All-regime Lagrangian-Remap numerical schemes for the gas dynamics equations. Applications to the large friction and low Mach coefficients

In this talk, we propose an all regime Lagrange-Projection like numerical scheme for the gas dynamics equations. By all regime, we mean that the numerical scheme is able to compute accurate approximate solutions with an under-resolved discretization with respect to the Mach number M, i.e. such that the ratio between the Mach number M and the mesh size or the time step is small with respect to 1. The key idea is to decouple acoustic and transport phenomenon and then alter the numerical flux in the acoustic approximation to obtain a uniform truncation error in term of M. This modified scheme is conservative and endowed with good stability properties with respect to the positivity of the density and the internal energy. A discrete entropy inequality under a condition on the modification is obtained thanks to a reinterpretation of the modified scheme in the Harten Lax and van Leer formalism. A natural extension to multi-dimensional problems discretized over unstructured mesh is proposed. Then a simple and efficient semi implicit scheme is also proposed. The resulting scheme is stable under a CFL condition driven by the (slow) material waves and not by the (fast) acoustic waves and so verifies the all regime property. Numerical evidences are proposed and show the ability of the scheme to deal with tests where the flow regime may vary from low to high Mach values.

Asymptotic preserving and time diminishing schemes for rarefied gas dynamic

In this work, we introduce a new class of numerical schemes for rarefied gas dynamic problems described by collisional kinetic equations. The idea consists in reformulating the problem using a micro-macro decomposition and successively in solving the microscopic part by using asymptotic preserving Monte Carlo methods. We consider two types of decompositions, the first leading to the Euler system of gas dynamics while the second to the Navier-Stokes equations for the macroscopic part. In addition, the particle method which solves the microscopic part is designed in such a way that the global scheme becomes computationally less expensive as the solution approaches the equilibrium state as opposite to standard methods for kinetic equations which computational cost increases with the number of interactions. At the same time, the statistical error due to the particle part of the solution decreases as the system approach the equilibrium state. This causes the method to degenerate to the sole solution of the macroscopic hydrodynamic equations (Euler or Navier-Stokes) in the limit of infinite number of collisions. In a last part, we will show the behaviors of this new approach in comparisons to standard Monte Carlo techniques for solving the kinetic equation by testing it on different problems which typically arise in rarefied gas dynamic simulations.

Comparison of five popular normalization methods using a spike-in proteomics data set

Mass spectrometry (MS)-based proteomics has seen significant technical advances during the past two decades and mass spectrometry has become a central tool in many biosciences. Despite the popularity of MS-based methods, the handling of the systematic non-biological variation in the data remains a common problem. This biasing variation can result from several sources ranging from sample handling to differences caused by the instrumentation. Normalization is the procedure which aims to account for this biasing variation and make samples comparable. Many normalization methods commonly used in proteomics have been adapted from the DNA-microarray world. Studies comparing normalization methods with proteomics data sets using some variability measures exist. However, a more thorough comparison looking at the quantitative and qualitative differences of the performance of the different normalization methods and at their ability in preserving the true differential expression signal of proteins, is lacking. In this thesis, several popular and widely used normalization methods (the Linear regression normalization, Local regression normalization, Variance stabilizing normalization, Quantile-normalization, Median central tendency normalization and also variants of some of the forementioned methods), representing different strategies in normalization are being compared and evaluated with a benchmark spike-in proteomics data set. The normalization methods are evaluated in several ways. The performance of the normalization methods is evaluated qualitatively and quantitatively on a global scale and in pairwise comparisons of sample groups. In addition, it is investigated, whether performing the normalization globally on the whole data or pairwise for the comparison pairs examined, affects the performance of the normalization method in normalizing the data and preserving the true differential expression signal. In this thesis, both major and minor differences in the performance of the different normalization methods were found. Also, the way in which the normalization was performed (global normalization of the whole data or pairwise normalization of the comparison pair) affected the performance of some of the methods in pairwise comparisons. Differences among variants of the same methods were also observed.

