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Materials which exhibit non-linear mechanical behaviors under large deformations are generally classified as “soft matter”. Elastomers represent an important class of soft materials which have wide commercial applications and isotropic non-linear behavior. In contrast, biological materials have anisotropic responses due to their heterogeneous and composite architectures. The underlying microstructure determines the arterial macroscopic behavior and is represented through constitutive models to describe the stress-strain relationships. Mechanical characterization and development of constitutive models that describe these non-linear and anisotropic properties are essential to our understanding of the structure-property relationships in these materials. In this study, we use two model systems to link the local microstructure to the overall macroscopic behaviors of soft matter. First, we delineate the roles of individual network topological factors in determining the overall macroscopic behavior of isotropic silicone elastomers using specimens fabricated with differential amounts of crosslinking. We performed mechanical experiments, within a theoretically motivated continuum mechanical framework, using a custom made planar biaxial testing instrument. These experiments demonstrate the contributions of physical entanglements and chemical crosslinks to the overall mechanical properties of silicone elastomers. Further, we show that the slip-link form of strain energy function is better suited to describe the material properties in the low to moderate regions of the stress-strain behavior. However, this model does not predict the stiffening response of elastomers at higher deformations, which is better captured using the Arruda-Boyce form of strain energy function. To explore the effects of individual topological factors on the overall network properties, we performed swelling experiments of silicone specimens in xylene and quantified variations in the polymer-solvent interaction parameter, χ, given by the Frenkel-Flory-Rehner (FFR) model. Further, we characterized the viscoelastic properties using dynamic mechanical analysis. Our results show that χ is not a constant, as assumed in the FFR model, but bears a linear relation to the equilibrium polymer volume fraction. To characterize the contribution of trapped entanglements to the overall mechanical behaviors, we use scaling laws in polymer physics and investigate the dependence of equilibrium volume fraction and experimentally obtained elastic moduli. Further, dynamic mechanical analysis demonstrated an increase in complex modulus with increase in the cross linking density. Finally, we examined variations in the uniaxial and the dynamical mechanical properties of silicone elastomers with storage time. Our results show that the time dependent increase in the modulus correlated with the formation of slip-links in the samples aged for a significantly long time in air. Together, these comprehensive studies show the importance of individual network features which affect the overall macroscopic properties of elastomers. Second, we use a multilayered and composite arterial model system to explore the passive material properties of arteries due to anisotropic layouts of extracellular matrix proteins, collagen and elastin. We characterized the mechanical properties of diseased human ascending thoracic aortic dissected (TAD) tissues, obtained from consenting patients undergoing emergency surgical repair to replace the diseased region, using multiple biaxial tests. We fit these results to micro structurally motivated Holzapfel-Gasser-Ogden model which is frequently used in the arterial mechanics literature. Our results show a higher stiffness for TAD tissues as compared to control aorta, without the presence of atherosclerotic plaques or other arterial disease. To study the directional variation in the mechanical properties of TAD tissues, we compared the stiffness in circumferential longitudinal directions at high and low stress region of equibiaxial experimental data. We observed no differences in the stiffness of TAD tissues in the circumferential and longitudinal directions. Further, we do not see any directional variations in the ultimate tensile stress, maximum extensibility, and modulus calculated in the low stretch region of uniaxial stress-strain response in TAD tissues. Histological analysis of TAD tissues showed a decrease in elastin content and an increase in collagen content as compared to control tissues. Higher TAD tissue stiffness also correlated with reduced elastin content in the arterial walls. To investigate the strain rate dependence of measured mechanical properties we use high testing rates of 1mm/sec to show that the TAD tissues have higher stiffness in the circumferential direction as compared to longitudinal direction. Finally, we used peel experiments to quantify the rupture potential of aortic dissected tissues. Our results show that TAD tissues have reduced delamination strength between layers as compared to control aortic tissues. To the best of our knowledge, no previous study has reported the mechanical property of human TAD tissues and these are the only biomechanical results on TAD tissues reported in specimens from South Asian patients. We hope that such studies will be useful for researchers who rely on microstructure based constitutive models to accurately describe the mechanical environment of cells which are important in the remodeling of tissues and in numerical models to assess mechanical criteria which may lead to the growth or dissection of arterial tissues.

