Dark matter substructure modelling and sensitivity of the Cherenkov Telescope Array to Galactic dark halos

Hierarchical structure formation leads to a clumpy distribution of dark matter in the Milky Way. These clumps are possible targets to search for dark matter annihilation with present and future $\gamma$-ray instruments. Many uncertainties exist on the clump distribution, leading to disputed conclusions about the expected number of detectable clumps and the ensuing limits that can be obtained from non-detection. In this paper, we use the CLUMPY code to simulate thousands of skymaps for several clump distributions. This allows us to statistically assess the typical properties (mass, distance, angular size, luminosity) of the detectable clumps. Varying parameters of the clump distributions allows us to identify the key quantities to which the number of detectable clumps is the most sensitive. Focusing our analysis on two extreme clump configurations, yet consistent with results from numerical simulations, we revisit and compare various calculations made for the Fermi-LAT instrument, in terms of number of dark clumps expected and the angular power spectrum for the Galactic signal. We then focus on the prospects of detecting dark clumps with the future CTA instrument, for which we make a detailed sensitivity analysis using open-source CTA software. Based on a realistic scenario for the foreseen CTA extragalactic survey, and accounting for a post-trial sensitivity in the survey, we show that we obtain competitive and complementary limits to those based on long observation of a single bright dwarf spheroidal galaxy.Comment: 29 pages + appendix, 15 figures. V2: Sects. 3.3, 4, and 5.3 extended, results unchanged (matching accepted JCAP version

Hydrogen production by the hyperthermophilic bacterium Thermotoga maritima part I: effects of sulfured nutriments, with thiosulfate as model, on hydrogen production and growth

International audienceBackground: Thermotoga maritima and T. neapolitana are hyperthermophile bacteria chosen by many research teams to produce bio-hydrogen because of their potential to ferment a wide variety of sugars with the highest theoretical H-2/glucose yields. However, to develop economically sustainable bio-processes, the culture medium formulation remained to be optimized. The main aim of this study was to quantify accurately and specifically the effect of thiosulfate, used as sulfured nutriment model, on T. maritima growth, yields and productivities of hydrogen. The results were obtained from batch cultures, performed into a bioreactor, carefully controlled, and specifically designed to prevent the back-inhibition by hydrogen. Results: Among sulfured nutriments tested, thiosulfate, cysteine, and sulfide were found to be the most efficient to stimulate T. maritima growth and hydrogen production. In particular, under our experimental conditions (glucose 60 mmol L-1 and yeast extract 1 g L-1), the cellular growth was limited by thiosulfate concentrations lower than 0.06 mmol L-1. Under these conditions, the cellular yield on thiosulfate (Y X/Thio) could be determined at 3617 mg mmol(-1). In addition, it has been shown that the limitations of T. maritima growth by thiosulfate lead to metabolic stress marked by a significant metabolic shift of glucose towards the production of extracellular polysaccharides (EPS). Finally, it has been estimated that the presence of thiosulfate in the T. maritima culture medium significantly increased the cellular and hydrogen productivities by a factor 6 without detectable sulfide production. Conclusions: The stimulant effects of thiosulfate at very low concentrations on T. maritima growth have forced us to reconsider its role in this species and more probably also in all thiosulfato-reducer hyperthermophiles. Henceforth, thiosulfate should be considered in T. maritima as (1) an essential sulfur source for cellular materials when it is present at low concentrations (about 0.3 mmol g(-1) of cells), and (2) as both sulfur source and detoxifying agent for H-2 when thiosulfate is present at higher concentrations and, when, simultaneously, the pH(2) is high. Finally, to improve the hydrogen production in bio-processes using Thermotoga species, it should be recommended to incorporate thiosulfate in the culture medium

Virtual MHD Jets on Grids

International audienceAs network performance has outpaced computational power and storage capacity, a new paradigm has evolved to enable the sharing of geographically distributed resources. This paradigm is known as Grid computing and aims to offer access to distributed resource irrespective of their physical location. Many national, European and international projects have been launched during the last years trying to explore the Grid and to change the way we are doing our everyday work. In Ireland, we have started the CosmoGrid project that is a collaborative project aimed to provide high performance super-computing environments. This will help to address complex problems such as magnetohydrodynamic outflows and jets in order to model and numerically simulate them. Indeed, the numerical modeling of plasma jets requires massive computations, due to the wide range of spatial-temporal scales involved. We present here the first jet simulations and their corresponding models that could help to understand results from laboratory experiments