The Becker-Döring equations with exponentially size-dependent rate coefficients

This paper is concerned with an analysis of the Becker-Döring equations which lie at the heart of a number of descriptions of non-equilibrium phase transitions and related complex dynamical processes. The Becker-Döring theory describes growth and fragmentation in terms of stepwise addition or removal of single particles to or from clusters of similar particles and has been applied to a wide range of problems of physicochemical and biological interest within recent years. Here we consider the case where the aggregation and fragmentation rates depend exponentially on cluster size. These choices of rate coefficients at least qualitatively correspond to physically realistic molecular clustering scenarios such as occur in, for example, simulations of simple fluids. New similarity solutions for the constant monomer Becker-Döring system are identified, and shown to be generic in the case of aggregation and fragmentation rates that depend exponentially on cluster size.

Fluorinated surfactants in solution: Diffusion coefficients of fluorinated alcohols in water

Intra-diffusion coefficients of three fluorinated alcohols, 2,2,3,3,3-pentafluoropropan-1-ol (PFP), 2,2,3,3,4,4,4-heptafluorobutan-1-ol (HFB) and 2,2,3,3,4,4,5,5,5-nonafluoropentan-1-ol (NFP) in water have been measured by the PFG–NMR spin-echo technique as a function of temperature and composition, focusing on the alcohol dilute region. For comparison, intra-diffusion coefficients of 2,2,2- trifluoroethanol (TFE) and HFB have also been measured in heavy water using the same method and conditions. As far as we know, these are the first experimental measurements of this property for these binary systems. Intra-diffusion coefficients for NFP in water and for TFE and HFB in heavy water have also been obtained by molecular dynamics simulation, complementing those for TFE, PFP and HFB reported in a previous work. The agreement between experimental and simulated results for PFP, HFB and NFP in water is reasonable, although presenting higher deviations than for the TFE/water system. From the dependence of the intra-diffusion coefficients on temperature, diffusion activation energies were estimated for all the solutes in water and heavy water.

Méthodes de Bootstrap pour les modèles à facteurs

Cette thèse développe des méthodes bootstrap pour les modèles à facteurs qui sont couram- ment utilisés pour générer des prévisions depuis l'article pionnier de Stock et Watson (2002) sur les indices de diffusion. Ces modèles tolèrent l'inclusion d'un grand nombre de variables macroéconomiques et financières comme prédicteurs, une caractéristique utile pour inclure di- verses informations disponibles aux agents économiques. Ma thèse propose donc des outils éco- nométriques qui améliorent l'inférence dans les modèles à facteurs utilisant des facteurs latents extraits d'un large panel de prédicteurs observés. Il est subdivisé en trois chapitres complémen- taires dont les deux premiers en collaboration avec Sílvia Gonçalves et Benoit Perron. Dans le premier article, nous étudions comment les méthodes bootstrap peuvent être utilisées pour faire de l'inférence dans les modèles de prévision pour un horizon de h périodes dans le futur. Pour ce faire, il examine l'inférence bootstrap dans un contexte de régression augmentée de facteurs où les erreurs pourraient être autocorrélées. Il généralise les résultats de Gonçalves et Perron (2014) et propose puis justifie deux approches basées sur les résidus : le block wild bootstrap et le dependent wild bootstrap. Nos simulations montrent une amélioration des taux de couverture des intervalles de confiance des coefficients estimés en utilisant ces approches comparativement à la théorie asymptotique et au wild bootstrap en présence de corrélation sérielle dans les erreurs de régression. Le deuxième chapitre propose des méthodes bootstrap pour la construction des intervalles de prévision permettant de relâcher l'hypothèse de normalité des innovations. Nous y propo- sons des intervalles de prédiction bootstrap pour une observation h périodes dans le futur et sa moyenne conditionnelle. Nous supposons que ces prévisions sont faites en utilisant un ensemble de facteurs extraits d'un large panel de variables. Parce que nous traitons ces facteurs comme latents, nos prévisions dépendent à la fois des facteurs estimés et les coefficients de régres- sion estimés. Sous des conditions de régularité, Bai et Ng (2006) ont proposé la construction d'intervalles asymptotiques sous l'hypothèse de Gaussianité des innovations. Le bootstrap nous permet de relâcher cette hypothèse et de construire des intervalles de prédiction valides sous des hypothèses plus générales. En outre, même en supposant la Gaussianité, le bootstrap conduit à des intervalles plus précis dans les cas où la dimension transversale est relativement faible car il prend en considération le biais de l'estimateur des moindres carrés ordinaires comme le montre une étude récente de Gonçalves et Perron (2014). Dans le troisième chapitre, nous suggérons des procédures de sélection convergentes pour les regressions augmentées de facteurs en échantillons finis. Nous démontrons premièrement que la méthode de validation croisée usuelle est non-convergente mais que sa généralisation, la validation croisée «leave-d-out» sélectionne le plus petit ensemble de facteurs estimés pour l'espace généré par les vraies facteurs. Le deuxième critère dont nous montrons également la validité généralise l'approximation bootstrap de Shao (1996) pour les regressions augmentées de facteurs. Les simulations montrent une amélioration de la probabilité de sélectionner par- cimonieusement les facteurs estimés comparativement aux méthodes de sélection disponibles. L'application empirique revisite la relation entre les facteurs macroéconomiques et financiers, et l'excès de rendement sur le marché boursier américain. Parmi les facteurs estimés à partir d'un large panel de données macroéconomiques et financières des États Unis, les facteurs fortement correlés aux écarts de taux d'intérêt et les facteurs de Fama-French ont un bon pouvoir prédictif pour les excès de rendement.

