Ex Situ X-ray Diffraction, X-ray Absorption Near Edge Structure, Electron Spin Resonance, and Transmission Electron Microscopy Study of the Hydrothermal Crystallization of Vanadium Oxide Nanotubes: An Insight into the Mechanism of Formation

The nucleation and growth of vanadium oxide nanotubes (VOx-NT) have been followed by a combination of numerous ex situ techniques. long the hydrothermal process. Intermediate solid phases extracted at different reaction times have been characterized by powder X-ray diffraction, scanning and transmission electron microscopy, electron spin resonance, and V-K edge :X-ray absorption near-edge structure spectroscopy. The supernatant vanadate solutions extracted during the hydrothermal treatment have been studied by liquid V-51 NMR and flame. spectroscopy. For short durations of the hydrothermal synthesis, the initial V2O5-surfactant intercalate. is progressively transformed into VOx-NT whose crystallization starts to be detected after a hydrothermal treatment of 24 h. Upon heating from 24 h to 7 days, VOx-NT are obtained in larger amount and with an improved crystallinity. The detection of soluble amines and cyclic metavanadate V4O12](4-) in the supernatant solution along the hydrothermal process suggests that VOx-NT result from a dissolution precipitation mechanism. Metavanadate species V4O12](4-) could behave as molecular precursors in the polymerization reactions leading to VOx-NT.

Determination of electric field at and near the focus of a cylindrical lens for applications in fluorescence microscopy

We present an explicit computable integral solution of the electric field generated at the focal region of a cylindrical lens. This representation is based on vectorial diffraction theory and further enables the computation of the system point spread function of a cylindrical lens. It is assumed that there is no back-scattering and the contribution from the evanescent field is negligible. Stationary phase approximation along with the Fresnel transmission coefficients are employed for evaluating the polarization dependent electric field components. Studies were carried out to determine the polarization effects and to calculate the system resolution. The effect of s -, p - and randomly polarized light is studied on the fixed sample (electric dipole is fixed in space). Proposed approach allows better understanding of electric field effects at the focus of a cylindrical aplanatic system. This opens up future developments in the field of fluorescence microscopy and optical imaging. (C) 2013 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Crystallization and preliminary X-ray diffraction studies of Staphylococcus aureus homoserine dehydrogenase

Staphylococcus aureus is a Gram-positive nosocomial pathogen. The prevalence of multidrug-resistant S. aureus strains in both hospital and community settings makes it imperative to characterize new drug targets to combat S. aureus infections. In this context, enzymes involved in cell-wall maintenance and essential amino-acid biosynthesis are significant drug targets. Homoserine dehydrogenase (HSD) is an oxidoreductase that is involved in the reversible conversion of l-aspartate semialdehyde to l-homoserine in a dinucleotide cofactor-dependent reduction reaction. HSD is thus a crucial intermediate enzyme linked to the biosynthesis of several essential amino acids such as lysine, methionine, isoleucine and threonine.

X-ray diffraction and Mossbauer spectroscopy studies of cementite dissolution in cold-drawn pearlitic steel

Cementite dissolution in cold-drawn pearlitic steel (0.8 wt.% carbon) wires has been studied by quantitative X-ray diffraction (XRD) and Mossbauer spectroscopy up to drawing strain 1.4. Quantification of cementite-phase fraction by Rietveld analysis has confirmed more than 50% dissolution of cementite phase at drawing strain 1.4. It is found that the lattice parameter of the ferrite phase determined by Rietveld refinement procedure remains nearly unchanged even after cementite dissolution. This confirms that the carbon atoms released after cementite dissolution do not dissolve in the ferrite lattice as Fe-C interstitial solid solution. Detailed analysis of broadening of XRD line profiles for the ferrite phase shows high density of dislocations (approximate to 10(15)/m(2)) in the ferrite matrix at drawing strain 1.4. The results suggest a dominant role of 111 screw dislocations in the cementite dissolution process. Post-deformation heat treatment leads to partial annihilation of dislocations and restoration of cementite phase. Based on these experimental observations, further supplemented by TEM studies, we have suggested an alternative thermodynamic mechanism of the dissolution process.

