Middleware for Long-running Applications on Batch Grids. Student Research Symposium poster

Computational grids with multiple batch systems (batch grids) can be powerful infrastructures for executing long-running multicomponent parallel applications. In this paper, we have constructed a middleware framework for executing such long-running applications spanning multiple submissions to the queues on multiple batch systems. We have used our framework for execution of a foremost long-running multi-component application for climate modeling, the Community Climate System Model (CCSM). Our framework coordinates the distribution, execution, migration and restart of the components of CCSM on the multiple queues where the component jobs of the different queues can have different queue waiting and startup times.

Counter-free input-determined timed automata

We identify a class of timed automata, which we call counter-free input-determined automata, which characterize the class of timed languages definable by several timed temporal logics in the literature, including MTL. We make use of this characterization to show that MTL+Past satisfies an “ultimate stability” property with respect to periodic sequences of timed words. Our results hold for both the pointwise and continuous semantics. Along the way we generalize the result of McNaughton-Papert to show a counter-free automata characterization of FO-definable finitely varying functions.

Running neutrino mass from six dimensions

In the present talk, we will discuss a six dimensional mass generation for the neutrinos. The SM neutrinos live on a 3-brane and interact via a brane localised mass term with a Weyl singlet neutrino residing in all the six dimensions. We present the physical neutrino mass spectrum and show that the active neutrino mass and the KK masses have a logarithmic cut-off dependence at the tree level. This translates in to a renormalisation group running of n -masses above the KK compactification scale coming from classical effects without any SM particles in the spectrum.This could have effects in neutrinoless double beta decay experiments.

Iodine-Catalyzed Amination of Benzoxazoles: A Metal-Free Route to 2-Aminobenzoxazoles under Mild Conditions

A facile metal-free route of oxidative amination of benzoxazole by activation of C-H bonds with secondary or primary amines in the presence of catalytic iodine in aqueous tert-butyl hydroperoxide proceeds smoothly at ambient temperature under neat reaction condition to furnish the high yield of the aminated product. This user-friendly method to form C-N bonds produces tertiary butanol and water as the byproduct, which are environmentally benign. The application of the methodology is demonsrated by synthesizing therapeutically active benzoxazoles.

Evolution of crystallinity of free gold agglomerates and shape transformation

We report the shape evolution of free gold agglomerates with different morphologies that transform to ellipsoidal and then to spherical shapes during the heating cycle. The shape transformation is associated with a structural transition from polycrystalline to single crystalline. The structural transition temperature is shown to be dependent on the final size of the particles and not on the initial morphologies of the agglomerates. It is also shown that the transition occurs well below the melting temperature which is in contrast with the melt-freeze process reported in the literature.

Computational Analysis of Flow through a Multiple Nozzle Driven Laser Cavity and Diffuser

Computations have been carried out for simulating supersonic flow through a set of converging-diverging nozzles with their expanding jets forming a laser cavity and flow patterns through diffusers, past the cavity. A thorough numerical investigation with 3-D RANS code is carried out to capture the flow distribution which comprises of shock patterns and multiple supersonic jet interactions. The analysis of pressure recovery characteristics during the flow through the diffusers is an important parameter of the simulation and is critical for the performance of the laser device. The results of the computation have shown a close agreement with the experimentally measured parameters as well as other established results indicating that the flow analysis done is found to be satisfactory.

Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies

Single chain fragment variables (ScFvs) have been extensively employed in studying the protein-protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)-luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG-LH receptor interactions. An anti-hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG-ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson-Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG-ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG-ScFv complexes. Superimposition of hCG-ScFv model onto a model of hCG complexed with the 51-266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure-function analysis of ligand-receptor interactions. Proteins 2011;79:3108-3122. (C) 2011 Wiley-Liss, Inc.