The transport of a biomolecule through a nanopore occurs in many biological functions such as, DNA or RNA transport across nuclear pores and the translocation of proteins across the eukaryotic endoplasmic reticulum. In addition to the biological processes, it has potential applications in technology such as, drug delivery, gene therapy, and single molecule sensing. The DNA translocation through a synthetic nanopore device is considered as the basis for cheap and fast sequencing technology. Motivated by the experimental advances, many theoretical models have been developed. In this thesis, we explore the dynamics of driven translocation of a semiflexible polymer through a nanopore in two dimensions (2D) using Langevin dynamics (LD) simulation. By carrying out extensive simulation as a function of different parameters such as, driving force, length and rigidity of the chain, viscosity of the solvent, and diameter of the nanopore, we provide a detailed description of the translocation process. Our studies are relevant for fundamental understanding of the translocation process which is essential for making accurate nano-pore based devices.

<p>The bending moduli and line tension of bilayer membranes self-assembled from diblock copolymers was calculated using the self-consistent field theory. The limitation of the linear elasticity theory (Helfrich model) was evaluated by calculating fourth- order curvature moduli in high curvature systems. It was found that in highly curved membranes, the fourth-order contributions to the bending energy becomes comparable to the low-order terms. The line tension (γL) of membrane pores was also investigated for mixtures of structurally different diblock copolymers. The line ten- sion was found to depend sensitively on the diblock chain topology. Addition of short hydrophobic copolymers was found to reduce the line tensions to negative values, showing that lipid mixtures may be used as pore stabilizers.</p> / Master of Science (MSc)

The goal of this thesis has been to find a means of i) designing an active square particle, and ii) continuously varying its degree of activity with the objective of understanding the effects of activity on the various phases of granular matter. The motivations, results and limitations of our methods of creating active particles are discussed in this thesis. The applicability of a stochastic model based on the Langevin equation in 2D as well as implications for future experiments are also discussed.

The unique features of flexoelectric and dielectric effects are investigated, and exploited for a variety of functions, in a wide range of helicoidal liquid crystal systems, including non-chiral, cholesteric and blue phases. Electrooptic techniques are developed to measure flexoelectric parameters in non-chiral and cholesteric liquid crystals using twisted nematic and Grandjean geometries respectively. A crystal rotation method, and using a lock-in amplifier, is used to enable the measurement of a very small e/K of 0.011 C/N^-1m^-1. Enhancement in chiral-flexoelectric switching is demonstrated theoretically in liquid crystals with negative dielectric anisotropy and in systems in which the pitch is constrained to be other than the natural pitch. A methodological framework for inducing stable Uniform Lying Helix alignment is developed based on weak homeotropic alignment conditions and a method to bias the helicoidal axis orientation; a series of approaches within this framework are demonstrated, including nano-grooved interfaces, periodic boundaries conditions, in-plane fields, and mould-templated micro-channels. The latter approach is potentially commercially viable for sub-millisecond electrooptic technology. The contribution to a cholesteric material's effective dielectric permittivity of flexoelectric polarization is formulated, and an ability to switch a cholesteric between Grandjean and lying-helix configurations based on the dispersion in the flexoelectric polarization and resultant relaxation in dielectric properties is demonstrated. The flexoelectric contribution to dielectric permittivity is exploited to enable switching in bistable reflective displays and alignment of the Uniform Lying Helix. The existence of a flexoelectric contribution to Kerr switching in blue phases is demonstrated, and a semi-empirical model for the effect is developed. The effect is the first known example of a non-polar flexoelectrooptic effect. Independent flexoelectric and dielectric contributions to Kerr switching in blue phases are measured experimentally by measuring the induced birefringence as a function of driving frequency in flexoelectric- and dielectric-dominated wide-temperature-range blue phase materials.

Swarms of animals exhibit aggregations whose behavior is a challenge for mathematicians to understand. We analyze this behavior numerically and analytically by using the pairwise interaction model known as the Morse potential. Our goal is to prove the global stability of the candidate local minimizer in 1D found in A Primer of Swarm Equilibria. Using the calculus of variations and eigenvalues analysis, we conclude that the candidate local minimizer is a global minimum with respect to all solution smaller than its support. In addition, we manage to extend the global stability condition to any solutions whose support has a single component. We are still examining the local minimizers with multiple components to determine whether the candidate solution is the minimum-energy configuration.

