MolBridge: a program for identifying nonbonded interactions in small molecules and biomolecular structures

Identification and analysis of nonbonded interactions within a molecule and with the surrounding molecules are an essential part of structural studies, given the importance of these interactions in defining the structure and function of any supramolecular entity. MolBridge is an easy to use algorithm based purely on geometric criteria that can identify all possible nonbonded interactions, such as hydrogen bond, halogen bond, cation-pi, pi-pi and van der Waals, in small molecules as well as biomolecules. The user can either upload three-dimensional coordinate files or enter the molecular ID corresponding to the relevant database. The program is available in a standalone form and as an interactive web server with Jmol and JME incorporated into it. The program is freely downloadable and the web server version is also available at http://nucleix.mbu.iisc.ernet.in/molbridge/index.php.

Dynamics of intermittent force fluctuations in vesicular nanotubulation

Irregular force fluctuations are seen in most nanotubulation experiments. The dynamics behind their presence has, however, been neither commented upon nor modeled. A simple estimate of the mean energy dissipated in force drops turns out to be several times the thermal energy. This coupled with the rate dependent nature of the deformation reported in several experiments point to a dynamical origin of the serrations. We simplify the whole process of tether formation through a three-stage model of successive deformations of sphere to ellipsoid, neck-formation, and tubule birth and extension. Based on this, we envisage a rate-softening frictional force at the neck that must be overcome before a nanotube can be pulled out. Our minimal model includes elastic and visco-elastic deformation of the vesicle, and has built-in dependence on pull velocity, vesicle radius, and other material parameters, enabling us to capture various kinds of serrated force-extension curves for different parameter choices. Serrations are predicted in the nanotubulation region. Other features of force-extension plots reported in the literature such as a plateauing serrated region beyond a force drop, serrated flow region with a small positive slope, an increase in the elastic threshold with pull velocity, force-extension curves for vesicles with larger radius lying lower than those for smaller radius, are all also predicted by the model. A toy model is introduced to demonstrate that the role of the friction law is limited to inducing stick-slip oscillations in the force, and all other qualitative and quantitative features emerging from the model can only be attributed to other physical mechanisms included in the deformation dynamics of the vesicle. (C) 2014 AIP Publishing LLC.

Structural and magnetic properties of ultra-small scale eutectic CoFeZr alloys

Aiming to develop high mechanical strength and toughness by tuning ultrafine lamellar spacing of magnetic eutectic alloys, we report the mechanical and magnetic properties of the binary eutectic alloys Co90.5Zr9.5 and Fe90.2Zr9.8, as well as the pseudo-binary eutectic alloys Co82.4Fe8Zr9.6, Co78Fe12.4Zr9.6 and Co49.2Fe49.2Zr9.6 developed by suction-casting. The lower lamellar spacing around 100 nm of the eutectics Co49.2Fe49.2Zr9.6 yields a high hardness of 713(+/- 20) VHN. Magnetic measurements reveal high magnetic moment of 1.92 mu B (at 5 K) and 1.82 mu B (at 300 K) per formula unit for this composition. The magnetization vs. applied field data at 5 K show a directional preference to some extent and therefore smaller non-collinear magnetization behavior compared to Co11Zr2 reported in the literature due to exchange frustration and transverse spin freezing owing to the presence of smaller Zr content. The decay of magnetization as a function of temperature along the easy axis of magnetization of all the eutectic compositions can be described fairly well by the spin wave excitation equation Delta M/M(0) = BT3/2 + CT5/2. (C) 2014 Elsevier B.V. All rights reserved.

Evaluating shock absorption behavior of small-sized systems under programmable electric field

A simple ball-drop impact tester is developed for studying the dynamic response of hierarchical, complex, small-sized systems and materials. The developed algorithm and set-up have provisions for applying programmable potential difference along the height of a test specimen during an impact loading; this enables us to conduct experiments on various materials and smart structures whose mechanical behavior is sensitive to electric field. The software-hardware system allows not only acquisition of dynamic force-time data at very fast sampling rate (up to 2 x 10(6) samples/s), but also application of a pre-set potential difference (up to +/- 10 V) across a test specimen for a duration determined by feedback from the force-time data. We illustrate the functioning of the set-up by studying the effect of electric field on the energy absorption capability of carbon nanotube foams of 5 x 5 x 1.2 mm(3) size under impact conditions. (C) 2014 AIP Publishing LLC.

