Search results for: crystallographic%20analysis.

Authors: Tudor Petreuş, Andrei Neamţu, Cristina Dascălu, Paul Dan Sîrbu, Carmen E. Cotrutz

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Matrix metalloproteinases (MMP) are a class of structural and functional related enzymes involved in altering the natural elements of the extracellular matrix. Most of the MMP structures are cristalographycally determined and published in WorldWide ProteinDataBank, isolated, in full structure or bound to natural or synthetic inhibitors. This study proposes an algorithm to replace missing crystallographic structures in PDB database. We have compared the results of a chosen docking algorithm with a known crystallographic structure in order to validate enzyme sites reconstruction there where crystallographic data are missing.

Keywords: matrix metalloproteinases, molecular docking, structure superposition, surface complementarity.

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Authors: Takashi Sakai, Itaru Kumisawa

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Because die drawing requires insertion of a die, a plug, or a mandrel, higher precision and efficiency are demanded for drawing equipment for a tube having smaller diameter. Manufacturing of such tubes is also accompanied by problems such as cracking and fracture. We specifically examine dieless drawing, which is less affected by these drawing-related difficulties. This deformation process is governed by a similar principle to that of reduction in diameter when pulling a heated glass tube. We conducted dieless drawing of SUS304 stainless steel microtubes under various conditions with three factor parameters of heating temperature, area reduction, and drawing speed. We used SEM-EBSD to observe the processing condition effects on microstructural elements. As the result of this study, crystallographic orientation of microtube is clear by using SEM-EBSD analysis.

Keywords: Microtube, dieless drawing, IPF, inverse pole figure, GOS, grain orientation spread, crystallographic analysis.

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Authors: S. Krishnan, J. Dumbre, S. Bhatt, Esther T. Akinlabi, R. Ramalingam

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The localized corrosion behavior of laser surface melted 304L austenitic stainless steel was studied by potentiodynamic polarization test. The extent of improvement in corrosion resistance was governed by the preferred orientation and the percentage of delta ferrite present on the surface of the laser melted sample. It was established by orientation imaging microscopy that the highest pitting potential value was obtained when grains were oriented in the most close- packed [101] direction compared to the random distribution of the base metal and other laser surface melted samples oriented in [001] direction. The sample with lower percentage of ferrite had good pitting resistance.

Keywords: Crystallographic orientation, Ferrite percentage, Laser melting, Pitting corrosion, 304L SS.

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Authors: Takashi Sakai, Saori Yoshikawa, Hideo Morimoto

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To understand the material characteristics of singleand poly-crystals of pure copper, the respective relationships between crystallographic orientations and microstructures, and the bending and mechanical properties were examined. And texture distribution is also analyzed. A bending test is performed in a SEM apparatus and while its behaviors are observed in situ. Furthermore, some analytical results related to crystal direction maps, inverse pole figures, and textures were obtained from EBSD analyses.

Keywords: Pure Copper, Bending, Single Crystal, SEM-EBSD Analysis, Texture, Microstructure

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Authors: Yuko Matayoshi, Takashi Sakai, Ying-jun Jin, Jun-ichi Koyama

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To elucidate the material characteristics of single crystals of pure aluminum and copper, the respective relations between crystallographic orientations and microstructures were examined, along with bending and mechanical properties. The texture distribution was also analysed. Bending tests were performed in a SEM apparatus while its behaviors were observed. Some analytical results related to crystal direction maps, inverse pole figures, and textures were obtained from electron backscatter diffraction (EBSD) analyses.

Keywords: Pure aluminum, Pure copper, Single crystal, Bending, SEM-EBSD analysis, Texture, Microstructure.

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Authors: Takashi Sakai, Hitoshi Omata, Jun-Ichi Koyama

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To improve the material characteristics of single- and poly-crystals of pure copper, the respective relationships between crystallographic orientations and microstructures, and the bending and mechanical properties were examined. And texture distribution is also analyzed. A grain refinement procedure was performed to obtain a grained structure. Furthermore, some analytical results related to crystal direction maps, inverse pole figures, and textures were obtained from SEM-EBSD analyses. Results showed that these grained metallic materials have peculiar springback characteristics with various bending angles.

