This thesis describes the results of experimental work on polyelectrolyte gels and their interaction with oppositely charged surfactants, and presents two new algorithms applicable to the simulation of colloid and polymer systems. The model systems investigated were crosslinked poly(acrylate) (PA) and poly(styrene sulphonate) (PSS), and the surfactant was dodecyl trimethylammonium bromide (DoTAB). Pure gel materials were studied using dynamic light scattering. It was shown that the diffusion coefficient (D) increases with increasing degree of swelling and the concentration dependence is larger than predicted by scaling arguments. For gels at swelling equilibrium D increases with increasing degree of crosslinking. In subsequent studies on gel particles in DoTAB solution, Raman spectra were recorded at different positions in the gel. For both types of gels two distinct regions could be observed. For PA the surfactant is localised in the outer phase without any surfactant in the core, while for PSS the surfactant was distributed such that it had the same concentration relative to the polymer throughout the gel. In a second experiment, the kinetics for the deswelling of microscopic PSS particles in DoTAB solution was studied. It was found that the final volume varied linearly with the DoTAB concentration, and the rate of volume decrease could be fitted to a single exponential indicating stagnant layer diffusion to be the rate limiting process for the deswelling of the PSS particles. In the second part, I first describe an algorithm showing an efficient way to detect percolation in simulations, with periodic boundary conditions, using recursion. Spherical boundary conditions is an alternative to periodic boundary conditions for systems with long-range interactions. In the last part, the possibility to use the surface of a hypersphere in four dimensions for simulations of polymer systems is investigated, and algorithms for Monte Carlo and Brownian dynamics simulations are described.

The thesis reports a contribution to the development of neural-like network- based element-free methods for the numerical simulation of some non-Newtonian fluid flow problems. The numerical approximation of functions and solution of the governing partial differential equations are mainly based on radial basis function networks. The resultant micro-macroscopic approaches do not require any element-based discretisation and only rely on a set of unstructured collocation points and hence are truly meshless or element-free. The development of the present methods begins with the use of the multi-layer perceptron networks (MLPNs) and radial basis function networks (RBFNs) to effectively eliminate the volume integrals in the integral formulation of fluid flow problems. An adaptive velocity gradient domain decomposition (AVGDD) scheme is incorporated into the computational algorithm. As a result, an improved feed forward neural network boundary-element-only method (FFNN- BEM) is created and verified. The present FFNN-BEM successfully simulates the flow of several Generalised Newtonian Fluids (GNFs), including the Carreau, Power-law and Cross models. To the best of the author's knowledge, the present FFNN-BEM is the first to achieve convergence for difficult flow situations when the power-law indices are very small (as small as 0.2). Although some elements are still used to discretise the governing equations, but only on the boundary of the analysis domain, the experience gained in the development of element-free approximation in the domain provides valuable skills for the progress towards an element-free approach. A least squares collocation RBFN-based mesh-free method is then developed for solving the governing PDEs. This method is coupled with the stochastic simulation technique (SST), forming the mesoscopic approach for analyzing viscoelastic flid flows. The velocity field is computed from the RBFN-based mesh-free method (macroscopic component) and the stress is determined by the SST (microscopic component). Thus the SST removes a limitation in traditional macroscopic approaches since closed form constitutive equations are not necessary in the SST. In this mesh-free method, each of the unknowns in the conservation equations is represented by a linear combination of weighted radial basis functions and hence the unknowns are converted from physical variables (e.g. velocity, stresses, etc) into network weights through the application of the general linear least squares principle and point collocation procedure. Depending on the type of RBFs used, a number of parameters will influence the performance of the method. These parameters include the centres in the case of thin plate spline RBFNs (TPS-RBFNs), and the centres and the widths in the case of multi-quadric RBFNs (MQ-RBFNs). A further improvement of the approach is achieved when the Eulerian SST is formulated via Brownian configuration fields (BCF) in place of the Lagrangian SST. The SST is made more efficient with the inclusion of the control variate variance reduction scheme, which allows for a reduction of the number of dumbbells used to model the fluid. A highly parallelised algorithm, at both macro and micro levels, incorporating a domain decomposition technique, is implemented to handle larger problems. The approach is verified and used to simulate the flow of several model dilute polymeric fluids (the Hookean, FENE and FENE-P models) in simple as well as non-trivial geometries, including shear flows (transient Couette, Poiseuille flows)), elongational flows (4:1 and 10:1 abrupt contraction flows) and lid-driven cavity flows.

