A theoretical formalism to reconstruct structural and dynamical properties of polymer liquids from their coarse-grained description is developed. This formalism relies on established earlier analytical coarse-graining of polymers derived from the first principles of liquid theory. The polymer chain is represented at a mesoscale level as a soft particle. Coarse-grained computer simulations provide input data to the reconstruction formalism and allow one to achieve the most gain in computational efficiency. The structure of polymer systems is reconstructed by combining global information from mesoscale simulations and local information from small united-atom simulations. The obtained monomer total correlation function is tested for a number of systems including polyethylene melts of different degrees of polymerization as well as melts with different local chemical structure. The agreement with full united-atom simulations is quantitative, and the procedure remains advantageous in computational time. The dynamics in mesoscale simulations is artificially accelerated due to the coarse-graining procedure and needs to be rescaled. The proposed formalism addresses two rescalings of the dynamics. First, the internal degrees of freedom averaged out during coarse-graining procedure are reintroduced in "a posteriori" manner, rescaling the simulation time. The second rescaling takes into account the change in friction when switching from a monomer level description to mesoscopic. Both friction coefficients for monomer and soft particle are calculated analytically and their ratio provides the rescaling factor for the diffusion coefficient. The formalism is extensively tested against the united-atom molecular dynamic simulations and experimental data. The reconstructed diffusive dynamics of the center-of-mass for polyethylene and polybutadiene melts of increasing degrees of polymerization show a quantitative agreement, supporting the foundation of the approach. Finally, from the center-of-mass diffusion the monomer friction coefficient is obtained and used as an input into Cooperative Dynamics theory. The dynamics of polymer chains at any length scale of interest is described through a Langevin equation. In summary, the proposed formalism reconstructs the structure and dynamics of polymer melts enhancing computational efficiency of molecular dynamic simulations. This dissertation includes previously published and unpublished co-authored material.

Nous avons étudié expérimentalement la dynamique de remontée de bulles dans des fluides complexes, allant de solutions de polymère à des milieux granulaires immergés, dans le cas d'une géométrie confinée (cellule de Hele-Shaw). Dans un premier temps, nous avons considéré la remontée d'une bulle unique dans une solution de polymère confinée. Le fluide choisi (PEO) est viscoélastique et rhéofluidifiant. Au-delà d'un volume critique, nous avons mis en évidence et caractérisé deux types d'instabilités : la bulle est défléchie de sa trajectoire verticale, ou se fragmente. L'extension de cette expérience au cas de l'injection continue d'air en base de la cellule a permis de quantifier la dynamique couplée entre les bulles et en particulier leur coalescence, qui dépend fortement du débit d'injection. Dans un deuxième temps, nous avons considéré le cas d'un milieu granulaire immergé : un lit de grains à surface libre, dans lequel de l'air est injecté à débit constant par un unique point d'injection en base de la cellule. En régime stationnaire, la mise en mouvement des grains par le passage répété de l'air conduit à la formation d'une zone fluide. Nous avons quantifié la dynamique des bulles dans cette zone et montré que même en variant la taille des grains et le débit de gaz, la fraction de gaz piégée dans la zone fluide reste constante. Enfin, nous avons considéré l'influence d'un obstacle fixe sur la dynamique du canal d'air central. Un diagramme des régimes est établi en fonction de la taille et de la hauteur de l'obstacle : soit le canal est stabilisé par l'obstacle, soit il est instable et explore de manière intermittente l'un ou l'autre côté de l'obstacle. / We have studied experimentally the dynamics of bubbles rising in complex fluids, from polymer solutions to immersed granular media, in a confined geometry (Hele-Shaw cell). In a first part, we considered the rise of a single bubble in a confined polymer solution. The fluid (PEO) is viscoelastic and shear-thinning. Above a critical volume, we have observed and characterized two types of instabilities : the bubble is deflected from its vertical trajectory, or fragments. The extension of this experiment to continuous air injection at of the cell bottom made it possible to quantify the coupled dynamics between bubbles and in particular their coalescence, which is highly dependent on the injection rate. In a second part, we considered the case of a immersed granular medium, in which air is injected at constant flow rate through a single nozzle at the cell bottom. In the steady state, the movement of the grains generated by the successive air pathways leads to the formation of a fluidized zone. We quantified the bubble dynamics in this zone and showed that even when varying the grains size and gas flow rate, the fraction of gas trapped in the fluidized zone remains constant. Finally, we considered the influence of a fixed obstacle on the dynamics of the central air channel. A phase diagram is established depending on the size and height of the obstacle: either the channel is stabilized by the obstacle, or it is unstable and intermittently explores each side of the obstacle.

