Parallel Computation of 2D Morse-Smale Complexes

The Morse-Smale complex is a useful topological data structure for the analysis and visualization of scalar data. This paper describes an algorithm that processes all mesh elements of the domain in parallel to compute the Morse-Smale complex of large two-dimensional data sets at interactive speeds. We employ a reformulation of the Morse-Smale complex using Forman's Discrete Morse Theory and achieve scalability by computing the discrete gradient using local accesses only. We also introduce a novel approach to merge gradient paths that ensures accurate geometry of the computed complex. We demonstrate that our algorithm performs well on both multicore environments and on massively parallel architectures such as the GPU.

Oneand twodimensional single quantumand multiplequantumNMR methodologies: tools for chiral analyses

It is well known that enantiomers cannot be distinguished by NMR spectroscopy unless diastereomorphic interactions are imposed. Several chiral aligning media have therefore been reported for their visualization, although extensive studies are carried out using the liquid crystal made of polypeptide poly-γ-benzyl-L-glutamate (PBLG) in organic solvent. In PBLG medium the spin systems are weakly coupled and the first order analyses of the spectra are generally possible. But due to large number of pair wise interactions of nuclear spins resulting in many degenerate transitions the 1H NMR spectra are not only complex but also broad and featureless, in addition to an indistinguishable overlap of the spectra of enantiomers. This enormous loss of resolution severely hinders the analyses of proton spectra, even for spin systems with 5–6 interacting protons, thereby restricting itsroutine application. In this review we discuss our recently developed several one and multidimensional NMR experiments to circumvent these difficulties taking specific examples of the molecules containing a single chiral centre.

Three-Component Chiral Derivatizing Protocols for NMR Spectroscopic Enantiodiscrimination of Hydroxy Acids and Primary Amines

The novel three-component chiral derivatization protocols have been derived for (1)H and (19)F NMR spectroscopic discrimination of a series of chiral hydroxy acids by their coordination and self-assembly with optically active a-methylbenzylamine and 2-formylphenylboronic acid. In addition, the optically pure (S)-mandelic acid in combination with 2-formylphenylboronic acid permits visualization of enantiomers of primary amines. These protocols have been demonstrated on enantiodiscrimination of chiral amines and hydroxy acids.

Real source-sink pair

This work is concerned with the interaction of a source-sink pair. The main parameters of the problem are source and sink flow rates, the axial and lateral separations of the source and sink, and the angle between the axes of source and sink. Of concern is the percentage of source fluid that enters the sink as a function of these parameters. The experiments have been carried using the source nozzle diameter of 6 mm and the sink pipe diameter of two sizes: 10 mm and 20 mm. The Reynolds numbers of the source jet is about 3200. The main diagnostics are flow visualization using dye, laser induced fluorescence (LIF), particle streak photographs and particle image velocimetry (Ply). To obtain the removal effectiveness (that is percentage of source fluid that is going through the sink pipe), titration method is used. The sink diameter and the angle between source and the sink axes do not influence efficiencies as do the sink flow rate and the lateral separation. Data from experiments have been consolidated so that these results can be used for designing sinks for removal of heat and pollutants. (C) 2011 Elsevier Ltd. All rights reserved.

Planform structure of turbulent free convection on horizontal surfaces

The planform structure of turbulent free convection over a heated horizontal surface has been visualized and analyzed for different boundary conditions at the top and for different aspect ratios, for flux Rayleigh numbers ranging from 10 exp 8 - 10 exp 10. The different boundary conditions correspond to Rayleigh-Benard convection, open convection with evaporation at the top and with an imposed external flow on the heated boundary. Without the external flow the planform is one randomly oriented line plume. At large Ra, these line plumes seem to align along the diagonal, persumably due to a large-scale flow along as visualized in the side view. When the external flow is imposed, the line plumes clearly align in the direction of external flow. Flow visualization reveals that at these Ra, the shear tends to break the plumes which otherwise would reach the opposite boundary. (Author)

In-situ measurements of concentration and temperature during transient solidification of aqueous solution of ammonium chloride using laser interferometry