Les métallacarboranes sont des clusters anioniques constitués d'atomes de bore, de carbone et d'hydrogène avec un cation métallique pris en « sandwich » au cœur de ce cluster (Co3+ en général) et hautement stable thermiquement que chimiquement. Ces entités sont représentées trivialement par la lettre grecque « thêta » où leurs pôles sont considérés comme hydrophobes et possèdent une charge négative délocalisée qui peut être contre balancée par un proton acide. Cette forte stabilité ainsi que ces diverses propriétés leur procurent un intérêt particulier dans des applications telles que la co-extraction du Cs et Sr dans les effluents nucléaires ou bien en médecine pour leur aptitude à inhiber la protéase du VIH de par ses liaisons hydrogènes. La chimie du bore étant relativement riche, une synthèse de quelques dérivés a été réalisée en laboratoire. Il est ainsi possible de substituer spécifiquement des atomes d'hydrogène par des atomes d'iode ou de chlore ou bien de changer le métal central par un cation Fe3+ formant respectivement les anions diiodo-COSAN (I2COSAN), dichloro-COSAN (Cl2COSAN) et ferrabisdicarbollide (FESAN). Ces métallacarboranes sont aussi considérés comme une nouvelle classe de tensioactif pour lesquels une première étude de leur auto-assemblage a été réalisée. Les résultats obtenus sur l'un d'entre eux, le cobaltabisdicarbollide ou COSAN, ont montré un effet sur la tension de surface ainsi qu'une structuration spontanée de ces clusters en forme de vésicule (à partir de 0,5 mmol/L) et par interaction Coulombienne, tendent à former des micelles à plus forte concentration (après 15 mmolL). Mais ces derniers offrent davantage de surprise de par la formation de phases lyotropes en solution aqueuse. En effet, ces phases, clairement identifiées par des techniques de diffusion au rayon-X et microscopie, montrent une dépendance en température mais aussi en concentration dont un diagramme de phase a pu être établi pour le I2COSAN en particulier. Cette thèse fait ainsi l'objet de la compréhension des phénomènes contrôlant cette agrégation de ces curieux composés. / Metallacarboranes are anionic clusters composed of boron, carbon and hydrogen with a metallic cation sandwiched at the heart of this cluster (Co3+ in general) and highly stable in thermic and chemical point of view. These entities are trivially represented by the Greek letter "theta" where the poles are considered hydrophobic and have a negative charge delocalized and counter-balanced by an acidic proton. This high stability as well as the various properties gives a particular interest in applications such as the co-extraction of Cs and Sr in nuclear waste or in medicine for their ability to inhibit HIV protease by its hydrogen bonds. The chemistry of boron is relatively rich; a synthesis of some derivatives was performed in laboratory. It is possible to substitute specifically hydrogen by iodine or chlorine atoms or change the metallic heart by other atom as Fe3+, respectively forming diiodo- COSAN (I2COSAN), dichloro-COSAN (Cl2COSAN) and ferrabisdicarbollide (FESAN) anions. Metallacarboranes are also considered as a new class of surfactant where a first study of their self-assembly has been performed. The results of one of them, cobaltabisdicarbollide or COSAN, have shown an effect at the surface tension and theses clusters formed spontaneously vesicles in dilute regime (from 0.5 mmol/L) and by Coulomb interactions, they form micelles at higher concentration (after 15 mmol/L). But they offer more surprise by the formation of lyotropic phases in aqueous solution. Indeed, these phases, clearly identified by X-ray scattering techniques and microscopy, showed temperature and concentration dependence where a phase diagram was established for the I2COSAN in particular. Therefore, the thesis is focused on the understanding of the phenomena controlling the aggregation of these curious compounds.

