Crowding, molecular volume and plasticity: An assessment involving crystallography, NMR and simulations

The discrepancy between the X-ray and NMR structures of Mycobacterium tuberculosis peptidyl-tRNA hydrolase in relation to the functionally important plasticity of the molecule led to molecular dynamics simulations. The X-ray and the NMR studies along with the simulations indicated an inverse correlation between crowding and molecular volume. A detailed comparison of proteins for which X-ray and the NMR structures appears to confirm this correlation. In consonance with the reported results of the investigations in cellular compartments and aqueous solution, the comparison indicates that the crowding results in compaction of the molecule as well as change in its shape, which could specifically involve regions of the molecule important in function. Crowding could thus influence the action of proteins through modulation of the functionally important plasticity of the molecule. Selvaraj M, Ahmad R, Varshney U and Vijayan M 2012 Crowding, molecular volume and plasticity: An assessment involving crystallography, NMR and simulations. J. Biosci. 37 953-963] DOI 10.1007/s12038-012-9276-5

SOLVING VOLUME INTEGRAL EQUATION USING ScaLAPACK

In this article, we investigate the performance of a volume integral equation code on BlueGene/L system. Volume integral equation (VIE) is solved for homogeneous and inhomogeneous dielectric objects for radar cross section (RCS) calculation in a highly parallel environment. Pulse basis functions and point matching technique is used to convert the volume integral equation into a set of simultaneous linear equations and is solved using parallel numerical library ScaLAPACK on IBM's distributed-memory supercomputer BlueGene/L by different number of processors to compare the speed-up and test the scalability of the code.

Multi-objective optimization of satellite image registration using discrete Pparticle swarm optimisation

A new multi-sensor image registration technique is proposed based on detecting the feature corner points using modified Harris Corner Detector (HDC). These feature points are matched using multi-objective optimization (distance condition and angle criterion) based on Discrete Particle Swarm Optimization (DPSO). This optimization process is more efficient as it considers both the distance and angle criteria to incorporate multi-objective switching in the fitness function. This optimization process helps in picking up three corresponding corner points detected in the sensed and base image and thereby using the affine transformation, the sensed image is aligned with the base image. Further, the results show that the new approach can provide a new dimension in solving multi-sensor image registration problems. From the obtained results, the performance of image registration is evaluated and is concluded that the proposed approach is efficient.

A method for measurement of planar liquid volume fraction in dense sprays

A methodology for measurement of planar liquid volume fraction in dense sprays using a combination of Planar Laser-Induced Fluorescence (PLIF) and Particle/Droplet Imaging Analysis (PDIA) is presented in this work. The PLIF images are corrected for loss of signal intensity due to laser sheet scattering, absorption and auto-absorption. The key aspect of this work pertains to simultaneously solving the equations involving the corrected PLIF signal and liquid volume fraction. From this, a quantitative estimate of the planar liquid volume fraction is obtained. The corrected PLIF signal and the corrected planar Mie scattering can be also used together to obtain the Sauter Mean Diameter (SMD) distribution by using data from the PDIA technique at a particular location for calibration. This methodology is applied to non-evaporating sprays of diesel and a more viscous pure plant oil at an injection pressure of 1000 bar and a gas pressure of 30 bar in a high pressure chamber. These two fuels are selected since their viscosity values are very different with a consequently very different spray structure. The spatial distribution of liquid volume fraction and SMD is obtained for two fuels. The proposed method is validated by comparing liquid volume fraction obtained by the current method with data from PDIA technique. (C) 2012 Elsevier Inc. All rights reserved.

Chapman-Enskog analysis for finite-volume formulation of lattice Boltzmann equation

The classical Chapman-Enskog expansion is performed for the recently proposed finite-volume formulation of lattice Boltzmann equation (LBE) method D.V. Patil, K.N. Lakshmisha, Finite volume TVD formulation of lattice Boltzmann simulation on unstructured mesh, J. Comput. Phys. 228 (2009) 5262-5279]. First, a modified partial differential equation is derived from a numerical approximation of the discrete Boltzmann equation. Then, the multi-scale, small parameter expansion is followed to recover the continuity and the Navier-Stokes (NS) equations with additional error terms. The expression for apparent value of the kinematic viscosity is derived for finite-volume formulation under certain assumptions. The attenuation of a shear wave, Taylor-Green vortex flow and driven channel flow are studied to analyze the apparent viscosity relation.