The variation in temperature and concentration plays a crucial role in predicting the final microstructure during solidification of a binary alloy. Most of the experimental techniques used to measure concentration and temperature are intrusive in nature and affect the flow field. In this paper, the main focus is laid on in-situ, non-intrusive, transient measurement of concentration and temperature during the solidification of a binary mixture of aqueous ammonium chloride solution (a metal-analog system) in a top cooled cavity using laser based Mach-Zehnder Interferometric technique. It was found from the interferogram, that the angular deviation of fringe pattern and the total number of fringes exhibit significant sensitivity to refractive index and hence are functions of the local temperature and concentration of the NH4Cl solution inside the cavity. Using the fringe characteristics, calibration curves were established for the range of temperature and concentration levels expected during the solidification process. In the actual solidification experiment, two hypoeutectic solutions (5% and 15% NH4Cl) were chosen. The calibration curves were used to determine the temperature and concentration of the solution inside the cavity during solidification of 5% and 15% NH4Cl solution at different instants of time. The measurement was carried out at a fixed point in the cavity, and the concentration variation with time was recorded as the solid-liquid interface approached the measurement point. The measurement exhibited distinct zones of concentration distribution caused by solute rejection and Rayleigh Benard convection. Further studies involving flow visualization with laser scattering confirmed the Rayleigh Benard convection. Computational modeling was also performed, which corroborated the experimental findings. (C) 2011 Elsevier Ltd. All rights reserved.

Experimental Studies on High-Pressure Spray Structure of Biofuels

The high-pressure spray characteristics of biofuels, specifically, Pongamia oil and its blends with diesel are studied for various gas pressures. Two single-hole solenoid injectors with nozzle diameters of 200 and 260 mu m are used along with a high-pressure common-rail direct-injection system to inject fuel into a high-pressure spray visualization chamber. The spray structure is characterized using a high-speed laser-based shadowgraphy technique. The spray structure of Pongamia oil revealed the presence of an intact liquid core at low gas pressure. At high gas pressures, the spray atomization of the Pongamia oil showed marked improvement. The spray tip penetration of Pongamia oil and its blends with diesel is higher compared to that of diesel for all test conditions. The spray cone angle of Pongamia oil and 50% Pongamia oil blend with diesel is lower as compared to that of diesel. Both these observations are attributed to the presence of large droplets carrying higher momentum in oil and blend. The droplet size is measured at an injection pressure of 1000 bar and gas pressure of 30 bar at 25 mm below the nozzle tip using the particle/droplet image.analysis (PDIA) method. The droplet size measurements have shown that the Sauter mean diameter (SMD) in the spray core of Pongamia oil is more than twice that of diesel. The spray tip penetration of the 20% blend of Pongamia with diesel (P20) is similar to that of diesel but the SMD is 50% higher. Based on experimental data, appropriate spray tip penetration correlation is proposed for the vegetable oil fuels such as Pongamia.

A novel variable resolution global spectral method on the sphere

A variable resolution global spectral method is created on the sphere using High resolution Tropical Belt Transformation (HTBT). HTBT belongs to a class of map called reparametrisation maps. HTBT parametrisation of the sphere generates a clustering of points in the entire tropical belt; the density of the grid point distribution decreases smoothly in the domain outside the tropics. This variable resolution method creates finer resolution in the tropics and coarser resolution at the poles. The use of FFT procedure and Gaussian quadrature for the spectral computations retains the numerical efficiency available with the standard global spectral method. Accuracy of the method for meteorological computations are demonstrated by solving Helmholtz equation and non-divergent barotropic vorticity equation on the sphere. (C) 2011 Elsevier Inc. All rights reserved.

Plumes Dynamics and Heat Transfer over Horizontal Grooved Surfaces

This study investigates the free convection and plumes dynamics over horizontal surfaces with parallel V-grooves. The convection is studied in a tank of water with the bottom surface being a smooth or grooved surface and the top of the water surface exposed to ambient. Two groove heights were used-10 mm and 3 mm-and the experiment was done with two values of aspect ratio-2.9 and 1.8 (aspect ratio is the width of the fluid layer/height of fluid layer). Heat flux at the bottom surface was from electrical heating. Beyond a certain critical temperature difference, enhanced heat transfer is obtained on the grooved surface compared to a smooth surface. Nusselt numbers are evaluated for both smooth and grooved surfaces and correlated using modified Rayleigh numbers. Visualization shows that the enhanced heat transport in the rough cavities cannot be ascribed to the increase in the contact area; rather, it must be the local dynamics of the thermal boundary layer.

Fragment Finder 2.0: a computing server to identify structurally similar fragments

Fragment Finder 2.0 is a web-based interactive computing server which can be used to retrieve structurally similar protein fragments from 25 and 90% nonredundant data sets. The computing server identifies structurally similar fragments using the protein backbone C alpha angles. In addition, the identified fragments can be superimposed using either of the two structural superposition programs, STAMP and PROFIT, provided in the server. The freely available Java plug-in Jmol has been interfaced with the server for the visualization of the query and superposed fragments. The server is the updated version of a previously developed search engine and employs an in-house-developed fast pattern matching algorithm. This server can be accessed freely over the World Wide Web through the URL http://cluster.physics.iisc.ernet.in/ff/.

