Sensitivity of polarization fluctuations to the nature of protein-water interactions: Study of biological water in four different protein-water systems

Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (similar to 80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solution's dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000-30000 water molecules (varied according to the protein size), providing a concentration in the range of similar to 2-3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water < dM(W) (0)delta M-W (t) > is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (similar to 50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4-5 layers away. We also calculate shellwise orientational correlation function and tetrahedral order parameter to understand the local dynamics and structural re-arrangement of water. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in the present work. (C) 2014 AIP Publishing LLC.

Reply to ``Comment on `Strongly magnetized cold degenerate electron gas: Mass-radius relation of the magnetized white dwarf'''

We show that the upper bound for the central magnetic field of a super-Chandrasekhar white dwarf calculated by Nityananda and Konar Phys. Rev. D 89, 103017 (2014)] and in the concerned comment, by the same authors, against our work U. Das and B. Mukhopadhyay, Phys. Rev. D 86, 042001 (2012)] is erroneous. This in turn strengthens the argument in favor of the stability of the recently proposed magnetized super-Chandrasekhar white dwarfs. We also point out several other numerical errors in their work. Overall we conclude that the arguments put forth by Nityananda and Konar are misleading.

On the strain rate sensitivity of plastic flow in metallic glasses

The nanoindentation technique was employed to examine the strain rate sensitivity, m, and its dependence on the structural state of a Zr-based bulk metallic glass (BMG). The free volume content in the BMG was varied by examining samples in the as-cast (AC), shot-peened (SP), and structurally relaxed (SR) states. Hardness values measured at different loading rates and over a temperature range of 300-423 K as well as the strain-rate jump tests conducted in the quasi-static regime at room temperature, show that m is always negative. All the load-displacement (P-h) curves in this temperature regime exhibit serrated load-displacement responses, indicating that the shear band mediated inhomogeneous plastic flow governs deformation. Such localization of flow and associated softening is the raison d'etre for the negative m. Significant levels of pile-up around the indents were also noted. The order in the average values of hardness, pile-up heights, and the displacement bursts on the P-h curves was always such that SR > AC > SP, which is also the order of increasing free volume content. These observations were utilized to discuss the reasons for the negative strain rate sensitivity, and its dependence on the structural state of metallic glasses. It is suggested that the positive values of m reported in the literature for them are possibly experimental artefacts that arise due to large pile ups around the indents which lead to erroneous estimation in hardness values. (C) 2014 Elsevier B.V. All rights reserved.

Sensitivity characteristics of Ag doped BaTiO3-CuO mixed oxide as Carbon-dioxide S ensor

Ag doped BaTiO3-CuO mixed oxide thin films are evaluated for their carbon-dioxide sensing characteristics. The metal oxide films of different thicknesses are deposited on oxidized p type Si < 100 > substrate by RF Sputtering. Sensing characteristics for different CO2 concentration, (300 ppm - 1000 ppm) are obtained for different operating temperatures, (100 degrees C - 400 degrees C). Optimum temperature for maximum sensitivity is found to be 250 degrees C. The effect of annealing on sensing properties is also evaluated. The unannealed films give better sensitivity than that of annealed films. Response time and recovery time are also calculated.

The cold mode: a phenomenological model for the evolution of density perturbations in the intracluster medium

Cool cluster cores are in global thermal equilibrium but are locally thermally unstable. We study a non-linear phenomenological model for the evolution of density perturbations in the intracluster medium (ICM) due to local thermal instability and gravity. We have analysed and extended a model for the evolution of an overdense blob in the ICM. We find two regimes in which the overdense blobs can cool to thermally stable low temperatures. One for large t(cool)/t(ff) (t(cool) is the cooling time and t(ff) is the free-fall time), where a large initial overdensity is required for thermal runaway to occur; this is the regime which was previously analysed in detail. We discover a second regime for t(cool)/t(ff) less than or similar to 1 (in agreement with Cartesian simulations of local thermal instability in an external gravitational field), where runaway cooling happens for arbitrarily small amplitudes. Numerical simulations have shown that cold gas condenses out more easily in a spherical geometry. We extend the analysis to include geometrical compression in weakly stratified atmospheres such as the ICM. With a single parameter, analogous to the mixing length, we are able to reproduce the results from numerical simulations; namely, small density perturbations lead to the condensation of extended cold filaments only if t(cool)/t(ff) less than or similar to 10.

