Quantifying diffusion in biofilms : from model hydrogels to living biofilms

Les biofilms sont des communautés de microorganismes incorporés dans une matrice exo-polymérique complexe. Ils sont reconnus pour jouer un rôle important comme barrière de diffusion dans les systèmes environnementaux et la santé humaine, donnant lieu à une résistance accrue aux antibiotiques et aux désinfectants. Comme le transfert de masse dans un biofilm est principalement dû à la diffusion moléculaire, il est primordial de comprendre les principaux paramètres influençant les flux de diffusion. Dans ce travail, nous avons étudié un biofilm de Pseudomonas fluorescens et deux hydrogels modèles (agarose et alginate) pour lesquels l’autodiffusion (mouvement Brownien) et les coefficients de diffusion mutuels ont été quantifiés. La spectroscopie par corrélation de fluorescence a été utilisée pour mesurer les coefficients d'autodiffusion dans une volume confocal de ca. 1 m3 dans les gels ou les biofilms, tandis que les mesures de diffusion mutuelle ont été faites par cellule de diffusion. En outre, la voltamétrie sur microélectrode a été utilisée pour évaluer le potentiel de Donnan des gels afin de déterminer son impact sur la diffusion. Pour l'hydrogel d'agarose, les observations combinées d'une diminution du coefficient d’autodiffusion et de l’augmentation de la diffusion mutuelle pour une force ionique décroissante ont été attribuées au potentiel de Donnan du gel. Des mesures de l'effet Donnan (différence de -30 mV entre des forces ioniques de 10-4 et 10-1 M) et l'accumulation correspondante d’ions dans l'hydrogel (augmentation d’un facteur de 13 par rapport à la solution) ont indiqué que les interactions électrostatiques peuvent fortement influencer le flux de diffusion de cations, même dans un hydrogel faiblement chargé tel que l'agarose. Curieusement, pour un gel plus chargé comme l'alginate de calcium, la variation de la force ionique et du pH n'a donné lieu qu'à de légères variations de la diffusion de sondes chargées dans l'hydrogel. Ces résultats suggèrent qu’en influençant la diffusion du soluté, l'effet direct des cations sur la structure du gel (compression et/ou gonflement induits) était beaucoup plus efficace que l'effet Donnan. De même, pour un biofilm bactérien, les coefficients d'autodiffusion étaient pratiquement constants sur toute une gamme de force ionique (10-4-10-1 M), aussi bien pour des petits solutés chargés négativement ou positivement (le rapport du coefficient d’autodiffusion dans biofilm sur celui dans la solution, Db/Dw ≈ 85 %) que pour des nanoparticules (Db/Dw≈ 50 %), suggérant que l'effet d'obstruction des biofilms l’emporte sur l'effet de charge. Les résultats de cette étude ont montré que parmi les divers facteurs majeurs qui affectent la diffusion dans un biofilm environnemental oligotrophe (exclusion stérique, interactions électrostatiques et hydrophobes), les effets d'obstruction semblent être les plus importants lorsque l'on tente de comprendre la diffusion du soluté. Alors que les effets de charge ne semblaient pas être importants pour l'autodiffusion de substrats chargés dans l'hydrogel d'alginate ou dans le biofilm bactérien, ils ont joué un rôle clé dans la compréhension de la diffusion à travers l’agarose. L’ensemble de ces résultats devraient être très utiles pour l'évaluation de la biodisponibilité des contaminants traces et des nanoparticules dans l'environnement.

Rapport M/L de disques de galaxies issus de modèles CSPE et contrôle des contraintes mécaniques dans la conception de revêtements optiques