Assessing the activity coefficients of water in cholinium-based ionic liquids: experimental measurements and COSMO-RS modeling

The vapor liquid-equilibrium of water + ionic liquids is relevant for a wide range of applications of these compounds. It is usually measured by ebulliometric techniques, but these are time consuming and expensive. In this work it is shown that the activity coefficients of water in a series of cholinium-based ionic liquids can be reliably and quickly estimated at 298.15K using a humidity meter instrument. The cholinium based ionic liquids were chosen to test this experimental methodology since data for water activities of quaternary ammonium salts are available in the literature allowing the validation of the proposed technique. The COSMO-RS method provides a reliable description of the data and was also used to understand the molecular interactions occurring on these binary systems. The estimated excess enthalpies indicate that hydrogen bonding between water and ionic liquid anion is the dominant interaction that governs the behavior of water and cholinium-based ionic liquids systems, while the electrostatic-misfit and van der Walls forces have a minor contribution to the total excess enthalpies.

Measurements of activity coefficients at infinite dilution of organic solutes and water on polar imidazolium-based ionic liquids

The activity coefficients at infinite dilution, gamma(infinity)(13), of 55 organic solutes and water in three ionic liquids with the common cation 1-butyl-3-methylimidazolium and the polar anions Cl--,Cl- [CH3SO3](-) and [(CH3)(2)PO4](-), were determined by (gas + liquid) chromatography at four temperatures in the range (358.15 to 388.15) K for alcohols and water, and T = (398.15 to 428.15) K for the other organic solutes including alkanes, cycloalkanes, alkenes, cycloalkenes, alkynes, ketones, ethers, cyclic ethers, aromatic hydrocarbons, esters, butyraldehyde, acetonitrile, pyridine, 1-nitropropane and thiophene. From the experimental gamma(infinity)(13) values, the partial molar excess Gibbs free energy, (G) over bar (E infinity)(m), enthalpy (H) over bar (E infinity)(m), and entropy (S) over bar (E infinity)(m), at infinite dilution, were estimated in order to provide more information about the interactions between the solutes and the ILs. Moreover, densities were measured and (gas + liquid) partition coefficients (KL) calculated. Selectivities at infinite dilution for some separation problems such as octane/benzene, cyclohexane/benzene and cyclohexane/thiophene were calculated using the measured gamma(infinity)(13), and compared with literature values for N-methyl-2-pyrrolidinone (NMP), sulfolane, and other ionic liquids with a common cation or anion of the ILs here studied. From the obtained infinite dilution selectivities and capacities, it can be concluded that the ILs studied may replace conventional entrainers applied for the separation processes of aliphatic/aromatic hydrocarbons.

