Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca

Rome, Italy

Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca

Rome, Italy

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Guerra R.,University of Modena and Reggio Emilia | Ippolito M.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Meloni S.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Meloni S.,University College Dublin | Ossicini S.,University of Modena and Reggio Emilia
Applied Physics Letters | Year: 2012

By means of ab-initio calculations, we investigate the optical properties of pure a-SiN x samples, with x ∈ [0. 4, 1. 8], and samples embedding silicon nanoclusters (NCs) of diameter 0. 5 ≤ d ≤ 1. 0 nm. In the pure samples, the optical absorption gap and the radiative recombination rate vary according to the concentration of Si-N bonds. In the presence of NCs, the radiative rate of the samples is barely affected, indicating that the intense photoluminescence of experimental samples is mostly due to the matrix itself rather than to the NCs. Besides, we evidence an important role of Si-N-Si bonds at the NC/matrix interface in the observed photoluminescence trend. © 2012 American Institute of Physics.


Orlandini S.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Orlandini S.,University of Rome La Sapienza | Meloni S.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Meloni S.,University College Dublin | And 3 more authors.
Physical Review B - Condensed Matter and Materials Physics | Year: 2010

We have investigated the Si and O self-diffusion in stoichiometric and substoichiometric amorphous SiO2 by means of molecular-dynamics simulations. The diffusivity and the migration energies at different Si concentrations are reported and the results in qualitative agreement with previous experimental and theoretical (ab initio) results. We prove that the diffusion of Si and O occurs through steplike events. In particular, we identify three mechanisms, associated with coordination and "local stoichiometry" defects, responsible for the diffusion. The migration energy and pre-exponential factor, as well as the relative relevance of these mechanisms, is computed as a function of the Si concentration and temperature. A model for interpreting our results is proposed and discussed. © 2010 The American Physical Society.


Orlandini S.,University of Rome La Sapienza | Orlandini S.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Meloni S.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Meloni S.,University College Dublin | And 2 more authors.
AIP Conference Proceedings | Year: 2011

We review a dynamical approach to non-equilibrium MD (D-NEMD). We show how, using a proper simulation setup, is possible to treat interesting cases in which the initial condition is a stationary non-equilibrium state produced by a suitable dynamical system. We then extend the class of non-equilibrium phenomena that can be studied by atomistic simulations to the case of complex initial conditions consisting in assigning a macroscopic value of a scalar or vector observable or a field. We illustrate the functioning of this method by applying it to the relaxation of an interface between two immiscible liquids. We have shown that our method generate unbiased results while this might not be the case for the often used short time average approach. © 2011 American Institute of Physics.


Lombardozzi V.,Third University of Rome | Castrignano T.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | D'Antonio M.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Casanova Municchia A.,Third University of Rome | Caneva G.,Third University of Rome
International Biodeterioration and Biodegradation | Year: 2012

Despite the wide spectrum of literature on stone biodeterioration associated with pitting, there has not been sufficient description of some general topics related to stone biopitting in terrestrial conditions, nor of the taxonomy of the organisms supporting it. In order to synthesize the information available in the literature, and to give a critical analysis of the bibliographic data, an interactive on-line database has been created. Among the about 800 papers selected in the first step of creating this database. Only 24 studies reported on biopitting, giving information on the object, material composition and associated organisms. These first data concern 83 different sites, for a total of 249 samples, coming mainly from the Mediterranean bioclimatic area, even though the biopitting phenomenon is not exclusive to this climate. The most commonly occurring organisms are cyanobacteria, and the associated environmental conditions are dryness, arising from various factors, such as the low porosity of the stone; the exposure conditions; and the bioclimate. These factors explain very high appearance of organisms and especially cyanobacteria in marble, their preference for vertical or subvertical surfaces, and their high occurrence in Mediterranean and desert climate. The lack of information describing the entire phenomenon i.e., type of stone, exposure conditions, and all biodeteriogens present, doesn't permit the full use of the database's interactive potential. © 2012 Elsevier Ltd.


D'Onorio De Meo P.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | D'Antonio M.,University of Bari | Griggio F.,University of Milan | Lupi R.,University of Milan | And 6 more authors.
Nucleic Acids Research | Year: 2012

The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa. © The Author(s) 2011. Published by Oxford University Press.