Successful data recovery from oscillation photographs containing strong polycrystalline diffraction rings from an unknown small-molecule contaminant: preliminary structure solution of Salmonella typhimurium pyridoxal kinase (PdxK)

Pyridoxal kinase (PdxK; EC 2.7.1.35) belongs to the phosphotransferase family of enzymes and catalyzes the conversion of the three active forms of vitamin B-6, pyridoxine, pyridoxal and pyridoxamine, to their phosphorylated forms and thereby plays a key role in pyridoxal 5 `-phosphate salvage. In the present study, pyridoxal kinase from Salmonella typhimurium was cloned and overexpressed in Escherichia coli, purified using Ni-NTA affinity chromatography and crystallized. X-ray diffraction data were collected to 2.6 angstrom resolution at 100 K. The crystal belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with unitcell parameters a = 65.11, b = 72.89, c = 107.52 angstrom. The data quality obtained by routine processing was poor owing to the presence of strong diffraction rings caused by a polycrystalline material of an unknown small molecule in all oscillation images. Excluding the reflections close to powder/polycrystalline rings provided data of sufficient quality for structure determination. A preliminary structure solution has been obtained by molecular replacement with the Phaser program in the CCP4 suite using E. coli pyridoxal kinase (PDB entry 2ddm) as the phasing model. Further refinement and analysis of the structure are likely to provide valuable insights into catalysis by pyridoxal kinases.

Diffraction tomography from intensity measurements: an evolutionary stochastic search to invert experimental data

We develop iterative diffraction tomography algorithms, which are similar to the distorted Born algorithms, for inverting scattered intensity data. Within the Born approximation, the unknown scattered field is expressed as a multiplicative perturbation to the incident field. With this, the forward equation becomes stable, which helps us compute nearly oscillation-free solutions that have immediate bearing on the accuracy of the Jacobian computed for use in a deterministic Gauss-Newton (GN) reconstruction. However, since the data are inherently noisy and the sensitivity of measurement to refractive index away from the detectors is poor, we report a derivative-free evolutionary stochastic scheme, providing strictly additive updates in order to bridge the measurement-prediction misfit, to arrive at the refractive index distribution from intensity transport data. The superiority of the stochastic algorithm over the GN scheme for similar settings is demonstrated by the reconstruction of the refractive index profile from simulated and experimentally acquired intensity data. (C) 2014 Optical Society of America

Efficient generation of diffraction-limited multi-sheet pattern for biological imaging

We demonstrate a new technique to generate multiple light-sheets for fluorescence microscopy. This is possible by illuminating the cylindrical lens using multiple copies of Gaussian beams. A diffraction grating placed just before the cylindrical lens splits the incident Gaussian beam into multiple beams traveling at different angles. Subsequently, this gives rise to diffraction-limited light-sheets after the Gaussian beams pass through the combined cylindrical lens-objective sub-system. Direct measurement of field at and around the focus of objective lens shows multi-sheet pattern with an average thickness of 7.5 mu m and inter-sheet separation of 380 mu m. Employing an independent orthogonal detection sub-system, we successfully imaged fluorescently-coated yeast cells (approximate to 4 mu m) encaged in agarose gel-matrix. Such a diffraction-limited sheet-pattern equipped with dedicated detection system may find immediate applications in the field of optical microscopy and fluorescence imaging. (C) 2015 Optical Society of America

Online_DPI: a web server to calculate the diffraction precision index for a protein structure

An online computing server, Online_DPI (where DPI denotes the diffraction precision index), has been created to calculate the `Cruickshank DPI' value for a given three-dimensional protein or macromolecular structure. It also estimates the atomic coordinate error for all the atoms available in the structure. It is an easy-to-use web server that enables users to visualize the computed values dynamically on the client machine. Users can provide the Protein Data Bank (PDB) identification code or upload the three-dimensional atomic coordinates from the client machine. The computed DPI value for the structure and the atomic coordinate errors for all the atoms are included in the revised PDB file. Further, users can graphically view the atomic coordinate error along with `temperature factors' (i.e. atomic displacement parameters). In addition, the computing engine is interfaced with an up-to-date local copy of the Protein Data Bank. New entries are updated every week, and thus users can access all the structures available in the Protein Data Bank. The computing engine is freely accessible online at http://cluster.physics.iisc.ernet.in/dpi/.

