ED Mathématiques et Informatique
Model order reduction with mesh adaptation
by Ishak TIFOUTI (IMB - Institut de Mathématiques de Bordeaux)
The defense will take place at 14h00 - Salle de conférences 350 Cr de la Liberation, Talence, 33400, France IMB Bat A33, Salle de conférences
in front of the jury composed of
- Nicolas BARRAL - Maître de conférences - Bordeaux INP - Directeur de these
- Tommaso TADDEI - Chargé de recherche - INRIA - CoDirecteur de these
- Anca-Claudia BELME - Maîtresse de conférences - Sorbonne Universite - Rapporteur
- Olga MULA - Full professor - University of Vienna - Rapporteur
- Frederic ALAUZET - Directeur de recherche - INRIA - Examinateur
- Luc MIEUSSENS - Professeur des universités - Bordeaux INP - Examinateur
- Masayuki YANO - Associate Professor - University of Toronto - Examinateur
- Virginie EHRLACHER - Professeure - Ecole des Ponts Paristech - Examinateur
A wealth of applications in science and engineering involve the solution to computational fluid dynamics (CFD) problems for many different system configurations. For this class of problems, it is important to reduce the marginal cost associated with a given simulation over a range of parameters. Model order reduction (MOR) techniques rely on an offline/online decomposition to reduce marginal costs. During the offline phase, we rely on high-fidelity (hf) simulations to generate a reduced-order model (ROM) to estimate the solution over a range of parameters. During the online or deployment phase, given a new value of the parameter, we query the ROM to estimate the solution field. We particularly focus on the development of automated procedures for both training and deployment stages. Approximation to advection-dominated PDEs poses several fundamental challenges to state-of-the-art model order reduction methods. First, despite the recent advances in high-performance computing and numerical analysis, hf numerical approximation of these problems requires extensive computational resources: limiting the number of solutions (snapshots) used to build the ROM. Second, linear-approximation-based methods are completely inadequate to deal with parameter-dependent discontinuities: this motivates the development of nonlinear approximation methods. Third, MOR techniques rely on the projection of the equation onto a unique shared hf discretization and thus rely on the assumption that the underlying hf discretization is accurate for all parameters in a prescribed range: for problems with parameter-dependent shocks, this requires accurate adaptive mesh refinement (AMR) over a broad portion of the spatial domain and is often unfeasible. Mesh adaptation aims at improving the accuracy of numerical simulations while reducing the computational cost through automatic optimisation of the mesh resolution during the computation. More precisely, in anisotropic mesh adaptation, the mesh elements sizes and orientations are modified in order to minimize a certain numerical error model, to guarantee an optimal mesh size for a desired accuracy. A non-linear process is considered that ensures convergence of the mesh/solution pair to the optimum with respect to the error model considered. Anisotropic mesh adaptation is also able to handle unsteady problems, with complex moving geometries. The aim of the PhD project is to study a novel integrated model reduction mesh adaptation approach for nonlinear advection-dominated systems of partial differential equations (PDEs), notably aerodynamic and hydraulic flows. Relevant solutions to these problems are characterized by parameter-dependent shocks and contact discontinuities. To this aim, registration-based model reduction will be combined with parametric mesh adaptation. Registration-based model reduction relies on a parametric mapping to identify and then track relevant features of the solution field and ultimately improve performance of linear compression methods such as proper orthogonal decomposition (POD). Parametric mesh adaptation refers to the task of determining an accurate mesh for a range of system configurations. Provided that the mapping is effective to track moving features of the solution, mesh adaptation should lead to considerably more parsimonious discretizations compared to uniform refinement, for any target accuracy.
ED Sciences Chimiques
Exploration of structural colors through surface structuration and oxide composition
by Julien CASTETS (ICMCB - Institut de Chimie de la Matière Condensée de Bordeaux)
The defense will take place at 10h00 - Amphithéâtre Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB), 87 Avenue du Dr Albert Schweitzer, 33600, Pessac
in front of the jury composed of
- Glenna DRISKO - Directrice de recherche - Laboratoire de Chimie ENS de Lyon - Directeur de these
- Beniamino SCIACCA - Chargé de recherche - Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), CNRS, UMR7325, Aix-Marseille University - Rapporteur
- Beatriz JULIáN-LóPEZ - Associate Professor - Institute of Advanced Materials (INAM) - Rapporteur
- Kevin VYNCK - Chargé de recherche - Institut Lumière Matière (iLM), UMR5306 - UCBL - CNRS - Examinateur
- Laurence CROGUENNEC - Directrice de recherche - Institut de Chimie de la Matière Condensée in Bordeaux (ICMCB) - Examinateur
- Julien LUMEAU - Directeur de recherche - Institut Fresnel, CNRS, Aix-Marseille Université - Examinateur
The perception of a surface's appearance is defined by its interaction with light, and the relative position of the observer and light source. Vivid structural colors are found in Nature, due to structures on a scale comparable to wavelengths of visible light. Novel optical functionalities can be achieved in thin films by controlling the structuration of scatterers at the nano/micron scale. Thus, we explored the synthesis of a disordered perforated silica layer through dip-coating and sol-gel chemistry. Perforations, which act to scatter light, are formed by water adsorption into the film from a humid environment, driven by the salinity of the film. By carefully choosing the synthetic conditions, the pore structure can be adapted, resulting in a higher degree of organization of the perforations. We explored another way to produce saturated structural colors, with a numerical and experimental investigation of the angular appearance of Bragg mirrors composed of alternating dielectrics, specifically silica and titania layers. A Bragg mirror is a photonic structure, with a periodic repetition of pairs of thin films, usually displaying vivid and iridescent colors. The angular colors generated by the stacks are explored by computing their spectral reflectance spectra, while fabricated Bragg mirrors are also angularly characterized, allowing for a comparison between measurements and simulations. Additionally, the dip-coating synthesis protocol of the layers is investigated to explore the effect on appearance of small deviations in the Bragg mirrors' thickness and refractive index. Finally, we explored the coating of a dense thin film with an ordered and disordered porous patterned layer. The morphologies of the structuration are investigated by AFM and SEM. Both structures are optically characterized. Light diffusion is observed from the disordered structure, while light diffraction is observed from the ordered structures. We studied the impact of the thin film's refractive index and thickness on the light diffraction and diffusion behavior, with simulations of the reflectance spectra being compared with optical measurements of the fabricated materials.