Ippolito M.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Meloni S.,University College Dublin
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

By means of molecular dynamics simulations based on the Billeter environment-dependent classical force field we studied the structural features of SiN x samples at various stoichiometries. Our results are in good agreement with experimental data and are able to reproduce some features which so far were not reproduced by simulations. In particular, we identified units containing N-N bonds, which are thought to be responsible for an unassigned peak in the radial distribution function obtained from neutron diffraction data and signals observed in electron spin resonance, x-ray photoemission spectroscopy, electron-energy-loss spectroscopy, and optical absorption experiments. We have identified defects which are thought to be responsible for the high concentration of charge traps that makes this material suitable for building nonvolatile memory devices. We analyzed the dependency of the concentration of these defects with the stoichiometry of the sample. © 2011 American Physical Society.


Giombini E.,University of Rome La Sapienza | Orsini M.,Center for Advanced Studies | Carrabino D.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Tramontano A.,University of Rome La Sapienza
BMC Bioinformatics | Year: 2010

Background: Bacterial infections represent a global health challenge. The identification of novel antibacterial targets for both therapy and vaccination is needed on a constant basis because resistance continues to spread worldwide at an alarming rate. Even infections that were once easy to treat are becoming difficult or, in some cases, impossible to cure. Ideal targets for both therapy and vaccination are bacterial proteins exposed on the surface of the organism, which are often involved in host-pathogen interaction. Their identification can greatly benefit from technologies such as bioinformatics, proteomics and DNA microarrays.Results: Here we describe a pipeline named SLEP (Surface Localization Extracellular Proteins), based on an automated optimal combination and sequence of usage of reliable available tools for the computational identification of the surfome, i.e. of the subset of proteins exposed on the surface of a bacterial cell.Conclusions: The tool not only simplifies the usage of these methods, but it also improves the results by selecting the specifying order and combination of the instruments. The tool is freely available at http://www.caspur.it/slep. © 2010 Giombini et al; licensee BioMed Central Ltd.


Orlandini S.,University of Rome La Sapienza | Orlandini S.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Meloni S.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Meloni S.,University College Dublin | Colombo L.,University of Cagliari
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

We investigated the relative stability of the amorphous versus crystalline nanoparticles of sizes ranging between 0.8 and 1.8 nm. We found that (at variance from bulk systems) at low T, small nanoparticles are amorphous and they undergo an amorphous-to-crystalline phase transition at high T. On the contrary, large nanoparticles recover the bulklike behavior: crystalline at low T and amorphous at high T. We also investigated the structure of crystalline nanoparticles, providing evidence that they are formed by an ordered core surrounded by a disordered periphery. Furthermore, we also provide evidence that the details of the structure of the crystalline core depend on the size of the nanoparticle. © 2011 American Physical Society.


Zazza C.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Coletta A.,University of Rome Tor Vergata | Sanna N.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Chillemi G.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | And 2 more authors.
Journal of Physical Chemistry B | Year: 2010

The low-lying valence electronic excitations of the topotecan anticancer drug, in two stable lactone forms, have been addressed in infinite dilute aqueous solution by combining time-dependent density functional theory calculations with nanoseconds time-scale classical molecular dynamics simulations at 298 K. The effects of the surrounding and fluctuating classical environment on the investigated topotecan forms are included in a perturbed electronic Hamiltonian, which is computed, and then diagonalized, at each frame stored during the molecular dynamics sampling in explicit solution. Current results clearly indicate that, at moderately acidic and physiological conditions, the valence UV-vis absorption spectra of topotecan drug are strongly affected by the surrounding dielectric media and by its perturbing trajectory as arising from finite-temperature fluctuations and supramolecular interactions. Furthermore, the extension of the proposed computational study to hydrated topotecan complexes in liquid water shows that all of the experimentally detected UV-vis spectroscopic features in solution are accurately reproduced only when direct solute-solvent intermolecular interactions are also explicitly taken into account in our simulating scenario. Finally, the present investigation opens up a chance regarding the computational prediction of the UV-vis absorption spectra of topotecan interacting, in silico, with the topoisomerase-DNA binary complex in physiological conditions (i.e., water dilute solution, room temperature). © 2010 American Chemical Society.


Picardi E.,University of Bari | D'Antonio M.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Carrabino D.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Castrignano T.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | And 2 more authors.
Bioinformatics | Year: 2011

Summary: ExpEdit is a web application for assessing RNA editing in human at known or user-specified sites supported by transcript data obtained by RNA-Seq experiments. Mapping data (in SAM/BAM format) or directly sequence reads [in FASTQ/short read archive (SRA) format] can be provided as input to carry out a comparative analysis against a large collection of known editing sites collected in DARNED database as well as other user-provided potentially edited positions. Results are shown as dynamic tables containing University of California, Santa Cruz (UCSC) links for a quick examination of the genomic context. © The Author 2011. Published by Oxford University Press. All rights reserved.

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