Asymptotic stability of a coupled Advection-Diffusion-Reaction system arising in bioreactor processes.

In this work, we perform an asymptotic analysis of a coupled system of two Advection-Diffusion-Reaction equations with Danckwerts boundary conditions, which models the interaction between a microbial population (e.g., bacterias), called biomass, and a diluted organic contaminant (e.g., nitrates), called substrate, in a continuous flow bioreactor. This system exhibits, under suitable conditions, two stable equilibrium states: one steady state in which the biomass becomes extinct and no reaction is produced, called washout, and another steady state, which corresponds to the partial elimination of the substrate. We use the method of linearization to give sufficient conditions for the asymptotic stability of the two stable equilibrium configurations. Finally, we compare our asymptotic analysis with the usual asymptotic analysis associated to the continuous bioreactor when it is modeled with ordinary differential equations.

ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

Background: Statistical analysis of DNA microarray data provides a valuable diagnostic tool for the investigation of genetic components of diseases. To take advantage of the multitude of available data sets and analysis methods, it is desirable to combine both different algorithms and data from different studies. Applying ensemble learning, consensus clustering and cross-study normalization methods for this purpose in an almost fully automated process and linking different analysis modules together under a single interface would simplify many microarray analysis tasks. Results: We present ArrayMining.net, a web-application for microarray analysis that provides easy access to a wide choice of feature selection, clustering, prediction, gene set analysis and cross-study normalization methods. In contrast to other microarray-related web-tools, multiple algorithms and data sets for an analysis task can be combined using ensemble feature selection, ensemble prediction, consensus clustering and cross-platform data integration. By interlinking different analysis tools in a modular fashion, new exploratory routes become available, e.g. ensemble sample classification using features obtained from a gene set analysis and data from multiple studies. The analysis is further simplified by automatic parameter selection mechanisms and linkage to web tools and databases for functional annotation and literature mining. Conclusion: ArrayMining.net is a free web-application for microarray analysis combining a broad choice of algorithms based on ensemble and consensus methods, using automatic parameter selection and integration with annotation databases.

Étude du nombre de polynômes irréductibles dans les corps finis avec certaines contraintes imposées aux coefficients

L'objectif de ce mémoire est de dénombrer les polynômes irréductibles unitaires sur un corps fini en prescrivant des contraintes sur les coefficients. Dans les prochaines pages, il sera question de fixer simplement des coefficients, ou simplement de fixer leur signe, leur cubicité ou leur quarticité.

Étude du nombre de polynômes irréductibles dans les corps finis avec certaines contraintes imposées aux coefficients

L'objectif de ce mémoire est de dénombrer les polynômes irréductibles unitaires sur un corps fini en prescrivant des contraintes sur les coefficients. Dans les prochaines pages, il sera question de fixer simplement des coefficients, ou simplement de fixer leur signe, leur cubicité ou leur quarticité.

Macroglial and retinal changes in hypercholesterolemic rabbits after normalization of cholesterol levels