Biomimetic lipopolymers and stimuli-responsive lipids to tailor membrane permeability
by Rosanna LE SCOUARNEC (Acides nucléiques : Régulations Naturelles et Artificielles)
The defense will take place at 9h00 - Amphi CRPP Centre de Recherche Paul Pascal (CRPP) 115 Avenue Schweitzer 33600 Pessac
in front of the jury composed of
- Jeanne LEBLOND CHAIN - Chargée de recherche - Université de Bordeaux - Directeur de these
- Andreas HEISE - Professor - Royal College of Surgeons - Rapporteur
- Paola LUCIANI - Full professor - University of Bern, Switzerland - Rapporteur
- Colin BONDUELLE - Directeur de recherche - Université de Bordeaux - CoDirecteur de these
- Martina STENZEL - Professor - University of New South Wales - Examinateur
- Jean-Christophe BARET - Professeur - Université de Bordeaux - Examinateur
Transmembrane transport of solutes is a critical feature to build synthetic cells or to develop therapeutic nanocarriers for nanomedicine. In Nature, the diffusion across the cellular membrane is either facilitated by proteins or by unique lipid dynamics. In order to achieve improved control over permeability in cell-like compartments, synthetic systems, such as those based on polypeptides, are particularly promising. These polymers possess similar properties to proteins, including their capacity to self-assemble via well-defined secondary structures, as well as stimuli-responsive properties, biocompatibility, and biodegradability. Anchoring these polymers in a cell membrane can be facilitated by lipid functionalization. Indeed, lipids represent an alternative strategy to generate membrane destabilization through the successful development of new stimuli-responsive lipids. Whether they are polymers or lipids, their common goal is to enhance their robustness while maintaining the reactivity and reversibility of their natural counterparts. This PhD thesis investigates the synthesis of polypeptides and switchable lipids, with a particular focus on their ability to provide stimuli-responsiveness to liposomes, i.e. thermoresponsiveness. The goal of the project was to mimic membrane transport processes mediated by phospholipid or protein membrane dynamics. We first designed lipid-polyproline conjugates in order to anchor them within liposomes' membrane. Once inserted, the conjugates induced reversible phase separation in a temperature-dependent manner. Such membrane modifications resulted in liposome permeability at different scales (micro- and nanoscale) and allowed the release of cargo molecules up to the size of proteins. These polymers were then combined with pH-switchable lipids to obtain vesicles whose permeability can be modulated by several stimuli. We then designed new switchable lipid structures responsive to metal cations, whose influence on membrane permeability was investigated.
ED Sciences de la Vie et de la Santé
“Development of an 'Intestine-On-chip' to study infections by opportunistic pathogenic yeast Candida with advanced customized optical microscopy.”
