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Guerrero G.D.,University of Chile | Imbernon B.,San Antonio de Murcia Catholic University | Perez-Sanchez H.,San Antonio de Murcia Catholic University | Sanz F.,Institute for Biocomputation and Physics of Complex Systems | And 2 more authors.
BioMed Research International | Year: 2014

Bioinformatics is an interdisciplinary research field that develops tools for the analysis of large biological databases, and, thus, the use of high performance computing (HPC) platforms is mandatory for the generation of useful biological knowledge. The latest generation of graphics processing units (GPUs) has democratized the use of HPC as they push desktop computers to cluster-level performance. Many applications within this field have been developed to leverage these powerful and low-cost architectures. However, these applications still need to scale to larger GPU-based systems to enable remarkable advances in the fields of healthcare, drug discovery, genome research, etc. The inclusion of GPUs in HPC systems exacerbates power and temperature issues, increasing the total cost of ownership (TCO). This paper explores the benefits of volunteer computing to scale bioinformatics applications as an alternative to own large GPU-based local infrastructures. We use as a benchmark a GPU-based drug discovery application called BINDSURF that their computational requirements go beyond a single desktop machine. Volunteer computing is presented as a cheap and valid HPC system for those bioinformatics applications that need to process huge amounts of data and where the response time is not a critical factor. © 2014 Ginés D. Guerrero et al. Source

Rosa A.,Institute for Biocomputation and Physics of Complex Systems | Becker N.B.,CNRS Physics Laboratory | Everaers R.,CNRS Physics Laboratory
Biophysical Journal | Year: 2010

Fluorescence in-situ hybridization (FISH) and chromosome conformation capture (3C) are two powerful techniques for investigating the three-dimensional organization of the genome in interphase nuclei. The use of these techniques provides complementary information on average spatial distances (FISH) and contact probabilities (3C) for specific genomic sites. To infer the structure of the chromatin fiber or to distinguish functional interactions from random colocalization, it Is useful to compare experimental data to predictions from statistical fiber models. The current estimates of the fiber stiffness derived from FISH and 3C differ by a factor of 5. They are based on the wormlike chain model and a heuristic modification of the ShimadaYamakawa theory of looping for unkinkable, unconstrained, zero-diameter filaments. Here, we provide an extended theoretical and computational framework to explain the currently available experimental data for various species on the basis of a unique, minimal model of decondensing chromosomes: a kinkable, topologically constraint, semiflexible polymer with the (FISH) Kuhn length of /K = 300 nm, 10 kinks per Mbp, and a contact distance of 45 nm. In particular: 1), we reconsider looping of finite-diameter filaments on the basis of an analytical approximation (novel, to our knowledge) of the wormlike chain radial density and show that unphysically large contact radii would be required to explain the 3C data based on the FISH estimate of the fiber stiffness; 2), we demonstrate that the observed interaction frequencies at short genomic lengths can be explained by the presence of a low concentration of curvature defects (kinks); and 3), we show that the most recent experimental 3C data for human chromosomes are in quantitative agreement with interaction frequencies extracted from our simulations of topologically confined model chromosomes. © 2010 by the Biophysical Society. Source

Rodriguez-Pascual M.,CIEMAT | Bustos A.,CIEMAT | Castejon F.,CIEMAT | Llorente I.M.,Complutense University of Madrid | And 2 more authors.
Plasma Physics and Controlled Fusion | Year: 2013

The numerical simulation of the dynamics of fast ions coming from neutral beam injection (NBI) heating is an important task in fusion devices, since these particles are used as sources to heat and fuel the plasma and their uncontrolled losses can damage the walls of the reactor. This paper shows a new application that simulates these dynamics on the grid: FastDEP. FastDEP plugs together two Monte Carlo codes used in fusion science, namely FAFNER2 and ISDEP, and add new functionalities. Physically, FAFNER2 provides the fast ion initial state in the device while ISDEP calculates their evolution in time; as a result, the fast ion distribution function in TJ-II stellerator has been estimated, but the code can be used on any other device. In this paper a comparison between the physics of the two NBI injectors in TJ-II is presented, together with the differences between fast ion confinement and the driven momentum in the two cases. The simulations have been obtained using Montera, a framework developed for achieving grid efficient executions of Monte Carlo applications. © 2013 IOP Publishing Ltd. Source

Javarone M.A.,University of Cagliari | Antonioni A.,University of Lausanne | Antonioni A.,Charles III University of Madrid | Antonioni A.,Institute for Biocomputation and Physics of Complex Systems | And 2 more authors.
EPL | Year: 2016

We investigate the spatial Public Goods Game in the presence of fitness-driven and conformity-driven agents. This framework usually considers only the former type of agents, i.e., agents that tend to imitate the strategy of their fittest neighbors. However, whenever we study social systems, the evolution of a population might be affected also by social behaviors as conformism, stubbornness, altruism, and selfishness. Although the term evolution can assume different meanings depending on the considered domain, here it corresponds to the set of processes that lead a system towards an equilibrium or a steady state. We map fitness to the agents' payoff so that richer agents are those most imitated by fitness-driven agents, while conformity-driven agents tend to imitate the strategy assumed by the majority of their neighbors. Numerical simulations aim to identify the nature of the transition, on varying the amount of the relative density of conformity-driven agents in the population, and to study the nature of related equilibria. Remarkably, we find that conformism generally fosters ordered cooperative phases and may also lead to bistable behaviors. © CopyrightEPLA, 2016. Source

Aniello P.,University of Naples Federico II | Clemente-Gallardo J.,Institute for Biocomputation and Physics of Complex Systems | Marmo G.,University of Naples Federico II | Volkert G.F.,University of Naples Federico II | Volkert G.F.,Ludwig Maximilians University of Munich
International Journal of Geometric Methods in Modern Physics | Year: 2010

The geometrical description of a Hilbert space associated with a quantum system considers a Hermitian tensor to describe the scalar inner product of vectors which are now described by vector fields. The real part of this tensor represents a flat Riemannian metric tensor while the imaginary part represents a symplectic two-form. The immersion of classical manifolds in the complex projective space associated with the Hilbert space allows to pull-back tensor fields related to previous ones, via the immersion map. This makes available, on these selected manifolds of states, methods of usual Riemannian and symplectic geometry. Here, we consider these pulled-back tensor fields when the immersed submanifold contains separable states or entangled states. Geometrical tensors are shown to encode some properties of these states. These results are not unrelated with criteria already available in the literature. We explicitly deal with some of these relations. © 2010 World Scientific Publishing Company. Source

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