La thèse qui suit est organisée en deux volets: un premier volet portant sur les modèles de masse de galaxies et un second volet sur la conception de revêtements optiques et le contrôle de leurs propriétés mécaniques. Les modèles de masse présentés dans cette thèse ont été réalisés sur un sous-échantillon de dix galaxies de l'étude SINGS comprenant neuf galaxies normales et une galaxie naine. Ce travail visait à fixer le rapport masse-luminosité du disque à tout rayon en utilisant les résultats de modèles d'évolution galactique chimio-spectrophotométriques ajustés spécifiquement à chaque galaxie grâce à son profil de photométrie multi-bandes. Les résultats montrent que les disques stellaires tels que normalisés par les rapports masse-luminosité issus des modèles ont des masses cohérentes dans toutes les bandes étudiées de l'ultra-violet, du visible ainsi que du proche infrarouge (bandes FUV à IRAC2). Ces disques peuvent être considérés comme maximaux par rapport aux données cinématiques des galaxies étudiées. Ceci est dû au fait que le rapport M/L est plus élevé au centre que sur les bords. Les disques étant maximaux et physiquement justifiés, on ne peut dès lors ignorer les effets de composants tels que les bulbes ou les barres et les corrections nécessaires doivent être apportées aux profils de luminosité et de vitesses de rotation de la galaxie. Dans les travaux de la seconde partie, le logiciel en développement libre OpenFilters a été modifié afin de tenir compte des contraintes mécaniques dans la conception numérique de revêtements optiques. Les contraintes mécaniques dans les couches minces ont un effet délétère sur leurs performances optiques. Un revêtement destiné à rendre réflectives les lames d'un étalon Fabry-Perot utilisé en astronomie a été conçu et fabriqué afin d'évaluer les performances réelles de la méthode. Ce cas a été choisi à cause de la diminution de la finesse d'un étalon Fabry-Perot apporté par la courbure des lames sous l'effet des contraintes. Les résultats montrent que les mesures concordent avec les modèles numériques et qu'il est donc possible à l'aide de ce logiciel d'optimiser les revêtements pour leur comportement mécanique autant que pour leurs propriétés optiques.

Studies on Pseudoscalar Meson Bound States and Semileptonic Decays in a Relativistic Potential Model

In this thesis quark-antiquark bound states are considered using a relativistic two-body equation for Dirac particles. The mass spectrum of mesons includes bound states involving two heavy quarks or one heavy and one light quark. In order to analyse these states within a unified formalism, it is desirable to have a two-fermion equation that limits to one body Dirac equation with a static interaction for the light quark when the other particle's mass tends to infinity. A suitable two-body equation has been developed by Mandelzweig and Wallace. This equation is solved in momentum space and is used to describe the complete spectrum of mesons. The potential used in this work contains a short range one-gluon exchange interaction and a long range linear confining and constant potential terms. This model is used to investigate the decay processes of heavy mesons. Semileptonic decays are more tractable since there is no final state interactions between the leptons and hadrons that would otherwise complicate the situation. Studies on B and D meson decays are helpful to understand the nonperturbative strong interactions of heavy mesons, which in turn is useful to extract the details of weak interaction process. Calculation of form factors of these semileptonic decays of pseudo scalar mesons are also presented.

Model of single-electron decay from a strongly isolated quantum dot

Recent measurements of electron escape from a nonequilibrium charged quantum dot are interpreted within a two-dimensional (2D) separable model. The confining potential is derived from 3D self-consistent Poisson-Thomas-Fermi calculations. It is found that the sequence of decay lifetimes provides a sensitive test of the confining potential and its dependence on electron occupation

Hysteresis and avalanches in the random anisotropy Ising model

ches. The critical point is characterized by a set of critical exponents, which are consistent with the universal values proposed from the study of other simpler models.

Closure of the Monte Carlo dynamical equation in the spherical Sherrington-Kirkpatrick model

We study the analytical solution of the Monte Carlo dynamics in the spherical Sherrington-Kirkpatrick model using the technique of the generating function. Explicit solutions for one-time observables (like the energy) and two-time observables (like the correlation and response function) are obtained. We show that the crucial quantity which governs the dynamics is the acceptance rate. At zero temperature, an adiabatic approximation reveals that the relaxational behavior of the model corresponds to that of a single harmonic oscillator with an effective renormalized mass.