A Novel Highly Efficient Device for Growing Micro-Aerophilic Microorganisms

This work describes a novel, simple and cost-effective culture system, named the Micro-Oxygenated Culture Device (MOCD), designed to grow microorganisms under particularly challenging oxygenation conditions. Two microaerophilic magnetotactic bacteria, a freshwater Magnetospirillum gryphiswaldense strain MSR-1 and a marine Magnetospira sp. strain QH-2, were used as biological models to prove the efficiency of the MOCD and to evaluate its specifications. Using the MOCD, growth rates of MSR-1 and QH-2 increased by four and twofold, respectively, when compared to traditional growing techniques using simple bottles. Oxystat-bioreactors have been typically used and specifically designed to control low dissolved oxygen concentrations, however, the MOCD, which is far less sophisticated was proven to be as efficient for both MSR-1 and QH-2 cultures with regard to growth rate, and even better for MSR-1 when looking at cell yield (70% increase). The MOCD enables a wide range of oxygenation conditions to be studied, including different O2-gradients. This makes it an innovative and ingenious culture device that opens up new parameters for growing microaerobic microorganisms

euHCVdb: the European hepatitis C virus database

The hepatitis C virus (HCV) genome shows remarkable sequence variability, leading to the classification of at least six major genotypes, numerous subtypes and a myriad of quasispecies within a given host. A database allowing researchers to investigate the genetic and structural variability of all available HCV sequences is an essential tool for studies on the molecular virology and pathogenesis of hepatitis C as well as drug design and vaccine development. We describe here the European Hepatitis C Virus Database (euHCVdb, ), a collection of computer-annotated sequences based on reference genomes. The annotations include genome mapping of sequences, use of recommended nomenclature, subtyping as well as three-dimensional (3D) molecular models of proteins. A WWW interface has been developed to facilitate database searches and the export of data for sequence and structure analyses. As part of an international collaborative effort with the US and Japanese databases, the European HCV Database (euHCVdb) is mainly dedicated to HCV protein sequences, 3D structures and functional analyses

Biological Roles of the Podospora anserina Mitochondrial Lon Protease and the Importance of Its N-Domain

Mitochondria have their own ATP-dependent proteases that maintain the functional state of the organelle. All multicellular eukaryotes, including filamentous fungi, possess the same set of mitochondrial proteases, unlike in unicellular yeasts, where ClpXP, one of the two matricial proteases, is absent. Despite the presence of ClpXP in the filamentous fungus Podospora anserina, deletion of the gene encoding the other matricial protease, PaLon1, leads to lethality at high and low temperatures, indicating that PaLON1 plays a main role in protein quality control. Under normal physiological conditions, the PaLon1 deletion is viable but decreases life span. PaLon1 deletion also leads to defects in two steps during development, ascospore germination and sexual reproduction, which suggests that PaLON1 ensures important regulatory functions during fungal development. Mitochondrial Lon proteases are composed of a central ATPase domain flanked by a large non-catalytic N-domain and a C-terminal protease domain. We found that three mutations in the N-domain of PaLON1 affected fungal life cycle, PaLON1 protein expression and mitochondrial proteolytic activity, which reveals the functional importance of the N-domain of the mitochondrial Lon protease. All PaLon1 mutations affected the C-terminal part of the N-domain. Considering that the C-terminal part is predicted to have an α helical arrangement in which the number, length and position of the helices are conserved with the solved structure of its bacterial homologs, we propose that this all-helical structure participates in Lon substrate interaction

The crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1: implications to protein function and drug design.