L'objectif de cette thèse porte sur l'étude des phénomènes de blocage dans un flux particules à faible densité dans un canal. Le blocage est induit par la géométrie du canal. L'essentiel de mes travaux concerne la description des situations où le blocage est contrôlé par les limites en capacité d'un canal. Le paramètre pertinent pour ce phénomène est donné par le nombre de particules minimum, N, conduisant à l'interruption du flux de particules. Un modèle stochastique simple introduit par Gabrielli et al. (PRL. 110, 170601, 2013) illustre ce comportement: des particules arrivent aléatoirement selon une distribution de Poisson à l'entrée d'un canal unidimensionnel et le traversent avec un temps constant, noté t. Le blocage survient lorsque N particules sont simultanément sur le pont. Le travail de cette thèse à été d'étudier les extensions de ce modèle. Les observables du système sont la probabilité de survie, le flux sortant ainsi que la statistique sur les particules sorties avant le blocage. Les différentes études ont permis pour le cas N>2, pour une distribution homogène quelconque et inhomogène d'entrée, pour un système de multi-canaux ainsi que pour une durée finie de blocage d'obtenir des résultats analytiques exactes ainsi que des approximations à l'aide d'outils statistique. Le dernier projet de cette thèse porte sur l'étude microscopique des phénomènes de blocage. Le modèle simple que nous avons étudié est un système bidimensionnel de particules browniennes soumis à une force de traînée et se déplaçant dans un canal avec rétrécissement. La présence d'un obstacle au milieu du canal peut causer un colmatage selon les valeurs des différents paramètres du système. / This manuscript presents a study of blocking phenomenon in particulate streams flowing through anarrow channel. In particular, it examines situations in which blocking is controlled by the limitedcarrying capacity of the channel. It builds on a simple stochastic model, introduced by Gabrielli etal. (Phys. Rev. Lett. 110, 170601, 2013), in which particles arrive randomly according to a Poissondistribution at the entrance of a one-dimensional channel with an intensity λ and, unless interrupted,exit after a transit time, τ. Blocking occurs instantaneously when N=2 particles are simultaneouslypresent in the channel. The quantities of interest include the probability that the channel is still openat time t (survival probability) and the flux and total number of exiting particles. The thesisexamines a number of generalizations including when more than two particles must be present toinduce blockage, N>2, a time dependent intensity, a finite blocking time, and multi-channelsystems. We obtain exact and approximate analytical results using tools such as the masterequations describing the evolution of the n-particle partial probabilities, large deviation theory andqueuing theory. The theoretical results are validated by comparison with the results of numericalsimulations. The final chapter of the thesis uses a different approach, namely a brownian dynamics simulation of a two dimensional system of soft particles subjected to an external driving and dragforces. The presence of an obstacle in the middle of the channel can cause irreversible orintermittent clogging depending on the system geometry, temperature and particle stiffness.