A diffuse-interface finite-element method has been applied to simulate the flow of two-component rheologically complex fluids. It treats the interfaces as having a finite thickness with a phase-field parameter varying continuously from one phase to the other. Adaptive meshing is applied to produce fine grid near the interface and coarse mesh in the bulk. It leads to accurate resolution of the interface at modest computational costs. An advantage of this method is that topological changes such as interfacial rupture and coalescence happen naturally under a short-range force resembling the van der Waals force. There is no need for manual intervention as in sharp-interface model to effect such event. Moreover, this energy-based formulation easily incorporates complex rheology as long as the free energy of the microstructures is known. The complex fluids considered in this thesis include viscoelastic fluids and nematic liquid crystals. Viscoelasticity is represented by the Oldroyd-B model, derived for a dilute polymer solution as linear elastic dumbbells suspended in a Newtonian solvent. The Leslie-Ericksen model is used for nematic liquid crystals，which features distortional elasticity and viscous anisotropy. The interfacial dynamics of such complex fluids are of both scientific and practical significance. The thesis describes seven computational studies of physically interesting problems. The numerical simulations of monodisperse drop formation in microfluidic devices have reproduced scenarios of jet breakup and drop formation observed in experiments. Parametric studies have shown dripping and jetting regimes for increasing flow rates, and elucidated the effects of flow and rheological parameters on the drop formation process and the final drop size. A simple liquid drop model is used to study the neutrophil, the most common type of white blood cell, transit in pulmonary capillaries. The cell size, viscosity and rheological properties are found to determine the transit time. A compound drop model is also employed to account for the cell nucleus. The other four cases concern drop and bubble dynamics in nematic liquid crystals, as determined by the coupling among interfacial anchoring, bulk elasticity and anisotropic viscosity. In particular, the simulations reproduce unusual bubble shapes seen in experiments, and predict self-assembly of microdroplets in nematic media. / Applied Science, Faculty of / Chemical and Biological Engineering, Department of / Graduate

Many coatings only need to either be durable or fast drying, usually sacrificing long term stability in favor of quick setting, or vice versa. One coating type that cannot afford to sacrifice either performance feature is traffic paint. These paints are made up of a weak polycation, an anionic latex, and a volatile base which evaporates upon application. The high pH in the initial formulation deprotonates the polycation, rendering it charge neutral. However, upon evaporation, the resulting drop in pH allows for the electrostatic complexation between the polycation and the latex. The electrostatic interactions used in these formulations parallels that of complex coacervation, an associative liquid-liquid phase separation. In this thesis, we will take advantage of model coacervate systems to elucidate the design parameters necessary for the formulations to serve as paints. We used a series of simplified systems, starting with a system consisting of a weakly cationic homopolymer and weakly anionic homopolymer before moving on to anionic copolymers with decreasing charge density, and ultimately an anionic latex. We investigated the effects of pH, charge stoichiometry, and salt concentration for each of these systems, using turbidimetry and optical microscopy as a means of measuring the extent of coacervation. We determined that, the removal of 99.9% of the charge on our polymers was necessary for coacervation to no longer occur. This can be achieved using either salt or pH, however, salt may be preferable, due to the inherent hazardous properties of highly acidic or basic solutions. Very excitingly, we were able to observe coacervation with latex particles. To our knowledge, there are no known observations of polymer-particle coacervation prior to this study. These results suggest that the underlying physics and design principles associated with fast setting paints can be explored using complex coacervation, and that a much broader range of parameters can be used to control the setting of these materials, beyond just pH used in existing technology. Future efforts are still needed to better understand the effect that polymer chemistry has on the complexation of these materials, and how it also affects the mechanical and adhesive properties of coating produced by such formulations.

