Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation-intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nano-indentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr-Cr interaction and the Morse potential for Cr-C interactions. We study the performance of our algorithm for a range of MPI-thread combinations and find the performance to depend strongly on the computational task and load sharing in the multi-core processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favorably with that achieved by standard MD packages. (C) 2013 Elsevier Inc. All rights reserved.

Free turbulent shear layer in a point vortex gas as a problem in nonequilibrium statistical mechanics

This paper attempts to unravel any relations that may exist between turbulent shear flows and statistical mechanics through a detailed numerical investigation in the simplest case where both can be well defined. The flow considered for the purpose is the two-dimensional (2D) temporal free shear layer with a velocity difference Delta U across it, statistically homogeneous in the streamwise direction (x) and evolving from a plane vortex sheet in the direction normal to it (y) in a periodic-in-x domain L x +/-infinity. Extensive computer simulations of the flow are carried out through appropriate initial-value problems for a ``vortex gas'' comprising N point vortices of the same strength (gamma = L Delta U/N) and sign. Such a vortex gas is known to provide weak solutions of the Euler equation. More than ten different initial-condition classes are investigated using simulations involving up to 32 000 vortices, with ensemble averages evaluated over up to 10(3) realizations and integration over 10(4)L/Delta U. The temporal evolution of such a system is found to exhibit three distinct regimes. In Regime I the evolution is strongly influenced by the initial condition, sometimes lasting a significant fraction of L/Delta U. Regime III is a long-time domain-dependent evolution towards a statistically stationary state, via ``violent'' and ``slow'' relaxations P.-H. Chavanis, Physica A 391, 3657 (2012)], over flow time scales of order 10(2) and 10(4)L/Delta U, respectively (for N = 400). The final state involves a single structure that stochastically samples the domain, possibly constituting a ``relative equilibrium.'' The vortex distribution within the structure follows a nonisotropic truncated form of the Lundgren-Pointin (L-P) equilibrium distribution (with negatively high temperatures; L-P parameter lambda close to -1). The central finding is that, in the intermediate Regime II, the spreading rate of the layer is universal over the wide range of cases considered here. The value (in terms of momentum thickness) is 0.0166 +/- 0.0002 times Delta U. Regime II, extensively studied in the turbulent shear flow literature as a self-similar ``equilibrium'' state, is, however, a part of the rapid nonequilibrium evolution of the vortex-gas system, which we term ``explosive'' as it lasts less than one L/Delta U. Regime II also exhibits significant values of N-independent two-vortex correlations, indicating that current kinetic theories that neglect correlations or consider them as O(1/N) cannot describe this regime. The evolution of the layer thickness in present simulations in Regimes I and II agree with the experimental observations of spatially evolving (3D Navier-Stokes) shear layers. Further, the vorticity-stream-function relations in Regime III are close to those computed in 2D Navier-Stokes temporal shear layers J. Sommeria, C. Staquet, and R. Robert, J. Fluid Mech. 233, 661 (1991)]. These findings suggest the dominance of what may be called the Kelvin-Biot-Savart mechanism in determining the growth of the free shear layer through large-scale momentum and vorticity dispersal.

A Harmonic Suppression Scheme for Open-End Winding Split-Phase IM Drive Using Capacitive Filters for the Full Speed Range

Voltage source inverter (VSI)-fed six-phase induction motor (IM) drives have high 6n +/- 1, n = odd-order harmonic currents. This is because these currents, driven by the corresponding harmonic voltages in the inverter output, are limited only by the stator leakage impedance, as these harmonics are absent in the back electromotive force of the motor. To suppress the harmonic currents, either bulky inductive harmonic filters or complex pulsewidth modulation (PWM) techniques have to be used. This paper proposes a harmonic elimination scheme using switched capacitor filters for a VSI-fed split-phase IM drive. Two 3-phase inverters fed from capacitors are used on the open-end side of the motor to suppress 6n +/- 1, n = odd-order harmonics. A PWM scheme that can suppress the harmonics as well as balance the capacitor voltage is also proposed. The capacitor fed inverters are switched so that the fundamental voltage is not affected, and the fundamental power is always drawn from the main inverters. The proposed scheme is verified with a detailed experimental study. The effectiveness of the scheme is demonstrated by comparing the results with those obtained by disabling the capacitor fed inverters.