Keywords: Pure Copper, Grain Refinement, Environmental Materials, SEM-EBSD Analysis, Texture, Microstructure

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Authors: Jun Yop An, Kyoung Ryoung Park, Jung-Gyu Lee, Hyung-Seop Youn, Jung-Yeon Kang, Gil Bu Kang, Soo Hyun Eom

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MinC plays an important role in bacterial cell division system by inhibiting FtsZ assembly. However, the molecular mechanism of the action is poorly understood. E. coli MinC Nterminus domain was purified and crystallized using 1.4 M sodium citrate pH 6.5 as a precipitant. X-ray diffraction data was collected and processed to 2.3 Å from a native crystal. The crystal belonged to space group P212121, with the unit cell parameters a = 52.7, b = 54.0, c = 64.7 Å. Assuming the presence of two molecules in the asymmetric unit, the Matthews coefficient value is 1.94 Å3 Da-1, which corresponds to a solvent content of 36.5%. The overall structure of MinCN is observed as a dimer form through anti-parallel ß-strand interaction.

Keywords: MinC, Cell division, Crystallization.

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Authors: Branko Skoric, Aleksandar Miletic, Pal Terek, Lazar Kovacevic, Milan Kukuruzovic

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In this paper, we present the results of a study of TiN thin films which are deposited by a Physical Vapour Deposition (PVD) and Ion Beam Assisted Deposition (IBAD). In the present investigation the subsequent ion implantation was provided with N⁵⁺ ions. The ion implantation was applied to enhance the mechanical properties of surface. The thin film deposition process exerts a number of effects such as crystallographic orientation, morphology, topography, densification of the films. A variety of analytic techniques were used for characterization, such as scratch test, calo test, Scanning electron microscopy (SEM), Atomic Force Microscope (AFM), X-ray diffraction (XRD) and Energy Dispersive X-ray analysis (EDAX).

Keywords: Steel, coating, super hard, ion implantation, nanohardness.

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Authors: Takashi Sakai, Shinsaku Kikuta, Jun-ichi Koyama

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Using a texture database, a statistical estimation of spring-back was conducted in this study on the basis of statistical analysis. Both spring-back in bending deformation and experimental data related to the crystal orientation show significant dispersion. Therefore, a probabilistic statistical approach was established for the proper quantification of these values. Correlation was examined among the parameters F(x) of spring-back, F(x) of the buildup fraction to three orientations after 92° bending, and F(x) at an as-received part on the basis of the three-parameter Weibull distribution. Consequent spring-back estimation using a texture database yielded excellent estimates compared with experimental values.

Keywords: Bending, Spring-back, Database, Crystallographic Orientation, Texture, SEM-EBSD, Weibull distribution, Statistical analysis.

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Authors: Mahendran Samykano, Ram Mohan, Shyam Aravamudhan

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The objective of this work is to study the effect of two key factors - external magnetic field and applied current density during template-based electrodeposition of nickel nanowires using an electrode distance of 20 mm. Morphology, length, crystallite size and crystallographic characterization of the grown nickel nanowires at an electrode distance of 20mm are presented. For this electrode distance of 20 mm, these two key electrodeposition factors when coupled was found to reduce crystallite size with a higher growth length and preferred orientation of Ni crystals. These observed changes can be inferred to be due to coupled interaction forces induced by the intensity of applied electric field (current density) and external magnetic field known as magnetohydrodynamic (MHD) effect during the electrodeposition process.

Keywords: Anodic alumina oxide, electrodeposition, nanowires, nickel.

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Authors: Syed Bahari Ramadzan Syed Adnan, Nor Sabirin Mohamed, Norwati K.A

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In this study, Li4SiO4 powder was successfully synthesized via sol gel method followed by drying at 150oC. Lithium oxide, Li2O and silicon oxide, SiO2 were used as the starting materials with citric acid as the chelating agent. The obtained powder was then sintered at various temperatures. Crystallographic phase analysis, morphology and ionic conductivity were investigated systematically employing X-ray diffraction, Fourier Transform Infrared, Scanning Electron Microscopy and AC impedance spectroscopy. XRD result showed the formation of pure monoclinic Li4SiO4 crystal structure with lattice parameters a = 5.140 Å, b = 6.094 Å, c = 5.293 Å, β = 90o in the sample sintered at 750oC. This observation was confirmed by FTIR analysis. The bulk conductivity of this sample at room temperature was 3.35 × 10-6 S cm-1 and the highest bulk conductivity of 1.16 × 10-4 S cm-1 was obtained at 100°C. The results indicated that, the Li4SiO4 compound has potential to be used as host for LISICON structured solid electrolyte for low temperature application.