Formation of gas bubbles in complex fluids and their subsequent rise due to buoyancy is a very important fundamental phenomenon both in nature and industry. Bubble size and bubble velocity are critical parameters which govern the interfacial transport phenomena and play an important role in gas-solid contact. These characteristics affect the operating parameters as well as the design of equipment in industrial applications. Non-Newtonian, Shear-thickening fluids have been studied extensively due to their immense potential for commercial use in shock absorbing and force damping applications, such as liquid body armor, sports and personal protection. Furthermore, a better understanding of shear-thickening fluid is pertinent to industrial processing for enhancing flow, preventing the breakage or clogging of mixing equipment, and preventing clogging in narrow orifices. Despite their significance, many aspects of the flow of these non-Newtonian fluids remain poorly understood. In the first part of this dissertation, we study the dynamics of rising bubbles in three dimensional fluidized beds using computational fluid dynamics-discrete element method (CFD-DEM) to shed light on the physics underpinning phenomena uncovered previously using magnetic resonance imaging (MRI). We were able to understand the underlying mechanism behind the anomalous collapse of a bubble in side-by-side injection as well as an alternating asynchronous pinch-off pattern due to jet interaction in a fluidized bed by looking into the gas streamlines and the drag force on the particles. In the second part of this dissertation, we study dynamics of rising bubbles in Newtonian fluids and non-Newtonian cornstarch-water suspensions experimentally using optical imaging. We were able to identify that Capillary number (Ca) is a key dimensionless parameter governing the regimes of interacting jets in water. We also observed a periodic coalescence of bubbles at the same points in space in cornstarch-water suspensions and attributed this behavior to leading bubbles entering a shear thickening regime. Further, we identified the key dimensionless parameters for wobbling behavior of single bubbles in cornstarch suspensions to be Bond (Bo), and Reynolds (Re) number, regardless of the bubble being in a Newtonian or a shear-thinning regime. We believe our findings can be applied in industry to optimize the mass transport and liquid mixing for a range of applications.

Knowledge of thermodynamic fluid properties, such as density and phase behavior, is important for the design, operation, and safety of several processes including drilling, extraction, transportation, and separation that are required in the petroleum. The knowledge is even more critical at extreme temperature and pressure conditions as the search for more crude oil reserves lead to harsher conditions. Currently, there is dearth of experimental data at these conditions and as such, the predictive capability of the existing modeling tools are unproven. The objective of this research is to develop a fundamental understanding of the impact of molecular architecture on fluid phase behavior at temperatures to 523 K (250 °C) and pressures to 275 MPa (40,000 psi). These high-temperature and high-pressure (HTHP) conditions are typical of operating conditions often encountered in petroleum exploration and recovery from ultra-deep wells that are encountered in the Gulf of Mexico. This PhD study focuses on the fluid phase behavior of a low molecular weight compound, two moderately high molecular weight compounds, three asymmetric binary mixtures of a light gas and a heavy hydrocarbon compound with varying molecular size. The compounds are selected to represent the family of saturated compounds found in typical crude oils. Furthermore, this study reports experimental data for two "dead" crude oil samples obtained from the Gulf of Mexico and their mixtures with methane from ambient to HTHP conditions. A variable-volume view cell coupled with a linear variable differential transformer is used to experimentally measure the high-pressure properties of these compounds and mixtures. The reported density data compare well to the limited available data in the literature with deviations that are less than 0.9%, which is the experimental uncertainty of the density data reported in this study. The phase behavior and density data obtained in this study are modeled using the Peng-Robinson (PR), the volume-translated (VT) PR, and the Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT) equations of state (EoS). The EoS pure component parameters, typically obtained from the open literature, are derived from fitting the particular EoS to, critical point, or to vapor pressure and saturated liquid density data, or to HTHP density data. For the density data reported here, the PREoS provided the worst predictions, while the VT-PREoS gives an improved performance as compared to the PREoS. However, the PC-SAFT EoS provided the best HTHP density predictions especially when using HTHP pure component