Transition in vortex breakdown modes in a coaxial isothermal unconfined swirling jet

This paper reports first observations of transition in recirculation pattern from an open-bubble type axisymmetric vortex breakdown to partially open bubble mode through an intermediate, critical regime of conical sheet formation in an unconfined, co-axial isothermal swirling flow. This time-mean transition is studied for two distinct flow modes which are characterized based on the modified Rossby number (Ro(m)), i.e., Ro(m) <= 1 and Ro(m) > 1. Flow modes with Ro(m) <= 1 are observed to first undergo cone-type breakdown and then to partially open bubble state as the geometric swirl number (S-G) is increased by similar to 20% and similar to 40%, respectively, from the baseline open-bubble state. However, the flow modes with Ro(m) > 1 fail to undergo such sequential transition. This distinct behavior is explained based on the physical significance associated with Ro(m) and the swirl momentum factor (xi). In essence, xi represents the ratio of angular momentum distributed across the flow structure to that distributed from central axis to the edge of the vortex core. It is observed that xi increases by similar to 100% in the critical swirl number band where conical breakdown occurs as compared to its magnitude in the S-G regime where open bubble state is seen. This results from the fact that flow modes with Ro(m) <= 1 are dominated by radial pressure gradient due to swirl/rotational effect when compared to radial pressure deficit arising from entrainment (due to the presence of co-stream). Consequently, the imparted swirl tends to penetrate easily towards the central axis causing it to spread laterally and finally undergo conical sheet breakdown. However, the flow modes with Ro(m) > 1 are dominated by pressure deficit due to entrainment effect. This blocks the radial inward penetration of imparted angular momentum thus preventing the lateral spread of these flow modes. As such these structures fail to undergo cone mode of vortex breakdown which is substantiated by a mere 30%-40% rise in xi in the critical swirl number range. (C) 2014 AIP Publishing LLC.

Micro-mechanical stages with enhanced range

We present concepts and an optimization-based methodology for the design of micro-mechanical stages that have not only high precision but also an enhanced range. Joint-free distributed compliant designs provide high precision and easy manufacturability at macro and micro scales. The range of motion is enhanced by using displacement-amplifying compliant mechanisms (DaCMs). The main issue addressed in this paper is how to retain the decoupling between the X and Y motions in the stage when it is equipped with DaCMs. The natural frequency of the stage is also not compromised in enhancing the range. The optimized design has 2.5 times more range than the designs reported in the literature. Furthermore, the sensitivity improved by a factor of two when the stage is optimized for an accelerometer.

12 V / kilo-Farad Range Lead-Carbon Hybrid Ultracapacitors and Their Envisaged Applications

12 V / kilo-Farad (kF) range substrate-integrated lead-carbon hybrid ultracapacitors (HUCs) wherein the conventional positive plates of lead-acid batteries are replaced with substrate-integrated PbO2 positive plates and the negative plates are replaced with carbon-coated graphitic electrodes, providing totally non-faradaic and corrosion-free electrodes, are developed and performance tested. Constant-current discharge data at varying load-currents, constant-power discharge data at varying power values, and the capacitance data at different temperature for a 12 V / kF range substrate-integrated lead-carbon HUC are described along with its resistance, leakage current, self-discharge and cycle-life characteristics.

A Stochastic Chemical Dynamic Approach to Correlate Autoimmunity and Optimal Vitamin-D Range

Motivated by several recent experimental observations that vitamin-D could interact with antigen presenting cells (APCs) and T-lymphocyte cells (T-cells) to promote and to regulate different stages of immune response, we developed a coarse grained but general kinetic model in an attempt to capture the role of vitamin-D in immunomodulatory responses. Our kinetic model, developed using the ideas of chemical network theory, leads to a system of nine coupled equations that we solve both by direct and by stochastic (Gillespie) methods. Both the analyses consistently provide detail information on the dependence of immune response to the variation of critical rate parameters. We find that although vitamin-D plays a negligible role in the initial immune response, it exerts a profound influence in the long term, especially in helping the system to achieve a new, stable steady state. The study explores the role of vitamin-D in preserving an observed bistability in the phase diagram (spanned by system parameters) of immune regulation, thus allowing the response to tolerate a wide range of pathogenic stimulation which could help in resisting autoimmune diseases. We also study how vitamin-D affects the time dependent population of dendritic cells that connect between innate and adaptive immune responses. Variations in dose dependent response of anti-inflammatory and pro-inflammatory T-cell populations to vitamin-D correlate well with recent experimental results. Our kinetic model allows for an estimation of the range of optimum level of vitamin-D required for smooth functioning of the immune system and for control of both hyper-regulation and inflammation. Most importantly, the present study reveals that an overdose or toxic level of vitamin-D or any steroid analogue could give rise to too large a tolerant response, leading to an inefficacy in adaptive immune function.