This thesis presents the results of computer simulation studies of the structure, dynamics, and deformation of cross-linked polymer gels. Obtaining a fundamental understanding of the interrelation between the detailed structure and the properties of polymer gels is a challenge and a key issue towards designing materials for specific purposes. A new off-lattice method for constructing a closed network is presented that is free from defects, such as looping chains and dangling ends. Using these model networks in Brownian dynamics simulations, I show results for the structure and dynamics of bulk gels and describe a novel approach using spherical boundary conditions as an alternative to the periodic boundary conditions commonly used in simulations. This algorithm was also applied for simulating the diffusion of tracer particles within a static and dynamic network, to illustrate the quantitative difference and importance of including network mobility for large particles, as dynamic chains facilitate the escape of particles that become entrapped. I further investigate two technologically relevant properties of polymer gels: their stimuli-responsive behaviour and their mechanical properties. The collapse of core-shell nanogels was studied for a range of parameters, including the cross-linking degree and shell thickness. Two distinct regimes of gel collapse could be observed, with a rapid formation of small clusters followed by a coarsening stage. It is shown that in some cases, a collapsing shell may lead to an inversion of the core-shell particle which exposes the core polymer chains to the environment. This thesis also explores the deformation of bimodal gels consisting of both short and long chains, subject to uniaxial elongation, with the aim to understand the role of both network composition as well as structural heterogeneity on the mechanical response and the reinforcement mechanism of these materials. It is shown that a bimodal molecular weight distribution alone is sufficient to strongly alter the mechanical properties of networks compared to the corresponding unimodal networks with the same number-average chain length. Furthermore, it is shown that heterogeneities in the form of high-density short-chain clusters affect the mechanical properties relative to a homogeneous network, primarily by providing extensibility.

This thesis consists of research work in the broad area of soft condensed matter theory with a focus on active matter. The study of long wavelength, low frequency collective behavior of active particles (bacterial suspensions, fish schools, motor-microtubule extracts, active gels) forms an interesting modification to liquid-crystal hydrodynamics, in which the constituent particles carry permanent stresses that stir the fluid. Activity introduces novel instabilities and many novel aspects emerge. Our works focus on the dynamics, order, fluctuations and instabilities in these systems. In particular, we investigated the dynamics, order and fluctuation properties emerging from effective hydrodynamic descriptions of translationally ordered active matter and also studied those in microwave-driven quantum Hall nematics. We also investigated the rheological properties of active suspensions subjected to an applied orienting field. A summary of the works carried out is as follows. Translationally ordered active phases – active smectics and active cholesterics: Active or self-propelled particles consume and dissipate energy generating permanent stresses that stir the fluid around them. The collective behavior of systems of active particles, in systems with translational order, pose interesting questions and possibilities of new physics that differ strikingly from those in systems at thermal equilibrium with the same spatial symmetry. We developed the hydrodynamic equations of motion for (a) an active system with spontaneously broken translational symmetry in one direction, i.e., smectic and (b) the simplest uniaxially ordered phase of active chiral objects, namely, an active cholesteric. We analyze the fluctuation properties as well as the nature of characteristic instabilities that these systems can display and make a number of predictions. For example, in the case of an active smectic, we show that active stresses generate an effective active layer tension which, if positive, sup-presses the Landau-Peierls effect, leading to long-range smectic order in dimension d =3 and quasi-long-range in d =2, in sharp contrast with thermal equilibrium systems. Negative active layer tension in bulk systems, however, lead to a spontaneous Helfrich-Hurault undulation instability of the layers, accompanied by spontaneous flow. Also, active smectics, unlike orientationally ordered active systems, normally have finite concentration fluctuations. Similarly, for the case of cholesterics we show that cholesteric elasticity intervenes to suppress some of the instabilities present in active nematics. xi Numerical simulation of active smectics: We present results from a Brownian Dynamics simulation, with no hydrodynamic interaction, of a system of apolar active particles form-ing translational liquid-crystalline order in a suspension. The particles interact through a prolate-ellipsoidal Gay-Berne potential. We model activity minimally through different noise temperatures for movement along and normal to the orientation axis of each particle. We present preliminary results on the disruptive effect of activity on smectic order for the parameter values investigated. Future work will test the predictions of our theory [1] on active smectics. Rheology of active suspensions near field-induced critical points : Shear induces orientation of active stresses in a suspension, through flow alignment. Depending on the sign, activity then either enhances or reduces the viscosity. The change in viscosity, in the zero frequency limit, is proportional to the product of the magnitude of active stress and the system relaxation time. A strong enough orienting field can make the system approach a critical point and the relaxation time diverges. We show that, this results in the divergence of viscosity at zero frequency making the system strongly viscoelastic. Depending on the sign, activity strengthens or reduces the effect of the field. We also investigate the rheological property of an active suspension with mixed polar and nematic oreder. Active quantum Hall systems: We construct the hydrodynamic theory for a 2d charged active nematic with 3d electrostatics. We have investigated the interplay of the Coulomb interaction and activity in these systems. We show that activity competes to enhance the charge density fluctuations normally suppressed by long-ranged Coulomb interactions. The charge structure factor Sq of the corresponding passive charged nematic goes to zero as q, whereas in charged active nematics, activity leads to a nonvanishing charge structure factor at small wavenumber. We also show how the effect of an applied magnetic field can be incorporated into the dynamics of the system and leave scope for further studies on these effects.