by Fernanda LOPEZ GARCIA (Microbiologie fondamentale et Pathogénicité)
The defense will take place at 14h00 - Module 2.6 146 Rue Léo Saignat, 33000 Bordeaux
in front of the jury composed of
- Delphine DELACOUR - Directrice de recherche - UMR 7288 - E2M - Marseille Developmental Biology Institute - Examinateur
- Pierre JOSEPH - Directeur de recherche - UPR 8001 - LAAS - Laboratoire d'Analyse et d'Architecture des Systèmes - Rapporteur
- Julie DECHANET-MERVILLE - Directrice de recherche - Universite de Bordeuax-UMR 5164 -Immunologie conceptuelle, expérimentale et translationnelle - Examinateur
- Lourdes BASABE - Directrice de recherche - University of the Basque Country-BIOMICs microfluidics Team - Examinateur
- Karine DEMENTHON - Maîtresse de conférences - Universite de Bordeaux- UMR 5234 - Microbiologie Fondamentale et Pathogénicité - Directeur de these
- Pierre NASSOY - Directeur de recherche - Universite de Bordeuax- UMR 5298 - Le Laboratoire Photonique, Numérique et Nanosciences - CoDirecteur de these
- Mathieu HAUTEFEUILLE - Professeur - UMR 8263 - Développement, Adaptation et Vieillissement - Rapporteur
Conventional in vitro models, such as cells cultured in Petri dishes or Transwell inserts, often fail to replicate the complex physiology of the human body. At the same time, the use of animal models is increasingly avoided due to ethical concerns and their limited translational relevance to human biology. Organs-on-chip (OOCs) provide a promising alternative by creating biomimetic environments that model organ functionality and recapitulate key physiological and pathological features under controlled in vitro conditions. This thesis addresses a critical limitation of current OOC designs, the difficulty of observing real-time cellular events under flow conditions within a culture-compatible environment. The primary objective is to develop a next-generation OOC that more closely mimics in vivo conditions by enabling the application of external mechanical cues, specifically fluidic shear stress. The project focuses on the design, fabrication, and thorough characterization of the microfluidic device, including a central porous membrane. Two membrane materials, PDMS and collagen type I, are compared through comprehensive characterization to determine which better supports physiologically relevant cell growth. Using this platform, a proof-of-concept study investigates the mechanisms of intestinal infection by the pathogenic yeast Candida albicans in the intestine. The research includes morphological characterization of the intestinal epithelial layer using markers such as ZO-1 for tight junctions and villin and actin for assessing cell polarization. Scanning electron microscopy (SEM) is employed to observe both healthy and infected cells, while permeability assays evaluate intestinal barrier integrity in both conditions. Arriving to the conclusion that it is possible to study in depth the infection process of the yeast and its effects on the intestinal epithelium, opening the way to future projects that will create a more complex system.
Characterisation of the spatiotemporal organisation of cholinergic inputs in the cortex during perception and learning
by Tomás GARNIER ARTINANO (Institut Interdisciplinaire de Neurosciences)
The defense will take place at 14h00 - ???? CARF, 146 rue Léo Saignat, 33076 Bordeaux Cedex
in front of the jury composed of
- Naoya TAKAHASHI - Chargé de recherche - Université de Bordeaux - Directeur de these
- Valérie EGO-STENGEL - Directrice de recherche - Université Paris-Saclay - Rapporteur
- Belen PARDI - Chargée de recherche - Université Paris-Cité - Rapporteur
- Isabelle FEREZOU - Directrice de recherche - NeuroPSI – Institut des Neurosciences Paris-Saclay - Examinateur
- Shauna PARKES - Directrice de recherche - Université de Bordeaux - Examinateur
Understanding how the brain detects sensory inputs is a key challenge in neuroscience. Brain states exert a powerful and dynamic influence over the perception of sensory stimuli, with neuromodulatory systems playing a crucial role in regulating these states. The perceptual threshold, defined as the lowest stimulus intensity detectable half the time, varies with context, behavioural state, experience, and mood. However, the mechanisms controlling this threshold remain largely unknown. Previous studies have demonstrated that cholinergic inputs modulate cortical activity, influencing the detection of sensory stimuli. Traditionally, neuromodulation was thought to have a widespread and uniform impact throughout the brain. However, recent anatomical evidence suggests that basal forebrain cholinergic neurones offer targeted innervation to different cortical regions, potentially leading to differences in cholinergic patterns between different subregions of the cortex. At the moment, there is limited evidence regarding the dynamics of cholinergic modulation in the cortex and its relevance to sensory perception. In my thesis, I aim to characterise the spatiotemporal organisation of cholinergic activity in the primary somatosensory cortex (S1) of mice engaged in tactile detection, by employing a whisker-based tactile detection task. I tested the role of S1 cholinergic activity in the mouse's sensitivity to detect tactile stimuli to the contralateral C2 whisker. Local pharmacological injections of acetylcholine receptor blockers show cholinergic modulation affects tactile detection sensitivity by acting through muscarinic acetylcholine receptors in the S1. By using a novel genetically encoded cholinergic sensor and wide-field microscopy, I was able to image cholinergic activity across the S1 during the task. I observed cholinergic activity decreasing prior to the onset of the stimulus to successful detection of near-threshold stimulations. This decrease in pre-stimulus cholinergic activity was seen across S1 subregions, with a moderate amplitude gradient more prominent in the paw-related S1 region compared to the whisker-related region. These spatial patterns in the pre-stimulus window were highly predictive of behavioural outcome - whether stimuli were detected or missed. Both the spatial and temporal patterns of cholinergic activity remained largely unchanged across behavioural conditions in which mice engaged in detecting stimulation of different body parts (contralateral C2 whisker, ipsilateral C2 whisker, and contralateral hindpaw), indicating that the cholinergic activity leading to detection is independent of the specific body part attended to. Together, these results paint a complex picture for cholinergic dynamics in the cortex, suggesting it works at mesoscale, not a single global signal but not fully local either.