204 research outputs found

    Microscopic calculations of Hugoniot curves of neat TATB and of its detonation products

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    We compute the Hugoniot curves of both neat TATB and its detonation products mixture using atomistic simulation tools. To compute the Hugoniot states, we adapted our "Sampling Constraints in Average" (SCA) method (Maillet et al., Applied Math. Research eXpress 2008, 2009) to Monte-Carlo simulations. For neat TATB, we show that the potential proposed by Rai (Rai et al., J. Chem. Phys. 129, 2008) is not accurate enough to predict the Hugoniot curve and requires some optimization of its parameters. Concerning detonation products, thermodynamic properties at chemical equilibrium are computed using a specific RxMC method (Bourasseau et al., Phys. Chem. Chem. Phys. 13, 2011) taking into account the presence of carbon clusters in the fluid mixture. We show that this explicit description of the solid phase immersed in the fluid phase modifies the chemical equilibrium

    Molecular Simulations of Hugoniots of detonation products mixtures at chemical equilibrium: Microscopic calculation of the Chapman-Jouguet State

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    International audienceIn this work, we used simultaneously the Reaction Ensemble Monte Carlo (ReMC) method and the Adaptive Erpenbeck Equation Of State (AE-EOS) method to directly calculate the thermodynamical and chemical equilibrium of mixtures of detonation products on the Hugoniot curve. The ReMC method (W. R. Smith and B. Triska, J. Chem. Phys. 100, pp 3019-3027 (1994)) allows to reach the chemical equilibrium of a reacting mixture, and the AE-EOS method (J. J. Erpenbeck, Phys. Rev. A, 46, p 6406 (1992)) constrains the system to satisfy the Hugoniot relation. Once the Hugoniot curve of the detonation products mixture is established, the CJ state of the explosive can be determined. Performing a NPT simulation at P(CJ) , T(CJ) , we then calculate the direct thermodynamic properties and the following derivative properties of the system using a fluctuation method: calorific capacities, sound velocity and Gruneisen coefficient. As the composition fluctuates, and the number of particles is not necessarily constant in this ensemble, a fluctuation formula has been developed to take into account the fluctuations of mole number and composition. This type of calculation has been applied to several usual energetic materials: nitromethane, tetranitromethane, hexanitroethane, PETN and RDX

    Handling temporal heterogeneous data for content-based management of large video collections

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    Video document retrieval is now an active part of the domain of multimedia retrieval. However, unlike for other media, the management of a collection of video documents adds the problem of efficiently handling an overwhelming volume of temporal data. Challenges include balancing efficient content modeling and storage against fast access at various levels. In this paper, we detail the framework we have built to accommodate our developments in content-based multimedia retrieval. We show that not only our framework facilitates the development of processing and indexing algorithms but it also opens the way to several other possibilities such as rapid interface prototyping or retrieval algorithm benchmarking. Here, we discuss our developments in relation to wider contexts such as MPEG-7 and the TREC Video Trac

    Molecular Simulations of Shock to Detonation Transition in Nitromethane

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    An extension of the model described in a previous work of Maillet, Soulard and Stoltz based on a Dissipative Particule Dynamics is presented and applied to liquid nitromethane. Large scale non-equilibrium simulations of reacting nitromethane under sustained shock conditions allow a better understanding of the shock-to-detonation transition in homogeneous explosives. Moreover, the propagation of the reactive wave appears discontinuous since ignition points in the shocked material can be activated by the compressive waves emitted from the onset of chemical reactions

    Comparaison de novo de données de séquençage issues de très grands échantillons métagénomiques (application sur le projet Tara Oceans)

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    La métagénomique vise à étudier le contenu génétique et génomique d'un échantillon provenant d'un environnement naturel. Cette discipline récente s'attache à étudier les génomes de différents organismes provenant d'un même milieu. La métagénomique pose de nouvelles questions, tant d'un point de vue biologique qu'informatique. Les masses de données générées par les études métagénomiques et la complexité des milieux étudiés, nécessitent de développer de nouvelles structures de données et de nouveaux algorithmes dédiés. Parmi les différentes approches existantes en métagénomique, la métagénomique comparative consiste à comparer plusieurs métagénomes afin d'en connaître les divers degrés de similarité. Lorsque cette comparaison se base uniquement sur le contenu brut des échantillons, sans faire appel à des connaissances externes, on parle de métagénomique comparative de novo. L'objectif des travaux que nous proposons est de développer une méthode permettant d'extraire les séquences similaires de deux jeux de données métagénomiques, où chaque jeu peut être composé de centaines de millions de courtes séquences. La comparaison proposée consiste à identifier les séquences d'un premier jeu similaires à au moins une séquence d'un second jeu. Afin d'être rapide et économe en mémoire, l'implémentation de notre méthode a nécessité la conception d'une nouvelle structure d'indexation, basée sur le filtre de bloom. Le logiciel final, nommé Compareads, a une consommation mémoire faible (de l'ordre de quelques go) et peut calculer l'intersection de deux échantillons de 100 millions de séquences chacun en une dizaine d'heures. Notre méthode est une heuristique qui génère un faible taux de faux positifs. Le logiciel Compareads est dédié à l'analyse de grands jeux de données métagénomiques. À l'heure actuelle, il est le seul outil capable de comparer de tels jeux. Compareads a été appliqué sur plusieurs projets métagénomiques. Notre outil produit des résultats robustes, biologiquement exploitables et en accord avec diverses méthodes fondamentalement différentes. Il est actuellement utilisé de manière intensive sur les échantillons provenant de l'expédition tara oceans. Sur ce projet, notre méthode à permis de mettre en évidence que les grands systèmes océaniques influent sur la répartition globale des micro-organismes marins.Metagenomics studies overall genomic information of multiple organisms coming from the same biotope. The information is generally provided by next generation sequencing technologies (NGS). Typical data are samples of short reads (i.e. reads of few hundred base pairs). To study such metagenomics information, we developed an original method for extracting similarities between two samples of reads. More precisely, this approach locates the set of common reads present in two samples. In order to fit with current memory capacities and to be time efficient, we used a modified Bloom filter data structure. Finding the common reads between multiple samples and crossing this information with the location of samples leads to visualize some biological processes like ubiquitous species or effect of water stream caring some species. Finally, the tool can also be used as a filter on metagenomics datas to remove for example only one specie. Our software, Compareads, is actually used on the Tara Oceans project where it shows that global dynamic of oceans seems to play a part on the dispersion of marine microorganisms.RENNES1-Bibl. électronique (352382106) / SudocSudocFranceF