parameters. The situation is however reversed in the modeling performance for the phase behavior data whereby the PC-SAFT EoS with HTHP parameters provided the worst vapor-liquid equilibria predictions. Better predictions are obtained with the PC-SAFT EoS when using parameters obtained from fit of the vapor pressure data and is comparable to the PREoS predictions. This reversal in performance is not surprising since the phase behavior data occur at moderately low pressures. The performance of the PC-SAFT EoS is extended to the experimental density data reported for the dead crude oil samples and their mixtures with methane. The PC-SAFT EoS with either set of pure component parameters yield similar predictions that are within 3% of the reported crude oil density data. However, when using the HTHP parameters, the PC-SAFT gives a good representation of the slope of experimental data, which is crucial in the calculation of second-derivative properties such has isothermal compressibility. The PC-SAFT EoS is also employed to model the crude oil HTHP density data for both the dead crude oils and their mixtures with methane using correlations for both the Low-P parameters and the HTHP parameters. The Low-P parameters are derived from fitting the PC-SAFT EoS to pure compound vapor pressure and saturated liquid density data, while the HTHP parameters are obtained from fitting the PC-SAFT EoS to pure compound HTHP liquid density data. Interestingly, the PC-SAFT EoS with the Low-P parameters provided better HTHP density predictions that are within 1.5% of the experimental data for the dead oils than the HTHP parameters that are within 2 to 4% of the data. Density predictions for the dead oil mixtures with methane are however comparable for both sets of parameters and are within 1% on average. However, the PC-SAFT EoS with HTHP parameters clearly provided better representation of the isothermal property, a derivative property obtained from density data, within 10% while predictions with the Low-P parameters can be as high as 37%. The successful completion of the thesis work expands the current knowledge base of fluid phase behavior at the extreme operating conditions encountered by engineers in the petroleum industries. Furthermore, the reported HTHP experimental data also provide a means to scientists and researchers for the development, improvement, and validation of equations with improved modeling performance.

Les écoulements de fluides complexes à l’échelle sub-micronique est une problématique rencontrée dans des domaines aussi divers que la récupération assistée du pétrole ou la lubrification des surfaces. Un fluide complexe a des propriétés rhéologiques riches, dues à la présence d’objets déformables en solution, comme les pelotes de polymère. Les phénomènes de surface, comme le glissement jouent un rôle important aux petites échelles. La question de l’effet du confinement sur la rhéologie de solutions de polymères est abordée. Nous caractérisons la taille des objets en solution et la rhéologie volumique des fluides. Grâce au développement d’une technique de photobleaching de fluorescence pour la mesure de vitesse d’écoulement dans des canaux sub-microniques, nous déterminons la viscosité effective des fluides en géométrie confinée. Cette approche expérimentale nous permet de montrer que le confinement induit une diminution de la viscosité effective des fluides. Une mesure directe des vitesses et longueurs de glissement est réalisée en microcanaux par vélocimétrie de particules (micro-PIV). Ces données mettent en évidence une réduction du glissement en géométrie confinée, qui est interprétée en termes de modification du mécanisme de glissement. Une distinction entre le comportement volumique et les phénomènes de surface ne permet plus de rendre compte du comportement du fluide à l’échelle sub-micronique. Une étude préliminaire des écoulements de solutions de tensioactifs à l’échelle sub-micronique est également proposée. / Rheology of high molecular weight polymer solutions at submicroscale is investigated, with a particular emphasis on the wall slip characterization. Our approach is to measure the velocity of a pressure-driven flow in sub-microchannels in order to determine an effective viscosity of fluids. We have been using fluorescence photobleaching as a non-invasive technique to evaluate the velocity of a pressure-driven flow in 175 to 4000 nm high channels. A striking reduction of the effective viscosity is observed with the confinement, as compared to the bulk one. Direct measurement of slip velocity in microchannels is performed, using z-resolved micro-Particle Image Velocimetry (PIV). This study enables to draw two important conclusions, which have never been experimentally demonstrated. Slippage of polymer solutions in the semi-dilute unentangled regime is greatly reduced by confinement. A distinction of bulk and surface phenomena seems no longer valid at the submicroscale. This experimental method is also adapted to the study of surfactant solutions flows at the submicroscale.