The research leading to these results received funding from the European Community’s Seventh Framework Programme under grant agreement No.602773 (Project KINDRED).The de novo crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSir2rp1) has been solved at 1.99Å in complex with an acetyl-lysine peptide substrate. The structure is broadly commensurate with Hst2/SIRT2 proteins of yeast and human origin, reproducing many of the structural features common to these sirtuin deacetylases, including the characteristic small zinc-binding domain, and the larger Rossmann-fold domain involved in NAD+-binding interactions. The two domains are linked via a cofactor binding loop ordered in open conformation. The peptide substrate binds to the LiSir2rp1 protein via a cleft formed between the small and large domains, with the acetyl-lysine side chain inserting further into the resultant hydrophobic tunnel. Crystals were obtained only with recombinant LiSir2rp1 possessing an extensive internal deletion of a proteolytically-sensitive region unique to the sirtuins of kinetoplastid origin. Deletion of 51 internal amino acids (P253-E303) from LiSir2rp1 did not appear to alter peptide substrate interactions in deacetylation assays, but was indispensable to obtain crystals. Removal of this potentially flexible region, that otherwise extends from the classical structural elements of the Rossmann-fold, specifically the β8-β9 connector, appears to result in lower accumulation of the protein when expressed from episomal vectors in L. infantum SIR2rp1 single knockout promastigotes. The biological function of the large serine-rich insertion in kinetoplastid/trypanosomatid sirtuins, highlighted as a disordered region with strong potential for post-translational modification, remains unknown but may confer additional cellular functions that are distinct from their human counterparts. These unique molecular features, along with the resolution of the first kinetoplastid sirtuin deacetylase structure, present novel opportunities for drug design against a protein target previously established as essential to parasite survival and proliferation.Publisher PDFPeer reviewe

Etude analytique et numérique des flots autour des étoiles jeunes

This thesis is built in two distinct parts, treating of two different astrophysical topics: i) in the first (and main) part, work related to star formation is presented whereas ii) the second part deals with cosmic rays.When a star forms, huge bipolar ejections of material, under the form of jets and molecular outflows, are observed as accretion proceeds onto the central object. After an introduction giving a large overview of the star formation process, we focus on the different ``standard'' approaches used to model molecular outflows. An alternative and complementary model is then built: the transit model. It is a self-similar MHD model where part of the infalling material is being diverted into an outflow when approaching the central object. It is shown that the transit allows to reach the huge mass rates observed in massive star formation, in opposition to the ``standard'' approaches. The model is thoughtfully studied with a Monte Carlo exploration of the parameter space and two families of solutions are put to the fore. The transit model gives a large-scale description of the protostellar environment, showing both density and velocity structures. It is in such a medium that a jet launched from the accretion disk will propagate and a preliminary numerical study of this propagation shows that the morphology and kinematics of the jet is strongly affected by the ambient medium. We conclude in the importance of a good description of the latter and the urge of leaving the ``uniform and motionless medium'' usually used in such simulations.The second part focuses on the nuclear component of the Galactic cosmic rays. After being accelerated in supernova remnants, these nuclei propagate through the Galaxy and its halo. Eventually, some of them reach the Earth where they are detected. A good understanding of the propagation processes is compulsory in order to derive the source abundances from the measured ones.In this work, we focus on ultra-heavy nuclei, in connexion with the UHCR Experiment, and study how the local structure of the Galaxy, the so-called ``local bubble'', affects the propagation. We find that the local sub-density surrounding the Solar neighbourhood does play an important role in the determination of the source abundances and that the effect tends towards a better agreement between the source abundances and the solar abundances for these heavy nuclei. Some very crude approximations have been used in this preliminary study and we give, in a final chapter, some future developments that should be implemented.Ce travail de thèse, s'intéresse dans deux parties distinctes à deux thématiques astrophysiques indépendantes : i) certains aspects de la formation stellaire sont traités dans une première partie, alors que la seconde, plus modeste, s'intéresse au rayonnement cosmique.Lorsqu'une étoile se forme, alors que l'accrétion sur l'objet central se poursuit, de gigantesques éjections de matière se produisent sous forme de jets et flots moléculaires bipolaires. Après uneintroduction donnant une vision globale de tous les éléments impliqués dans la formation stellaire, nous présentons les modèles "standards" pour les flots moléculaires. Dans untroisième temps, nous construisons un modèle alternatif et complémentaire aux approches standards~: le modèle de transit. Il s'agit d'un modèle MHD, autosimilaire et qui considère le renversement d'un partie de l'écoulement lorsque le gaz en chute approche de l'objet central. Les résultats montrent notamment que le modèle permet de rendre compte des taux de masses observés lors de la formation des étoiles massives, taux que les modèles standards atteignent difficilement. Le modèle est étudié de façon extensive grâce à une exploration Monte Carlo de l'espace des paramètres et la mise en évidence de deux grandes familles de solutions. Le modèle de transit donne une description à grande échelle de l'environnement proto-stellaire et montre une forte structuration du milieu autant en densité qu'en vitesse. C'est dans un tel milieu que le jet issu du disque d'accrétion se propage, et une étude numérique préliminaire de cette propagation montre que la morphologie et la cinématique du jet est fortement affectée par le milieu ambiant. Nous en déduisons l'importance d'avoir un bonne description de ce dernier et la nécessité de ne pas se contenter des milieux "uniformes et au repos" généralement considérés. La seconde partie est consacrée à la partie nucléaire du rayonnement cosmique Galactique. Ce "rayonnement" est constitué de noyaux qui se sont propagés dans la Galaxie et son halo diffusif, après avoir été accélérés dans les chocs de supernovae. Certains de ces noyaux atteignent la Terre où ilssont détectés. Comprendre la propagation de ces noyaux est essentiel pour remonter, à partir des mesures, aux abondances des noyaux dans les sources. Dans ce travail, nous nous intéressons spécifiquement au cas des noyaux lourds, en connection avec l'expérience UHCRE, et regardons comment la structure locale de la Galaxie, la "bulle locale", affecte la propagation des lourds. Nous trouvons que la sous-densité locale du voisinnage solaire joue effectivement un rôle dans la détermination des abondances sources et que l'effet tend à réduire les différences entre les abondances sources et les abondances solaires des noyaux. Nous donnons enfin dans un dernier chapitre quelques perspectives pour la poursuite de cette étude