    Potential optimization for the calculation of shocked liquid nitromethane properties

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    International audienceWe present the results of the optimization of a classical molecular force field used to calculate the properties of shocked nitromethane by Monte Carlo simulations. The optimization technique allows a good transferability of the potential parameters on a broad range of thermodynamic conditions (temperature and pressure) since a large variety of reference data can be used in the optimization procedure, including densities, vaporization enthalpies or pressures along the Hugoniot curve. Results of calculated properties of shocked nitromethane are in good agreement with experimental shock hugoniot data, including temperature measurements of second shock hugoniot

    Caffeic Acid Phenethyl Ester and Its Amide Analogue Are Potent Inhibitors of Leukotriene Biosynthesis in Human Polymorphonuclear Leukocytes

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    BACKGROUND: 5-lipoxygenase (5-LO) catalyses the transformation of arachidonic acid (AA) into leukotrienes (LTs), which are important lipid mediators of inflammation. LTs have been directly implicated in inflammatory diseases like asthma, atherosclerosis and rheumatoid arthritis; therefore inhibition of LT biosynthesis is a strategy for the treatment of these chronic diseases. METHODOLOGY/PRINCIPAL FINDINGS: Analogues of caffeic acid, including the naturally-occurring caffeic acid phenethyl ester (CAPE), were synthesized and evaluated for their capacity to inhibit 5-LO and LTs biosynthesis in human polymorphonuclear leukocytes (PMNL) and whole blood. Anti-free radical and anti-oxidant activities of the compounds were also measured. Caffeic acid did not inhibit 5-LO activity or LT biosynthesis at concentrations up to 10 µM. CAPE inhibited 5-LO activity (IC(50) 0.13 µM, 95% CI 0.08-0.23 µM) more effectively than the clinically-approved 5-LO inhibitor zileuton (IC(50) 3.5 µM, 95% CI 2.3-5.4 µM). CAPE was also more effective than zileuton for the inhibition of LT biosynthesis in PMNL but the compounds were equipotent in whole blood. The activity of the amide analogue of CAPE was similar to that of zileuton. Inhibition of LT biosynthesis by CAPE was the result of the inhibition of 5-LO and of AA release. Caffeic acid, CAPE and its amide analog were free radical scavengers and antioxidants with IC(50) values in the low µM range; however, the phenethyl moiety of CAPE was required for effective inhibition of 5-LO and LT biosynthesis. CONCLUSIONS: CAPE is a potent LT biosynthesis inhibitor that blocks 5-LO activity and AA release. The CAPE structure can be used as a framework for the rational design of stable and potent inhibitors of LT biosynthesis

    Marine diatoms change their gene expression profile when exposed to microscale turbulence under nutrient replete conditions

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    Diatoms are a fundamental microalgal phylum that thrives in turbulent environments. Despite several experimental and numerical studies, if and how diatoms may profit from turbulence is still an open question. One of the leading arguments is that turbulence favours nutrient uptake. Morphological features, such as the absence of flagella, the presence of a rigid exoskeleton and the micrometre size would support the possible passive but beneficial role of turbulence on diatoms. We demonstrate that in fact diatoms actively respond to turbulence in non-limiting nutrient conditions. TURBOGEN, a prototypic instrument to generate natural levels of microscale turbulence, was used to expose diatoms to the mechanical stimulus. Differential expression analyses, coupled with microscopy inspections, enabled us to study the morphological and transcriptional response of Chaetoceros decipiens to turbulence. Our target species responds to turbulence by activating energy storage pathways like fatty acid biosynthesis and by modifying its cell chain spectrum. Two other ecologically important species were examined and the occurrence of a morphological response was confirmed. These results challenge the view of phytoplankton as unsophisticated passive organisms
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