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.

Kannada WordNet - a lexical database

This paper presents the preliminary analysis of Kannada WordNet and the set of relevant computational tools. Although the design has been inspired by the famous English WordNet, and to certain extent, by the Hindi WordNet, the unique features of Kannada WordNet are graded antonyms and meronymy relationships, nominal as well as verbal compoundings, complex verb constructions and efficient underlying database design (designed to handle storage and display of Kannada unicode characters). Kannada WordNet would not only add to the sparse collection of machine-readable Kannada dictionaries, but also will give new insights into the Kannada vocabulary. It provides sufficient interface for applications involved in Kannada machine translation, spell checker and semantic analyser.

Pleiotropic Roles of a Ribosomal Protein in Dictyostelium discoideum

The cell cycle phase at starvation influences post-starvation differentiation and morphogenesis in Dictyostelium discoideum. We found that when expressed in Saccharomyces cerevisiae, a D. discoideum cDNA that encodes the ribosomal protein S4 (DdS4) rescues mutations in the cell cycle genes cdc24, cdc42 and bem1. The products of these genes affect morphogenesis in yeast via a coordinated moulding of the cytoskeleton during bud site selection. D. discoideum cells that over-or under-expressed DdS4 did not show detectable changes in protein synthesis but displayed similar developmental aberrations whose intensity was graded with the extent of over-or under-expression. This suggested that DdS4 might influence morphogenesis via a stoichiometric effect - specifically, by taking part in a multimeric complex similar to the one involving Cdc24p, Cdc42p and Bem1p in yeast. In support of the hypothesis, the S. cerevisiae proteins Cdc24p, Cdc42p and Bem1p as well as their D. discoideum cognates could be co-precipitated with antibodies to DdS4. Computational analysis and mutational studies explained these findings: a C-terminal domain of DdS4 is the functional equivalent of an SH3 domain in the yeast scaffold protein Bem1p that is central to constructing the bud site selection complex. Thus in addition to being part of the ribosome, DdS4 has a second function, also as part of a multi-protein complex. We speculate that the existence of the second role can act as a safeguard against perturbations to ribosome function caused by spontaneous variations in DdS4 levels.

Theory and Algorithms for Hop-Count-Based Localization with Random Geometric Graph Models of Dense Sensor Networks

Wireless sensor networks can often be viewed in terms of a uniform deployment of a large number of nodes in a region of Euclidean space. Following deployment, the nodes self-organize into a mesh topology with a key aspect being self-localization. Having obtained a mesh topology in a dense, homogeneous deployment, a frequently used approximation is to take the hop distance between nodes to be proportional to the Euclidean distance between them. In this work, we analyze this approximation through two complementary analyses. We assume that the mesh topology is a random geometric graph on the nodes; and that some nodes are designated as anchors with known locations. First, we obtain high probability bounds on the Euclidean distances of all nodes that are h hops away from a fixed anchor node. In the second analysis, we provide a heuristic argument that leads to a direct approximation for the density function of the Euclidean distance between two nodes that are separated by a hop distance h. This approximation is shown, through simulation, to very closely match the true density function. Localization algorithms that draw upon the preceding analyses are then proposed and shown to perform better than some of the well-known algorithms present in the literature. Belief-propagation-based message-passing is then used to further enhance the performance of the proposed localization algorithms. To our knowledge, this is the first usage of message-passing for hop-count-based self-localization.

Electrical properties of buckled multiwalled carbon nanotube arrays in the diffusive regime

We report the geometrical effect of graded buckled multiwalled carbon nanotube arrays on the electrical transport properties in the diffusive regime, via successive breakdown caused by the Joule heating. This breakdown occurs in the straighter region. Empirical relations involving the current-carrying ability, resistance, breakdown power, threshold voltage, diameter and length of carbon nanotube arrays are discussed on the basis of an extensive set of experimental data along with justification. The experimental results are corroborated by the density functional tight-binding calculations of electronic band structure. The band gap decreases as buckleness increases leading to the enhancement in the current-carrying ability and elucidating the role of buckleness in carbon nanotubes. Copyright (c) EPLA, 2012

Demonstrating the Usefulness of CAELinux for Computer Aided Engineering using an Example of the Three Dimensional Reconstruction of a Pig Liver

CAELinux is a Linux distribution which is bundled with free software packages related to Computer Aided Engineering (CAE). The free software packages include software that can build a three dimensional solid model, programs that can mesh a geometry, software for carrying out Finite Element Analysis (FEA), programs that can carry out image processing etc. Present work has two goals: 1) To give a brief description of CAELinux 2) To demonstrate that CAELinux could be useful for Computer Aided Engineering, using an example of the three dimensional reconstruction of a pig liver from a stack of CT-scan images. One can note that instead of using CAELinux, using commercial software for reconstructing the liver would cost a lot of money. One can also note that CAELinux is a free and open source operating system and all software packages that are included in the operating system are also free. Hence one can conclude that CAELinux could be a very useful tool in application areas like surgical simulation which require three dimensional reconstructions of biological organs. Also, one can see that CAELinux could be a very useful tool for Computer Aided Engineering, in general.

