i) a focused ion beam microscope for the determination of the physical growth angles of the whiskers with respect to a specimen (reference) coordinate system and (ii) an electron backscatter detector in a scanning electron microscope for the determination of the crystallographic orientation of the whiskers. The Sn whiskers were found to grow preferentially along low-index directions of the β-Sn crystal structure. The experimental findings of this study (and most of the results presented in the literature as well) were explained by applying, in a modified way, the Hartman–Perdok concept of periodic bond chains, i.e. chains of strong bonds running uninterruptedly through the structure, to the Sn whisker-growth phenomenon

LTE modeling of inhomogeneous chromospheric structure using high-resolution limb observations

Science.gov (United States)

Lindsey, C.

1987-01-01

The paper discusses considerations relevant to LTE modeling of rough atmospheres. Particular attention is given to the application of recent high-resolution observations of the solar limb in the far-infrared and radio continuum to the modeling of chromospheric spicules. It is explained how the continuum limb observations can be combined with morphological knowledge of spicule structure to model the physical conditions in chromospheric spicules. This discussion forms the basis for a chromospheric model presented in a parallel publication based on observations ranging from 100 microns to 2.6 mm.

Preliminary crystallographic analysis of two hypothetical ribose-5-phosphate isomerases from Streptococcus mutans

International Nuclear Information System (INIS)

Wang, Chen; Fan, Xuexin; Cao, Xiaofang; Liu, Xiang; Li, Lanfen; Su, Xiaodong

2012-01-01

Two hypothetical ribose-5-phosphate isomerases from S. mutans have been produced in E. coli and crystallized. The crystals diffracted to high resolutions suitable for crystallographic analyses. Study of the enzymes from sugar metabolic pathways may provide a better understanding of the pathogenesis of the human oral pathogen Streptococcus mutans. Bioinformatics, biochemical and crystallization methods were used to characterize and understand the function of two putative ribose-5-phosphate isomerases: SMU1234 and SMU2142. The proteins were cloned and constructed with N-terminal His tags. Protein purification was performed by Ni 2+ -chelating and size-exclusion chromatography. The crystals of SUM1234 diffracted to 1.9 Å resolution and belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 48.97, b = 98.27, c = 101.09 Å, α = β = γ = 90°. The optimized SMU2142 crystals diffracted to 2.7 Å resolution and belonged to space group P1, with unit-cell parameters a = 53.7, b = 54.1, c = 86.5 Å, α = 74.2, β = 73.5, γ = 83.7°. Initial phasing of both proteins was attempted by molecular replacement; the structure of SMU1234 could easily be solved, but no useful results were obtained for SMU2142. Therefore, SeMet-labelled SMU2142 will be prepared for phasing

Structural characterization of ether lipids from the archaeon Sulfolobus islandicus by high-resolution shotgun lipidomics

DEFF Research Database (Denmark)

Jensen, Sara Munk; Brandl, Martin; Treusch, Alexander H

2015-01-01

The molecular structures, biosynthetic pathways and physiological functions of membrane lipids produced by organisms in the domain Archaea are poorly characterized as compared with that of counterparts in Bacteria and Eukaryota. Here we report on the use of high-resolution shotgun lipidomics......-resolution Fourier transform mass spectrometry using an ion trap-orbitrap mass spectrometer. This analysis identified five clusters of molecular ions that matched ether lipids in the database with sub-ppm mass accuracy. To structurally characterize and validate the identities of the potential lipid species, we...... performed structural analysis using multistage activation on the ion trap-orbitrap instrument as well as tandem mass analysis using a quadrupole time-of-flight machine. Our analysis identified four ether lipid species previously reported in Archaea, and one ether lipid species that had not been described...

Recovery of crystallographic texture in remineralized dental enamel.

Directory of Open Access Journals (Sweden)

Samera Siddiqui

Full Text Available Dental caries is the most prevalent disease encountered by people of all ages around the world. Chemical changes occurring in the oral environment during the caries process alter the crystallography and microstructure of dental enamel resulting in loss of mechanical function. Little is known about the crystallographic effects of demineralization and remineralization. The motivation for this study was to develop understanding of the caries process at the crystallographic level in order to contribute towards a long term solution. In this study synchrotron X-ray diffraction combined with scanning electron microscopy and scanning microradiography have been used to correlate enamel crystallography, microstructure and mineral concentration respectively in enamel affected by natural caries and following artificial demineralization and remineralization regimes. In particular, the extent of destruction and re-formation of this complex structure has been measured. 2D diffraction patterns collected at the European Synchrotron Radiation Facility were used to quantify changes in the preferred orientation (crystallographic texture and position of the (002 Bragg reflection within selected regions of interest in each tooth slice, and then correlated with the microstructure and local mineral mass. The results revealed that caries and artificial demineralization cause a large reduction in crystallographic texture which is coupled with the loss of mineral mass. Remineralization restores the texture to the original level seen in healthy enamel and restores mineral density. The results also showed that remineralization promotes ordered formation of new crystallites and growth of pre-existing crystallites which match the preferred orientation of healthy enamel. Combining microstructural and crystallographic characterization aids the understanding of caries and erosion processes and assists in the progress towards developing therapeutic treatments to allow affected

High-resolution structure of the recombinant sweet-tasting protein thaumatin I

International Nuclear Information System (INIS)

Masuda, Tetsuya; Ohta, Keisuke; Mikami, Bunzo; Kitabatake, Naofumi

2011-01-01

The structure of a recombinant form of the sweet-tasting protein thaumatin I was determined at 1.1 Å resolution and refined to an R work of 9.1% and an R free of 11.7%. Comparisons with plant thaumatin revealed the electron density of recombinant thaumatin I to be significantly improved, especially around Asn46 and Ser63. Thaumatin, an intensely sweet-tasting plant protein, elicits a sweet taste at a concentration of 50 nM. The crystal structure of a recombinant form of thaumatin I produced in the yeast Pichia pastoris has been determined to a resolution of 1.1 Å. The model was refined with anisotropic B parameters and riding H atoms. A comparison of the diffraction data and refinement statistics for recombinant thaumatin I with those for plant thaumatin I revealed no significant differences in the diffraction data. The R values for recombinant thaumatin I and plant thaumatin I (F o > 4σ) were 9.11% and 9.91%, respectively, indicating the final model to be of good quality. Notably, the electron-density maps around Asn46 and Ser63, which differ between thaumatin variants, were significantly improved. Furthermore, a number of H atoms became visible in an OMIT map and could be assigned. The high-quality structure of recombinant thaumatin with H atoms should provide details about sweetness determinants in thaumatin and provide valuable insights into the mechanism of its interaction with taste receptors

Design and development of high-resolution atomic beam fluorescence spectroscopy facility for isotope shift and hyperfine structure measurements

International Nuclear Information System (INIS)

Acharyulu, G.V.S.G.; Sankari, M.; Kiran Kumar, P.V.; Suryanarayana, M.V.

2012-01-01

A high-resolution atomic beam fluorescence spectroscopy facility for the determination of isotope shifts and hyperfine structure in atomic species has been designed and developed. A resistively heated graphite tube atomic beam source was designed, tested and integrated into a compact interaction chamber for atomic beam fluorescence experiments. The design of the laser-atom interaction chamber and the source has been modified in a phased manner so as to achieve sub-Doppler resolution. The system has been used to record the hyperfine spectrum of the D2 transitions of Rb and K isotopes. The spectral resolution achieved is ∼ 26 MHz and is adequate to carry out high resolution measurement of isotope shifts and hyperfine structure of various atomic species. The other major advantage of the source is that it requires very small amounts of sample for achieving very good signal to noise ratio. (author)

Mobile and embedded fast high resolution image stitching for long length rectangular monochromatic objects with periodic structure

Science.gov (United States)

Limonova, Elena; Tropin, Daniil; Savelyev, Boris; Mamay, Igor; Nikolaev, Dmitry

2018-04-01

In this paper we describe stitching protocol, which allows to obtain high resolution images of long length monochromatic objects with periodic structure. This protocol can be used for long length documents or human-induced objects in satellite images of uninhabitable regions like Arctic regions. The length of such objects can reach notable values, while modern camera sensors have limited resolution and are not able to provide good enough image of the whole object for further processing, e.g. using in OCR system. The idea of the proposed method is to acquire a video stream containing full object in high resolution and use image stitching. We expect the scanned object to have straight boundaries and periodic structure, which allow us to introduce regularization to the stitching problem and adapt algorithm for limited computational power of mobile and embedded CPUs. With the help of detected boundaries and structure we estimate homography between frames and use this information to reduce complexity of stitching. We demonstrate our algorithm on mobile device and show image processing speed of 2 fps on Samsung Exynos 5422 processor

Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints

International Nuclear Information System (INIS)

Furuita, Kyoko; Kataoka, Saori; Sugiki, Toshihiko; Hattori, Yoshikazu; Kobayashi, Naohiro; Ikegami, Takahisa; Shiozaki, Kazuhiro; Fujiwara, Toshimichi; Kojima, Chojiro

2015-01-01

NMR structure determination of soluble proteins depends in large part on distance restraints derived from NOE. In this study, we examined the impact of paramagnetic relaxation enhancement (PRE)-derived distance restraints on protein structure determination. A high-resolution structure of the loop-rich soluble protein Sin1 could not be determined by conventional NOE-based procedures due to an insufficient number of NOE restraints. By using the 867 PRE-derived distance restraints obtained from the NOE-based structure determination procedure, a high-resolution structure of Sin1 could be successfully determined. The convergence and accuracy of the determined structure were improved by increasing the number of PRE-derived distance restraints. This study demonstrates that PRE-derived distance restraints are useful in the determination of a high-resolution structure of a soluble protein when the number of NOE constraints is insufficient

Demonstrating the Uneven Importance of Fine-Scale Forest Structure on Snow Distributions using High Resolution Modeling

Science.gov (United States)

Broxton, P. D.; Harpold, A. A.; van Leeuwen, W.; Biederman, J. A.

2016-12-01

Quantifying the amount of snow in forested mountainous environments, as well as how it may change due to warming and forest disturbance, is critical given its importance for water supply and ecosystem health. Forest canopies affect snow accumulation and ablation in ways that are difficult to observe and model. Furthermore, fine-scale forest structure can accentuate or diminish the effects of forest-snow interactions. Despite decades of research demonstrating the importance of fine-scale forest structure (e.g. canopy edges and gaps) on snow, we still lack a comprehensive understanding of where and when forest structure has the largest impact on snowpack mass and energy budgets. Here, we use a hyper-resolution (1 meter spatial resolution) mass and energy balance snow model called the Snow Physics and Laser Mapping (SnowPALM) model along with LIDAR-derived forest structure to determine where spatial variability of fine-scale forest structure has the largest influence on large scale mass and energy budgets. SnowPALM was set up and calibrated at sites representing diverse climates in New Mexico, Arizona, and California. Then, we compared simulations at different model resolutions (i.e. 1, 10, and 100 m) to elucidate the effects of including versus not including information about fine scale canopy structure. These experiments were repeated for different prescribed topographies (i.e. flat, 30% slope north, and south-facing) at each site. Higher resolution simulations had more snow at lower canopy cover, with the opposite being true at high canopy cover. Furthermore, there is considerable scatter, indicating that different canopy arrangements can lead to different amounts of snow, even when the overall canopy coverage is the same. This modeling is contributing to the development of a high resolution machine learning algorithm called the Snow Water Artificial Network (SWANN) model to generate predictions of snow distributions over much larger domains, which has implications

High resolution NMR in zeolites

International Nuclear Information System (INIS)

Diaz, Anix

1991-01-01

In this work 29 Si and 27 Al NMR spectroscopy was used to study various types of zeolites. The corresponding spectra were used to measure the Si/Al ratios, to follow chemical modifications induced by acid and hydrothermal treatments, to determine non-equivalent crystallographic sites in highly dealuminated mordenites, and to detect modifications of faujasites due to the insertion of titanium atoms in the lattice. (author)

High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor-binding domain of botulinum neurotoxin serotype D

International Nuclear Information System (INIS)

Zhang, Yanfeng; Gao, Xiaoli; Qin, Ling; Buchko, Garry W.; Robinson, Howard; Varnum, Susan M.

2010-01-01

The receptor-binding domain of botulinum neurotoxin serotype D was expressed in E. coli using a codon-optimized cDNA. The highly purified protein crystallized in space group P2 1 2 1 2 1 , with unit-cell parameters a = 60.8, b = 89.7, c = 93.9 Å, and the crystals diffracted to 1.65 Å resolution. Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D-HCR was expressed at a high level (150–200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D-HCR was obtained. The recombinant BoNT/D-HCR was crystallized and the crystals diffracted to 1.65 Å resolution. The crystals belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 60.8, b = 89.7, c = 93.9 Å. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit

Valence band structure of binary chalcogenide vitreous semiconductors by high-resolution XPS

International Nuclear Information System (INIS)

Kozyukhin, S.; Golovchak, R.; Kovalskiy, A.; Shpotyuk, O.; Jain, H.

2011-01-01

High-resolution X-ray photoelectron spectroscopy (XPS) is used to study regularities in the formation of valence band electronic structure in binary As x Se 100−x , As x S 100−x , Ge x Se 100−x and Ge x S 100−x chalcogenide vitreous semiconductors. It is shown that the highest occupied energetic states in the valence band of these materials are formed by lone pair electrons of chalcogen atoms, which play dominant role in the formation of valence band electronic structure of chalcogen-rich glasses. A well-expressed contribution from chalcogen bonding p electrons and more deep s orbitals are also recorded in the experimental valence band XPS spectra. Compositional dependences of the observed bands are qualitatively analyzed from structural and compositional points of view.

Valence band structure of binary chalcogenide vitreous semiconductors by high-resolution XPS

Energy Technology Data Exchange (ETDEWEB)

Kozyukhin, S., E-mail: sergkoz@igic.ras.ru [Russian Academy of Science, Institute of General and Inorganic Chemistry (Russian Federation); Golovchak, R. [Lviv Scientific Research Institute of Materials of SRC ' Carat' (Ukraine); Kovalskiy, A. [Lehigh University, Department of Materials Science and Engineering (United States); Shpotyuk, O. [Lviv Scientific Research Institute of Materials of SRC ' Carat' (Ukraine); Jain, H. [Lehigh University, Department of Materials Science and Engineering (United States)

2011-04-15

High-resolution X-ray photoelectron spectroscopy (XPS) is used to study regularities in the formation of valence band electronic structure in binary As{sub x}Se{sub 100-x}, As{sub x}S{sub 100-x}, Ge{sub x}Se{sub 100-x} and Ge{sub x}S{sub 100-x} chalcogenide vitreous semiconductors. It is shown that the highest occupied energetic states in the valence band of these materials are formed by lone pair electrons of chalcogen atoms, which play dominant role in the formation of valence band electronic structure of chalcogen-rich glasses. A well-expressed contribution from chalcogen bonding p electrons and more deep s orbitals are also recorded in the experimental valence band XPS spectra. Compositional dependences of the observed bands are qualitatively analyzed from structural and compositional points of view.

Expression, crystallization and preliminary crystallographic study of GluB from Corynebacterium glutamicum

International Nuclear Information System (INIS)

Liu, Qingbo; Li, Defeng; Hu, Yonglin; Wang, Da-Cheng

2013-01-01

GluB, a substrate-binding protein from C. glutamicum, was expressed, purified and crystallized, followed by X-ray diffraction data collection and preliminary crystallographic analysis. GluB is a substrate-binding protein (SBP) which participates in the uptake of glutamic acid in Corynebacterium glutamicum, a Gram-positive bacterium. It is part of an ATP-binding cassette (ABC) transporter system. Together with the transmembrane proteins GluC and GluD and the cytoplasmic protein GluA, which couples the hydrolysis of ATP to the translocation of glutamate, they form a highly active glutamate-uptake system. As part of efforts to study the amino-acid metabolism, especially the metabolism of glutamic acid by C. glutamicum, a bacterium that is widely used in the industrial production of glutamic acid, the GluB protein was expressed, purified and crystallized, an X-ray diffraction data set was collected to a resolution of 1.9 Å and preliminary crystallographic analysis was performed. The crystal belonged to space group P3 1 21 or P3 2 21, with unit-cell parameters a = b = 82.50, c = 72.69 Å

Crystallographic theory of the martensitic transformation

Directory of Open Access Journals (Sweden)

Edwar A. Torres-López

2014-08-01

Full Text Available The martensitic transformation is one of the most researched topics in the materials science during the 20th century. The second half of this century was mainly remembered by the development of several theories related with the kinetics of phase transformation, the mechanisms involved in the nucleation phenomenon, and the way as the crystallographic change is produced. In this paper are described the fundamental concepts that are defined in the crystallographic framework of the martensitic transformation. The study is focused on the application of the most outstanding crystallographic models: the Bain; the Wechsler, Lieberman & Read; and the Bowles & Mackenzie. The topic is presented based upon the particular features of the martensitic transformation, such as its non-diffusional character, type of interface between parent (austenite and product (martensite phases, the formation of substructural defects, and the shape change; all of these features are mathematically described by equations aimed to predict how the transformation will take place rather than to explain the actual movement of the atoms within the structure. This mathematical development is known as the Phenomenological Theory of Martensite Crystallography (PTMC.

High-resolution AFM structure of DNA G-wires in aqueous solution.

Science.gov (United States)

Bose, Krishnashish; Lech, Christopher J; Heddi, Brahim; Phan, Anh Tuân

2018-05-17

We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G 4 T 2 G 4 ] in physiologically relevant aqueous solution using atomic force microscopy (AFM). Wire-like structures (G-wires) of 3.0 nm height with well-defined surface periodic features were observed. Analysis of high-resolution AFM images allowed their classification based on the periodicity of these features. A major species is identified with periodic features of 4.3 nm displaying left-handed ridges or zigzag features on the molecular surface. A minor species shows primarily left-handed periodic features of 2.2 nm. In addition to 4.3 and 2.2 nm ridges, background features with periodicity of 0.9 nm are also observed. Using molecular modeling and simulation, we identify a molecular structure that can explain both the periodicity and handedness of the major G-wire species. Our results demonstrate the potential structural diversity of G-wire formation and provide valuable insight into the structure of higher-order intermolecular G-quadruplexes. Our results also demonstrate how AFM can be combined with simulation to gain insight into biomolecular structure.

Realization of highly crystallographic three-dimensional nanosheets by a stress-induced oriented-diffusion method

Energy Technology Data Exchange (ETDEWEB)

Gharooni, M.; Hosseini, M.; Mohajerzadeh, S., E-mail: mohajer@ut.ac.ir; Taghinejad, M.; Taghinejad, H. [Thin Film and Nanoelectronics Lab, Nanoelectronics Center of Excellence, School of Electrical and Computer Engineering, University of Tehran, Tehran 143957131 (Iran, Islamic Republic of); Abdi, Y. [Nano-Physics Research Lab, Department of Physics, University of Tehran, Tehran 1439955961 (Iran, Islamic Republic of)

2014-07-28

Morphologically controlled nanostructures have been increasingly important because of their strongly shape dependent physical and chemical properties. Formation of nanoscale silicon based structures that employ high levels of strain, intentional, and unintentional twins or grain boundaries can be dramatically different from the commonly conceived bulk processes. We report, realization of highly crystallographic 3D nanosheets with unique morphology and ultra-thin thickness by a stress-induced oriented-diffusion method, based on plasma processing of metal layer deposited on Si substrate and its post deep reactive ion etching. Annealing in plasma ambient creates rod-like metal alloy precursors which induce stress at its interface with Si substrate due to the mismatch of lattice constants. This stress opens facilitated gateways for orientated-diffusion of metal atoms in 〈110〉 directions and leads to formation of NSs (nanosheets) with [111] crystalline essence. Nanosheets are mainly triangular, hexagonal, or pseudo hexagonal in shape and their thicknesses are well controlled from several to tens of nanometers. The structural and morphological evolution of features were investigated in detail using transmission electron microscope, atomic force microscope, scanning electron microscope and possible mechanism is proposed to explain the formation of the thermodynamically unfavorable morphology of nanosheets. Significant photoemission capability of NSs was also demonstrated by photoluminescence spectroscopy.

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.

Science.gov (United States)

Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R; Murshudov, Garib N; Short, Judith M; Scheres, Sjors H W; Henderson, Richard

2013-12-01

Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an

An atlas of high-resolution IRAS maps on nearby galaxies

Science.gov (United States)

Rice, Walter

1993-01-01

An atlas of far-infrared IRAS maps with near 1 arcmin angular resolution of 30 optically large galaxies is presented. The high-resolution IRAS maps were produced with the Maximum Correlation Method (MCM) image construction and enhancement technique developed at IPAC. The MCM technique, which recovers the spatial information contained in the overlapping detector data samples of the IRAS all-sky survey scans, is outlined and tests to verify the structural reliability and photometric integrity of the high-resolution maps are presented. The infrared structure revealed in individual galaxies is discussed. The atlas complements the IRAS Nearby Galaxy High-Resolution Image Atlas, the high-resolution galaxy images encoded in FITS format, which is provided to the astronomical community as an IPAC product.

Preliminary X-ray crystallographic analysis of the d-xylulose 5-phosphate phosphoketolase from Lactococcus lactis

International Nuclear Information System (INIS)

Petrareanu, Georgiana; Balasu, Mihaela C.; Zander, Ulrich; Scheidig, Axel J.; Szedlacsek, Stefan E.

2010-01-01

The expression, purification, preliminary crystallization and crystallographic analysis of phosphoketolase from L. lactis ssp. lactis (strain IL 1403) are reported. Phosphoketolases are thiamine diphosphate-dependent enzymes which play a central role in the pentose-phosphate pathway of heterofermentative lactic acid bacteria. They belong to the family of aldehyde-lyases and in the presence of phosphate ion cleave the carbon–carbon bond of the specific substrate d-xylulose 5-phosphate (or d-fructose 6-phosphate) to give acetyl phosphate and d-glyceraldehyde 3-phosphate (or d-erythrose 4-phosphate). Structural information about phosphoketolases is particularly important in order to fully understand their mechanism as well as the steric course of phosphoketolase-catalyzed reactions. Here, the purification, preliminary crystallization and crystallographic characterization of d-xylulose 5-phosphate phosphoketolase from Lactococcus lactis are reported. The presence of thiamine diphosphate during purification was essential for the enzymatic activity of the purified protein. The crystals belonged to the monoclinic space group P2 1 . Diffraction data were obtained to a resolution of 2.2 Å

Water polygons in high-resolution protein crystal structures.

Science.gov (United States)

Lee, Jonas; Kim, Sung-Hou

2009-07-01

We have analyzed the interstitial water (ISW) structures in 1500 protein crystal structures deposited in the Protein Data Bank that have greater than 1.5 A resolution with less than 90% sequence similarity with each other. We observed varieties of polygonal water structures composed of three to eight water molecules. These polygons may represent the time- and space-averaged structures of "stable" water oligomers present in liquid water, and their presence as well as relative population may be relevant in understanding physical properties of liquid water at a given temperature. On an average, 13% of ISWs are localized enough to be visible by X-ray diffraction. Of those, averages of 78% are water molecules in the first water layer on the protein surface. Of the localized ISWs beyond the first layer, almost half of them form water polygons such as trigons, tetragons, as well as expected pentagons, hexagons, higher polygons, partial dodecahedrons, and disordered networks. Most of the octagons and nanogons are formed by fusion of smaller polygons. The trigons are most commonly observed. We suggest that our observation provides an experimental basis for including these water polygon structures in correlating and predicting various water properties in liquid state.

Super-resolution thermographic imaging using blind structured illumination

Science.gov (United States)

Burgholzer, Peter; Berer, Thomas; Gruber, Jürgen; Mayr, Günther

2017-07-01

Using an infrared camera for thermographic imaging allows the contactless temperature measurement of many surface pixels simultaneously. From the measured surface data, the structure below the surface, embedded inside a sample or tissue, can be reconstructed and imaged, if heated by an excitation light pulse. The main drawback in active thermographic imaging is the degradation of the spatial resolution with the imaging depth, which results in blurred images for deeper lying structures. We circumvent this degradation by using blind structured illumination combined with a non-linear joint sparsity reconstruction algorithm. We demonstrate imaging of a line pattern and a star-shaped structure through a 3 mm thick steel sheet with a resolution four times better than the width of the thermal point-spread-function. The structured illumination is realized by parallel slits cut in an aluminum foil, where the excitation coming from a flashlight can penetrate. This realization of super-resolution thermographic imaging demonstrates that blind structured illumination allows thermographic imaging without high degradation of the spatial resolution for deeper lying structures. The groundbreaking concept of super-resolution can be transferred from optics to diffusive imaging by defining a thermal point-spread-function, which gives the principle resolution limit for a certain signal-to-noise ratio, similar to the Abbe limit for a certain optical wavelength. In future work, the unknown illumination pattern could be the speckle pattern generated by a short laser pulse inside a light scattering sample or tissue.

High resolution Neutron and Synchrotron Powder Diffraction

International Nuclear Information System (INIS)

Hewat, A.W.

1986-01-01

The use of high-resolution powder diffraction has grown rapidly in the past years, with the development of Rietveld (1967) methods of data analysis and new high-resolution diffractometers and multidetectors. The number of publications in this area has increased from a handful per year until 1973 to 150 per year in 1984, with a ten-year total of over 1000. These papers cover a wide area of solid state-chemistry, physics and materials science, and have been grouped under 20 subject headings, ranging from catalysts to zeolites, and from battery electrode materials to pre-stressed superconducting wires. In 1985 two new high-resolution diffractometers are being commissioned, one at the SNS laboratory near Oxford, and one at the ILL in Grenoble. In different ways these machines represent perhaps the ultimate that can be achieved with neutrons and will permit refinement of complex structures with about 250 parameters and unit cell volumes of about 2500 Angstrom/sp3/. The new European Synchotron Facility will complement the Grenoble neutron diffractometers, and extend the role of high-resolution powder diffraction to the direct solution of crystal structures, pioneered in Sweden

Microbeam high-resolution diffraction and x-ray standing wave methods applied to semiconductor structures

International Nuclear Information System (INIS)

Kazimirov, A; Bilderback, D H; Huang, R; Sirenko, A; Ougazzaden, A

2004-01-01

A new approach to conditioning x-ray microbeams for high angular resolution x-ray diffraction and scattering techniques is introduced. We combined focusing optics (one-bounce imaging capillary) and post-focusing collimating optics (miniature Si(004) channel-cut crystal) to generate an x-ray microbeam with a size of 10 μm and ultimate angular resolution of 14 μrad. The microbeam was used to analyse the strain in sub-micron thick InGaAsP epitaxial layers grown on an InP(100) substrate by the selective area growth technique in narrow openings between the oxide stripes. For the structures for which the diffraction peaks from the substrate and the film overlap, the x-ray standing wave technique was applied for precise measurements of the strain with a Δd/d resolution of better than 10 -4 . (rapid communication)

Evolution of dislocation structures following a change in loading conditions studied by in situ high resolution reciprocal space mapping

DEFF Research Database (Denmark)

Wejdemann, Christian

or to a strain of 7% at a temperature of -196 ○C, and the samples were characterized by electron microscopy and mechanical tests. Transmission electron microscopy showed that the pre-deformation produced a characteristic dislocation cell structure consisting of regions with relatively high dislocation density...... the pre-deformation axis. In the X-ray diffraction experiments a technique was employed with which it is possible to obtain high-resolution reciprocal space maps from individual bulk grains. The high-resolution reciprocal space maps contain features related to the dislocation structure in the grains......: A spread-out ‘cloud’ of low intensity caused by diffraction from the dislocation walls and a number of sharp peaks of high intensity caused by diffraction from the individual subgrains. By acquiring reciprocal space maps at a number of different strain levels the evolution of the dislocation structures can...

High resolution NMR in zeolites

Energy Technology Data Exchange (ETDEWEB)

Diaz, Anix [INTEVEP, Filial de Petroleos de Venezuela, SA, Caracas (Venezuela). Dept. de Analisis y Evalucion

1992-12-31

In this work {sup 29} Si and {sup 27} Al NMR spectroscopy was used to study various types of zeolites. The corresponding spectra were used to measure the Si/Al ratios, to follow chemical modifications induced by acid and hydrothermal treatments, to determine non-equivalent crystallographic sites in highly dealuminated mordenites, and to detect modifications of faujasites due to the insertion of titanium atoms in the lattice. (author) 7 refs., 7 figs., 2 tabs.

High-resolution X-ray diffraction with no sample preparation.

Science.gov (United States)

Hansford, G M; Turner, S M R; Degryse, P; Shortland, A J

2017-07-01

It is shown that energy-dispersive X-ray diffraction (EDXRD) implemented in a back-reflection geometry is extremely insensitive to sample morphology and positioning even in a high-resolution configuration. This technique allows high-quality X-ray diffraction analysis of samples that have not been prepared and is therefore completely non-destructive. The experimental technique was implemented on beamline B18 at the Diamond Light Source synchrotron in Oxfordshire, UK. The majority of the experiments in this study were performed with pre-characterized geological materials in order to elucidate the characteristics of this novel technique and to develop the analysis methods. Results are presented that demonstrate phase identification, the derivation of precise unit-cell parameters and extraction of microstructural information on unprepared rock samples and other sample types. A particular highlight was the identification of a specific polytype of a muscovite in an unprepared mica schist sample, avoiding the time-consuming and difficult preparation steps normally required to make this type of identification. The technique was also demonstrated in application to a small number of fossil and archaeological samples. Back-reflection EDXRD implemented in a high-resolution configuration shows great potential in the crystallographic analysis of cultural heritage artefacts for the purposes of scientific research such as provenancing, as well as contributing to the formulation of conservation strategies. Possibilities for moving the technique from the synchrotron into museums are discussed. The avoidance of the need to extract samples from high-value and rare objects is a highly significant advantage, applicable also in other potential research areas such as palaeontology, and the study of meteorites and planetary materials brought to Earth by sample-return missions.

Crystallographic computing system JANA2006: General features

Czech Academy of Sciences Publication Activity Database

Petříček, Václav; Dušek, Michal; Palatinus, Lukáš

2014-01-01

Roč. 229, č. 5 (2014), s. 345-352 ISSN 0044-2968 R&D Projects: GA ČR(CZ) GAP204/11/0809; GA ČR(CZ) GA14-03276S Grant - others:AV ČR(CZ) Praemium Academiae Institutional support: RVO:68378271 Keywords : JANA2006 * aperiodic structures * magnetic structures * crystallographic computing Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.310, year: 2014

Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement

International Nuclear Information System (INIS)

Chen, Xiaorui; Lu, Mingyang; Poon, Billy K.; Wang, Qinghua; Ma, Jianpeng

2009-01-01

The structural model of the unliganded and fully glycosylated simian immunodeficiency virus gp120 core determined to 4.0 Å resolution was substantially improved using a recently developed normal-mode-based anisotropic B-factor refinement method. The envelope protein gp120/gp41 of simian and human immunodeficiency viruses plays a critical role in viral entry into host cells. However, the extraordinarily high structural flexibility and heavy glycosylation of the protein have presented enormous difficulties in the pursuit of high-resolution structural investigation of some of its conformational states. An unliganded and fully glycosylated gp120 core structure was recently determined to 4.0 Å resolution. The rather low data-to-parameter ratio limited refinement efforts in the original structure determination. In this work, refinement of this gp120 core structure was carried out using a normal-mode-based refinement method that has been shown in previous studies to be effective in improving models of a supramolecular complex at 3.42 Å resolution and of a membrane protein at 3.2 Å resolution. By using only the first four nonzero lowest-frequency normal modes to construct the anisotropic thermal parameters, combined with manual adjustments and standard positional refinement using REFMAC5, the structural model of the gp120 core was significantly improved in many aspects, including substantial decreases in R factors, better fitting of several flexible regions in electron-density maps, the addition of five new sugar rings at four glycan chains and an excellent correlation of the B-factor distribution with known structural flexibility. These results further underscore the effectiveness of this normal-mode-based method in improving models of protein and nonprotein components in low-resolution X-ray structures

High resolution (transformers.

Science.gov (United States)

Garcia-Souto, Jose A; Lamela-Rivera, Horacio

2006-10-16

A novel fiber-optic interferometric sensor is presented for vibrations measurements and analysis. In this approach, it is shown applied to the vibrations of electrical structures within power transformers. A main feature of the sensor is that an unambiguous optical phase measurement is performed using the direct detection of the interferometer output, without external modulation, for a more compact and stable implementation. High resolution of the interferometric measurement is obtained with this technique (transformers are also highlighted.

High-resolution polypeptide structure and dynamics in anisotropic environments: The gramicidin channel

Energy Technology Data Exchange (ETDEWEB)

Cross, T.A.; Lee, K.C.; Ketchem, R.R.; Hu, W.; Lazo, N.D.; Huo, S. [Florida State Univ., Tallahassee, FL (United States)

1994-12-01

To understand the details of macromolecular function, high-resolution structural and dynamic detail is essential. The polypeptide fold of the gramicidin channel has been effectively modeled for the past 20 years, yet the functional changes in conductance and channel lifetime associated with amino acid substitutions cannot be predicted. To accomplish this goal, high-resolution electrostatic modeling and the precise orientation of all dipoles are required. Furthermore, an enhanced knowledge of the complex molecular environment of this membrane-bound peptide is needed. An aqueous environment is relatively uniform and achiral. The membrane environment is very heterogenous and chiral. A knowledge of the interactions, specific and nonspecific, between peptide and lipid will aid in developing a better understanding of this environment. To accomplish this goal, it is necessary to study the peptide in an extended lipid bilayer, rather than in a vesicular or micellar form. These latter environments are likely to possess increased dynamics, increased water penetration, and distorted interactions between the polypeptide and membrane surface. To perform NMR studies on bilayer bound peptides, solid state NMR methods are required, and for specific site information, isotopic labels are incorporated using solid phase peptide synthesis.

Super-resolution optical microscopy for studying membrane structure and dynamics.

Science.gov (United States)

Sezgin, Erdinc

2017-07-12

Investigation of cell membrane structure and dynamics requires high spatial and temporal resolution. The spatial resolution of conventional light microscopy is limited due to the diffraction of light. However, recent developments in microscopy enabled us to access the nano-scale regime spatially, thus to elucidate the nanoscopic structures in the cellular membranes. In this review, we will explain the resolution limit, address the working principles of the most commonly used super-resolution microscopy techniques and summarise their recent applications in the biomembrane field.

High tracking resolution detectors. Final Technical Report

International Nuclear Information System (INIS)

Vasile, Stefan; Li, Zheng

2010-01-01

High-resolution tracking detectors based on Active Pixel Sensor (APS) have been valuable tools in Nuclear Physics and High-Energy Physics research, and have contributed to major discoveries. Their integration time, radiation length and readout rate is a limiting factor for the planed luminosity upgrades in nuclear and high-energy physics collider-based experiments. The goal of this program was to demonstrate and develop high-gain, high-resolution tracking detector arrays with faster readout, and shorter radiation length than APS arrays. These arrays may operate as direct charged particle detectors or as readouts of high resolution scintillating fiber arrays. During this program, we developed in CMOS large, high-resolution pixel sensor arrays with integrated readout, and reset at pixel level. Their intrinsic gain, high immunity to surface and moisture damage, will allow operating these detectors with minimal packaging/passivation requirements and will result in radiation length superior to APS. In Phase I, we designed and fabricated arrays with calorimetric output capable of sub-pixel resolution and sub-microsecond readout rate. The technical effort was dedicated to detector and readout structure development, performance verification, as well as to radiation damage and damage annealing.

Asymmetric Rolling Process Simulations by Dynamic Explicit Crystallographic Homogenized Finite Element Method

International Nuclear Information System (INIS)

Ngoc Tam, Nguyen; Nakamura, Yasunori; Terao, Toshihiro; Kuramae, Hiroyuki; Nakamachi, Eiji; Sakamoto, Hidetoshi; Morimoto, Hideo

2007-01-01

Recently, the asymmetric rolling (ASR) has been applied to the material processing of aluminum alloy sheet to control micro-crystal structure and texture in order to improve the mechanical properties. Previously, several studies aimed at high formability sheet generation have been carried out experimentally, but finite element simulations to predict the deformation induced texture evolution of the asymmetrically rolled sheet metals have not been investigated rigorously. In this study, crystallographic homogenized finite element (FE) codes are developed and applied to analyze the asymmetrical rolling processes. The textures of sheet metals were measured by electron back scattering diffraction (EBSD), and compared with FE simulations. The results from the dynamic explicit type Crystallographic homogenization FEM code shows that this type of simulation is a comprehensive tool to predict the plastic induced texture evolution

Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage

Science.gov (United States)

Pintilie, Grigore; Chen, Dong-Hua; Haase-Pettingell, Cameron A.; King, Jonathan A.; Chiu, Wah

2016-01-01

CryoEM continues to produce density maps of larger and more complex assemblies with multiple protein components of mixed symmetries. Resolution is not always uniform throughout a cryoEM map, and it can be useful to estimate the resolution in specific molecular components of a large assembly. In this study, we present procedures to 1) estimate the resolution in subcomponents by gold-standard Fourier shell correlation (FSC); 2) validate modeling procedures, particularly at medium resolutions, which can include loop modeling and flexible fitting; and 3) build probabilistic models that combine high-accuracy priors (such as crystallographic structures) with medium-resolution cryoEM densities. As an example, we apply these methods to new cryoEM maps of the mature bacteriophage P22, reconstructed without imposing icosahedral symmetry. Resolution estimates based on gold-standard FSC show the highest resolution in the coat region (7.6 Å), whereas other components are at slightly lower resolutions: portal (9.2 Å), hub (8.5 Å), tailspike (10.9 Å), and needle (10.5 Å). These differences are indicative of inherent structural heterogeneity and/or reconstruction accuracy in different subcomponents of the map. Probabilistic models for these subcomponents provide new insights, to our knowledge, and structural information when taking into account uncertainty given the limitations of the observed density. PMID:26743049

High-resolution anatomy of the human brain stem using 7-T MRI: improved detection of inner structures and nerves?

Energy Technology Data Exchange (ETDEWEB)

Gizewski, Elke R. [Medical University Innsbruck, Department of Neuroradiology, Innsbruck (Austria); Maderwald, Stefan [University Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); Linn, Jennifer; Bochmann, Katja [LMU Munich, Department of Neuroradiology, Munich (Germany); Dassinger, Benjamin [Medical University Innsbruck, Department of Neuroradiology, Innsbruck (Austria); Justus-Liebig-University Giessen, Department of Neuroradiology, Giessen (Germany); Forsting, Michael [University Hospital, University Duisburg-Essen, Departments of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany); Ladd, Mark E. [University Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); University Hospital, University Duisburg-Essen, Departments of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany)

2014-03-15

The purpose of this paper is to assess the value of 7 Tesla (7 T) MRI for the depiction of brain stem and cranial nerve (CN) anatomy. Six volunteers were examined at 7 T using high-resolution SWI, MPRAGE, MP2RAGE, 3D SPACE T2, T2, and PD images to establish scanning parameters targeted at optimizing spatial resolution. Direct comparisons between 3 and 7 T were performed in two additional subjects using the finalized sequences (3 T: T2, PD, MPRAGE, SWAN; 7 T: 3D T2, MPRAGE, SWI, MP2RAGE). Artifacts and the depiction of structures were evaluated by two neuroradiologists using a standardized score sheet. Sequences could be established for high-resolution 7 T imaging even in caudal cranial areas. High in-plane resolution T2, PD, and SWI images provided depiction of inner brain stem structures such as pons fibers, raphe, reticular formation, nerve roots, and periaqueductal gray. MPRAGE and MP2RAGE provided clear depiction of the CNs. 3D T2 images improved depiction of inner brain structure in comparison to T2 images at 3 T. Although the 7-T SWI sequence provided improved contrast to some inner structures, extended areas were influenced by artifacts due to image disturbances from susceptibility differences. Seven-tesla imaging of basal brain areas is feasible and might have significant impact on detection and diagnosis in patients with specific diseases, e.g., trigeminal pain related to affection of the nerve root. Some inner brain stem structures can be depicted at 3 T, but certain sequences at 7 T, in particular 3D SPACE T2, are superior in producing anatomical in vivo images of deep brain stem structures. (orig.)

High-resolution anatomy of the human brain stem using 7-T MRI: improved detection of inner structures and nerves?

International Nuclear Information System (INIS)

Gizewski, Elke R.; Maderwald, Stefan; Linn, Jennifer; Bochmann, Katja; Dassinger, Benjamin; Forsting, Michael; Ladd, Mark E.

2014-01-01

The purpose of this paper is to assess the value of 7 Tesla (7 T) MRI for the depiction of brain stem and cranial nerve (CN) anatomy. Six volunteers were examined at 7 T using high-resolution SWI, MPRAGE, MP2RAGE, 3D SPACE T2, T2, and PD images to establish scanning parameters targeted at optimizing spatial resolution. Direct comparisons between 3 and 7 T were performed in two additional subjects using the finalized sequences (3 T: T2, PD, MPRAGE, SWAN; 7 T: 3D T2, MPRAGE, SWI, MP2RAGE). Artifacts and the depiction of structures were evaluated by two neuroradiologists using a standardized score sheet. Sequences could be established for high-resolution 7 T imaging even in caudal cranial areas. High in-plane resolution T2, PD, and SWI images provided depiction of inner brain stem structures such as pons fibers, raphe, reticular formation, nerve roots, and periaqueductal gray. MPRAGE and MP2RAGE provided clear depiction of the CNs. 3D T2 images improved depiction of inner brain structure in comparison to T2 images at 3 T. Although the 7-T SWI sequence provided improved contrast to some inner structures, extended areas were influenced by artifacts due to image disturbances from susceptibility differences. Seven-tesla imaging of basal brain areas is feasible and might have significant impact on detection and diagnosis in patients with specific diseases, e.g., trigeminal pain related to affection of the nerve root. Some inner brain stem structures can be depicted at 3 T, but certain sequences at 7 T, in particular 3D SPACE T2, are superior in producing anatomical in vivo images of deep brain stem structures. (orig.)

Taking MAD to the extreme: ultrafast protein structure determination

International Nuclear Information System (INIS)

Walsh, M.A.; Dementieva, I.; Evans, G.; Sanishvili, R.; Joachimiak, A.