Etude analytique et numérique des flots autour des étoiles jeunes

LORS DU PROCESSUS DE FORMATION STELLAIRE, DE FORMIDABLES EJECTIONS BIPOLAIRES DE MATIERE SONT OBSERVEES, EN PLUS DE L'ACCRETION SUR L'OBJET CENTRAL. DEUX COMPOSANTES CONSTITUENT CES FLOTS BIPOLAIRES : LES JETS (RAPIDES, COLLIMATES ET LEGERS) ET LES FLOTS MOLECULAIRES (PLUS LENTS, LARGES ET DENSES). IL EST SOUVENT ADMIS QUE LE JET EST RESPONSABLE DU FLOT MOLECULAIRE, LORSQUE CE PREMIER ENTRAINE PAR EFFET CHASSE-NEIGE LE MILIEU AMBIANT DANS LEQUEL IL SE PROPAGE. DANS CETTE THESE, NOUS NOUS INTERESSONS PRINCIPALEMENT AUX FLOTS MOLECULAIRES PAR L'ETUDE D'UN MODELE ALTERNATIF ET COMPLEMENTAIRE DE LA VISION STANDARD MENTIONNEE CI-DESSUS. DANS CE MODELE DE >, UNE PARTIE DU GAZ EN CHUTE EN DIRECTION DE L'OBJET CENTRAL EST DEVIEE (TRANSIT) DANS LES DIRECTIONS BIPOLAIRES, EN RAISON DE L'AUGMENTATION DE LA TEMPERATURE ET DE LA DENSITE LORSQUE LA DISTANCE A LA PROTO-ETOILE DIMINUE. NOUS MONTRONS QUE DES SOLUTIONS EXISTENT SANS QU'UN CHAMP MAGNETIQUE SOIT PRESENT, IMPLIQUANT UNE NATURE THERMODYNAMIQUE DU PROCESSUS QUE NOUS DECRIVONS. LES SOLUTIONS MAGNETISEES SONT CEPENDANT EN MEILLEUR ACCORD AVEC LES OBSERVATIONS, CONFIRMANT QUE LE CHAMP MAGNETIQUE EST UN INGRDIENT IMPORTANT DU PROCESSUS DE FORMATION STELLAIRE. GRACE A CE MODELE, NOUS PARVENONS SANS DIFFICULTE A ATTEINDRE LES ENORMES MASSES CHARRIEES DANS LES FLOTS D'ETOILES MASSIVES PUISQUE LE MODELE N'EST PAS LIMITE A CE QU'UN JET PEUT ENTRAINER. LA COMPOSITION DU MILIEU INFLUE EGALEMENT SUR LES SOLUTIONS OBTENUES ET IL EST MONTRE QUE L'ABSENCE DE POUSSIERES DANS LE MILIEU ENTRIANE POTENTIELLEMENT LA FORMATION D'ETOILES PLUS MASSIVES QUE CELLES QUI SE FORMENT DANS L'UNIVERS ACTUEL (OU LA POUSSIERE EST PRESENTE).WHEN A STAR FORMS, NOT ONLY GAS ACCRETES ONTO THE CENTRAL OBJECT BUT POWERFUL BIPOLAR EJECTIONS OF MATERIAL ARE ALSO OBSERVED. THESE BIPOLAR OUTFLOWS ARE GENERALLY SEPERATED INTO TWO COMPONENTS: THE JETS (FAST, HIGHLY COLLIMATED AND LIGHT) AND THE MOLECULAR OUTFLOWS (SLOWER, WIDER AND DENSER). IT IS USELY ACCEPTED THAT THE JETS ARE THE CAUSE OF THE MOLECULAR OUTFLOWS AS THEY ENTRAIN THE GAS OF THE MEDIUM THEY ARE PROPAGATING IN, VIA