At : Salle Itzykson, IPhT Saclay , on 14:00

At : Amphi Charpak , on 14:00

Le transport dans le tube digestif est important pour l’absorption des nutriments, ainsi que pour la dynamique du microbiote intestinal. Cependant, le transport dans le tube digestif est mal caractérisé. Cette thèse modélise plusieurs aspects de ce transport. Dans une première partie, la densité de structures comme les villosités et les cryptes intestinales qui maximisent l’absorption est calculée analytiquement, en supposant que le transport est diffusif à leur proximité. Alors qu’on pense souvent que davantage de surface permet forcément d’augmenter l’absorption, des structures trop proches limitent la diffusion. Il y a donc une distance optimale finie entre ces structures. Dans une deuxième partie, on se focalise sur l’effet inverse: comme les parois du tube digestif sur lesquelles sont les villis bougent, l’espace entre villi peut varier, ce qui entraîne un écoulement. Des simulations de dynamique computationnelle des fluides permettent d’explorer systématiquement l’impact de la période spatiale de la vague de contraction sur l’épaisseur de la couche où le mouvement des villi entraîne un mélange, et sur l’écoulement net résultant dans la lumière intestinale. Ce dernier correspond à ce qu’une approximation analytique prédit. La troisième partie est le résultat d’une collaboration avec des expérimentateurs. L’analyse d’images du duodenum permet d’en déduire des conditions aux bords réalistes, qui sont ensuite implémentées dans des simulations numériques d’écoulements. Dans ces simulations, les trajectoires de particules sont suivies, analysées, et comparées à des approximations analytiques. Le but est d’obtenir une meilleure description approchée du transport dans le système digestif. Dans une dernière partie, on regarde l’impact du transport sur la compétition entre souches bactérienne. Ce travail contribue à une meilleure compréhension des mécanismes physiques impliqués dans les fonctions digestives et la dynamique du microbiote.

At : , on 14:00

At : amphithéâtre Bloch, IPhT Saclay, CEA, Orme des Merisiers – Bâtiment 774, 91191 Gif‑sur‑Yvette, France , on 14:00

At : IV Conf IV, 24 rue Lhomond, 75005, Paris , on 14:00

At : Campus Jussieu, 4 pl. Jussieu, Paris 5è, Tour 22-23, Étage 4, Salle de Conférences (401) , on 10:00

Numerical calculation methods are essential tools for supporting experimental research in chemical-physical problems, as their diversity and accessibility enable the study of a large number of systems. At thermodynamic equilibrium, the properties of the electronic ground state of a molecule or a solid can be studied using ab initio methods based on the evaluation of the electronic wavefunction or the electronic density, through the formalism of density functional theory (DFT). Among the many interactions, electronic exchange and correlation effects are the most complicated to evaluate. Advanced approaches, such as quantum Monte Carlo (QMC) or coupled cluster (CC), are able to provide an accurate description of these interactions, but at a high computational cost, which limits their application to the simplest systems. Thus, the ratio between the precision achieved and the numerical cost associated with the calculation is a decisive criterion in the choice of methods. This search of balance has represented an essential step in establishing this thesis work. On an apparently simple system — the hydrogen dimer (H2)2 — we found that only methods with an advanced description of exchange and correlation interactions are able to provide a satisfactory description of its potential energy surface. While some of the less advanced methods are able to return good results around the equilibrium geometry, they fail to describe the potential energy surface when the intermolecular bond distance of the dimer is compressed to values similar to those observed in solid hydrogen phases formed under megabar pressures. Of all the methods tested, those based on the random phase approximation (RPA) offer the best accuracy-cost ratio. This observation, in line with works we carried out prior to this thesis on the II-III phase transition of solid hydrogen, led us to consider extending the use of such methods to the calculation of physical quantities other than the energy. From this viewpoint, the determination of atomic forces is particularly relevant, as their knowledge allows us to understand the evolution of a system, identify its equilibrium geometry or calculate its harmonic vibration modes. We therefore sought to implement the analytical calculation of forces for the RPA method within the ACFDT extension of the Quantum ESPRESSO distribution, which uses plane waves and relies on the DFT formalism. This work has been successfully carried out in two distinct cases, with and without a self-consistent solving procedure of the Kohn-Sham equations. Because of the DFT formalism used, a self-consistent solution requires obtaining the RPA exchange-correlation potential through the optimized effective potential (OEP) approach. In both cases, forces of good quality have been calculated. Their evaluation at the RPA level shows a systematic improvement in the structural properties and vibration frequencies of molecules and solids compared with less advanced DFT methods. As the exact exchange potential formalism is similar between RPA and hybrid DFT methods, we also extended our force implementation to the latter. We were able to demonstrate that a self-consistent solution to the Kohn-Sham equations is often not necessary for computing any of the force-related properties. This work paves the way for a wider application of hybrid DFT and RPA methods to the calculation of additional physical quantities.