In order to associate with the cytoplasmic leaflet of the plasma membrane, many cytosolic signalling proteins possess a distinct lipid binding domain as part of their overall fold. Here, a multiscale simulation approach has been used to investigate three membrane-binding proteins involved in cellular processes such as growth and proliferation. The pleckstrin homology (PH) domain from the general receptor for phosphoinositides 1 (GRP1-PH) binds phosphatidylinositol (3,4,5)-trisphosphate (PI(3,4,5)P₃) with high affinity and specificity. To investigate how this peripheral protein is able to locate its target lipid in the complex membrane environment, Brownian dynamics (BD) simulations were employed to explore association pathways for GRP1-PH binding to PI(3,4,5)P₃ embedded in membranes with different surface charge densities and distributions. The results indicated that non-PI(3,4,5)P₃ lipids can act as decoys to disrupt PI(3,4,5)P₃ binding, but that at approximately physiological anionic lipid concentrations steering towards PI(3,4,5)P₃ is actually enhanced. Atomistic molecular dynamics (MD) simulations revealed substantial membrane penetration of membrane-bound GRP1-PH, evident when non-equilibrium, steered MD simulations were used to forcibly dissociate the protein from the membrane surface. Atomistic and coarse grained (CG) MD simulations of the phosphatase and tensin homologue deleted on chromosome ten (PTEN) tumour suppressor, which also binds PI(3,4,5)P₃, detected numerous non-specific protein-lipid contacts and anionic lipid clustering around PTEN that can be modulated by selective in silico mutagenesis. These results suggested a dual recognition model of membrane binding, with non-specific membrane interactions complementing the protein-ligand interaction. Molecular docking and MD simulations were used to characterise the lipid binding properties of kindlin-1 PH. Simulations demonstrated that a dynamic salt bridge was responsible for controlling the accessibility of the binding site. Electrostatics calculations applied to a variety of PH domains suggested that their molecular dipole moments are typically aligned with their ligand binding sites, which has implications for steering and ligand electrostatic funnelling.

The homo and hetero dimerisation of two spectroscopically different chromophores were studied, namely: 4,4-difluoro-4-bora-3a,4a-diazas-indacene (g-BODIPY) and its 5-styryl-derivative (r-BODIPY). Various spectroscopic properties of the r-BODIPY in different common solvents were determined. It was shown that g- and r-BODIPY in the ground state can form homo- as well as hetero dimers. We demonstrate that the ganglioside GM1 in lipid bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) exhibits a non-uniform lateral distribution, which is an argument in favour of self-aggregation of GM1 being an intrinsic property of the GM1. This was concluded from energy transfer/migration studies of BODIPY-labelled gangliosides. An algorithm is presented that quantitatively accounts for donor–donor energy migration (DDEM) among fluorophore-labelled proteins forming regular non-covalent polymers. The DDEM algorithm is based on Monte Carlo (MC) and Brownian dynamics (BD) simulations and applies to the calculation of fluorescence depolarisation data, such as the fluorescence anisotropy. Thereby local orientations, as well as reorienting motions of the fluorescent groups are considered in the absence and presence of DDEM among them. A new method, in which a genetic algorithm (GA) was combined with BD and MC simulations, was developed to analyse fluorescence depolarisation data collected by the time-correlated single photon counting technique. It was applied to study g-BODIPY-labelled filamentous actin (F-actin). The technique registered the local order and reorienting motions of the fluorophores, which were covalently coupled to cysteine 374 (C374) in actin and interacted by means of electronic energy migration within the polymer. Analyses of F-actin samples composed of different fractions of labelled actin molecules revealed the known helical organiszation of F-actin, and demonstrated the usefulness of this technique for structure determination of complex protein polymers. The distance from the filament axis to the fluorophore was found to be considerably less than expected from the proposed position of C374 at a high filament radius. In addition, polymerisation experiments with BODIPY-actin suggest a 25-fold more efficient signal for filament formation than pyrene-actin.