Numerical Investigation of Heat Transfer from a Two-Dimensional Sudden Expansion Flow Using Nanofluids

Laminar forced convection heat transfer from two-dimensional sudden expansion flow of different nanofluids is studied numerically. The governing equations are solved using the unsteady stream function-vorticity method. The effect of volume fraction of the nanoparticles and type of nanoparticles on heat transfer is examined and found to have a significant impact. Local and average Nusselt numbers are reported in connection with various nanoparticle, volume fraction, and Reynolds number for expansion ratio 2. The Nusselt number reaches peak values near the reattachment point and reaches asymptotic value in the downstream. Bottom wall eddy and volume fraction shows a significant impact on the average Nusselt number.

Determination of alpha(s)(M-tau(2)) from improved fixed order perturbation theory

We revisit the extraction of alpha(s)(M-tau(2)) from the QCD perturbative corrections to the hadronic tau branching ratio, using an improved fixed-order perturbation theory based on the explicit summation of all renormalization-group accessible logarithms, proposed some time ago in the literature. In this approach, the powers of the coupling in the expansion of the QCD Adler function are multiplied by a set of functions D-n, which depend themselves on the coupling and can be written in a closed form by iteratively solving a sequence of differential equations. We find that the new expansion has an improved behavior in the complex energy plane compared to that of the standard fixed-order perturbation theory (FOPT), and is similar but not identical to the contour-improved perturbation theory (CIPT). With five terms in the perturbative expansion we obtain in the (MS) over bar scheme alpha(s)(M-tau(2)) = 0.338 +/- 0.010, using as input a precise value for the perturbative contribution to the hadronic width of the tau lepton reported recently in the literature.

A study on seismicity and seismic hazard for Karnataka State

This paper presents a detailed study on the seismic pattern of the state of Karnataka and also quantifies the seismic hazard for the entire state. In the present work, historical and instrumental seismicity data for Karnataka (within 300 km from Karnataka political boundary) were compiled and hazard analysis was done based on this data. Geographically, Karnataka forms a part of peninsular India which is tectonically identified as an intraplate region of Indian plate. Due to the convergent movement of the Indian plate with the Eurasian plate, movements are occurring along major intraplate faults resulting in seismic activity of the region and hence the hazard assessment of this region is very important. Apart from referring to seismotectonic atlas for identifying faults and fractures, major lineaments in the study area were also mapped using satellite data. The earthquake events reported by various national and international agencies were collected until 2009. Declustering of earthquake events was done to remove foreshocks and aftershocks. Seismic hazard analysis was done for the state of Karnataka using both deterministic and probabilistic approaches incorporating logic tree methodology. The peak ground acceleration (PGA) at rock level was evaluated for the entire state considering a grid size of 0.05A degrees x 0.05A degrees. The attenuation relations proposed for stable continental shield region were used in evaluating the seismic hazard with appropriate weightage factors. Response spectra at rock level for important Tier II cities and Bangalore were evaluated. The contour maps showing the spatial variation of PGA values at bedrock are presented in this work.

INST: An Integrated Steering Framework for Critical Weather Applications

Online remote visualization and steering of critical weather applications like cyclone tracking are essential for effective and timely analysis by geographically distributed climate science community. A steering framework for controlling the high-performance simulations of critical weather events needs to take into account both the steering inputs of the scientists and the criticality needs of the application including minimum progress rate of simulations and continuous visualization of significant events. In this work, we have developed an integrated user-driven and automated steering framework INST for simulations, online remote visualization, and analysis for critical weather applications. INST provides the user control over various application parameters including region of interest, resolution of simulation, and frequency of data for visualization. Unlike existing efforts, our framework considers both the steering inputs and the criticality of the application, namely, the minimum progress rate needed for the application, and various resource constraints including storage space and network bandwidth to decide the best possible parameter values for simulations and visualization.

Confinement and viscoelastic effects on chain closure dynamics

Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to cellular biochemistry - the diffusion-limited cyclization of long chain polymers - is influenced by such confinement and crowding effects. More specifically, starting from the Rouse model of polymer dynamics, and invoking the Wilemski-Fixman approximation, we determine the scaling relationship between the mean closure time t(c) of a flexible chain (no excluded volume or hydrodynamic interactions) and the length N of its contour under the following separate conditions: (a) confinement of the chain to a sphere of radius d and (b) modulation of its dynamics by colored Gaussian noise. Among other results, we find that in case (a) when d is much smaller than the size of the chain, t(c) similar to Nd-2, and that in case (b), t(c) similar to N-2/(2 (2H)), H being a number between 1/2 and 1 that characterizes the decay of the noise correlations. H is not known a priori, but values of about 0.7 have been used in the successful characterization of protein conformational dynamics. At this value of H (selected for purposes of illustration), t(c) similar to N-3.4, the high scaling exponent reflecting the slow relaxation of the chain in a viscoelastic medium. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4729041]