Mono layer to Interdigitated Partial Bilayer Smectic C Transition in Thiophene-Based Spacer Mesogens: X-ray Diffraction and C-13 Nuclear Magnetic Resonance Studies

Mesophase organization of molecules built with thiophene at the center and linked via flexible spacers to rigid side arm core units and terminal alkoxy chains has been investigated. Thirty homologues realized by varying the span of the spacers as well as the length of the terminal chains have been studied. In addition to the enantiotropic nematic phase observed for all the mesogens, the increase of the spacer as well as the terminal chain lengths resulted in the smectic C phase. The molecular organization in the smectic phase as investigated by temperature dependent X-ray diffraction measurements revealed an interesting behavior that depended on the length of the spacer vis-a-vis the length of the terminal chain. Thus, a tilted interdigitated partial bilayer organization was observed for molecules with a shorter spacer length, while a tilted monolayer arrangement was observed for those with a longer spacer length. High-resolution solid state C-13 NMR studies carried out for representative mesogens indicated a U-shape for all the molecules, indicating that intermolecular interactions and molecular dynamics rather than molecular shape are responsible for the observed behavior. Models for the mesophase organization have been considered and the results understood in terms of segregation of incompatible parts of the mesogens combined with steric frustration leading to the observed lamellar order.

Neutron powder diffraction study of Ba3ZnRu2-xIrxO9 (x=0, 1, 2) with 6H-type perovskite structure

The triple perovskites Ba3ZnRu2-xIrxO9 with x = 0, 1, and 2 are insulating compounds in which Ru(Ir) cations form a dimer state. Polycrystalline samples of these materials were studied using neutron powder diffraction (NPD) at 10 and 295 K. No structural transition nor evidence of long range magnetic order was observed within the investigated temperature range. The results from structural refinements of the NPD data and its polyhedral analysis are presented, and discussed as a function of Ru/Ir content. (C) 2015 Elsevier Masson SAS. All rights reserved.

Neutron diffraction, Mossbauer effect and Electron Paramagnetic Resonance studies on multiferroic Pb(Fe2/3W1/3)O-3

Multiferroic Pb(Fe2/3W1/3)O-3 ceramics were synthesized via a modified two-stage Columbite method. Single phase formation was confirmed from the analysis of x-ray and neutron diffraction patterns recorded at room temperature. Structural analysis of the diffraction data reveals cubic phase (space group Pm-3m) for the title compound. Magnetic structure of the title compound at room temperature exhibits G-type antiferromagnetic structure. The Mossbauer spectroscopy and Electron Paramagnetic Resonance (EPR) studies were carried out at 300 K. The isomer shift and quadrupole splitting of the Mossbauer spectra confirms the trivalent state of iron (Fe3+). The Mossbauer spectra also suggest that the iron and tungsten are randomly distributed at the octahedral, B site. EPR spectra show a single broad line associated with Fe3+ ions. Both spectra clearly exhibit weak ferromagnetic behaviour of Pb(Fe2/3W1/3)O-3 ceramic at 300 K. Considering neutron diffraction, Mossbauer and EPR results together, it may be stated here that Pb(Fe2/3W1/3)O-3 exhibits antiferromagnetic behavior along with weak ferromagnetism at room temperature.

Magnetic structures and magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied by neutron powder diffraction

The magnetic structures and the magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied using neutron powder diffraction are reported. Magnetic phase transitions are identified at T-N(Fe/Mn) approximate to 295K where a paramagnetic-to-antiferromagnetic transition occurs in the Fe/Mn sublattice, T-SR(Fe/Mn) approximate to 26K where a spin-reorientation transition occurs in the Fe/Mn sublattice and T-N(R) approximate to 2K where Tb-ordering starts to manifest. At 295 K, the magnetic structure of the Fe/Mn sublattice in TbFe0.5Mn0.5O3 belongs to the irreducible representation Gamma(4) (G(x)A(y)F(z) or Pb'n'm). A mixed-domain structure of (Gamma(1) + Gamma(4)) is found at 250K which remains stable down to the spin re-orientation transition at T-SR(Fe/Mn) approximate to 26K. Below 26K and above 250 K, the majority phase (>80%) is that of Gamma(4). Below 10K the high-temperature phase Gamma(4) remains stable till 2K. At 2 K, Tb develops a magnetic moment value of 0.6(2) mu(B)/f.u. and orders long-range in F-z compatible with the Gamma(4) representation. Our study confirms the magnetic phase transitions reported already in a single crystal of TbFe0.5Mn0.5O3 and, in addition, reveals the presence of mixed magnetic domains. The ratio of these magnetic domains as a function of temperature is estimated from Rietveld refinement of neutron diffraction data. Indications of short-range magnetic correlations are present in the low-Q region of the neutron diffraction patterns at T < T-SR(Fe/Mn). These results should motivate further experimental work devoted to measure electric polarization and magnetocapacitance of TbFe0.5Mn0.5O3. (C) 2016 AIP Publishing LLC.