Dans cette thèse, nous présentons une nouvelle méthode smoothed particle hydrodynamics (SPH) pour la résolution des équations de Navier-Stokes incompressibles, même en présence des forces singulières. Les termes de sources singulières sont traités d'une manière similaire à celle que l'on retrouve dans la méthode Immersed Boundary (IB) de Peskin (2002) ou de la méthode régularisée de Stokeslets (Cortez, 2001). Dans notre schéma numérique, nous mettons en oeuvre une méthode de projection sans pression de second ordre inspirée de Kim et Moin (1985). Ce schéma évite complètement les difficultés qui peuvent être rencontrées avec la prescription des conditions aux frontières de Neumann sur la pression. Nous présentons deux variantes de cette approche: l'une, Lagrangienne, qui est communément utilisée et l'autre, Eulerienne, car nous considérons simplement que les particules SPH sont des points de quadrature où les propriétés du fluide sont calculées, donc, ces points peuvent être laissés fixes dans le temps. Notre méthode SPH est d'abord testée à la résolution du problème de Poiseuille bidimensionnel entre deux plaques infinies et nous effectuons une analyse détaillée de l'erreur des calculs. Pour ce problème, les résultats sont similaires autant lorsque les particules SPH sont libres de se déplacer que lorsqu'elles sont fixes. Nous traitons, par ailleurs, du problème de la dynamique d'une membrane immergée dans un fluide visqueux et incompressible avec notre méthode SPH. La membrane est représentée par une spline cubique le long de laquelle la tension présente dans la membrane est calculée et transmise au fluide environnant. Les équations de Navier-Stokes, avec une force singulière issue de la membrane sont ensuite résolues pour déterminer la vitesse du fluide dans lequel est immergée la membrane. La vitesse du fluide, ainsi obtenue, est interpolée sur l'interface, afin de déterminer son déplacement. Nous discutons des avantages à maintenir les particules SPH fixes au lieu de les laisser libres de se déplacer. Nous appliquons ensuite notre méthode SPH à la simulation des écoulements confinés des solutions de polymères non dilués avec une interaction hydrodynamique et des forces d'exclusion de volume. Le point de départ de l'algorithme est le système couplé des équations de Langevin pour les polymères et le solvant (CLEPS) (voir par exemple Oono et Freed (1981) et Öttinger et Rabin (1989)) décrivant, dans le cas présent, les dynamiques microscopiques d'une solution de polymère en écoulement avec une représentation bille-ressort des macromolécules. Des tests numériques de certains écoulements dans des canaux bidimensionnels révèlent que l'utilisation de la méthode de projection d'ordre deux couplée à des points de quadrature SPH fixes conduit à un ordre de convergence de la vitesse qui est de deux et à une convergence d'ordre sensiblement égale à deux pour la pression, pourvu que la solution soit suffisamment lisse. Dans le cas des calculs à grandes échelles pour les altères et pour les chaînes de bille-ressort, un choix approprié du nombre de particules SPH en fonction du nombre des billes N permet, en l'absence des forces d'exclusion de volume, de montrer que le coût de notre algorithme est d'ordre O(N). Enfin, nous amorçons des calculs tridimensionnels avec notre modèle SPH. Dans cette optique, nous résolvons le problème de l'écoulement de Poiseuille tridimensionnel entre deux plaques parallèles infinies et le problème de l'écoulement de Poiseuille dans une conduite rectangulaire infiniment longue. De plus, nous simulons en dimension trois des écoulements confinés entre deux plaques infinies des solutions de polymères non diluées avec une interaction hydrodynamique et des forces d'exclusion de volume. / In this thesis we develop a new smoothed particle hydrodynamics (SPH) method suitable for solving the incompressible Navier-Stokes equations, even with singular forces. Singular source terms are handled in a manner similar to that in the immersed boundary (IB) method of Peskin (2002) or in the method of regularized Stokeslets (Cortez, 2001). The numerical scheme implements a second-order pressure-free projection method due to Kim and Moin (1985) and completely obviates the difficulties that may be faced in prescribing Neumann pressure boundary conditions. We present two variants of this approach, one Langrangian which is commonly used and one Eulerian, simply because we consider that the SPH particles are quadrature points on which the fluid properties are calculated, therefore, these points can be kept fixed in time. The proposed SPH method is first tested on