Neste trabalho usamos simulações computacionais para estudar inicialmente a estrutura das redes de ligação de hidrogênio (HB) formadas pelas misturas de metanol--água e 1-propanol--água e em seguida como essas misturas afetam as propriedades eletrônicas da sonda solvatocrômica 1-metilquinolin-8-olato (QB). Para a primeira parte fizemos uso do formalismo de redes complexas na análise das redes de HB formadas nas misturas. Com essa abordagem foi possível verificar o comportamento do sistema como um todo em diferentes concentrações de água nas misturas por meio do cálculo de diversas propriedades de rede. Da análise dessas propriedades pudemos, por exemplo, constatar bastante similaridade na conectividade dos dois tipos de misturas, entender melhor comportamentos anômalos, observar microssegregação, e verificar uma mudança na conectividade das moléculas de água em misturas com 1-propanol. Na parte seguinte, onde investigamos os efeitos das misturas nas propriedades eletrônicas da QB, foi necessário modelar uma parametrização adequada para o campo de força da sonda utilizado nas simulações. Essa parametrização incluiu adaptação de parâmetros geométricos da sonda e do conjunto de cargas atômicas polarizadas. Nessa último tópico, adaptamos o procedimento iterativo de polarização, dentro de uma abordagem sequencial de mecânica quântica e mecânica molecular. De posse desses parâmetros realizamos a simulação da QB em misturas de álcool--água em sete frações molares de água distintas. Analisamos a distribuição do solvente ao redor da QB e a solvatação preferencial. Em configurações amostradas nas simulações calculamos os efeitos das misturas no dipolo induzido, comprimento de onda de excitação eletrônica, índices globais de reatividade e blindagem magnética da QB. Fomos especialmente atentos em correlacionar esses efeitos com as propriedades estruturais do sistema, e percebemos quais das propriedades eletrônicas calculadas para a QB podem ser divididas nas duas classes: as que são mais susceptíveis às interações de curto alcance, como HB com o solvente e a solvatação preferencial; e as que são mais susceptíveis às interações de longo alcance. / In this work we use computer simulations to initially study the hydrogen bond (HB) networks formed in mixtures of methanol--water and 1-propanol--water and subsequently how these mixtures can affect the electronic properties of the solvatocromic probe 1-methylquinolin-8-olate (QB). For the first part, we use the complex networks formalism to analyse HB networks formed in mixtures. With this approach it was possible to verify the behavior of the system as a whole in different water concentrations by calculating several network properties. As a result we note, for example, the connectivities of the two types of mixtures are quite similar. We were also able to better understand the system anomalous behavior, observe microsegregation and verify a change in the connectivity of water molecules in mixtures with 1-propanol. In the following part, in which we investigated the effects of mixtures on the electronic properties of the QB, it was necessary to model an appropriate parameterization for the force field of the probe used in the simulations. This parameterization included adjustments for both the geometric parameters and the polarized atomic charges. In this last topic, we adapt the iterative polarization process within a sequential approach using quantum mechanics and molecular mechanics. With these parameters we performed the simulation of the QB in mixtures of alcohol--water in seven distinct water fractions. We analyzed the solvent distribution around the QB and the preferential solvation. Using configurations sampled in the simulations we calculate the mixtures effects on induced dipole, wavelength electronic excitation, global indices of reactivity and magnetic shielding of the QB. We were especially attentive to correlate these effects with the structural properties of the system, and realize that of the electronic properties calculated for the QB can be divided into two classes: those that are more susceptible to short-range interactions, such as solute-solvent HB and preferential solvation, and those which are more susceptible to long-range interactions.