1999-01-01

Multiwavelength anomalous diffraction data were measured in 23 min from a 16 kDa selenomethionyl-substituted protein, producing experimental phases to 2.25 (angstrom) resolution. The data were collected on a mosaic 3 x 3 charge-coupled device using undulator radiation from the Structural Biology Center 19ID beamline at the Argonne National Laboratory's Advanced Photon Source. The phases were independently obtained semiautomatically by two crystallographic program suites, CCP4 and CNS. The quality and speed of this data acquisition exemplify the opportunities at third-generation synchrotron sources for high-throughput protein crystal structure determination

HCN Polymers: Toward Structure Comprehension Using High Resolution Mass Spectrometry

Science.gov (United States)

Bonnet, Jean-Yves; Thissen, Roland; Frisari, Ma; Vuitton, Veronique; Quirico, Eric; Le Roy, Léna; Fray, Nicolas; Cottin, Hervé; Horst, Sarah; Yelle, Roger

A lot of solar system materials, including cometary ices and Titan aerosols, contain dark matter that can be interpreted as complex nitrogen bearing organic matter [1]. In laboratory experi-ments, HCN polymers are thus analogs of great interest. In fact they may be present in Titan atmosphere and in comet nuclei and then reprocessed as a CN distributed source [2], when ices began to sublimate and ejects from the nucleus organic matter grains [3]. The presence of HCN polymers is suggested because HCN molecule has been directly observed in 1P/Halley comet [4] and others. HCN polymers are also of prebiotic interest [5] as it can form amino acid under hydrolysis conditions. Even if they have been studied during the last decades, their chemical composition and structure are still poorly understood, and a great analytical effort has to be continued. In this way we present a high resolution mass spectrometry (HRMS) and a high resolution tandem mass spectrometry (MS/HRMS) analysis of HCN polymers. It was shown [6] that this is a suitable technique to elucidate composition and structure of the soluble part of tholins analogs of Titan's atmosphere aerosols. HCN polymers have never been studied by HRMS, thus we used a LTQ-Orbitrap XL high resolution mass spectrometer to analyse the HCN polymers. These are produced at LISA by direct polymerisation of pure liquid HCN, catalyzed by ammonia. HCN polymers have been completely dissolved in methanol and then injected in the mass spectrometer by ElectroSpray Ionization (ESI). This atmospheric pressure ionization process produces protonated or deprotonated ions, but it does not fragment molecules. Thus HRMS, allows a direct access to the stoechiometry of all the ionizable molecules present in the samples. Fragmentation analyses (MS/MS) of selected ions have also been performed. Thess analysis provide information about the different chemical fonctionnalities present in HCN poly-mers and also about their structure. Thus we are able to

HIGH RESOLUTION MICROTOMOGRAPHY FOR DENSITY AND SPATIAL INFORMATION ABOUT WOOD STRUCTURES.

Energy Technology Data Exchange (ETDEWEB)

ILLMAN,B.

1999-07-22

Microtomography has successfully been used to characterize loss of structural integrity of wood. Tomographic images were generated with the newly developed third generation x-ray computed microtomography (XCMT) instrument at the X27A beamline at the National Synchrotron Light Source (NSLS). The beamline is equipped with high-flux x-ray monochromator based on multilayer optics developed for this application. The sample is mounted on a translation stage with which to center the sample rotation, a rotation stage to perform the rotation during data collection and a motorized goniometer head for small alignment motions. The absorption image is recorded by a single-crystal scintillator, an optical microscope and a cooled CCD array detector. Data reconstruction has provided three-dimensional geometry of the heterogeneous wood matrix in microtomographic images. Wood is a heterogeneous material composed of long lignocellulose vessels. Although wood is a strong natural product, fungi have evolved chemical systems that weaken the strength properties of wood by degrading structural vessels. Tomographic images with a resolution of three microns were obtained nonintrusively to characterize the compromised structural integrity of wood. Computational tools developed by Lindquist et al (1996) applied to characterize the microstructure of the tomographic volumes.

Lateral resolution of eddy current imaging

International Nuclear Information System (INIS)

Hassan, W.; Blodgett, M.; Nagy, P.B.

2002-01-01

Analytical, finite element simulation, and experimental methods were used to investigate the lateral resolution of eddy current microscopy. It was found that the lateral resolution of eddy current imaging is ultimately limited by the probe-coil geometry and dimensions, but both the inspection frequency and the phase angle can be used to optimize the resolution, to some degree, at the expense of sensitivity. Electric anisotropy exhibited by noncubic crystallographic classes of materials such as titanium alloys can play a very similar role in electromagnetic materials characterization of polycrystalline metals to that of elastic anisotropy in ultrasonic materials characterization. Our results demonstrate that eddy current microscopy can be enhanced via a high-resolution, small diameter probe-coil which delivers a unique materials characterization tool well suited for the evaluation of Ti alloys

Precision mechanical structure of an ultra-high-resolution spectrometer for inelastic X-ray scattering instrument

Science.gov (United States)

Shu, Deming; Shvydko, Yuri; Stoupin, Stanislav A.; Khachatryan, Ruben; Goetze, Kurt A.; Roberts, Timothy

2015-04-14

A method and an ultrahigh-resolution spectrometer including a precision mechanical structure for positioning inelastic X-ray scattering optics are provided. The spectrometer includes an X-ray monochromator and an X-ray analyzer, each including X-ray optics of a collimating (C) crystal, a pair of dispersing (D) element crystals, anomalous transmission filter (F) and a wavelength (W) selector crystal. A respective precision mechanical structure is provided with the X-ray monochromator and the X-ray analyzer. The precision mechanical structure includes a base plate, such as an aluminum base plate; positioning stages for D-crystal alignment; positioning stages with an incline sensor for C/F/W-crystal alignment, and the positioning stages including flexure-based high-stiffness structure.

Resolution enhancement of low-quality videos using a high-resolution frame

Science.gov (United States)

Pham, Tuan Q.; van Vliet, Lucas J.; Schutte, Klamer

2006-01-01

This paper proposes an example-based Super-Resolution (SR) algorithm of compressed videos in the Discrete Cosine Transform (DCT) domain. Input to the system is a Low-Resolution (LR) compressed video together with a High-Resolution (HR) still image of similar content. Using a training set of corresponding LR-HR pairs of image patches from the HR still image, high-frequency details are transferred from the HR source to the LR video. The DCT-domain algorithm is much faster than example-based SR in spatial domain 6 because of a reduction in search dimensionality, which is a direct result of the compact and uncorrelated DCT representation. Fast searching techniques like tree-structure vector quantization 16 and coherence search1 are also key to the improved efficiency. Preliminary results on MJPEG sequence show promising result of the DCT-domain SR synthesis approach.

Low resolution solution structure of HAMLET and the importance of its alpha-domains in tumoricidal activity.

Science.gov (United States)

Ho, C S James; Rydstrom, Anna; Manimekalai, Malathy Sony Subramanian; Svanborg, Catharina; Grüber, Gerhard

2012-01-01

HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) is the first member in a new family of protein-lipid complexes with broad tumoricidal activity. Elucidating the molecular structure and the domains crucial for HAMLET formation is fundamental for understanding its tumoricidal function. Here we present the low-resolution solution structure of the complex of oleic acid bound HAMLET, derived from small angle X-ray scattering data. HAMLET shows a two-domain conformation with a large globular domain and an extended part of about 2.22 nm in length and 1.29 nm width. The structure has been superimposed into the related crystallographic structure of human α-lactalbumin, revealing that the major part of α-lactalbumin accommodates well in the shape of HAMLET. However, the C-terminal residues from L105 to L123 of the crystal structure of the human α-lactalbumin do not fit well into the HAMLET structure, resulting in an extended conformation in HAMLET, proposed to be required to form the tumoricidal active HAMLET complex with oleic acid. Consistent with this low resolution structure, we identified biologically active peptide epitopes in the globular as well as the extended domains of HAMLET. Peptides covering the alpha1 and alpha2 domains of the protein triggered rapid ion fluxes in the presence of sodium oleate and were internalized by tumor cells, causing rapid and sustained changes in cell morphology. The alpha peptide-oleate bound forms also triggered tumor cell death with comparable efficiency as HAMLET. In addition, shorter peptides corresponding to those domains are biologically active. These findings provide novel insights into the structural prerequisites for the dramatic effects of HAMLET on tumor cells.

Correlation between Crystallographic and Magnetic Domains at Co/NiO(001) Interfaces

Energy Technology Data Exchange (ETDEWEB)

Ohldag, H.; van der Laan, G.; Arenholz, E.

2008-12-18

Using soft x-ray spectromicroscopy we show that NiO(001) exhibits a crystallographic and magnetic domain structure near the surface identical to that of the bulk. Upon Co deposition a perpendicular coupling between the Ni and Co moments is observed that persists even after formation of uncompensated Ni spins at the interface through annealing. The chemical composition at the interface alters its crystallographic structure and leads to a reorientation of the Ni moments from the <112> to the <110> direction. We show that this reorientation is driven by changes in the magnetocrystalline anisotropy rather than exchange coupling mediated by residual uncompensated spins.

Deriving Quantitative Crystallographic Information from the Wavelength-Resolved Neutron Transmission Analysis Performed in Imaging Mode

Directory of Open Access Journals (Sweden)

Hirotaka Sato

2017-12-01

Full Text Available Current status of Bragg-edge/dip neutron transmission analysis/imaging methods is presented. The method can visualize real-space distributions of bulk crystallographic information in a crystalline material over a large area (~10 cm with high spatial resolution (~100 μm. Furthermore, by using suitable spectrum analysis methods for wavelength-dependent neutron transmission data, quantitative visualization of the crystallographic information can be achieved. For example, crystallographic texture imaging, crystallite size imaging and crystalline phase imaging with texture/extinction corrections are carried out by the Rietveld-type (wide wavelength bandwidth profile fitting analysis code, RITS (Rietveld Imaging of Transmission Spectra. By using the single Bragg-edge analysis mode of RITS, evaluations of crystal lattice plane spacing (d-spacing relating to macro-strain and d-spacing distribution’s FWHM (full width at half maximum relating to micro-strain can be achieved. Macro-strain tomography is performed by a new conceptual CT (computed tomography image reconstruction algorithm, the tensor CT method. Crystalline grains and their orientations are visualized by a fast determination method of grain orientation for Bragg-dip neutron transmission spectrum. In this paper, these imaging examples with the spectrum analysis methods and the reliabilities evaluated by optical/electron microscope and X-ray/neutron diffraction, are presented. In addition, the status at compact accelerator driven pulsed neutron sources is also presented.

Integration of first-principles methods and crystallographic database searches for new ferroelectrics: Strategies and explorations

International Nuclear Information System (INIS)

Bennett, Joseph W.; Rabe, Karin M.

2012-01-01

In this concept paper, the development of strategies for the integration of first-principles methods with crystallographic database mining for the discovery and design of novel ferroelectric materials is discussed, drawing on the results and experience derived from exploratory investigations on three different systems: (1) the double perovskite Sr(Sb 1/2 Mn 1/2 )O 3 as a candidate semiconducting ferroelectric; (2) polar derivatives of schafarzikite MSb 2 O 4 ; and (3) ferroelectric semiconductors with formula M 2 P 2 (S,Se) 6 . A variety of avenues for further research and investigation are suggested, including automated structure type classification, low-symmetry improper ferroelectrics, and high-throughput first-principles searches for additional representatives of structural families with desirable functional properties. - Graphical abstract: Integration of first-principles methods with crystallographic database mining, for the discovery and design of novel ferroelectric materials, could potentially lead to new classes of multifunctional materials. Highlights: ► Integration of first-principles methods and database mining. ► Minor structural families with desirable functional properties. ► Survey of polar entries in the Inorganic Crystal Structural Database.

Design and analysis of a cross-type structured-illumination confocal microscope for high speed and high resolution

International Nuclear Information System (INIS)

Kim, Young-Duk; Ahn, MyoungKi; Kim, Taejoong; Gweon, DaeGab; Yoo, Hongki

2012-01-01

There have been many studies about a super resolution microscope for many years. A super resolution microscope can detect the physical phenomena or morphology of a biological sample more precisely than conventional microscopes. The structured-illumination microscope (SIM) is one of the technologies that demonstrate super resolution. However, the conventional SIM requires more time to obtain one resolution-enhanced image than other super resolution microscopes. More specifically, the conventional SIM uses three images with a 120° phase difference for each direction and three different directions are image-processed to make one resolution enhancement by increasing the optical transfer function in three directions. In this paper, we present a novel cross structured-illumination confocal microscope (CSICM) that takes the advantage of the technology of both SIM and the confocal microscope. The CSICM uses only two directions with three phase difference images, for a total of six images. By reducing the number of images that must be obtained, the total image acquisition time and image reconstruction time in obtaining the final output images can be decreased, and the confocal microscope provides axial information of the sample automatically. We demonstrate our method of cross illumination and evaluate the performance of the CSICM and compare it to the conventional SIM and the confocal microscope. (paper)

Localization-based super-resolution imaging of cellular structures.

Science.gov (United States)

Kanchanawong, Pakorn; Waterman, Clare M

2013-01-01

Fluorescence microscopy allows direct visualization of fluorescently tagged proteins within cells. However, the spatial resolution of conventional fluorescence microscopes is limited by diffraction to ~250 nm, prompting the development of super-resolution microscopy which offers resolution approaching the scale of single proteins, i.e., ~20 nm. Here, we describe protocols for single molecule localization-based super-resolution imaging, using focal adhesion proteins as an example and employing either photoswitchable fluorophores or photoactivatable fluorescent proteins. These protocols should also be easily adaptable to imaging a broad array of macromolecular assemblies in cells whose components can be fluorescently tagged and assemble into high density structures.

Solving the RNA polymerase I structural puzzle

Energy Technology Data Exchange (ETDEWEB)

Moreno-Morcillo, María [European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany); Taylor, Nicholas M. I. [Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid (Spain); Gruene, Tim [Georg-August-University, Tammannstrasse 4, 37077 Göttingen (Germany); Legrand, Pierre [SOLEIL Synchrotron, L’Orme de Merisiers, Saint Aubin, Gif-sur-Yvette (France); Rashid, Umar J. [European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany); Ruiz, Federico M. [Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid (Spain); Steuerwald, Ulrich; Müller, Christoph W. [European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany); Fernández-Tornero, Carlos, E-mail: cftornero@cib.csic.es [Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid (Spain); European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany)

2014-10-01

Details of the RNA polymerase I crystal structure determination provide a framework for solution of the structures of other multi-subunit complexes. Simple crystallographic experiments are described to extract relevant biological information such as the location of the enzyme active site. Knowing the structure of multi-subunit complexes is critical to understand basic cellular functions. However, when crystals of these complexes can be obtained they rarely diffract beyond 3 Å resolution, which complicates X-ray structure determination and refinement. The crystal structure of RNA polymerase I, an essential cellular machine that synthesizes the precursor of ribosomal RNA in the nucleolus of eukaryotic cells, has recently been solved. Here, the crucial steps that were undertaken to build the atomic model of this multi-subunit enzyme are reported, emphasizing how simple crystallographic experiments can be used to extract relevant biological information. In particular, this report discusses the combination of poor molecular replacement and experimental phases, the application of multi-crystal averaging and the use of anomalous scatterers as sequence markers to guide tracing and to locate the active site. The methods outlined here will likely serve as a reference for future structural determination of large complexes at low resolution.

Synthesis, structure and magnetic properties of crystallographically aligned CuCr{sub 2}Se{sub 4} thin films

Energy Technology Data Exchange (ETDEWEB)

Esters, Marco [Department of Chemistry, University of Oregon, Eugene, OR 97403 (United States); Liebig, Andreas [Institut für Physik, Universität Augsburg, 86159 Augsburg (Germany); Ditto, Jeffrey J.; Falmbigl, Matthias [Department of Chemistry, University of Oregon, Eugene, OR 97403 (United States); Albrecht, Manfred [Institut für Physik, Universität Augsburg, 86159 Augsburg (Germany); Johnson, David C., E-mail: davej@uoregon.edu [Department of Chemistry, University of Oregon, Eugene, OR 97403 (United States)

2016-06-25

We report the low temperature synthesis of highly textured CuCr{sub 2}Se{sub 4} thin films using the modulated elemental reactant (MER) method. The structure of CuCr{sub 2}Se{sub 4} is determined for the first time in its thin film form and exhibits cell parameters that are smaller than found in bulk CuCr{sub 2}Se{sub 4}. X-ray diffraction and precession electron diffraction show a strong degree of crystallographic alignment of the crystallites, where the <111> axis is oriented perpendicular to the substrate surface, while being rotationally disordered within the plane. Temperature and field dependent in-plane and out-of-plane magnetization measurements show that the film is ferromagnetic with a Curie temperature of 406 K CuCr{sub 2}Se{sub 4} synthesized utilizing the MER method shows stronger magnetic anisotropy (effective anisotropy: 1.82 × 10{sup 6} erg cm{sup −3}; shape anisotropy: 1.07 × 10{sup 6} erg cm{sup −3}), with the easy axis lying out of plane, and a larger magnetic moment (6 μ{sub B}/f.u.) than bulk CuCr{sub 2}Se{sub 4}. - Highlights: • Crystallographically aligned, phase pure CuCr{sub 2}Se{sub 4} were synthesized. • The degree of alignment decreases with annealing time. • The films are ferromagnetic with the easy axis along the <111> direction. • The magnetization is larger than bulk CuCr{sub 2}Se{sub 4} or other CuCr{sub 2}Se{sub 4} films made to date.

The effect of crystallographic orientation on the active corrosion of pure magnesium

International Nuclear Information System (INIS)

Liu Ming; Qiu Dong; Zhao Mingchun; Song, Guangling; Atrens, Andrej

2008-01-01

An improved method was used to investigate the influence of crystallographic orientation on the corrosion of pure magnesium in 0.1 N HCl. The corrosion depth and orientation of surface features were mapped against crystallographic orientation (obtained by electron backscatter diffraction) for many off-principal magnesium crystals. The grains near (0 0 0 1) orientation are the most corrosion resistant. Most grains exhibited a striated structure of long and narrow hillocks with a unique direction

A Color-Texture-Structure Descriptor for High-Resolution Satellite Image Classification

Directory of Open Access Journals (Sweden)

Huai Yu

2016-03-01

Full Text Available Scene classification plays an important role in understanding high-resolution satellite (HRS remotely sensed imagery. For remotely sensed scenes, both color information and texture information provide the discriminative ability in classification tasks. In recent years, substantial performance gains in HRS image classification have been reported in the literature. One branch of research combines multiple complementary features based on various aspects such as texture, color and structure. Two methods are commonly used to combine these features: early fusion and late fusion. In this paper, we propose combining the two methods under a tree of regions and present a new descriptor to encode color, texture and structure features using a hierarchical structure-Color Binary Partition Tree (CBPT, which we call the CTS descriptor. Specifically, we first build the hierarchical representation of HRS imagery using the CBPT. Then we quantize the texture and color features of dense regions. Next, we analyze and extract the co-occurrence patterns of regions based on the hierarchical structure. Finally, we encode local descriptors to obtain the final CTS descriptor and test its discriminative capability using object categorization and scene classification with HRS images. The proposed descriptor contains the spectral, textural and structural information of the HRS imagery and is also robust to changes in illuminant color, scale, orientation and contrast. The experimental results demonstrate that the proposed CTS descriptor achieves competitive classification results compared with state-of-the-art algorithms.

World directory of crystallographers and of other scientists employing crystallographic methods

CERN Document Server

Filippini, G; Hashizume, H; Torriani, I; Duax, W

1995-01-01

The 9th edition of the World Directory of Crystallographers and of Other Scientists Employing Crystallographic Methods, which contains 7907 entries embracing 72 countries, differs considerably from the 8th edition, published in 1990. The content has been updated, and the methods used to acquire the information presented and to produce this new edition of the Directory have involved the latest advances in technology. The Directory is now also available as a regularly updated electronic database, accessible via e-mail, Telnet, Gopher, World-Wide Web, and Mosaic. Full details are given in an Appendix to the printed edition.

Electron diffraction study of {alpha}-AlMnSi crystals including non-crystallographic axes

Energy Technology Data Exchange (ETDEWEB)

Song, G.L.; Bursill, L.A.

1997-06-01

The structure of crystalline {alpha}-AlMnSi is examined by electron diffraction. Six distinct zone axes are examined, including both normal crystallographic and non-crystallographic zones axes, allowing the space group symmetry to be studied. Electron diffraction patterns characteristic of Pm3-bar were obtained for thicker specimens. However, for very thin specimens, as used for HRTEM imaging, the electron diffraction patterns were characteristic of Im3-bar space group symmetry. The structural basis of the Pm3-bar to Im3-bar transformation may be understood in terms of an analysis of the icosahedral structural elements located at the corners and body-centers of the cubic unit cell. A method for indexing the non-crystallographic zone axis diffraction patterns is described. An electron diffraction pattern of the 5-fold axis of the quasicrystalline phase i-AlMnSi is also included; this is compared with the experimental results and calculations for the [0{tau}1] axis of Pm3-bar and Im3-bar crystalline phases. 26 refs., 4 tabs., 7 figs.

Multi element high resolution scintillator structure

International Nuclear Information System (INIS)

Cusano, D.A.

1980-01-01

A gamma camera scintillator structure, suitable for detecting high energy gamma photons which, in a single scintillator camera, would require a comparatively thick scintillator crystal, so resulting in unacceptable dispersion of light photons, comprises a collimator array of a high Z material with elongated, parallel wall channels with the scintillator material being disposed in one end of the channels so as to form an integrated collimator/scintillator structure. The collimator channel walls are preferably coated with light reflective material and further light reflective surfaces being translucent to gamma photons, may be provided in each channel. The scintillators may be single crystals or preferably comprise a phosphor dispersed in a thermosetting translucent matrix as disclosed in GB2012800A. The light detectors of the assembled camera may be photomultiplier tubes charge coupled devices or charge injection devices. (author)

Crystallographic Analysis of a Japanese Sword by using Bragg Edge Transmission Spectroscopy

Science.gov (United States)

Shiota, Yoshinori; Hasemi, Hiroyuki; Kiyanagi, Yoshiaki

Neutron imaging using a pulsed neutron source can give crystallographic information over wide area of a sample by analysing position dependent transmission spectra. With the use of a Bragg edge imaging method we non-destructively obtained crystallographic information of a Japanese sword, signed by Bishu Osafune Norimitsu, in order to know position dependent crystallographic characteristics and to check usefulness of the method for the Japanese sword investigation. Strong texture appeared on the back side. On the other hand in the middle area almost isotropic feature appeared and edge side showed feature between them. Rather isotropic area in the centre area gradually reduced from the grip side to the tip side. The crystallite size was smaller near the edge and became larger towards the back side. The smaller crystallite size will be due to quenching around the edge and this trend disappeared in the grip (nakago) area. The larger crystallite size will be due to strong hammering. Coarse grains were also observed directly as transmission images with the use of a high spatial resolution detector. The spatial distribution of the grains was not uniform but the reason have not been understood. Furthermore, a white area around a tip area was proved to be a void by looking at the Brag edge transmission spectra. This void may be formed during forging process of two kinds of steel. It is suggested that consideration on differences in the texture and the crystallite size depending on position will give information to clarify the manufacturing process, and Bragg edge analysis will be a profitable tool for research of Japanese sword.

Crystallographic and oxidation kinetic study of uranium dioxide by high temperature X-ray diffractometry

International Nuclear Information System (INIS)

Teixeira, S.R.

1981-01-01

The structural behavior of UO 2 sintered plates was studied as a function of temperature by X-ray diffractometry. All the experiments were carried out under an inert atmosphere with low oxygen content (approximated 140 ppm). The thermal expansion coefficient of UO 2 05 was found to be 10,5 x 10 - 6 0 C - 1 for temperatures above 165 0 C. Structural transformations during oxidation were observed at 170,235 and 275 0 C. The isothermal oxidation of UO 2 to U 3 O 7 follows a parabolic form and the diffusion of oxygen through the product layer U 4 O 9 is the mechanism controlling the oxidation rate. The phases observed were UO 2 (cubic) - U 4 O 9 (cubic) - U 3 O 7 (tetragonal). Activation energies of oxidation were found for different crystallographic planes (hkl). From this one can conclude that there is a preferential occupation of interstitial oxygen within the UO 2 structure. (Author) [pt

Magnetic structure of holmium-yttrium superlattices

DEFF Research Database (Denmark)

Jehan, D.A.; McMorrow, D.F.; Cowley, R.A.

1993-01-01

We present the results of a study of the chemical and magnetic structures of a series of holmium-yttrium superlattices and a 5000 angstrom film of holmium, all grown by molecular-beam epitaxy. By combining the results of high-resolution x-ray diffraction with detailed modeling, we show...... that the superlattices have high crystallographic integrity: the structural coherence length parallel to the growth direction is typically almost-equal-to 2000 angstrom, while the interfaces between the two elements are well defined and extend over approximately four lattice planes. The magnetic structures were...... determined using neutron-scattering techniques. The moments on the Ho3+ ions in the superlattices form a basal-plane helix. From an analysis of the superlattice structure factors of the primary magnetic satellites, we are able to determine separately the contributions made by the holmium and yttrium...

Assessing resolution in live cell structured illumination microscopy

Science.gov (United States)

Pospíšil, Jakub; Fliegel, Karel; Klíma, Miloš

2017-12-01

Structured Illumination Microscopy (SIM) is a powerful super-resolution technique, which is able to enhance the resolution of optical microscope beyond the Abbe diffraction limit. In the last decade, numerous SIM methods that achieve the resolution of 100 nm in the lateral dimension have been developed. The SIM setups with new high-speed cameras and illumination pattern generators allow rapid acquisition of the live specimen. Therefore, SIM is widely used for investigation of the live structures in molecular and live cell biology. Quantitative evaluation of resolution enhancement in a real sample is essential to describe the efficiency of super-resolution microscopy technique. However, measuring the resolution of a live cell sample is a challenging task. Based on our experimental findings, the widely used Fourier ring correlation (FRC) method does not seem to be well suited for measuring the resolution of SIM live cell video sequences. Therefore, the resolution assessing methods based on Fourier spectrum analysis are often used. We introduce a measure based on circular average power spectral density (PSDca) estimated from a single SIM image (one video frame). PSDca describes the distribution of the power of a signal with respect to its spatial frequency. Spatial resolution corresponds to the cut-off frequency in Fourier space. In order to estimate the cut-off frequency from a noisy signal, we use a spectral subtraction method for noise suppression. In the future, this resolution assessment approach might prove useful also for single-molecule localization microscopy (SMLM) live cell imaging.

HIGH-RESOLUTION HELIOSEISMIC IMAGING OF SUBSURFACE STRUCTURES AND FLOWS OF A SOLAR ACTIVE REGION OBSERVED BY HINODE

International Nuclear Information System (INIS)

Zhao Junwei; Kosovichev, Alexander G.; Sekii, Takashi

2010-01-01

We analyze a solar active region observed by the Hinode Ca II H line using the time-distance helioseismology technique, and infer wave-speed perturbation structures and flow fields beneath the active region with a high spatial resolution. The general subsurface wave-speed structure is similar to the previous results obtained from Solar and Heliospheric Observatory/Michelson Doppler Imager observations. The general subsurface flow structure is also similar, and the downward flows beneath the sunspot and the mass circulations around the sunspot are clearly resolved. Below the sunspot, some organized divergent flow cells are observed, and these structures may indicate the existence of mesoscale convective motions. Near the light bridge inside the sunspot, hotter plasma is found beneath, and flows divergent from this area are observed. The Hinode data also allow us to investigate potential uncertainties caused by the use of phase-speed filter for short travel distances. Comparing the measurements with and without the phase-speed filtering, we find out that inside the sunspot, mean acoustic travel times are in basic agreement, but the values are underestimated by a factor of 20%-40% inside the sunspot umbra for measurements with the filtering. The initial acoustic tomography results from Hinode show a great potential of using high-resolution observations for probing the internal structure and dynamics of sunspots.

Design of a high-resolution high-stability positioning mechanism for crystal optics

International Nuclear Information System (INIS)

Shu, D.; Toellner, T. S.; Alp, E. E.

1999-01-01

The authors present a novel miniature multi-axis driving structure that will allow positioning of two crystals with better than 50-nrad angular resolution and nanometer linear driving sensitivity.The precision and stability of this structure allow the user to align or adjust an assembly of crystals to achieve the same performance as does a single channel-cut crystal, so they call it an artificial channel-cut crystal. In this paper, the particular designs and specifications, as well as the test results,for a two-axis driving structure for a high-energy-resolution artificial channel-cut crystal monochromator are presented

Imaging collagen type I fibrillogenesis with high spatiotemporal resolution

International Nuclear Information System (INIS)

Stamov, Dimitar R; Stock, Erik; Franz, Clemens M; Jähnke, Torsten; Haschke, Heiko

2015-01-01

Fibrillar collagens, such as collagen type I, belong to the most abundant extracellular matrix proteins and they have received much attention over the last five decades due to their large interactome, complex hierarchical structure and high mechanical stability. Nevertheless, the collagen self-assembly process is still incompletely understood. Determining the real-time kinetics of collagen type I formation is therefore pivotal for better understanding of collagen type I structure and function, but visualising the dynamic self-assembly process of collagen I on the molecular scale requires imaging techniques offering high spatiotemporal resolution. Fast and high-speed scanning atomic force microscopes (AFM) provide the means to study such processes on the timescale of seconds under near-physiological conditions. In this study we have applied fast AFM tip scanning to study the assembly kinetics of fibrillar collagen type I nanomatrices with a temporal resolution reaching eight seconds for a frame size of 500 nm. By modifying the buffer composition and pH value, the kinetics of collagen fibrillogenesis can be adjusted for optimal analysis by fast AFM scanning. We furthermore show that amplitude-modulation imaging can be successfully applied to extract additional structural information from collagen samples even at high scan rates. Fast AFM scanning with controlled amplitude modulation therefore provides a versatile platform for studying dynamic collagen self-assembly processes at high resolution. - Highlights: • Continuous non-invasive time-lapse investigation of collagen I fibrillogenesis in situ. • Imaging of collagen I self-assembly with high spatiotemporal resolution. • Application of setpoint modulation to study the hierarchical structure of collagen I. • Observing real-time formation of the D-banding pattern in collagen I

Imaging collagen type I fibrillogenesis with high spatiotemporal resolution

Energy Technology Data Exchange (ETDEWEB)

Stamov, Dimitar R, E-mail: stamov@jpk.com [JPK Instruments AG, Bouchéstrasse 12, 12435 Berlin (Germany); Stock, Erik [JPK Instruments AG, Bouchéstrasse 12, 12435 Berlin (Germany); Franz, Clemens M [DFG-Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1a, 76131 Karlsruhe (Germany); Jähnke, Torsten; Haschke, Heiko [JPK Instruments AG, Bouchéstrasse 12, 12435 Berlin (Germany)

2015-02-15

Fibrillar collagens, such as collagen type I, belong to the most abundant extracellular matrix proteins and they have received much attention over the last five decades due to their large interactome, complex hierarchical structure and high mechanical stability. Nevertheless, the collagen self-assembly process is still incompletely understood. Determining the real-time kinetics of collagen type I formation is therefore pivotal for better understanding of collagen type I structure and function, but visualising the dynamic self-assembly process of collagen I on the molecular scale requires imaging techniques offering high spatiotemporal resolution. Fast and high-speed scanning atomic force microscopes (AFM) provide the means to study such processes on the timescale of seconds under near-physiological conditions. In this study we have applied fast AFM tip scanning to study the assembly kinetics of fibrillar collagen type I nanomatrices with a temporal resolution reaching eight seconds for a frame size of 500 nm. By modifying the buffer composition and pH value, the kinetics of collagen fibrillogenesis can be adjusted for optimal analysis by fast AFM scanning. We furthermore show that amplitude-modulation imaging can be successfully applied to extract additional structural information from collagen samples even at high scan rates. Fast AFM scanning with controlled amplitude modulation therefore provides a versatile platform for studying dynamic collagen self-assembly processes at high resolution. - Highlights: • Continuous non-invasive time-lapse investigation of collagen I fibrillogenesis in situ. • Imaging of collagen I self-assembly with high spatiotemporal resolution. • Application of setpoint modulation to study the hierarchical structure of collagen I. • Observing real-time formation of the D-banding pattern in collagen I.

Structure of δ-Bi2O3 from density functional theory: A systematic crystallographic analysis

International Nuclear Information System (INIS)

Aidhy, Dilpuneet S.; Sinnott, Susan B.; Wachsman, Eric D.; Phillpot, Simon R.; Nino, Juan C.

2009-01-01

A systematic crystallographic analysis of the and vacancy-ordered structure of cubic δ-Bi 2 O 3 obtained from electronic-structure calculations is presented. The ordering of vacancies leads to a doubling of the unit-cell that results in a 2x2x2 fluorite super-structure, with an associated reduction in its space group symmetry from Fm3-barm to Fm3-bar. The Bi atoms present inside the vacancy-ordered oxygen sublattice have equal Bi-O bond lengths, whereas, those present inside the vacancy-ordered oxygen sublattice have three different pairs of Bi-O bond lengths. The specific ionic displacements and electronic charge configurations also depend on the nature of vacancy ordering in the oxygen sub-lattice. - Graphical abstract: 1/8 of a 2x2x2 δ-Bi 2 O 3 superstructure having Fm3-bar space group. Every oxygen (black) has three possible positions, only one of which is filled either by O1 (red) or O 2 (blue).

Coupling physics and biogeochemistry thanks to high-resolution observations of the phytoplankton community structure in the northwestern Mediterranean Sea

Science.gov (United States)

Marrec, Pierre; Grégori, Gérald; Doglioli, Andrea M.; Dugenne, Mathilde; Della Penna, Alice; Bhairy, Nagib; Cariou, Thierry; Hélias Nunige, Sandra; Lahbib, Soumaya; Rougier, Gilles; Wagener, Thibaut; Thyssen, Melilotus

2018-03-01

Fine-scale physical structures and ocean dynamics strongly influence and regulate biogeochemical and ecological processes. These processes are particularly challenging to describe and understand because of their ephemeral nature. The OSCAHR (Observing Submesoscale Coupling At High Resolution) campaign was conducted in fall 2015 in which a fine-scale structure (1-10 km/1-10 days) in the northwestern Mediterranean Ligurian subbasin was pre-identified using both satellite and numerical modeling data. Along the ship track, various variables were measured at the surface (temperature, salinity, chlorophyll a and nutrient concentrations) with ADCP current velocity. We also deployed a new model of the CytoSense automated flow cytometer (AFCM) optimized for small and dim cells, for near real-time characterization of the surface phytoplankton community structure of surface waters with a spatial resolution of a few kilometers and an hourly temporal resolution. For the first time with this optimized version of the AFCM, we were able to fully resolve Prochlorococcus picocyanobacteria in addition to the easily distinguishable Synechococcus. The vertical physical dynamics and biogeochemical properties of the studied area were investigated by continuous high-resolution CTD profiles thanks to a moving vessel profiler (MVP) during the vessel underway associated with a high-resolution pumping system deployed during fixed stations allowing sampling of the water column at a fine resolution (below 1 m). The observed fine-scale feature presented a cyclonic structure with a relatively cold core surrounded by warmer waters. Surface waters were totally depleted in nitrate and phosphate. In addition to the doming of the isopycnals by the cyclonic circulation, an intense wind event induced Ekman pumping. The upwelled subsurface cold nutrient-rich water fertilized surface waters and was marked by an increase in Chl a concentration. Prochlorococcus and pico- and nano-eukaryotes were more

Expression, purification, crystallization and X-ray crystallographic studies of different redox states of the active site of thioredoxin 1 from the whiteleg shrimp Litopenaeus vannamei

International Nuclear Information System (INIS)

Campos-Acevedo, Adam A.; Garcia-Orozco, Karina D.; Sotelo-Mundo, Rogerio R.; Rudiño-Piñera, Enrique

2013-01-01

Analysis of the different redox states of the catalytic cysteines in four crystallographic structures of thioredoxin 1 from the Pacific whiteleg shrimp L. vannamei highlights their reactivity and corroborates the existence of a structural dimer mediated by an interface of 12 residues which includes a disulfide bridge between the Cys73 residues of each monomer. Thioredoxin (Trx) is a 12 kDa cellular redox protein that belongs to a family of small redox proteins which undergo reversible oxidation to produce a cystine disulfide bond through the transfer of reducing equivalents from the catalytic site cysteine residues (Cys32 and Cys35) to a disulfide substrate. In this study, crystals of thioredoxin 1 from the Pacific whiteleg shrimp Litopenaeus vannamei (LvTrx) were successfully obtained. One data set was collected from each of four crystals at 100 K and the three-dimensional structures of the catalytic cysteines in different redox states were determined: reduced and oxidized forms at 2.00 Å resolution using data collected at a synchrotron-radiation source and two partially reduced structures at 1.54 and 1.88 Å resolution using data collected using an in-house source. All of the crystals belonged to space group P3 2 12, with unit-cell parameters a = 57.5 (4), b = 57.5 (4), c = 118.1 (8) Å. The asymmetric unit contains two subunits of LvTrx, with a Matthews coefficient (V M ) of 2.31 Å 3 Da −1 and a solvent content of 46%. Initial phases were determined by molecular replacement using the crystallographic model of Trx from Drosophila melanogaster as a template. In the present work, LvTrx was overexpressed in Escherichia coli, purified and crystallized. Structural analysis of the different redox states at the Trx active site highlights its reactivity and corroborates the existence of a dimer in the crystal. In the crystallographic structures the dimer is stabilized by several interactions, including a disulfide bridge between Cys73 of each LvTrx monomer, a

High-resolution electron microscopy of advanced materials

Energy Technology Data Exchange (ETDEWEB)

Mitchell, T.E.; Kung, H.H.; Sickafus, K.E.; Gray, G.T. III; Field, R.D.; Smith, J.F. [Los Alamos National Lab., NM (United States). Materials Science and Technology Div.

1997-11-01

This final report chronicles a three-year, Laboratory Directed Research and Development (LDRD) project at Los Alamos National Laboratory (LANL). The High-Resolution Electron Microscopy Facility has doubled in size and tripled in quality since the beginning of the three-year period. The facility now includes a field-emission scanning electron microscope, a 100 kV field-emission scanning transmission electron microscope (FE-STEM), a 300 kV field-emission high-resolution transmission electron microscope (FE-HRTEM), and a 300 kV analytical transmission electron microscope. A new orientation imaging microscope is being installed. X-ray energy dispersive spectrometers for chemical analysis are available on all four microscopes; parallel electron energy loss spectrometers are operational on the FE-STEM and FE-HRTEM. These systems enable evaluation of local atomic bonding, as well as chemical composition in nanometer-scale regions. The FE-HRTEM has a point-to-point resolution of 1.6 {angstrom}, but the resolution can be pushed to its information limit of 1 {angstrom} by computer reconstruction of a focal series of images. HRTEM has been used to image the atomic structure of defects such as dislocations, grain boundaries, and interfaces in a variety of materials from superconductors and ferroelectrics to structural ceramics and intermetallics.

High-resolution X-ray television and high-resolution video recorders

International Nuclear Information System (INIS)

Haendle, J.; Horbaschek, H.; Alexandrescu, M.

1977-01-01

The improved transmission properties of the high-resolution X-ray television chain described here make it possible to transmit more information per television image. The resolution in the fluoroscopic image, which is visually determined, depends on the dose rate and the inertia of the television pick-up tube. This connection is discussed. In the last few years, video recorders have been increasingly used in X-ray diagnostics. The video recorder is a further quality-limiting element in X-ray television. The development of function patterns of high-resolution magnetic video recorders shows that this quality drop may be largely overcome. The influence of electrical band width and number of lines on the resolution in the X-ray television image stored is explained in more detail. (orig.) [de

The use of Fourier reverse transforms in crystallographic phase refinement

Energy Technology Data Exchange (ETDEWEB)

Ringrose, Sharon [Iowa State Univ., Ames, IA (United States)

1997-10-08

Often a crystallographer obtains an electron density map which shows only part of the structure. In such cases, the phasing of the trial model is poor enough that the electron density map may show peaks in some of the atomic positions, but other atomic positions are not visible. There may also be extraneous peaks present which are not due to atomic positions. A method for determination of crystal structures that have resisted solution through normal crystallographic methods has been developed. PHASER is a series of FORTRAN programs which aids in the structure solution of poorly phased electron density maps by refining the crystallographic phases. It facilitates the refinement of such poorly phased electron density maps for difficult structures which might otherwise not be solvable. The trial model, which serves as the starting point for the phase refinement, may be acquired by several routes such as direct methods or Patterson methods. Modifications are made to the reverse transform process based on several assumptions. First, the starting electron density map is modified based on the fact that physically the electron density map must be non-negative at all points. In practice a small positive cutoff is used. A reverse Fourier transform is computed based on the modified electron density map. Secondly, the authors assume that a better electron density map will result by using the observed magnitudes of the structure factors combined with the phases calculated in the reverse transform. After convergence has been reached, more atomic positions and less extraneous peaks are observed in the refined electron density map. The starting model need not be very large to achieve success with PHASER; successful phase refinement has been achieved with a starting model that consists of only 5% of the total scattering power of the full molecule. The second part of the thesis discusses three crystal structure determinations.

CIRS High-Resolution Thermal Scans and the Structure of Saturn's B Ring

Science.gov (United States)

Brooks, S. M.; Spilker, L. J.; Showalter, M.; Pilorz, S.; Edgington, S. G.

2017-12-01

The flyby of Titan on November 29, 2016, sent the Cassini spacecraft on a trajectory that would take it within 10,000 kilometers of Saturn's F ring multiple times before a subsequent Titan encounter on April 22, 2017, would send it on ballistic trajectory carrying it between Saturn's cloud tops and the planet's D ring for several flybys. This geometry has proven beneficial for high-resolution studies of the rings, not just because of Cassini's proximity to the rings, but also because of the spacecraft's high elevation angle above the rings, which reduces the foreshortening that tends to degrade resolution in the ring plane. We will report on several observations of Saturn's main rings at the high spatial resolutions enabled by the end-of-mission geometry, particulary the B ring, with the Composite Infrared Spectrometer onboard Cassini during the F-ring and proximal orbits. CIRS' three infrared detectors cover a combined spectral range of 10 to 1400 cm-1 (1 mm down to 7 microns). We focus on data from Focal Plane 1, which covers the 10 to 600 cm-1 range (1 mm to 16 microns). The apodized spectral resolution of the instrument can be varied from 15 cm-1 to 0.5 cm-1 (Flasar et al. 2004). FP1's wavelength range makes it well-suited to sensing thermal emission from objects at temperatures typical of Saturn's rings. Correlating ring optical depth with temperatures retrieved from scans of the face of the rings exposed to direct solar illumination (the lit face) and the opposite (unlit) face suggests differences in ring structure or particle transport between the lit and unlit sides of the rings in different regions of the B ring. Lit side temperatures in the core of the B ring range between 82 and 87 K; temperatures on the unlit side of the core vary from 66 K up to 74 K. Ferrari and Reffet (2013) and Pilorz et al. (2015) published thorough analyses of the thermal throughput across this optically thick ring. We will discuss these recent CIRS rings observations and their

Challenges in quantitative crystallographic characterization of 3D thin films by ACOM-TEM.