the planar start-up Poiseuille problem and a detailed error analysis is performed. For this problem, the results are similar whether the SPH particles are free to move or fixed on a regular grid. Our hybrid SPH-IB method is then used to calculate the dynamics of a stretched immersed elastic membrane. The membrane is represented by a cubic spline along which the tension in the membrane is computed and transmitted to the surrounding fluid. The Navier-Stokes equations with singular force due to the membrane are then solved to determine the velocity of the fluid in which the membrane is immersed. The fluid velocity thus obtained is interpolated on the interface, to determine its displacement. We discuss the advantages, in this problem, of fixing the SPH particles, rather than allowing them to move with the fluid. A new coupled Brownian dynamics-SPH method for the computation of confined flows of non-dilute polymer solutions with full hydrodynamic interaction and excluded volume forces is next presented. The starting point for the algorithm is the system of coupled Langevin equations for polymer and solvent (CLEPS) (see Oono and Freed (1981) and Öttinger and Rabin (1989), for example) describing, in the present case, the microscopic dynamics of a flowing polymer solution with a bead-spring representation of the macromolecules. Numerical tests of some two-dimensional channel flows reveal that use of a second-order projection scheme coupled with fixed SPH quadrature points leads to second-order velocity convergence and almost second-order pressure convergence, provided that the solution is sufficiently smooth. In the case of large-scale dumbbell and bead-spring chain calculations, an appropriate scaling of the number of grid points as a function of the number of beads N ensures, in the absence of excluded volume forces, that the cost of our algorithm is O(N) flops. Finally, we begin calculations in three dimensions with our SPH model. To this end, we solve in three dimensions the problem of Poiseuille flow between two infinite and parallel plates and the problem of Poiseuille flow in a rectangular infinitely long duct. In addition, we carry out three dimensional computations of confined flows of non-dilute polymer solutions with full hydrodynamic interaction and excluded volume forces.

Dans cette thèse, nous présentons une nouvelle méthode smoothed particle hydrodynamics (SPH) pour la résolution des équations de Navier-Stokes incompressibles, même en présence des forces singulières. Les termes de sources singulières sont traités d'une manière similaire à celle que l'on retrouve dans la méthode Immersed Boundary (IB) de Peskin (2002) ou de la méthode régularisée de Stokeslets (Cortez, 2001). Dans notre schéma numérique, nous mettons en oeuvre une méthode de projection sans pression de second ordre inspirée de Kim et Moin (1985). Ce schéma évite complètement les difficultés qui peuvent être rencontrées avec la prescription des conditions aux frontières de Neumann sur la pression. Nous présentons deux variantes de cette approche: l'une, Lagrangienne, qui est communément utilisée et l'autre, Eulerienne, car nous considérons simplement que les particules SPH sont des points de quadrature où les propriétés du fluide sont calculées, donc, ces points peuvent être laissés fixes dans le temps. Notre méthode SPH est d'abord testée à la résolution du problème de Poiseuille bidimensionnel entre deux plaques infinies et nous effectuons une analyse détaillée de l'erreur des calculs. Pour ce problème, les résultats sont similaires autant lorsque les particules SPH sont libres de se déplacer que lorsqu'elles sont fixes. Nous traitons, par ailleurs, du problème de la dynamique d'une membrane immergée dans un fluide visqueux et incompressible avec notre méthode SPH. La membrane est représentée par une spline cubique le long de laquelle la tension présente dans la membrane est calculée et transmise au fluide environnant. Les équations de Navier-Stokes, avec une force singulière issue de la membrane sont ensuite résolues pour déterminer la vitesse du fluide dans lequel est immergée la membrane. La vitesse du fluide, ainsi obtenue, est interpolée sur l'interface, afin de déterminer son déplacement. Nous discutons des avantages à maintenir les particules SPH fixes au lieu de les laisser libres de se déplacer. Nous appliquons ensuite notre méthode SPH à la simulation des écoulements confinés des solutions de polymères non dilués avec une interaction hydrodynamique et des forces d'exclusion de volume. Le point de départ de l'algorithme est le système couplé des équations de Langevin