An adaptive singular ES-FEM for mechanics problems with singular field of arbitrary order

This paper presents a singular edge-based smoothed finite element method (sES-FEM) for mechanics problems with singular stress fields of arbitrary order. The sES-FEM uses a basic mesh of three-noded linear triangular (T3) elements and a special layer of five-noded singular triangular elements (sT5) connected to the singular-point of the stress field. The sT5 element has an additional node on each of the two edges connected to the singular-point. It allows us to represent simple and efficient enrichment with desired terms for the displacement field near the singular-point with the satisfaction of partition-of-unity property. The stiffness matrix of the discretized system is then obtained using the assumed displacement values (not the derivatives) over smoothing domains associated with the edges of elements. An adaptive procedure for the sES-FEM is proposed to enhance the quality of the solution with minimized number of nodes. Several numerical examples are provided to validate the reliability of the present sES-FEM method. (C) 2012 Elsevier B.V. All rights reserved.

Flux density calibration in diffuse optical tomographic systems

The solution of the forward equation that models the transport of light through a highly scattering tissue material in diffuse optical tomography (DOT) using the finite element method gives flux density (Phi) at the nodal points of the mesh. The experimentally measured flux (U-measured) on the boundary over a finite surface area in a DOT system has to be corrected to account for the system transfer functions (R) of various building blocks of the measurement system. We present two methods to compensate for the perturbations caused by R and estimate true flux density (Phi) from U-measured(cal). In the first approach, the measurement data with a homogeneous phantom (U-measured(homo)) is used to calibrate the measurement system. The second scheme estimates the homogeneous phantom measurement using only the measurement from a heterogeneous phantom, thereby eliminating the necessity of a homogeneous phantom. This is done by statistically averaging the data (U-measured(hetero)) and redistributing it to the corresponding detector positions. The experiments carried out on tissue mimicking phantom with single and multiple inhomogeneities, human hand, and a pork tissue phantom demonstrate the robustness of the approach. (C) 2013 Society of Photo-Optical Instrumentation Engineers (SPIE) DOI: 10.1117/1.JBO.18.2.026023]

Information dissemination in socially aware networks under the linear threshold model

We provide new analytical results concerning the spread of information or influence under the linear threshold social network model introduced by Kempe et al. in, in the information dissemination context. The seeder starts by providing the message to a set of initial nodes and is interested in maximizing the number of nodes that will receive the message ultimately. A node's decision to forward the message depends on the set of nodes from which it has received the message. Under the linear threshold model, the decision to forward the information depends on the comparison of the total influence of the nodes from which a node has received the packet with its own threshold of influence. We derive analytical expressions for the expected number of nodes that receive the message ultimately, as a function of the initial set of nodes, for a generic network. We show that the problem can be recast in the framework of Markov chains. We then use the analytical expression to gain insights into information dissemination in some simple network topologies such as the star, ring, mesh and on acyclic graphs. We also derive the optimal initial set in the above networks, and also hint at general heuristics for picking a good initial set.

Seismic site classification and correlation between standard penetration test N value and shear wave velocity for Lucknow city in Indo-Gangetic basin

Subsurface lithology and seismic site classification of Lucknow urban center located in the central part of the Indo-Gangetic Basin (IGB) are presented based on detailed shallow subsurface investigations and borehole analysis. These are done by carrying out 47 seismic surface wave tests using multichannel analysis of surface waves (MASW) and 23 boreholes drilled up to 30 m with standard penetration test (SPT) N values. Subsurface lithology profiles drawn from the drilled boreholes show low- to medium-compressibility clay and silty to poorly graded sand available till depth of 30 m. In addition, deeper boreholes (depth >150 m) were collected from the Lucknow Jal Nigam (Water Corporation), Government of Uttar Pradesh to understand deeper subsoil stratification. Deeper boreholes in this paper refer to those with depth over 150 m. These reports show the presence of clay mix with sand and Kankar at some locations till a depth of 150 m, followed by layers of sand, clay, and Kankar up to 400 m. Based on the available details, shallow and deeper cross-sections through Lucknow are presented. Shear wave velocity (SWV) and N-SPT values were measured for the study area using MASW and SPT testing. Measured SWV and N-SPT values for the same locations were found to be comparable. These values were used to estimate 30 m average values of N-SPT (N-30) and SWV (V-s(30)) for seismic site classification of the study area as per the National Earthquake Hazards Reduction Program (NEHRP) soil classification system. Based on the NEHRP classification, the entire study area is classified into site class C and D based on V-s(30) and site class D and E based on N-30. The issue of larger amplification during future seismic events is highlighted for a major part of the study area which comes under site class D and E. Also, the mismatch of site classes based on N-30 and V-s(30) raises the question of the suitability of the NEHRP classification system for the study region. Further, 17 sets of SPT and SWV data are used to develop a correlation between N-SPT and SWV. This represents a first attempt of seismic site classification and correlation between N-SPT and SWV in the Indo-Gangetic Basin.