Breakup processes of pressure swirl spray in gaseous cross-flow

Injection of liquid fuel in cross flowing air has been a strategy for future aircraft engines in order to control the emissions. In this context, breakup of a pressure swirl spray in gaseous cross-flow is investigated experimentally. The atomizer discharges a conical swirling sheet of liquid that interacts with cross-flowing air. This complex interaction and the resulting spray structures at various flow conditions are studied through flow visualization using still as well as high speed photography. Experiments are performed over a wide range of aerodynamic Weber number (2-300) and liquid-to-air momentum flux ratio (5-150). Various breakup regimes exhibiting different breakup processes are mapped on a parameter space based on flow conditions. This map shows significant variations from breakup regime map for a plain liquid jet in cross-flow. It is observed that the breakup of leeward side of the sheet is dominated by bag breakup and the windward side of the sheet undergoes breakup through surface waves. Similarities and differences between bag breakup present in plain liquid jet in cross-flow and swirl spray in cross-flow are explained. Multimodal drop size distribution from bag breakup, frequency of bag breakup, wavelength of surface waves and trajectory of spray in cross-flow are measured by analyzing the spray images and parametric study of their variations is also presented. (C) 2014 Elsevier Ltd. All rights reserved.

Angular momentum transport and evolution of lopsided galaxies

The surface brightness distribution in the majority of stellar galactic discs falls off exponentially. Often what lies beyond such a stellar disc is the neutral hydrogen gas whose distribution also follows a nearly exponential profile at least for a number of nearby disc galaxies. Both the stars and gas are commonly known to host lopsided asymmetry especially in the outer parts of a galaxy. The role of such asymmetry in the dynamical evolution of a galaxy has not been explored so far. Following Lindblad's original idea of kinematic density waves, we show that the outer part of an exponential disc is ideally suitable for hosting lopsided asymmetry. Further, we compute the transport of angular momentum in the combined stars and gas disc embedded in a dark matter halo. We show that in a pure star and gas disc, there is a transition point where the free precession frequency of a lopsided mode, Omega - kappa, changes from retrograde to prograde and this in turn reverses the direction of angular momentum flow in the disc leading to an unphysical behaviour. We show that this problem is overcome in the presence of a dark matter halo, which sets the angular momentum flow outwards as required for disc evolution, provided the lopsidedness is leading in nature. This, plus the well-known angular momentum transport in the inner parts due to spiral arms, can facilitate an inflow of gas from outside perhaps through the cosmic filaments.

Long range emission enhancement and anisotropy in coupled quantum dots induced by aligned gold nanoantenna

Quantum dot arrays have been projected as the material of choice for next generation displays and photodetectors. Extensive ongoing research aims at improving optical and electrical efficiencies of such devices. We report experimental results on non-local long range emission intensity enhancement and anisotropy in quantum dot assemblies induced by isolated and partially aligned gold nanoantennas. Spatially resolved photoluminescence clearly demonstrate that the effect is maximum, when the longitudinal surface plasmon resonance of the nanoantenna is resonant with the emission maxima of the quantum dots. We estimated the decay length of this enhancement to be similar to 2.6 mu m, which is considerably larger than the range of near field interaction of metal nanoantenna. Numerical simulations qualitatively capture the near field behavior of the nanorods but fail to match the experimentally observed non-local effects. We have suggested how strong interactions of quantum dots in the close packed assemblies, mediated by the nanoantennas, could lead to such observed behavior. (C) 2014 AIP Publishing LLC.

Orientational order as the origin of the long-range hydrophobic effect

The long range attractive force between two hydrophobic surfaces immersed in water is observed to decrease exponentially with their separation-this distance-dependence of effective force is known as the hydrophobic force law (HFL). We explore the microscopic origin of HFL by studying distance-dependent attraction between two parallel rods immersed in 2D Mercedes Benz model of water. This model is found to exhibit a well-defined HFL. Although the phenomenon is conventionally explained by density-dependent theories, we identify orientation, rather than density, as the relevant order parameter. The range of density variation is noticeably shorter than that of orientational heterogeneity. The latter is comparable to the observed distances of hydrophobic force. At large separation, attraction between the rods arises primarily from a destructive interference among the inwardly propagating oppositely oriented heterogeneity generated in water by the two rods. As the rods are brought closer, the interference increases leading to a decrease in heterogeneity and concomitant decrease in free energy of the system, giving rise to the effective attraction. We notice formation of hexagonal ice-like structures at the onset of attractive region which suggests that metastable free energy minimum may play a role in the origin of HFL. (C) 2015 AIP Publishing LLC.

HCN channels enhance spike phase coherence and regulate the phase of spikes and LFPs in the theta-frequency range