This study evaluates hypercholesterolemic rabbits, examining the retinal changes in Müller cells and astrocytes as well as their variations after a period of normal blood-cholesterol values induced by a standard diet. New Zealand rabbits were divided into three groups: G0, fed a standard diet; G1A, fed a 0.5% cholesterol-enriched diet for 8 months; and G1B, fed as G1A followed by standard diet for 6 months. Eyes were processed for transmission electron microscopy and immunohistochemistry (GFAP). While G1B resembled G0 more than did G1A, they shared alterations with G1A: a) as in G1A, Müller cells were GFAP+, filled spaces left by axonal degeneration, formed glial scars and their nuclei were displaced to the nerve-fibre layer. The area occupied by the astrocytes associated with the nerve-fibre bundles (AANFB) and by perivascular astrocytes (PVA) in G1A and G1B was significantly lower than in controls. However, no significant differences in PVA were found between G1A and G1B. In G1B, type I PVA was absent and replaced by hypertrophic type II cells; b) Bruch's membrane (BM) was thinner in G1B than in G1A; c) the retinal pigment epithelium (RPE) cytoplasm contained fewer lipids in G1B than in G1A; d) in G1A and G1B choriocapillaris and retinal vessel showed alterations with respect to G0; e) cell death and axonal degeneration in the retina were similar in G1A and G1B. The substitution of a hyperlipemic diet by a standard one normalizes blood-lipid levels. However, the persistence of damage at retinal vessels and BM-RPE could trigger chronic ischemia.

Estimation of water use and crop coefficients for an intensive olive orchard using sap flow measurements and modeled data

Olive tree sap flow measurements were collected in an intensive orchard near Évora, Portugal, during the irrigation seasons of 2013 and 2014, to calculate daily tree transpiration rates (T_SF). Meteorological variables were also collected to calculate reference evapotranspiration (ETo). Both data were used to assess values of basal crop coefficient (Kcb) for the period of the sap flow observations. The soil water balance model SIMDualKc was calibrated with soil, biophysical ground data and sap flow measurements collected in 2013. Validated in 2014 with collected sap flow observations, the model was used to provide estimates of dual e single crop coefficients for 2014 crop growing season. Good agreement between model simulated daily transpiration rates and those obtained with sapflow measurements was observed for 2014 (R2=0.76, RMSE=0.20 mm d-1), the year of validation, with an estimation average absolute error (AAE) of 0.20 mm d-1. Olive modeled daily actual evapotranspiration resulted in atual ETc values of 0.87, 2.05 and 0.77 mm d-1 for 2014 initial, mid- and end-season, respectively. Actual crop coefficient (Kc act) values of 0.51, 0.43 and 0.67 were also obtained for the same periods, respectively. Higher Kc values during spring (initial stage) and autumn (end-stage) were published in FAO56, varying between 0.65 for Kc ini and 0.70 for Kc end. The lower Kc mid value of 0.43 obtained for the summer (mid-season) is also inconsistent with the FAO56 expected Kc mid value of 0.70 for the period. The modeled Kc results are more consistent with the ones published by Allen & Pereira [1] for olive orchards with effective ground cover of 0.25 to 0.5, which vary between 0.40 and 0.80 for Kc ini, 0.40–0.60 for Kc mid with no active ground cover, and 0.35–0.75 for Kc end, depending on ground cover. The SIMDualKc simulation model proved to be appropriate for obtaining evapotranspiration and crop coefficient values for our intensive olive orchard in southern Portugal.

Olive water use and crop coefficients from energy balance and radiometric canopy temperatures

Biophysical and meteorological variables as well as radiometric canopy temperatures were collected in an intensive orchard near Évora, Portugal, with 28% ground cover by canopy and combined in a simplified two-source energy balance model (STSEB) to independently calculate the olive tree transpiration (T_STSEB) component of the total evapotranspiration (ETc). Sap flow observations were simultaneously taken in the same orchard allowing also for independent calculations of tree transpiration (T_SF). Model water use results were compared with water use estimates from the sap flow measurements. Good agreement was observed (R2=0.86, RMSE=0.20 mm d-1), with an estimation average absolute error (AAE) of 0.17 mm d-1. From June to August, on average olive water use were 1.92 and 1.89 mm d-1 for sap flow and STSEB model respectively, and 1.38 and 1.58 mm d-1 for the month of September. Results were also used to assess the olive basal crop coefficients (Kcb). Kcb estimates of 0.33 were obtained for sap flow and STSEB model, respectively, for June to August, and of 0.44 and 0.53 for the month of September. Basal crop coefficients were lower than the suggested FAO56 average Kcb values of 0.65 for June to August, the crop mid-season growth stage, and of 0.65 for the month of September, the end-season.