The behaviour of colloidal particles in two-dimensional (2D) systems is addressed in real space and time using magnetic fields, optical tweezers and optical video microscopy. First, the fluctuations of a grain boundary in a 2D colloidal crystal are analysed. A real space analogue of the capillary fluctuation method is derived and successfully employed to extract the key parameters that characterise the grain boundary. Good agreement is also found with a fluctuation-dissipation based method recently suggested in simulation. Following on from analysis of the interface fluctuations, the properties of the individual grain boundary particles are analysed to investigate the long standing hypothesis that suggests that grain boundary particle dynamics are similar to those in supercooled liquids. The grain boundary particle dynamics display cage breaking at long times, highly heterogeneous particle dynamics and the formation of cooperatively moving regions along the interface, all typical behaviour of a supercooled liquid. Next, the frustration induced by confining colloidal particles inside a pentagonal environment is investigated. The state of the system is adjusted via two separate control parameters: the inter-particle interaction potential and the number density. A gradual crystalline to confined liquid-like transition is observed as the repulsive inter-particle interaction potential is decreased. In contrast, re-entrant orientational ordering and dynamical effects result as the number density of the confined colloidal particles is increased. Finally, the dynamics of colloidal particles distributed amongst a random array of fixed obstacle particles is probed as a function of both the mobile particle and fixed obstacle particle number densities. Increasing the mobile and the obstacle particle number density drives the system towards a glass transition. The dynamics of the free particles are shown to behave in a similar way to the normal glass transition at low obstacle density and more analogous to a localisation glass transition at high obstacle density.

Dans ce manuscrit, nous mesurons la réponse mécanique à l’échelle nanométrique de divers systèmes issus de la matière molle en utilisant un microscope à force atomique basé sur un diapason à quartz. Utilisé comme un nano-rhéomètre, cet instrument permet une mesure quantitative des propriétés viscoélastiques des matériaux et des processus frictionnels et dissipatifs aux nanoéchelles. Nous montrons d’abord que les liquides ioniques confinés aux nanoéchelles peuvent subir un changement dramatique de leurs propriétés mécaniques, suggérant une solidification capillaire. Cette transition est favorisée par la nature métallique des interfaces confinantes, montrant la présence d’effets électrostatiques subtils dans ces électrolytes denses. Nous étudions ensuite les mécanismes de plasticité à l’échelle atomique en mesurant la réponse viscoélastique de jonctions d’or de quelques atomes de diamètre. Nous mettons en évidence une transition sous cisaillement entre un régime élastique, puis plastique, jusqu’à la liquéfaction complète de la jonction. Nous caractérisons ainsi de manière fine les mécanismes de plasticité dans ces systèmes moléculaires. Finalement, nous montrons les effets profonds que les interactions à l’échelle nanométrique peuvent avoir sur le comportement macroscopique de la matière molle. Nous mesurons le profil frictionnel entre paires de particules de suspensions de PVC et de maïzena. Nos mesures mettent en lumière le rôle dominant des interactions locales entre particules dans la rhéologie non-newtonienne des suspensions. / In this manuscript, we use a tuning fork based atomic force microscope to measure the mechanical response of various soft matter systems at the nanoscale. This instrument is used as a nano-rheometer, allowing quantitative measurements of viscoelastic material properties, and unprecedented characterization of friction and dissipation at the nanoscale. First, we show that ionic liquids can undergo a dramatic change in their mechanical properties when confined at the nanoscale, pointing to a capillary freezing transition. This transition is favored by the metallic nature of the confining substrates, suggesting the occurrence of subtle electrostatic effects in those dense electrolytes. Second, we probe plasticity at the individual atomic level, by measuring the viscoelastic rheological response of gold junctions of few atoms diameter. For increasing shear, we uncover a transition from a purely elastic regime to a plastic flow regime, up to the complete shear-induced melting of the junction. Our measurements give unprecedented insights on the plastic mechanisms at play in those molecular systems. Finally, we show that nanoscale interactions can have profound effects on the macroscopic behavior of soft materials. Focusing on the nonnewtonian flow behavior of concentrated suspensions of particles, we measure the nanoscale frictional force profile between pairs of particles of PVC and cornstarch suspensions. Our measurements highlight the dominant role of local interparticle interactions on the macroscale rheology of suspensions.

