WISDOM: A Grid-Enabled Drug Discovery Initiative Against Malaria

The goal of this chapter is to present the WISDOM initiative, which is one of the main accomplishments in the use of grids for biomedical sciences achieved on grid infrastructures in Europe. Researchers in life sciences are among the most active scientifi c communities on the EGEE infrastructure. As a consequence, the biomedical virtual organization stands fourth in terms of resources consumed in 2007, with an average of 7000 jobs submitted every day to the grid and more than 4 million hours of CPU consumed in the last 12 months. Only three experiments on the CERN Large Hadron Collider have used more resources. Compared to particle physics, the use of resources is much less centralized as about 40 different scientifi c applications are now currently deployed on EGEE. Each of them requires an amount of CPU which ranges from a few to a few hundred CPU years. Thanks to the 20,000 processors available to the users of the biomedical virtual organization, crunching factors in the hundreds are witnessed routinely. Such performances were already achieved on supercomputers but at the cost of reservation and long delays in the access to resources. On the contrary, grid infrastructures are constantly open to the user communities. Such changes in the scale of the computing resources made continuously available to the researchers in biomedical sciences open opportunities for exploring new fi elds or changing the approach to existing challenges. In this chapter, we would like to show the potential impact of grids in the fi eld of drug discovery through the example of the WISDOM initiative

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

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

A Global Plate Model Including Lithospheric Deformation Along Major Rifts and Orogens Since the Triassic

Global deep‐time plate motion models have traditionally followed a classical rigid plate approach, even though plate deformation is known to be significant. Here we present a global Mesozoic–Cenozoic deforming plate motion model that captures the progressive extension of all continental margins since the initiation of rifting within Pangea at ~240 Ma. The model also includes major failed continental rifts and compressional deformation along collision zones. The outlines and timing of regional deformation episodes are reconstructed from a wealth of published regional tectonic models and associated geological and geophysical data. We reconstruct absolute plate motions in a mantle reference frame with a joint global inversion using hot spot tracks for the last 80 million years and minimizing global trench migration velocities and net lithospheric rotation. In our optimized model, net rotation is consistently below 0.2°/Myr, and trench migration scatter is substantially reduced. Distributed plate deformation reaches a Mesozoic peak of 30 × 106 km2 in the Late Jurassic (~160–155 Ma), driven by a vast network of rift systems. After a mid‐Cretaceous drop in deformation, it reaches a high of 48 x 106 km2 in the Late Eocene (~35 Ma), driven by the progressive growth of plate collisions and the formation of new rift systems. About a third of the continental crustal area has been deformed since 240 Ma, partitioned roughly into 65% extension and 35% compression. This community plate model provides a framework for building detailed regional deforming plate networks and form a constraint for models of basin evolution and the plate‐mantle system

Potential Sinks for Geologic Storage of CO2 Generated in the Carolinas

This document summarizes a scoping study of the current state of knowledge of carbon storage options for our geographic area. The focus is on one aspect of carbon capture and storage—identification of deep saline aquifers in which carbon dioxide (CO2 ) generated in the Carolinas might be stored. The study does not address other aspects of CO2 storage projects, such as capture and compression of the gas, well construction and development, or injection. Transport of CO2 is touched upon in this study but has not been fully addressed. The information contained in this document is primarily from review of published geologic literature and unpublished data. No field data collection has been completed as part of this study. Further work will be necessary to increase confidence in the suitability of the potential CO2 storage sites identified in this report. This study does not address the regulatory, environmental, or public policy issues associated with carbon storage, which are under development at this time.Duke Energy, Progress Energy, Santee Cooper Power, South Carolina Electric and Gas, Electric Power Research Institute (EPRI), Southern States Energy Board (SSEB)Bureau of Economic Geolog

Euclidean Preferences, Option Sets and Strategy Proofness

In this note, we use the technique of option sets to sort out the implications of coalitional strategyproofness in the spatial setting. We also discuss related issues and open problems

CHEMICALLY MODIFIED PHOTOSYNTHETIC BACTERIAL REACTION CENTERS: CIRCULAR DICHROISM, RAMAN RESONANCE, LOW TEMPERATURE ABSORPTION, FLUORESCENCE AND ODMR SPECTRA AND POLYPEPTIDE COMPOSITION OF BOROHYDRIDE TREATED REACTION CENTERS FROM Rhodobacter sphaeroides R26

Reaction centers from Rhodobacter sphaeroides have been modified by treatment with sodium borohydride similar to the original procedure [Ditson et al., Biochim. Biophys. Acta 766, 623 (1984)], and investigated spectroscopically and by gel electrophoresis. (1) Low temperature (1.2 K) absorption, fluorescence, absorption- and fluorescence-detected ODMR, and microwave-induced singlet-triplet absorption difference spectra (MIA) suggest that the treatment produces a spectroscopically homogeneous preparation with one of the ‘additional’ bacteriochlorophylls being removed. The modification does not alter the zero field splitting parameters of the primary donor triplet (TP870). (2) From the circular dichroism and Raman resonance spectra in the1500–1800 cm-1 region, the removed pigment is assigned to BchlM, e.g. the "extra" Bchl on the "inactive" M-branch. (3) A strong coupling among all pigment molecules is deduced from the circular dichroism spectra, because pronounced band-shifts and/or intensity changes occur in the spectral components assigned to all pigments. This is supported by distinct differences among the MIA spectra of untreated and modified reaction centers, as well as by Raman resonance. (4) The modification is accompanied by partial proteolytic cleavage of the M-subunit. The preparation is thus spectroscopically homogeneous, but biochemically heterogenous

Las playas de Tulum en la Riviera maya mexicana: caracterización y diagnóstico como base del manejo integrado costero

En el contexto del Programa Hacia la Certificación de la Calidad de las Playas de Tulum, que viene desarrollando la Unidad de Atención a Playas - Tulum, adscripta a la Fundación Orígenes de Quintana Roo (México), durante el primer trimestre del año 2008 se realizó un exhaustivo trabajo de campo que permitió actualizar la Caracterización general y el Diagnóstico físico-ambiental de este sector costero. En este trabajo se presenta una descripción sintetizada de los rasgos físicogeográficos de las playas y se identifican los principales problemas ambientales que las afectan actualmente, para finalmente esbozar los lineamientos generales que perrrútirán continuar avanzando hacia la conformación de un Programa de Manejo integrado costero y Certificación de las playas de Tulum.By the context of the "Programa Hacia la Certificación de la Calidad de las Playas de Tulum", which is developing by the "Unidad de Atención a Playas - Tulum" , attached to the "Fundación Orígenes de Quintana Roo" (Mexico), during the first quarter of 2008, was a comprehensive work allowing field upgrade a physical-environment characterization and diagnostics of this coastal sector. This paper presents a summary description of the physical-geographical features of the beaches and identifies the main environmental problems that affect them now, and finally outline the general guidelines that allow us to continue moving toward the establishment of an Integrated Coastal Management Program and Certification from the beaches of Tulum