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At : , on 15:00

At : Institut d’astrophysique de Paris, 98 bis boulevard Arago, Amphi. Rez de chaussée , on 14:00

At : , on 14:00

At : Salle Itzykson Orme des meresiers, Bât. 774 - Point courrier 136 F-91191 Gif-sur-Yvette Cédex. , on 14:00

At : Amphithéâtre Charpak , on 15:00

La communication cellule-cellule participe à la régulation et à la synchronisation des fonctions cellulaires. Dans les tissus, le transport des ions et des molécules d’une cellule à l’autre s’effectue notamment à travers des pores protéiques nanométriques inclus dans la membrane cellulaire. De tels nanopores peuvent être inertes (simples nano-trous) ou mécanosensibles avec une perméabilité ionique/moléculaire qui dépend de la contrainte agissant sur la membrane. Ce projet propose une approche biomimétique de la communication cellule-cellule dans les tissus. Les tissus sont mimés avec des réseaux 2D de gouttelettes aqueuses reliées par des membranes lipidiques décorées de protéines transmembranaires, inertes ou mécanosensibles. Les protéines mécanosensibles sont synthétisées directement dans les gouttelettes à l’aide d’outils de biologie synthétique. Pour les réseaux inertes, nous étudions par microscopie à épifluorescence comment la diffusion des molécules de calcéine dépend de la topologie du réseau et de la concentration des pores. Nos résultats sont directement confrontés à des modèles de physique statistique du transport moléculaire basés sur des marches aléatoires en temps continu.Nous présentons également un système d’excitation mécanique mis en place pour déformer des réseaux de gouttes et les méthodes de biologie synthétique utilisées. Nous développons ces dernières dans le but d’insérer des protéines mécanosensibles dans la membrane DIB, afin d’obtenir une perméabilité moléculaire dépendante du stress, comme observée dans certains types de jonctions communicantes.

At : , on 16:00

Current classical simulations of physical phenomena face many limitations, particularly when dealing with complex systems such as turbulent fluids, plasmas or strongly correlated quantum materials. These simulations often struggle with high computational costs, limited scalability across multiple dimensions and time scales, and difficulties in capturing inherently non-linear or chaotic behaviors. Even with access to powerful high performance computing (HPC) resources, accurately resolving fine-scale dynamics or long time evolutions remains a significant challenge. The development of novel numerical methods is therefore essential for both academic research and industrial applications. Quantum computers emerge as novel numerical tools for studying such systems and solving the partial differential equations that model them. Thanks to the superposition and entanglement properties of qubits, digital computations can be performed in novel ways, offering promising theoretical speedups for certain problems. In this context, this thesis contributes to the development and understanding of quantum algorithms, ranging from the design of quantum circuits to the numerical solutions of partial and ordinary differential equations. First, efficient quantum circuits are presented for the implementation of crucial routines that are prevalent in quantum algorithms (multi-controlled operations, quantum state preparation, diagonal operations), and for a novel routine: the quantum Laplace transform. These routines limited the efficiency of quantum algorithms due to generic implementations that required complexities scaling exponentially with the number of qubits. Now, these tasks can be performed with tailored quantum circuits that leverage the structure of the physical problems. In the second part, quantum numerical schemes are introduced to address anisotropic transport equations and non-linear Hamiltonian ODEs. These schemes are composed of three steps (initialization, evolution, and measurement) and are based on high-ordered finite-difference and product formula approximations, also known as Trotterization. Efficient protocols to measure quantities of interest are presented, and a novel numerical analysis based on the vector norm instead of the generic operator norm is introduced, proving that the number of time-steps can be reduced by a factor that scales exponentially with the number of qubits while reaching similar accuracy. Additionally, non-linear Madelung transforms are studied to solve fluid equations on quantum computers. The various results of this thesis are illustrated with classical simulations of the quantum algorithms and simulations on real quantum hardware. This work lays the foundations for the practical simulations of classical physical systems on both current noisy-intermediate-scale quantum devices and future fault-tolerant quantum computers.