In the last few decades, an increasing number of physicists specialized in soft matter, including polymers, have turned their attention to biologically relevant materials. The properties of various molecules and fibres, such as DNA, RNA, proteins, and filaments of all sorts, are studied to better understand their behaviours and functions. Self-assembled biological membranes, or lipid bilayers, are also the focus of much attention as many life processes depend on these. Small lipid bilayers vesicles dubbed liposomes are also frequently used in the pharmaceutical and cosmetic industries. In this thesis, work is presented on both the elastic properties of polymers and the response of lipid bilayer vesicles to extrusion in narrow-channels. These two areas of research may seem disconnected but they both concern deformed soft materials. The thesis contains four articles: the first presenting a fundamental study of the entropic elasticity of circular chains; the second, a simple universal description of the effect of sequence on the elasticity of linear polymers such as DNA; the third, a model of the symmetric thermophoretic stretch of a nano-confined polymer; the fourth, a model that predicts the final sizes of vesicles obtained by pressure extrusion. These articles are preceded by an extensive introduction that covers all of the essential concepts and theories necessary to understand the work that has been done.

Load management is an essential and important factor for distributed simulations running on shared resources due to load imbalances that can caused considerable performance loss. High Level Architecture (HLA) -based simulation is a framework that works to facilitate the design and management of distributed simulations. HLA coordinates the interaction between simulation entities (federates). However, HLA-based simulation standards do not present the ability to manage resources or help detect load imbalances that could directly cause decrease of performance. Focusing on this constraint, a migration-aware dynamic balancing system has been designed for HLA simulations to offer an efficient load-balancing scheme that works in large-scale environments. This system presents some limitations on estimating costs and benefits, so we propose an enhancement to this existing load balancing system, which improves the accuracy of estimating the number of migrations for the next load redistribution. The proposed scheme detects the load imbalances by evaluating the recourses overhead. The scheme classifies the recourses based on the overhead as overloaded and underloaded, followed by matching the highest overloaded recourses with the lowest underloaded recourses. Furthermore, the proposed scheme aims to precisely estimate the number of migrations by evaluating and analyzing the recourses to obtain the best number of migrations. Therefore, certain migrations that do not contribute to an improvement in the simulation performance are avoided. This avoidance is based on comparing time delay and time gain. Moreover, to be considered for migration, the overall sum of the time gains should be larger than the overall sum of the time delays. The proposed scheme has shown an improvement on decreasing the execution time.

Vesicles are simple structures, but display complex, non-linear dynamics in fluid flow. I investigate the deformation of nanometer-sized vesicles, both fully-inflated and those with excess area, as they travel in tightly confined capillaries. By varying both channel size and flow strength, I simulate vesicles as they transition from steady-state to unstable shapes, and then rupture in strong flow fields. By employing a molecular dynamics model of the vesicle, fluid, and capillary system one is able to rupture the lipid bilayer of these vesicles. This is unique in that most other numerical methods for modelling vesicles are unable to show rupture. The rupture of fully-inflated vesicles is applicable to drug delivery in which the release of the encapsulated medicine needs to be controlled. The deformation and rupture of vesicles with excess area could be applicable to red blood cells which have similar rheological properties.

Cette thèse doctorale se focalise sur l'étude du procédé d'usinage au moyen de l'outil numérique de calcul par Eléments finis (MEF). Concrètement, il s'agit d'étudier les phénomènes thermomécaniques qui ont lieu, lors de l'opération d'arrachement de matière, à l'interface et qui contrôlent le type de contact entre l'outil et le copeau. Pour cela, un modèle numérique de coupe orthogonale sous la formulation ALE (Arbitrary Lagrangian Eulerian) a été développé avec le code de calcul par MEF Abaqus/Explicit. Plusieurs études paramétriques ont été menées à bien pour découpler les effets des variables locales, tant sur les résultats macroscopiques (forces...), comme dans la zone de l'interface (température...). Les résultats numériques montrent que ce sont les effets combinés du type de modèle de frottement implémenté à l'interface, avec l'adoucissement thermique du matériau, qui conditionnent l'apparition du type de contact collant, et par conséquent, régissent le contact outil/copeau. On propose deux nouveaux modèles de frottement variable en fonction de la vitesse, pour améliorer la définition du frottement à l'interface. D'autre part, la validité du modèle numérique est vérifiée en observant une bonne corrélation entre les forces numériques obtenues, et les forces de coupe expérimentales obtenues pour le même matériau et dans les mêmes conditions de coupe / This doctoral thesis is focused on the study of the process of machining by means of the numerical tool for calculation by Finite Element Method (FEM). Concretely, it is a question of studying the thermomechanical phenomena which take place, during an operation of material removal, at the interface and that control the type of contact between the tool and the chip. for that, a numerical model of orthogonal cutting under the ALE formulation (Arbitrary Lagrangian Eulerian) was developed with the code Abaqus/Explicit. Several parametric studies were carried out to uncouple the effects of the local variables, on the macroscopic results (forces...), as in the interface (temperature...). The numerical results show that in fact the combined effects of the type of the implemented friction model at the interface, both with the thermal softening of the material, condition the appearence of the sticking contact, and consequently, govern the tool/chip contact type. Two new models of variable friction with to velocity are proposed, to improve the definition of friction in the interface. Finally, the validity of the numerical model is checked by observing a good correlation between the obtained numerical forces, and the experimental cutting forces obtained for same material and under the same cutting conditions