Superheavy nuclei in relativistic effective Lagrangian model

Isotopic and isotonic chains of superheavy nuclei are analyzed to search for spherical double shell closures beyond Z=82 and N=126 within the new effective field theory model of Furnstahl, Serot, and Tang for the relativistic nuclear many-body problem. We take into account several indicators to identify the occurrence of possible shell closures, such as two-nucleon separation energies, two-nucleon shell gaps, average pairing gaps, and the shell correction energy. The effective Lagrangian model predicts N=172 and Z=120 and N=258 and Z=120 as spherical doubly magic superheavy nuclei, whereas N=184 and Z=114 show some magic character depending on the parameter set. The magicity of a particular neutron (proton) number in the analyzed mass region is found to depend on the number of protons (neutrons) present in the nucleus.

Multilevel multitrait-multimethod model: application to the measurement of egocentered social networks

Our goal in this paper is to assess reliability and validity of egocentered network data using multilevel analysis (Muthen, 1989, Hox, 1993) under the multitrait-multimethod approach. The confirmatory factor analysis model for multitrait-multimethod data (Werts & Linn, 1970; Andrews, 1984) is used for our analyses. In this study we reanalyse a part of data of another study (Kogovšek et al., 2002) done on a representative sample of the inhabitants of Ljubljana. The traits used in our article are the name interpreters. We consider egocentered network data as hierarchical; therefore a multilevel analysis is required. We use Muthen's partial maximum likelihood approach, called pseudobalanced solution (Muthen, 1989, 1990, 1994) which produces estimations close to maximum likelihood for large ego sample sizes (Hox & Mass, 2001). Several analyses will be done in order to compare this multilevel analysis to classic methods of analysis such as the ones made in Kogovšek et al. (2002), who analysed the data only at group (ego) level considering averages of all alters within the ego. We show that some of the results obtained by classic methods are biased and that multilevel analysis provides more detailed information that much enriches the interpretation of reliability and validity of hierarchical data. Within and between-ego reliabilities and validities and other related quality measures are defined, computed and interpreted

Body mass index as a standard of living measure: a different interpretation for the case of Colombia

We analyze the Body Mass Index (BMI) in a distinct way of its traditional use and it lets us use it as a proxy of standard of living for the case of Colombia. Our approach is focused on studying how far the people are from the normal range and not on the score of each one and this lets us to treat equally extreme cases as severe thinness and obesity. We use a probabilistic model (Ordered Probit) that evaluates the probability of being within the normal range or another level. We found that socioeconomic variables have a significant effect on the dependent variable and that there are no linear effects. Besides, people with difficulties for walking and adults have less probability of having a normal BMI.

A new efficient approach to the direct restricted active space self-consistent field method

An implicitly parallel method for integral-block driven restricted active space self-consistent field (RASSCF) algorithms is presented. The approach is based on a model space representation of the RAS active orbitals with an efficient expansion of the model subspaces. The applicability of the method is demonstrated with a RASSCF investigation of the first two excited states of indole

Automatic mass segmentation in mammographic images

Aquesta tesi està emmarcada dins la detecció precoç de masses, un dels símptomes més clars del càncer de mama, en imatges mamogràfiques. Primerament, s'ha fet un anàlisi extensiu dels diferents mètodes de la literatura, concloent que aquests mètodes són dependents de diferent paràmetres: el tamany i la forma de la massa i la densitat de la mama. Així, l'objectiu de la tesi és analitzar, dissenyar i implementar un mètode de detecció robust i independent d'aquests tres paràmetres. Per a tal fi, s'ha construït un patró deformable de la massa a partir de l'anàlisi de masses reals i, a continuació, aquest model és buscat en les imatges seguint un esquema probabilístic, obtenint una sèrie de regions sospitoses. Fent servir l'anàlisi 2DPCA, s'ha construït un algorisme capaç de discernir aquestes regions són realment una massa o no. La densitat de la mama és un paràmetre que s'introdueix de forma natural dins l'algorisme.

