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Reports & scientific papers

Reports and scientific papers on EU-IndiaGrid2 User communities fields of interest are collected in this section.

Other EUIG2 papers are currently under preparation and / or waiting for publication in 2012. The list provided in below:

 

  • Amit Das, J. L. Ferrer and M. V. Hosur (2011): Mechanism of resistance through X-ray structure of M36I mutant of HIV-1 protease complexed with the inhibitor Ritonavir. (part of Ph. D. thesis submitted to Homi Bhabha National Institute)
  • Subhash Chandra Bihani, J. L. Ferrer and M. V. Hosur (2011): 1.8 Å X-ray structures of drug-resistant HIV-1 protease mutant N88S complexed with protease inhibitors Nelfinavir and Saquinavir (Manuscript under preparation)
  • D.Vaddi, S.Cozzini, Regional Climate Simulations on EU-INDIA grid infrastructure: methodologies and performance, submitted to
  • Sükösd, Z., Schmidt, H.G., and Lipkow, K. Evidence for stochastic opening of chromosomal domains by molecular simulation. In preparation, to be submitted to PNAS.
  • Collins, W.A., Howlett, A.P., Prosseda, P., Dannewitz, S., Sewitz, S., and Lipkow, K. Dynamic Localisation of CheZ Phosphatase: Experimental proof and computational insights. In preparation.
  • Schmidt, H.G., Sewitz, S., Zhang, N., Oliver, S.G. and Lipkow, K.* Effects of nuclear architecture on transcription – an integrated study. In preparation.
  • Lipkow, K. Simulating bacterial chemotaxis at high spatial resolution. Commissioned review for a special issue on Computational Cell Biology in Current Chemical Biology.
  • Lipkow, K. , Claeys Bouuaert, C. +, Andrews, S.S., and Chalmers, R. Autoregulation of mariner transposition. In preparation, to be submitted to Cell or PLoS Biology.
  • S Khan, TS Reese, NM Rajpoot, A Shabbir
Spatiotemporal Maps of CaMKII in Dendritic Spines
Journal of Computational Neuroscience (Revision under review)
 October 2011

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A. Magrin, A. Peresan, F. Vaccari, S. Cozzini, B.K. Rastogi, I.A. Parvez, G.F. Panza

Department of Mathematics and Geosciences, University of Trieste, via Weiss 4, 34127. Trieste - Italy.
The Abdus Salam International Centre for Theoretical Physics, ICTP SAND Group. Trieste - Italy
Consiglio Nazionale delle Ricerche, Istituto Officina dei Materiali, CNR/IOM uos Democritos. Trieste - Italy.

Institute of Seismological Research, Raisan, Gandhinagar, Gujarat, India

CSIR Centre for Mathematical Modelling and Computer Simulation (C-MMACS), NAL Belur Campus, Bangalore, India


Abstract
. Seismic hazard assessment can be performed following a neo-deterministic approach (NDSHA), which allows to give a realistic description of the seismic ground motion due to an earthquake of given distance and magnitude. The approach is based on modelling techniques that have been developed from a detailed knowledge of both the seismic source process and the propagation of seismic waves.
This permits us to define a set of earthquake scenarios and to simulate the associated synthetic signals without having to wait for a strong event to occur. NDSHA can be applied at the regional scale, computing seismograms at the nodes of a grid with the desired spacing, or at the local scale, taking into account the source characteristics, the path and local geological and geotechnical conditions. Synthetic signals can be produced in a short time and at a very low cost/benefit ratio. They can be used as seismic input in subsequent engineering analyses aimed at the computation of the full non-linear seismic response of the structure or simply the earthquake damaging potential.
Massive parametric tests, to explore the influence not only of deterministic source parameters
and structural models but also of random properties of the same source model, enable realistic
estimate of seismic hazard and their uncertainty. This is particular true in those areas for which scarce (or no) historical or instrumental information is available.
The use of the EU-India Grid infrastructure allows to conduct massive parametric tests for evaluating the uncertainties in the computed hazard maps. In the framework of cooperation project between three Italian partners (DMG, University of Trieste; ICTP SAND Group; CNR/IOM uos Democritos) and two Indian partners (ISR, Gujarat; CSIR C-MMACS, Bangalore) a system will be set up for the scenario-based characterization of the seismic hazard, integrated with the e-infrastructures of the European project EU-India Grid.