Ce manuscrit de thèse porte sur l'étude de deux projets distincts. Le premier fait état de la conception expérimentale ainsi que de l'étude théorique d'un tout nouveau type de moteur basé sur des fibres de polymères : le fiberdrive. Le fonctionnement de ce moteur s'appuie sur un nouveau concept physique décrit ici, les modes de déformation à énergie élastique nulle. Ces modes de déformation sont entraînés par un flux d'énergie qui provoque une déformation élastique au sein du matériau. Le présent manuscrit développe un modèle théorique qui est confronté à la première réalisation expérimentale de ce type de moteur. Le système réalisé est le moteur le plus simple au monde, un stator sans rotor. La deuxième partie du manuscrit introduit le concept de confotronique, l'étude de système composés d'unités commutables individuellement coopérant à grande échelle. Ce concept est mis en oeuvre dans la réalisation d'une fibre confotronique à base d'ADN ainsi que dans la conception d'un moteur moléculaire à base d'ADN. / This thesis manuscript deals with the study of two distinct projects. The first deals with the experimental design as well as the theoretical study of a brand new type of engine based on polymer fibers: the fiberdrive. The operation of this engine is based on a new physical concept described here, deformation modes with zero elastic energy (ZEEMs). These deformation modes are driven by a flow of energy that causes elastic deformation within the material. This manuscript develops a theoretical model that is confronted with the first experimental realization of this type of engine. The realized system is the simplest engine in the world, a stator without rotor.The second part of the manuscript introduces the concept of confotronics, the study of system composed of individually switchable units cooperating on a large scale. This concept is implemented in the realization of a DNA-based confotronic fiber as well as in the design of a DNA-based molecular engine.

Although dynamical systems have a multitude of classical uses in physics and applied mathematics, new research in theoretical computer science shows that dynamical systems can also be used as a highly secure method of encrypting data. Properties of Lorenz and similar systems of equations yield chaotic outputs that are good at masking the underlying data both physically and mathematically. This paper aims to show how Lorenz systems may be used to encrypt text and image data, as well as provide a framework for how physical mechanisms may be built using these properties to transmit encrypted wave signals.

Les composites élastomères sont actuellement utilisés dans de nombreuses applications commerciales et ont montré de grandes promesses pour l'utilisation dans les nouvelles technologies. Cela soulève la pratique, ainsi que théorique nécessaire pour comprendre le lien entre la microstructure sous-jacente de composites en élastomère et de leurs propriétés mécaniques et physiques, et comment celui-ci peut être améliorée avec des changements dans l'ancienne. Dans ce contexte, l'objectif principal de cette thèse est le développement d'une analyse, le cadre homogénéisation non linéaire pour déterminer la réponse globale des composites élastomères soumis à des déformations finies. Les comptes-cadre pour l'évolution de la microstructure sous-jacente, ce qui entraîne des changements dans la géométrie finie induite par la charge appliquée. Ce point est essentiel que l'évolution de la microstructure peut avoir un assouplissement significatif géométrique (ou raidissage) effet sur la réponse globale du matériau, qui, à son tour, peut conduire à l'élaboration éventuelle d'instabilités macroscopiques. Le concept principal derrière la méthode d'homogénéisation non linéaire proposé est la construction de principes variationnels appropriés en utilisant l'idée d'un "portail composite linéaire», qui a finalement permettre la conversion des estimations disponibles homogénéisation linéaire dans les estimations analytiques pour la grande déformation de réponse global de l' non linéaire des composites en élastomère. Cette thèse comprend des applications de la théorie proposée pour les différentes classes des élastomères renforcés et poreux aléatoire et des microstructures périodiques. Une analyse complète du comportement efficace, l'évolution de la microstructure et le développement d'instabilités macroscopiques est prévu pour toutes ces applications.