Science.gov (United States)

Kobler, A; Kübel, C

2017-02-01

Automated crystal orientation mapping for transmission electron microscopy (ACOM-TEM) has become an easy to use method for the investigation of crystalline materials and complements other TEM methods by adding local crystallographic information over large areas. It fills the gap between high resolution electron microscopy and electron back scatter diffraction in terms of spatial resolution. Recent investigations showed that spot diffraction ACOM-TEM is a quantitative method with respect to sample parameters like grain size, twin density, orientation density and others. It can even be used in combination with in-situ tensile or thermal testing. However, there are limitations of the current method. In this paper we discuss some of the challenges and discuss solutions, e.g. we present an ambiguity filter that reduces the number of pixels with a '180° ambiguity problem'. For that an ACOM-TEM tilt series of nanocrystalline Pd thin films with overlapping crystallites was acquired and analyzed. Copyright © 2017. Published by Elsevier B.V.

Automated method for relating regional pulmonary structure and function: integration of dynamic multislice CT and thin-slice high-resolution CT

Science.gov (United States)

Tajik, Jehangir K.; Kugelmass, Steven D.; Hoffman, Eric A.

1993-07-01

We have developed a method utilizing x-ray CT for relating pulmonary perfusion to global and regional anatomy, allowing for detailed study of structure to function relationships. A thick slice, high temporal resolution mode is used to follow a bolus contrast agent for blood flow evaluation and is fused with a high spatial resolution, thin slice mode to obtain structure- function detail. To aid analysis of blood flow, we have developed a software module, for our image analysis package (VIDA), to produce the combined structure-function image. Color coded images representing blood flow, mean transit time, regional tissue content, regional blood volume, regional air content, etc. are generated and imbedded in the high resolution volume image. A text file containing these values along with a voxel's 3-D coordinates is also generated. User input can be minimized to identifying the location of the pulmonary artery from which the input function to a blood flow model is derived. Any flow model utilizing one input and one output function can be easily added to a user selectable list. We present examples from our physiologic based research findings to demonstrate the strengths of combining dynamic CT and HRCT relative to other scanning modalities to uniquely characterize pulmonary normal and pathophysiology.

Numerical simulation study for atomic-resolution x-ray fluorescence holography

International Nuclear Information System (INIS)

Xie Honglan; Gao Hongyi; Chen Jianwen; Xiong Shisheng; Xu Zhizhan; Wang Junyue; Zhu Peiping; Xian Dingchang

2003-01-01

Based on the principle of x-ray fluorescence holography, an iron single crystal model of a body-centred cubic lattice is numerically simulated. From the fluorescence hologram produced numerically, the Fe atomic images were reconstructed. The atomic images of the (001), (100), (010) crystallographic planes were consistent with the corresponding atomic positions of the model. The result indicates that one can obtain internal structure images of single crystals at atomic-resolution by using x-ray fluorescence holography

Dianthraceno[a,e]pentalenes: Synthesis, crystallographic structures and applications in organic field-effect transistors

KAUST Repository

Dai, Gaole

2015-01-01

Two soluble and stable dianthraceno[a,e]pentalenes with two (DAP1) and six (DAP2) phenyl substituents were synthesized. Both compounds possess a small energy band gap and show amphoteric redox behaviour due to intramolecular donor-accepter interactions. X-ray crystallographic analysis revealed that DAP2 has a closely packed structure with multi-dimensional [C-H⋯π] interactions although there are no π-π interactions between the dianthraceno[a,e]pentalene cores. As a result, solution-processed field effect transistors based on DAP2 exhibited an average hole mobility of 0.65 cm2 V-1 s-1. Under similar conditions, DAP1 showed an average field effect hole mobility of 0.001 cm2 V-1 s-1. This journal is

On the use of distorted fcc structures for describing high-pressure phases

International Nuclear Information System (INIS)

Gerward, L.; Staun Olsen, J.; Benedict, U.

1986-01-01

The paper describes distorted lattices that can be derived from the face-centred cubic Bravais lattice. Crystallographic principles are outlined and it is discussed how various lattices can be identified from the observed splitting of X-ray powder diffraction lines. Examples are taken from recent high-pressure studies of actinide rocksalt structure compounds and cerium metal. (orig.)

Preliminary X-ray crystallographic analysis of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans

International Nuclear Information System (INIS)

Zhang, Yanfei; Cherney, Maia M.; Solomonson, Matthew; Liu, Jianshe; James, Michael N. G.; Weiner, Joel H.

2009-01-01

The sulfide:quinone oxidoreductase from A. ferrooxidans ATCC 23270 was overexpressed in E. coli and purified. Crystallization and preliminarily X-ray crystallographic analysis were performed for the recombinant enzyme. The gene product of open reading frame AFE-1293 from Acidithiobacillus ferrooxidans ATCC 23270 is annotated as encoding a sulfide:quinone oxidoreductase, an enzyme that catalyses electron transfer from sulfide to quinone. Following overexpression in Escherichia coli, the enzyme was purified and crystallized using the hanging-drop vapour-diffusion method. The native crystals belonged to the tetragonal space group P4 2 2 1 2, with unit-cell parameters a = b = 131.7, c = 208.8 Å, and diffracted to 2.3 Å resolution. Preliminary crystallographic analysis indicated the presence of a dimer in the asymmetric unit, with an extreme value of the Matthews coefficient (V M ) of 4.53 Å 3 Da −1 and a solvent content of 72.9%

Purification, crystallization and preliminary crystallographic analysis of human cystathionine β-synthase

International Nuclear Information System (INIS)

Oyenarte, Iker; Majtan, Tomas; Ereño, June; Corral-Rodríguez, María Angeles; Kraus, Jan P.; Martínez-Cruz, Luis Alfonso

2012-01-01

This article describes the crystallization and preliminary crystallographic analysis of a protein construct (hCBS 516–525 ) that contains the full-length cystathionine β-synthase from Homo sapiens (hCBS) and just lacks amino-acid residues 516–525. Human cystathionine β-synthase (CBS) is a pyridoxal-5′-phosphate-dependent hemeprotein, whose catalytic activity is regulated by S-adenosylmethionine. CBS catalyzes the β-replacement reaction of homocysteine (Hcy) with serine to yield cystathionine. CBS is a key regulator of plasma levels of the thrombogenic Hcy and deficiency in CBS is the single most common cause of homocystinuria, an inherited metabolic disorder of sulfur amino acids. The properties of CBS enzymes, such as domain organization, oligomerization degree or regulatory mechanisms, are not conserved across the eukaryotes. The current body of knowledge is insufficient to understand these differences and their impact on CBS function and physiology. To overcome this deficiency, we have addressed the crystallization and preliminary crystallographic analysis of a protein construct (hCBS 516–525 ) that contains the full-length CBS from Homo sapiens (hCBS) and just lacks amino-acid residues 516–525, which are located in a disordered loop. The human enzyme yielded crystals belonging to space group I222, with unit-cell parameters a = 124.98, b = 136.33, c = 169.83 Å and diffracting X-rays to a resolution of 3.0 Å. The crystal structure appears to contain two molecules in the asymmetric unit which presumably correspond to a dimeric form of the enzyme

Ultrahigh resolution radiation imaging system using an optical fiber structure scintillator plate.

Science.gov (United States)

Yamamoto, Seiichi; Kamada, Kei; Yoshikawa, Akira

2018-02-16

High resolution imaging of radiation is required for such radioisotope distribution measurements as alpha particle detection in nuclear facilities or high energy physics experiments. For this purpose, we developed an ultrahigh resolution radiation imaging system using an optical fiber structure scintillator plate. We used a ~1-μm diameter fiber structured GdAlO 3 :Ce (GAP) /α-Al 2 O 3 scintillator plate to reduce the light spread. The fiber structured scintillator plate was optically coupled to a tapered optical fiber plate to magnify the image and combined with a lens-based high sensitivity CCD camera. We observed the images of alpha particles with a spatial resolution of ~25 μm. For the beta particles, the images had various shapes, and the trajectories of the electrons were clearly observed in the images. For the gamma photons, the images also had various shapes, and the trajectories of the secondary electrons were observed in some of the images. These results show that combining an optical fiber structure scintillator plate with a tapered optical fiber plate and a high sensitivity CCD camera achieved ultrahigh resolution and is a promising method to observe the images of the interactions of radiation in a scintillator.

A High-resolution Atlas and Statistical Model of the Vocal Tract from Structural MRI.

Science.gov (United States)

Woo, Jonghye; Lee, Junghoon; Murano, Emi Z; Xing, Fangxu; Al-Talib, Meena; Stone, Maureen; Prince, Jerry L

Magnetic resonance imaging (MRI) is an essential tool in the study of muscle anatomy and functional activity in the tongue. Objective assessment of similarities and differences in tongue structure and function has been performed using unnormalized data, but this is biased by the differences in size, shape, and orientation of the structures. To remedy this, we propose a methodology to build a 3D vocal tract atlas based on structural MRI volumes from twenty normal subjects. We first constructed high-resolution volumes from three orthogonal stacks. We then removed extraneous data so that all 3D volumes contained the same anatomy. We used an unbiased diffeomorphic groupwise registration using a cross-correlation similarity metric. Principal component analysis was applied to the deformation fields to create a statistical model from the atlas. Various evaluations and applications were carried out to show the behaviour and utility of the atlas.

Coupling physics and biogeochemistry thanks to high-resolution observations of the phytoplankton community structure in the northwestern Mediterranean Sea

Directory of Open Access Journals (Sweden)

P. Marrec

2018-03-01

Full Text Available Fine-scale physical structures and ocean dynamics strongly influence and regulate biogeochemical and ecological processes. These processes are particularly challenging to describe and understand because of their ephemeral nature. The OSCAHR (Observing Submesoscale Coupling At High Resolution campaign was conducted in fall 2015 in which a fine-scale structure (1–10 km∕1–10 days in the northwestern Mediterranean Ligurian subbasin was pre-identified using both satellite and numerical modeling data. Along the ship track, various variables were measured at the surface (temperature, salinity, chlorophyll a and nutrient concentrations with ADCP current velocity. We also deployed a new model of the CytoSense automated flow cytometer (AFCM optimized for small and dim cells, for near real-time characterization of the surface phytoplankton community structure of surface waters with a spatial resolution of a few kilometers and an hourly temporal resolution. For the first time with this optimized version of the AFCM, we were able to fully resolve Prochlorococcus picocyanobacteria in addition to the easily distinguishable Synechococcus. The vertical physical dynamics and biogeochemical properties of the studied area were investigated by continuous high-resolution CTD profiles thanks to a moving vessel profiler (MVP during the vessel underway associated with a high-resolution pumping system deployed during fixed stations allowing sampling of the water column at a fine resolution (below 1 m. The observed fine-scale feature presented a cyclonic structure with a relatively cold core surrounded by warmer waters. Surface waters were totally depleted in nitrate and phosphate. In addition to the doming of the isopycnals by the cyclonic circulation, an intense wind event induced Ekman pumping. The upwelled subsurface cold nutrient-rich water fertilized surface waters and was marked by an increase in Chl a concentration. Prochlorococcus and pico

High resolution orientation mapping of secondary phases in ATI 718Plus® alloy

Directory of Open Access Journals (Sweden)

Krakow Robert

2014-01-01

Full Text Available The polycrystalline superalloy ATI 718Plus ® (hereafter 718Plus has been developed to replace the established alloy Inconel 718 by offering higher temperature capability for applications in gas turbines. The alloy exhibits two secondary phases in the austenitic matrix; it is strengthened by the γ′-phase with η-phase discontinuously precipitated at the grain boundaries. It can be utilized to control grain growth during forging. Generally, hexagonal η phase has been reported to possess a defined crystallographic orientation with the matrix. However, the material studied here exhibits blocky η-phase that has been precipitated and grown during thermo-mechanical processing. Therefore a measurable change in orientation relationship is expected. The standard technique for orientation mapping is electron back-scattered diffraction with spatial resolution of 100 nm. That is insufficient for studying η-phase in 718Plus. By applying high resolution orientation mapping in the transmission electron microscope (Philips CM 300 FEGTEM equipped with a Nanomegas ASTARTM system a resolution of 3 nm was achieved. The indexed diffraction data was analysed using the Matlab Toolbox Mtex. The analysis included grain reconstruction and exclusion of low confidence measurements. The data set allows generating phase boundary maps indicating interfaces characteristics. Quantitative assessment shows that only 19% of the γ-η-interfaces fulfil the orientation relationship.

Carbohydrate structure: the rocky road to automation.

Science.gov (United States)

Agirre, Jon; Davies, Gideon J; Wilson, Keith S; Cowtan, Kevin D

2017-06-01

With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to 'protein standards' will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most. Copyright © 2016 Elsevier Ltd. All rights reserved.

Crystal structure of the sweet-tasting protein thaumatin II at 1.27 A

International Nuclear Information System (INIS)

Masuda, Tetsuya; Ohta, Keisuke; Tani, Fumito; Mikami, Bunzo; Kitabatake, Naofumi

2011-01-01

Highlights: → X-ray crystallographic structure of sweet-tasting protein, thaumatin II, was determined at a resolution of 1.27 A. → The overall structure of thaumatin II is similar to that of thaumatin I, but a slight shift of the Cα atom of G96 in thaumatin II was observed. → The side chain of two critical residues, 67 and 82, for sweetness was modeled in two alternative conformations. → The flexibility and fluctuation of side chains at 67 and 82 seems to be suitable for interaction of thaumatin molecules with sweet receptors. -- Abstract: Thaumatin, an intensely sweet-tasting protein, elicits a sweet taste sensation at 50 nM. Here the X-ray crystallographic structure of one of its variants, thaumatin II, was determined at a resolution of 1.27 A. Overall structure of thaumatin II is similar to thaumatin I, but a slight shift of the Cα atom of G96 in thaumatin II was observed. Furthermore, the side chain of residue 67 in thaumatin II is highly disordered. Since residue 67 is one of two residues critical to the sweetness of thaumatin, the present results suggested that the critical positive charges at positions 67 and 82 are disordered and the flexibility and fluctuation of these side chains would be suitable for interaction of thaumatin molecules with sweet receptors.

Crystal structure of the sweet-tasting protein thaumatin II at 1.27 A

Energy Technology Data Exchange (ETDEWEB)

Masuda, Tetsuya, E-mail: t2masuda@kais.kyoto-u.ac.jp [Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Department Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Uji, Kyoto 611-0011 (Japan); Ohta, Keisuke; Tani, Fumito [Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Department Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Uji, Kyoto 611-0011 (Japan); Mikami, Bunzo [Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Kitabatake, Naofumi [Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 (Japan); Department Natural Resources, Graduate School of Global Environmental Studies, Kyoto University, Uji, Kyoto 611-0011 (Japan)

2011-07-08

Highlights: {yields} X-ray crystallographic structure of sweet-tasting protein, thaumatin II, was determined at a resolution of 1.27 A. {yields} The overall structure of thaumatin II is similar to that of thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. {yields} The side chain of two critical residues, 67 and 82, for sweetness was modeled in two alternative conformations. {yields} The flexibility and fluctuation of side chains at 67 and 82 seems to be suitable for interaction of thaumatin molecules with sweet receptors. -- Abstract: Thaumatin, an intensely sweet-tasting protein, elicits a sweet taste sensation at 50 nM. Here the X-ray crystallographic structure of one of its variants, thaumatin II, was determined at a resolution of 1.27 A. Overall structure of thaumatin II is similar to thaumatin I, but a slight shift of the C{alpha} atom of G96 in thaumatin II was observed. Furthermore, the side chain of residue 67 in thaumatin II is highly disordered. Since residue 67 is one of two residues critical to the sweetness of thaumatin, the present results suggested that the critical positive charges at positions 67 and 82 are disordered and the flexibility and fluctuation of these side chains would be suitable for interaction of thaumatin molecules with sweet receptors.

A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP)

International Nuclear Information System (INIS)

Tsuruta, Osamu; Yokoyama, Hideshi; Fujii, Satoshi

2012-01-01

A new crystal lattice structure of H. pylori neutrophil-activating protein has been determined. Iron loading causes a series of conformational changes at the ferroxidase centre. A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP) has been determined in two forms: the native state (Apo) at 2.20 Å resolution and an iron-loaded form (Fe-load) at 2.50 Å resolution. The highly solvated packing of the dodecameric shell is suitable for crystallographic study of the metal ion-uptake pathway. Like other bacterioferritins, HP-NAP forms a spherical dodecamer with 23 symmetry including two kinds of channels. Iron loading causes a series of conformational changes of amino-acid residues (Trp26, Asp52 and Glu56) at the ferroxidase centre

Structure of Se-rich As-Se glasses by high-resolution x-ray photoelectron spectroscopy

International Nuclear Information System (INIS)

Golovchak, R.; Kovalskiy, A.; Miller, A. C.; Jain, H.; Shpotyuk, O.

2007-01-01

To establish the validity of various proposed structural models, we have investigated the structure of the binary As x Se 100-x chalcogenide glass family (x≤40) by high-resolution x-ray photoelectron spectroscopy. From the composition dependence of the valence band, the contributions to the density of states from the 4p lone pair electrons of Se and the 4p bonding states and 4s electrons of Se and As are identified in the top part of the band. The analysis of Se 3d and As 3d core-level spectra supports the so-called chain crossing model for the atomic structure of Se-rich As x Se 100-x bulk glasses. The results also indicate small deviations (∼3-8%) from this model, especially for glass compositions with short Se chains (25 40 Se 60 and of Se-Se-Se fragments in a glass with composition x=30 is established

Structural Characterisation of Acetogenins from Annona muricata by Supercritical Fluid Chromatography Coupled to High-Resolution Tandem Mass Spectrometry.

Science.gov (United States)

Laboureur, Laurent; Bonneau, Natacha; Champy, Pierre; Brunelle, Alain; Touboul, David

2017-11-01

Acetogenins are plant polyketides known to be cytotoxic and proposed as antitumor candidates. They are also suspected to be alimentary neurotoxins. Their occurrence as complex mixtures renders their dereplication and structural identification difficult using liquid chromatography coupled to tandem mass spectrometry and efforts are required to improve the methodology. To develop a supercritical fluid chromatography (SFC) high-resolution tandem mass spectrometry method, involving lithium post-column cationisation, for the structural characterisation of Annonaceous acetogenins in crude extracts. The seeds of Annona muricata L. were extracted with methanol. Supercritical fluid chromatography of the extract, using a 2-ethylpyridine stationary phase column, was monitored using a high-resolution quadrupole time-of-flight mass spectrometer. Lithium iodide was added post-column in the make-up solvent. For comparison, the same extract was analysed using high-pressure liquid chromatography coupled to the same mass spectrometer, with a column based on solid core particles. Sensitivity was similar for both HPLC and SFC approaches. Retention behaviour and fragmentation pathways of three different isomer groups are described. A previously unknown group of acetogenins was also evidenced for the first time. The use of SFC-MS/MS allows the reduction of the time of analysis, of environmental impact and an increase in the chromatographic resolution, compared to liquid chromatography. This new methodology enlightened a new group of acetogenins, isomers of montanacin-D. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

High pressure structural phase transition of neodymium mono pnictides

International Nuclear Information System (INIS)

Pagare, Gitanjali; Ojha, P.; Sanyal, S.P.; Aynyas, Mahendra

2007-01-01

We have investigated theoretically the high-pressure structural phase transition of two neodymium mono NdX (X=As, Sb) using an interionic potential theory with necessary modification to include the effect of Coulomb screening by the delocalized f electrons of Nd ion. These compounds exhibits first order crystallographic phase transition from their NaCl (B 1 ) phase to body centered tetragonal (BCT) at 27 GPa and 15.3 GPa respectively. We also calculated the Nd-Nd distance as a function of pressure. (author)

Multi-resolution voxel phantom modeling: a high-resolution eye model for computational dosimetry.

Science.gov (United States)

Caracappa, Peter F; Rhodes, Ashley; Fiedler, Derek

2014-09-21

Voxel models of the human body are commonly used for simulating radiation dose with a Monte Carlo radiation transport code. Due to memory limitations, the voxel resolution of these computational phantoms is typically too large to accurately represent the dimensions of small features such as the eye. Recently reduced recommended dose limits to the lens of the eye, which is a radiosensitive tissue with a significant concern for cataract formation, has lent increased importance to understanding the dose to this tissue. A high-resolution eye model is constructed using physiological data for the dimensions of radiosensitive tissues, and combined with an existing set of whole-body models to form a multi-resolution voxel phantom, which is used with the MCNPX code to calculate radiation dose from various exposure types. This phantom provides an accurate representation of the radiation transport through the structures of the eye. Two alternate methods of including a high-resolution eye model within an existing whole-body model are developed. The accuracy and performance of each method is compared against existing computational phantoms.

Local dynamics of proteins and DNA evaluated from crystallographic B factors

International Nuclear Information System (INIS)

Schneider, Bohdan; Gelly, Jean-Christophe; Brevern, Alexandre G. de; Černý, Jiří

2014-01-01

surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified

Local dynamics of proteins and DNA evaluated from crystallographic B factors

Energy Technology Data Exchange (ETDEWEB)

Schneider, Bohdan, E-mail: bohdan.schneider@gmail.com [Institute of Biotechnology AS CR, Videnska 1083, 142 20 Prague (Czech Republic); Gelly, Jean-Christophe; Brevern, Alexandre G. de [INSERM, U1134, DSIMB, 75739 Paris (France); Université Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, 75739 Paris (France); Institut National de la Transfusion Sanguine (INTS), 75739 Paris (France); Laboratoire d’Excellence GR-Ex, 75739 Paris (France); Černý, Jiří [Institute of Biotechnology AS CR, Videnska 1083, 142 20 Prague (Czech Republic)

2014-09-01

surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified.

ANL high resolution injector

International Nuclear Information System (INIS)

Minehara, E.; Kutschera, W.; Hartog, P.D.; Billquist, P.

1985-01-01

The ANL (Argonne National Laboratory) high-resolution injector has been installed to obtain higher mass resolution and higher preacceleration, and to utilize effectively the full mass range of ATLAS (Argonne Tandem Linac Accelerator System). Preliminary results of the first beam test are reported briefly. The design and performance, in particular a high-mass-resolution magnet with aberration compensation, are discussed. 7 refs., 5 figs., 2 tabs

Structure of the orthorhombic form of human inosine triphosphate pyrophosphatase

International Nuclear Information System (INIS)

Porta, Jason; Kolar, Carol; Kozmin, Stanislav G.; Pavlov, Youri I.; Borgstahl, Gloria E. O.

2006-01-01

X-ray crystallographic analysis of human inosine triphosphate pyrophosphohydrolase provided the secondary structure and active-site structure at 1.6 Å resolution in an orthorhombic crystal form. The structure gives a framework for future structure–function studies employing site-directed mutagenesis and for the identification of substrate/product-binding sites. The structure of human inosine triphosphate pyrophosphohydrolase (ITPA) has been determined using diffraction data to 1.6 Å resolution. ITPA contributes to the accurate replication of DNA by cleansing cellular dNTP pools of mutagenic nucleotide purine analogs such as dITP or dXTP. A similar high-resolution unpublished structure has been deposited in the Protein Data Bank from a monoclinic and pseudo-merohedrally twinned crystal. Here, cocrystallization of ITPA with a molar ratio of XTP appears to have improved the crystals by eliminating twinning and resulted in an orthorhombic space group. However, there was no evidence for bound XTP in the structure. Comparison with substrate-bound NTPase from a thermophilic organism predicts the movement of residues within helix α1, the loop before α6 and helix α7 to cap off the active site when substrate is bound

Expression, purification and preliminary crystallographic analysis of sucrose phosphate synthase (SPS) from Halothermothrix orenii

International Nuclear Information System (INIS)

Huynh, Frederick; Tan, Tien-Chye; Swaminathan, Kunchithapadam; Patel, Bharat K. C.

2004-01-01

The first crystallographic study of a sucrose phosphate synthase from H. orenii, an organism that is both thermophilic and halophilic, is reported. The protein crystal diffracts X-rays to 3.01 Å. This is the first report of the crystallization of a sucrose phosphate synthase (SPS; EC 2.4.1.14). It also constitutes the first study of a sucrose phosphate synthase from a non-photosynthetic thermohalophilic anaerobic bacterium, Halothermothrix orenii. The purified recombinant spsA protein has been crystallized in the monoclinic space group C2, with unit-cell parameters a = 154.2, b = 47.9, c = 72.3 Å, β = 103.16°, using the hanging-drop vapour-diffusion method. The crystal diffracts X-rays to a resolution limit of 3.01 Å. Heavy-metal and halide-soaking trials are currently in progress to solve the structure

Structure of a thermostable serralysin from Serratia sp. FS14 at 1.1 Å resolution.

Science.gov (United States)

Wu, Dongxia; Ran, Tinting; Wang, Weiwu; Xu, Dongqing

2016-01-01

Serralysin is a well studied metalloprotease, and typical serralysins are not thermostable. The serralysin isolated from Serratia sp. FS14 was found to be thermostable, and in order to reveal the mechanism responsible for its thermostability, the crystal structure of serralysin from Serratia sp. FS14 was solved to a crystallographic R factor of 0.1619 at 1.10 Å resolution. Similar to its homologues, it mainly consists of two domains: an N-terminal catalytic domain and a `parallel β-roll' C-terminal domain. Comparative studies show that the shape of the catalytic active-site cavity is more open owing to the 189-198 loop, with a short 310-helix protruding further from the molecular surface, and that the β-sheets comprising the `parallel β-roll' are longer than those in its homologues. The formation of hydrogen bonds from one of the nonconserved residues (Asn200) to Lys27 may contribute to the thermostability.

High-resolution 3D imaging of polymerized photonic crystals by lab-based x-ray nanotomography with 50-nm resolution

Science.gov (United States)

Yin, Leilei; Chen, Ying-Chieh; Gelb, Jeff; Stevenson, Darren M.; Braun, Paul A.

2010-09-01

High resolution x-ray computed tomography is a powerful non-destructive 3-D imaging method. It can offer superior resolution on objects that are opaque or low contrast for optical microscopy. Synchrotron based x-ray computed tomography systems have been available for scientific research, but remain difficult to access for broader users. This work introduces a lab-based high-resolution x-ray nanotomography system with 50nm resolution in absorption and Zernike phase contrast modes. Using this system, we have demonstrated high quality 3-D images of polymerized photonic crystals which have been analyzed for band gap structures. The isotropic volumetric data shows excellent consistency with other characterization results.

Absorbed dose estimates to structures of the brain and head using a high-resolution voxel-based head phantom

International Nuclear Information System (INIS)

Evans, Jeffrey F.; Blue, Thomas E.; Gupta, Nilendu

2001-01-01

The purpose of this article is to demonstrate the viability of using a high-resolution 3-D head phantom in Monte Carlo N-Particle (MCNP) for boron neutron capture therapy (BNCT) structure dosimetry. This work describes a high-resolution voxel-based model of a human head and its use for calculating absorbed doses to the structures of the brain. The Zubal head phantom is a 3-D model of a human head that can be displayed and manipulated on a computer. Several changes were made to the original head phantom which now contains over 29 critical structures of the brain and head. The modified phantom is a 85x109x120 lattice of voxels, where each voxel is 2.2x2.2x1.4 mm 3 . This model was translated into MCNP lattice format. As a proof of principle study, two MCNP absorbed dose calculations were made (left and right lateral irradiations) using a uniformly distributed neutron disk source with an 1/E energy spectrum. Additionally, the results of these two calculations were combined to estimate the absorbed doses from a bilateral irradiation. Radiobiologically equivalent (RBE) doses were calculated for all structures and were normalized to 12.8 Gy-Eq. For a left lateral irradiation, the left motor cortex receives the limiting RBE dose. For a bilateral irradiation, the insula cortices receive the limiting dose. Among the nonencephalic structures, the parotid glands receive RBE doses that were within 15% of the limiting dose

Phormidium phycoerythrin forms hexamers in crystals: a crystallographic study

Science.gov (United States)

Sonani, Ravi Raghav; Sharma, Mahima; Gupta, Gagan Deep; Kumar, Vinay; Madamwar, Datta

2015-01-01

The crystallographic analysis of a marine cyanobacterium (Phormidium sp. A09DM) phycoerythrin (PE) that shows distinct sequence features compared with known PE structures from cyanobacteria and red algae is reported. Phormidium PE was crystallized using the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant. Diffraction data were collected on the protein crystallography beamline at the Indus-2 synchrotron. The crystals diffracted to about 2.1 Å resolution at 100 K. The crystals, with an apparent hexagonal morphology, belonged to space group P1, with unit-cell parameters a = 108.3, b = 108.4 Å, c = 116.6 Å, α = 78.94, β = 82.50, γ = 60.34°. The molecular-replacement solution confirmed the presence of 12 αβ monomers in the P1 cell. The Phormidium PE elutes as an (αβ)3 trimer of αβ monomers from a molecular-sieve column and exists as [(αβ)3]2 hexamers in the crystal lattice. Unlike red algal PE proteins, the hexamers of Phormidium PE do not form higher-order structures in the crystals. The existence of only one characteristic visual absorption band at 564 nm suggests the presence of phycoerythrobilin chromophores, and the absence of any other types of bilins, in the Phormidium PE assembly. PMID:26249689

NMR structure of the protein NP-247299.1: comparison with the crystal structure

International Nuclear Information System (INIS)

Jaudzems, Kristaps; Geralt, Michael; Serrano, Pedro; Mohanty, Biswaranjan; Horst, Reto; Pedrini, Bill; Elsliger, Marc-André; Wilson, Ian A.; Wüthrich, Kurt

2010-01-01

Comparison of the NMR and crystal structures of a protein determined using largely automated methods has enabled the interpretation of local differences in the highly similar structures. These differences are found in segments of higher B values in the crystal and correlate with dynamic processes on the NMR chemical shift timescale observed in solution. The NMR structure of the protein NP-247299.1 in solution at 313 K has been determined and is compared with the X-ray crystal structure, which was also solved in the Joint Center for Structural Genomics (JCSG) at 100 K and at 1.7 Å resolution. Both structures were obtained using the current largely automated crystallographic and solution NMR methods used by the JCSG. This paper assesses the accuracy and precision of the results from these recently established automated approaches, aiming for quantitative statements about the location of structure variations that may arise from either one of the methods used or from the different environments in solution and in the crystal. To evaluate the possible impact of the different software used for the crystallographic and the NMR structure determinations and analysis, the concept is introduced of reference structures, which are computed using the NMR software with input of upper-limit distance constraints derived from the molecular models representing the results of the two structure determinations. The use of this new approach is explored to quantify global differences that arise from the different methods of structure determination and analysis versus those that represent interesting local variations or dynamics. The near-identity of the protein core in the NMR and crystal structures thus provided a basis for the identification of complementary information from the two different methods. It was thus observed that locally increased crystallographic B values correlate with dynamic structural polymorphisms in solution, including that the solution state of the protein involves

High resolution satellite imagery : from spies to pipeline management

Energy Technology Data Exchange (ETDEWEB)

Adam, S. [Canadian Geomatic Solutions Ltd., Calgary, AB (Canada); Farrell, M. [TransCanada Transmission, Calgary, AB (Canada)

2000-07-01

The launch of Space Imaging's IKONOS satellite in September 1999 has opened the door for corridor applications. The technology has been successfully implemented by TransCanada PipeLines in mapping over 1500 km of their mainline. IKONOS is the world's first commercial high resolution satellite which collects data at 1-meter black/white and 4-meter multi-spectral. Its use is regulated by the U.S. government. It is the best source of high resolution satellite image data. Other sources include the Indian Space Agency's IRS-1 C/D satellite and the Russian SPIN-2 which provides less reliable coverage. In addition, two more high resolution satellites may be launched this year to provide imagery every day of the year. IKONOS scenes as narrow as 5 km can be purchased. TransCanada conducted a pilot study to determine if high resolution satellite imagery is as effective as ortho-photos for identifying population structures within a buffer of TransCanada's east line right-of-way. The study examined three unique segments where residential, commercial, industrial and public features were compared. It was determined that IKONOS imagery is as good as digital ortho-photos for updating structures from low to very high density areas. The satellite imagery was also logistically easier than ortho-photos to acquire. This will be even more evident when the IKONOS image archives begins to grow. 4 tabs., 3 figs.

Electron diffraction and high-resolution transmission electron microscopy of the high temperature crystal structures of GexSb2Te3+x (x=1,2,3) phase change material

NARCIS (Netherlands)

Kooi, B.J.; de Hosson, J.T.M.

2002-01-01

The crystal structures of GeSb2Te4, Ge2Sb2Te5, and Ge3Sb2Te6 were determined using electron diffraction and high-resolution transmission electron microscopy. The structure determined for the former two crystals deviates from the ones proposed in the literature. These crystal structures were

Three dimensional imaging of damage in structural materials using high resolution micro-tomography

Energy Technology Data Exchange (ETDEWEB)

Buffiere, J.-Y. [GEMPPM UMR CNRS 5510, INSA Lyon, 20 Av. A. Einstein, 69621 Villeurbanne Cedex (France)]. E-mail: jean-yves.buffiere@insa-lyon.fr; Proudhon, H. [GEMPPM UMR CNRS 5510, INSA Lyon, 20 Av. A. Einstein, 69621 Villeurbanne Cedex (France); Ferrie, E. [GEMPPM UMR CNRS 5510, INSA Lyon, 20 Av. A. Einstein, 69621 Villeurbanne Cedex (France); Ludwig, W. [GEMPPM UMR CNRS 5510, INSA Lyon, 20 Av. A. Einstein, 69621 Villeurbanne Cedex (France); Maire, E. [GEMPPM UMR CNRS 5510, INSA Lyon, 20 Av. A. Einstein, 69621 Villeurbanne Cedex (France); Cloetens, P. [ESRF Grenoble (France)

2005-08-15

This paper presents recent results showing the ability of high resolution synchrotron X-ray micro-tomography to image damage initiation and development during mechanical loading of structural metallic materials. First, the initiation, growth and coalescence of porosities in the bulk of two metal matrix composites have been imaged at different stages of a tensile test. Quantitative data on damage development has been obtained and related to the nature of the composite matrix. Second, three dimensional images of fatigue crack have been obtained in situ for two different Al alloys submitted to fretting and/or uniaxial in situ fatigue. The analysis of those images shows the strong interaction of the cracks with the local microstructure and provides unique experimental data for modelling the behaviour of such short cracks.

Three dimensional imaging of damage in structural materials using high resolution micro-tomography

International Nuclear Information System (INIS)

Buffiere, J.-Y.; Proudhon, H.; Ferrie, E.; Ludwig, W.; Maire, E.; Cloetens, P.

2005-01-01

This paper presents recent results showing the ability of high resolution synchrotron X-ray micro-tomography to image damage initiation and development during mechanical loading of structural metallic materials. First, the initiation, growth and coalescence of porosities in the bulk of two metal matrix composites have been imaged at different stages of a tensile test. Quantitative data on damage development has been obtained and related to the nature of the composite matrix. Second, three dimensional images of fatigue crack have been obtained in situ for two different Al alloys submitted to fretting and/or uniaxial in situ fatigue. The analysis of those images shows the strong interaction of the cracks with the local microstructure and provides unique experimental data for modelling the behaviour of such short cracks

Low-resolution structure of Drosophila translin

Science.gov (United States)

Kumar, Vinay; Gupta, Gagan D.

2012-01-01

Crystals of native Drosophila melanogaster translin diffracted to 7 Å resolution. Reductive methylation of the protein improved crystal quality. The native and methylated proteins showed similar profiles in size-exclusion chromatography analyses but the methylated protein displayed reduced DNA-binding activity. Crystals of the methylated protein diffracted to 4.2 Å resolution at BM14 of the ESRF synchrotron. Crystals with 49% solvent content belonged to monoclinic space group P21 with eight protomers in the asymmetric unit. Only 2% of low-resolution structures with similar low percentage solvent content were found in the PDB. The crystal structure, solved by molecular replacement method, refined to Rwork (Rfree) of 0.24 (0.29) with excellent stereochemistry. The crystal structure clearly shows that drosophila protein exists as an octamer, and not as a decamer as expected from gel-filtration elution profiles. The similar octameric quaternary fold in translin orthologs and in translin–TRAX complexes suggests an up-down dimer as the basic structural subunit of translin-like proteins. The drosophila oligomer displays asymmetric assembly and increased radius of gyration that accounts for the observed differences between the elution profiles of human and drosophila proteins on gel-filtration columns. This study demonstrates clearly that low-resolution X-ray structure can be useful in understanding complex biological oligomers. PMID:23650579

Accelerated high-resolution photoacoustic tomography via compressed sensing

Science.gov (United States)

Arridge, Simon; Beard, Paul; Betcke, Marta; Cox, Ben; Huynh, Nam; Lucka, Felix; Ogunlade, Olumide; Zhang, Edward

2016-12-01

Current 3D photoacoustic tomography (PAT) systems offer either high image quality or high frame rates but are not able to deliver high spatial and temporal resolution simultaneously, which limits their ability to image dynamic processes in living tissue (4D PAT). A particular example is the planar Fabry-Pérot (FP) photoacoustic scanner, which yields high-resolution 3D images but takes several minutes to sequentially map the incident photoacoustic field on the 2D sensor plane, point-by-point. However, as the spatio-temporal complexity of many absorbing tissue structures is rather low, the data recorded in such a conventional, regularly sampled fashion is often highly redundant. We demonstrate that combining model-based, variational image reconstruction methods using spatial sparsity constraints with the development of novel PAT acquisition systems capable of sub-sampling the acoustic wave field can dramatically increase the acquisition speed while maintaining a good spatial resolution: first, we describe and model two general spatial sub-sampling schemes. Then, we discuss how to implement them using the FP interferometer and demonstrate the potential of these novel compressed sensing PAT devices through simulated data from a realistic numerical phantom and through measured data from a dynamic experimental phantom as well as from in vivo experiments. Our results show that images with good spatial resolution and contrast can be obtained from highly sub-sampled PAT data if variational image reconstruction techniques that describe the tissues structures with suitable sparsity-constraints are used. In particular, we examine the use of total variation (TV) regularization enhanced by Bregman iterations. These novel reconstruction strategies offer new opportunities to dramatically increase the acquisition speed of photoacoustic scanners that employ point-by-point sequential scanning as well as reducing the channel count of parallelized schemes that use detector arrays.

High-resolution crystal structure of Streptococcus pyogenes β-NAD+ glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

International Nuclear Information System (INIS)

Yoon, Ji Young; An, Doo Ri; Yoon, Hye-Jin; Kim, Hyoun Sook; Lee, Sang Jae; Im, Ha Na; Jang, Jun Young; Suh, Se Won

2013-01-01

The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD + glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules. One of the virulence factors produced by Streptococcus pyogenes is β-NAD + glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38–451) and the full-length IFS (residues 1–161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPN ct –IFS complex, which consists of the SPN C-terminal domain (SPN ct ; residues 193–451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPN ct and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope

Macromolecular crystallographic results obtained using a 2048x2048 CCD detector at CHESS

International Nuclear Information System (INIS)

Thiel, D.J.; Ealick, S.E.; Tate, M.W.; Gruner, S.M.; Eikenberry, E.F.

1996-01-01

We present results of macromolecular crystallographic experiments performed at the Cornell High Energy Synchrotron Source (CHESS) with a new CCD-based detector. This detector, installed in January 1995, complements a 1024x1024 CCD detector that has been in continuous operation at CHESS since December 1993. The new detector is based on a 4-port, 2048x2048 pixel CCD that is directly coupled to a Gd 2 O 2 S:Tb phosphor by a 3:1 tapered fiber optic. The active area of the phosphor is a square 82 mm on an edge. The readout time is 7 seconds. In the standard mode of operation, the pixel size at the active area is 41 μm on the edge leading to the capability of resolving approximately 200 orders of diffraction across the detector face. The detector also operates in a 1024x1024 mode in which the pixel size is electronically increased by a factor of 4 in area resulting in smaller data files and faster detector readout but at the expense of spatial resolution. Most of the data that has been collected by this detector has been collected in this mode. Dozens of data sets have been collected by many experimenters using this detector at CHESS during the four month period from its installation until the start of the six-month down period of the storage ring. The capabilities of the detector will be illustrated with results from various crystallographic measurements including experiments in which the recorded diffraction patterns extend in resolution as far as 1 A. The results demonstrate that this detector is capable of collecting data of quality at least equal to that of imaging plates but, in many circumstances, with much greater beamline efficiency. copyright 1996 American Institute of Physics

Automated identification of crystallographic ligands using sparse-density representations

International Nuclear Information System (INIS)

Carolan, C. G.; Lamzin, V. S.

2014-01-01

A novel procedure for identifying ligands in macromolecular crystallographic electron-density maps is introduced. Density clusters in such maps can be rapidly attributed to one of 82 different ligands in an automated manner. A novel procedure for the automatic identification of ligands in macromolecular crystallographic electron-density maps is introduced. It is based on the sparse parameterization of density clusters and the matching of the pseudo-atomic grids thus created to conformationally variant ligands using mathematical descriptors of molecular shape, size and topology. In large-scale tests on experimental data derived from the Protein Data Bank, the procedure could quickly identify the deposited ligand within the top-ranked compounds from a database of candidates. This indicates the suitability of the method for the identification of binding entities in fragment-based drug screening and in model completion in macromolecular structure determination

Crystallographic analysis of human hemoglobin elucidates the structural basis of the potent and dual antisickling activity of pyridyl derivatives of vanillin

Energy Technology Data Exchange (ETDEWEB)

Abdulmalik, Osheiza [The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 (United States); Ghatge, Mohini S.; Musayev, Faik N.; Parikh, Apurvasena [Virginia Commonwealth University, Richmond, VA 23298 (United States); Chen, Qiukan; Yang, Jisheng [The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 (United States); Nnamani, Ijeoma [Duke University Medical Center, Durham, NC 27710 (United States); Danso-Danquah, Richmond [Virginia Commonwealth University, Richmond, VA 23298 (United States); Eseonu, Dorothy N. [Virginia Union University, Richmond, VA 23220 (United States); Asakura, Toshio [Duke University Medical Center, Durham, NC 27710 (United States); Abraham, Donald J.; Venitz, Jurgen; Safo, Martin K., E-mail: msafo@vcu.edu [Virginia Commonwealth University, Richmond, VA 23298 (United States); The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 (United States)

2011-11-01

Pyridyl derivatives of vanillin increase the fraction of the more soluble oxygenated sickle hemoglobin and/or directly increase the solubility of deoxygenated sickle hemoglobin. Crystallographic analysis reveals the structural basis of the potent and dual antisickling activity of these derivatives. Vanillin has previously been studied clinically as an antisickling agent to treat sickle-cell disease. In vitro investigations with pyridyl derivatives of vanillin, including INN-312 and INN-298, showed as much as a 90-fold increase in antisickling activity compared with vanillin. The compounds preferentially bind to and modify sickle hemoglobin (Hb S) to increase the affinity of Hb for oxygen. INN-312 also led to a considerable increase in the solubility of deoxygenated Hb S under completely deoxygenated conditions. Crystallographic studies of normal human Hb with INN-312 and INN-298 showed that the compounds form Schiff-base adducts with the N-terminus of the α-subunits to constrain the liganded (or relaxed-state) Hb conformation relative to the unliganded (or tense-state) Hb conformation. Interestingly, while INN-298 binds and directs its meta-positioned pyridine-methoxy moiety (relative to the aldehyde moiety) further down the central water cavity of the protein, that of INN-312, which is ortho to the aldehyde, extends towards the surface of the protein. These studies suggest that these compounds may act to prevent sickling of SS cells by increasing the fraction of the soluble high-affinity Hb S and/or by stereospecific inhibition of deoxygenated Hb S polymerization.