Magnetic structures and magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied by neutron powder diffraction

The magnetic structures and the magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied using neutron powder diffraction are reported. Magnetic phase transitions are identified at T-N(Fe/Mn) approximate to 295K where a paramagnetic-to-antiferromagnetic transition occurs in the Fe/Mn sublattice, T-SR(Fe/Mn) approximate to 26K where a spin-reorientation transition occurs in the Fe/Mn sublattice and T-N(R) approximate to 2K where Tb-ordering starts to manifest. At 295 K, the magnetic structure of the Fe/Mn sublattice in TbFe0.5Mn0.5O3 belongs to the irreducible representation Gamma(4) (G(x)A(y)F(z) or Pb'n'm). A mixed-domain structure of (Gamma(1) + Gamma(4)) is found at 250K which remains stable down to the spin re-orientation transition at T-SR(Fe/Mn) approximate to 26K. Below 26K and above 250 K, the majority phase (>80%) is that of Gamma(4). Below 10K the high-temperature phase Gamma(4) remains stable till 2K. At 2 K, Tb develops a magnetic moment value of 0.6(2) mu(B)/f.u. and orders long-range in F-z compatible with the Gamma(4) representation. Our study confirms the magnetic phase transitions reported already in a single crystal of TbFe0.5Mn0.5O3 and, in addition, reveals the presence of mixed magnetic domains. The ratio of these magnetic domains as a function of temperature is estimated from Rietveld refinement of neutron diffraction data. Indications of short-range magnetic correlations are present in the low-Q region of the neutron diffraction patterns at T < T-SR(Fe/Mn). These results should motivate further experimental work devoted to measure electric polarization and magnetocapacitance of TbFe0.5Mn0.5O3. (C) 2016 AIP Publishing LLC.

Development of a spin polarized low energy electron diffraction system

We have designed and constructed a spin polarized low energy electron diffraction system working in the reflected electron pulse counting mode. This system is capable of measuring asymmetries due to spin-orbit and exchange interactions. Photoemission from a strained GaAs/GaAsP super lattice is used as the source of spin polarized electrons. Spin-orbit asymmetry is evaluated for Ir(100) single crystal at various energies. Subsequently, exchange asymmetry has been evaluated on 40 monolayer Fe deposited on Ir(100). This instrument proves to be useful in understanding structure and magnetism at surfaces. (C) 2016 AIP Publishing LLC.

Magnetic structures and magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied by neutron powder diffraction

The magnetic structures and the magnetic phase transitions in the Mn-doped orthoferrite TbFeO3 studied using neutron powder diffraction are reported. Magnetic phase transitions are identified at T-N(Fe/Mn) approximate to 295K where a paramagnetic-to-antiferromagnetic transition occurs in the Fe/Mn sublattice, T-SR(Fe/Mn) approximate to 26K where a spin-reorientation transition occurs in the Fe/Mn sublattice and T-N(R) approximate to 2K where Tb-ordering starts to manifest. At 295 K, the magnetic structure of the Fe/Mn sublattice in TbFe0.5Mn0.5O3 belongs to the irreducible representation Gamma(4) (G(x)A(y)F(z) or Pb'n'm). A mixed-domain structure of (Gamma(1) + Gamma(4)) is found at 250K which remains stable down to the spin re-orientation transition at T-SR(Fe/Mn) approximate to 26K. Below 26K and above 250 K, the majority phase (>80%) is that of Gamma(4). Below 10K the high-temperature phase Gamma(4) remains stable till 2K. At 2 K, Tb develops a magnetic moment value of 0.6(2) mu(B)/f.u. and orders long-range in F-z compatible with the Gamma(4) representation. Our study confirms the magnetic phase transitions reported already in a single crystal of TbFe0.5Mn0.5O3 and, in addition, reveals the presence of mixed magnetic domains. The ratio of these magnetic domains as a function of temperature is estimated from Rietveld refinement of neutron diffraction data. Indications of short-range magnetic correlations are present in the low-Q region of the neutron diffraction patterns at T < T-SR(Fe/Mn). These results should motivate further experimental work devoted to measure electric polarization and magnetocapacitance of TbFe0.5Mn0.5O3. (C) 2016 AIP Publishing LLC.