High indium non-polar InGaN clusters with infrared sensitivity grown by PAMBE

Studies on the optical properties of InGaN alloy of relatively higher indium content are of potential interest to understand the effect of indium content on the optical band gap of epitaxial InGaN. We report the growth of self assembled non-polar high indium clusters of In0.55Ga0.45N over non-polar (11-20) a-plane In0.17Ga0.83N epilayer grown on a-plane (11-20) GaN/(1-102) r-plane sapphire substrate using plasma assisted molecular beam epitaxy (PAMBE). Such structures are potential candidates for high brightness LEDs emitting in longer wavelengths. The high resolution X-ray diffraction studies revealed the formation of two distinct compositions of InxGa1-xN alloys, which were further confirmed by photoluminescence studies. A possible mechanism for the formation of such structure was postulated which was supported with the results obtained by energy dispersive X-ray analysis. The structure hence grown when investigated for photo-detecting properties, showed sensitivity to both infrared and ultraviolet radiations due to the different composition of InGaN region. (C) 2015 Author(s).

Thermal Response on the Microstructure and Texture of ECAP and Cold-Rolled Pure Magnesium

This paper deals with dynamic recrystallization (DRX), static recrystallization, and grain growth phenomena of pure magnesium after equal channel angular pressing (ECAP) by route A and B-C at 523 K (250 A degrees C) followed by 80 pct cold rolling. The ECAP-deformed and the subsequently rolled samples were annealed at 373 K and 773 K (100 A degrees C and 500 A degrees C). The associated changes in the microstructure and texture were studied using electron back-scattered diffraction. ECAP produced an average grain size of 12 to 18 A mu m with B and C-2 fiber textures. Subsequent rolling led to an average grain size 8 to 10 A mu m with basal texture fiber parallel to ND. There was no noticeable increase in the average grain size on annealing at 373 K (100 A degrees C). However, significant increase in the average grain size occurred at 773 K (500 A degrees C). The occurrence of different DRX mechanisms was detected: discontinuous dynamic recrystallization was attributed to basal slip activity and continuous dynamic recovery and recrystallization to prismatic/pyramidal slip systems. Only continuous static recrystallization could be observed on annealing.

Study on effect of optical wavelength on photo induced strain sensitivity in carbon nanotubes using fiber Bragg grating

In this work, the role of optical wavelength on the photo induced strain in carbon nanotubes (CNT) is probed using a Fiber Bragg Grating (FBG), upon exposure to infrared (IR) (21 mu epsilon mW(-1)) and visible (9 mu epsilon mW(-1)) radiations. The strain sensitivity in CNT is monitored over a smaller range (10(-3) to 10(-9) epsilon) by exposing to a low optical power varying in the range 10(-3) to 10(-6) W. In addition, the wavelength dependent response and recovery periods of CNT under IR (tau(rise) = 150 ms, tau(fall) = 280 ms) and visible (tau(rise) = 1.07 s, tau(fall) = 1.18 s) radiations are evaluated in detail. This study can be further extended to measure the sensitivity of nano-scale photo induced strains in nano materials and opens avenues to control mechanical actuation using various optical wavelengths.