Crystallographic analysis of human hemoglobin elucidates the structural basis of the potent and dual antisickling activity of pyridyl derivatives of vanillin

International Nuclear Information System (INIS)

Abdulmalik, Osheiza; Ghatge, Mohini S.; Musayev, Faik N.; Parikh, Apurvasena; Chen, Qiukan; Yang, Jisheng; Nnamani, Ijeoma; Danso-Danquah, Richmond; Eseonu, Dorothy N.; Asakura, Toshio; Abraham, Donald J.; Venitz, Jurgen; Safo, Martin K.

2011-01-01

Pyridyl derivatives of vanillin increase the fraction of the more soluble oxygenated sickle hemoglobin and/or directly increase the solubility of deoxygenated sickle hemoglobin. Crystallographic analysis reveals the structural basis of the potent and dual antisickling activity of these derivatives. Vanillin has previously been studied clinically as an antisickling agent to treat sickle-cell disease. In vitro investigations with pyridyl derivatives of vanillin, including INN-312 and INN-298, showed as much as a 90-fold increase in antisickling activity compared with vanillin. The compounds preferentially bind to and modify sickle hemoglobin (Hb S) to increase the affinity of Hb for oxygen. INN-312 also led to a considerable increase in the solubility of deoxygenated Hb S under completely deoxygenated conditions. Crystallographic studies of normal human Hb with INN-312 and INN-298 showed that the compounds form Schiff-base adducts with the N-terminus of the α-subunits to constrain the liganded (or relaxed-state) Hb conformation relative to the unliganded (or tense-state) Hb conformation. Interestingly, while INN-298 binds and directs its meta-positioned pyridine-methoxy moiety (relative to the aldehyde moiety) further down the central water cavity of the protein, that of INN-312, which is ortho to the aldehyde, extends towards the surface of the protein. These studies suggest that these compounds may act to prevent sickling of SS cells by increasing the fraction of the soluble high-affinity Hb S and/or by stereospecific inhibition of deoxygenated Hb S polymerization

Overexpression, purification and crystallographic analysis of a unique adenosine kinase from Mycobacterium tuberculosis

Energy Technology Data Exchange (ETDEWEB)

Wang, Yimin; Long, Mary C.; Ranganathan, Senthil; Escuyer, Vincent; Parker, William B.; Li, Rongbao, E-mail: li@sri.org [Southern Research Institute, 2000 Ninth Avenue South, Birmingham, Alabama 35205 (United States)

2005-06-01

Adenosine kinase from M. tuberculosis has been overexpressed, purified and crystallized in the presence of adenosine. Structure determination using molecular replacement with diffraction data collected at 2.2 Å reveals a dimeric structure. Adenosine kinase from Mycobacterium tuberculosis is the only prokaryotic adenosine kinase that has been isolated and characterized. The enzyme catalyzes the phosphorylation of adenosine to adenosine monophosphate and is involved in the activation of 2-methyladenosine, a compound that has demonstrated selective activity against M. tuberculosis. The mechanism of action of 2-methyladenosine is likely to be different from those of current tuberculosis treatments and this compound (or other adenosine analogs) may prove to be a novel therapeutic intervention for this disease. The M. tuberculosis adenosine kinase was overexpressed in Escherichia coli and the enzyme was purified with activity comparable to that reported previously. The protein was crystallized in the presence of adenosine using the vapour-diffusion method. The crystals diffracted X-rays to high resolution and a complete data set was collected to 2.2 Å using synchrotron radiation. The crystal belonged to space group P3{sub 1}21, with unit-cell parameters a = 70.2, c = 111.6 Å, and contained a single protein molecule in the asymmetric unit. An initial structural model of the protein was obtained by the molecular-replacement method, which revealed a dimeric structure. The monomers of the dimer were related by twofold crystallographic symmetry. An understanding of how the M. tuberculosis adenosine kinase differs from the human homolog should aid in the design of more potent and selective antimycobacterial agents that are selectively activated by this enzyme.

Overexpression, purification and crystallographic analysis of a unique adenosine kinase from Mycobacterium tuberculosis

International Nuclear Information System (INIS)

Wang, Yimin; Long, Mary C.; Ranganathan, Senthil; Escuyer, Vincent; Parker, William B.; Li, Rongbao

2005-01-01

Adenosine kinase from M. tuberculosis has been overexpressed, purified and crystallized in the presence of adenosine. Structure determination using molecular replacement with diffraction data collected at 2.2 Å reveals a dimeric structure. Adenosine kinase from Mycobacterium tuberculosis is the only prokaryotic adenosine kinase that has been isolated and characterized. The enzyme catalyzes the phosphorylation of adenosine to adenosine monophosphate and is involved in the activation of 2-methyladenosine, a compound that has demonstrated selective activity against M. tuberculosis. The mechanism of action of 2-methyladenosine is likely to be different from those of current tuberculosis treatments and this compound (or other adenosine analogs) may prove to be a novel therapeutic intervention for this disease. The M. tuberculosis adenosine kinase was overexpressed in Escherichia coli and the enzyme was purified with activity comparable to that reported previously. The protein was crystallized in the presence of adenosine using the vapour-diffusion method. The crystals diffracted X-rays to high resolution and a complete data set was collected to 2.2 Å using synchrotron radiation. The crystal belonged to space group P3 1 21, with unit-cell parameters a = 70.2, c = 111.6 Å, and contained a single protein molecule in the asymmetric unit. An initial structural model of the protein was obtained by the molecular-replacement method, which revealed a dimeric structure. The monomers of the dimer were related by twofold crystallographic symmetry. An understanding of how the M. tuberculosis adenosine kinase differs from the human homolog should aid in the design of more potent and selective antimycobacterial agents that are selectively activated by this enzyme

Super-resolution biomolecular crystallography with low-resolution data.

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Schröder, Gunnar F; Levitt, Michael; Brunger, Axel T

2010-04-22

X-ray diffraction plays a pivotal role in the understanding of biological systems by revealing atomic structures of proteins, nucleic acids and their complexes, with much recent interest in very large assemblies like the ribosome. As crystals of such large assemblies often diffract weakly (resolution worse than 4 A), we need methods that work at such low resolution. In macromolecular assemblies, some of the components may be known at high resolution, whereas others are unknown: current refinement methods fail as they require a high-resolution starting structure for the entire complex. Determining the structure of such complexes, which are often of key biological importance, should be possible in principle as the number of independent diffraction intensities at a resolution better than 5 A generally exceeds the number of degrees of freedom. Here we introduce a method that adds specific information from known homologous structures but allows global and local deformations of these homology models. Our approach uses the observation that local protein structure tends to be conserved as sequence and function evolve. Cross-validation with R(free) (the free R-factor) determines the optimum deformation and influence of the homology model. For test cases at 3.5-5 A resolution with known structures at high resolution, our method gives significant improvements over conventional refinement in the model as monitored by coordinate accuracy, the definition of secondary structure and the quality of electron density maps. For re-refinements of a representative set of 19 low-resolution crystal structures from the Protein Data Bank, we find similar improvements. Thus, a structure derived from low-resolution diffraction data can have quality similar to a high-resolution structure. Our method is applicable to the study of weakly diffracting crystals using X-ray micro-diffraction as well as data from new X-ray light sources. Use of homology information is not restricted to X

Recent applications of gas chromatography with high-resolution mass spectrometry.

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Špánik, Ivan; Machyňáková, Andrea

2018-01-01

Gas chromatography coupled to high-resolution mass spectrometry is a powerful analytical method that combines excellent separation power of gas chromatography with improved identification based on an accurate mass measurement. These features designate gas chromatography with high-resolution mass spectrometry as the first choice for identification and structure elucidation of unknown volatile and semi-volatile organic compounds. Gas chromatography with high-resolution mass spectrometry quantitative analyses was previously focused on the determination of dioxins and related compounds using magnetic sector type analyzers, a standing requirement of many international standards. The introduction of a quadrupole high-resolution time-of-flight mass analyzer broadened interest in this method and novel applications were developed, especially for multi-target screening purposes. This review is focused on the development and the most interesting applications of gas chromatography coupled to high-resolution mass spectrometry towards analysis of environmental matrices, biological fluids, and food safety since 2010. The main attention is paid to various approaches and applications of gas chromatography coupled to high-resolution mass spectrometry for non-target screening to identify contaminants and to characterize the chemical composition of environmental, food, and biological samples. The most interesting quantitative applications, where a significant contribution of gas chromatography with high-resolution mass spectrometry over the currently used methods is expected, will be discussed as well. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

Science.gov (United States)

2013-01-01

Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

Crystallographically uniform arrays of ordered (In)GaN nanocolumns

Energy Technology Data Exchange (ETDEWEB)

Gačević, Ž., E-mail: gacevic@isom.upm.es; Bengoechea-Encabo, A.; Albert, S.; Calleja, E. [ETSIT-ISOM, Universidad Politécnica de Madrid, Avda. Complutense s/n, 28040 Madrid (Spain); Torres-Pardo, A.; González-Calbet, J. M. [Dept. Química Inorgánica, Universidad Complutense, 28040 Madrid (Spain); CEI Campus Moncloa, UCM-UPM, Madrid (Spain)

2015-01-21

In this work, through a comparative study of self-assembled (SA) and selective area grown (SAG) (In)GaN nanocolumn (NC) ensembles, we first give a detailed insight into improved crystallographic uniformity (homogeneity of crystallographic tilts and twists) of the latter ones. The study, performed making use of: reflective high energy electron diffraction, X-ray diffraction and scanning electron microscopy, reveals that unlike their SA counterparts, the ensembles of SAG NCs show single epitaxial relationship to both sapphire(0001) and Si(111) underlying substrates. In the second part of the article, making use of X-ray diffraction, we directly show that the selective area growth leads to improved compositional uniformity of InGaN NC ensembles. This further leads to improved spectral purity of their luminescence, as confirmed by comparative macro-photoluminescence measurements performed on SA and SAG InGaN NC ensembles. An improved crystallographic uniformity of NC ensembles facilitates their integration into optoelectronic devices, whereas their improved compositional uniformity allows for their employment in single-color optoelectronic applications.

High resolution spectroscopy in the microwave and far infrared

Science.gov (United States)

Pickett, Herbert M.

1990-01-01

High resolution rotational spectroscopy has long been central to remote sensing techniques in atmospheric sciences and astronomy. As such, laboratory measurements must supply the required data to make direct interpretation of data for instruments which sense atmospheres using rotational spectra. Spectral measurements in the microwave and far infrared regions are also very powerful tools when combined with infrared measurements for characterizing the rotational structure of vibrational spectra. In the past decade new techniques were developed which have pushed high resolution spectroscopy into the wavelength region between 25 micrometers and 2 mm. Techniques to be described include: (1) harmonic generation of microwave sources, (2) infrared laser difference frequency generation, (3) laser sideband generation, and (4) ultrahigh resolution interferometers.

Microwave structure of quiescent solar filaments at high resolution

International Nuclear Information System (INIS)

Gary, D.E.

1986-01-01

High resolution very low altitude maps of a quiescent filament at three frequencies are presented. The spatial resolution (approx. 15'' at 1.45 GHz, approx. 6'' at 4.9 GHz, and approx. 2'' at 15 GHz) is several times better than previously attained. At each frequency, the filament appears as a depression in the quiet Sun background. The depression is measurably wider and longer in extent than the corresponding H alpha filament at 1.45 GHz and 4.9 GHz, indicating that the depression is due in large part to a deficit in coronal density associated with the filament channel. In contrast, the shape of the radio depression at 15 CHz closely matches that of the H alpha filament. In addition, the 15 GHz map shows enhanced emission along both sides of the radio depression. A similar enhancement is seen in an observation of a second filament 4 days later, which suggests that the enhancement is a general feature of filaments. Possible causes of the enhanced emission are explored

Ultra high spatial and temporal resolution breast imaging at 7T.

Science.gov (United States)

van de Bank, B L; Voogt, I J; Italiaander, M; Stehouwer, B L; Boer, V O; Luijten, P R; Klomp, D W J

2013-04-01

There is a need to obtain higher specificity in the detection of breast lesions using MRI. To address this need, Dynamic Contrast-Enhanced (DCE) MRI has been combined with other structural and functional MRI techniques. Unfortunately, owing to time constraints structural images at ultra-high spatial resolution can generally not be obtained during contrast uptake, whereas the relatively low spatial resolution of functional imaging (e.g. diffusion and perfusion) limits the detection of small lesions. To be able to increase spatial as well as temporal resolution simultaneously, the sensitivity of MR detection needs to increase as well as the ability to effectively accelerate the acquisition. The required gain in signal-to-noise ratio (SNR) can be obtained at 7T, whereas acceleration can be obtained with high-density receiver coil arrays. In this case, morphological imaging can be merged with DCE-MRI, and other functional techniques can be obtained at higher spatial resolution, and with less distortion [e.g. Diffusion Weighted Imaging (DWI)]. To test the feasibility of this concept, we developed a unilateral breast coil for 7T. It comprises a volume optimized dual-channel transmit coil combined with a 30-channel receive array coil. The high density of small coil elements enabled efficient acceleration in any direction to acquire ultra high spatial resolution MRI of close to 0.6 mm isotropic detail within a temporal resolution of 69 s, high spatial resolution MRI of 1.5 mm isotropic within an ultra high temporal resolution of 6.7 s and low distortion DWI at 7T, all validated in phantoms, healthy volunteers and a patient with a lesion in the right breast classified as Breast Imaging Reporting and Data System (BI-RADS) IV. Copyright © 2012 John Wiley & Sons, Ltd.

X-ray metrology for ULSI structures

International Nuclear Information System (INIS)

Bowen, D. K.; Matney, K. M.; Wormington, M.

1998-01-01

Non-destructive X-ray metrological methods are discussed for application to both process development and process control of ULSI structures. X-ray methods can (a) detect the unacceptable levels of internal defects generated by RTA processes in large wafers, (b) accurately measure the thickness and roughness of layers between 1 and 1000 nm thick and (c) can monitor parameters such as crystallographic texture and the roughness of buried interfaces. In this paper we review transmission X-ray topography, thin film texture measurement, grazing-incidence X-ray reflectivity and high-resolution X-ray diffraction. We discuss in particular their suitability as on-line sensors for process control

Crystallographic study of one turn of G/C-rich B-DNA.

Science.gov (United States)

Heinemann, U; Alings, C

1989-11-20

The DNA decamer d(CCAGGCCTGG) has been studied by X-ray crystallography. At a nominal resolution of 1.6 A, the structure was refined to R = 16.9% using stereochemical restraints. The oligodeoxyribonucleotide forms a straight B-DNA double helix with crystallographic dyad symmetry and ten base-pairs per turn. In the crystal lattice, DNA fragments stack end-to-end along the c-axis to form continuous double helices. The overall helical structure and, notably, the groove dimensions of the decamer are more similar to standard, fiber diffraction-determined B-DNA than A-tract DNA. A unique stacking geometry is observed at the CA/TG base-pair step, where an increased rotation about the helix axis and a sliding motion of the base-pairs along their long axes leads to a superposition of the base rings with neighboring carbonyl and amino functions. Three-center (bifurcated) hydrogen bonds are possible at the CC/GG base-pair steps of the decamer. In their common sequence elements, d(CCAGGCCTGG) and the related G.A mismatch decamer d(CCAAGATTGG) show very similar three-dimensional structures, except that d(CCAGGCCTGG) appears to have a less regularly hydrated minor groove. The paucity of minor groove hydration in the center of the decamer may be a general feature of G/C-rich DNA and explain its relative instability in the B-form of DNA.

High Resolution Orientation Distribution Function

DEFF Research Database (Denmark)

Schmidt, Søren; Gade-Nielsen, Nicolai Fog; Høstergaard, Martin

2012-01-01

from the deformed material. The underlying mathematical formalism supports all crystallographic space groups and reduces the problem to solving a (large) set of linear equations. An implementation on multi-core CPUs and Graphical Processing Units (GPUs) is discussed along with an example on simulated...

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation.

Science.gov (United States)

Koebernick, Nicolai; Daly, Keith R; Keyes, Samuel D; George, Timothy S; Brown, Lawrie K; Raffan, Annette; Cooper, Laura J; Naveed, Muhammad; Bengough, Anthony G; Sinclair, Ian; Hallett, Paul D; Roose, Tiina

2017-10-01

In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root-soil interface during the early stage of crop establishment. This was achieved by use of high-resolution (c. 5 μm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant-soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare), with and without root hairs, were grown for 8 d in microcosms packed with sandy loam soil at 1.2 g cm -3 dry bulk density. Root hairs were visualised within air-filled pore spaces, but not in the fine-textured soil regions. We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (> 5 μm) in the rhizosphere, as compared with the no-hair mutants. Both genotypes showed decreasing pore space between 0.8 and 0.1 mm from the root surface. Interestingly the root-hair-bearing genotype had a significantly greater soil pore volume-fraction at the root-soil interface. Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image-based modelling. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

High resolution X-ray tomography for stationary multiphase flows

International Nuclear Information System (INIS)

Schmitz, D.; Reinecke, N.; Petritsch, G.; Mewes, D.

1998-01-01

The high resolution which can be obtained by computer assisted tomography is used to investigate the liquid distribution and void fraction in random and structured packing. With a spatial resolution of 0.4x0.4mm 2 it is possible even to detect thin liquid films on structured packings. The experimental set-up consists of a custom-built second generation tomograph. The imaged object consists of a column filled with either a random ceramic packing of spheres or a structured metal packing. The liquid and void fraction distribution in random and structured packings with a quiescent gaseous phase is visualized. The water/air system is used. The liquid distributor consists of a perforated plate. The experimental hold-up values averaged over the column cross-section are in good agreement with empirical equations. (author)

Structure and function of proteins investigated by crystallographic and spectroscopic time-resolved methods

Science.gov (United States)

Purwar, Namrta

Biomolecules play an essential role in performing the necessary functions for life. The goal of this thesis is to contribute to an understanding of how biological systems work on the molecular level. We used two biological systems, beef liver catalase (BLC) and photoactive yellow protein (PYP). BLC is a metalloprotein that protects living cells from the harmful effects of reactive oxygen species by converting H2O2 into water and oxygen. By binding nitric oxide (NO) to the catalase, a complex was generated that mimics the Cat-H2O2 adduct, a crucial intermediate in the reaction promoted by the catalase. The Cat-NO complex is obtained by using a convenient NO generator (1-(N,N-diethylamino)diazen-1-ium-1,2-diolate). Concentrations up to 100˜200 mM are reached by using a specially designed glass cavity. With this glass apparatus and DEANO, sufficient NO occupation is achieved and structure determination of the catalase with NO bound to the heme iron becomes possible. Structural changes upon NO binding are minute. NO has a slightly bent geometry with respect to the heme normal, which results in a substantial overlap of the NO orbitals with the iron-porphyrin molecular orbitals. From the structure of the iron-NO complex, conclusions on the electronic properties of the heme iron can be drawn that ultimately lead to an insight into the catalytic properties of this enzyme. Enzyme kinetics is affected by additional parameters such as temperature and pH. Additionally, in crystallography, the absorbed X-ray dose may impair protein function. To address the effect of these parameters, we performed time-resolved crystallographic experiments on a model system, PYP. By collecting multiple time-series on PYP at increasing X-ray dose levels, we determined a kinetic dose limit up to which kinetically meaningful X-ray data sets can be collected. From this, we conclude that comprehensive time-series spanning up to 12 orders of magnitude in time can be collected from a single PYP

Ligand Binding Induces Conformational Changes in Human Cellular Retinol-binding Protein 1 (CRBP1) Revealed by Atomic Resolution Crystal Structures.

Science.gov (United States)

Silvaroli, Josie A; Arne, Jason M; Chelstowska, Sylwia; Kiser, Philip D; Banerjee, Surajit; Golczak, Marcin

2016-04-15

Important in regulating the uptake, storage, and metabolism of retinoids, cellular retinol-binding protein 1 (CRBP1) is essential for trafficking vitamin A through the cytoplasm. However, the molecular details of ligand uptake and targeted release by CRBP1 remain unclear. Here we report the first structure of CRBP1 in a ligand-free form as well as ultra-high resolution structures of this protein bound to either all-trans-retinol or retinylamine, the latter a therapeutic retinoid that prevents light-induced retinal degeneration. Superpositioning of human apo- and holo-CRBP1 revealed major differences within segments surrounding the entrance to the retinoid-binding site. These included α-helix II and hairpin turns between β-strands βC-βD and βE-βF as well as several side chains, such as Phe-57, Tyr-60, and Ile-77, that change their orientations to accommodate the ligand. Additionally, we mapped hydrogen bond networks inside the retinoid-binding cavity and demonstrated their significance for the ligand affinity. Analyses of the crystallographic B-factors indicated several regions with higher backbone mobility in the apoprotein that became more rigid upon retinoid binding. This conformational flexibility of human apo-CRBP1 facilitates interaction with the ligands, whereas the more rigid holoprotein structure protects the labile retinoid moiety during vitamin A transport. These findings suggest a mechanism of induced fit upon ligand binding by mammalian cellular retinol-binding proteins. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

High-resolution ultrasound biomicroscopy for monitoring ovarian structures in mice

Directory of Open Access Journals (Sweden)

Singh Jaswant

2009-07-01

Full Text Available Abstract Background Until recently, the limit of spatial resolution of ultrasound systems has prevented characterization of structures Methods Experiment 1 was a pilot study to develop methods of immobilization (physical restraint vs. general anesthesia and determine technical factors affecting ovarian images using ultrasound bio-microscopy in rats vs. mice. The hair coat was removed over the thoraco-lumber area using depilation cream, and a highly viscous acoustic gel was applied while the animals were maintained in sternal recumbency. In Experiment 2, changes in ovarian structures during the estrous cycle were monitored by twice daily ultrasonography in 10 mice for 2 estrous cycles. Results Ovarian images were not distinct in rats due to attenuation of ultrasound waves. Physical restraint, without general anesthesia, was insufficient for immobilization in mice. By placing the transducer face over the dorsal flank, the kidney was visualized initially as a point of reference. A routine of moving the transducer a few millimetres caudo-laterally from the kidney was established to quickly and consistently localize the ovaries; the total time to scan both ovaries in a mouse was about 10 minutes. By comparing vaginal cytology with non-anesthetized controls, repeated exposure to anesthesia did not affect the estrous cycle. Temporal changes in the number of follicles in 3 different size categories support the hypothesis that follicles ≥ 20 microns develop in a wave-like fashion. Conclusion The mouse is a suitable model for the study of ovarian dynamics using transcutaneous ultrasound bio-microscopy. Repeated general anesthesia for examination had no apparent effect on the estrous cycle, and preliminary results revealed a wave-like pattern of ovarian follicle development in mice.

Fortuitous structure determination of ‘as-isolated’ Escherichia coli bacterioferritin in a novel crystal form

International Nuclear Information System (INIS)

Eerde, André van; Wolterink-van Loo, Suzanne; Oost, John van der; Dijkstra, Bauke W.

2006-01-01

E. coli bacterioferritin was crystallized in a novel crystal form from different conditions and the structure was solved. The crystals belonged to space group P2 1 3 and diffracted to a resolution of 2.5 Å. Escherichia coli bacterioferritin was serendipitously crystallized in a novel cubic crystal form and its structure could be determined to 2.5 Å resolution despite a high degree of merohedral twinning. This is the first report of crystallographic data on ‘as-isolated’ E. coli bacterioferritin. The ferroxidase active site contains positive difference density consistent with two metal ions that had co-purified with the protein. X-ray fluorescence studies suggest that the metal composition is different from that of previous structures and is a mix of zinc and native iron ions. The ferroxidase-centre configuration displays a similar flexibility as previously noted for other bacterioferritins

High Resolution Higher Energy X-ray Microscope for Mesoscopic Materials

International Nuclear Information System (INIS)

Snigireva, I; Snigirev, A

2013-01-01

We developed a novel X-ray microscopy technique to study mesoscopically structured materials, employing compound refractive lenses. The easily seen advantage of lens-based methodology is the possibility to retrieve high resolution diffraction pattern and real-space images in the same experimental setup. Methodologically the proposed approach is similar to the studies of crystals by high resolution transmission electron microscopy. The proposed microscope was applied for studying of mesoscopic materials such as natural and synthetic opals, inverted photonic crystals

Hyper-resolution urban flood modeling using high-resolution radar precipitation and LiDAR data

Science.gov (United States)

Noh, S. J.; Lee, S.; Lee, J.; Seo, D. J.

2016-12-01

Floods occur most frequently among all natural hazards, often causing widespread economic damage and loss of human lives. In particular, urban flooding is becoming increasingly costly and difficult to manage with a greater concentration of population and assets in urban centers. Despite of known benefits for accurate representation of small scale features and flow interaction among different flow domains, which have significant impact on flood propagation, high-resolution modeling has not been fully utilized due to expensive computation and various uncertainties from model structure, input and parameters. In this study, we assess the potential of hyper-resolution hydrologic-hydraulic modeling using high-resolution radar precipitation and LiDAR data for improved urban flood prediction and hazard mapping. We describe a hyper-resolution 1D-2D coupled urban flood model for pipe and surface flows and evaluate the accuracy of the street-level inundation information produced. For detailed geometric representation of urban areas and for computational efficiency, we use 1 m-resolution topographical data, processed from LiDAR measurements, in conjunction with adaptive mesh refinement. For street-level simulation in large urban areas at grid sizes of 1 to 10 m, a hybrid parallel computing scheme using MPI and openMP is also implemented in a high-performance computing system. The modeling approach developed is applied for the Johnson Creek Catchment ( 40 km2), which makes up the Arlington Urban Hydroinformatics Testbed. In addition, discussion will be given on availability of hyper-resolution simulation archive for improved real-time flood mapping.

Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase.

Science.gov (United States)

Daughtry, Kelly D; Xiao, Youli; Stoner-Ma, Deborah; Cho, Eunsun; Orville, Allen M; Liu, Pinghua; Allen, Karen N

2012-02-08

Herein, the structure resulting from in situ turnover in a chemically challenging quaternary ammonium oxidative demethylation reaction was captured via crystallographic analysis and analyzed via single-crystal spectroscopy. Crystal structures were determined for the Rieske-type monooxygenase, stachydrine demethylase, in the unliganded state (at 1.6 Å resolution) and in the product complex (at 2.2 Å resolution). The ligand complex was obtained from enzyme aerobically cocrystallized with the substrate stachydrine (N,N-dimethylproline). The ligand electron density in the complex was interpreted as proline, generated within the active site at 100 K by the absorption of X-ray photon energy and two consecutive demethylation cycles. The oxidation state of the Rieske iron-sulfur cluster was characterized by UV-visible spectroscopy throughout X-ray data collection in conjunction with resonance Raman spectra collected before and after diffraction data. Shifts in the absorption band wavelength and intensity as a function of absorbed X-ray dose demonstrated that the Rieske center was reduced by solvated electrons generated by X-ray photons; the kinetics of the reduction process differed dramatically for the liganded complex compared to unliganded demethylase, which may correspond to the observed turnover in the crystal.

Routine phasing of coiled-coil protein crystal structures with AMPLE

Directory of Open Access Journals (Sweden)

Jens M. H. Thomas

2015-03-01

Full Text Available Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.

Crystal structure of the catalytic core domain of the family 6 cellobiohydrolase II, Cel6A, from Humicola insolens, at 1.92 A resolution.

Science.gov (United States)

Varrot, A; Hastrup, S; Schülein, M; Davies, G J

1999-01-15

The three-dimensional structure of the catalytic core of the family 6 cellobiohydrolase II, Cel6A (CBH II), from Humicola insolens has been determined by X-ray crystallography at a resolution of 1.92 A. The structure was solved by molecular replacement using the homologous Trichoderma reesei CBH II as a search model. The H. insolens enzyme displays a high degree of structural similarity with its T. reesei equivalent. The structure features both O- (alpha-linked mannose) and N-linked glycosylation and a hexa-co-ordinate Mg2+ ion. The active-site residues are located within the enclosed tunnel that is typical for cellobiohydrolase enzymes and which may permit a processive hydrolysis of the cellulose substrate. The close structural similarity between the two enzymes implies that kinetics and chain-end specificity experiments performed on the H. insolens enzyme are likely to be applicable to the homologous T. reesei enzyme. These cast doubt on the description of cellobiohydrolases as exo-enzymes since they demonstrated that Cel6A (CBH II) shows no requirement for non-reducing chain-ends, as had been presumed. There is no crystallographic evidence in the present structure to support a mechanism involving loop opening, yet preliminary modelling experiments suggest that the active-site tunnel of Cel6A (CBH II) is too narrow to permit entry of a fluorescenyl-derivatized substrate, known to be a viable substrate for this enzyme.

Preliminary crystallographic characterization of an RNA helicase from Kunjin virus

International Nuclear Information System (INIS)

Mastrangelo, Eloise; Bollati, Michela; Milani, Mario; Brisbarre, Nadège; Lamballerie, Xavier de; Coutard, Bruno; Canard, Bruno; Khromykh, Alexander; Bolognesi, Martino

2006-01-01

The C-terminal 440 amino acids of the NS3 protein from Kunjin virus (Flaviviridae) code for a helicase. The protein has been overexpressed and crystallized. Characterization of the isolated monoclinic crystal form and diffraction data (at 3.0 Å resolution) are presented, together with a preliminary molecular-replacement solution. Kunjin virus is a member of the Flavivirus genus and is an Australian variant of West Nile virus. The C-terminal domain of the Kunjin virus NS3 protein displays helicase activity. The protein is thought to separate daughter and template RNA strands, assisting the initiation of replication by unwinding RNA secondary structure in the 3′ nontranslated region. Expression, purification and preliminary crystallographic characterization of the NS3 helicase domain are reported. It is shown that Kunjin virus helicase may adopt a dimeric assembly in absence of nucleic acids, oligomerization being a means to provide the helicases with multiple nucleic acid-binding capability, facilitating translocation along the RNA strands. Kunjin virus NS3 helicase domain is an attractive model for studying the molecular mechanisms of flavivirus replication, while simultaneously providing a new basis for the rational development of anti-flaviviral compounds

Structure of a 14-3-3σ–YAP phosphopeptide complex at 1.15 Å resolution

International Nuclear Information System (INIS)

Schumacher, Benjamin; Skwarczynska, Malgorzata; Rose, Rolf; Ottmann, Christian

2010-01-01

The first structure of a 14-3-3 protein–phosphopeptide complex is reported at 1.15 Å resolution. The YAP 14-3-3-binding motif is revealed for the first time using crystallographic tools. The 14-3-3 proteins are a class of eukaryotic acidic adapter proteins, with seven isoforms in humans. 14-3-3 proteins mediate their biological function by binding to target proteins and influencing their activity. They are involved in pivotal pathways in the cell such as signal transduction, gene expression, enzyme activation, cell division and apoptosis. The Yes-associated protein (YAP) is a WW-domain protein that exists in two transcript variants of 48 and 54 kDa in humans. By transducing signals from the cytoplasm to the nucleus, YAP is important for transcriptional regulation. In both variants, interaction with 14-3-3 proteins after phosphorylation of Ser127 is important for nucleocytoplasmic trafficking, via which the localization of YAP is controlled. In this study, 14-3-3σ has been cloned, purified and crystallized in complex with a phosphopeptide from the YAP 14-3-3-binding domain, which led to a crystal that diffracted to 1.15 Å resolution. The crystals belonged to space group C222 1 , with unit-cell parameters a = 82.3, b = 112.1, c = 62.9 Å

Preliminary X-ray crystallographic analysis of the glycosyltransferase from a marine Streptomyces species

International Nuclear Information System (INIS)

Gong, Liping; Xiao, Yi; Liu, Qiang; Li, Sumei; Zhang, Changsheng; Liu, Jinsong

2010-01-01

The recombinant glycosyltransferase ElaGT from the elaiophylin-producing marine Streptomyces sp. SCSIO 01934 has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.9 Å resolution. ElaGT is a glycosyltransferase from a marine Streptomyces species that is involved in the biosynthesis of elaiophylin. Here, the molecular cloning, protein expression and purification, preliminary crystallization and crystallographic characterization of ElaGT are reported. The rod-shaped crystals belonged to space group P2 1 22, with unit-cell parameters a = 66.7, b = 131.7, c = 224.6 Å, α = 90, β = 90, γ = 90°. Data were collected to 2.9 Å resolution. A preliminary molecular-replacement solution implied the presence of two ElaGT molecules in the asymmetric unit

Geological survey by high resolution electrical survey on granite areas

International Nuclear Information System (INIS)

Sugimoto, Yoshihiro; Yamada, Naoyuki

2002-03-01

As an Integral part of the geological survey in 'The study of the regions ground water flow system' that we are carrying out with Tono Geoscience Center, we proved the relation between the uncontinuation structure such as lineament in the base rock and resistivity structure (resistivity distribution), for the purpose of that confirms the efficacy of the high resolution electrical survey as geological survey, we carried out high resolution electrical survey on granite area. We obtained the following result, by the comparison of resistivity distribution with established geological survey, lineament analysis and investigative drilling. 1. The resistivity structure of this survey area is almost able to classify it into the following four range. 1) the low resistivity range of 50-800 Ωm, 2) The resistivity range like the middle of 200-2000 Ωm, 3) The high resistivity range of 2000 Ωm over, 4) The low resistivity range of depth of the survey line 400-550 section. 2. The low resistivity range of 4) that correspond with the established geological data is not admitted. 3. It was confirmed that resistivity structure almost correspond to geological structure by the comparison with the established data. 4. The small-scale low resistivity area is admitted in the point equivalent to the lineament position of established. 5. We carried out it with the simulation method about the low resistivity range of 4). As a result, it understood that it has the possibility that the narrow ratio low resistivity area is shown as the wide ratio resistivity range in the analysis section. In the survey in this time, it is conceivable that the resistivity distribution with the possibility of the unhomogeneous and uncontinuation structure of the base rock is being shown conspicuously, the efficacy of the high resolution resistivity survey as geological survey on granite was shown. (author)

High resolution structure of the ba3 cytochrome c oxidase from Thermus thermophilus in a lipidic environment.

Directory of Open Access Journals (Sweden)

Theresa Tiefenbrunn

Full Text Available The fundamental chemistry underpinning aerobic life on Earth involves reduction of dioxygen to water with concomitant proton translocation. This process is catalyzed by members of the heme-copper oxidase (HCO superfamily. Despite the availability of crystal structures for all types of HCO, the mode of action for this enzyme is not understood at the atomic level, namely how vectorial H(+ and e(- transport are coupled. Toward addressing this problem, we report wild type and A120F mutant structures of the ba(3-type cytochrome c oxidase from Thermus thermophilus at 1.8 Å resolution. The enzyme has been crystallized from the lipidic cubic phase, which mimics the biological membrane environment. The structures reveal 20 ordered lipid molecules that occupy binding sites on the protein surface or mediate crystal packing interfaces. The interior of the protein encloses 53 water molecules, including 3 trapped in the designated K-path of proton transfer and 8 in a cluster seen also in A-type enzymes that likely functions in egress of product water and proton translocation. The hydrophobic O(2-uptake channel, connecting the active site to the lipid bilayer, contains a single water molecule nearest the Cu(B atom but otherwise exhibits no residual electron density. The active site contains strong electron density for a pair of bonded atoms bridging the heme Fe(a3 and Cu(B atoms that is best modeled as peroxide. The structure of ba(3-oxidase reveals new information about the positioning of the enzyme within the membrane and the nature of its interactions with lipid molecules. The atomic resolution details provide insight into the mechanisms of electron transfer, oxygen diffusion into the active site, reduction of oxygen to water, and pumping of protons across the membrane. The development of a robust system for production of ba(3-oxidase crystals diffracting to high resolution, together with an established expression system for generating mutants, opens the

Subwavelength resolution from multilayered structure (Conference Presentation)

Science.gov (United States)

Cheng, Bo Han; Jen, Yi-Jun; Liu, Wei-Chih; Lin, Shan-wen; Lan, Yung-Chiang; Tsai, Din Ping

2016-10-01

Breaking optical diffraction limit is one of the most important issues needed to be overcome for the demand of high-density optoelectronic components. Here, a multilayered structure which consists of alternating semiconductor and dielectric layers for breaking optical diffraction limitation at THz frequency region are proposed and analyzed. We numerically demonstrate that such multilayered structure not only can act as a hyperbolic metamaterial but also a birefringence material via the control of the external temperature (or magnetic field). A practical approach is provided to control all the diffraction signals toward a specific direction by using transfer matrix method and effective medium theory. Numerical calculations and computer simulation (based on finite element method, FEM) are carried out, which agree well with each other. The temperature (or magnetic field) parameter can be tuned to create an effective material with nearly flat isofrequency feature to transfer (project) all the k-space signals excited from the object to be resolved to the image plane. Furthermore, this multilayered structure can resolve subwavelength structures at various incident THz light sources simultaneously. In addition, the resolution power for a fixed operating frequency also can be tuned by only changing the magnitude of external magnetic field. Such a device provides a practical route for multi-functional material, photolithography and real-time super-resolution image.

Production, purification, crystallization and structure determination of H-1 Parvovirus

International Nuclear Information System (INIS)

Halder, Sujata; Nam, Hyun-Joo; Govindasamy, Lakshmanan; Vogel, Michèle; Dinsart, Christiane; Salomé, Nathalie; McKenna, Robert; Agbandje-McKenna, Mavis

2012-01-01

The production, purification, crystallization and crystallographic analysis of H-1 Parvovirus, a gene-therapy vector, are reported. Crystals of H-1 Parvovirus (H-1PV), an antitumor gene-delivery vector, were obtained for DNA-containing capsids and diffracted X-rays to 2.7 Å resolution using synchrotron radiation. The crystals belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 255.4, b = 350.4, c = 271.6 Å, β = 90.34°. The unit cell contained two capsids, with one capsid per crystallographic asymmetric unit. The H-1PV structure has been determined by molecular replacement and is currently being refined

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.

Science.gov (United States)

Borbulevych, Oleg Y; Plumley, Joshua A; Martin, Roger I; Merz, Kenneth M; Westerhoff, Lance M

2014-05-01

Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein-ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

High-Resolution Powder Diffractometer HRPT for Thermal Neutrons at SINQ

International Nuclear Information System (INIS)

Fischer, P.; Koch, M.; Koennecke, M.; Pomjakushin, V.; Schefer, J.; Schlumpf, N.

1999-01-01

The new neutron powder diffractometer at the Swiss continuous spallation neutron source SINQ is designed as a flexible instrument for high resolution [best values δd/d: ( -3 with d = lattice spacing in the high resolution or high intensity modes, respectively]. It uses large scattering angles 2Θ M = 120 deg or 90 deg of the monochromator, a 28 cm high, vertically focusing wafer type Ge(hkk) monochromator and a position-sensitive 3 He detector(3.6 bar) produced by Cerca at Romans, France. It has 1600 (25x64) detectors with an angular separation of 0.1 deg and includes modern electronics developed by E. Berruyer, Cerca and PSI. The SICS software of PSI controls the instrument with a server running on an unix workstation and clients written in Java through the TCP/IP network. The design principles and first experiences are presented. The interdisciplinary applications of HRPT will permit high-resolution refinement of chemical and magnetic structures as well as phase analysis including the detection of defects and internal microstrain. In particular real-time investigations of chemical or structural changes and of magnetic phase transitions in crystalline, quasicrystalline, amorphous and liquid samples including technically interesting new materials are possible. (author)

Development of a high-resolution cavity-beam position monitor

Directory of Open Access Journals (Sweden)

Yoichi Inoue

2008-06-01

Full Text Available We have developed a high-resolution cavity-beam position monitor (BPM to be used at the focal point of the ATF2, which is a test beam line that is now being built to demonstrate stable orbit control at ∼nanometer resolution. The design of the cavity structure was optimized for the Accelerator Test Facility (ATF beam in various ways. For example, the cavity has a rectangular shape in order to isolate two dipole modes in orthogonal directions, and a relatively thin gap that is less sensitive to trajectory inclination. A two stage homodyne mixer with highly sensitive electronics and phase-sensitive detection was also developed. Two BPM blocks, each containing two cavity BPMs, were installed in the existing ATF beam line using a rigid support frame. After testing the basic characteristics, we measured the resolution using three BPMs. The system demonstrated 8.7 nm position resolution over a dynamic range of 5  μm.

Development of a high-resolution cavity-beam position monitor

Science.gov (United States)

Inoue, Yoichi; Hayano, Hitoshi; Honda, Yosuke; Takatomi, Toshikazu; Tauchi, Toshiaki; Urakawa, Junji; Komamiya, Sachio; Nakamura, Tomoya; Sanuki, Tomoyuki; Kim, Eun-San; Shin, Seung-Hwan; Vogel, Vladimir

2008-06-01

We have developed a high-resolution cavity-beam position monitor (BPM) to be used at the focal point of the ATF2, which is a test beam line that is now being built to demonstrate stable orbit control at ˜nanometer resolution. The design of the cavity structure was optimized for the Accelerator Test Facility (ATF) beam in various ways. For example, the cavity has a rectangular shape in order to isolate two dipole modes in orthogonal directions, and a relatively thin gap that is less sensitive to trajectory inclination. A two stage homodyne mixer with highly sensitive electronics and phase-sensitive detection was also developed. Two BPM blocks, each containing two cavity BPMs, were installed in the existing ATF beam line using a rigid support frame. After testing the basic characteristics, we measured the resolution using three BPMs. The system demonstrated 8.7 nm position resolution over a dynamic range of 5μm.