A SNOW-PLOW EFFECT. IN THIS THESIS, WE ARE PRIMARILY INTERESTED BY MOLECULAR OUTFLOWS AND STUDY AN ALTERNATIVE AND COMPLEMENTARY MODEL OF THE STANDARD JET-DRIVEN MODEL DESCRIBED ABOVE. IN OUR SO-CALLED "TRANSIT MODEL", PART OF THE INFALLING GAZ IS BEING DIVERTED INTO A BIPOLAR OUTFLOW AS THE DENSITY AND TEMPERATURE INCREASE WITH DECREASING DISTANCE TO THE CENTRAL OBJECT. WE SOLVE THE SYSTEM OF EQUATIONS DESCRIBING THE MODEL IN BOTH THE UNMAGNETISED AND MAGNETISED CASE. THE EXISTENCE OF PURELY HYDRODYNAMICAL SOLUTIONS SHOW THAT THE FUNDAMENTAL NATURE OF THE PROCESS DESCRIBED HERE IS THERMODYNAMICAL. HOWEVER, MAGNETISED SOLUTIONS COMPARE BETTER WITH OBSERVATIONS, CONFIRMING THE IMPORTANCE OF THE MAGNETIC FIELD IN THE STAR FORMATION PROCESS. WITH THE TRANSIT MODEL, IT IS POSSIBLE TO REACH WITHOUT DIFFICULTIES THE HUGE MASS OBSERVED IN THE OUTFLOWS OF MASSIVE FORMING STARS : INDEED, IN THE MODEL, THE MASS IN THE MOLECULAR OUTFLOW IS NOT LIMITED TO THE MASS THAT CAN BE ENTRAINED BY AN UNDERLYING JET. WE ALSO STUDIED THE INFLUENCE O F THE COMPOSITION OF THE GAS ON THE SOLUTIONS AND FOUND THAT MORE MASSIVE STARS CAN POTENTIALLY FORM WHEN DUST DOES NOT DOMINATE THE COOLING OF THE GAS, AS IT IS IN THE PRESENT-DAY UNIVERSE.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

CLUMPY v3: γ\gamma-ray and ν\nu signals from dark matter at all scales

International audienceWe present the third release of the CLUMPY code for calculating γ -ray and ν signals from annihilations or decays in dark matter structures. This version includes the mean extragalactic signal with several pre-defined options and keywords related to cosmological parameters, mass functions for the dark matter structures, and γ -ray absorption up to high redshift. For more flexibility and consistency, dark matter halo masses and concentrations are now defined with respect to a user-defined overdensity Δ . We have also made changes for the user’s benefit: distribution and versioning of the code via git , less dependencies and a simplified installation, better handling of options in run command lines, consistent naming of parameters, and a new Sphinx documentation at http://lpsc.in2p3.fr/clumpy/