Neben ihrer Bedeutung in industriellen Anwendungen dienen Kolloide als Modellsysteme in Experimenten und in der Theorie, um die Struktur und Dynamik von kondensierter Materie zu untersuchen. Kürzlich wurde experimentell gezeigt, dass eine kleine Anisotropie ausreicht, um die viskoelastische Antwort im Vergleich zu harten Kugeln drastisch zu ändern. Die mikroskopischen Ursachen hierfür sind bisher nicht verstanden. In dieser Arbeit werden daher Nichtgleichgewichts-Brownsche-Dynamik-Simulationen (NEBD) von harten kolloidalen Dumbbells in oszillatorischen Scherfeldern entwickelt und eingesetzt, um diese Resultate mit Verbindung zu Rheologie- und Neutronenstreuexperimenten zu erklären. Weiterhin wird die Bedeutung der Anisotropie für Struktur und Dynamik von solchen Suspensionen im Gleichgewicht mit Hilfe von "Linear-Response"-Theorie und Brownsche-Dynamik-Simulationen analysiert. Im linearen Limit zeigt die Scherviskosität bei hohen Packungsdichten einen dramatischen Anstieg jenseits eines kritischen Anisotropieparameters. Dies weist darauf hin, dass schon bei den kleinen Anisotropien kollektive Rotations-Translations-Kopplungen für langsame Zeitskalen verantwortlich sind. Weiterhin wird ein Nichtgleichgewichtsübergang mittels NEBD-Simulationen von Suspensionen harter Dumbbells im PC unter oszillatorischer Scherung ersichtlich. Es wird gezeigt, dass der kontinuierliche Übergang nur für sehr kleine Aspektverhältnisse erhalten bleibt. Oberhalb eines bestimmten Aspektverhältnisses wird der Übergang durch einen ungeordneten Zustand vermittelt. Außerdem wird ein Sliding-Layer Zustand mit kollektiver Ordnung der Teilchenausrichtung bei hohen Scheramplituden beobachtet. Somit zeigt diese Arbeit, dass die NEBD-Simulationen Phänomene in Rheologie- und Streuexperimenten erklären. Angesichts dieser Experimente wird gezeigt, dass der Orientierungsfreiheitsgrad einen starken Einfluss auf den strukturellen Übergang bei steigenden Amplituden hat. / Besides being important for industrial applications, colloidal suspensions have long served as model systems for investigating the structure and dynamics of condensed matter. Recently, it has been demonstrated experimentally that apparently a small particle anisotropy is sufficient to dramatically change the viscoelastic response under external shearing fields, of which the microscopic mechanisms are not yet sufficiently understood. In the present work, NEBD simulations of colloidal hard dumbbells in oscillatory shear fields are developed and employed to elucidate the novel findings in close connection with comprehensive rheology and SANS experiments. Furthermore, by utilising BD simulations and linear response theory, the impact of anisotropy on structure and dynamics of such suspensions in equilibrium is analysed. In the linear response limit, the shear viscosity exhibits a dramatic increase at high packing fractions beyond a critical anisotropy of the particles. This indicates that newly occurring, collective rotational-translational couplings must be made responsible for slow time scales appearing in the PC. Moreover, a non-equilibrium transition emerging at moderate aspect ratios is revealed by NEBD of plastic crystalline suspensions under oscillatory shear. This transition behaviour is systematically studied. It is demonstrated that the continuous nature of the transition is retained for very low aspect ratios only. Above a certain aspect ratio, the transition is mediated by an intermediate disordered state. Furthermore, a partially oriented sliding layer state featuring a finite collective order in the particles'' orientations is observed at high strains. Hence, this thesis demonstrates that the NEBD simulations explain novel phenomena in rheology and scattering experiments. In the light of these experiments, it is shown that the orientational degree of freedom has a vigorous impact on the structural transition under increasing oscillatory shear.

No description available.