Image Quality in High-resolution and High-cadence Solar Imaging

Science.gov (United States)

Denker, C.; Dineva, E.; Balthasar, H.; Verma, M.; Kuckein, C.; Diercke, A.; González Manrique, S. J.

2018-03-01

Broad-band imaging and even imaging with a moderate bandpass (about 1 nm) provides a photon-rich environment, where frame selection (lucky imaging) becomes a helpful tool in image restoration, allowing us to perform a cost-benefit analysis on how to design observing sequences for imaging with high spatial resolution in combination with real-time correction provided by an adaptive optics (AO) system. This study presents high-cadence (160 Hz) G-band and blue continuum image sequences obtained with the High-resolution Fast Imager (HiFI) at the 1.5-meter GREGOR solar telescope, where the speckle-masking technique is used to restore images with nearly diffraction-limited resolution. The HiFI employs two synchronized large-format and high-cadence sCMOS detectors. The median filter gradient similarity (MFGS) image-quality metric is applied, among others, to AO-corrected image sequences of a pore and a small sunspot observed on 2017 June 4 and 5. A small region of interest, which was selected for fast-imaging performance, covered these contrast-rich features and their neighborhood, which were part of Active Region NOAA 12661. Modifications of the MFGS algorithm uncover the field- and structure-dependency of this image-quality metric. However, MFGS still remains a good choice for determining image quality without a priori knowledge, which is an important characteristic when classifying the huge number of high-resolution images contained in data archives. In addition, this investigation demonstrates that a fast cadence and millisecond exposure times are still insufficient to reach the coherence time of daytime seeing. Nonetheless, the analysis shows that data acquisition rates exceeding 50 Hz are required to capture a substantial fraction of the best seeing moments, significantly boosting the performance of post-facto image restoration.

Challenges in quantitative crystallographic characterization of 3D thin films by ACOM-TEM

Energy Technology Data Exchange (ETDEWEB)

Kobler, A. [Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen (Germany); Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen (Germany); Kübel, C., E-mail: christian.kuebel@kit.edu [Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen (Germany); Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen (Germany)

2017-02-15

Automated crystal orientation mapping for transmission electron microscopy (ACOM-TEM) has become an easy to use method for the investigation of crystalline materials and complements other TEM methods by adding local crystallographic information over large areas. It fills the gap between high resolution electron microscopy and electron back scatter diffraction in terms of spatial resolution. Recent investigations showed that spot diffraction ACOM-TEM is a quantitative method with respect to sample parameters like grain size, twin density, orientation density and others. It can even be used in combination with in-situ tensile or thermal testing. However, there are limitations of the current method. In this paper we discuss some of the challenges and discuss solutions, e.g. we present an ambiguity filter that reduces the number of pixels with a ‘180° ambiguity problem’. For that an ACOM-TEM tilt series of nanocrystalline Pd thin films with overlapping crystallites was acquired and analyzed. - Highlights: • Tilt series of nanocrystalline Pd thin films. • Quantitative ACOM-TEM data processing, including a rotation map of crystallites. • Noise filter for orientation data: Ambiguity Filter and min. distance filter.

High resolution solar observations

International Nuclear Information System (INIS)

Title, A.

1985-01-01

Currently there is a world-wide effort to develop optical technology required for large diffraction limited telescopes that must operate with high optical fluxes. These developments can be used to significantly improve high resolution solar telescopes both on the ground and in space. When looking at the problem of high resolution observations it is essential to keep in mind that a diffraction limited telescope is an interferometer. Even a 30 cm aperture telescope, which is small for high resolution observations, is a big interferometer. Meter class and above diffraction limited telescopes can be expected to be very unforgiving of inattention to details. Unfortunately, even when an earth based telescope has perfect optics there are still problems with the quality of its optical path. The optical path includes not only the interior of the telescope, but also the immediate interface between the telescope and the atmosphere, and finally the atmosphere itself

High speed, High resolution terahertz spectrometers

International Nuclear Information System (INIS)

Kim, Youngchan; Yee, Dae Su; Yi, Miwoo; Ahn, Jaewook

2008-01-01

A variety of sources and methods have been developed for terahertz spectroscopy during almost two decades. Terahertz time domain spectroscopy (THz TDS)has attracted particular attention as a basic measurement method in the fields of THz science and technology. Recently, asynchronous optical sampling (AOS)THz TDS has been demonstrated, featuring rapid data acquisition and a high spectral resolution. Also, terahertz frequency comb spectroscopy (TFCS)possesses attractive features for high precision terahertz spectroscopy. In this presentation, we report on these two types of terahertz spectrometer. Our high speed, high resolution terahertz spectrometer is demonstrated using two mode locked femtosecond lasers with slightly different repetition frequencies without a mechanical delay stage. The repetition frequencies of the two femtosecond lasers are stabilized by use of two phase locked loops sharing the same reference oscillator. The time resolution of our terahertz spectrometer is measured using the cross correlation method to be 270 fs. AOS THz TDS is presented in Fig. 1, which shows a time domain waveform rapidly acquired on a 10ns time window. The inset shows a zoom into the signal with 100ps time window. The spectrum obtained by the fast Fourier Transformation (FFT)of the time domain waveform has a frequency resolution of 100MHz. The dependence of the signal to noise ratio (SNR)on the measurement time is also investigated

Multishell structure formation in Ni nanowire under uniaxial strain along <0 0 1> crystallographic direction: A molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Wang Li, E-mail: wanglihxf@sdu.edu.c [School of Mechanical and Electrical Engineering, Shandong University at Weihai, 180 Wenhuaxi Road, Weihai 264209 (China); Peng Chuanxiao [Key Laboratory of Liquid Structure and Heredity of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Gong Jianhong [School of Mechanical and Electrical Engineering, Shandong University at Weihai, 180 Wenhuaxi Road, Weihai 264209 (China)

2010-04-01

Molecular dynamics simulations based upon embedded-atom-method potential are employed to explore the fracture behavior of Ni nanowire along <0 0 1> crystallographic direction at temperature of 300 K. We find the formation of (5,5) multishell structure (MS), which is transformed from (6,5) MS at the necking region of nanowire under the strain rate of 0.02%ps{sup -1}. A reorientation transformation from <0 0 1> to <1 1 0> is first detected before formation of (6,5) MS. The formed (5,5) MS is more stable and can be tensioned longer as lower strain rate is loaded.

High resolution NMR spectroscopy of nanocrystalline proteins at ultra-high magnetic field

International Nuclear Information System (INIS)

Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Lipton, Andrew S.; Berthold, Deborah A.; Rienstra, Chad M.

2010-01-01

Magic-angle spinning (MAS) solid-state NMR (SSNMR) spectroscopy of uniformly- 13 C, 15 N labeled protein samples provides insight into atomic-resolution chemistry and structure. Data collection efficiency has advanced remarkably in the last decade; however, the study of larger proteins is still challenged by relatively low resolution in comparison to solution NMR. In this study, we present a systematic analysis of SSNMR protein spectra acquired at 11.7, 17.6 and 21.1 Tesla ( 1 H frequencies of 500, 750, and 900 MHz). For two protein systems-GB1, a 6 kDa nanocrystalline protein and DsbA, a 21 kDa nanocrystalline protein-line narrowing is demonstrated in all spectral regions with increasing field. Resolution enhancement is greatest in the aliphatic region, including methine, methylene and methyl sites. The resolution for GB1 increases markedly as a function of field, and for DsbA, resolution in the C-C region increases by 42%, according to the number of peaks that can be uniquely picked and integrated in the 900 MHz spectra when compared to the 500 MHz spectra. Additionally, chemical exchange is uniquely observed in the highest field spectra for at least two isoleucine Cδ1 sites in DsbA. These results further illustrate the benefits of high-field MAS SSNMR spectroscopy for protein structural studies.

High resolution studies of barium Rydberg states

International Nuclear Information System (INIS)

Eliel, E.R.

1982-01-01

The subtle structure of Rydberg states of barium with orbital angular momentum 0, 1, 2 and 3 is investigated. Some aspects of atomic theory for a configuration with two valence electrons are reviewed. The Multi Channel Quantum Defect Theory (MQDT) is concisely introduced as a convenient way to describe interactions between Rydberg series. Three high-resolution UV studies are presented. The first two, presenting results on a transition in indium and europium serve as an illustration of the frequency doubling technique. The third study is of hyperfine structure and isotope shifts in low-lying p states in Sr and Ba. An extensive study of the 6snp and 6snf Rydberg states of barium is presented with particular emphasis on the 6snf states. It is shown that the level structure cannot be fully explained with the model introduced earlier. Rather an effective two-body spin-orbit interaction has to be introduced to account for the observed splittings, illustrating that high resolution studies on Rydberg states offer an unique opportunity to determine the importance of such effects. Finally, the 6sns and 6snd series are considered. The hyperfine induced isotope shift in the simple excitation spectra to 6sns 1 S 0 is discussed and attention is paid to series perturbers. It is shown that level mixing parameters can easily be extracted from the experimental data. (Auth.)

High-resolution intravital microscopy.

Directory of Open Access Journals (Sweden)

Volker Andresen

Full Text Available Cellular communication constitutes a fundamental mechanism of life, for instance by permitting transfer of information through synapses in the nervous system and by leading to activation of cells during the course of immune responses. Monitoring cell-cell interactions within living adult organisms is crucial in order to draw conclusions on their behavior with respect to the fate of cells, tissues and organs. Until now, there is no technology available that enables dynamic imaging deep within the tissue of living adult organisms at sub-cellular resolution, i.e. detection at the level of few protein molecules. Here we present a novel approach called multi-beam striped-illumination which applies for the first time the principle and advantages of structured-illumination, spatial modulation of the excitation pattern, to laser-scanning-microscopy. We use this approach in two-photon-microscopy--the most adequate optical deep-tissue imaging-technique. As compared to standard two-photon-microscopy, it achieves significant contrast enhancement and up to 3-fold improved axial resolution (optical sectioning while photobleaching, photodamage and acquisition speed are similar. Its imaging depth is comparable to multifocal two-photon-microscopy and only slightly less than in standard single-beam two-photon-microscopy. Precisely, our studies within mouse lymph nodes demonstrated 216% improved axial and 23% improved lateral resolutions at a depth of 80 µm below the surface. Thus, we are for the first time able to visualize the dynamic interactions between B cells and immune complex deposits on follicular dendritic cells within germinal centers (GCs of live mice. These interactions play a decisive role in the process of clonal selection, leading to affinity maturation of the humoral immune response. This novel high-resolution intravital microscopy method has a huge potential for numerous applications in neurosciences, immunology, cancer research and

High-Resolution Intravital Microscopy

Science.gov (United States)

Andresen, Volker; Pollok, Karolin; Rinnenthal, Jan-Leo; Oehme, Laura; Günther, Robert; Spiecker, Heinrich; Radbruch, Helena; Gerhard, Jenny; Sporbert, Anje; Cseresnyes, Zoltan; Hauser, Anja E.; Niesner, Raluca

2012-01-01

Cellular communication constitutes a fundamental mechanism of life, for instance by permitting transfer of information through synapses in the nervous system and by leading to activation of cells during the course of immune responses. Monitoring cell-cell interactions within living adult organisms is crucial in order to draw conclusions on their behavior with respect to the fate of cells, tissues and organs. Until now, there is no technology available that enables dynamic imaging deep within the tissue of living adult organisms at sub-cellular resolution, i.e. detection at the level of few protein molecules. Here we present a novel approach called multi-beam striped-illumination which applies for the first time the principle and advantages of structured-illumination, spatial modulation of the excitation pattern, to laser-scanning-microscopy. We use this approach in two-photon-microscopy - the most adequate optical deep-tissue imaging-technique. As compared to standard two-photon-microscopy, it achieves significant contrast enhancement and up to 3-fold improved axial resolution (optical sectioning) while photobleaching, photodamage and acquisition speed are similar. Its imaging depth is comparable to multifocal two-photon-microscopy and only slightly less than in standard single-beam two-photon-microscopy. Precisely, our studies within mouse lymph nodes demonstrated 216% improved axial and 23% improved lateral resolutions at a depth of 80 µm below the surface. Thus, we are for the first time able to visualize the dynamic interactions between B cells and immune complex deposits on follicular dendritic cells within germinal centers (GCs) of live mice. These interactions play a decisive role in the process of clonal selection, leading to affinity maturation of the humoral immune response. This novel high-resolution intravital microscopy method has a huge potential for numerous applications in neurosciences, immunology, cancer research and developmental biology

High-resolution crystal structure of Streptococcus pyogenes β-NAD{sup +} glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

Energy Technology Data Exchange (ETDEWEB)

Yoon, Ji Young; An, Doo Ri; Yoon, Hye-Jin [Seoul National University, Seoul 151-747 (Korea, Republic of); Kim, Hyoun Sook [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-742 (Korea, Republic of); Lee, Sang Jae [Seoul National University, Seoul 151-742 (Korea, Republic of); Im, Ha Na; Jang, Jun Young [Seoul National University, Seoul 151-747 (Korea, Republic of); Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-747 (Korea, Republic of)

2013-11-01

The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD{sup +} glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules. One of the virulence factors produced by Streptococcus pyogenes is β-NAD{sup +} glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38–451) and the full-length IFS (residues 1–161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPN{sub ct}–IFS complex, which consists of the SPN C-terminal domain (SPN{sub ct}; residues 193–451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPN{sub ct} and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope.

Purification, identification and preliminary crystallographic studies of a 2S albumin seed protein from Lens culinaris

International Nuclear Information System (INIS)

Gupta, Pankaj; Gaur, Vineet; Salunke, Dinakar M.

2008-01-01

A 2S albumin from L. culinaris was purified and crystallized and preliminary crystallographic studies were carried out. Lens culinaris (lentil) is a widely consumed high-protein-content leguminous crop. A 2S albumin protein (26.5 kDa) has been identified using NH 2 -terminal sequencing from a 90% ammonium sulfate saturation fraction of total L. culinaris seed protein extract. The NH 2 -terminal sequence shows very high homology to PA2, an allergy-related protein from Pisum sativum. The 2S albumin protein was purified using a combination of size-exclusion and ion-exchange chromatography. Crystals of the 2S seed albumin obtained using the hanging-drop vapour-diffusion method diffracted to 2.5 Å resolution and were indexed in space group P4 1 (or P4 3 ), with unit-cell parameters a = b = 78.6, c = 135.2 Å

High-resolution Crystal Structure of Dimeric VP40 From Sudan ebolavirus.

Science.gov (United States)

Clifton, Matthew C; Bruhn, Jessica F; Atkins, Kateri; Webb, Terry L; Baydo, Ruth O; Raymond, Amy; Lorimer, Donald D; Edwards, Thomas E; Myler, Peter J; Saphire, Erica Ollmann

2015-10-01

Ebolaviruses cause severe hemorrhagic fever. Central to the Ebola life cycle is the matrix protein VP40, which oligomerizes and drives viral budding. Here we present the crystal structure of the Sudan virus (SUDV) matrix protein. This structure is higher resolution (1.6 Å) than previously achievable. Despite differences in the protein purification, we find that it still forms a stable dimer in solution, as was noted for other Ebola VP40s. Although the N-terminal domain interface by which VP40 dimerizes is conserved between Ebola virus and SUDV, the C-terminal domain interface by which VP40 dimers may further assemble is significantly smaller in this SUDV assembly. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Voltage-Gated Potassium Channels: A Structural Examination of Selectivity and Gating

Science.gov (United States)

Kim, Dorothy M.; Nimigean, Crina M.

2016-01-01

Voltage-gated potassium channels play a fundamental role in the generation and propagation of the action potential. The discovery of these channels began with predictions made by early pioneers, and has culminated in their extensive functional and structural characterization by electrophysiological, spectroscopic, and crystallographic studies. With the aid of a variety of crystal structures of these channels, a highly detailed picture emerges of how the voltage-sensing domain reports changes in the membrane electric field and couples this to conformational changes in the activation gate. In addition, high-resolution structural and functional studies of K+ channel pores, such as KcsA and MthK, offer a comprehensive picture on how selectivity is achieved in K+ channels. Here, we illustrate the remarkable features of voltage-gated potassium channels and explain the mechanisms used by these machines with experimental data. PMID:27141052

High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure.

Science.gov (United States)

Rosa-Garrido, Manuel; Chapski, Douglas J; Schmitt, Anthony D; Kimball, Todd H; Karbassi, Elaheh; Monte, Emma; Balderas, Enrique; Pellegrini, Matteo; Shih, Tsai-Ting; Soehalim, Elizabeth; Liem, David; Ping, Peipei; Galjart, Niels J; Ren, Shuxun; Wang, Yibin; Ren, Bing; Vondriska, Thomas M

2017-10-24

Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined. To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype. Transcriptome analyses by RNA-seq were conducted as a functional readout of the epigenomic structural changes. Depletion of CTCF was sufficient to induce heart failure in mice, and human patients with heart failure receiving mechanical unloading via left ventricular assist devices show increased CTCF abundance. Chromatin structural analyses revealed interactions within the cardiac myocyte genome at 5-kb resolution, enabling examination of intra- and interchromosomal events, and providing a resource for future cardiac epigenomic investigations. Pressure overload or CTCF depletion selectively altered boundary strength between topologically associating domains and A/B compartmentalization, measurements of genome accessibility. Heart failure involved decreased stability of chromatin interactions around disease-causing genes. In addition, pressure overload or CTCF depletion remodeled long-range interactions of cardiac enhancers, resulting in a significant decrease in local chromatin interactions around these functional elements. These findings provide a high-resolution chromatin architecture resource for cardiac epigenomic investigations and demonstrate that global structural remodeling of chromatin underpins heart failure. The newly identified principles of endogenous chromatin structure have key implications for epigenetic therapy. © 2017 The Authors.

Dependence of Crystallographic Orientation on Pitting Corrosion Behavior of Ni-Fe-Cr Alloy 028

Science.gov (United States)

Zhang, LiNa; Szpunar, Jerzy A.; Dong, JianXin; Ojo, Olanrewaju A.; Wang, Xu

2018-03-01

The influence of crystallographic orientation on the pitting corrosion behavior of Ni-Fe-Cr alloy 028 was studied using a combination of X-ray diffraction (XRD), electron backscatter diffraction (EBSD), potentiodynamic polarization technique, and atomic force microscopy (AFM). The results show that there is anisotropy of pitting corrosion that strongly depends on crystallographic orientation of the surface plane. The distribution of pit density in a standard stereographic triangle indicates that the crystallographic planes close to {100} are more prone to pitting corrosion compared to planes {110} and {111}. The surface energy calculation of (001) and (111) shows that the plane with a high atomic packing density has a low surface energy with concomitant strong resistance to pitting corrosion. A correlation function between crystallographic orientation and pitting corrosion susceptibility suggests a method that not only predicts the pitting resistance of known textured materials, but also could help to improve corrosion resistance by controlling material texture.

Linear versus non-linear structural information limit in high-resolution transmission electron microscopy

International Nuclear Information System (INIS)

Van Aert, S.; Chen, J.H.; Van Dyck, D.

2010-01-01

A widely used performance criterion in high-resolution transmission electron microscopy (HRTEM) is the information limit. It corresponds to the inverse of the maximum spatial object frequency that is linearly transmitted with sufficient intensity from the exit plane of the object to the image plane and is limited due to partial temporal coherence. In practice, the information limit is often measured from a diffractogram or from Young's fringes assuming a weak phase object scattering beyond the inverse of the information limit. However, for an aberration corrected electron microscope, with an information limit in the sub-angstrom range, weak phase objects are no longer applicable since they do not scatter sufficiently in this range. Therefore, one relies on more strongly scattering objects such as crystals of heavy atoms observed along a low index zone axis. In that case, dynamical scattering becomes important such that the non-linear and linear interaction may be equally important. The non-linear interaction may then set the experimental cut-off frequency observed in a diffractogram. The goal of this paper is to quantify both the linear and the non-linear information transfer in terms of closed form analytical expressions. Whereas the cut-off frequency set by the linear transfer can be directly related with the attainable resolution, information from the non-linear transfer can only be extracted using quantitative, model-based methods. In contrast to the historic definition of the information limit depending on microscope parameters only, the expressions derived in this paper explicitly incorporate their dependence on the structure parameters as well. In order to emphasize this dependence and to distinguish from the usual information limit, the expressions derived for the inverse cut-off frequencies will be referred to as the linear and non-linear structural information limit. The present findings confirm the well-known result that partial temporal coherence has

High-Resolution Sonars: What Resolution Do We Need for Target Recognition?

Directory of Open Access Journals (Sweden)

Pailhas Yan

2010-01-01

Full Text Available Target recognition in sonar imagery has long been an active research area in the maritime domain, especially in the mine-counter measure context. Recently it has received even more attention as new sensors with increased resolution have been developed; new threats to critical maritime assets and a new paradigm for target recognition based on autonomous platforms have emerged. With the recent introduction of Synthetic Aperture Sonar systems and high-frequency sonars, sonar resolution has dramatically increased and noise levels decreased. Sonar images are distance images but at high resolution they tend to appear visually as optical images. Traditionally algorithms have been developed specifically for imaging sonars because of their limited resolution and high noise levels. With high-resolution sonars, algorithms developed in the image processing field for natural images become applicable. However, the lack of large datasets has hampered the development of such algorithms. Here we present a fast and realistic sonar simulator enabling development and evaluation of such algorithms.We develop a classifier and then analyse its performances using our simulated synthetic sonar images. Finally, we discuss sensor resolution requirements to achieve effective classification of various targets and demonstrate that with high resolution sonars target highlight analysis is the key for target recognition.

Quantifying vegetation distribution and structure using high resolution drone-based structure-from-motion photogrammetry

Science.gov (United States)

Zhang, J.; Okin, G.

2017-12-01

Vegetation is one of the most important driving factors of different ecosystem processes in drylands. The structure of vegetation controls the spatial distribution of moisture and heat in the canopy and the surrounding area. Also, the structure of vegetation influences both airflow and boundary layer resistance above the land surface. Multispectral satellite remote sensing has been widely used to monitor vegetation coverage and its change; however, it can only capture 2D images, which do not contain the vertical information of vegetation. In situ observation uses different methods to measure the structure of vegetation, and their results are accurate; however, these methods are laborious and time-consuming, and susceptible to undersampling in spatial heterogeneity. Drylands are sparsely covered by short plants, which allows the drone fly at a relatively low height to obtain ultra-high resolution images. Structure-from-motion (SfM) is a photogrammetric method that was proved to produce 3D model based on 2D images. Drone-based remote sensing can obtain the multiangle images for one object, which can be used to constructed 3D models of vegetation in drylands. Using these images detected by the drone, the orthomosaics and digital surface model (DSM) can be built. In this study, the drone-based remote sensing was conducted in Jornada Basin, New Mexico, in the spring of 2016 and 2017, and three derived vegetation parameters (i.e., canopy size, bare soil gap size, and plant height) were compared with those obtained with field measurement. The correlation coefficient of canopy size, bare soil gap size, and plant height between drone images and field data are 0.91, 0.96, and 0.84, respectively. The two-year averaged root-mean-square error (RMSE) of canopy size, bare soil gap size, and plant height between drone images and field data are 0.61 m, 1.21 m, and 0.25 cm, respectively. The two-year averaged measure error (ME) of canopy size, bare soil gap size, and plant height

Crystallization and preliminary X-ray crystallographic studies of DnaJ from Streptococcus pneumoniae

International Nuclear Information System (INIS)

Zhao, Shasha; Jin, Li; Niu, Siqiang; Yang, Wei; Zhang, Shaocheng; Guo, Zhen; Zhang, Hongpeng; Huang, Ailong; Yin, Yibing; Wang, Deqiang

2013-01-01

DnaJ from Streptococcus pneumoniae (SpDnaJ) is involved in the infectious disease process and is being developed as a potential vaccine to prevent bacterial infection. Here the expression, purification, crystallization and preliminary crystallographic analysis of SpDnaJ are reported. DnaJ, cooperating with DnaK and GrpE, promotes the folding of unfolded hydrophobic polypeptides, dissociates protein complexes and translocates protein across membranes. Additionally, DnaJ from Streptococcus pneumoniae (SpDnaJ) is involved in the infectious disease process and is being developed as a potential vaccine to prevent bacterial infection. Here the expression, purification, crystallization and preliminary crystallographic analysis of SpDnaJ are reported. The crystals belong to space groups I222 or I2 1 2 1 2 1 and the diffraction resolution is 3.0 Å with unit-cell parameters a = 47.68, b = 104.45, c = 234.57 Å. The crystal most likely contains one molecule in the asymmetric unit, with a V M value of 3.24 Å 3 Da −1 and a solvent content of 62.1%

High-resolution solution-state NMR of unfractionated plant cell walls

Science.gov (United States)

John Ralph; Fachuang Lu; Hoon Kim; Dino Ress; Daniel J. Yelle; Kenneth E. Hammel; Sally A. Ralph; Bernadette Nanayakkara; Armin Wagner; Takuya Akiyama; Paul F. Schatz; Shawn D. Mansfield; Noritsugu Terashima; Wout Boerjan; Bjorn Sundberg; Mattias Hedenstrom

2009-01-01

Detailed structural studies on the plant cell wall have traditionally been difficult. NMR is one of the preeminent structural tools, but obtaining high-resolution solution-state spectra has typically required fractionation and isolation of components of interest. With recent methods for dissolution of, admittedly, finely divided plant cell wall material, the wall can...

Monitoring Termite-Mediated Ecosystem Processes Using Moderate and High Resolution Satellite Imagery

Science.gov (United States)

Lind, B. M.; Hanan, N. P.

2016-12-01

Termites are considered dominant decomposers and prominent ecosystem engineers in the global tropics and they build some of the largest and architecturally most complex non-human-made structures in the world. Termite mounds significantly alter soil texture, structure, and nutrients, and have major implications for local hydrological dynamics, vegetation characteristics, and biological diversity. An understanding of how these processes change across large scales has been limited by our ability to detect termite mounds at high spatial resolutions. Our research develops methods to detect large termite mounds in savannas across extensive geographic areas using moderate and high resolution satellite imagery. We also investigate the effect of termite mounds on vegetation productivity using Landsat-8 maximum composite NDVI data as a proxy for production. Large termite mounds in arid and semi-arid Senegal generate highly reflective `mound scars' with diameters ranging from 10 m at minimum to greater than 30 m. As Sentinel-2 has several bands with 10 m resolution and Landsat-8 has improved calibration, higher radiometric resolution, 15 m spatial resolution (pansharpened), and improved contrast between vegetated and bare surfaces compared to previous Landsat missions, we found that the largest and most influential mounds in the landscape can be detected. Because mounds as small as 4 m in diameter are easily detected in high resolution imagery we used these data to validate detection results and quantify omission errors for smaller mounds.

High voltage/high resolution studies of metal and semiconductor interfaces

International Nuclear Information System (INIS)

Westmacott, K.H.; Dahmen, U.

1989-11-01

The application of high resolution transmission electron microscopy to the study of homo- or hetero-phase interface structures requires specimens that meet stringent criteria. In some systems the necessary geometric imaging conditions are established naturally, thus greatly simplifying the analysis. This is illustrated for a diamond-hexagonal/diamond-cubic interface in deformed silicon, a Σ99 tilt boundary in a pure aluminum bicrystal, and a germanium precipitate in an aluminum matrix. 13 refs., 5 figs

Crystallographic properties of fertilizer compounds

Energy Technology Data Exchange (ETDEWEB)

Frazier, A.W.; Dillard, E.F.; Thrasher, R.D.; Waerstad, K.R.; Hunter, S.R.; Kohler, J.J.; Scheib, R.M.

1991-02-01

This bulletin is a compilation of crystallographic data collected at NFERC on 450 fertilizer-related compounds. In TVA's fertilizer R and D program, petrographic examination, XRD, and infrared spectroscopy are combined with conventional chemical analysis methods in identifying the individual compounds that occur in fertilizer materials. This handbook brings together the results of these characterization studies and supplemental crystallographic data from the literature. It is in one-compound-per-page, loose-leaf format, ordered alphabetically by IUPAC name. Indexes provided include IUPAC name, formula, group, alternate formula, synonyms, x-ray data, optical data. Tables are given for solids, compounds in commercial MAP and DAP, and matrix materials in phosphate rock.

Nitrogen in highly crystalline carbon nanotubes

International Nuclear Information System (INIS)

Ducati, C; Koziol, K; Stavrinadis, A; Friedrichs, S; Windle, A H; Midgley, P A

2006-01-01

Multiwall carbon nanotubes (MWCNTs) with an unprecedented degree of internal order were synthesised by chemical vapour deposition (CVD) adding a nitrogen-containing compound to the hydrocarbon feedstock. Ferrocene was used as the metal catalyst precursor. The remarkable crystallinity of these nanotubes lies both in the isochirality and in the crystallographic register of their walls, as demonstrated by electron diffraction and high resolution electron microscopy experiments. High resolution transmission electron microscopy analysis shows that the walls of the nanotubes consist of truncated stacked cones, instead of perfect cylinders, with a range of apex angles that appears to be related to the nitrogen concentration in the synthesis process. The structure of armchair, zigzag and chiral nanotubes is modelled and discussed in terms of density of topological defects, providing an interesting comparison with our microscopy experiments. A growth mechanism based on the interplay of base- and tip-growth is proposed to account for our experimental observations

A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures

International Nuclear Information System (INIS)

Rovira, Carme; Alfonso-Prieto, Mercedes; Biarnes, Xevi; Carpena, Xavi; Fita, Ignacio; Loewen, Peter C.

2006-01-01

Density functional molecular dynamics simulations using a QM/MM approach are used to get insight into the binding modes of formic acid in catalase. Two ligand binding sites are found, named A and B, in agreement with recent high resolution structures of catalase with bound formic acid. In addition, the calculations show that the His56 residue is protonated and the ligand is present as a formate anion. The lowest energy minimum structure (A) corresponds to the ligand interacting with both the heme iron and the catalytic residues (His56 and Asn129). The second minimum energy structure (B) corresponds to the situation in which the ligand interacts solely with the catalytic residues. A mechanism for the process of formic acid binding in catalase is suggested

A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures

Energy Technology Data Exchange (ETDEWEB)

Rovira, Carme [Centre especial de Recerca en Quimica Teorica, Parc Cientific de Barcelona, Josep Samitier 1-5, 08028 Barcelona (Spain)], E-mail: crovira@pcb.ub.es; Alfonso-Prieto, Mercedes [Centre especial de Recerca en Quimica Teorica, Parc Cientific de Barcelona, Josep Samitier 1-5, 08028 Barcelona (Spain); Biarnes, Xevi [Centre especial de Recerca en Quimica Teorica, Parc Cientific de Barcelona, Josep Samitier 1-5, 08028 Barcelona (Spain); Carpena, Xavi [Consejo Superior de Investigaciones Cientificas y Parc Cientific de Barcelona (CSIC-PCB), Josep Samitier 1-5, 08028 Barcelona (Spain); Fita, Ignacio [Consejo Superior de Investigaciones Cientificas y Parc Cientific de Barcelona (CSIC-PCB), Josep Samitier 1-5, 08028 Barcelona (Spain); Loewen, Peter C. [Department of Microbiology, University of Manitoba, Winnipeg, Canada MB R3T 2N2 (Canada)

2006-03-31

Density functional molecular dynamics simulations using a QM/MM approach are used to get insight into the binding modes of formic acid in catalase. Two ligand binding sites are found, named A and B, in agreement with recent high resolution structures of catalase with bound formic acid. In addition, the calculations show that the His56 residue is protonated and the ligand is present as a formate anion. The lowest energy minimum structure (A) corresponds to the ligand interacting with both the heme iron and the catalytic residues (His56 and Asn129). The second minimum energy structure (B) corresponds to the situation in which the ligand interacts solely with the catalytic residues. A mechanism for the process of formic acid binding in catalase is suggested.

High-Resolution Spore Coat Architecture and Assembly of Bacillus Spores

Energy Technology Data Exchange (ETDEWEB)

Malkin, A J; Elhadj, S; Plomp, M

2011-03-14

Elucidating the molecular architecture of bacterial and cellular surfaces and its structural dynamics is essential to understanding mechanisms of pathogenesis, immune response, physicochemical interactions, environmental resistance, and provide the means for identifying spore formulation and processing attributes. I will discuss the application of in vitro atomic force microscopy (AFM) for studies of high-resolution coat architecture and assembly of several Bacillus spore species. We have demonstrated that bacterial spore coat structures are phylogenetically and growth medium determined. We have proposed that strikingly different species-dependent coat structures of bacterial spore species are a consequence of sporulation media-dependent nucleation and crystallization mechanisms that regulate the assembly of the outer spore coat. Spore coat layers were found to exhibit screw dislocations and two-dimensional nuclei typically observed on inorganic and macromolecular crystals. This presents the first case of non-mineral crystal growth patterns being revealed for a biological organism, which provides an unexpected example of nature exploiting fundamental materials science mechanisms for the morphogenetic control of biological ultrastructures. We have discovered and validated, distinctive formulation-specific high-resolution structural spore coat and dimensional signatures of B. anthracis spores (Sterne strain) grown in different formulation condition. We further demonstrated that measurement of the dimensional characteristics of B. anthracis spores provides formulation classification and sample matching with high sensitivity and specificity. I will present data on the development of an AFM-based immunolabeling technique for the proteomic mapping of macromolecular structures on the B. anthracis surfaces. These studies demonstrate that AFM can probe microbial surface architecture, environmental dynamics and the life cycle of bacterial and cellular systems at near

Impact of AlN seeding layer growth rate in MOVPE growth of semi-polar gallium nitride structures on high index silicon

Energy Technology Data Exchange (ETDEWEB)

Ravash, Roghaiyeh; Blaesing, Juergen; Hempel, Thomas; Noltemeyer, Martin; Dadgar, Armin; Christen, Juergen; Krost, Alois [Otto-von-Guericke-University Magdeburg, FNW/IEP/AHE, Postfach 4120, 39016 Magdeburg (Germany)

2011-03-15

We present metal organic vapor phase epitaxy growth of semi-polar GaN structures on high index silicon surfaces. The crystallographic structure of GaN grown on Si(112), (115), and (117) substrates is investigated by X-ray analysis and scanning electron microscopy. X-ray diffraction was performed in Bragg Brentano geometry as well as pole figure measurements. The results demonstrate that the orientation of GaN crystallites on Si is significantly dependent on thickness of the AlN seeding layer and TMAl-flow rate. We observe that the crystallographic structures of GaN by applying thin AlN seeding layers grown with high TMAl-flow rate depend on Si surface direction while they are independent for thicker layers. By applying such seeding layer we obtain single crystalline semi-polar GaN on Si(112), while GaN structures grown with the same growth parameters on Si(117) show four components of GaN(0002). (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Analyzing shear band formation with high resolution X-ray diffraction

Energy Technology Data Exchange (ETDEWEB)

Pagan, Darren C.; Obstalecki, Mark; Park, Jun-Sang; Miller, Matthew P.

2018-04-01

Localization of crystallographic slip into shear bands during uniaxial compression of a copper single crystal is studied using very far-field high-energy diffraction microscopy (vff-HEDM). Diffracted intensity was collected in-situ as the crystal deformed using a unique mobile detector stage that provided access to multiple diffraction peaks with high-angular resolution. From the diffraction data, single crystal orientation pole figures (SCPFs) were generated and are used to track the evolution of the distribution of lattice orientation that develops as slip localizes. To aid the identification of 'signatures' of shear band formation and analyze the SCPF data, a model of slip-driven lattice reorientation within shear bands is introduced. Confidence is built in conclusions drawn from the SCPF data about the character of internal slip localization through comparisons with strain fields on the sample surface measured simultaneously using digital image correlation. From the diffraction data, we find that the active slip direction and slip plane are not directly aligned with the orientation of the shear bands that formed. In fact, by extracting the underlying slip system activity from the SCPF data, we show that intersecting shear bands measured on the surface of the sample arise from slip primarily on the same underlying single slip system. These new vff-HEDM results raise significant questions on the use of surface measurements for slip system activity estimation. (C) 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

High resolution solar observations from first principles to applications

Science.gov (United States)

Verdoni, Angelo P.

2009-10-01

The expression "high-resolution observations" in Solar Physics refers to the spatial, temporal and spectral domains in their entirety. High-resolution observations of solar fine structure are a necessity to answer many of the intriguing questions related to solar activity. However, a researcher building instruments for high-resolution observations has to cope with the fact that these three domains often have diametrically opposed boundary conditions. Many factors have to be considered in the design of a successful instrument. Modern post-focus instruments are more closely linked with the solar telescopes that they serve than in past. In principle, the quest for high-resolution observations already starts with the selection of the observatory site. The site survey of the Advanced Technology Solar Telescope (ATST) under the stewardship of the National Solar Observatory (NSO) has identified Big Bear Solar Observatory (BBSO) as one of the best sites for solar observations. In a first step, the seeing characteristics at BBSO based on the data collected for the ATST site survey are described. The analysis will aid in the scheduling of high-resolution observations at BBSO as well as provide useful information concerning the design and implementation of a thermal control system for the New Solar Telescope (NST). NST is an off-axis open-structure Gregorian-style telescope with a 1.6 m aperture. NST will be housed in a newly constructed 5/8-sphere ventilated dome. With optics exposed to the surrounding air, NST's open-structure design makes it particularly vulnerable to the effects of enclosure-related seeing. In an effort to mitigate these effects, the initial design of a thermal control system for the NST dome is presented. The goal is to remediate thermal related seeing effects present within the dome interior. The THermal Control System (THCS) is an essential component for the open-telescope design of NST to work. Following these tasks, a calibration routine for the

Crystallographic disorder and magnetism in UPd2-xSn

International Nuclear Information System (INIS)

Suellow, S.; Mattheus, C.C.; Becker, B.; Snel, C.E.; Nieuwenhuys, G.J.; Mydosh, J.A.; Schenck, A.

1997-01-01

The intermetallic compound UPd 2 Sn has been shown in previous investigations to crystallize in an orthorhombic structure (space group Pnma). No indications for magnetic or superconducting transitions were found. However, if the Pd content is reduced, then, similar to UNi 2 Sn, a structural transition occurs. We prepared UPd 1.85 Sn and found it to crystallize as a Heusler compound in the MnCu 2 Al-structure (space group Fm anti 3m). Now the system undergoes a transition into a disordered magnetic state at T mag ≅ 28 K. Here, we present our measurements of the specific heat, susceptibility and muon relaxation of UPd 1.85 Sn, and discuss the nature of the magnetic state in relation to the crystallographic structure. (orig.)

Modeling the characteristic etch morphologies along specific crystallographic orientations by anisotropic chemical etching

Directory of Open Access Journals (Sweden)

Kun-Dar Li

2018-02-01

Full Text Available To improve the advanced manufacturing technology for functional materials, a sophisticated control of chemical etching process is highly demanded, especially in the fields of environment and energy related applications. In this study, a phase-field-based model is utilized to investigate the etch morphologies influenced by the crystallographic characters during anisotropic chemical etching. Three types of etching modes are inspected theoretically, including the isotropic, and preferred oriented etchings. Owing to the specific etching behavior along the crystallographic directions, different characteristic surface structures are presented in the simulations, such as the pimple-like, pyramidal hillock and ridge-like morphologies. In addition, the processing parameters affecting the surface morphological formation and evolution are also examined systematically. According to the numerical results, the growth mechanism of surface morphology in a chemical etching is revealed distinctly. While the etching dynamics plays a dominant role on the surface formation, the characteristic surface morphologies corresponding to the preferred etching direction become more apparent. As the atomic diffusion turned into a determinative factor, a smoothened surface would appear, even under the anisotropic etching conditions. These simulation results provide fundamental information to enhance the development and application of anisotropic chemical etching techniques.

Modeling the characteristic etch morphologies along specific crystallographic orientations by anisotropic chemical etching

Science.gov (United States)

Li, Kun-Dar; Miao, Jin-Ru

2018-02-01

To improve the advanced manufacturing technology for functional materials, a sophisticated control of chemical etching process is highly demanded, especially in the fields of environment and energy related applications. In this study, a phase-field-based model is utilized to investigate the etch morphologies influenced by the crystallographic characters during anisotropic chemical etching. Three types of etching modes are inspected theoretically, including the isotropic, and preferred oriented etchings. Owing to the specific etching behavior along the crystallographic directions, different characteristic surface structures are presented in the simulations, such as the pimple-like, pyramidal hillock and ridge-like morphologies. In addition, the processing parameters affecting the surface morphological formation and evolution are also examined systematically. According to the numerical results, the growth mechanism of surface morphology in a chemical etching is revealed distinctly. While the etching dynamics plays a dominant role on the surface formation, the characteristic surface morphologies corresponding to the preferred etching direction become more apparent. As the atomic diffusion turned into a determinative factor, a smoothened surface would appear, even under the anisotropic etching conditions. These simulation results provide fundamental information to enhance the development and application of anisotropic chemical etching techniques.

Novel high resolution tactile robotic fingertips

DEFF Research Database (Denmark)

Drimus, Alin; Jankovics, Vince; Gorsic, Matija

2014-01-01

This paper describes a novel robotic fingertip based on piezoresistive rubber that can sense pressure tactile stimuli with a high spatial resolution over curved surfaces. The working principle is based on a three-layer sandwich structure (conductive electrodes on top and bottom and piezoresistive...... with specialized data acquisition electronics that acquire 500 frames per second provides rich information regarding contact force, shape and angle for bio- inspired robotic fingertips. Furthermore, a model of estimating the force of contact based on values of the cells is proposed....

Computationally-optimized bone mechanical modeling from high-resolution structural images.

Directory of Open Access Journals (Sweden)

Jeremy F Magland

Full Text Available Image-based mechanical modeling of the complex micro-structure of human bone has shown promise as a non-invasive method for characterizing bone strength and fracture risk in vivo. In particular, elastic moduli obtained from image-derived micro-finite element (μFE simulations have been shown to correlate well with results obtained by mechanical testing of cadaveric bone. However, most existing large-scale finite-element simulation programs require significant computing resources, which hamper their use in common laboratory and clinical environments. In this work, we theoretically derive and computationally evaluate the resources needed to perform such simulations (in terms of computer memory and computation time, which are dependent on the number of finite elements in the image-derived bone model. A detailed description of our approach is provided, which is specifically optimized for μFE modeling of the complex three-dimensional architecture of trabecular bone. Our implementation includes domain decomposition for parallel computing, a novel stopping criterion, and a system for speeding up convergence by pre-iterating on coarser grids. The performance of the system is demonstrated on a dual quad-core Xeon 3.16 GHz CPUs equipped with 40 GB of RAM. Models of distal tibia derived from 3D in-vivo MR images in a patient comprising 200,000 elements required less than 30 seconds to converge (and 40 MB RAM. To illustrate the system's potential for large-scale μFE simulations, axial stiffness was estimated from high-resolution micro-CT images of a voxel array of 90 million elements comprising the human proximal femur in seven hours CPU time. In conclusion, the system described should enable image-based finite-element bone simulations in practical computation times on high-end desktop computers with applications to laboratory studies and clinical imaging.