 

The International Symposium on Grids and Clouds (ISGC) 2012, February 26 - March 2, 2012 Academia Sinica, Taipei, Taiwan



M. V. Hosur (2010)

INSA NEWS, Issue 202, page 5, published by the Indian National Science Academy, New Delhi

Giorgi, F., Coppola, E., Solmon, F., Mariotti, L., Sylla, M., Bi, X., Elguindi, N., Diro, G. T., Nair, V., Giuliani, G., Cozzini, S., Guettler, I., O’Brien, T. A., Tawfik, A., Shalaby, A., Za- key, A., Steiner, A., Stordal, F., Sloan, L., and Brankovic, C.:

Clim. Rev., accepted, 2011.
pp. 3439, 3441

These results show RegCM-UW as a nascent mesoscale stratocumulus model that is 15 appropriate for stratocumulus investigations at scales ranging from hourly to decadal.
The source code for RegCM-UW is publicly available, under the GNU license, through the International Centre for Theoretical Physics.

Giuseppe Facchetti, Giovanni Iacono, and Claudio Altafini, International School for Advanced Studies, via Bonomea 265, 34136 Trieste, Italy

Edited by Giorgio Parisi, University of Rome, Italy, and approved October 26, 2011

PNAS
URL: http://www.pnas.org/content/108/52/20953.abstract

Abstract. Structural balance theory affirms that signed social networks (i.e., graphs whose signed edges represent friendly/hostile interactions among individuals) tend to be organized so as to avoid conflictual situations, corresponding to cycles of negative parity. Using an algorithm for ground-state calculation in large-scale Ising spin glasses, in this paper we compute the global level of balance of very large online social networks and verify that currently available networks are indeed extremely balanced. This property is explainable in terms of the high degree of skewness of the sign distributions on the nodes of the graph. In particular, individuals linked by a large majority of negative edges create mostly “apparent disorder,” rather than true “frustration.”

Ideh Heidari, Sandip De, S. M. Ghazi, Stefan Goedecker, and D. G. Kanhere
Department of Chemistry, University of Pune, Ganeshkhind, Pune 411 007, India
Department of Physics and Center for Modeling and Simulation, University of Pune, Ganeshkhind, Pune 411 007, India
Physical Chemistry Division, National Chemical Laboratory, Pune 411 008, India
Department of Physics, Universitat Basel, Klingelbergstr. 82, 4056 Basel, Switzerland

J. Phys. Chem. A, 2011, 115 (44), pp 12307–12314
DOI: 10.1021/jp204442e

URL: http://pubs.acs.org/doi/abs/10.1021/jp204442e

Publication Date (Web): September 21, 2011
Copyright © 2011 American Chemical Society

Abstract. Using the minima hopping global geometry optimization method on density functional potential energy surface, we have studied the structural and electronic properties of magnesium clusters for a size range of MgN where N = 10–56. Our exhaustive search reveals that most of our global minima are nonsymmetric in the size range above N = 20. We elucidate the evolutionary trend of the entire series and present more details about the peculiar growth of the clusters. For N > 20, it is possible to divide the cluster into two regions: the core region and the surface region. It turns out that the growth follows a peculiar cyclic pattern where the core and surface grow alternatively. The surface energy, as a function of number of atoms shows a clear signature as the number of atoms in the core increases by one. We have also carried out stability analysis and the stable sizes(magic numbers) agree very well with the experimental magic numbers reported by Diederich [ J. Chem. Phys. 2011, 134, 124302]. We point out the similarities and differences between our results and sodium clusters.