Small-Signal Stability Analysis of an Open-loop Induction Motor Drive Including the Effect of Inverter Dead-Time

This paper demonstrates light-load instability in open-loop induction motor drives on account of inverter dead-time. The dynamic equations of an inverter fed induction motor, incorporating the effect of dead-time, are considered. A procedure to derive the small-signal model of the motor, including the effect of inverter dead-time, is presented. Further, stability analysis is carried out on a 100-kW, 415V, 3-phase induction motor considering no-load. For voltage to frequency (i.e. V/f) ratios between 0.5 and 1 pu, the analysis brings out regions of instability on the V-f plane, in the frequency range between 5Hz and 20Hz. Simulation and experimental results show sub-harmonic oscillations in the motor current in this region, confirming instability as predicted by the analysis.

Performance Assessment of a Small Biogas-fuelled Power Generator Prototype

This study reports the development and performance evaluation of prototypes of biogas-fuelled stationary power generators in the range of 1 kW. Strategies to achieve high engine efficiency namely pulsed manifold injection, electronic throttle control and dual spark plugs, have been incorporated in the prototype. A complete closed-loop control of the engine operation to maintain a steady engine speed of 3000 rpm (+/- 5%) across the entire load range while maintaining an optimum fuel-air equivalence ratio is made possible by an electronic control unit (ECU) controlling the injection duration, ignition timing and throttle position. This study specifically focuses on the response of the generator to transient loads, and the overall efficiency obtained. The results obtained from testing the prototype have been found to be satisfactory and show that biogas power generators for low power applications can be made efficient (overall efficiency of 19% at electrical load of 640 W) using the strategies of biogas fuel injection.

Solution processable diketopyrrolopyrrole (DPP) cored small molecules with BODIPY end groups as novel donors for organic solar cells

Two novel triads based on a diketopyrrolopyrrole (DPP) central core and two 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) units attached by thiophene rings have been synthesised having high molar extinction coefficients. These triads were characterised and used as donor materials in small molecule, solution processable organic solar cells. Both triads were blended with PC71BM as an acceptor in different ratios by wt% and their photovoltaic properties were studied. For both the triads a modest photovoltaic performance was observed, having an efficiency of 0.65%. Moreover, in order to understand the ground and excited state properties and vertical absorption profile of DPP and BODIPY units within the triads, theoretical DFT and TDDFT calculations were performed.

Adaptive mesh generation for singularly perturbed fourth-order ordinary differential equations

In this paper, we consider a singularly perturbed boundary-value problem for fourth-order ordinary differential equation (ODE) whose highest-order derivative is multiplied by a small perturbation parameter. To solve this ODE, we transform the differential equation into a coupled system of two singularly perturbed ODEs. The classical central difference scheme is used to discretize the system of ODEs on a nonuniform mesh which is generated by equidistribution of a positive monitor function. We have shown that the proposed technique provides first-order accuracy independent of the perturbation parameter. Numerical experiments are provided to validate the theoretical results.

Simple three parameter equations for correlating liquid phase compositions in subcritical and supercritical systems

Two Chrastil type expressions have been developed to model the solubility of supercritical fluids/gases in liquids. The three parameter expressions proposed correlates the solubility as a function of temperature, pressure and density. The equation can also be used to check the self-consistency of the experimental data of liquid phase compositions for supercritical fluid-liquid equilibria. Fifty three different binary systems (carbon-dioxide + liquid) with around 2700 data points encompassing a wide range of compounds like esters, alcohols, carboxylic acids and ionic liquids were successfully modeled for a wide range of temperatures and pressures. Besides the test for self-consistency, based on the data at one temperature, the model can be used to predict the solubility of supercritical fluids in liquids at different temperatures. (C) 2014 Elsevier B.V. All rights reserved.

An insight to the low temperature conduction mechanism of c-axis grown Al-doped ZnO, a widely used transparent conducting oxide

Al-doped ZnO thin films were synthesized from oxygen reactive co-sputtering of Al and Zn targets. Explicit doping of Al in the highly c-axis oriented crystalline films of ZnO was manifested in terms of structural optical and electrical properties. Electrical conduction with different extent of Al doping into the crystal lattice of ZnO (AZnO) were characterized by frequency dependent (40 Hz-50 MHz) resistance. From the frequency dependent resistance, the ac conduction of them, and correlations of localized charge particles in the crystalline films were studied. The dc conduction at the low frequency region was found to increase from 8.623 mu A to 1.14 mA for the samples AZnO1 (1 wt% Al) and AZnO2 (2 wt% Al), respectively. For the sample AZnO10 (10 wt% Al) low frequency dc conduction was not found due to the electrode polarization effect. The measure of the correlation length by inverse of threshold frequency (omega(0)) showed that on application of a dc electric field such length decreases and the decrease in correlation parameter(s) indicates that the correlation between potentials wells of charge particles decreases for the unidirectional nature of dc bias. The comparison between the correlation length and the extent of correlation in the doped ZnO could not be made due to the observation of several threshold frequencies at the extent of higher doping. Such threshold frequencies were explained by the population possibility of correlated charge carriers that responded at different frequencies. For AZnO2 (2% Al), the temperature dependent (from 4.5 to 288 K) resistance study showed that the variable range hopping mechanism was the most dominating conduction mechanism at higher temperature whereas at low temperature region it was influenced by the small polaronic hopping conduction mechanism. There was no significant influence found in these mechanisms on applications of 1, 2 and 3 V as biases.