La fenêtre pariéto-dynamique est un système « passif » de récupération de chaleur. Son principe de fonctionnement consiste à faire circuler l’air neuf de ventilation entre les lames de verre avant son introduction dans le volume habitable. Une partie de la chaleur traversant les vitrages est alors récupérée par l’écoulement d’air. La fenêtre Paziaud® est une fenêtre pariéto-dynamique particulière, composée de trois vitrages séparés par des lames d’air ventilées qui forment un conduit en U. Alors que la mise en place d’un système de ventilation double flux est complexe dans un contexte de réhabilitation, ce type de fenêtre présente une alternative intéressante moyennant un surcoût d’environ 20% par rapport à une fenêtre double vitrage classique mais permettant une récupération de chaleur non négligeable.Afin de caractériser les performances de la fenêtre Paziaud®, des études numériques et expérimentales ont été entreprises et ont confirmé le potentiel du dispositif. Par ailleurs, la prise en compte de ce genre de système dans les codes de simulation thermique des bâtiments n’est pas satisfaisante. Pour répondre à ce besoin, ont été développés plusieurs modèles simplifiés basés sur un bilan thermique représentable par analogie électrique. Une attention particulière a été portée sur le traitement des échanges convectifs dans les lames d’air. Les résultats ont permis de valider un modèle simplifié, qui pourra être utilisé par la suite dans un code de thermique de l’habitat. / The ventilated window is a passive system of heat recovery. It draws fresh air circulating between window’s glasses from the outside to the inside. A part of the heat which crosses the glasses is then recovered by the air flow. The Paziaud® window is composed of three glasses separated by ventilated air spaces in U-shape. While the implementation of a double-flow ventilation system for the housing retrofitting is complex, this Paziaud® window costs only 20% more than a conventional double-glazed window but improves significantly the heat recovery.In order to study the performance of the Paziaud® window, numerical and experimental works have been undertaken and have confirmed the potentiality of such windows. However, a thermal code able to take into account the heat exchange is not available for such system. Considering this lack of simulations, several simplified models based on electrical analogy have been developed. Particular attention is paid to the convective exchange process in the ventilated air spaces. The numerical results could validate a simplified thermal model which can be integrated to the building codes.

Dust and gas in protoplanetary disks are the building blocks of planets. In this thesis, we study the dynamics of the gas and dust, which are crucial for the planet formation theory, using observational and numerical approaches. The observational part contains the case study of a rare circumtriple disk around the GW Ori hierarchical triple system. We present Atacama Large Millimeter/submillimeter Array (ALMA) observations of 1.3 mm dust continuum and 12CO J = 2-1 molecular gas emission of the disk. For the first time, we identify three dust rings in the GW Ori disk at ~46, 188, and 338 au, with the outermost ring being the largest dust ring ever found in protoplanetary disks. We use visibility modeling of the dust continuum and kinematics modeling of CO lines to show that the disk has misaligned parts, and the innermost dust ring is eccentric. We interpret these substructures as evidence of ongoing dynamical interactions between the triple stars and the circumtriple disk. In the numerical part, we study whether or not dust around gas gaps opened by planets can remain settled by performing three-dimensional, dust-plus-gas simulations of protoplanetary disks with an embedded planet. We find planets that open gas gaps 'puff up' small, sub-mm-sized grains at the gap edges, where the dust scale-height can reach 80% of the gas scale-height. We attribute this dust 'puff-up' to the planet-induced meridional gas flows previously identified by Fung and Chiang. We thus emphasize the importance of explicit 3D simulations to obtain the vertical distribution of sub-mm-sized grains around planet gaps. We caution that the gas-gap-opening planet interpretation of well-defined dust rings is only self-consistent with large grains exceeding mm in size. / Graduate

This thesis focuses mainly on the consequences that single mutations have on structural, functional and energetic aspects of the protein cyanovirin-N. In order to estimate the free energy of single mutations, we have applied thermodynamics integration and Bennett acceptance ratio techniques. Replica exchange molecular dynamics has been applied to accelerate simulations for complicated scenarios. Our studies suggest that certain single mutations may be promising to improve binding affinity to Manα1→2Manα but we also learned that the simplistic view of a strong hydrogen bond correlating to a high binding affinity may not always be correct. Finally, we explored in detail the widely used mutation P51G for its impact on protein rigidity at the very important hinge region as well as for its possible effect on glycan binding.