Cette thèse couvre l'auto-assemblage de particules dipolaires (magnétiques/électriques). Ces systèmes sont abondants en physique de la matière condensée (molécules et nanoparticules magnétiques, particules colloïdales magnétiques, bactérie magnétotactique, etc.). Sur un plan fondamental, ils représentent un défi important en raison de l'anisotropie et de la longue portée de l'interaction de paire. Le principal objectif de ce travail de recherche est de prédire les microstructures de ces systèmes en tenant compte de façon adéquate de l'interaction complexe dipôle-dipôle ainsi que des effets stériques et ceux dus à un éventuel confinement. Comprendre et revisiter les interactions de filaments dipolaires tels que des aiguilles et des chaînes faites de billes dipolaires est une première étape importante de cette thèse. En effet, les chaînes sont les constituants élémentaires de nombreux systèmes dipolaires, notamment sous l'effet d'un champ magnétique extérieur appliqué. Ensuite, l'agrégation colonnaire des chaînes dipolaires est examinée, ce qui conduit aussi naturellement à l'étude des cristaux dipolaires massifs où une nouvelle phase est découverte. Le cas plus générique des chaînes hélicoïdales est discuté en considérant les situations limites que sont les chaînes linéaires droites et en zigzag. L'association des chaînes dipolaires, dans le cas bidimensionnel, forme des rubans, puis une monocouche avec un réseau hexagonal. La réponse non triviale d'un tel réseau à un champ magnétique perpendiculaire imposé est aussi étudiée. Il est démontré qu'un réseau rhombique peut être induit de cette façon. Finalement, la sédimentation de particules paramagnétiques dans une monocouche inclinée en présence d'un champ magnétique est explorée via une étude mêlant expériences, théorie et simulations. L'ordre induit par gravité s'avère être une voie prometteuse pour l'élaboration contrôlée de réseaux bidimensionnels / This thesis covers the self-assembly of dipolar (magnetic/dielectric) particles. These systems are abundant in condensed matter physics (magnetic molecules and nanoparticles, magnetic colloidal particles, magnetotactic bacteria, etc). They also represent a fundamental challenge owing to the both long range and anisotropic nature of the pair interaction. The main objective of this research work is to predict the microstructures of these systems by properly handling the intricate dipole-dipole interaction combined with steric and possibly confinement effects. Understanding and revisiting the interaction of dipolar filaments such as needles or chains made up of dipolar beads is a first important achievement in this thesis. Indeed, the chains are the fundamental building blocks of many dipolar systems especially under applied external magnetic field. Then, the columnar aggregation of dipolar chains is investigated which naturally leads to the study of the bulk dipolar crystals. A new phase is discovered there. The more generic case of helical chains is discussed by considering limiting situations such as straight linear chains and zigzag chains. The association of dipolar chains in two-dimensions forms ribbons then a monolayer with triangular lattice symmetry. The interesting response of such a layer to an imposed perpendicular magnetic is addressed as well. It is demonstrated that rhombicity can be induced that way. Finally, sedimenting paramagnetic particles in a tilted monolayer in presence of a magnetic field are investigated by experiments, theory and simulations. The gravity-mediated ordering is found to be a promising route to elaborate tailored two-dimensional patterns

En médecine, les nanotechnologies permettent le développement de nouvelles techniques de soin comme l’hyperthermie local ou la délivrance ciblée de médicaments. Ces applications impliquent de nouveaux défis scientifiques concernant la conception de nanosystems et les propriétés de leur environnement biologique. Dans cette thèse, nous avons analysé plusieurs aspects de la relaxation thermique de tels systèmes. Nous avons mise en œuvre la fois des simulations de Dynamique Moléculaire et des mesures expérimentales de microscopie d’imagerie en temps de vie de fluorescence. Nous présentons une étude numérique du transfert thermique depuis une nanoparticule en solution aqueuse et montrons qu’attacher un polymère à sa surface permet de réduire la résistance thermique entre la particule et son environnement. Nous avons modélisé des bicouches lipidiques pour calculer leurs propriétés diélectriques et leur viscosité a été étudiée par microscopie de fluorescence. Ces expériences sont réalisées sur des membranes suspendues et des vésicules unilamellaires géantes et démontrent que la viscosité des bicouches lipidiques diminue avec la température et l’application d’une tension transmembranaire induisant un changement de structure. / In medicine, nanotechnologies give the opportunity to create new care practices such as local hyperthermia and targeted drug delivery. These applications imply new scientific challenges concerning the design of nanodevices and the properties of their biological environment. In this thesis, we have analysed several aspects of heat relaxation of such systems. We have used both Molecular Dynamics numerical simulations and Fluorescence-lifetime imaging microscopy experiments. We present a study of heat transfer from a solvated nanoparticle and show that attaching a polymer on its surface reduces the thermal resistance between the particle and its aqueous environment. We have modelled lipid bilayers to compute their dielectric properties and their viscosity have been investigated by fluorescence imaging. The experiments conducted on both suspended lipid membrane and giant unilamellar vesicles show that the viscosity decreases when the temperature increases and when a transmembrane voltage is applied to inducing a structural change.