Wall-mode instability in plane shear flow of viscoelastic fluid over a deformable solid

The linear stability analysis of a plane Couette flow of an Oldroyd-B viscoelastic fluid past a flexible solid medium is carried out to investigate the role of polymer addition in the stability behavior. The system consists of a viscoelastic fluid layer of thickness R, density rho, viscosity eta, relaxation time lambda, and retardation time beta lambda flowing past a linear elastic solid medium of thickness HR, density rho, and shear modulus G. The emphasis is on the high-Reynolds-number wall-mode instability, which has recently been shown in experiments to destabilize the laminar flow of Newtonian fluids in soft-walled tubes and channels at a significantly lower Reynolds number than that for flows in rigid conduits. For Newtonian fluids, the linear stability studies have shown that the wall modes become unstable when flow Reynolds number exceeds a certain critical value Re c which scales as Sigma(3/4), where Reynolds number Re = rho VR/eta, V is the top-plate velocity, and dimensionless parameter Sigma = rho GR(2)/eta(2) characterizes the fluid-solid system. For high-Reynolds-number flow, the addition of polymer tends to decrease the critical Reynolds number in comparison to that for the Newtonian fluid, indicating a destabilizing role for fluid viscoelasticity. Numerical calculations show that the critical Reynolds number could be decreased by up to a factor of 10 by the addition of small amount of polymer. The critical Reynolds number follows the same scaling Re-c similar to Sigma(3/4) as the wall modes for a Newtonian fluid for very high Reynolds number. However, for moderate Reynolds number, there exists a narrow region in beta-H parametric space, corresponding to very dilute polymer solution (0.9 less than or similar to beta < 1) and thin solids (H less than or similar to 1.1), in which the addition of polymer tends to increase the critical Reynolds number in comparison to the Newtonian fluid. Thus, Reynolds number and polymer properties can be tailored to either increase or decrease the critical Reynolds number for unstable modes, thus providing an additional degree of control over the laminar-turbulent transition.

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.

Small signal Nonquasi-Static Model for Common Double-Gate MOSFETs Adapted to Gate Oxide Thickness Asymmetry

We present a physics-based closed form small signal Nonquasi-static (NQS) model for a long channel Common Double Gate MOSFET (CDG) by taking into account the asymmetry that may prevail between the gate oxide thickness. We use the unique quasi-linear relationship between the surface potentials along the channel to solve the governing continuity equation (CE) in order to develop the analytical expressions for the Y parameters. The Bessel function based solution of the CE is simplified in form of polynomials so that it could be easily implemented in any circuit simulator. The model shows good agreement with the TCAD simulation at-least till 4 times of the cut-off frequency for different device geometries and bias conditions.

Equilibrium and equivariant triangulations of some small covers with minimum number of vertices

Small covers were introduced by Davis and Januszkiewicz in 1991. We introduce the notion of equilibrium triangulations for small covers. We study equilibrium and vertex minimal 4-equivariant triangulations of 2-dimensional small covers. We discuss vertex minimal equilibrium triangulations of RP3#RP3, S-1 x RP2 and a nontrivial S-1 bundle over RP2. We construct some nice equilibrium triangulations of the real projective space RPn with 2(n) + n 1 vertices. The main tool is the theory of small covers.

Bayesian parameter identification in dynamic state space models using modified measurement equations

When Markov chain Monte Carlo (MCMC) samplers are used in problems of system parameter identification, one would face computational difficulties in dealing with large amount of measurement data and (or) low levels of measurement noise. Such exigencies are likely to occur in problems of parameter identification in dynamical systems when amount of vibratory measurement data and number of parameters to be identified could be large. In such cases, the posterior probability density function of the system parameters tends to have regions of narrow supports and a finite length MCMC chain is unlikely to cover pertinent regions. The present study proposes strategies based on modification of measurement equations and subsequent corrections, to alleviate this difficulty. This involves artificial enhancement of measurement noise, assimilation of transformed packets of measurements, and a global iteration strategy to improve the choice of prior models. Illustrative examples cover laboratory studies on a time variant dynamical system and a bending-torsion coupled, geometrically non-linear building frame under earthquake support motions. (C) 2015 Elsevier Ltd. All rights reserved.