This work addresses the application of non-premixed filtered tabulated chemistry as a turbulent combustion modeling strategy in the LES framework. On the first part of this study the effects of the filtering operation on non-premixed flamelets are carefully appraised, considering an individual flamelet and the entire manifold. Subsequently, a systematic approach is followed where first the numerical implementation is verified. Afterwards validation is done on a coflow laminar diffusion flame, where promising results encourage the further model appraisal on a more complex turbulent configuration. This is finally achieved under turbulent conditions of Flames D and E, where the formalism including a SGS wrinkling modeling function adequately describes the wrinkled flame front features. The formalism assessment on a laminar coflow diffusion flame reveals a considerable sensitivity to the flame dimensionality. A flame sensor based on the mixture fraction gradient, with a tolerance to take into account the numerical grid resolution, is introduced and proves to deliver satisfactory results. The sensor-determined model activation allows to adequately represent the underlying physics behind flame filtering and so it endorses the consistency of the numerical procedure. The evaluation of the non-premixed FTACLES model on turbulent flames D and E demonstrates that the formalism coupling with a SGS wrinkling modeling function can adequately describe the wrinkled flame front condition. The model performs significantly well employing a three-dimensional tabulation strategy, where the numerical grid is coupled with the model by the third parameter, i.e. the computational cell size. The predictions for both the major stable species and the minor ones accurately correspond with the undergoing physics. The obtained results have a deep theoretical implication for the combustion research. First, they confirm the idea that SGS closure in diffusive combustion can be derived based on filtering arguments, and not only based on statistical approaches. Second, they demonstrate the enormous potential of the non-premixed FTACLES formalism once a sound flame sensor and a SGS wrinkling modeling function are included. / Doctorat en Sciences de l'ingénieur et technologie / info:eu-repo/semantics/nonPublished

Methane/air premixed and partially premixed turbulent flames at high Reynolds number are characterized using Direct Numerical Simulations (DNS) with detailed chemistry in a spatially evolving slot Bunsen configuration. Two sets of simulations are performed. A first set of simulations with fully premixed inlet conditions is considered in order to assess the effect of turbulence on the flame. Four simulations are performed at increasing Reynolds number and up to 22400, defined based on the bulk velocity, slot width, and the reactants' properties, and 22 billion grid points, making it one of the largest simulations in turbulent combustion. The simulations feature finite rate chemistry with a 16 species mechanism. To perform these simulations, few preliminary steps were required: (i) two skeletal mechanisms were developed reducing GRI-3.0; (ii) a convergence study is performed to select the proper spatial and temporal discretization and (iii) simulations of fully developed turbulent channel flows are preformed to generate the inlet conditions of the jet. The study covers different aspects of flame-turbulence interaction. It is found that the thickness of the reaction zone is similar to that of a laminar flame, while the preheat zone has a lower mean temperature gradient, indicating flame thickening. The characteristic length scales of turbulence are investigated and the effect of the Reynolds number on these quantities is assessed. The tangential rate of strain is responsible for the production of flame surface in the mean and surface destruction is due to the curvature term. A second set of simulations with inhomogeneous inlet conditions is performed to study how partial premixing and turbulence interact with the flame and with each other. The jet Reynolds number is 5600, and a 33 species mechanism is used. The effect of the inlet fluctuations is reflected on heat release rate fluctuations, however the conditional mean is not affected. The flames show thickening of the preheat zone, and for the lowest level of mixing a slight thickening of the reaction zone is observed. The effect of partially mixed mixture on the NOx formation is analyzed and no major impact was found.

Density dependent flow occurs in areas where high-salinity groundwater interacts with low-salinity groundwater to create a brine-to-freshwater interface that defies common assumptions about groundwater movement. Yet the geologic and hydrologic factors that impact interface dynamics and migration remain poorly defined. With less than 20 mm•yr-1 of precipitation and with an extremely dense (i.e. 1.2 g•cm-3) naturally occurring brine, Chile’s Salar de Atacama (SdA) provides an excellent analog for exploring interface dynamics in other arid regions. Site-specific 2-D models of the interface in the southeastern region of SdA, with interpretations of the hydrostratigraphic framework, provide an analysis for density-driven response rates to climatic change. A separate parametric, equally probable series of distributions of hydraulic conductivity provides a means for expanding analysis to other similar arid salar (i.e. “salt flat”) environments. Comparing the modeled interface’s geometry and response to perturbations in the rates of lateral recharge in each hydrostratigraphic realization yields insight into the dynamics of interface migration to coupled climatic and geologic conditions. Changes in hydrologic conditions, informed by paleoclimatic interpretations and previously modeled climate predictions, are introduced to each hydrostratigraphic realization following the interface reaching an initial dynamic equilibrium, and the interface’s response is assessed subsequent to it reaching a new dynamic equilibrium. Metrics for model evaluation include migration rate, change in the interface’s areal extent, change in interface slope, and the response rate following the introduction to a perturbation in the aquifer’s hydrology. Model analyses suggest that evaporation rates strongly control the interface’s geometry and sensitivity despite climatic and geologic conditions; continuity of high-permeability pathways controls interface slope; increasing continuity also decreases interface stability in terms of time required to reach a new steady state. While these results have implications for interface dynamics in both salars specifically and arid climates in general, they also indicate the importance of considering hydrostatigraphic continuity for saline water intrusion in coastal regions. They also provide a compelling method for assessing interface dynamics in other climatic and geologic conditions.