Global response sensitivity analysis using probability distance measures and generalization of Sobol's analysis

The study introduces two new alternatives for global response sensitivity analysis based on the application of the L-2-norm and Hellinger's metric for measuring distance between two probabilistic models. Both the procedures are shown to be capable of treating dependent non-Gaussian random variable models for the input variables. The sensitivity indices obtained based on the L2-norm involve second order moments of the response, and, when applied for the case of independent and identically distributed sequence of input random variables, it is shown to be related to the classical Sobol's response sensitivity indices. The analysis based on Hellinger's metric addresses variability across entire range or segments of the response probability density function. The measure is shown to be conceptually a more satisfying alternative to the Kullback-Leibler divergence based analysis which has been reported in the existing literature. Other issues addressed in the study cover Monte Carlo simulation based methods for computing the sensitivity indices and sensitivity analysis with respect to grouped variables. Illustrative examples consist of studies on global sensitivity analysis of natural frequencies of a random multi-degree of freedom system, response of a nonlinear frame, and safety margin associated with a nonlinear performance function. (C) 2015 Elsevier Ltd. All rights reserved.

COOL CORE CYCLES: COLD GAS AND AGN JET FEEDBACK IN CLUSTER CORES

Using high-resolution 3D and 2D (axisymmetric) hydrodynamic simulations in spherical geometry, we study the evolution of cool cluster cores heated by feedback-driven bipolar active galactic nuclei (AGNs) jets. Condensation of cold gas, and the consequent enhanced accretion, is required for AGN feedback to balance radiative cooling with reasonable efficiencies, and to match the observed cool core properties. A feedback efficiency (mechanical luminosity approximate to epsilon(M) over dot(acc)c(2); where (M) over dot(acc). is the mass accretion rate at 1 kpc) as small as 6 x 10(-5) is sufficient to reduce the cooling/accretion rate by similar to 10 compared to a pure cooling flow in clusters (with M-200 less than or similar to 7 x 10(14) M-circle dot). This value is much smaller compared to the ones considered earlier, and is consistent with the jet efficiency and the fact that only a small fraction of gas at 1 kpc is accreted onto the supermassive black hole (SMBH). The feedback efficiency in earlier works was so high that the cluster core reached equilibrium in a hot state without much precipitation, unlike what is observed in cool-core clusters. We find hysteresis cycles in all our simulations with cold mode feedback: condensation of cold gas when the ratio of the cooling-time to the free-fall time (t(cool)/t(ff)) is less than or similar to 10 leads to a sudden enhancement in the accretion rate; a large accretion rate causes strong jets and overheating of the hot intracluster medium such that t(cool)/t(ff) > 10; further condensation of cold gas is suppressed and the accretion rate falls, leading to slow cooling of the core and condensation of cold gas, restarting the cycle. Therefore, there is a spread in core properties, such as the jet power, accretion rate, for the same value of core entropy t(cool)/t(ff). A smaller number of cycles is observed for higher efficiencies and for lower mass halos because the core is overheated to a longer cooling time. The 3D simulations show the formation of a few-kpc scale, rotationally supported, massive (similar to 10(11) M-circle dot) cold gas torus. Since the torus gas is not accreted onto the SMBH, it is largely decoupled from the feedback cycle. The radially dominant cold gas (T < 5 x 10(4) K; vertical bar v(r)vertical bar >vertical bar v(phi vertical bar)) consists of fast cold gas uplifted by AGN jets and freely infalling cold gas condensing out of the core. The radially dominant cold gas extends out to 25 kpc for the fiducial run (halo mass 7 x 10(14) M-circle dot and feedback efficiency 6 x 10(-5)), with the average mass inflow rate dominating the outflow rate by a factor of approximate to 2. We compare our simulation results with recent observations.

Notch sensitivity in nanoscale metallic glass specimens: Insights from continuum simulations

Recent experiments have shown that nano-sized metallic glass (MG) specimens subjected to tensile loading exhibit increased ductility and work hardening. Failure occurs by necking as opposed to shear banding which is seen in bulk samples. Also, the necking is generally observed at shallow notches present on the specimen surface. In this work, continuum finite element analysis of tensile loading of nano-sized notched MG specimens is conducted using a thermodynamically consistent non-local plasticity model to clearly understand the deformation behavior from a mechanics perspective. It is found that plastic zone size in front of the notch attains a saturation level at the stage when a dominant shear band forms extending across the specimen. This size scales with an intrinsic material length associated with the interaction stress between flow defects. A transition in deformation behavior from quasi-brittle to ductile becomes possible when this critical plastic zone size is larger than the uncracked ligament length. These observations corroborate with atomistic simulations and experimental results. (C) 2015 Elsevier Ltd. All rights reserved.

