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

Anisotropic merging and splitting of dipolar Bose-Einstein condensates

We study the merging and splitting of quasi-two-dimensional Bose-Einstein condensates with strong dipolar interactions. We observe that if the dipoles have a non-zero component in the plane of the condensate, the dynamics of merging or splitting along two orthogonal directions, parallel and perpendicular to the projection of dipoles on the plane of the condensate, are different. The anisotropic merging and splitting of the condensate is a manifestation of the anisotropy of the roton-like mode in the dipolar system. The difference in dynamics disappears if the dipoles are oriented at right angles to the plane of the condensate as in this case the Bogoliubov dispersion, despite having roton-like features, is isotropic.

Nonlinear analysis of a thin pre-twisted and delaminated anisotropic strip

The present work is aimed at the development of an efficient mathematical model to assess the degradation in the stiffness properties of an anisotropic strip due to delamination. In particular, the motive is to capture those nonlinear effects in a strip that arise due to the geometry of the structure, in the presence of delamination. The variational asymptotic method (VAM) is used as a mathematical tool to simplify the original 3D problem to a 1D problem. Further simplification is achieved by modeling the delaminated structure by a sublaminate approach. By VAM, a 2D nonlinear sectional analysis is carried out to determine compact expression for the stiffness terms. The stiffness terms, both linear and nonlinear, are derived as functions of delamination length and location in closed form. In general, the results from the analysis include fully coupled nonlinear 1D stiffness coefficients, 3D strain field, 3D stress field, and in-plane and warping fields. In this work, the utility of the model is demonstrated for a static case, and its capability to capture the trapeze effect in the presence of delamination is investigated and compared with results available in the literature.

Instabilities in a fluid overlying an inclined anisotropic and inhomogeneous porous layer

In this paper, linear stability analysis on a Newtonian fluid film flowing under the effect of gravity over an inclined porous medium saturated with the same fluid in isothermal condition is carried out. The focus is placed on the effect of the anisotropic and inhomogeneous variations in the permeability of the porous medium on the shear mode and surface mode instabilities. The fluid-porous system is modelled by a coupled two-dimensional Navier-Stokes/Darcy problem. The perturbation equations are solved numerically using the Chebyshev collocation method. Detailed stability characteristics as a function of the depth ratio (the ratio of the depth of the fluid layer to that of the porous layer), the anisotropic parameter (the ratio of the permeability in the direction of the basic flow to that in the direction transverse to the basic flow) and the inhomogeneity functions are presented.

A strongly coupled anisotropic fluid from dilaton driven holography

We consider a system consisting of 5 dimensional gravity with a negative cosmological constant coupled to a massless scalar, the dilaton. We construct a black brane solution which arises when the dilaton satisfies linearly varying boundary conditions in the asymptotically AdS(5) region. The geometry of this black brane breaks rotational symmetry while preserving translational invariance and corresponds to an anisotropic phase of the system. Close to extremality, where the anisotropy is big compared to the temperature, some components of the viscosity tensor become parametrically small compared to the entropy density. We study the quasi normal modes in considerable detail and find no instability close to extremality. We also obtain the equations for fluid mechanics for an anisotropic driven system in general, working upto first order in the derivative expansion for the stress tensor, and identify additional transport coefficients which appear in the constitutive relation. For the fluid of interest we find that the parametrically small viscosity can result in a very small force of friction, when the fluid is enclosed between appropriately oriented parallel plates moving with a relative velocity.

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

Anisotropic isometric fluctuation relations in experiment and theory on a self-propelled rod

The isometric fluctuation relation (IFR) P. I. Hurtado et al., Proc. Natl. Acad. Sci. USA 108, 7704 (2011)] relates the relative probability of current fluctuations of fixed magnitude in different spatial directions. We test its validity in an experiment on a tapered rod, rendered motile by vertical vibration and immersed in a sea of spherical beads. We analyze the statistics of the velocity vector of the rod and show that they depart significantly from the IFR of Hurtado et al. Aided by a Langevin-equation model we show that our measurements are largely described by an anisotropic generalization of the IFR R. Villavicencio et al., Europhys. Lett. 105, 30009 (2014)], with no fitting parameters, but with a discrepancy in the prefactor whose origin may lie in the detailed statistics of the microscopic noise. The experimentally determined large-deviation function of the velocity vector has a kink on a curve in the plane.

Viscosity bound for anisotropic superfluids in higher derivative gravity

In the present paper, based on the principles of gauge/gravity duality we analytically compute the shear viscosity to entropy (eta/s) ratio corresponding to the super fluid phase in Einstein Gauss-Bonnet gravity. From our analysis we note that the ratio indeed receives a finite temperature correction below certain critical temperature (T < T-c). This proves the non universality of eta/s ratio in higher derivative theories of gravity. We also compute the upper bound for the Gauss-Bonnet coupling (lambda) corresponding to the symmetry broken phase and note that the upper bound on the coupling does not seem to change as long as we are close to the critical point of the phase diagram. However the corresponding lower bound of the eta/s ratio seems to get modified due to the finite temperature effects.

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/.

Stability of Poiseuille flow in a fluid overlying an anisotropic and inhomogeneous porous layer

We present the linear stability analysis of horizontal Poiseuille flow in a fluid overlying a porous medium with anisotropic and inhomogeneous permeability. The generalized Darcy model is used to describe the flow in the porous medium with the Beavers-Joseph condition at the interface of the two layers and the eigenvalue problem is solved numerically. The effect of major system parameters on the stability characteristics is addressed in detail. It is shown that the anisotropic and inhomogeneous modulation of the permeability of the underlying porous layer provides an effective means for passive control of the flow stability.

Anisotropic magnetic couplings and structure-driven canted to collinear transitions in Sr2IrO4 by magnetically constrained noncollinear DFT

We study the canted magnetic state in Sr2IrO4 using fully relativistic density functional theory (DFT) including an on-site Hubbard U correction. A complete magnetic phase diagram with respect to the tetragonal distortion and the rotation of IrO6 octahedra is constructed, revealing the presence of two types of canted to collinear magnetic transitions: a spin-flop transition with increasing tetragonal distortion and a complete quenching of the basal weak ferromagnetic moment below a critical octahedral rotation. Moreover, we put forward a scheme to study the anisotropic magnetic couplings by mapping magnetically constrained noncollinear DFT onto a general spin Hamiltonian. This procedure allows for the simultaneous account and direct control of the lattice, spin, and orbital interactions within a fully ab initio scheme. We compute the isotropic, single site anisotropy and Dzyaloshinskii-Moriya (DM) coupling parameters, and clarify that the origin of the canted magnetic state in Sr2IrO4 arises from the structural distortions and the competition between isotropic exchange and DM interactions.