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.

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.

ABOUT FORMS OF ELECTRONIC AND IONIC DEVICES WITH THERMIONIC CATHODES.

The miniaturization of electronic and ionic devices with thermionic cathodes and thc improvement of their vacuum properties are questions of very great interest to the electronic engineer. However there have bcen no proposals so far to analyse the problem of miniaturization of such devices In a fundamental way. The present work suggests a choice of the geometrical shape of the cathode, the anode and the envelope of the device, that may help towards such a fundamcnlal approach.It is shown that a design, in which the cathode and the envelope of the tube are made of thm prismatic shape and the anode coincides with the cnvclope, offers a slriknrg advantage over the conventional cylindrical design, in respect of over-all size. The use of the prismatic shape will lead to considerable economy in msterials and may facilitate simpler prodoct~ont echn~ques. I n respect of the miin criteria of vacuum, namely the grade of vacuum, the internal volume occupied by residual gases, the evolution of gases in the internal space and the diffusion of gases from outside into the devicc, it is shown that the prismatic form is at least as good as, if not somewhat superior lo, the cylindrical form.In the actual construction of thin prismatic tubes, manv practical problems will arise, the most important being the mechanical strength and stablity of the structure. But the changeover from the conventional cylindrical to the new prirmaiic form, with its basic advantages, is a development that merits close attention.

Epoch extraction based on integrated linear prediction residual using plosion index

Epoch is defined as the instant of significant excitation within a pitch period of voiced speech. Epoch extraction continues to attract the interest of researchers because of its significance in speech analysis. Existing high performance epoch extraction algorithms require either dynamic programming techniques or a priori information of the average pitch period. An algorithm without such requirements is proposed based on integrated linear prediction residual (ILPR) which resembles the voice source signal. Half wave rectified and negated ILPR (or Hilbert transform of ILPR) is used as the pre-processed signal. A new non-linear temporal measure named the plosion index (PI) has been proposed for detecting `transients' in speech signal. An extension of PI, called the dynamic plosion index (DPI) is applied on pre-processed signal to estimate the epochs. The proposed DPI algorithm is validated using six large databases which provide simultaneous EGG recordings. Creaky and singing voice samples are also analyzed. The algorithm has been tested for its robustness in the presence of additive white and babble noise and on simulated telephone quality speech. The performance of the DPI algorithm is found to be comparable or better than five state-of-the-art techniques for the experiments considered.

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.

Large-MIMO Receiver based on Linear Regression of MMSE Residual

Multiple input multiple output (MIMO) systems with large number of antennas have been gaining wide attention as they enable very high throughputs. A major impediment is the complexity at the receiver needed to detect the transmitted data. To this end we propose a new receiver, called LRR (Linear Regression of MMSE Residual), which improves the MMSE receiver by learning a linear regression model for the error of the MMSE receiver. The LRR receiver uses pilot data to estimate the channel, and then uses locally generated training data (not transmitted over the channel), to find the linear regression parameters. The proposed receiver is suitable for applications where the channel remains constant for a long period (slow-fading channels) and performs quite well: at a bit error rate (BER) of 10(-3), the SNR gain over MMSE receiver is about 7 dB for a 16 x 16 system; for a 64 x 64 system the gain is about 8.5 dB. For large coherence time, the complexity order of the LRR receiver is the same as that of the MMSE receiver, and in simulations we find that it needs about 4 times as many floating point operations. We also show that further gain of about 4 dB is obtained by local search around the estimate given by the LRR receiver.

Analytical Determination of Residual Strength and Linkup Strength for Flat Panels, with Multiple Site Damage

The problem of multiple site damage in aged airplane fuselage is handled in this paper. The analytical and numerical procedures used for the estimation of the strength of a flat panel with such multi-site damage are presented. Further, numerical results are presented on the residual strength of the panel using fracture mechanics-based approach and the stress levels when the leading crack is likely to link up with multiple site damage cracks. The presence of multiple site damage cracks in the vicinity of leading crack significantly decreases the residual strength of the panel. The model is verified using experimental data from the open literature and the predictions are in good agreement with the measured residual strength.

Energy loss due to adhesion in longitudinal impact of elastic cylinders

Adhesive interaction between impacting bodies can cause energy loss, even in an otherwise elastic impact. Adhesion force induces tensile stress in the bodies, which modifies the stress wave profile and influences the restitution behavior. We investigate this effect by developing a finite element framework, which incorporates a Lennard-Jones-type potential for modeling the adhesive interaction between volume elements. With this framework, the classical problems in contact mechanics can be revisited without the restrictive surface-force approximation. In this paper, we study the longitudinal impact of an elastic cylinder on a rigid half-space with adhesion. In the absence of adhesion, this problem reduces to the impact between two identical cylinders in which there is no energy loss. Adhesion causes a fraction of energy in the stress waves to remain in the cylinder as residual stress waves. This apparent loss in kinetic energy is shown to be a unique function of maximum tensile strain energy. We have developed a 1-D model in terms of interaction force parameters, velocity and material properties to estimate the tensile stain energy. We show that this model can be used to predict practically important phenomena like capture wherein the impacting bodies stick together. (C) 2013 Elsevier Masson SAS. 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.