What are the implications for the existence of subthreshold ion channels, their localization profiles, and plasticity on local field potentials (LFPs)? Here, we assessed the role of hyperpolarization-activated cyclic-nucleotide-gated (HCN) channels in altering hippocampal theta-frequency LFPs and the associated spike phase. We presented spatiotemporally randomized, balanced theta-modulated excitatory and inhibitory inputs to somatically aligned, morphologically realistic pyramidal neuron models spread across a cylindrical neuropil. We computed LFPs from seven electrode sites and found that the insertion of an experimentally constrained HCN-conductance gradient into these neurons introduced a location- dependent lead in the LFP phase without significantly altering its amplitude. Further, neurons fired action potentials at a specific theta phase of the LFP, and the insertion of HCN channels introduced large lags in this spike phase and a striking enhancement in neuronal spike-phase coherence. Importantly, graded changes in either HCN conductance or its half-maximal activation voltage resulted in graded changes in LFP and spike phases. Our conclusions on the impact of HCN channels on LFPs and spike phase were invariant to changes in neuropil size, to morphological heterogeneity, to excitatory or inhibitory synaptic scaling, and to shifts in the onset phase of inhibitory inputs. Finally, we selectively abolished the inductive lead in the impedance phase introduced by HCN channels without altering neuronal excitability and found that this inductive phase lead contributed significantly to changes in LFP and spike phase. Our results uncover specific roles for HCN channels and their plasticity in phase-coding schemas and in the formation and dynamic reconfiguration of neuronal cell assemblies.

Airblast spray in crossflow - Structure, trajectory and droplet sizing

This study reports results of an experimental investigation of airblast spray of water and ethanol in crossflow. Laser shadowgraphy and Particle/Droplet Imaging Analysis (PDIA) are used to derive spray trajectory and drop size information while Particle Tracking Velocimetry (PTV) is used to measure droplet velocities. A new phenomenon of spray bifurcation is observed for low Gas to Liquid Ratio (GLR) cases. The reasons for the spatial bifurcation can be attributed to a combination of reasons. These are (a) presence of large ligaments and droplets in the near-nozzle region for low GLRs (b) secondary breakup experienced by ligaments/droplets leading to formation of a large number of small droplets, and (c) the crossflow causing differential dispersion of the small and large droplets. A novel correlation for spray trajectory is proposed incorporating the momentum ratio and liquid surface tension. This correlation is shown to be effective in predicting the non-linear spray trajectory over a large range of conditions for not only water but ethanol and Jet-A also. It is observed that the larger droplets penetrate further into the crossflow, in the direction of injection. Thus, with increase in height of the measurement location from the injection plane, the droplet Sauter Mean Diameter (SMD) is found to increase. Moreover, as the droplets travel downstream in the crossflow direction, the droplet SMD is observed to decrease. The effect of drag is assessed by comparing velocity of different sizes of droplets at various locations. Smaller droplets are entrained into the crossflow at much lower elevations, whereas larger droplets tend to penetrate further into the crossflow. (C) 2015 Elsevier Ltd. All rights reserved.

Electric field induced short range to long range structural ordering and its influence on the Eu+3 photoluminescence in the lead-free ferroelectric Na1/2Bi1/2TiO3

Eu+3 was incorporated into the lattice of a lead-free ferroelectric Na1/2Bi1/2TiO3 (NBT) as per the nominal formula Na0.5Bi0.5-xEuxTiO3. This system was investigated with regard to the Eu+3 photoluminescence (PL) and structural behaviour as a function of composition and electric field. Electric field was found to irreversibly change the features in the PL spectra and also in the x-ray diffraction patterns below the critical composition x = 0.025. Detailed analysis revealed that below the critical composition, electric field irreversibly suppresses the structural heterogeneity inherent of the host matrix NBT and brings about a long range ferroelectric state with rhombohedral (R3c) distortion. It is shown that the structural disorder on the nano-scale opens a new channel for radiative transition which manifests as a new emission line branching off from the main D-5(0)-> F-7(0) line along with a concomitant change in the relative intensity of the other crystal field induced Stark lines with different J values. The study suggests that Eu+3 luminescence can be used to probe the relative degree of field induced structural ordering in relaxor ferroelectrics and also in high performance piezoelectric alloys where electric field couples very strongly with the lattice and structural degrees of freedom. (C) 2015 AIP Publishing LLC.

HYDROMAGNETICS OF ADVECTIVE ACCRETION FLOWS AROUND BLACK HOLES: REMOVAL OF ANGULAR MOMENTUM BY LARGE-SCALE MAGNETIC STRESSES

We show that the removal of angular momentum is possible in the presence of large-scale magnetic stresses in geometrically thick, advective, sub-Keplerian accretion flows around black holes in steady state, in the complete absence of alpha-viscosity. The efficiency of such an angular momentum transfer could be equivalent to that of alpha-viscosity with alpha = 0.01-0.08. Nevertheless, the required field is well below its equipartition value, leading to a magnetically stable disk flow. This is essentially important in order to describe the hard spectral state of the sources when the flow is non/sub-Keplerian. We show in our simpler 1.5 dimensional, vertically averaged disk model that the larger the vertical-gradient of the azimuthal component of the magnetic field is, the stronger the rate of angular momentum transfer becomes, which in turn may lead to a faster rate of outflowing matter. Finding efficient angular momentum transfer in black hole disks via magnetic stresses alone, is very interesting when the generic origin of alpha-viscosity is still being explored.