Grid Added Value to Address Malaria

Through this paper, we call for a distributed, internet-based collaboration to address one of the worst plagues of our present world, malaria. The spirit is a non-proprietary peer-production of information-embedding goods. And we propose to use the grid technology to enable such a world wide "open source" like collaboration. The first step towards this vision has been achieved during the summer on the EGEE grid infrastructure where 46 million ligands were docked for a total amount of 80 CPU years in 6 weeks in the quest for new drugs.Comment: 7 pages, 1 figure, 6th IEEE International Symposium on Cluster Computing and the Grid, Singapore, 16-19 may 2006, to appear in the proceeding

Generating Gowdy cosmological models

Using the analogy with stationary axisymmetric solutions, we present a method to generate new analytic cosmological solutions of Einstein's equation belonging to the class of $T^3$ Gowdy cosmological models. We show that the solutions can be generated from their data at the initial singularity and present the formal general solution for arbitrary initial data. We exemplify the method by constructing the Kantowski-Sachs cosmological model and a generalization of it that corresponds to an unpolarized $T^3$ Gowdy model.Comment: Latex, 15 pages, no figure

Continued evaluation of potential for geologic storage of carbon dioxide in the southeastern United States

Southern States Energy Board Duke Energy Santee Cooper Power Southern CompanyBureau of Economic Geolog

Palaeoecology of the Cenomanian amber forest of Sarthe (western France)

Cretaceous ambers have been discovered in France since the beginning of the 18th century. The best known are those from south-western France which are Late Albian-Early Cenomanian in age, but there are other important amber deposits in other regions. Here, we summarise the data on one of these other Cretaceous amber regions, the Sarthe Department. These deposits have been mentioned in the literature since the end of the 18th century, but they have remained relatively unknown. The material, that has been studied during the 1970's and 1980's, yielded a well-diversified arthropod fauna (72 arthropod specimens, including arachnids, cockroaches, bugs, beetles, flies, wasps...) dated to late Early-Middle Cenomanian. In the last decade, 4 types of bacteria, a possible testate amoeba and fungal remains were also found. A re-examination of the historical collections of the Sarthe amber, housed in the "Musée Vert" (Le Mans, France), allows to estimate the geographical extent of the amber deposits in the Sarthe Department. The study of the microfossils of these samples provides new data on their palaeoenvironment

Stress response function of a two-dimensional ordered packing of frictional beads

We study the stress profile of an ordered two-dimensional packing of beads in response to the application of a vertical overload localized at its top surface. Disorder is introduced through the Coulombic friction between the grains which gives some indeterminacy and allows the choice of one constrained random number per grain in the calculation of the contact forces. The so-called `multi-agent' technique we use, lets us deal with systems as large as $1000\times1000$ grains. We show that the average response profile has a double peaked structure. At large depth $z$, the position of these peaks grows with $cz$, while their widths scales like $\sqrt{Dz}$. $c$ and $D$ are analogous to `propagation' and `diffusion' coefficients. Their values depend on that of the friction coefficient $\mu$. At small $\mu$, we get $c_0-c \propto \mu$ and $D \propto \mu^\beta$, with $\beta \sim 2.5$, which means that the peaks get closer and wider as the disorder gets larger. This behavior is qualitatively what was predicted in a model where a stochastic relation between the stress components is assumed.Comment: 7 pages, 7 figures, accepted version to Europhys. Let

Replication and update of molecular biology databases in a grid environment

PCSV, présenté par V. Breton, à paraître dans les proceedingsUpdate of molecular biology databases is a growing burden on the biomedical research community. As the grid allows to share and replicate data, we propose a service to automatically update the biology databases from a single changing reference using web services. In this paper we report the components, the architecture and the deployment of the update service on the french RUGBI grid infrastructure. RUGBI is a computing grid infrastructure based on existing middleware and technologies for the community of scientists in bioinformatics