pour les polymères et le solvant (CLEPS) (voir par exemple Oono et Freed (1981) et Öttinger et Rabin (1989)) décrivant, dans le cas présent, les dynamiques microscopiques d'une solution de polymère en écoulement avec une représentation bille-ressort des macromolécules. Des tests numériques de certains écoulements dans des canaux bidimensionnels révèlent que l'utilisation de la méthode de projection d'ordre deux couplée à des points de quadrature SPH fixes conduit à un ordre de convergence de la vitesse qui est de deux et à une convergence d'ordre sensiblement égale à deux pour la pression, pourvu que la solution soit suffisamment lisse. Dans le cas des calculs à grandes échelles pour les altères et pour les chaînes de bille-ressort, un choix approprié du nombre de particules SPH en fonction du nombre des billes N permet, en l'absence des forces d'exclusion de volume, de montrer que le coût de notre algorithme est d'ordre O(N). Enfin, nous amorçons des calculs tridimensionnels avec notre modèle SPH. Dans cette optique, nous résolvons le problème de l'écoulement de Poiseuille tridimensionnel entre deux plaques parallèles infinies et le problème de l'écoulement de Poiseuille dans une conduite rectangulaire infiniment longue. De plus, nous simulons en dimension trois des écoulements confinés entre deux plaques infinies des solutions de polymères non diluées avec une interaction hydrodynamique et des forces d'exclusion de volume. / In this thesis we develop a new smoothed particle hydrodynamics (SPH) method suitable for solving the incompressible Navier-Stokes equations, even with singular forces. Singular source terms are handled in a manner similar to that in the immersed boundary (IB) method of Peskin (2002) or in the method of regularized Stokeslets (Cortez, 2001). The numerical scheme implements a second-order pressure-free projection method due to Kim and Moin (1985) and completely obviates the difficulties that may be faced in prescribing Neumann pressure boundary conditions. We present two variants of this approach, one Langrangian which is commonly used and one Eulerian, simply because we consider that the SPH particles are quadrature points on which the fluid properties are calculated, therefore, these points can be kept fixed in time. The proposed SPH method is first tested on the planar start-up Poiseuille problem and a detailed error analysis is performed. For this problem, the results are similar whether the SPH particles are free to move or fixed on a regular grid. Our hybrid SPH-IB method is then used to calculate the dynamics of a stretched immersed elastic membrane. The membrane is represented by a cubic spline along which the tension in the membrane is computed and transmitted to the surrounding fluid. The Navier-Stokes equations with singular force due to the membrane are then solved to determine the velocity of the fluid in which the membrane is immersed. The fluid velocity thus obtained is interpolated on the interface, to determine its displacement. We discuss the advantages, in this problem, of fixing the SPH particles, rather than allowing them to move with the fluid. A new coupled Brownian dynamics-SPH method for the computation of confined flows of non-dilute polymer solutions with full hydrodynamic interaction and excluded volume forces is next presented. The starting point for the algorithm is the system of coupled Langevin equations for polymer and solvent (CLEPS) (see Oono and Freed (1981) and Öttinger and Rabin (1989), for example) describing, in the present case, the microscopic dynamics of a flowing polymer solution with a bead-spring representation of the macromolecules. Numerical tests of some two-dimensional channel flows reveal that use of a second-order projection scheme coupled with fixed SPH quadrature points leads to second-order velocity convergence and almost second-order pressure convergence, provided that the solution is sufficiently smooth. In the case of large-scale dumbbell and bead-spring chain calculations, an appropriate scaling of the number of grid points as a function of the number of beads N ensures, in the absence of excluded volume forces, that the cost of our algorithm is O(N) flops. Finally, we begin calculations in three dimensions with our SPH model. To this end, we solve in three dimensions the problem of Poiseuille flow between two infinite and parallel plates and the problem of Poiseuille flow in a rectangular infinitely long duct. In addition, we carry out three dimensional computations of confined flows of non-dilute polymer solutions with full hydrodynamic interaction and excluded volume forces.