Global response sensitivity analysis of uncertain structures

The problem of characterizing global sensitivity indices of structural response when system uncertainties are represented using probabilistic and (or) non-probabilistic modeling frameworks (which include intervals, convex functions, and fuzzy variables) is considered. These indices are characterized in terms of distance measures between a fiducial model in which uncertainties in all the pertinent variables are taken into account and a family of hypothetical models in which uncertainty in one or more selected variables are suppressed. The distance measures considered include various probability distance measures (Hellinger,l(2), and the Kantorovich metrics, and the Kullback-Leibler divergence) and Hausdorff distance measure as applied to intervals and fuzzy variables. Illustrations include studies on an uncertainly parametered building frame carrying uncertain loads. (C) 2015 Elsevier Ltd. All rights reserved.

Damage Detection Sensitivity, Specificity and Classification Data Analysis for SHM Systems Design, Verification and Validation

In this paper, we consider applying derived knowledge base regarding the sensitivity and specificity of damage(s) to be detected by an SHM system being designed and qualified. These efforts are necessary toward developing capabilities in SHM system to classify reliably various probable damages through sequence of monitoring, i.e., damage precursor identification, detection of damage and monitoring its progression. We consider the particular problem of visual and ultrasonic NDE based SHM system design requirements, where the damage detection sensitivity and specificity data definitions for a class of structural components are established. Methodologies for SHM system specification creation are discussed in details. Examples are shown to illustrate how the physics of damage detection scheme limits particular damage detection sensitivity and specificity and further how these information can be used in algorithms to combine various different NDE schemes in an SHM system to enhance efficiency and effectiveness. Statistical and data driven models to determine the sensitivity and probability of damage detection (POD) has been demonstrated for plate with varying one-sided line crack using optical and ultrasonic based inspection techniques.

Plasmonic Lipid Bilayer Membranes for Enhanced Detection Sensitivity of Biolabeling Fluorophores

Plasmonics based sensing, using the surface plasmon resonance of metal nanoparticles, has been effectively demonstrated in various applications. Extending this methodology to cell and artificial lipid bilayer membranes is extremely beneficial in enhancing the sensitivity of the detection of binding and cellular transport of molecules across such membranes. Here, the creation of an artificial plasmonic biomembrane template is demonstrated and used to show the enhanced detection sensitivity of certain widely used biomarker molecules. The efficacy of these templates is explained in terms of the ability of the hydrophobic polymer grafted gold nanoparticles used to organize, penetrate, and fluidize the membranes. The enhancement of photoluminescence of the dye molecules used occurs over a reasonably large spectral range as compared to the plasmon resonance of gold nanoparticles. The results could, possibly, be extended to cellular membranes with relevant modifications, as well as to the detection of any other biological molecule appropriately labeled with fluorescent dye molecules, and demonstrate the versatility of these plasmonic bioinspired platforms as potential biochemical sensors.

Global Response Sensitivity Analysis of Randomly Excited Dynamic Structures

The response of structural dynamical systems excited by multiple random excitations is considered. Two new procedures for evaluating global response sensitivity measures with respect to the excitation components are proposed. The first procedure is valid for stationary response of linear systems under stationary random excitations and is based on the notion of Hellinger's metric of distance between two power spectral density functions. The second procedure is more generally valid and is based on the l2 norm based distance measure between two probability density functions. Specific cases which admit exact solutions are presented, and solution procedures based on Monte Carlo simulations for more general class of problems are outlined. Illustrations include studies on a parametrically excited linear system and a nonlinear random vibration problem involving moving oscillator-beam system that considers excitations attributable to random support motions and guide-way unevenness. (C) 2015 American Society of Civil Engineers.