High resolution X radiography imaging detector-micro gap chamber

International Nuclear Information System (INIS)

Long Huqiang; Wang Yun; Xu Dong; Xie Kuanzhong; Bian Jianjiang

2007-01-01

Micro gap chamber (MGC) is a new type of Two-Dimensional position sensitive detector having excellent properties on the space and time resolution, counting rate, 2D compact structure and the flexible of application. It will become a candidate of a new tracking detector for high energy physics experiment. The basic structure and properties of MGC as well as its main research subjects are presented in this paper. Furthermore, the feasibility and validity of utilizing diamond films as the MGC gap material were also discussed in detail. So, a potential radiography imaging detector is provided in order to realize X image and X ray diffraction experiment having very good spatial and time resolution in the 3rd Generation of Synchrotron Radiation Facility. (authors)

Triple aldose reductase/α-glucosidase/radical scavenging high-resolution profiling combined with high-performance liquid chromatography – high-resolution mass spectrometry – solid-phase extraction – nuclear magnetic resonance spectroscopy for identification of antidiabetic constituents in crude, extract of Radix Scutellariae

DEFF Research Database (Denmark)

Tahtah, Yousof; Kongstad, Kenneth Thermann; Wubshet, Sileshi Gizachew

2015-01-01

high-performance liquid chromatography – high-resolution mass spectrometry – solid-phase extraction – nuclear magnetic resonance spectroscopy. The only α-glucosidase inhibitor was baicalein, whereas main aldose reductase inhibitors in the crude extract were baicalein and skullcapflavone II, and main....../α-glucosidase/radical scavenging high-resolution inhibition profile - allowing proof of concept with Radix Scutellariae crude extract as a polypharmacological herbal drug. The triple bioactivity high-resolution profiles were used to pinpoint bioactive compounds, and subsequent structure elucidation was performed with hyphenated...

Auxeticity of Yukawa Systems with Nanolayers in the (111 Crystallographic Plane

Directory of Open Access Journals (Sweden)

Paweł M. Pigłowski

2017-11-01

Full Text Available Elastic properties of model crystalline systems, in which the particles interact via the hard potential (infinite when any particles overlap and zero otherwise and the hard-core repulsive Yukawa interaction, were determined by Monte Carlo simulations. The influence of structural modifications, in the form of periodic nanolayers being perpendicular to the crystallographic axis [111], on auxetic properties of the crystal was investigated. It has been shown that the hard sphere nanolayers introduced into Yukawa crystals allow one to control the elastic properties of the system. It has been also found that the introduction of the Yukawa monolayers to the hard sphere crystal induces auxeticity in the [ 11 1 ¯ ] [ 112 ] -direction, while maintaining the negative Poisson’s ratio in the [ 110 ] [ 1 1 ¯ 0 ] -direction, thus expanding the partial auxeticity of the system to an additional important crystallographic direction.

Dynamical X-ray scattering from the relaxed structures

International Nuclear Information System (INIS)

Benediktovitch, A.; Feranchuk, I.; Ulyanenkov, A.

2009-01-01

High-resolution X-ray diffraction is now widely used analytical tool for investigation of nano scale multilayered structures in semiconductor and optical technologies. The HRXRD method delivers unique information on the crystallographic lattice of the samples, concentration of solid solutions, lattice mismatches, layer thicknesses, defect distribution, and relaxation degree of the epitaxial layers. The evaluation of the experimental results, however, requires a robust and precise theory due to complex dynamical scattering of X-rays from near perfect crystallographic structure of the samples. Usually, the Takagi-Taupin approach [1] or the recurrent matrix methods [2] are used for the simulation of the X-ray diffraction profiles from the epitaxial multilayered structures. The use of these theories, however, becomes essentially difficult, when the lateral lattice mismatches are present in multilayers, for example, in the case of partially or fully relaxed epitaxially grown samples. In the present work, the general solution of this problem is found analytically. The angular divergence of the incident beam is also considered and the algorithm for the diffracted profile mapping in the reciprocal space is developed. The experimental reciprocal space mapping of typical AlGaN/GaN/AlN samples with partially relaxed layers is compared to the simulated maps, which describe well the location and character of the diffraction spots caused by different layers. (author)

Purification, crystallization and preliminary crystallographic studies on 2-dehydro-3-deoxygalactarate aldolase from Leptospira interrogans

Energy Technology Data Exchange (ETDEWEB)

Li, Xu; Huang, Hua [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Song, Xiaomin [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Wang, Yanli; Xu, Hang [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Teng, Maikun [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Gong, Weimin, E-mail: wgong@sun5.ibp.ac.cn [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

2006-12-01

Preliminary crystallographic studies on 2-dehydro-3-deoxygalactarate aldolase from L. interrogans. 2-Dehydro-3-deoxygalactarate (DDG) aldolase is a member of the class II aldolase family and plays an important role in the pyruvate-metabolism pathway, catalyzing the reversible aldol cleavage of DDG to pyruvate and tartronic semialdehyde. As it is a potential novel antibiotic target, it is necessary to elucidate the catalytic mechanism of DDG aldolase. To determine the crystal structure, crystals of DDG aldolase from Leptospira interrogans were obtained by the hanging-drop vapour-diffusion method. The crystals diffracted to 2.2 Å resolution using a Cu Kα rotating-anode X-ray source. The crystal belonged to space group C2, with unit-cell parameters a = 293.5, b = 125.6, c = 87.6 Å, β = 100.9°. The V{sub M} is calculated to be 2.4 Å{sup 3} Da{sup −1}, assuming there to be 12 protein molecules in the asymmetric unit.

Purification, crystallization and preliminary crystallographic studies on 2-dehydro-3-deoxygalactarate aldolase from Leptospira interrogans

International Nuclear Information System (INIS)

Li, Xu; Huang, Hua; Song, Xiaomin; Wang, Yanli; Xu, Hang; Teng, Maikun; Gong, Weimin

2006-01-01

Preliminary crystallographic studies on 2-dehydro-3-deoxygalactarate aldolase from L. interrogans. 2-Dehydro-3-deoxygalactarate (DDG) aldolase is a member of the class II aldolase family and plays an important role in the pyruvate-metabolism pathway, catalyzing the reversible aldol cleavage of DDG to pyruvate and tartronic semialdehyde. As it is a potential novel antibiotic target, it is necessary to elucidate the catalytic mechanism of DDG aldolase. To determine the crystal structure, crystals of DDG aldolase from Leptospira interrogans were obtained by the hanging-drop vapour-diffusion method. The crystals diffracted to 2.2 Å resolution using a Cu Kα rotating-anode X-ray source. The crystal belonged to space group C2, with unit-cell parameters a = 293.5, b = 125.6, c = 87.6 Å, β = 100.9°. The V M is calculated to be 2.4 Å 3 Da −1 , assuming there to be 12 protein molecules in the asymmetric unit

Berkeley High-Resolution Ball

International Nuclear Information System (INIS)

Diamond, R.M.

1984-10-01

Criteria for a high-resolution γ-ray system are discussed. Desirable properties are high resolution, good response function, and moderate solid angle so as to achieve not only double- but triple-coincidences with good statistics. The Berkeley High-Resolution Ball involved the first use of bismuth germanate (BGO) for anti-Compton shield for Ge detectors. The resulting compact shield permitted rather close packing of 21 detectors around a target. In addition, a small central BGO ball gives the total γ-ray energy and multiplicity, as well as the angular pattern of the γ rays. The 21-detector array is nearly complete, and the central ball has been designed, but not yet constructed. First results taken with 9 detector modules are shown for the nucleus 156 Er. The complex decay scheme indicates a transition from collective rotation (prolate shape) to single- particle states (possibly oblate) near spin 30 h, and has other interesting features

Principles of high resolution NMR in solids

CERN Document Server

Mehring, Michael

1983-01-01

The field of Nuclear Magnetic Resonance (NMR) has developed at a fascinating pace during the last decade. It always has been an extremely valuable tool to the organic chemist by supplying molecular "finger print" spectra at the atomic level. Unfortunately the high resolution achievable in liquid solutions could not be obtained in solids and physicists and physical chemists had to live with unresolved lines open to a wealth of curve fitting procedures and a vast amount of speculations. High resolution NMR in solids seemed to be a paradoxon. Broad structure­ less lines are usually encountered when dealing with NMR in solids. Only with the recent advent of mUltiple pulse, magic angle, cross-polarization, two-dimen­ sional and multiple-quantum spectroscopy and other techniques during the last decade it became possible to resolve finer details of nuclear spin interactions in solids. I have felt that graduate students, researchers and others beginning to get involved with these techniques needed a book which trea...

High resolution NMR theory and chemical applications

CERN Document Server

Becker, Edwin D

1999-01-01

High Resolution NMR provides a broad treatment of the principles and theory of nuclear magnetic resonance (NMR) as it is used in the chemical sciences. It is written at an "intermediate" level, with mathematics used to augment, rather than replace, clear verbal descriptions of the phenomena. The book is intended to allow a graduate student, advanced undergraduate, or researcher to understand NMR at a fundamental level, and to see illustrations of the applications of NMR to the determination of the structure of small organic molecules and macromolecules, including proteins. Emphasis is on the study of NMR in liquids, but the treatment also includes high resolution NMR in the solid state and the principles of NMR imaging and localized spectroscopy. Careful attention is given to developing and interrelating four approaches - steady state energy levels, the rotating vector picture, the density matrix, and the product operator formalism. The presentation is based on the assumption that the reader has an acquaintan...

Crystallographic structure and substrate-binding interactions of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri.

Science.gov (United States)

Balan, Andrea; Santacruz-Pérez, Carolina; Moutran, Alexandre; Ferreira, Luís Carlos Souza; Neshich, Goran; Gonçalves Barbosa, João Alexandre Ribeiro

2008-02-01

In Xanthomonas axonopodis pv. citri (Xac or X. citri), the modA gene codes for a periplasmic protein (ModA) that is capable of binding molybdate and tungstate as part of the ABC-type transporter required for the uptake of micronutrients. In this study, we report the crystallographic structure of the Xac ModA protein with bound molybdate. The Xac ModA structure is similar to orthologs with known three-dimensional structures and consists of two nearly symmetrical domains separated by a hinge region where the oxyanion-binding site lies. Phylogenetic analysis of different ModA orthologs based on sequence alignments revealed three groups of molybdate-binding proteins: bacterial phytopathogens, enterobacteria and soil bacteria. Even though the ModA orthologs are segregated into different groups, the ligand-binding hydrogen bonds are mostly conserved, except for Archaeglobus fulgidus ModA. A detailed discussion of hydrophobic interactions in the active site is presented and two new residues, Ala38 and Ser151, are shown to be part of the ligand-binding pocket.

Structural insights into the adaptation of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii to a high-salt environment

International Nuclear Information System (INIS)

Morgunova, Ekaterina; Gray, Fiona C.; MacNeill, Stuart A.; Ladenstein, Rudolf

2009-01-01

The crystal structure of PCNA from the halophilic archaeon H. volcanii reveals specific features of the charge distribution on the protein surface that reflect adaptation to a high-salt environment and suggests a different type of interaction with DNA in halophilic PCNAs. The sliding clamp proliferating cell nuclear antigen (PCNA) plays vital roles in many aspects of DNA replication and repair in eukaryotic cells and in archaea. Realising the full potential of archaea as a model for PCNA function requires a combination of biochemical and genetic approaches. In order to provide a platform for subsequent reverse genetic analysis, PCNA from the halophilic archaeon Haloferax volcanii was subjected to crystallographic analysis. The gene was cloned and expressed in Escherichia coli and the protein was purified by affinity chromatography and crystallized by the vapour-diffusion technique. The structure was determined by molecular replacement and refined at 3.5 Å resolution to a final R factor of 23.7% (R free = 25%). PCNA from H. volcanii was found to be homotrimeric and to resemble other homotrimeric PCNA clamps but with several differences that appear to be associated with adaptation of the protein to the high intracellular salt concentrations found in H. volcanii cells

Modelling high-resolution electron microscopy based on core-loss spectroscopy

International Nuclear Information System (INIS)

Allen, L.J.; Findlay, S.D.; Oxley, M.P.; Witte, C.; Zaluzec, N.J.

2006-01-01

There are a number of factors affecting the formation of images based on core-loss spectroscopy in high-resolution electron microscopy. We demonstrate unambiguously the need to use a full nonlocal description of the effective core-loss interaction for experimental results obtained from high angular resolution electron channelling electron spectroscopy. The implications of this model are investigated for atomic resolution scanning transmission electron microscopy. Simulations are used to demonstrate that core-loss spectroscopy images formed using fine probes proposed for future microscopes can result in images that do not correspond visually with the structure that has led to their formation. In this context, we also examine the effect of varying detector geometries. The importance of the contribution to core-loss spectroscopy images by dechannelled or diffusely scattered electrons is reiterated here

Crystal structure and defects of Zr4Co4Si7( V-phase) investigated by high resolution transmission electron microscope

International Nuclear Information System (INIS)

Mao, J.F.; Ye, H.Q.; Ning, X.G.; He, L.L.; Yang, D.Z.

1997-01-01

The results of high resolution transmission electron microscope (HRTEM) observation and image simulation show that Zr 4 Co 4 Si 7 possesses the same structure type of Zr 4 Co 4 Ge 7 . Adding of Fe or Ni into the Zr 4 Co 4 Si 7 compound, except that the dimensions changed slightly, does not change the lattice type and coordination in the crystal structure, maintaining the V-phase structure. Also, twins with coherent boundaries and with partially coherent at interfaces are observed. The image conditions of Zr 4 Co 4 Si 7 and the structure differences between Zr 4 Co 4 Si 7 and tetrahedral close-packed phases are also discussed. copyright 1997 Materials Research Society

Ocean acidification reduces the crystallographic control in juvenile mussel shells.

Science.gov (United States)

Fitzer, Susan C; Cusack, Maggie; Phoenix, Vernon R; Kamenos, Nicholas A

2014-10-01

Global climate change threatens the oceans as anthropogenic carbon dioxide causes ocean acidification and reduced carbonate saturation. Future projections indicate under saturation of aragonite, and potentially calcite, in the oceans by 2100. Calcifying organisms are those most at risk from such ocean acidification, as carbonate is vital in the biomineralisation of their calcium carbonate protective shells. This study highlights the importance of multi-generational studies to investigate how marine organisms can potentially adapt to future projected global climate change. Mytilus edulis is an economically important marine calcifier vulnerable to decreasing carbonate saturation as their shells comprise two calcium carbonate polymorphs: aragonite and calcite. M. edulis specimens were cultured under current and projected pCO2 (380, 550, 750 and 1000μatm), following 6months of experimental culture, adults produced second generation juvenile mussels. Juvenile mussel shells were examined for structural and crystallographic orientation of aragonite and calcite. At 1000μatm pCO2, juvenile mussels spawned and grown under this high pCO2 do not produce aragonite which is more vulnerable to carbonate under-saturation than calcite. Calcite and aragonite were produced at 380, 550 and 750μatm pCO2. Electron back scatter diffraction analyses reveal less constraint in crystallographic orientation with increased pCO2. Shell formation is maintained, although the nacre crystals appear corroded and crystals are not so closely layered together. The differences in ultrastructure and crystallography in shells formed by juveniles spawned from adults in high pCO2 conditions may prove instrumental in their ability to survive ocean acidification. Copyright © 2014 Elsevier Inc. All rights reserved.

Use of noncrystallographic symmetry for automated model building at medium to low resolution

International Nuclear Information System (INIS)

Wiegels, Tim; Lamzin, Victor S.

2012-01-01

Noncrystallographic symmetry is automatically detected and used to achieve higher completeness and greater accuracy of automatically built protein structures at resolutions of 2.3 Å or poorer. A novel method is presented for the automatic detection of noncrystallographic symmetry (NCS) in macromolecular crystal structure determination which does not require the derivation of molecular masks or the segmentation of density. It was found that throughout structure determination the NCS-related parts may be differently pronounced in the electron density. This often results in the modelling of molecular fragments of variable length and accuracy, especially during automated model-building procedures. These fragments were used to identify NCS relations in order to aid automated model building and refinement. In a number of test cases higher completeness and greater accuracy of the obtained structures were achieved, specifically at a crystallographic resolution of 2.3 Å or poorer. In the best case, the method allowed the building of up to 15% more residues automatically and a tripling of the average length of the built fragments

3D high-resolution radar imaging of small body interiors

Science.gov (United States)

Sava, Paul; Asphaug, Erik

2017-10-01

Answering fundamental questions about the origin and evolution of small planetary bodies hinges on our ability to image their interior structure in detail and at high resolution (Asphaug, 2009). We often infer internal structure from surface observations, e.g. that comet 67P/Churyumov-Gerasimenko is a primordial agglomeration of cometesimals (Massironi et al., 2015). However, the interior structure is not easily accessible without systematic imaging using, e.g., radar transmission and reflection data, as suggested by the CONSERT experiment on Rosetta. Interior imaging depends on observations from multiple viewpoints, as in medical tomography.We discuss radar imaging using methodology adapted from terrestrial exploration seismology (Sava et al., 2015). We primarily focus on full wavefield methods that facilitate high quality imaging of small body interiors characterized by complex structure and large contrasts of physical properties. We consider the case of a monostatic system (co-located transmitters and receivers) operated at two frequency bands, centered around 5 and 15 MHz, from a spacecraft in slow polar orbit around a spinning comet nucleus. Assuming that the spin period is significantly (e.g. 5x) faster than the orbital period, this configuration allows repeated views from multiple directions (Safaeinili et al., 2002)Using realistic numerical experiments, we argue that (1) the comet/asteroid imaging problem is intrinsically 3D and conventional SAR methodology does not satisfy imaging, sampling and resolution requirements; (2) imaging at different frequency bands can provide information about internal surfaces (through migration) and internal volumes (through tomography); (3) interior imaging can be accomplished progressively as data are being acquired through successive orbits around the studied object; (4) imaging resolution can go beyond the apparent radar frequency band by deconvolution of the point-spread-function characterizing the imaging system; and (5

New generation of efficient high resolution detector for 30-100 keV photons

DEFF Research Database (Denmark)

Olsen, Ulrik Lund

between pores. The potential of the structured scintillator is explored through Monte Carlo simulations. A spatial resolution of 1 µm is obtainable and for scintillators with a resolution between 1 µm and 8 µm the efficiency could be more than 15 times higher than a regular scintillator with corresponding...... detector. This establishes an inverse correlation between the spatial resolution and the detection efficiency which limits the performance of existing x-ray detectors. The purpose of this Ph.D. project is to explore alternative paths of research, to develop x-ray detectors for the 30-100 keV energy range...... with single micrometre resolution without compromising efficiency. A number of detector types have been evaluated for this purpose. Structured scintillators are found to exhibit a high potential in terms of performance and also in terms of realizing an actual detector. The structured scintillator consists...

Glacio-tectonic thrust and deformation structures in the Vejle Fjord, Denmark revealed by high-resolution subbottom-profile data

DEFF Research Database (Denmark)

Andresen, Katrine Juul; Boldreel, Lars Ole; Wahlgreen, Katrine Bak

Surface geomorphological features and partial cliff exposures up till now represent the predominant source of information of glaciation related deformation in Denmark. In this study we apply high-resolution marine reflection seismic data from the Vejle Fjord area, supported by gravity and Rumohr...... coring, to document intense glacio-tectonic deformation in the shallow subsurface of Denmark. The subbottom profiler seismic data have a peak frequency around 13 kHz and a vertical resolution in the order of 10-20 cm. The data reveal several variations of glacio-tectonic deformation structures, primarily...... movements from outcrops and shallow cores. The subbottom profiler data provides larger (longer and deeper) sectional views on for instance deformation and deposition complexes related to ice progressions and retreats and thus represents a very good supplement and valuable input to field mapping and outcrops...

High resolution muon computed tomography at neutrino beam facilities

International Nuclear Information System (INIS)

Suerfu, B.; Tully, C.G.

2016-01-01

X-ray computed tomography (CT) has an indispensable role in constructing 3D images of objects made from light materials. However, limited by absorption coefficients, X-rays cannot deeply penetrate materials such as copper and lead. Here we show via simulation that muon beams can provide high resolution tomographic images of dense objects and of structures within the interior of dense objects. The effects of resolution broadening from multiple scattering diminish with increasing muon momentum. As the momentum of the muon increases, the contrast of the image goes down and therefore requires higher resolution in the muon spectrometer to resolve the image. The variance of the measured muon momentum reaches a minimum and then increases with increasing muon momentum. The impact of the increase in variance is to require a higher integrated muon flux to reduce fluctuations. The flux requirements and level of contrast needed for high resolution muon computed tomography are well matched to the muons produced in the pion decay pipe at a neutrino beam facility and what can be achieved for momentum resolution in a muon spectrometer. Such an imaging system can be applied in archaeology, art history, engineering, material identification and whenever there is a need to image inside a transportable object constructed of dense materials

High-Resolution PET Detector. Final report

International Nuclear Information System (INIS)

Karp, Joel

2014-01-01

The objective of this project was to develop an understanding of the limits of performance for a high resolution PET detector using an approach based on continuous scintillation crystals rather than pixelated crystals. The overall goal was to design a high-resolution detector, which requires both high spatial resolution and high sensitivity for 511 keV gammas. Continuous scintillation detectors (Anger cameras) have been used extensively for both single-photon and PET scanners, however, these instruments were based on NaI(Tl) scintillators using relatively large, individual photo-multipliers. In this project we investigated the potential of this type of detector technology to achieve higher spatial resolution through the use of improved scintillator materials and photo-sensors, and modification of the detector surface to optimize the light response function.We achieved an average spatial resolution of 3-mm for a 25-mm thick, LYSO continuous detector using a maximum likelihood position algorithm and shallow slots cut into the entrance surface

Estimating structure quality trends in the Protein Data Bank by equivalent resolution.

Science.gov (United States)

Bagaria, Anurag; Jaravine, Victor; Güntert, Peter

2013-10-01

The quality of protein structures obtained by different experimental and ab-initio calculation methods varies considerably. The methods have been evolving over time by improving both experimental designs and computational techniques, and since the primary aim of these developments is the procurement of reliable and high-quality data, better techniques resulted on average in an evolution toward higher quality structures in the Protein Data Bank (PDB). Each method leaves a specific quantitative and qualitative "trace" in the PDB entry. Certain information relevant to one method (e.g. dynamics for NMR) may be lacking for another method. Furthermore, some standard measures of quality for one method cannot be calculated for other experimental methods, e.g. crystal resolution or NMR bundle RMSD. Consequently, structures are classified in the PDB by the method used. Here we introduce a method to estimate a measure of equivalent X-ray resolution (e-resolution), expressed in units of Å, to assess the quality of any type of monomeric, single-chain protein structure, irrespective of the experimental structure determination method. We showed and compared the trends in the quality of structures in the Protein Data Bank over the last two decades for five different experimental techniques, excluding theoretical structure predictions. We observed that as new methods are introduced, they undergo a rapid method development evolution: within several years the e-resolution score becomes similar for structures obtained from the five methods and they improve from initially poor performance to acceptable quality, comparable with previously established methods, the performance of which is essentially stable. Copyright © 2013 Elsevier Ltd. All rights reserved.

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package

Energy Technology Data Exchange (ETDEWEB)

Borbulevych, Oleg Y.; Plumley, Joshua A.; Martin, Roger I. [QuantumBio Inc., 2790 West College Avenue, State College, PA 16801 (United States); Merz, Kenneth M. Jr [University of Florida, Gainesville, Florida (United States); Westerhoff, Lance M., E-mail: lance@quantumbioinc.com [QuantumBio Inc., 2790 West College Avenue, State College, PA 16801 (United States)

2014-05-01

Semiempirical quantum-chemical X-ray macromolecular refinement using the program DivCon integrated with PHENIX is described. Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein–ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

Fabrication of thin TEM sample of ionic liquid for high-resolution ELNES measurements

Energy Technology Data Exchange (ETDEWEB)

Miyata, Tomohiro, E-mail: tomo-m@iis.u-tokyo.ac.jp; Mizoguchi, Teruyasu, E-mail: teru@iis.u-tokyo.ac.jp

2017-07-15

Investigation of the local structure, ionic and molecular behavior, and chemical reactions at high spatial resolutions in liquids has become increasingly important. Improvements in these areas help to develop efficient batteries and improve organic syntheses. Transmission electron microscopy (TEM) and scanning-TEM (STEM) have excellent spatial resolution, and the electron energy-loss near edge structure (ELNES) measured by the accompanied electron energy-loss spectroscopy (EELS) is effective to analyze the liquid local structure owing to reflecting the electronic density of states. In this study, we fabricate a liquid-layer-only sample with thickness of single to tens nanometers using an ionic liquid. Because the liquid film has a thickness much less than the inelastic mean free path (IMFP) of the electron beam, the fine structure of the C-K edge electron energy loss near edge structure (ELNES) can be measured with sufficient resolution to allow meaningful analysis. The ELNES spectrum from the thin liquid film has been interpreted using first principles ELNES calculations. - Highlights: • A fabrication method of thin liquid film samples for STEM-EELS observations is proposed. • The thickness of the fabricated thin liquid film is about 10 nm. • An ELNES is measured from the thin liquid with a high energy resolution. • The peaks of the ELNES are interpreted using first principles calculations.

Low-cost, high-resolution scanning laser ophthalmoscope for the clinical environment

Science.gov (United States)

Soliz, P.; Larichev, A.; Zamora, G.; Murillo, S.; Barriga, E. S.

2010-02-01

Researchers have sought to gain greater insight into the mechanisms of the retina and the optic disc at high spatial resolutions that would enable the visualization of small structures such as photoreceptors and nerve fiber bundles. The sources of retinal image quality degradation are aberrations within the human eye, which limit the achievable resolution and the contrast of small image details. To overcome these fundamental limitations, researchers have been applying adaptive optics (AO) techniques to correct for the aberrations. Today, deformable mirror based adaptive optics devices have been developed to overcome the limitations of standard fundus cameras, but at prices that are typically unaffordable for most clinics. In this paper we demonstrate a clinically viable fundus camera with auto-focus and astigmatism correction that is easy to use and has improved resolution. We have shown that removal of low-order aberrations results in significantly better resolution and quality images. Additionally, through the application of image restoration and super-resolution techniques, the images present considerably improved quality. The improvements lead to enhanced visualization of retinal structures associated with pathology.

Analysis of phase transitions and crystal structures of novel benzothiophene derivatives

Science.gov (United States)

Zhang, Shuo

Although single crystal X-ray diffraction remains the most important technique for analyzing periodically ordered structures at atomic resolution, single crystal X-ray diffraction of organic macromolecules is challenged by difficulty in growing single crystals of desired size and quality. Electron crystallography of organic macromolecules, on the other hand, is limited by image resolution due to radiation damage and highly dependent on high-resolution instrumentation. Novel alkylated benzothiophene derivatives synthesized previously can be readily fabricated into semiconductor devices for various applications (photodetectors, explosive sensors, field-effect transistors, light-emitting diodes, etc.) via solution process. The object of this research is to identify phase transitions of organic macromolecules of this kind via differential scanning calorimetry and temperature-resolved wide angle X-ray diffraction, and to determine their lattice parameters and space groups by reconstruction of their reciprocal space via transmission electron microscopy/selected area electron diffraction followed by refinement with X-ray diffraction, supplemented by polarized light microscopy. Computer simulation was performed to rationalize the molecular packing schemes, so as to understand the origin of their electronic performance from crystallographic perspective.

Comparison of the free volume sizes and shapes determined from crystallographic and PALS data

Directory of Open Access Journals (Sweden)

Tydda Maciej

2015-12-01

Full Text Available Two different classes of molecular crystals were investigated. The first group was benzenediols, which are characterized by the same chemical composition but a different organization of their crystallographic structures; all of the compounds from this group have only one kind of free volumes. The second class was represented by olanzapine, which has more complex chemical composition and two kinds of free volumes in the structure. The o-Ps lifetime values determined from positron annihilation lifetime spectroscopy (PALS measurements agree quite well with those calculated for sizes found from crystallographic data for benzenediols (agreement within 10% of the lifetime values. For olanzapine, a good agreement is observed in the case of cuboidal free volumes, while for the other kind of void, the agreement is less satisfactory. Positronium diffusion coefficient determined from o-Ps redistribution in olanzapine agrees with these found for polymers.

Transmission/Scanning Transmission Electron Microscopy | Materials Science

Science.gov (United States)

crystallographic structure of a material. Amplitude-contrast images yield information about the chemistry and microstructure of a material and its defects. Phase-contrast imaging or high-resolution (HR) TEM imaging gives information about the microstructure of a material and its defects at an atomic resolution. With scanning

Use of high-resolution satellite images for detection of geological structures related to Calerias geothermal field, Chile

Science.gov (United States)

Arellano-Baeza, A. A.; Urzua, L.

2011-12-01

Chile has enormous potential to use the geothermal resources for electric energy generation. The main geothermal fields are located in the Central Andean Volcanic Chain in the North, between the Central valley and the border with Argentina in the center, and in the fault system Liquiñe-Ofqui in the South of the country. High resolution images from the LANDSAT and ASTER satellites have been used to delineate the geological structures related to the Calerias geothermal field located at the northern end of the Southern Volcanic Zone of Chile. It was done by applying the lineament extraction technique developed by authors. These structures have been compared with the distribution of main geological structures obtained in the field. It was found that the lineament density increases in the areas of the major heat flux indicating that the lineament analysis could be a power tool for the detection of faults and joint zones associated to the geothermal fields.

HIGH SPATIAL RESOLUTION OBSERVATIONS OF LOOPS IN THE SOLAR CORONA

Energy Technology Data Exchange (ETDEWEB)

Brooks, David H.; Ugarte-Urra, Ignacio [College of Science, George Mason University, 4400 University Drive, Fairfax, VA 22030 (United States); Warren, Harry P. [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States); Winebarger, Amy R. [NASA Marshall Space Flight Center, ZP 13, Huntsville, AL 35812 (United States)

2013-08-01

Understanding how the solar corona is structured is of fundamental importance to determine how the Sun's upper atmosphere is heated to high temperatures. Recent spectroscopic studies have suggested that an instrument with a spatial resolution of 200 km or better is necessary to resolve coronal loops. The High Resolution Coronal Imager (Hi-C) achieved this performance on a rocket flight in 2012 July. We use Hi-C data to measure the Gaussian widths of 91 loops observed in the solar corona and find a distribution that peaks at about 270 km. We also use Atmospheric Imaging Assembly data for a subset of these loops and find temperature distributions that are generally very narrow. These observations provide further evidence that loops in the solar corona are often structured at a scale of several hundred kilometers, well above the spatial scale of many proposed physical mechanisms.

High resolution eddy current microscopy

Science.gov (United States)

Lantz, M. A.; Jarvis, S. P.; Tokumoto, H.

2001-01-01

We describe a sensitive scanning force microscope based technique for measuring local variations in resistivity by monitoring changes in the eddy current induced damping of a cantilever with a magnetic tip oscillating above a conducting sample. To achieve a high sensitivity, we used a cantilever with an FeNdBLa particle mounted on the tip. Resistivity measurements are demonstrated on a silicon test structure with a staircase doping profile. Regions with resistivities of 0.0013, 0.0041, and 0.022 Ω cm are clearly resolved with a lateral resolution of approximately 180 nm. For this range of resistivities, the eddy current induced damping is found to depend linearly on the sample resistivity.

Mapping Urban Tree Canopy Coverage and Structure using Data Fusion of High Resolution Satellite Imagery and Aerial Lidar

Science.gov (United States)

Elmes, A.; Rogan, J.; Williams, C. A.; Martin, D. G.; Ratick, S.; Nowak, D.

2015-12-01

Urban tree canopy (UTC) coverage is a critical component of sustainable urban areas. Trees provide a number of important ecosystem services, including air pollution mitigation, water runoff control, and aesthetic and cultural values. Critically, urban trees also act to mitigate the urban heat island (UHI) effect by shading impervious surfaces and via evaporative cooling. The cooling effect of urban trees can be seen locally, with individual trees reducing home HVAC costs, and at a citywide scale, reducing the extent and magnitude of an urban areas UHI. In order to accurately model the ecosystem services of a given urban forest, it is essential to map in detail the condition and composition of these trees at a fine scale, capturing individual tree crowns and their vertical structure. This paper presents methods for delineating UTC and measuring canopy structure at fine spatial resolution (body of methods, relying on a data fusion method to combine the information contained in high resolution WorldView-3 satellite imagery and aerial lidar data using an object-based image classification approach. The study area, Worcester, MA, has recently undergone a large-scale tree removal and reforestation program, following a pest eradication effort. Therefore, the urban canopy in this location provides a wide mix of tree age class and functional type, ideal for illustrating the effectiveness of the proposed methods. Early results show that the object-based classifier is indeed capable of identifying individual tree crowns, while continued research will focus on extracting crown structural characteristics using lidar-derived metrics. Ultimately, the resulting fine resolution UTC map will be compared with previously created UTC maps of the same area but for earlier dates, producing a canopy change map corresponding to the Worcester area tree removal and replanting effort.

Multi Scale Finite Element Analyses By Using SEM-EBSD Crystallographic Modeling and Parallel Computing

International Nuclear Information System (INIS)

Nakamachi, Eiji

2005-01-01

A crystallographic homogenization procedure is introduced to the conventional static-explicit and dynamic-explicit finite element formulation to develop a multi scale - double scale - analysis code to predict the plastic strain induced texture evolution, yield loci and formability of sheet metal. The double-scale structure consists of a crystal aggregation - micro-structure - and a macroscopic elastic plastic continuum. At first, we measure crystal morphologies by using SEM-EBSD apparatus, and define a unit cell of micro structure, which satisfy the periodicity condition in the real scale of polycrystal. Next, this crystallographic homogenization FE code is applied to 3N pure-iron and 'Benchmark' aluminum A6022 polycrystal sheets. It reveals that the initial crystal orientation distribution - the texture - affects very much to a plastic strain induced texture and anisotropic hardening evolutions and sheet deformation. Since, the multi-scale finite element analysis requires a large computation time, a parallel computing technique by using PC cluster is developed for a quick calculation. In this parallelization scheme, a dynamic workload balancing technique is introduced for quick and efficient calculations

Improving axial resolution in confocal microscopy with new high refractive index mounting media.

Science.gov (United States)

Fouquet, Coralie; Gilles, Jean-François; Heck, Nicolas; Dos Santos, Marc; Schwartzmann, Richard; Cannaya, Vidjeacoumary; Morel, Marie-Pierre; Davidson, Robert Stephen; Trembleau, Alain; Bolte, Susanne

2015-01-01

Resolution, high signal intensity and elevated signal to noise ratio (SNR) are key issues for biologists who aim at studying the localisation of biological structures at the cellular and subcellular levels using confocal microscopy. The resolution required to separate sub-cellular biological structures is often near to the resolving power of the microscope. When optimally used, confocal microscopes may reach resolutions of 180 nm laterally and 500 nm axially, however, axial resolution in depth is often impaired by spherical aberration that may occur due to refractive index mismatches. Spherical aberration results in broadening of the point-spread function (PSF), a decrease in peak signal intensity when imaging in depth and a focal shift that leads to the distortion of the image along the z-axis and thus in a scaling error. In this study, we use the novel mounting medium CFM3 (Citifluor Ltd., UK) with a refractive index of 1.518 to minimize the effects of spherical aberration. This mounting medium is compatible with most common fluorochromes and fluorescent proteins. We compare its performance with established mounting media, harbouring refractive indices below 1.500, by estimating lateral and axial resolution with sub-resolution fluorescent beads. We show furthermore that the use of the high refractive index media renders the tissue transparent and improves considerably the axial resolution and imaging depth in immuno-labelled or fluorescent protein labelled fixed mouse brain tissue. We thus propose to use those novel high refractive index mounting media, whenever optimal axial resolution is required.

Improving axial resolution in confocal microscopy with new high refractive index mounting media.

Directory of Open Access Journals (Sweden)

Coralie Fouquet

Full Text Available Resolution, high signal intensity and elevated signal to noise ratio (SNR are key issues for biologists who aim at studying the localisation of biological structures at the cellular and subcellular levels using confocal microscopy. The resolution required to separate sub-cellular biological structures is often near to the resolving power of the microscope. When optimally used, confocal microscopes may reach resolutions of 180 nm laterally and 500 nm axially, however, axial resolution in depth is often impaired by spherical aberration that may occur due to refractive index mismatches. Spherical aberration results in broadening of the point-spread function (PSF, a decrease in peak signal intensity when imaging in depth and a focal shift that leads to the distortion of the image along the z-axis and thus in a scaling error. In this study, we use the novel mounting medium CFM3 (Citifluor Ltd., UK with a refractive index of 1.518 to minimize the effects of spherical aberration. This mounting medium is compatible with most common fluorochromes and fluorescent proteins. We compare its performance with established mounting media, harbouring refractive indices below 1.500, by estimating lateral and axial resolution with sub-resolution fluorescent beads. We show furthermore that the use of the high refractive index media renders the tissue transparent and improves considerably the axial resolution and imaging depth in immuno-labelled or fluorescent protein labelled fixed mouse brain tissue. We thus propose to use those novel high refractive index mounting media, whenever optimal axial resolution is required.

Correlating Atom Probe Crystallographic Measurements with Transmission Kikuchi Diffraction Data.

Science.gov (United States)

Breen, Andrew J; Babinsky, Katharina; Day, Alec C; Eder, K; Oakman, Connor J; Trimby, Patrick W; Primig, Sophie; Cairney, Julie M; Ringer, Simon P

2017-04-01

Correlative microscopy approaches offer synergistic solutions to many research problems. One such combination, that has been studied in limited detail, is the use of atom probe tomography (APT) and transmission Kikuchi diffraction (TKD) on the same tip specimen. By combining these two powerful microscopy techniques, the microstructure of important engineering alloys can be studied in greater detail. For the first time, the accuracy of crystallographic measurements made using APT will be independently verified using TKD. Experimental data from two atom probe tips, one a nanocrystalline Al-0.5Ag alloy specimen collected on a straight flight-path atom probe and the other a high purity Mo specimen collected on a reflectron-fitted instrument, will be compared. We find that the average minimum misorientation angle, calculated from calibrated atom probe reconstructions with two different pole combinations, deviate 0.7° and 1.4°, respectively, from the TKD results. The type of atom probe and experimental conditions appear to have some impact on this accuracy and the reconstruction and measurement procedures are likely to contribute further to degradation in angular resolution. The challenges and implications of this correlative approach will also be discussed.

High-resolution ultrasonic spectroscopy

Directory of Open Access Journals (Sweden)

V. Buckin

2018-03-01

Full Text Available High-resolution ultrasonic spectroscopy (HR-US is an analytical technique for direct and non-destructive monitoring of molecular and micro-structural transformations in liquids and semi-solid materials. It is based on precision measurements of ultrasonic velocity and attenuation in analysed samples. The application areas of HR-US in research, product development, and quality and process control include analysis of conformational transitions of polymers, ligand binding, molecular self-assembly and aggregation, crystallisation, gelation, characterisation of phase transitions and phase diagrams, and monitoring of chemical and biochemical reactions. The technique does not require optical markers or optical transparency. The HR-US measurements can be performed in small sample volumes (down to droplet size, over broad temperature range, at ambient and elevated pressures, and in various measuring regimes such as automatic temperature ramps, titrations and measurements in flow.

Origin of intragranular crystallographic misorientations in hot-dip Al-Zn-Si coatings

International Nuclear Information System (INIS)

Niederberger, Ch.; Michler, J.; Jacot, A.

2008-01-01

The origin of intragranular variations of the crystallographic orientation in hot-dip Al-Zn-Si coatings is discussed based on new experimental results and modelling. The solidification microstructure in as-received 55Al-43.4Zn-1.6Si (in wt.%) coatings deposited on steel plates in an industrial production line was analyzed by electron backscattered diffraction, glow-discharge optical emission spectroscopy and atomic force microscopy (AFM). The results were compared with those obtained in coatings re-solidified under different cooling and mechanical loading conditions. Continuous variations of the crystallographic orientation as large as 35 deg. were observed within individual grains of Al-Zn-Si, consistent with previous studies. However, the mechanisms previously proposed for the origin of intragranular crystallographic misorientations had to be revisited. The new experimental data acquired during this study indicate that the solidification shrinkage accumulating in the area of the grain envelope is the driving force for the formation of intragranular misorientations. The solidification shrinkage leads to the development of tensile stresses in the oxide film covering the coating while it solidifies. Estimations based on AFM profiles and phase field simulations of the dendritic structure indicate that the stresses applied on the dendrite network are sufficient to deform plastically the dendrite arms during solidification

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data.

Science.gov (United States)

Terwilliger, Thomas C; Bricogne, Gerard

2014-10-01

Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

Carbides crystalline structure of AISI M2 high-speed steel

International Nuclear Information System (INIS)

Serna, M.M.; Galego, E.; Rossi, J.L.