Heterogeneous locational optimisation using a generalised Voronoi partition

In this paper a generalisation of the Voronoi partition is used for locational optimisation of facilities having different service capabilities and limited range or reach. The facilities can be stationary, such as base stations in a cellular network, hospitals, schools, etc., or mobile units, such as multiple unmanned aerial vehicles, automated guided vehicles, etc., carrying sensors, or mobile units carrying relief personnel and materials. An objective function for optimal deployment of the facilities is formulated, and its critical points are determined. The locally optimal deployment is shown to be a generalised centroidal Voronoi configuration in which the facilities are located at the centroids of the corresponding generalised Voronoi cells. The problem is formulated for more general mobile facilities, and formal results on the stability, convergence and spatial distribution of the proposed control laws responsible for the motion of the agents carrying facilities, under some constraints on the agents' speed and limit on the sensor range, are provided. The theoretical results are supported with illustrative simulation results.

Optimisation of an asymmetric polymerase chain reaction assay for the amplification of single-stranded DNA from Wuchereria bancrofti for electrochemical detection

Single-stranded DNA (ssDNA) is a prerequisite for electrochemical sensor-based detection of parasite DNA and other diagnostic applications. To achieve this detection, an asymmetric polymerase chain reaction method was optimised. This method facilitates amplification of ssDNA from the human lymphatic filarial parasite Wuchereria bancrofti. This procedure produced ssDNA fragments of 188 bp in a single step when primer pairs (forward and reverse) were used at a 100:1 molar ratio in the presence of double-stranded template DNA. The ssDNA thus produced was suitable for immobilisation as probe onto the surface of an Indium tin oxide electrode and hybridisation in a system for sequence-specific electrochemical detection of W. bancrofti. The hybridisation of the ssDNA probe and target ssDNA led to considerable decreases in both the anodic and the cathodic currents of the system's redox couple compared with the unhybridised DNA and could be detected via cyclic voltammetry. This method is reproducible and avoids many of the difficulties encountered by conventional methods of filarial parasite DNA detection; thus, it has potential in xenomonitoring.

Nanoindentation behavior of nanotwinned Cu: Influence of indenter angle on hardness, strain rate sensitivity and activation volume

The influence of strain on the mechanical properties and deformation kinetic parameters of nanotwinned (at) copper is investigated by a series of nanoindentation experiments, which were performed by employing sharp indenters with five varying centerline-to-face angles (psi). Comparison experiments were also conducted on (1 1 0) single crystalline Cu. Experimental results indicate that, unlike coarsegrained materials, nt-Cu is prone to plastic flow softening with large material pile-up around the indentation impression at high levels of strains. Localized detwinning becomes more significant with decreasing psi, concomitant with reduced strain-rate sensitivity (m) and enhanced activation volume (V*). The m of nt-Cu is found to depend sensitively on psi with a variation of more than a factor of 3, whereas V* exhibits a much less sensitive trend. This paper discusses the validation of the experimental techniques and the implications of various deformation kinetic parameters on the underlying deformation mechanisms of nt-Ca. 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Detailed investigation of contact deformation in ZrN/Zr multiplayer-understanding the role of volume fraction, bilayer spacing, and morphology of interfaces

A systematic study was done to understand the influence of volume fractions and bilayer spacings for metal/nitride multilayer coating using finite element method (FEM). An axisymmetric model was chosen to model the real situation by incorporating metal and substrate plasticity. Combinations of volume fractions and bilayer spacings were chosen for FEM analysis consistent with experimental results. The model was able to predict trends in cracking with respect to layer spacing and volume fraction. Metal layer plasticity is seen to greatly influence the stress field inside nitride. It is seen that the thicker metal induces higher tensile stresses inside nitride and hence leads to lower cracking loads. Thin metal layers < 10 nm were seen to have curved interfaces, and hence, the deformation mode was interfacial delamination in combination with edge cracking. There is an optimum seen with respect to volume fraction similar to 13% and metal layer thickness similar to 30 nm, which give maximum crack resistance.