Large scale deployment of molecular docking application on computational grid infrastructures for combating malaria

PCSVInternational audienceComputational grids are solutions for several biological applications like virtual screening or molecular dynamics where large amounts of computing power and storage are required. The WISDOM project successfully deployed virtual screening at large scale on EGEE grid infrastructures in the summer 2005 and achieved 46 million dockings in 45 days, which is equivalent to 80 CPU years. WISDOM is one good example of a successful deployment of an embarrassingly parallel application. In this paper, we describe the improvements in our deployment. We screened ZINC database against four targets implicated in malaria. During more than 2 months and a half, we have achieved 140 million dockings, representing an average throughput of almost 80,000 dockings per hour. This was made possible by the availability of thousands of CPUs through different infrastructures worldwide. Through the acquired experience, the WISDOM production environment is evolving to enable an easy and fault-tolerant deployment of biological tool

Validation of the GATE Monte Carlo simulation platform for modelling a CsI(Tl) scintillation camera dedicated to small animal imaging

Monte Carlo simulations are increasingly used in scintigraphic imaging to model imaging systems and to develop and assess tomographic reconstruction algorithms and correction methods for improved image quantitation. GATE (GEANT 4 Application for Tomographic Emission) is a new Monte Carlo simulation platform based on GEANT4 dedicated to nuclear imaging applications. This paper describes the GATE simulation of a prototype of scintillation camera dedicated to small animal imaging and consisting of a CsI(Tl) crystal array coupled to a position sensitive photomultiplier tube. The relevance of GATE to model the camera prototype was assessed by comparing simulated 99mTc point spread functions, energy spectra, sensitivities, scatter fractions and image of a capillary phantom with the corresponding experimental measurements. Results showed an excellent agreement between simulated and experimental data: experimental spatial resolutions were predicted with an error less than 100 mu m. The difference between experimental and simulated system sensitivities for different source-to-collimator distances was within 2%. Simulated and experimental scatter fractions in a [98-182 keV] energy window differed by less than 2% for sources located in water. Simulated and experimental energy spectra agreed very well between 40 and 180 keV. These results demonstrate the ability and flexibility of GATE for simulating original detector designs. The main weakness of GATE concerns the long computation time it requires: this issue is currently under investigation by the GEANT4 and the GATE collaboration

Long Term Study of the Double Pulsar J0737-3039 with XMM-Newton: pulsar timing

The relativistic double neutron star binary PSR J0737-3039 shows clear evidence of orbital phase-dependent wind-companion interaction, both in radio and X-rays. In this paper we present the results of timing analysis of PSR J0737-3039 performed during 2006 and 2011 XMM-Newton Large Programs that collected ~20,000 X-ray counts from the system. We detected pulsations from PSR J0737-3039A (PSR A) through the most accurate timing measurement obtained by XMM-Newton so far, the spin period error being of 2x10^-13 s. PSR A's pulse profile in X-rays is very stable despite significant relativistic spin precession that occurred within the time span of observations. This yields a constraint on the misalignment between the spin axis and the orbital momentum axis Delta_A ~6.6^{+1.3}_{-5.4} deg, consistent with estimates based on radio data. We confirmed pulsed emission from PSR J0737-3039B (PSR B) in X-rays even after its disappearance in radio. The unusual phenomenology of PSR B's X-ray emission includes orbital pulsed flux and profile variations as well as a loss of pulsar phase coherence on time scales of years. We hypothesize that this is due to the interaction of PSR A's wind with PSR B's magnetosphere and orbital-dependent penetration of the wind plasma onto PSR B closed field lines. Finally, the analysis of the full XMM-Newton dataset provided evidences of orbital flux variability (~7%) for the first time, involving a bow-shock scenario between PSR A's wind and PSR B's magnetosphere.Comment: Comments: 16 Pages, 6 Figures. Accepted for publication in Astrophysical Journal (Draft Version