S. A. Blundell, SPSMS, UMR-E CEA/UJF-Grenoble 1, INAC, Grenoble, F-38054, France
Soumyajyoti Haldary, Centre for Modeling and Simulation, University of Pune, Ganeshkhind, Pune 411 007, India and Department of Physics, University of Pune, Ganeshkhind, Pune 411 007, India.
D. G. Kanherez, Department of Physics, University of Pune, Ganeshkhind, Pune 411 007, India.

Dated: March 2, 2011

Abstract. We determine the structure and melting behavior of supported metallic clusters using an ab intio density-functional-based treatment of intracluster interactions and an approximate treatment of the surface as an idealized smooth plane yielding an e ective Lennard-Jones interaction with the ions of the cluster. We apply this model to sodium clusters containing from 4 to 22 atoms, treating the cluster-surface interaction strength as a variable parameter. For a strong cluster-surface interaction, the clusters form monolayer structures; comparisons with calculations of structure and dissociation energy performed with a classical Gupta interatomic potential show clearly the role of quantum shell e ects in the metallic binding in this case, and evidence is presented that these shell e ects correspond to those for a con ned two-dimensional electron gas. The melting behavior of a supported Na20 cluster is considered in detail using the model. Some qualitative similarities are observed in the melting dynamics between the density-functional and Gupta treatments of the cluster, involving either interlayer hops or in-plane melting according to the cluster-surface interaction strength, but there are quantitative di erences in the speci c-heat curves and melting temperatures observed.

 

In: Phys. Rev. B 84, 075430 (2011)

S. A. Blundell and S. Chackoy, SPSMS, UMR-E CEA/UJF-Grenoble 1, INAC, Grenoble, F-38054, France.

Dated: March 14, 2011

Abstract. An accurate con guation-interaction method employing a mean- eld basis set is used to study the excitation spectrum of localized Wigner states in the strongly interacting regime of a quasi-twodimensional parabolic quantum dot with N = 6 electrons. The approach achieves errors of order 1 part in 104 (or better) in the energies of low-lying states for a Wigner-Seitz radius rs = 12 a 0{16 a 0 , and is used to study low-lying spin, rotational, vibrational, and  isomeric excitations. The vibrational excitations at rs = 50 a 0 are shown to correspond qualitatively with the classical normal modes of the N = 6 electron dot, although the excitation energies agree only semiquantitatively with the classical normal-mode frequencies as a result of residual quantum uctuations.

 

In:Physical Review B, Volume 83, Issue 19
URL: http://link.aps.org/doi/10.1103/PhysRevB.83.195444

Giuseppe Andronico, Valeria Ardizzone, Roberto Barbera · Bruce Becker, Riccardo Bruno, Antonio Calanducci, Diego Carvalho, Leandro Ciuffo, Marco Fargetta, Emidio Giorgio Giuseppe La Rocca, Alberto Masoni, Marco Paganoni · Federico Ruggieri, Diego Scardaci

Published online: 24 March 2011
© Springer Science+Business Media B.V. 2011

Abstract.
In the last 10 years, a new way of doing science is spreading in the world thank to the development of virtual research communities across many geographic and administrative boundaries.
Avirtual research community is awidely dispersed group of researchers and associated scientific instruments working together in a common virtual environment. This new kind of scientific environment, usually addressed as a “collaboratory”, is based on the availability of high-speed networks and broadband access, advanced virtual tools and Grid-middleware technologies which, altogether, are the elements of the e-Infrastructures. The European Commission has heavily invested in promoting this new way of collaboration among scientists funding several international projects with the aim of creating e-Infrastructures to enable
the European Research Area and connect the European researchers with their colleagues
based in Africa, Asia and Latin America. In this paper we describe the actual status of these e- Infrastructures and present a complete picture of the virtual research communities currently using them. Information on the scientific domains and on the applications supported are provided together with their geographic distribution.

Giuseppe Andronico, Valeria Ardizzone, Roberto Barbera, Bruce Becker, Riccardo Bruno, Antonio Calanducci, Diego Carvalho, Leandro Ciuffo, Marco Fargetta and Emidio Giorgio, et al.