Target reliability-based optimisation for internal seismic stability of reinforced soil structures

In this paper, an approach for target component and system reliability-based design optimisation (RBDO) to evaluate safety for the internal seismic stability of geosynthetic-reinforced soil (GRS) structures is presented. Three modes of failure are considered: tension failure of the bottom-most layer of reinforcement, pullout failure of the topmost layer of reinforcement, and total pullout failure of all reinforcement layers. The analysis is performed by treating backfill properties, geometric and strength properties of reinforcement as random variables. The optimum number of reinforcement layers and optimum pullout length needed to maintain stability against tension failure, pullout failure and total pullout failure for different coefficients of variation of friction angle of the backfill, design strength of the reinforcement and horizontal seismic acceleration coefficients by targeting various system reliability indices are proposed. The results provide guidelines for the total length of reinforcement required, considering the variability of backfill as well as seismic coefficients. One illustrative example is presented to explain the evaluation of reliability for internal stability of reinforced soil structures using the proposed approach. In the second illustration (the stability of five walls), the Kushiro wall subjected to the Kushiro-Oki earthquake, the Seiken wall subjected to the Chiba-ken Toho-Oki earthquake, the Ta Kung wall subjected to the Ji-Ji earthquake, and the Gould and Valencia walls subjected to Northridge earthquake are re-examined.

Influence of surface area to volume ratio of fuel particles on gasification process in a fixed bed

The paper addresses the effect of particle size on tar generation in a fixed bed gasification system. Pyrolysis, a diffusion limited process, depends on the heating rate and the surface area of the particle influencing the release of the volatile fraction leaving behind residual char. The flaming time has been estimated for different biomass samples. It is found that the flaming time for wood flakes is almost one fourth than that of coconut shells for same equivalent diameter fuel samples. The particle density of the coconut shell is more than twice that of wood spheres, and almost four times compared with wood flakes; having a significant influence on the flaming time. The ratio of the particle surface area to that of an equivalent diameter is nearly two times higher for flakes compared with wood pieces. Accounting for the density effect, on normalizing with density of the particle, the flaming rate is double in the case of wood flakes or coconut shells compared with the wood sphere for an equivalent diameter. This is due to increased surface area per unit volume of the particle. Experiments are conducted on estimation of tar content in the raw gas for wood flakes and standard wood pieces. It is observed that the tar level in the raw gas is about 80% higher in the case of wood flakes compared with wood pieces. The analysis suggests that the time for pyrolysis is lower with a higher surface area particle and is subjected to fast pyrolysis process resulting in higher tar fraction with low char yield. Increased residence time with staged air flow has a better control on residence time and lower tar in the raw gas. (C) 2014 International Energy Initiative. Published by Elsevier Inc. All rights reserved.

Diffusing-wave spectroscopy in an inhomogeneous object: Local viscoelastic spectra from ultrasound-assisted measurement of correlation decay arising from the ultrasound focal volume

We demonstrate diffusing-wave spectroscopy (DWS) in a localized region of a viscoelastically inhomogeneous object by measurement of the intensity autocorrelation g(2)(tau)] that captures only the decay introduced by the temperature-induced Brownian motion in the region. The region is roughly specified by the focal volume of an ultrasound transducer which introduces region specific mechanical vibration owing to insonification. Essential characteristics of the localized non-Markovian dynamics are contained in the decay of the modulation depth M(tau)], introduced by the ultrasound forcing in the focal volume selected, on g(2)(tau). The modulation depth M(tau(i)) at any delay time tau(i) can be measured by short-time Fourier transform of g(2)(tau) and measurement of the magnitude of the spectrum at the ultrasound drive frequency. By following the established theoretical framework of DWS, we are able to connect the decay in M(tau) to the mean-squared displacement (MSD) of scattering centers and the MSD to G*(omega), the complex viscoelastic spectrum. A two-region composite polyvinyl alcohol phantom with different viscoelastic properties is selected for demonstrating local DWS-based recovery of G*(omega) corresponding to these regions from the measured region specific M(tau(i))vs tau(i). The ultrasound-assisted measurement of MSD is verified by simulating, using a generalized Langevin equation (GLE), the dynamics of the particles in the region selected as well as by the usual DWS experiment without the ultrasound. It is shown that whereas the MSD obtained by solving the GLE without the ultrasound forcing agreed with its experimental counterpart covering small and large values of tau, the match was good only in the initial transients in regard to experimental measurements with ultrasound.