Keywords: Conductivity, LISICON, Li4SiO4, Solid electrolyte, Structure.

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Authors: Kamyar Shameli, Mansor Bin Ahmad, Wan Md Zin Wan Yunus, Nor Azowa Ibrahim, Maryam Jokar, Majid Darroudi

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Silver/polylactide nanocomposites (Ag/PLA-NCs) were synthesized via chemical reduction method in diphase solvent. Silver nitrate and sodium borohydride were used as a silver precursor and reducing agent in the polylactide (PLA). The properties of Ag/PLA-NCs were studied as a function of the weight percentages of silver nanoparticles (8, 16 and 32 wt% of Ag-NPs) relative to the weight of PLA. The Ag/PLA-NCs were characterized by Xray diffraction (XRD), transmission electron microscopy (TEM), electro-optical microscopy (EOM), UV-visible spectroscopy (UV-vis) and Fourier transform infrared spectroscopy (FT-IR). XRD patterns confirmed that Ag-NPs crystallographic planes were face centered cubic (fcc) type. TEM images showed that mean diameters of Ag-NPs were 3.30, 3.80 and 4.80 nm. Electro-optical microscopy revealed excellent dispersion and interaction between Ag-NPs and PLA films. The generation of silver nanoparticles was confirmed from the UVvisible spectra. FT-IR spectra showed that there were no significant differences between PLA and Ag/PLA-NCs films. The synthesized Ag/PLA-NCs were stable in organic solution over a long period of time without sign of precipitation.

Keywords: Nanocomposites, Polylactide, Silver Nanoparticles, Sodium Borohydride, Transmission Electron Microscopy.

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Authors: Anushree, Chhaya Sharma, Satish Kumar

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Catalytic wet air oxidation (CWAO) is normally carried out at elevated temperature and pressure. This work investigates the potential of NiO-CeO₂ nano-catalyst in CWAO of paper industry wastewater under milder operating conditions of 90 °C and 1 atm. The NiO-CeO₂ nano-catalysts were synthesized by a simple co-precipitation method and characterized by X-ray diffraction (XRD), before and after use, in order to study any crystallographic change during experiment. The extent of metal-leaching from the catalyst was determined using the inductively coupled plasma optical emission spectrometry (ICP-OES). The catalytic activity of nano-catalysts was studied in terms of total organic carbon (TOC), adsorbable organic halides (AOX) and chlorophenolics (CHPs) removal. Interestingly, mixed oxide catalysts exhibited higher activity than the corresponding single-metal oxides. The maximum removal efficiency was achieved with Ce₄₀Ni₆₀ catalyst. The results indicate that the CWAO process is efficient in removing the priority organic pollutants from wastewater, as it exhibited up to 59% TOC, 55% AOX, and 54 % CHPs removal.

Keywords: Nano-materials, NiO-CeO2, wastewater, wet air oxidation.

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Authors: Abada Ahmed, Hiadsi Said, Ouahrani Tarik, Amrani Bouhalouane, Amara Kadda

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Using the first-principles full-potential linearized augmented plane wave plus local orbital (FP-LAPW+lo) method based on density functional theory (DFT), we have investigated the electronic structure and magnetism of full Heusler alloys Co2ZrGe and Co2NbB. These compounds are predicted to be half-metallic ferromagnets (HMFs) with a total magnetic moment of 2.000
B per formula unit, well consistent with the Slater-Pauling rule. Calculations show that both the alloys have an indirect band gaps, in the minority-spin channel of density of states (DOS), with values of 0.58 eV and 0.47 eV for Co2ZrGe and Co2NbB, respectively. Analysis of the DOS and magnetic moments indicates that their magnetism is mainly related to the d-d hybridization between the Co and Zr (or Nb) atoms. The half-metallicity is found to be relatively robust against volume changes. In addition, an atom inside molecule AIM formalism and an electron localization function ELF were also adopted to study the bonding properties of these compounds, building a bridge between their electronic and bonding behavior. As they have a good crystallographic compatibility with the lattice of semiconductors used industrially and negative calculated cohesive energies with considerable absolute values these two alloys could be promising magnetic materials in the spintronic field.