Journal of Grid Computing
Volume 9, Number 2, 155-184

URL: http://www.springerlink.com/content/81268575123q1p49/

 

Abstract. In the last 10 years, a new way of doing science is spreading in the world thank to the development of virtual research communities across many geographic and administrative boundaries. A virtual research community is a widely dispersed group of researchers and associated scientific instruments working together in a common virtual environment. This new kind of scientific environment, usually addressed as a “collaboratory”, is based on the availability of high-speed networks and broadband access, advanced virtual tools and Grid-middleware technologies which, altogether, are the elements of the e-Infrastructures. The European Commission has heavily invested in promoting this new way of collaboration among scientists funding several international projects with the aim of creating e-Infrastructures to enable the European Research Area and connect the European researchers with their colleagues based in Africa, Asia and Latin America. In this paper we describe the actual status of these e-Infrastructures and present a complete picture of the virtual research communities currently using them. Information on the scientific domains and on the applications supported are provided together with their geographic distribution.

Alberto Masoni, INFN Italy,
The International Symposium on Grids and Clouds and the Open Grid Forum
Academia Sinica, Taipei, Taiwan
March 19 - 25, 2011

2010 has been an eventful year for e-Infrastructures across Europe and India with a number of important achievements. EUIndiagrid2, basing on the achievements of the previous EU-IndiaGrid project and on the active role of its partners was at the core of all these events that contributed significantly to the project progress towards its objectives. The present article reviews the most recent e-Infrastructures developments in India and their relationship with respect to Europe and the Asia-Pacific area.

Alberto Masoni, INFN Italy
13th International Workshop on Advanced Computing and Analysis Techniques in Physics Research - ACAT 2010, Jaipur, India
February 22–27 2010

This article was prepared in occasion 13th International Workshop on Advanced Computing and Analysis Techniques in Physics Research - ACAT 2010 - held in Jaipur, India, in February. It provides an overview of the EU-IndiaGrid and EU-IndiaGrid2 activities in the context of the Indian e-Science scenario.

R. Balachandar, T. Selvi, M. Kashif, A.Masoni and S. Cozzini

Published in Journal Multiagent and Grid Systems archive
Volume 6 Issue 3, August 2010

ACM Digital Library URL: http://dl.acm.org/citation.cfm?id=1842423&CFID=84467293&CFTOKEN=25247749

 

Abstract. This paper investigates the interoperability issues between European and Indian Grid infrastructure and implements methodologies to overcome some of them. The main objective of EU-India Grid interoperability project is to aggregate the computational resources available across Europe and India, and to use them effectively in solving computationally intensive scientific applications. As both European and Indian Grid is based on different middleware, the interoperability initiative leads to several issues with respect to job submission, resource management and monitoring, security, and data transfers. The European Grid is based on gLite middleware and Indian Grid Garuda is a combination of in-house software's developed by C-DAC (Centre for Development of Advanced Computing), India, Globus toolkit and industry grade components. In this work, several interoperability issues have been investigated and a preliminary interoperable system to facilitate remote job submission, resource discovery between gLite and Garuda Grid infrastructure is proposed. An ExtendedUI is created to interoperate between the middleware and its prototype implementation is presented. This ExtendedUI consists of all the libraries and adapters for job submission across globus and gLite based Grid resources. GridSeed tool is used to setup experimental Grid infrastructure consists of resources based on both gLite and globus middleware and the extendedUI has been tested for job submission and information aggregation.

"Climate change is one of the greatest challenges of the world today. The consequences of the decisions we take in the next few months will be mainly borne by future generations and inaction will be very costly". Lars-Olof Lindgren, Ambassador of Sweden to India, Representing the Presidency of the Council of the European Union.

"The European Union stands ready to step up its cooperation with India on environment and climate/energy related policies and programmes". Danièle Smadja, Ambassador and Head of the Delegation of the European Union to India.

Find out more about how the EC is working with India to address climate change issues in this special report.

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