A molecular dynamics study of ambient and high pressure phases of silica: Structure and enthalpy variation with molar volume

Extensive molecular dynamics studies of 13 different silica polymorphs are reported in the isothermal-isobaric ensemble with the Parrinello-Rahman variable shape simulation cell. The van Beest-Kramer-van Santen (BKS) potential is shown to predict lattice parameters for most phases within 2%-3% accuracy, as well as the relative stabilities of different polymorphs in agreement with experiment. Enthalpies of high-density polymorphs - CaCl2-type, alpha-PbO2-type, and pyrite-type for which no experimental data are available as yet, are predicted here. Further, the calculated enthalpies exhibit two distinct regimes as a function of molar volume-for low and medium-density polymorphs, it is almost independent of volume, while for high-pressure phases a steep dependence is seen. A detailed analysis indicates that the increased short-range contributions to enthalpy in the high-density phases arise not only from an increased coordination number of silicon but also shorter Si-O bond lengths. Our results indicate that amorphous phases of silica exhibit better optimization of short-range interactions than crystalline phases at the same density while the magnitude of Coulombic contributions is lower in the amorphous phase. (C) 2014 AIP Publishing LLC.

Isotropic finite volume discretization

Finite volume methods traditionally employ dimension by dimension extension of the one-dimensional reconstruction and averaging procedures to achieve spatial discretization of the governing partial differential equations on a structured Cartesian mesh in multiple dimensions. This simple approach based on tensor product stencils introduces an undesirable grid orientation dependence in the computed solution. The resulting anisotropic errors lead to a disparity in the calculations that is most prominent between directions parallel and diagonal to the grid lines. In this work we develop isotropic finite volume discretization schemes which minimize such grid orientation effects in multidimensional calculations by eliminating the directional bias in the lowest order term in the truncation error. Explicit isotropic expressions that relate the cell face averaged line and surface integrals of a function and its derivatives to the given cell area and volume averages are derived in two and three dimensions, respectively. It is found that a family of isotropic approximations with a free parameter can be derived by combining isotropic schemes based on next-nearest and next-next-nearest neighbors in three dimensions. Use of these isotropic expressions alone in a standard finite volume framework, however, is found to be insufficient in enforcing rotational invariance when the flux vector is nonlinear and/or spatially non-uniform. The rotationally invariant terms which lead to a loss of isotropy in such cases are explicitly identified and recast in a differential form. Various forms of flux correction terms which allow for a full recovery of rotational invariance in the lowest order truncation error terms, while preserving the formal order of accuracy and discrete conservation of the original finite volume method, are developed. Numerical tests in two and three dimensions attest the superior directional attributes of the proposed isotropic finite volume method. Prominent anisotropic errors, such as spurious asymmetric distortions on a circular reaction-diffusion wave that feature in the conventional finite volume implementation are effectively suppressed through isotropic finite volume discretization. Furthermore, for a given spatial resolution, a striking improvement in the prediction of kinetic energy decay rate corresponding to a general two-dimensional incompressible flow field is observed with the use of an isotropic finite volume method instead of the conventional discretization. (C) 2014 Elsevier Inc. All rights reserved.

Effect of hydrogen on the yielding behavior and shear transformation zone volume in metallic glass ribbons

The effect of hydrogen (H) charging on the shear yield strength (tau(max)) and shear transformation zone volume (Omega) of Ni-Nb-Zr metallic glass ribbons, with varying Zr content, were studied through the first pop-in loads during nanoindentation. Weight gain measurements after H charging and desorption studies were utilized to identify how the total H absorbed during charging is partitioned into mobile and immobile (or trapped) parts. These, in turn, indicate the significant role of H mobility in the amorphous structure on the yielding behavior. In high-Zr alloys, tau(max) increases significantly whereas Omega decreases. In low-Zr alloys, a slight decrease in tau(max) and increase in Omega were noted. These experimental observations are rationalized in terms of the mobility of the absorbed H in the amorphous structure and the possible role of it in the shear transformation zone dynamics during deformation of the metallic glass. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.