Many cells exploit the bending or rotation of flagellar filaments in order to self-propel in viscous fluids. Often swimming occurs in complex, nonlinear fluids, e.g. mucus. Futhermore even in simple Newtonian fluids, if swimming appendages are deformable then locomotion is subject to fluid-structure interactions. The fundamental question addressed in this thesis is how exactly locomotion is impacted, in particular if it is faster or slower, with or without these effects. First we study locomotion in shear-thinning and viscoelastic fluids with rigid swimming appendages. Following the introductory Chapter, in Chapter 2 we propose empirical extensions of the classical Newtonian resistive-force theory to model the waving of slender filaments in non-Newtonian fluids, based on experimental measurements for the motion of rigid rods in non-Newtonian fluids and on the Carreau fluid model. We then use our models to address waving locomotion in shear-thinning fluids, and show that the resulting swimming speeds are systematically lowered a result which we are able to capture asymptotically and to interpret physically. In Chapter 3 we consider swimming using small-amplitude periodic waves in a viscoelastic fluid described by the Oldroyd-B constitutive relationship. Using Taylor’s swimming sheet model, we show that if all travelling waves move in the same direction, the locomotion speed of the organism is systematically decreased. However, if we allow waves to travel in two opposite directions, we show that this can lead to enhancement of the swimming speed, which is physically interpreted as due to asymmetric viscoelastic damping of waves with different frequencies. A change of the swimming direction is also possible. Secondly we consider the affect of fluid-structure interactions. In Chapter 4, we use Taylor’s swimming sheet model to describe an active swimmer immersed in an Oldroyd-B fluid. We solve for the shape of an active swimmer as a balance between the external fluid stresses, the internal driving moments, and the passive elastic resistance. We show that this dynamic balance leads to a generic transition from hindered rigid swimming to enhanced flexible locomotion. The results are physically interpreted as due to a viscoelastic suction increasing the swimming amplitude in a non-Newtonian fluid and overcoming viscoelastic damping. In Chapter 5 we consider peritrichously flagellated bacteria, such as Escherichia coli. The rotation of each motor is transmitted to a flexible rod called the hook which in turns transmits it to a helical filament, leading to swimming. The motors are randomly distributed over the body of the organism, and thus one expects the propulsive forces from the filament to almost cancel out leading to negligible swimming. We show that the transition to swimming is an elasto-hydrodynamic instability arising when the flexibility of the hook is below a critical threshold.

On s'attache à étudier des modèles mathématiques multi-échelles pour des domaines variés : la rhéologie des matériaux vitreux, la biochimie dans la balnéothérapie et la biomécanique des sutures craniofaciales. Pour les matériaux vitreux, nous étudions un modèle de type cinétique et justifions mathématiquement des propriétés macroscopiques (transition vitreuse à faible cisaillement et comportement de type fluide newtonien à fort taux de cisaillement) après avoir remarqué une certaine analogie avec la pénalisation d'obstacles en mécanique des fluides. Nous proposons également une généralisation multi-dimensionnelle de ce modèle afin de prendre en compte des types d'écoulements généraux. En biochimie nous présentons un premier modèle très simplifié de réaction-diffusion et montrons comment concevoir un schéma numérique adapté en utilisant les hypothèses de modélisation. Enfin nous proposons un modèle de couplage biomécanique pour le développement des sutures qui rend compte du phénomène d'interdigitation que l'on observe en pratique. / We study multiscale mathematical models for various scientific fields: soft glassy rheology, biochemistry for balneotherapy, and the biomechanics of craniofacial suture development. In soft flassy rheology, we study a kinetic-type of model and justify mathematically some macroscopic properties of the model (especially the glass transition at low shear rate and the Newtonian behaviour at large shear rate) by noticing an analogy with the problem of obstacle penalization in fluid mechanics. Moreover, we propose a multidimensional generalization of this model in order to handle more general flow types. In biochemistry, we introduce a first, very simplified model and show how we can design a numerical scheme based on the modelling hypotheses. Finally we present a model for suture growth coupling biology and mechanics which accounts for the interdigitation pattern observed in practice.