Simulation of the diurnal cycle in a climate model and its evaluation using data from Meteosat 7

The representation of the diurnal cycle in the Hadley Centre climate model is evaluated using simulations of the infrared radiances observed by Meteosat 7. In both the window and water vapour channels, the standard version of the model with 19 levels produces a good simulation of the geographical distributions of the mean radiances and of the amplitude of the diurnal cycle. Increasing the vertical resolution to 30 levels leads to further improvements in the mean fields. The timing of the maximum and minimum radiances reveals significant model errors, however, which are sensitive to the frequency with which the radiation scheme is called. In most regions, these errors are consistent with well documented errors in the timing of convective precipitation, which peaks before noon in the model, in contrast to the observed peak in the late afternoon or evening. When the radiation scheme is called every model time step (half an hour), as opposed to every three hours in the standard version, the timing of the minimum radiance is improved for convective regions over central Africa, due to the creation of upper-level layer-cloud by detrainment from the convection scheme, which persists well after the convection itself has dissipated. However, this produces a decoupling between the timing of the diurnal cycles of precipitation and window channel radiance. The possibility is raised that a similar decoupling may occur in reality and the implications of this for the retrieval of the diurnal cycle of precipitation from infrared radiances are discussed.

Statistical inference of OH concentrations and air mass dilution rates from successive observations of non-methane hydrocarbons in single air masses

Bayesian inference has been used to determine rigorous estimates of hydroxyl radical concentrations () and air mass dilution rates (K) averaged following air masses between linked observations of nonmethane hydrocarbons (NMHCs) spanning the North Atlantic during the Intercontinental Transport and Chemical Transformation (ITCT)-Lagrangian-2K4 experiment. The Bayesian technique obtains a refined (posterior) distribution of a parameter given data related to the parameter through a model and prior beliefs about the parameter distribution. Here, the model describes hydrocarbon loss through OH reaction and mixing with a background concentration at rate K. The Lagrangian experiment provides direct observations of hydrocarbons at two time points, removing assumptions regarding composition or sources upstream of a single observation. The estimates are sharpened by using many hydrocarbons with different reactivities and accounting for their variability and measurement uncertainty. A novel technique is used to construct prior background distributions of many species, described by variation of a single parameter . This exploits the high correlation of species, related by the first principal component of many NMHC samples. The Bayesian method obtains posterior estimates of , K and following each air mass. Median values are typically between 0.5 and 2.0 × 106 molecules cm−3, but are elevated to between 2.5 and 3.5 × 106 molecules cm−3, in low-level pollution. A comparison of estimates from absolute NMHC concentrations and NMHC ratios assuming zero background (the “photochemical clock” method) shows similar distributions but reveals systematic high bias in the estimates from ratios. Estimates of K are ∼0.1 day−1 but show more sensitivity to the prior distribution assumed.

Biologically motivated model for object detection and identification in real-world scenes

The classical computer vision methods can only weakly emulate some of the multi-level parallelisms in signal processing and information sharing that takes place in different parts of the primates’ visual system thus enabling it to accomplish many diverse functions of visual perception. One of the main functions of the primates’ vision is to detect and recognise objects in natural scenes despite all the linear and non-linear variations of the objects and their environment. The superior performance of the primates’ visual system compared to what machine vision systems have been able to achieve to date, motivates scientists and researchers to further explore this area in pursuit of more efficient vision systems inspired by natural models. In this paper building blocks for a hierarchical efficient object recognition model are proposed. Incorporating the attention-based processing would lead to a system that will process the visual data in a non-linear way focusing only on the regions of interest and hence reducing the time to achieve real-time performance. Further, it is suggested to modify the visual cortex model for recognizing objects by adding non-linearities in the ventral path consistent with earlier discoveries as reported by researchers in the neuro-physiology of vision.

Consistent Dirichlet Boundary Conditions for Numerical Solution of Moving Boundary Problems

We consider the imposition of Dirichlet boundary conditions in the finite element modelling of moving boundary problems in one and two dimensions for which the total mass is prescribed. A modification of the standard linear finite element test space allows the boundary conditions to be imposed strongly whilst simultaneously conserving a discrete mass. The validity of the technique is assessed for a specific moving mesh finite element method, although the approach is more general. Numerical comparisons are carried out for mass-conserving solutions of the porous medium equation with Dirichlet boundary conditions and for a moving boundary problem with a source term and time-varying mass.