2005-01-01

The aim of this study was to identify the crystallographic structure of the extracted carbides of AISI M2 steel spray formed The structure determination of these carbides. The structure determination of these carbides is a very hard work. Since these structures were formed by atom migration it is not possible to reproduce them by a controlled process with a determined chemical composition. The solution of this problem is to obtain the carbide by chemical extraction from the steel. (Author)

High resolution sequence stratigraphy in China

International Nuclear Information System (INIS)

Zhang Shangfeng; Zhang Changmin; Yin Yanshi; Yin Taiju

2008-01-01

Since high resolution sequence stratigraphy was introduced into China by DENG Hong-wen in 1995, it has been experienced two development stages in China which are the beginning stage of theory research and development of theory research and application, and the stage of theoretical maturity and widely application that is going into. It is proved by practices that high resolution sequence stratigraphy plays more and more important roles in the exploration and development of oil and gas in Chinese continental oil-bearing basin and the research field spreads to the exploration of coal mine, uranium mine and other strata deposits. However, the theory of high resolution sequence stratigraphy still has some shortages, it should be improved in many aspects. The authors point out that high resolution sequence stratigraphy should be characterized quantitatively and modelized by computer techniques. (authors)

Development of AMS high resolution injector system

International Nuclear Information System (INIS)

Bao Yiwen; Guan Xialing; Hu Yueming

2008-01-01

The Beijing HI-13 tandem accelerator AMS high resolution injector system was developed. The high resolution energy achromatic system consists of an electrostatic analyzer and a magnetic analyzer, which mass resolution can reach 600 and transmission is better than 80%. (authors)

Calibration of reconstruction parameters in atom probe tomography using a single crystallographic orientation

International Nuclear Information System (INIS)

Suram, Santosh K.; Rajan, Krishna

2013-01-01

The purpose of this work is to develop a methodology to estimate the APT reconstruction parameters when limited crystallographic information is available. Reliable spatial scaling of APT data currently requires identification of multiple crystallographic poles from the field desorption image for estimating the reconstruction parameters. This requirement limits the capacity of accurately reconstructing APT data for certain complex systems, such as highly alloyed systems and nanostructured materials wherein more than one pole is usually not observed within one grain. To overcome this limitation, we develop a quantitative methodology for calibrating the reconstruction parameters in an APT dataset by ensuring accurate inter-planar spacing and optimizing the curvature correction for the atomic planes corresponding to a single crystallographic orientation. We validate our approach on an aluminum dataset and further illustrate its capabilities by computing geometric reconstruction parameters for W and Al–Mg–Sc datasets. - Highlights: ► Quantitative approach is developed to accurately reconstruct APT data. ► Curvature of atomic planes in APT data is used to calibrate the reconstruction. ► APT reconstruction parameters are determined from a single crystallographic axis. ► Quantitative approach is demonstrated on W, Al and Al–Mg–Sc systems. ► Accurate APT reconstruction of complex materials is now possible

Resolution enhancement of low quality videos using a high-resolution frame

NARCIS (Netherlands)

Pham, T.Q.; Van Vliet, L.J.; Schutte, K.

2006-01-01

This paper proposes an example-based Super-Resolution (SR) algorithm of compressed videos in the Discrete Cosine Transform (DCT) domain. Input to the system is a Low-Resolution (LR) compressed video together with a High-Resolution (HR) still image of similar content. Using a training set of

Longitudinal profile diagnostic scheme with subfemtosecond resolution for high-brightness electron beams

Directory of Open Access Journals (Sweden)

G. Andonian

2011-07-01

Full Text Available High-resolution measurement of the longitudinal profile of a relativistic electron beam is of utmost importance for linac based free-electron lasers and other advanced accelerator facilities that employ ultrashort bunches. In this paper, we investigate a novel scheme to measure ultrashort bunches (subpicosecond with exceptional temporal resolution (hundreds of attoseconds and dynamic range. The scheme employs two orthogonally oriented deflecting sections. The first imparts a short-wavelength (fast temporal resolution horizontal angular modulation on the beam, while the second imparts a long-wavelength (slow angular kick in the vertical dimension. Both modulations are observable on a standard downstream screen in the form of a streaked sinusoidal beam structure. We demonstrate, using scaled variables in a quasi-1D approximation, an expression for the temporal resolution of the scheme and apply it to a proof-of-concept experiment at the UCLA Neptune high-brightness injector facility. The scheme is also investigated for application at the SLAC NLCTA facility, where we show that the subfemtosecond resolution is sufficient to resolve the temporal structure of the beam used in the echo-enabled free-electron laser. We employ beam simulations to verify the effect for typical Neptune and NLCTA parameter sets and demonstrate the feasibility of the concept.

High-Resolution Integrated Optical System

Science.gov (United States)

Prakapenka, V. B.; Goncharov, A. F.; Holtgrewe, N.; Greenberg, E.

2017-12-01

Raman and optical spectroscopy in-situ at extreme high pressure and temperature conditions relevant to the planets' deep interior is a versatile tool for characterization of wide range of properties of minerals essential for understanding the structure, composition, and evolution of terrestrial and giant planets. Optical methods, greatly complementing X-ray diffraction and spectroscopy techniques, become crucial when dealing with light elements. Study of vibrational and optical properties of minerals and volatiles, was a topic of many research efforts in past decades. A great deal of information on the materials properties under extreme pressure and temperature has been acquired including that related to structural phase changes, electronic transitions, and chemical transformations. These provide an important insight into physical and chemical states of planetary interiors (e.g. nature of deep reservoirs) and their dynamics including heat and mass transport (e.g. deep carbon cycle). Optical and vibrational spectroscopy can be also very instrumental for elucidating the nature of the materials molten states such as those related to the Earth's volatiles (CO2, CH4, H2O), aqueous fluids and silicate melts, planetary ices (H2O, CH4, NH3), noble gases, and H2. The optical spectroscopy study performed concomitantly with X-ray diffraction and spectroscopy measurements at the GSECARS beamlines on the same sample and at the same P-T conditions would greatly enhance the quality of this research and, moreover, will provide unique new information on chemical state of matter. The advanced high-resolution user-friendly integrated optical system is currently under construction and expected to be completed by 2018. In our conceptual design we have implemented Raman spectroscopy with five excitation wavelengths (266, 473, 532, 660, 946 nm), confocal imaging, double sided IR laser heating combined with high temperature Raman (including coherent anti-Stokes Raman scattering) and

Moessbauer spectroscopy with a high velocity resolution: advances in biomedical, pharmaceutical, cosmochemical and nano technological research

International Nuclear Information System (INIS)

Oshtrakha, M.I.; Semionkina, V.A.

2011-01-01

. Characteristics of this system demonstrated a high stability, precision and accuracy in the measurement of Moessbauer spectra in 4096 channels. In spite of substantial increase in the measurement time, spectra measured with a high velocity resolution permitted to obtain Moessbauer hyperfine parameters with systematic errors at least 8 times less than in the case of spectra measurement in 512 channels as well as to fit complicated Moessbauer spectra with better quality. Various applications of Moessbauer spectroscopy with a high velocity resolution demonstrated new possibilities of technique. Biomedical applications. New results were obtained in the study of human liver ferritin, its pharmaceutically important models as well as liver and spleen tissues from normal and leukemia chicken; in comparative study of various human and animals' normal oxyhemoglobins and oxyhemoglobins from patients; in the study of iron containing pharmaceutical products. Cosmochemical applications. In the study of various meteorites new results were obtained in analysis of Fe-Ni alloys with variations in Ni concentration, in the study of silicate phases and Fe-Ni phosphides with crystallographically non-equivalent sites for Fe. Nanotechnological applications. New results were obtained in the study of cupric ferrite nanoparticles with tin oxide adding as well as in the study of ferric oxide nanoparticles developed for magnetic fluids for biomedical purposes. (author)

High resolution, high speed ultrahigh vacuum microscopy

International Nuclear Information System (INIS)

Poppa, Helmut

2004-01-01

The history and future of transmission electron microscopy (TEM) is discussed as it refers to the eventual development of instruments and techniques applicable to the real time in situ investigation of surface processes with high resolution. To reach this objective, it was necessary to transform conventional high resolution instruments so that an ultrahigh vacuum (UHV) environment at the sample site was created, that access to the sample by various in situ sample modification procedures was provided, and that in situ sample exchanges with other integrated surface analytical systems became possible. Furthermore, high resolution image acquisition systems had to be developed to take advantage of the high speed imaging capabilities of projection imaging microscopes. These changes to conventional electron microscopy and its uses were slowly realized in a few international laboratories over a period of almost 40 years by a relatively small number of researchers crucially interested in advancing the state of the art of electron microscopy and its applications to diverse areas of interest; often concentrating on the nucleation, growth, and properties of thin films on well defined material surfaces. A part of this review is dedicated to the recognition of the major contributions to surface and thin film science by these pioneers. Finally, some of the important current developments in aberration corrected electron optics and eventual adaptations to in situ UHV microscopy are discussed. As a result of all the path breaking developments that have led to today's highly sophisticated UHV-TEM systems, integrated fundamental studies are now possible that combine many traditional surface science approaches. Combined investigations to date have involved in situ and ex situ surface microscopies such as scanning tunneling microscopy/atomic force microscopy, scanning Auger microscopy, and photoemission electron microscopy, and area-integrating techniques such as x-ray photoelectron

Strategies for dereplication of natural compounds using high-resolution tandem mass spectrometry.

Science.gov (United States)

Kind, Tobias; Fiehn, Oliver

2017-09-01

Complete structural elucidation of natural products is commonly performed by nuclear magnetic resonance spectroscopy (NMR), but annotating compounds to most likely structures using high-resolution tandem mass spectrometry is a faster and feasible first step. The CASMI contest 2016 (Critical Assessment of Small Molecule Identification) provided spectra of eighteen compounds for the best manual structure identification in the natural products category. High resolution precursor and tandem mass spectra (MS/MS) were available to characterize the compounds. We used the Seven Golden Rules, Sirius2 and MS-FINDER software for determination of molecular formulas, and then we queried the formulas in different natural product databases including DNP, UNPD, ChemSpider and REAXYS to obtain molecular structures. We used different in-silico fragmentation tools including CFM-ID, CSI:FingerID and MS-FINDER to rank these compounds. Additional neutral losses and product ion peaks were manually investigated. This manual and time consuming approach allowed for the correct dereplication of thirteen of the eighteen natural products.

X-ray crystallographic characterization of rhesus macaque MHC Mamu-A*02 complexed with an immunodominant SIV-Gag nonapeptide

International Nuclear Information System (INIS)

Feng, Youjun; Qi, Jianxun; Zhang, Huimin; Wang, Jinzi; Liu, Jinhua; Jiang, Fan; Gao, Feng

2005-01-01

X-ray crystallographic characterization of rhesus macaque MHC Mamu-A*02 complexed with an immunodominant SIV-Gag nonapeptide. Simian immunodeficiency virus (SIV) in the rhesus macaque is regarded as a classic animal model, playing a crucial role in HIV vaccine strategies and therapeutics by characterizing various cytotoxic T-lymphocyte (CTL) responses in macaque monkeys. However, the availability of well documented structural reports focusing on rhesus macaque major histocompatibility complex class I (MHC I) molecules remains extremely limited. Here, a complex of the rhesus macaque MHC I molecule (Mamu-A*02) with human β 2 m and an immunodominant SIV-Gag nonapeptide, GESNLKSLY (GY9), has been crystallized. The crystal diffracts X-rays to 2.7 Å resolution and belongs to space group C2, with unit-cell parameters a = 124.11, b = 110.45, c = 100.06 Å, and contains two molecules in the asymmetric unit. The availability of the structure, which is being solved by molecular replacement, will provide new insights into rhesus macaque MHC I (Mamu-A*02) presenting pathogenic SIV peptides

X-ray crystallographic characterization of rhesus macaque MHC Mamu-A*02 complexed with an immunodominant SIV-Gag nonapeptide

Energy Technology Data Exchange (ETDEWEB)

Feng, Youjun [Laboratory of Molecular Immunology and Molecular Virology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080 (China); Graduate School, Chinese Academy of Sciences, Beijing (China); Qi, Jianxun [Graduate School, Chinese Academy of Sciences, Beijing (China); Institute of Physics, Chinese Academy of Sciences, Beijing 100080 (China); Zhang, Huimin; Wang, Jinzi [Laboratory of Molecular Immunology and Molecular Virology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080 (China); Liu, Jinhua [College of Veterinary Medicine, China Agricultural University, Beijing 100094 (China); Jiang, Fan [Institute of Physics, Chinese Academy of Sciences, Beijing 100080 (China); Gao, Feng, E-mail: gaofeng@im.ac.cn [Laboratory of Molecular Immunology and Molecular Virology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080 (China); College of Veterinary Medicine, China Agricultural University, Beijing 100094 (China)

2006-01-01

X-ray crystallographic characterization of rhesus macaque MHC Mamu-A*02 complexed with an immunodominant SIV-Gag nonapeptide. Simian immunodeficiency virus (SIV) in the rhesus macaque is regarded as a classic animal model, playing a crucial role in HIV vaccine strategies and therapeutics by characterizing various cytotoxic T-lymphocyte (CTL) responses in macaque monkeys. However, the availability of well documented structural reports focusing on rhesus macaque major histocompatibility complex class I (MHC I) molecules remains extremely limited. Here, a complex of the rhesus macaque MHC I molecule (Mamu-A*02) with human β{sub 2}m and an immunodominant SIV-Gag nonapeptide, GESNLKSLY (GY9), has been crystallized. The crystal diffracts X-rays to 2.7 Å resolution and belongs to space group C2, with unit-cell parameters a = 124.11, b = 110.45, c = 100.06 Å, and contains two molecules in the asymmetric unit. The availability of the structure, which is being solved by molecular replacement, will provide new insights into rhesus macaque MHC I (Mamu-A*02) presenting pathogenic SIV peptides.

High-resolution He beam scattering as a tool for the investigation of the structural and dynamical properties of surface soliton dislocations

International Nuclear Information System (INIS)

El-Batanouny, M.; Martini, K.M.

1986-01-01

We discuss the applicability of high-resolution-He-beam/surface scattering to the investigation of the structural and dynamic properties of soliton-like surface misfit dislocations and associated phase transitions. We present evidence, based on recent He diffraction measurements, for the existence of double-sine-Gordon soliton-like dislocations on the reconstructed Au(111) surface. 18 refs., 3 figs., 1 tab

A Journey into Reciprocal Space; A crystallographer's perspective

Science.gov (United States)

Glazer, A. M.

2017-10-01

This book introduces undergraduate and graduate students to a crystallographer's view of real and reciprocal space, a concept that has been of particular use by crystallographers to understand the patterns of spots when x-rays are diffracted by crystals. It then proceeds to develop the concept in a form suitable for physics applications; such as how solid-state physicists use reciprocal space to explain various solid-state properties such as thermal and electrical phenomena.

Crystallographic investigation of grain selection during initial solidification

International Nuclear Information System (INIS)

Esaka, H; Shinozuka, K; Kataoka, Y

2016-01-01

Normally, macroscopic solidified structure consists of chill, columnar and equiaxed zones. In a chill zone, many fine grains nucleate on the mold surface and grow their own preferred growth direction. Only a few of them continue to grow because of grain selection. In order to understand the grain selection process, crystallographic investigation has been carried out in the zone of initial solidification in this study. 10 g of Al-6 wt%Si alloy was melted at 850 °C and poured on the thick copper plate. Longitudinal cross section of the solidified shell was observed by a SEM and analyzed by EBSD. The result of EBSD mapping reveals that crystallographic orientation was random in the range of initial solidification. Further, some grains are elongated along their <100> direction. Columnar grains, whose growth directions are almost parallel to the heat flow direction, develop via grain selection. Here, a dendrite whose growth direction is close to the heat flow direction overgrows the other dendrite whose growth direction is far from the heat flow direction. However, sometimes we observed that dendrite, whose zenith angle is large, overgrew the other dendrite. It can be deduced that the time of nucleation on the mold surface is not constant. (paper)

A high resolution solar atlas for fluorescence calculations

Science.gov (United States)

Hearn, M. F.; Ohlmacher, J. T.; Schleicher, D. G.

1983-01-01

The characteristics required of a solar atlas to be used for studying the fluorescence process in comets are examined. Several sources of low resolution data were combined to provide an absolutely calibrated spectrum from 2250 A to 7000A. Three different sources of high resolution data were also used to cover this same spectral range. The low resolution data were then used to put each high resolution spectrum on an absolute scale. The three high resolution spectra were then combined in their overlap regions to produce a single, absolutely calibrated high resolution spectrum over the entire spectral range.

High-resolution inelastic neutron scattering and neutron powder diffraction study of the adsorption of dihydrogen by the Cu(II) metal-organic framework material HKUST-1

Science.gov (United States)

Callear, Samantha K.; Ramirez-Cuesta, Anibal J.; David, William I. F.; Millange, Franck; Walton, Richard I.

2013-12-01

We present new high-resolution inelastic neutron scattering (INS) spectra (measured using the TOSCA and MARI instruments at ISIS) and powder neutron diffraction data (measured on the diffractometer WISH at ISIS) from the interaction of the prototypical metal-organic framework HKUST-1 with various dosages of dihydrogen gas. The INS spectra show direct evidence for the sequential occupation of various distinct sites for dihydrogen in the metal-organic framework, whose population is adjusted during increasing loading of the guest. The superior resolution of TOSCA reveals subtle features in the spectra, not previously reported, including evidence for split signals, while complementary spectra recorded on MARI present full information in energy and momentum transfer. The analysis of the powder neutron patterns using the Rietveld method shows a consistent picture, allowing the crystallographic indenisation of binding sites for dihydrogen, thus building a comprehensive picture of the interaction of the guest with the nanoporous host.

High-resolution electron microscopy and its applications.

Science.gov (United States)

Li, F H

1987-12-01

A review of research on high-resolution electron microscopy (HREM) carried out at the Institute of Physics, the Chinese Academy of Sciences, is presented. Apart from the direct observation of crystal and quasicrystal defects for some alloys, oxides, minerals, etc., and the structure determination for some minute crystals, an approximate image-contrast theory named pseudo-weak-phase object approximation (PWPOA), which shows the image contrast change with crystal thickness, is described. Within the framework of PWPOA, the image contrast of lithium ions in the crystal of R-Li2Ti3O7 has been observed. The usefulness of diffraction analysis techniques such as the direct method and Patterson method in HREM is discussed. Image deconvolution and resolution enhancement for weak-phase objects by use of the direct method are illustrated. In addition, preliminary results of image restoration for thick crystals are given.

High spatial resolution soft-x-ray microscopy

Energy Technology Data Exchange (ETDEWEB)

Meyer-Ilse, W.; Medecki, H.; Brown, J.T. [Ernest Orlando Lawrence Berkeley National Lab., CA (United States)] [and others

1997-04-01

A new soft x-ray microscope (XM-1) with high spatial resolution has been constructed by the Center for X-ray Optics. It uses bending magnet radiation from beamline 6.1 at the Advanced Light Source, and is used in a variety of projects and applications in the life and physical sciences. Most of these projects are ongoing. The instrument uses zone plate lenses and achieves a resolution of 43 nm, measured over 10% to 90% intensity with a knife edge test sample. X-ray microscopy permits the imaging of relatively thick samples, up to 10 {mu}m thick, in water. XM-1 has an easy to use interface, that utilizes visible light microscopy to precisely position and focus the specimen. The authors describe applications of this device in the biological sciences, as well as in studying industrial applications including structured polymer samples.

Radial super-resolution in digital holographic microscopy using structured illumination with circular symmetry

Science.gov (United States)

Yin, Yujian; Su, Ping; Ma, Jianshe

2018-01-01

A method to improve the radial resolution using special structured light is proposed in the field of digital holographic microscopy (DHM). A specimen is illuminated with circular symmetrical structured light that makes the spectrum have radial movement, so that high frequency components of the specimen are moved into the passband of the receiver to overcome the diffraction limit. In the DHM imaging system, Computer Generated Hologram (CGH) technology is used to generate the required structured light grating. Then the grating is loaded into a spatial light modulator (SLM) to obtain specific structured illumination. After recording the hologram, digital reconstruction, for the microstructure of a binary optical element that needs to observe radial distribution, the radial resolution of the specimen is improved experimentally compare it with the result of one-dimensional sinusoidal structured light imaging. And a method of designing structured light is presented.

Structure from motion, a low cost, very high resolution method for surveying glaciers using GoPros and opportunistic helicopter flights

Science.gov (United States)

Girod, L.; Nuth, C.; Schellenberger, T.

2014-12-01

The capability of structure from motion techniques to survey glaciers with a very high spatial and temporal resolution is a promising tool for better understanding the dynamic changes of glaciers. Modern software and computing power allow us to produce accurate data sets from low cost surveys, thus improving the observational capabilities on a wider range of glaciers and glacial processes. In particular, highly accurate glacier volume change monitoring and 3D movement computations will be possible Taking advantage of the helicopter flight needed to survey the ice stakes on Kronenbreen, NW Svalbard, we acquired high resolution photogrammetric data over the well-studied Midre Lovénbreen in September 2013. GoPro Hero 2 cameras were attached to the landing gear of the helicopter, acquiring two images per second. A C/A code based GPS was used for registering the stereoscopic model. Camera clock calibration is obtained through fitting together the shapes of the flight given by both the GPS logger and the relative orientation of the images. A DEM and an ortho-image are generated at 30cm resolution from 300 images collected. The comparison with a 2005 LiDAR DEM (5 meters resolution) shows an absolute error in the direct registration of about 6±3m in 3D which could be easily reduced to 1,5±1m by using fine point cloud alignment algorithms on stable ground. Due to the different nature of the acquisition method, it was not possible to use tie point based co-registration. A combination of the DEM and ortho-image is shown with the point cloud in figure below. A second photogrammetric data set will be acquired in September 2014 to survey the annual volume change and movement. These measurements will then be compared to the annual resolution glaciological stake mass balance and velocity measurements to assess the precision of the method to monitor at an annual resolution.

Shape and crystallographic orientation of nanodiamonds for quantum sensing.

Science.gov (United States)

Ong, S Y; Chipaux, M; Nagl, A; Schirhagl, R

2017-05-03

Nanodiamonds with dimensions down to a few tens of nanometers containing nitrogen-vacancy (NV) color centers have revealed their potential as powerful and versatile quantum sensors with a unique combination of spatial resolution and sensitivity. The NV centers allow transducing physical properties, such as strain, temperature, and electric or magnetic field, to an optical transition that can be detected in the single photon range. For example, this makes it possible to sense a single electron spin or a few nuclear spins by detecting their magnetic resonance. The location and orientation of these defects with respect to the diamond surface play a crucial role in interpreting the data and predicting their sensitivities. Despite its relevance, the geometry of these nanodiamonds has never been thoroughly investigated. Without accurate data, spherical models have been applied to interpret or predict results in the past. With the use of High Resolution Transmission Electron Microscopy (HR-TEM), Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM), we investigated nanodiamonds with an average hydrodynamic diameter of 25 nm (the most common type for quantum sensing) and found a flake-like geometry, with 23.2 nm and 4.5 nm being the average lateral and vertical dimensions. We have also found evidence for a preferred crystallographic orientation of the main facet in the (110) direction. Furthermore, we discuss the consequences of this difference in geometry on diamond-based applications. Shape not only influences the creation efficiency of nitrogen-vacancy centers and their quantum coherence properties (and thus sensing performance), but also the optical properties of the nanodiamonds, their interaction with living cells, and their surface chemistry.

High-resolution phylogenetic microbial community profiling

Energy Technology Data Exchange (ETDEWEB)

Singer, Esther; Coleman-Derr, Devin; Bowman, Brett; Schwientek, Patrick; Clum, Alicia; Copeland, Alex; Ciobanu, Doina; Cheng, Jan-Fang; Gies, Esther; Hallam, Steve; Tringe, Susannah; Woyke, Tanja

2014-03-17

The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

A high resolution ion microscope for cold atoms

International Nuclear Information System (INIS)

Stecker, Markus; Schefzyk, Hannah; Fortágh, József; Günther, Andreas

2017-01-01

We report on an ion-optical system that serves as a microscope for ultracold ground state and Rydberg atoms. The system is designed to achieve a magnification of up to 1000 and a spatial resolution in the 100 nm range, thereby surpassing many standard imaging techniques for cold atoms. The microscope consists of four electrostatic lenses and a microchannel plate in conjunction with a delay line detector in order to achieve single particle sensitivity with high temporal and spatial resolution. We describe the design process of the microscope including ion-optical simulations of the imaging system and characterize aberrations and the resolution limit. Furthermore, we present the experimental realization of the microscope in a cold atom setup and investigate its performance by patterned ionization with a structure size down to 2.7 μ m. The microscope meets the requirements for studying various many-body effects, ranging from correlations in cold quantum gases up to Rydberg molecule formation. (paper)

Platinum Group Thiophenoxyimine Complexes: Syntheses,Crystallographic and Computational Studies of Structural Properties

Energy Technology Data Exchange (ETDEWEB)

Krinsky, Jamin L.; Arnold, John; Bergman, Robert G.

2006-10-03

Monomeric thiosalicylaldiminate complexes of rhodium(I) and iridium(I) were prepared by ligand transfer from the homoleptic zinc(II) species. In the presence of strongly donating ligands, the iridium complexes undergo insertion of the metal into the imine carbon-hydrogen bond. Thiophenoxyketimines were prepared by non-templated reaction of o-mercaptoacetophenone with anilines, and were complexed with rhodium(I), iridium(I), nickel(II) and platinum(II). X-ray crystallographic studies showed that while the thiosalicylaldiminate complexes display planar ligand conformations, those of the thiophenoxyketiminates are strongly distorted. Results of a computational study were consistent with a steric-strain interpretation of the difference in preferred ligand geometries.

Investigations and characterization of the microstructure of special ceramic materials using the high-resolution electron microscope

International Nuclear Information System (INIS)

Kirn, M.

1979-01-01

The possibilities to characterize phases and microstructures by direct lattice imaging are indicated in the following work. Ceramic materials are particularly suitable for this as these exhibit a high mechanical stability in the investigation in the transmission electron microscope. First of all the fundamentals of the high-resolution electron microscopy are introduced and the various resulting possibilities to characterize microstructures are presented. A report then follows on experimental observations on undisturbed crystals of special ceramics on a Si 3 N 4 basis. Furthermore, it is shown that the high-resolution electron microscope provides valuable contributions to the determination of structure, in particular of twin variants. Finally, revealing information on the structure of the interfaces was obtained with the help of high-resolution electron microscopy. (orig./IHOE) [de

High-resolution SPECT for small-animal imaging

International Nuclear Information System (INIS)

Qi Yujin

2006-01-01

This article presents a brief overview of the development of high-resolution SPECT for small-animal imaging. A pinhole collimator has been used for high-resolution animal SPECT to provide better spatial resolution and detection efficiency in comparison with a parallel-hole collimator. The theory of imaging characteristics of the pinhole collimator is presented and the designs of the pinhole aperture are discussed. The detector technologies used for the development of small-animal SPECT and the recent advances are presented. The evolving trend of small-animal SPECT is toward a multi-pinhole and a multi-detector system to obtain a high resolution and also a high detection efficiency. (authors)

High resolution iridocorneal angle imaging system by axicon lens assisted gonioscopy

Science.gov (United States)

Perinchery, Sandeep Menon; Shinde, Anant; Fu, Chan Yiu; Jeesmond Hong, Xun Jie; Baskaran, Mani; Aung, Tin; Murukeshan, Vadakke Matham

2016-07-01

Direct visualization and assessment of the iridocorneal angle (ICA) region with high resolution is important for the clinical evaluation of glaucoma. However, the current clinical imaging systems for ICA do not provide sufficient structural details due to their poor resolution. The key challenges in achieving high quality ICA imaging are its location in the anterior region of the eye and the occurrence of total internal reflection due to refractive index difference between cornea and air. Here, we report an indirect axicon assisted gonioscopy imaging probe with white light illumination. The illustrated results with this probe shows significantly improved visualization of structures in the ICA including TM region, compared to the current available tools. It could reveal critical details of ICA and expected to aid management by providing information that is complementary to angle photography and gonioscopy.

A high-resolution study of mesospheric fine structure with the Jicamarca MST radar

Science.gov (United States)

Sheth, R.; Kudeki, E.; Lehmacher, G.; Sarango, M.; Woodman, R.; Chau, J.; Guo, L.; Reyes, P.

2006-07-01

Correlation studies performed on data from recent mesospheric experiments conducted with the 50-MHz Jicamarca radar in May 2003 and July 2004 are reported. The study is based on signals detected from a combination of vertical and off-vertical beams. The nominal height resolution was 150 m and spectral estimates were obtained after ~1 min integration. Spectral widths and backscattered power generally show positive correlations at upper mesospheric heights in agreement with earlier findings (e.g., Fukao et al., 1980) that upper mesospheric echoes are dominated by isotropic Bragg scatter. In many instances in the upper mesosphere, a weakening of positive correlation away from layer centers (towards top and bottom boundaries) was observed with the aid of improved height resolution. This finding supports the idea that layer edges are dominated by anisotropic turbulence. The data also suggests that negative correlations observed at lower mesospheric heights are caused by scattering from anisotropic structures rather than reflections from sharp vertical gradients in electron density.

A high-resolution study of mesospheric fine structure with the Jicamarca MST radar

Directory of Open Access Journals (Sweden)

R. Sheth

2006-07-01

Full Text Available Correlation studies performed on data from recent mesospheric experiments conducted with the 50-MHz Jicamarca radar in May 2003 and July 2004 are reported. The study is based on signals detected from a combination of vertical and off-vertical beams. The nominal height resolution was 150 m and spectral estimates were obtained after ~1 min integration. Spectral widths and backscattered power generally show positive correlations at upper mesospheric heights in agreement with earlier findings (e.g., Fukao et al., 1980 that upper mesospheric echoes are dominated by isotropic Bragg scatter. In many instances in the upper mesosphere, a weakening of positive correlation away from layer centers (towards top and bottom boundaries was observed with the aid of improved height resolution. This finding supports the idea that layer edges are dominated by anisotropic turbulence. The data also suggests that negative correlations observed at lower mesospheric heights are caused by scattering from anisotropic structures rather than reflections from sharp vertical gradients in electron density.

High-resolution studies of the structure of the solar atmosphere using a new imaging algorithm

Science.gov (United States)

Karovska, Margarita; Habbal, Shadia Rifai

1991-01-01

The results of the application of a new image restoration algorithm developed by Ayers and Dainty (1988) to the multiwavelength EUV/Skylab observations of the solar atmosphere are presented. The application of the algorithm makes it possible to reach a resolution better than 5 arcsec, and thus study the structure of the quiet sun on that spatial scale. The results show evidence for discrete looplike structures in the network boundary, 5-10 arcsec in size, at temperatures of 100,000 K.

The high resolution shear wave seismic reflection technique

International Nuclear Information System (INIS)

Johnson, W.J.; Clark, J.C.

1991-04-01

This report presents the state-of-the-art of the high resolution S-wave reflection technique. Published and unpublished literature has been reviewed and discussions have been held with experts. Result is to confirm that the proposed theoretical and practical basis for identifying aquifer systems using both P- and S-wave reflections is sound. Knowledge of S-wave velocity and P-wave velocity is a powerful tool for assessing the fluid characteristics of subsurface layers. Material properties and lateral changes in material properties such as change from clay to sand, can be inferred from careful dual evaluation of P and S-wave records. The high resolution S-wave reflection technique has seen its greatest application to date as part of geotechnical studies for building foundations in the Far East. Information from this type of study has been evaluated and will be incorporated in field studies. In particular, useful information regarding S-wave sources, noise suppression and recording procedures will be incorporated within the field studies. Case histories indicate that the best type of site for demonstrating the power of the high resolution S-wave technique will be in unconsolidated soil without excessive structural complexities. More complex sites can form the basis for subsequent research after the basic principles of the technique can be established under relatively uncomplicated conditions

Similarity of High-Resolution Tandem Mass Spectrometry Spectra of Structurally Related Micropollutants and Transformation Products

Science.gov (United States)

Schollée, Jennifer E.; Schymanski, Emma L.; Stravs, Michael A.; Gulde, Rebekka; Thomaidis, Nikolaos S.; Hollender, Juliane

2017-12-01

High-resolution tandem mass spectrometry (HRMS2) with electrospray ionization is frequently applied to study polar organic molecules such as micropollutants. Fragmentation provides structural information to confirm structures of known compounds or propose structures of unknown compounds. Similarity of HRMS2 spectra between structurally related compounds has been suggested to facilitate identification of unknown compounds. To test this hypothesis, the similarity of reference standard HRMS2 spectra was calculated for 243 pairs of micropollutants and their structurally related transformation products (TPs); for comparison, spectral similarity was also calculated for 219 pairs of unrelated compounds. Spectra were measured on Orbitrap and QTOF mass spectrometers and similarity was calculated with the dot product. The influence of different factors on spectral similarity [e.g., normalized collision energy (NCE), merging fragments from all NCEs, and shifting fragments by the mass difference of the pair] was considered. Spectral similarity increased at higher NCEs and highest similarity scores for related pairs were obtained with merged spectra including measured fragments and shifted fragments. Removal of the monoisotopic peak was critical to reduce false positives. Using a spectral similarity score threshold of 0.52, 40% of related pairs and 0% of unrelated pairs were above this value. Structural similarity was estimated with the Tanimoto coefficient and pairs with higher structural similarity generally had higher spectral similarity. Pairs where one or both compounds contained heteroatoms such as sulfur often resulted in dissimilar spectra. This work demonstrates that HRMS2 spectral similarity may indicate structural similarity and that spectral similarity can be used in the future to screen complex samples for related compounds such as micropollutants and TPs, assisting in the prioritization of non-target compounds. [Figure not available: see fulltext.

High-resolution crystal structure of a polyextreme GH43 glycosidase from Halothermothrix orenii with α-l-arabinofuranosidase activity

International Nuclear Information System (INIS)

Hassan, Noor; Kori, Lokesh D.; Gandini, Rosaria; Patel, Bharat K. C.; Divne, Christina; Tan, Tien Chye

2015-01-01

The crystal structure of the H. orenii glycosidase was determined by molecular replacement and refined at 1.10 Å resolution. A gene from the heterotrophic, halothermophilic marine bacterium Halothermothrix orenii has been cloned and overexpressed in Escherichia coli. This gene encodes the only glycoside hydrolase of family 43 (GH43) produced by H. orenii. The crystal structure of the H. orenii glycosidase was determined by molecular replacement and refined at 1.10 Å resolution. As for other GH43 members, the enzyme folds as a five-bladed β-propeller. The structure features a metal-binding site on the propeller axis, near the active site. Based on thermal denaturation data, the H. orenii glycosidase depends on divalent cations in combination with high salt for optimal thermal stability against unfolding. A maximum melting temperature of 76°C was observed in the presence of 4 M NaCl and Mn 2+ at pH 6.5. The gene encoding the H. orenii GH43 enzyme has previously been annotated as a putative α-l-arabinofuranosidase. Activity was detected with p-nitrophenyl-α-l-arabinofuranoside as a substrate, and therefore the name HoAraf43 was suggested for the enzyme. In agreement with the conditions for optimal thermal stability against unfolding, the highest arabinofuranosidase activity was obtained in the presence of 4 M NaCl and Mn 2+ at pH 6.5, giving a specific activity of 20–36 µmol min −1 mg −1 . The active site is structurally distinct from those of other GH43 members, including arabinanases, arabinofuranosidases and xylanases. This probably reflects the special requirements for degrading the unique biomass available in highly saline aqueous ecosystems, such as halophilic algae and halophytes. The amino-acid distribution of HoAraf43 has similarities to those of mesophiles, thermophiles and halophiles, but also has unique features, for example more hydrophobic amino acids on the surface and fewer buried charged residues

High-resolution crystal structure of a polyextreme GH43 glycosidase from Halothermothrix orenii with α-l-arabinofuranosidase activity

Energy Technology Data Exchange (ETDEWEB)

Hassan, Noor [KTH Royal Institute of Technology, Stockholm (Sweden); Karolinska Institutet, Stockholm (Sweden); Kori, Lokesh D. [Griffith University, Brisbane, QLD 4111 (Australia); Baylor College of Medicine, Houston, TX 77030 (United States); Gandini, Rosaria [KTH Royal Institute of Technology, Stockholm (Sweden); Karolinska Institutet, Stockholm (Sweden); Patel, Bharat K. C. [Griffith University, Brisbane, QLD 4111 (Australia); Divne, Christina; Tan, Tien Chye, E-mail: tantc@kth.se [KTH Royal Institute of Technology, Stockholm (Sweden); Karolinska Institutet, Stockholm (Sweden)

2015-02-19

The crystal structure of the H. orenii glycosidase was determined by molecular replacement and refined at 1.10 Å resolution. A gene from the heterotrophic, halothermophilic marine bacterium Halothermothrix orenii has been cloned and overexpressed in Escherichia coli. This gene encodes the only glycoside hydrolase of family 43 (GH43) produced by H. orenii. The crystal structure of the H. orenii glycosidase was determined by molecular replacement and refined at 1.10 Å resolution. As for other GH43 members, the enzyme folds as a five-bladed β-propeller. The structure features a metal-binding site on the propeller axis, near the active site. Based on thermal denaturation data, the H. orenii glycosidase depends on divalent cations in combination with high salt for optimal thermal stability against unfolding. A maximum melting temperature of 76°C was observed in the presence of 4 M NaCl and Mn{sup 2+} at pH 6.5. The gene encoding the H. orenii GH43 enzyme has previously been annotated as a putative α-l-arabinofuranosidase. Activity was detected with p-nitrophenyl-α-l-arabinofuranoside as a substrate, and therefore the name HoAraf43 was suggested for the enzyme. In agreement with the conditions for optimal thermal stability against unfolding, the highest arabinofuranosidase activity was obtained in the presence of 4 M NaCl and Mn{sup 2+} at pH 6.5, giving a specific activity of 20–36 µmol min{sup −1} mg{sup −1}. The active site is structurally distinct from those of other GH43 members, including arabinanases, arabinofuranosidases and xylanases. This probably reflects the special requirements for degrading the unique biomass available in highly saline aqueous ecosystems, such as halophilic algae and halophytes. The amino-acid distribution of HoAraf43 has similarities to those of mesophiles, thermophiles and halophiles, but also has unique features, for example more hydrophobic amino acids on the surface and fewer buried charged residues.

Crystallographic Structure Analysis of a Ti-Ta Thin Film Materials Library Fabricated by Combinatorial Magnetron Sputtering.

Science.gov (United States)

Kadletz, Peter M; Motemani, Yahya; Iannotta, Joy; Salomon, Steffen; Khare, Chinmay; Grossmann, Lukas; Maier, Hans Jürgen; Ludwig, Alfred; Schmahl, Wolfgang W

2018-03-12

Ti-Ta thin films exhibit properties that are of interest for applications as microactuators and as biomedical implants. A Ti-Ta thin film materials library was deposited at T = 25 °C by magnetron sputtering employing the combinatorial approach, which led to a compositional range of Ti 87 Ta 13 to Ti 14 Ta 86 . Subsequent high-throughput characterization methods permitted a quick and comprehensive study of the crystallographic, microstructural, and morphological properties, which strongly depend on the chemical composition. SEM investigation revealed a columnar morphology having pyramidal, sharp tips with coarser columns in the Ti-rich and finer columns in the Ta-rich region. By grazing incidence X-ray diffraction four phases were identified, from Ta-lean to Ta-rich: ω phase, α″ martensite, β phase, and a tetragonal Ta-rich phase (Ta (tetr) ). The crystal structure and microstructure were analyzed by Rietveld refinement and clear trends could be determined as a function of Ta-content. The lattice correspondences between β as the parent phase and α″ and ω as derivative phases were expressed in matrix form. The β ⇌ α″ phase transition shows a discontinuity at the composition where the martensitic transformation temperatures fall below room temperature (between 34 and 38 at. % Ta) rendering it first order and confirming its martensitic nature. A short study of the α″ martensite employing the Landau theory is included for a mathematical quantification of the spontaneous lattice strain at room temperature (ϵ̂ max = 22.4(6) % for pure Ti). Martensitic properties of Ti-Ta are beneficial for the development of high-temperature actuators with actuation response at transformation temperatures higher than 100 °C.

Active x-ray optics for high resolution space telescopes

Science.gov (United States)

Doel, Peter; Atkins, Carolyn; Brooks, D.; Feldman, Charlotte; Willingale, Richard; Button, Tim; Rodriguez Sanmartin, Daniel; Meggs, Carl; James, Ady; Willis, Graham; Smith, Andy

2017-11-01

The Smart X-ray Optics (SXO) Basic Technology project started in April 2006 and will end in October 2010. The aim is to develop new technologies in the field of X-ray focusing, in particular the application of active and adaptive optics. While very major advances have been made in active/adaptive astronomical optics for visible light, little was previously achieved for X-ray optics where the technological challenges differ because of the much shorter wavelengths involved. The field of X-ray astronomy has been characterized by the development and launch of ever larger observatories with the culmination in the European Space Agency's XMM-Newton and NASA's Chandra missions which are currently operational. XMM-Newton uses a multi-nested structure to provide modest angular resolution ( 10 arcsec) but large effective area, while Chandra sacrifices effective area to achieve the optical stability necessary to provide sub-arc second resolution. Currently the European Space Agency (ESA) is engaged in studies of the next generation of X-ray space observatories, with the aim of producing telescopes with increased sensitivity and resolution. To achieve these aims several telescopes have been proposed, for example ESA and NASA's combined International X-ray Observatory (IXO), aimed at spectroscopy, and NASA's Generation-X. In the field of X-ray astronomy sub 0.2 arcsecond resolution with high efficiency would be very exciting. Such resolution is unlikely to be achieved by anything other than an active system. The benefits of a such a high resolution would be important for a range of astrophysics subjects, for example the potential angular resolution offered by active X-ray optics could provide unprecedented structural imaging detail of the Solar Wind bowshock interaction of comets, planets and similar objects and auroral phenomena throughout the Solar system using an observing platform in low Earth orbit. A major aim of the SXO project was to investigate the production of thin

Tungsten heavy metal alloys relations between the crystallographic texture and the internal stress distribution

International Nuclear Information System (INIS)

Nicolas, G.; Voltz, M.

2001-01-01

Quite often the W-Ni-Fe-Co heavy alloys are subjected to a thermomechanical processing of swaging and aging in order to obtain the highest possible level of resistance. Within the framework of this plastic deformation on cylindrical parts, the swaging leads to the distribution of morphological and crystallographic texture as well as specific internal stresses. The resulting mechanical characteristics are correlated to structural and sub-structural variations. (author)

High spatial resolution mapping of folds and fractures using Unmanned Aerial Vehicle (UAV) photogrammetry

Science.gov (United States)

Cruden, A. R.; Vollgger, S.

2016-12-01

The emerging capability of UAV photogrammetry combines a simple and cost-effective method to acquire digital aerial images with advanced computer vision algorithms that compute spatial datasets from a sequence of overlapping digital photographs from various viewpoints. Depending on flight altitude and camera setup, sub-centimeter spatial resolution orthophotographs and textured dense point clouds can be achieved. Orientation data can be collected for detailed structural analysis by digitally mapping such high-resolution spatial datasets in a fraction of time and with higher fidelity compared to traditional mapping techniques. Here we describe a photogrammetric workflow applied to a structural study of folds and fractures within alternating layers of sandstone and mudstone at a coastal outcrop in SE Australia. We surveyed this location using a downward looking digital camera mounted on commercially available multi-rotor UAV that autonomously followed waypoints at a set altitude and speed to ensure sufficient image overlap, minimum motion blur and an appropriate resolution. The use of surveyed ground control points allowed us to produce a geo-referenced 3D point cloud and an orthophotograph from hundreds of digital images at a spatial resolution automatically extracted from these high-resolution datasets using open-source software. This resulted in an extensive and statistically relevant orientation dataset that was used to 1) interpret the progressive development of folds and faults in the region, and 2) to generate a 3D structural model that underlines the complex internal structure of the outcrop and quantifies spatial variations in fold geometries. Overall, our work highlights how UAV photogrammetry can contribute to new insights in structural analysis.

Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module

Energy Technology Data Exchange (ETDEWEB)

Deng, Liulin; Ibrahim, Yehia M.; Hamid, Ahmed M.; Garimella, Sandilya V. B.; Webb, Ian K.; Zheng, Xueyun; Prost, Spencer A.; Sandoval, Jeremy A.; Norheim, Randolph V.; Anderson, Gordon A.; Tolmachev, Aleksey V.; Baker, Erin S.; Smith, Richard D.

2016-09-20

We report the development and initial evaluation of a 13-m path length Structures for Lossless Manipulations (SLIM) module for achieving high resolution separations using traveling waves (TW) with ion mobility (IM) spectrometry. The TW SLIM module was fabricated using two mirror-image printed circuit boards with appropriately configured RF, DC and TW electrodes and positioned with a 2.75-mm inter-surface gap. Ions were effective confined between the surfaces by RF-generated pseudopotential fields and moved losslessly through a serpentine path including 44 “U” turns using TWs. The ion mobility resolution was characterized at different pressures, gaps between the SLIM surfaces, TW and RF parameters. After initial optimization the SLIM IM-MS module provided about 5-fold higher resolution separations than present commercially available drift tube or traveling wave IM-MS platforms. Peak capacity and peak generation rates achieved were 246 and 370 s-1, respectively, at a TW speed of 148 m/s. The high resolution achieved in the TW SLIM IM-MS enabled e.g., isomeric sugars (Lacto-N-fucopentaose I and Lacto-N-fucopentaose II) to be baseline resolved, and peptides from a albumin tryptic digest much better resolved than with existing commercial IM-MS platforms. The present work also provides a foundation for the development of much higher resolution SLIM devices based upon both considerably longer path lengths and multi-pass designs.

High resolution time integration for SN radiation transport

International Nuclear Information System (INIS)

Thoreson, Greg; McClarren, Ryan G.; Chang, Jae H.

2009-01-01

First-order, second-order, and high resolution time discretization schemes are implemented and studied for the discrete ordinates (S N ) equations. The high resolution method employs a rate of convergence better than first-order, but also suppresses artificial oscillations introduced by second-order schemes in hyperbolic partial differential equations. The high resolution method achieves these properties by nonlinearly adapting the time stencil to use a first-order method in regions where oscillations could be created. We employ a quasi-linear solution scheme to solve the nonlinear equations that arise from the high resolution method. All three methods were compared for accuracy and convergence rates. For non-absorbing problems, both second-order and high resolution converged to the same solution as the first-order with better convergence rates. High resolution is more accurate than first-order and matches or exceeds the second-order method

Recombinant ACHT1 from Arabidopsis thaliana: crystallization and X-ray crystallographic analysis.

Science.gov (United States)

Pan, Weimin; Wang, Junchao; Yang, Ye; Liu, Lin; Zhang, Min

2017-07-01

Thioredoxins (Trxs) play important roles in chloroplasts by linking photosynthetic light reactions to a series of plastid functions. They execute their function by regulating the oxidation and reduction of disulfide bonds. ACHT1 (atypical cysteine/histidine-rich Trx1) is a thylakoid-associated thioredoxin-type protein found in the Arabidopsis thaliana chloroplast. Recombinant ACHT1 protein was overexpressed in Escherichia coli, purified and crystallized by the vapour-diffusion method. The crystal diffracted to 1.7 Å resolution and a complete X-ray data set was collected. Preliminary crystallographic analysis suggested that the crystals belonged to space group C222 1 , with unit-cell parameters a = 102.7, b = 100.6, c = 92.8 Å.

Structural evolution of a deformed Σ=9 (122) grain boundary in silicon. A high resolution electron microscopy study

International Nuclear Information System (INIS)

Putaux, Jean-Luc

1991-01-01

This research thesis addresses the study by high resolution electron microscopy of the evolution of a silicon bi-crystal under deformation at different temperatures. The author notably studied the structural evolution of the boundary as well as that of grains at the vicinity of the boundary. Two observation scales have been used: the evolution of sub-structures of dislocations induced by deformation in grains and in boundary, and the structure of all defects at an atomic scale. After a presentation of experimental tools (the necessary perfect quality of the electronic optics is outlined), the author recalls some descriptive aspects of grain boundaries (geometric network concepts to describe coinciding networks, concepts of delimiting boundaries and of structural unit to describe grain boundary atomic structure), recalls the characteristics of the studied bi-crystal, and the conditions under which it is deformed. He presents the structures of all perfectly coinciding boundaries, describes defects obtained by deformation at the vicinity of the boundary, describes the entry of dissociated dislocations into the boundaries, and discusses the characterization of boundary dislocations (the notion of Burgers vector is put into question again), and the atomic mechanism of displacement of dislocations in boundaries [fr

High resolution crustal structure for the region between the Chilenia and Cuyania terrane above the Pampean flat slab of Argentina from local receiver function and petrological analyses

Science.gov (United States)

Ammirati, J. B.; Alvarado, P. M.; Pérez, S. B.; Beck, S. L.; Porter, R. C.; Zandt, G.

2015-12-01

Jean-Baptiste Ammirati 1,Sofía Perez 1, Patricia Alvarado 1, Susan L. Beck 2, Ryan Porter 3 and George Zandt 2(1) CIGEOBIO-CONICET, Universidad Nacional de San Juan, Argentina (2) The University of Arizona, USA (3) Northern Arizona University, USA At ~31ºS, The subduction of the Nazca plate under the South American plate presents along-strike variations of its dip angle referred to the Chilean-Pampean flat slab. Geological observations suggest that the regional crustal structure is inherited from the accretion of different terranes at Ordovician times and later reactivated during Andean compression since Miocene. Geophysical observations confirmed that the structure is extending in depth with décollement levels that accommodate crustal shortening in the region. In order to get a better insight on the shallow tectonics we computed high frequency local receiver functions from slab seismicity (~100 km depth). Local earthquakes present a higher frequency content that permits a better vertical resolution. Using a common conversion point (CCP) stacking method we obtained cross sections showing high-resolution crustal structure in the western part of the Pampean flat slab region, at the transition between the Precordillera and the Frontal Cordillera. Our results show a well-defined structure and their lateral extent for both units down to 80 km depth. In good agreement with previous studies, our higher resolution images better identify very shallow discontinuities putting more constraints on the relationships with the regional structural geology. Recent petrological analyses combined with RF high-resolution structure also allow us to better understand the regional crustal composition. Interestingly, we are able to observe a shifting structure beneath the Uspallata-Calingasta Valley, highlighting the differences in terms of crustal structure between the Precordillera and the Frontal Cordillera. Previously determined focal mechanisms in the region match well this

High resolution interface nanochemistry and structure

International Nuclear Information System (INIS)

1993-01-01

A summary is given of results on nanospectroscopy etc. during the previous three years, divided into the following subsections: development of methods and instrumentation for interface/boundary chemical analysis, interface and boundary structure in ceramic matrix composites, quantitative composition measurements of thin films and inclusions, theoretical calculations for electron energy loss near edge fine structure and grain boundary structure, and small probe radiation effects in ceramics. Materials studied include SiC whisker-reinforced Si3N4, SiC, Si oxides, Si, Si oxynitride, other ceramics. Methods mentioned include field emission, EELS (electron energy loss spectroscopy), nanospectroscopy, electron nanoprobe, etc

Crystal Structure of α-Galactosidase from Lactobacillus acidophilus NCFM: Insight into Tetramer Formation and Substrate Binding

DEFF Research Database (Denmark)

Fredslund, Folmer; Abou Hachem, Maher; Larsen, Rene Jonsgaard

2011-01-01

structure of α-Gal from L. acidophilus NCFM (LaMel36A) of glycoside hydrolase (GH) family 36 (GH36) is determined by single-wavelength anomalous dispersion. In addition, a 1.58-Å-resolution crystallographic complex with α-d-galactose at substrate binding subsite −1 was determined. LaMel36A has a large N...

Crystallization and preliminary crystallographic analysis of human LR11 Vps10p domain

International Nuclear Information System (INIS)

Nakata, Zenzaburo; Nagae, Masamichi; Yasui, Norihisa; Bujo, Hideaki; Nogi, Terukazu; Takagi, Junichi

2010-01-01

LR11/sorLA contains in its extracellular region a large (∼700-residue) Vps10p domain that is implicated in its intracellular protein-trafficking function. Here, the expression, purification, crystallization and preliminary crystallographic characterization of this domain are described. Low-density lipoprotein receptor (LDLR) relative with 11 binding repeats (LR11; also known as sorLA) is genetically associated with late-onset Alzheimer’s disease and is thought to be involved in neurodegenerative processes. LR11 contains a vacuolar protein-sorting 10 protein (Vps10p) domain. As this domain has been implicated in protein–protein interaction in other receptors, its structure and function are of great biological interest. Human LR11 Vps10p domain was expressed in mammalian cells and the purified protein was crystallized using the hanging-drop vapour-diffusion method. Enzymatic deglycosylation of the sample was critical to obtaining diffraction-quality crystals. Deglycosylated LR11 Vps10p-domain crystals belonged to the hexagonal space group P6 1 22. A diffraction data set was collected to 2.4 Å resolution and a clear molecular-replacement solution was obtained

Atomic resolution structure of the E. coli YajR transporter YAM domain

Energy Technology Data Exchange (ETDEWEB)

Jiang, Daohua [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Zhao, Yan [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Fan, Junping; Liu, Xuehui; Wu, Yan; Feng, Wei [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China); Zhang, Xuejun C., E-mail: zhangc@ibp.ac.cn [National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101 (China)

2014-07-25

Highlights: • We report the crystal structure of the YAM domain of YajR transporter at 1.07 Å. • The YAM dimerization is related to the halogen-dependent high thermal stability. • A belt of poly-pentagonal water molecules was observed in the dimer interface. - Abstract: YajR is an Escherichia coli transporter that belongs to the major facilitator superfamily. Unlike most MFS transporters, YajR contains a carboxyl terminal, cytosolic domain of 67 amino acid residues termed YAM domain. Although it is speculated that the function of this small soluble domain is to regulate the conformational change of the 12-helix transmembrane domain, its precise regulatory role remains unclear. Here, we report the crystal structure of the YAM domain at 1.07-Å resolution, along with its structure determined using nuclear magnetic resonance. Detailed analysis of the high resolution structure revealed a symmetrical dimer in which a belt of well-ordered poly-pentagonal water molecules is embedded. A mutagenesis experiment and a thermal stability assay were used to analyze the putative role of this dimerization in response to changes in halogen concentration.

Crystal structures of β-galactosidase from Penicillium sp. and its complex with galactose

International Nuclear Information System (INIS)

Rojas, A.L.; Nagem, R.A.P.; Garratt, R.C.; Polikarpov, I.; Neustroev, K.N.; Eneyskaya, E.V.; Kulminskaya, A.A.; Golubev, A.M.; Arand, M.; Adamska, M.

2004-01-01

Glycosidase belong to a group of enzymes displaying a great variety of protein folds and substrate specificities. Two critically located acidic residues make up the catalytic machinery of these enzymes, which are responsible for the cleavage of glycosidic bonds. The applications of glycosidase in textile, food, and pulp processing and in catalysts and oligosaccharide synthesis have encouraged the engineering of these proteins to improve their catalytic properties and stability. Furthermore, structural studies broaden our understanding of the catalytic mechanism and the role of glycosidase in the recognition processes of their different substrates. In this work, we describe crystallographic studies of a fungi glycosidase. The crystallographic structures of β-galactosidase from Penicillium sp. and its complex with galactose were solved at 1.90 A and 2.10 A resolution, respectively. The X-ray structure of the enzyme-galactose complex was useful in identifying the residue Glu200 as the proton donor and residue Glu 299 as the nucleophiles involved in catalysis. (author)

Crystal structures of {beta}-galactosidase from Penicillium sp. and its complex with galactose

Energy Technology Data Exchange (ETDEWEB)

Rojas, A.L.; Nagem, R.A.P.; Garratt, R.C.; Polikarpov, I. [Universidade de Sao Paulo, Sao Carlos, SP (Brazil); Neustroev, K.N.; Eneyskaya, E.V.; Kulminskaya, A.A.; Golubev, A.M. [St. Petersburg, Gatchina (Russian Federation); Arand, M.; Adamska, M. [University of Wuerzburg (Germany)

2004-07-01

Glycosidase belong to a group of enzymes displaying a great variety of protein folds and substrate specificities. Two critically located acidic residues make up the catalytic machinery of these enzymes, which are responsible for the cleavage of glycosidic bonds. The applications of glycosidase in textile, food, and pulp processing and in catalysts and oligosaccharide synthesis have encouraged the engineering of these proteins to improve their catalytic properties and stability. Furthermore, structural studies broaden our understanding of the catalytic mechanism and the role of glycosidase in the recognition processes of their different substrates. In this work, we describe crystallographic studies of a fungi glycosidase. The crystallographic structures of {beta}-galactosidase from Penicillium sp. and its complex with galactose were solved at 1.90 A and 2.10 A resolution, respectively. The X-ray structure of the enzyme-galactose complex was useful in identifying the residue Glu200 as the proton donor and residue Glu 299 as the nucleophiles involved in catalysis. (author)

High Resolution X-ray Diffraction Dataset for Bacillus licheniformis Gamma Glutamyl Transpeptidase-acivicin complex: SUMO-Tag Renders High Expression and Solubility.

Science.gov (United States)

Kumari, Shobha; Pal, Ravi Kant; Gupta, Rani; Goel, Manisha

2017-02-01

Gamma glutamyl transpeptidase, (GGT) is a ubiquitous protein which plays a central role in glutathione metabolism and has myriad clinical implications. It has been shown to be a virulence factor for pathogenic bacteria, inhibition of which results in reduced colonization potential. However, existing inhibitors are effective but toxic and therefore search is on for novel inhibitors, which makes it imperative to understand the interactions of various inhibitors with the protein in substantial detail. High resolution structures of protein bound to different inhibitors can serve this purpose. Gamma glutamyl transpeptidase from Bacillus licheniformis is one of the model systems that have been used to understand the structure-function correlation of the protein. The structures of the native protein (PDB code 4OTT), of its complex with glutamate (PDB code 4OTU) and that of its precursor mimic (PDB code 4Y23) are available, although at moderate/low resolution. In the present study, we are reporting the preliminary analysis of, high resolution X-ray diffraction data collected for the co-crystals of B. licheniformis, Gamma glutamyl transpeptidase, with its inhibitor, Acivicin. Crystals belong to the orthorhombic space group P2 1 2 1 2 1 and diffract X-ray to 1.45 Å resolution. This is the highest resolution data reported for all GGT structures available till now. The use of SUMO fused expression system enhanced yield of the target protein in the soluble fraction, facilitating recovery of protein with high purity. The preliminary analysis of this data set shows clear density for the inhibitor, acivicin, in the protein active site.

High-resolution geophysical profiling using a stepped-frequency ground penetrating radar

Energy Technology Data Exchange (ETDEWEB)

Noon, D; Longstaff, D [The University of Queensland, (Australia)

1996-05-01

This paper describes the results of a ground penetrating radar (GPR) system which uses stepped-frequency waveforms to obtain high-resolution geophysical profiles. The main application for this system is the high-resolution mapping of thin coal seam structures, in order to assist surface mining operations in open-cut coal mines. The required depth of penetration is one meter which represents the maximum thickness of coal seams that are designated `thin`. A resolution of five centimeters is required to resolve the minimum thickness of coal (or shale partings) which can be economically recovered in an open-cut coal mine. For this application, a stepped-frequency GPR system has been developed, because of its ultrawide bandwidth (1 to 2 GHz) and high external loop sensitivity (155 dB). The field test results of the stepped-frequency GPR system on a concrete pavement and at two Australian open-cut coal mines are also presented. 7 refs., 5 figs.

High Resolution Energetic X-ray Imager (HREXI)

Science.gov (United States)

Grindlay, Jonathan

IR telescope in spece, will enable GRBs to be used as probes of the formation of the first stars and structure in the Universe. HREXI on its own, with broad bandwidth and high spectral and spatial resolution, will extend both Galactic surveys for obscured young supernova remnants (44Ti sources) and for transients, black holes and flaring AGN and TDEs well at greatly increased sensitivity and spatial/spectral resolution than has been done with Swift or INTEGRAL. If the HREXI-1 technology is developed in the first year of this proposed effort, it could be used on the upcoming Brazil-US MIRAX telescope on the Lattes satellite, scheduled for a 2018 launch with imaging detector planes to be provided (under contract) by our group. Finally, the 3D stacking technology development proposed here for imaging detector arrays has broad application to Wide Field soft X-ray imaging, to CMB polarization mode (B mode) imaging detectors with very high detector-pixel count, and to Homeland Security.

The High-Resolution IRAS Galaxy Atlas

Science.gov (United States)

Cao, Yu; Terebey, Susan; Prince, Thomas A.; Beichman, Charles A.; Oliversen, R. (Technical Monitor)

1997-01-01

An atlas of the Galactic plane (-4.7 deg is less than b is less than 4.7 deg), along with the molecular clouds in Orion, rho Oph, and Taurus-Auriga, has been produced at 60 and 100 microns from IRAS data. The atlas consists of resolution-enhanced co-added images with 1 min - 2 min resolution and co-added images at the native IRAS resolution. The IRAS Galaxy Atlas, together with the Dominion Radio Astrophysical Observatory H(sub I) line/21 cm continuum and FCRAO CO (1-0) Galactic plane surveys, which both have similar (approx. 1 min) resolution to the IRAS atlas, provides a powerful tool for studying the interstellar medium, star formation, and large-scale structure in our Galaxy. This paper documents the production and characteristics of the atlas.

High-resolution structure of the antibiotic resistance protein NimA from Deinococcus radiodurans

International Nuclear Information System (INIS)

Leiros, Hanna-Kirsti S.; Tedesco, Consiglia; McSweeney, Seán M.

2008-01-01

In this paper, the 1.2 Å atomic resolution crystal structure of the 5-nitroimidazole antibiotic resistance protein NimA from Deinococcus radiodurans (DrNimA) is presented. Many anaerobic human pathogenic bacteria are treated using 5-nitroimidazole-based (5-Ni) antibiotics, a class of inactive prodrugs that contain a nitro group. The nitro group must be activated in an anaerobic one-electron reduction and is therefore dependent on the redox system in the target cells. Antibiotic resistance towards 5-Ni drugs is found to be related to the nim genes (nimA, nimB, nimC, nimD, nimE and nimF), which are proposed to encode a reductase that is responsible for converting the nitro group of the antibiotic into a nonbactericidal amine. A mechanism for the Nim enzyme has been proposed in which two-electron reduction of the nitro group leads to the generation of nontoxic derivatives and confers resistance against these antibiotics. The cofactor was found to be important in the mechanism and was found to be covalently linked to the reactive His71. In this paper, the 1.2 Å atomic resolution crystal structure of the 5-nitroimidazole antibiotic resistance protein NimA from Deinococcus radiodurans (DrNimA) is presented. A planar cofactor is clearly visible and well defined in the electron-density map adjacent to His71, the identification of the cofactor and its properties are discussed

Computerized tomography using high resolution X-ray imaging system with a microfocus source

International Nuclear Information System (INIS)

Zaprazny, Z.; Korytar, D.; Konopka, P.; Ac, V.; Bielecki, J.

2011-01-01

In recent years there is an effort to image an internal structure of an object by using not only conventional 2D X-ray radiography but also using high resolution 3D tomography which is based on reconstruction of multiple 2D projections at various angular positions of the object. We have previously reported [1] the development and basic parameters of a high resolution x-ray imaging system with a microfocus source. We report the recent progress using this high resolution X-ray laboratory system in this work. These first findings show that our system is particularly suitable for light weight and nonmetallic objects such as biological objects, plastics, wood, paper, etc. where phase contrast helps to increase the visibility of the finest structures of the object. Phase-contrast X-ray Computerized Tomography is of our special interest because it is an emerging imaging technique that can be implemented at third generation synchrotron radiation sources and also in laboratory conditions using a microfocus X-ray tube or beam conditioning optics. (authors)

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

Energy Technology Data Exchange (ETDEWEB)

Morshed, Nader [University of California, Berkeley, CA 94720 (United States); Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Echols, Nathaniel, E-mail: nechols@lbl.gov [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Adams, Paul D., E-mail: nechols@lbl.gov [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California, Berkeley, CA 94720 (United States)

2015-05-01

A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

Three-dimensional structure of brain tissue at submicrometer resolution

Energy Technology Data Exchange (ETDEWEB)

Saiga, Rino; Mizutani, Ryuta, E-mail: ryuta@tokai-u.jp [Department of Applied Biochemistry, Tokai University, Hiratsuka, Kanagawa 259-1292 (Japan); Inomoto, Chie; Takekoshi, Susumu; Nakamura, Naoya; Tsuboi, Akio; Osawa, Motoki [Tokai University School of Medicine, Isehara, Kanagawa 259-1193 (Japan); Arai, Makoto; Oshima, Kenichi; Itokawa, Masanari [Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo 156-8506 (Japan); Uesugi, Kentaro; Takeuchi, Akihisa; Terada, Yasuko; Suzuki, Yoshio [Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), Sayo, Hyogo 679-5198 (Japan)

2016-01-28

Biological objects are composed of submicrometer structures such as cells and organelles that are essential for their functions. Here, we report on three-dimensional X-ray visualization of cells and organelles at resolutions up to 100 nm by imaging microtomography (micro-CT) equipped with Fresnel zone plate optics. Human cerebral tissue, fruit fly cephalic ganglia, and Escherichia coli bacteria labeled with high atomic-number elements were embedded in epoxy resin and subjected to X-ray microtomography at the BL37XU and BL47XU beamlines of the SPring-8 synchrotron radiation facility. The obtained results indicated that soft tissue structures can be visualized with the imaging microtomography.

A high resolution portable spectroscopy system

International Nuclear Information System (INIS)

Kulkarni, C.P.; Vaidya, P.P.; Paulson, M.; Bhatnagar, P.V.; Pande, S.S.; Padmini, S.

2003-01-01

Full text: This paper describes the system details of a High Resolution Portable Spectroscopy System (HRPSS) developed at Electronics Division, BARC. The system can be used for laboratory class, high-resolution nuclear spectroscopy applications. The HRPSS consists of a specially designed compact NIM bin, with built-in power supplies, accommodating a low power, high resolution MCA, and on-board embedded computer for spectrum building and communication. A NIM based spectroscopy amplifier and a HV module for detector bias are integrated (plug-in) in the bin. The system communicates with a host PC via a serial link. Along-with a laptop PC, and a portable HP-Ge detector, the HRPSS offers a laboratory class performance for portable applications

Internal structure of InP/ZnS nanocrystals unraveled by high-resolution soft X-ray photoelectron spectroscopy.

Science.gov (United States)

Huang, Kai; Demadrille, Renaud; Silly, Mathieu G; Sirotti, Fausto; Reiss, Peter; Renault, Olivier

2010-08-24

High-energy resolution photoelectron spectroscopy (DeltaE InP/ZnS core/shell nanocrystals synthesized using a single-step procedure (core and shell precursors added at the same time), a homogeneously alloyed InPZnS core structure is evidenced by quantitative analysis of their In3d(5/2) spectra recorded at variable excitation energy. When using a two-step method (core InP nanocrystal synthesis followed by subsequent ZnS shell growth), XPS analysis reveals a graded core/shell interface. We demonstrate the existence of In-S and S(x)-In-P(1-x) bonding states in both types of InP/ZnS nanocrystals, which allows a refined view on the underlying reaction mechanisms.

Developmental approach towards high resolution optical coherence tomography for glaucoma diagnostics

Science.gov (United States)

Kemper, Björn; Ketelhut, Steffi; Heiduschka, Peter; Thorn, Marie; Larsen, Michael; Schnekenburger, Jürgen

2018-02-01

Glaucoma is caused by a pathological rise in the intraocular pressure, which results in a progressive loss of vision by a damage to retinal cells and the optical nerve head. Early detection of pressure-induced damage is thus essential for the reduction of eye pressure and to prevent severe incapacity or blindness. Within the new European Project GALAHAD (Glaucoma Advanced, Label free High Resolution Automated OCT Diagnostics), we will develop a new low-cost and high-resolution OCT system for the early detection of glaucoma. The device is designed to improve diagnosis based on a new system of optical coherence tomography. Although OCT systems are at present available in ophthalmology centres, high-resolution devices are extremely expensive. The novelty of the new Galahad system is its super wideband light source to achieve high image resolution at a reasonable cost. Proof of concept experiments with cell and tissue Glaucoma test standards and animal models are planned for the test of the new optical components and new algorithms performance for the identification of Glaucoma associated cell and tissue structures. The intense training of the software systems with various samples should result in a increased sensitivity and specificity of the OCT software system.

PEPSI, the High-Resolution Optical-IR Spectrograph for the LBT

Science.gov (United States)

Andersen, Michael; Strassmeier, Klaus; Hoffman, Axel; Woche, Manfred; Spano, Paolo

PEPSI is a high resolution fibre feed optical-IR polarimetric echelle spectrograph for the Large Binocular Telescope (LBT). PEPSI utilizes the two 8.4m LBT apertures to simultaneously record four polarization states at a resolution of 120.000. The extension of the coverage towards the IR is mainly motivated by the larger Zeeman splitting of IR lines, which would allow to study weaker/fainter magnetic structures on stars. The two optical arms, which also have an integral light mode with R up to 300.000, are under construction, while the IR arm is being designed.

High-heat tank safety issue resolution program plan

International Nuclear Information System (INIS)

Wang, O.S.

1993-12-01

The purpose of this program plan is to provide a guide for selecting corrective actions that will mitigate and/or remediate the high-heat waste tank safety issue for single-shell tank (SST) 241-C-106. This program plan also outlines the logic for selecting approaches and tasks to mitigate and resolve the high-heat safety issue. The identified safety issue for high-heat tank 241-C-106 involves the potential release of nuclear waste to the environment as the result of heat-induced structural damage to the tank's concrete, if forced cooling is interrupted for extended periods. Currently, forced ventilation with added water to promote thermal conductivity and evaporation cooling is used to cool the waste. At this time, the only viable solution identified to resolve this safety issue is the removal of heat generating waste in the tank. This solution is being aggressively pursued as the permanent solution to this safety issue and also to support the present waste retrieval plan. Tank 241-C-106 has been selected as the first SST for retrieval. The program plan has three parts. The first part establishes program objectives and defines safety issues, drivers, and resolution criteria and strategy. The second part evaluates the high-heat safety issue and its mitigation and remediation methods and alternatives according to resolution logic. The third part identifies major tasks and alternatives for mitigation and resolution of the safety issue. Selected tasks and best-estimate schedules are also summarized in the program plan

Crystallization and preliminary crystallographic studies of a cysteine protease inhibitor from the human nematode parasite Ascaris lumbricoides

International Nuclear Information System (INIS)

Liu, Sanling; Dong, Jianmei; Mei, Guoqiang; Liu, Guiyun; Xu, Wei; Su, Zhong; Liu, Jinsong

2011-01-01

A recombinant cysteine protease inhibitor from the human nematode parasite A. lumbricoides has been overexpressed in E. coli, purified and crystallized. Diffraction data were collected to 2.1 Å resolution. The cysteine protease inhibitor from Ascaris lumbricoides, a roundworm that lives in the human intestine, may be involved in the suppression of human immune responses. Here, the molecular cloning, protein expression and purification, preliminary crystallization and crystallographic characterization of the cysteine protease inhibitor from A. lumbricoides are reported. The rod-shaped crystal belonged to space group C2, with unit-cell parameters a = 99.40, b = 37.52, c = 62.92 Å, β = 118.26°. The crystal diffracted to 2.1 Å resolution and contained two molecules in the asymmetric unit

High Resolution Elevation Contours

Data.gov (United States)

Minnesota Department of Natural Resources — This dataset contains contours generated from high resolution data sources such as LiDAR. Generally speaking this data is 2 foot or less contour interval.

40-Godišnjica institucije Cambridge Crystallographic Data Centre posvećene pohranjivanju podataka o molekularnim i kristalnim strukturama -

Directory of Open Access Journals (Sweden)

Molčanov, K.

2006-06-01

Full Text Available The article is dedicated to 40th anniversary of The Cambridge Crystallographic Data Centre (CCDC, the world-known centre (http://www.ccdc.cam.ac.uk responsible for deposition and control of crystallographic data, including atomic coordinates that define the three-dimensional structures of organic molecules and metal complexes containing organic ligands. Cambride Structural Database (CSD, one among the first established electronic databases, nowadays is the most significant crystallographic database in the world. CSD has about 400,000 deposited structures. The use of the extensive database, which is growing rapidly, needs support of efficient and sophisticated software for searching, analysing and visualising structural data. The seminal role of CSD in the research related to crystallography, chemistry, material sciences, solid state physics and chemistry, life sciences, pharmacology, and in particular in drug design, has been documented in more than 1300 scientific papers. The important issues of CCDC are the accuracy of deposited data and development of software that enables a wide variety of applications. Such demanding project requires higly competent team of experts; thus the article brings into focus the scientific approach of the team based on the long tradition in crystallography, modelling and informatics. The article is not dedicated to 40th anniversary of the centre only, but it also reveals how Cambridge Structural Database can be used in the research and teaching. The use of electronic media and computer graphics makes “data mining" very efficient and useful but also esthetically appealing due to the molecular architecture. At the Rudjer Bošković Institute, Zagreb, Croatia there is The National Affiliated Centre of Cambridge Crystallographic Data Centre responsible for communication and dissemination of CSD in Croatia, Slovenia and Macedonia. The use of CSD is illustrated by two examples performed and published by the presenting

Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

Energy Technology Data Exchange (ETDEWEB)

Zeng, Ying-Xu [Department of Chemistry, University of Bergen, PO Box 7803, N-5020 Bergen (Norway); Mjøs, Svein Are, E-mail: svein.mjos@kj.uib.no [Department of Chemistry, University of Bergen, PO Box 7803, N-5020 Bergen (Norway); David, Fabrice P.A. [Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne (Switzerland); Schmid, Adrien W. [Proteomics Core Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne (Switzerland)

2016-03-31

Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. - Highlights: • A flexible strategy for analyzing MS and LC-MS data of lipid molecules is proposed. • Isotope distribution spectra of theoretically possible compounds were generated. • High resolution MS and LC-MS data were resolved by least squares spectral resolution. • The method proposed compounds that are likely to occur in the analyzed samples. • The proposed compounds matched results from manual interpretation of fragment spectra.

Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

International Nuclear Information System (INIS)

Zeng, Ying-Xu; Mjøs, Svein Are; David, Fabrice P.A.; Schmid, Adrien W.

2016-01-01

Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. - Highlights: • A flexible strategy for analyzing MS and LC-MS data of lipid molecules is proposed. • Isotope distribution spectra of theoretically possible compounds were generated. • High resolution MS and LC-MS data were resolved by least squares spectral resolution. • The method proposed compounds that are likely to occur in the analyzed samples. • The proposed compounds matched results from manual interpretation of fragment spectra.

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

International Nuclear Information System (INIS)

Terwilliger, Thomas C.; Bricogne, Gerard

2014-01-01

Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

Energy Technology Data Exchange (ETDEWEB)

Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States); Bricogne, Gerard, E-mail: terwilliger@lanl.gov [Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX (United Kingdom); Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States)

2014-10-01

Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

Ultra-high resolution coded wavefront sensor

KAUST Repository

Wang, Congli

2017-06-08

Wavefront sensors and more general phase retrieval methods have recently attracted a lot of attention in a host of application domains, ranging from astronomy to scientific imaging and microscopy. In this paper, we introduce a new class of sensor, the Coded Wavefront Sensor, which provides high spatio-temporal resolution using a simple masked sensor under white light illumination. Specifically, we demonstrate megapixel spatial resolution and phase accuracy better than 0.1 wavelengths at reconstruction rates of 50 Hz or more, thus opening up many new applications from high-resolution adaptive optics to real-time phase retrieval in microscopy.

Direct fabrication of high-resolution three-dimensional polymeric scaffolds using electrohydrodynamic hot jet plotting

International Nuclear Information System (INIS)

Wei, Chuang; Dong, Jingyan

2013-01-01

This paper presents the direct three-dimensional (3D) fabrication of polymer scaffolds with sub-10 µm structures using electrohydrodynamic jet (EHD-jet) plotting of melted thermoplastic polymers. Traditional extrusion-based fabrication approaches of 3D periodic porous structures are very limited in their resolution, due to the excessive pressure requirement for extruding highly viscous thermoplastic polymers. EHD-jet printing has become a high-resolution alternative to other forms of nozzle deposition-based fabrication approaches by generating micro-scale liquid droplets or a fine jet through the application of a large electrical voltage between the nozzle and the substrate. In this study, we successfully apply EHD-jet plotting technology with melted biodegradable polymer (polycaprolactone, or PCL) for the fabrication of 2D patterns and 3D periodic porous scaffold structures in potential tissue engineering applications. Process conditions (e.g. electrical voltage, pressure, plotting speed) have been thoroughly investigated to achieve reliable jet printing of fine filaments. We have demonstrated for the first time that the EHD-jet plotting process is capable of the fabrication of 3D periodic structures with sub-10 µm resolution, which has great potential in advanced biomedical applications, such as cell alignment and guidance. (paper)

RCrane: semi-automated RNA model building

International Nuclear Information System (INIS)

Keating, Kevin S.; Pyle, Anna Marie

2012-01-01

RCrane is a new tool for the partially automated building of RNA crystallographic models into electron-density maps of low or intermediate resolution. This tool helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RNA crystals typically diffract to much lower resolutions than protein crystals. This low-resolution diffraction results in unclear density maps, which cause considerable difficulties during the model-building process. These difficulties are exacerbated by the lack of computational tools for RNA modeling. Here, RCrane, a tool for the partially automated building of RNA into electron-density maps of low or intermediate resolution, is presented. This tool works within Coot, a common program for macromolecular model building. RCrane helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RCrane then allows the crystallographer to review the newly built structure and select alternative backbone conformations where desired. This tool can also be used to automatically correct the backbone structure of previously built nucleotides. These automated corrections can fix incorrect sugar puckers, steric clashes and other structural problems

Simultaneous observations of structure function parameter of refractive index using a high-resolution radar and the DataHawk small airborne measurement system

Science.gov (United States)

Scipión, Danny E.; Lawrence, Dale A.; Milla, Marco A.; Woodman, Ronald F.; Lume, Diego A.; Balsley, Ben B.

2016-09-01

The SOUSY (SOUnding SYstem) radar was relocated to the Jicamarca Radio Observatory (JRO) near Lima, Peru, in 2000, where the radar controller and acquisition system were upgraded with state-of-the-art parts to take full advantage of its potential for high-resolution atmospheric sounding. Due to its broad bandwidth (4 MHz), it is able to characterize clear-air backscattering with high range resolution (37.5 m). A campaign conducted at JRO in July 2014 aimed to characterize the lower troposphere with a high temporal resolution (8.1 Hz) using the DataHawk (DH) small unmanned aircraft system, which provides in situ atmospheric measurements at scales as small as 1 m in the lower troposphere and can be GPS-guided to obtain measurements within the beam of the radar. This was a unique opportunity to make coincident observations by both systems and to directly compare their in situ and remotely sensed parameters. Because SOUSY only points vertically, it is only possible to retrieve vertical radar profiles caused by changes in the refractive index within the resolution volume. Turbulent variations due to scattering are described by the structure function parameter of refractive index Cn2. Profiles of Cn2 from the DH are obtained by combining pressure, temperature, and relative humidity measurements along the helical trajectory and integrated at the same scale as the radar range resolution. Excellent agreement is observed between the Cn2 estimates obtained from the DH and SOUSY in the overlapping measurement regime from 1200 m up to 4200 m above sea level, and this correspondence provides the first accurate calibration of the SOUSY radar for measuring Cn2.

The structure of the ISM in the Zone of Avoidance by high-resolution multi-wavelength observations

Science.gov (United States)

Tóth, L. V.; Doi, Y.; Pinter, S.; Kovács, T.; Zahorecz, S.; Bagoly, Z.; Balázs, L. G.; Horvath, I.; Racz, I. I.; Onishi, T.

2018-05-01

We estimate the column density of the Galactic foreground interstellar medium (GFISM) in the direction of extragalactic sources. All-sky AKARI FIS infrared sky survey data might be used to trace the GFISM with a resolution of 2 arcminutes. The AKARI based GFISM hydrogen column density estimates are compared with similar quantities based on HI 21cm measurements of various resolution and of Planck results. High spatial resolution observations of the GFISM may be important recalculating the physical parameters of gamma-ray burst (GRB) host galaxies using the updated foreground parameters.

Proposal for a semiconductor high resolution tracking detector

International Nuclear Information System (INIS)

Rehak, P.

1983-01-01

A 'new' concept for detection and tracking of charged particles in high energy physics experiments is proposed. It combines a well known high purity semiconductor diode detector (HPSDD) with a heterojunction structure (HJ) and a negative electron affinity (NEA) surface. The detector should be capable of providing a two dimensional view (few cm 2 ) of multi-track events with the following properties: a) position resolution down to a few μm (10 8 position elements); b) high density of information (10 2 -10 3 dots per mm of minimum ionizing track); c) high rate capabilities (few MHz); d) live operation with options to be triggered and/or the information from the detector can be used as an input for the decision to record an event. (orig.)

Tuberculous otitis media: findings on high-resolution CT

International Nuclear Information System (INIS)

Lungenschmid, D.; Buchberger, W.; Schoen, G.; Schoepf, R.; Mihatsch, T.; Birbamer, G.; Wicke, K.

1993-01-01

We describe two cases of tuberculous otitis media studied with high-resolution computed tomography (CT). Findings included extensive soft tissue densities with fluid levels in the tympanic cavity, the antrum, the mastoid and petrous air cells. Multifocal bony erosions and reactive bone sclerosis were seen as well. CT proved valuable for planning therapy by accurately displaying the involvement of the various structures of the middle and inner ear. However, the specific nature of the disease could only be presumed. (orig.)

High resolution data acquisition

Science.gov (United States)

Thornton, Glenn W.; Fuller, Kenneth R.

1993-01-01

A high resolution event interval timing system measures short time intervals such as occur in high energy physics or laser ranging. Timing is provided from a clock (38) pulse train (37) and analog circuitry (44) for generating a triangular wave (46) synchronously with the pulse train (37). The triangular wave (46) has an amplitude and slope functionally related to the time elapsed during each clock pulse in the train. A converter (18, 32) forms a first digital value of the amplitude and slope of the triangle wave at the start of the event interval and a second digital value of the amplitude and slope of the triangle wave at the end of the event interval. A counter (26) counts the clock pulse train (37) during the interval to form a gross event interval time. A computer (52) then combines the gross event interval time and the first and second digital values to output a high resolution value for the event interval.

High resolution time integration for Sn radiation transport

International Nuclear Information System (INIS)

Thoreson, Greg; McClarren, Ryan G.; Chang, Jae H.

2008-01-01

First order, second order and high resolution time discretization schemes are implemented and studied for the S n equations. The high resolution method employs a rate of convergence better than first order, but also suppresses artificial oscillations introduced by second order schemes in hyperbolic differential equations. All three methods were compared for accuracy and convergence rates. For non-absorbing problems, both second order and high resolution converged to the same solution as the first order with better convergence rates. High resolution is more accurate than first order and matches or exceeds the second order method. (authors)

High-resolution electron microscopy

CERN Document Server

Spence, John C H

2013-01-01

This new fourth edition of the standard text on atomic-resolution transmission electron microscopy (TEM) retains previous material on the fundamentals of electron optics and aberration correction, linear imaging theory (including wave aberrations to fifth order) with partial coherence, and multiple-scattering theory. Also preserved are updated earlier sections on practical methods, with detailed step-by-step accounts of the procedures needed to obtain the highest quality images of atoms and molecules using a modern TEM or STEM electron microscope. Applications sections have been updated - these include the semiconductor industry, superconductor research, solid state chemistry and nanoscience, and metallurgy, mineralogy, condensed matter physics, materials science and material on cryo-electron microscopy for structural biology. New or expanded sections have been added on electron holography, aberration correction, field-emission guns, imaging filters, super-resolution methods, Ptychography, Ronchigrams, tomogr...

High Resolution Thz and FIR Spectroscopy of SOCl_2

Science.gov (United States)

Martin-Drumel, M. A.; Cuisset, A.; Sadovskii, D. A.; Mouret, G.; Hindle, F.; Pirali, O.

2013-06-01

Thionyl chloride (SOCl_2) is an extremely powerful oxidant widely used in industrial processes and playing a role in the chemistry of the atmosphere. In addition, it has a molecular configuration similar to that of phosgene (COCl_2), and is therefore of particular interest for security and defense applications. Low resolution vibrational spectra of gas phase SOCl_2 as well as high resolution pure rotational transitions up to 25 GHz have previously been investigated. To date no high resolution data are reported at frequencies higher than 25 GHz. We have investigated the THz absorption spectrum of SOCl_2 in the spectral region 70-650 GHz using a frequency multiplier chain coupled to a 1 m long single path cell containing a pressure of about 15 μbar. At the time of the writing, about 8000 pure rotational transitions of SO^{35}Cl_2 with highest J and K_a values of 110 and 50 respectively have been assigned on the spectrum. We have also recorded the high resolution FIR spectra of SOCl_2 in the spectral range 50-700 wn using synchrotron radiation at the AILES beamline of SOLEIL facility. A White-type cell aligned with an absorption path length of 150 m has been used to record, at a resolution of 0.001 wn, two spectra at pressures of 5 and 56 μbar of SOCl_2. On these spectra all FIR modes of SOCl_2 are observed (ν_2 to ν_6) and present a resolved rotational structure. Their analysis is in progress. T. J. Johnson et al., J. Phys. Chem. A 107, 6183 (2003) D. E. Martz and R. T. Lagemann, J. Chem. Phys. 22,1193 (1954) H. S. P. Müller and M. C. L. Gerry, J. Chem. Soc. Faraday Trans. 90, 3473 (1994)

Effect of pre-existing crystallographic preferred orientation on the rheology of Carrara marble

NARCIS (Netherlands)

de Raadt, W.S.; Burlini, L.; Kunze, K.; Spiers, C.J.

2014-01-01

Abstract Localized deformation during high temperature plastic flow is frequently attributed to mechanical weakening caused by grain size reduction and, in some cases, by the development of a crystallographic preferred orientation (CPO). This study aims to investigate experimentally the contribution