Interface capturing simulations of acoustically driven bubble dynamics in and near tissue

Tissue injury during therapeutic ultrasound or lithotripsy is thought, in cases, to be due to the action of cavitation bubbles. Assessing this and mitigating it is challenging since bubble dynamics in the complex confinement of tissues or in small blood vessels are challenging to predict. Simulations tools require specialized algorithms to simultaneously represent strong acoustic waves and shocks, topologically complex liquid‐vapor phase boundaries, and the complex viscoelastic material dynamics of tissue. We discuss advances in a simulation tool for such situations. A single‐mesh Eulerian solver is used to solve the governing equations. Special sharpening terms maintain the liquid‐vapor interface in face of the finite numerical dissipation included in the scheme to accurately capture shocks. A recent enhancement to this formulation has significantly improved this interface capturing procedure, which is demonstrated for simulation of the Rayleigh collapse of a bubble. The solver also transports elastic stresses and can thus be used to assess the effects of elastic properties on bubble dynamics. A shock‐induced bubble collapse adjacent to a model elastic tissue is used to demonstrate this and draw some conclusions regarding the injury suppressing role that tissue elasticity might play.

A h-Adaptive Algorithm Using Residual Error Estimates for Fluid Flows

Algorithms for adaptive mesh refinement using a residual error estimator are proposed for fluid flow problems in a finite volume framework. The residual error estimator, referred to as the R-parameter is used to derive refinement and coarsening criteria for the adaptive algorithms. An adaptive strategy based on the R-parameter is proposed for continuous flows, while a hybrid adaptive algorithm employing a combination of error indicators and the R-parameter is developed for discontinuous flows. Numerical experiments for inviscid and viscous flows on different grid topologies demonstrate the effectiveness of the proposed algorithms on arbitrary polygonal grids.

Biomechanics of Substrate Boring by Fig Wasps: Role of Zinc in Insect Cuticle

There are many biomechanical challenges that a female insect must meet to successfully oviposit and ensure her evolutionary success. These begin with selection of a suitable substrate through which the ovipositor must penetrate without itself buckling or fracturing. The second phase corresponds to steering and manipulating the ovipositor to deliver eggs at desired locations. Finally, the insect must retract her ovipositor fast to avoid possible predation and repeat this process multiple times during her lifetime. From a materials perspective, insect oviposition is a fascinating problem and poses many questions. Specifically, are there diverse mechanisms that insects use to drill through hard substrates without itself buckling or fracturing? What are the structure-property relationships in the ovipositor material? These are some of the questions we address with a model system consisting of a parasitoid fig wasp - fig substrate system. To characterize the structure of ovipositors, we use scanning electron microscopy with a detector to quantify the presence of transition elements. Our results show that parasitoid ovipositors have teeth like structures on their tips and contain high amounts of zinc as compared to remote regions. Sensillae are present along the ovipositor to aid detection of chemical species and mechanical deformations. To quantify the material properties of parasitoid ovipositors, we use an atomic force microscope and show that tip regions have higher modulus as compared to remote regions. Finally, we use videography to show that ovipositors buckle during oviposition and estimate the forces needed to cause substrate boring based on Euler buckling analysis. Such methods may be useful for the design of functionally graded surgical tools.

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.

Efficient asynchronous executions of AMR computations and visualization on a GPU system

Adaptive Mesh Refinement is a method which dynamically varies the spatio-temporal resolution of localized mesh regions in numerical simulations, based on the strength of the solution features. In-situ visualization plays an important role for analyzing the time evolving characteristics of the domain structures. Continuous visualization of the output data for various timesteps results in a better study of the underlying domain and the model used for simulating the domain. In this paper, we develop strategies for continuous online visualization of time evolving data for AMR applications executed on GPUs. We reorder the meshes for computations on the GPU based on the users input related to the subdomain that he wants to visualize. This makes the data available for visualization at a faster rate. We then perform asynchronous executions of the visualization steps and fix-up operations on the CPUs while the GPU advances the solution. By performing experiments on Tesla S1070 and Fermi C2070 clusters, we found that our strategies result in 60% improvement in response time and 16% improvement in the rate of visualization of frames over the existing strategy of performing fix-ups and visualization at the end of the timesteps.