Plusieurs indices suggèrent que le repliement du chromosome et la régulation de l’expression génétique sont étroitement liés. Par exemple, la co-expression d’un grand nombre de gènes est favorisée par leur rapprochement dans l’espace cellulaire. En outre, le repliement du chromosome permet de faire émerger des structures fonctionnelles. Celles-ci peuvent être des amas condensés et fibrillaires, interdisant l’accès à l’ADN, ou au contraire des configurations plus ouvertes de l’ADN avec quelques amas globulaires, comme c’est le cas avec les usines de transcription. Bien que dissemblables au premier abord, de telles structures sont rendues possibles par l’existence de protéines bivalentes, capable d’apparier des régions parfois très éloignées sur la séquence d’ADN. Le système physique ainsi constitué du chromosome et de protéines bivalentes peut être très complexe. C’est pourquoi les mécanismes régissant le repliement du chromosome sont restés majoritairement incompris.Nous avons étudié des modèles d’architecture du chromosome en utilisant le formalisme de la physique statistique. Notre point de départ est la représentation du chromosome sous la forme d’un polymère rigide, pouvant interagir avec une solution de protéines liantes. Les structures résultant de ces interactions ont été caractérisées à l’équilibre thermodynamique. De plus, nous avons utilisé des simulations de dynamique Brownienne en complément des méthodes théoriques, car elles permettent de prendre en considération une plus grande complexité dans les phénomènes biologiques étudiés.Les principaux aboutissements de cette thèse ont été : (i) de fournir un modèle pour l’existence des usines de transcriptions caractérisées in vivo à l’aide de microscopie par fluorescence ; (ii) de proposer une explication physique pour une conjecture portant sur un mécanisme de régulation de la transcription impliquant la formation de boucles d’ADN en tête d’épingle sous l’effet de la protéine H-NS, qui a été émise suite à l’observation de ces boucles au microscope à force atomique ; (iii) de proposer un modèle du chromosome qui reproduise les contacts mesurés à l’aide des techniques Hi-C. Les conséquences de ces mécanismes sur la régulation de la transcription ont été systématiquement discutées. / Increasing evidences suggest that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space. Furthermore, functional structures can result from the particular folding of the chromosome. These can be rather compact bundle-like aggregates that prevent the access to DNA, or in contrast, open coil configurations with several (presumably) globular clusters like transcription factories. Such phenomena have in common to result from the binding of divalent proteins that can bridge regions sometimes far away on the DNA sequence. The physical system consisting of the chromosome interacting with divalent proteins can be very complex. As such, most of the mechanisms responsible for chromosome folding and for the formation of functional structures have remained elusive.Using methods from statistical physics, we investigated models of chromosome architecture. A common denominator of our approach has been to represent the chromosome as a polymer with bending rigidity and consider its interaction with a solution of DNA-binding proteins. Structures entailed by the binding of such proteins were then characterized at the thermodynamical equilibrium. Furthermore, we complemented theoretical results with Brownian dynamics simulations, allowing to reproduce more of the biological complexity.The main contributions of this thesis have been: (i) to provide a model for the existence of transcrip- tion factories characterized in vivo with fluorescence microscopy; (ii) to propose a physical basis for a conjectured regulatory mechanism of the transcription involving the formation of DNA hairpin loops by the H-NS protein as characterized with atomic-force microscopy experiments; (iii) to propose a physical model of the chromosome that reproduces contacts measured in chromosome conformation capture (CCC) experiments. Consequences on the regulation of transcription are discussed in each of these studies.