Keywords: Electronic properties, full Heusler alloys, halfmetallic ferromagnets, magnetic properties.

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Authors: I. Kurashvili, A. Sichinava, G. Bokuchava, G. Darsavelidze

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Si-Ge solid solutions (bulk poly- and mono-crystalline samples, thin films) are characterized by high perspectives for application in semiconductor devices, in particular, optoelectronics and microelectronics. From this point of view, complex studying of structural state of the defects and structural-sensitive physical properties of Si-Ge solid solutions depending on the contents of Si and Ge components is very important. Present work deals with the investigations of microstructure, microhardness, internal friction and shear modulus of Si1-xGex(x≤0,02) bulk monocrystals conducted at room temperature. Si-Ge bulk crystals were obtained by Czochralski method in [111] crystallographic direction. Investigated monocrystalline Si-Ge samples are characterized by p-type conductivity and carriers’ concentration 5.1014-1.1015cm-3. Microhardness was studied on Dynamic Ultra Micro hardness Tester DUH-201S with Berkovich indenter. Investigate samples are characterized with 0,5x0,5x(10-15)mm3 sizes, oriented along [111] direction at torsion oscillations ≈1Hz, multistage changing of internal friction and shear modulus has been revealed in an interval of strain amplitude of 10-5-5.10-3. Critical values of strain amplitude have been determined at which hysteretic changes of inelastic characteristics and microplasticity are observed. The critical strain amplitude and elasticity limit values are also determined. Dynamic mechanical characteristics decreasing trend is shown with increasing Ge content in Si-Ge solid solutions. Observed changes are discussed from the point of view of interaction of various dislocations with point defects and their complexes in a real structure of Si-Ge solid solutions.

Keywords: Internal friction, microhardness, relaxation processes, shear modulus, Si-Ge.

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Authors: Qing Liu, Jean-Fabien Capsal, Claude Richard

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In this current contribution, authors are dedicated to investigate influence of the crystal lamellae orientation on electromechanical behaviors of relaxor ferroelectric Poly (vinylidene fluoride –trifluoroethylene -chlorotrifluoroethylene) (P(VDF-TrFE-CTFE)) films by control of polymer microstructure, aiming to picture the full map of structure-property relationship. In order to define their crystal orientation films, terpolymer films were fabricated by solution-casting, stretching and hot-pressing process. Differential scanning calorimetry, impedance analyzer, and tensile strength techniques were employed to characterize crystallographic parameters, dielectric permittivity, and elastic Young’s modulus respectively. In addition, large electrical induced out-of-plane electrostrictive strain was obtained by cantilever beam mode. Consequently, as-casted pristine films exhibited surprisingly high electrostrictive strain 0.1774% due to considerably small value of elastic Young’s modulus although relatively low dielectric permittivity. Such reasons contributed to large mechanical elastic energy density. Instead, due to 2 folds increase of elastic Young’s modulus and less than 50% augmentation of dielectric constant, fullycrystallized film showed weak electrostrictive behavior and mechanical energy density as well. And subjected to mechanical stretching process, Film C exhibited stronger dielectric constant and out-performed electrostrictive strain over Film B because edge-on crystal lamellae orientation induced by uniaxially mechanical stretch. Hot-press films were compared in term of cooling rate. Rather large electrostrictive strain of 0.2788% for hot-pressed Film D in quenching process was observed although its dielectric permittivity equivalent to that of pristine as-casted Film A, showing highest mechanical elastic energy density value of 359.5 J/m3. In hot-press cooling process, dielectric permittivity of Film E saw values at 48.8 concomitant with ca.100% increase of Young’s modulus. Films with intermediate mechanical energy density were obtained.

Keywords: Crystal orientation, electrostrictive strain, mechanical energy density, permittivity, relaxor ferroelectric.

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Authors: Alan Luo, Hunter N. B. Moseley

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Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for X-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across X-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: Biomacromolecular structure, coenzyme, electron density discrepancy analysis, X-ray crystallography.

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