<p>X-ray and neutron crystallography are the predominant methods for obtaining atomic-scale information on bimolecular macromolecules. Despite the success of these techniques, generating well diffracting crystals critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. </p><p>The fields of structural biology and soft matter have independently sought out fundamental principles to rationalize protein crystallization. Yet the conceptual differences and limited overlap between the two disciplines may have prevented a comprehensive understanding of the phenomenon to emerge. Part of this dissertation focuses on computational studies of rubredoxin and human uniquitin that bridge the two fields.</p><p>Using atomistic simulations, the protein crystal contacts are characterized, and patchy particle models are accordingly parameterized. Comparing the phase diagrams of these schematic models with experimental results enables the critical review of the assumptions behind the two approaches, and reveals insights about protein-protein interactions that can be leveraged to crystallize proteins more generally. In addition, exploration of the model parameter space provides a rationale for several experimental observations, such as the success and occasional failure of George and Wilson's proposal for protein crystallization conditions and the competition between different crystal forms.</p><p>These simple physical models enlighten the connection between protein phase behavior and protein-protein interactions, which are, however, remarkably sensitive to the protein chemical environment. To help determine relationships between the physico-chemical protein properties and crystallization propensity, statistical models are trained on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.</p><p>To conclude, the behavior of water in protein crystals is specifically examined. Water is not only essential for the correct functioning and folding of proteins, but it is also a key player in protein crystal assembly. Although water occupies up to 80% of the volume fraction of a protein crystal, its structure has so far received little attention and it is often overly simplified in the structural refinement process. Merging information derived from molecular dynamics simulations and original structural information provides a way to better understand the behavior of water in crystals and to develop a method that enriches standard structural refinement.</p> / Dissertation

Ce travail de thèse concerne le développement de nouvelles architectures hôte et invité à base de polysaccharide et leur application dans la conception de nanoparticules molles à structure hiérarchique et d’hydrogels supramoléculaires pour l’encapsulation et la libération de médicaments. Dans la première partie du manuscrit, nous décrivons une voie de synthèse de polymères hôtes et invités comprenant des chaînons espaceurs poly(éthylène glycol) hydrophile (PEG) entre le squelette de dextrane et soit le groupement b-cyclodextrine (bCD)(polymère hôte) ou le groupement adamantane (Ada) (polymère invité). La présence des bras espaceurs PEG a conduit à une amélioration substantielle de la disponibilité des groupes Ada du polymère invité par rapport à la situation avec un bras espaceur court et hydrophobe. Nous avons ensuite étudié la formation de nanoassemblages entre les différents types de polymères hôtes et invités. Une fois de plus, les espaceurs PEG ont eu un impact significatif sur la taille et la structure interne des nanoassemblages. La deuxième partie de ce travail décrit la synthèse d’une nouvelle série de dextranes greffés par des chaînons PEG et Ada, préparés par réactions de cycloaddition d'azoture-alcyne catalysées le cuivre (I) (CuAAC). Les degrés substitution (DS) en chaînons PEG greffés (5000 g/mole) sont de l’ordre de 20 mol.% tandis que les DS par les groupements Ada sont variés de 0 à 10 mol.%. L’affinité de ces polymères pour la bCD native, ainsi que leur capacité à former des couches superficielles avec des polymères de b-cyclodextrine (pbCD et pbCDN+), s'avèrent dépendre fortement du DS en groupements Ada, ce qui résulte de la coopérativité des interactions impliquées. Dans la dernière partie, nous avons décrit une stratégie de modification non covalente de microgels sensibles à la température à base de poly (N- isopropylacrylamide) (pNIPAm), pour les recouvrir d’une couronne de pbCDN+. Cette stratégie s'appuie sur l’auto-assemblage électrostatique entre pbCDN+ et les chaînes de poly(acide acrylique) chargés négativement (pAAc) et greffées à la surface des microgels. Dans le cas d’une charge globalement neutre des microgels pNIPAm/bCDN, la stabilisation colloïdale a pu être réalisée à l’aide de dextranes greffés (PEG, Ada) en utilisant une procédure d’assemblage hiérarchique. Enfin, à l'aide de dextrane modifié par des groupements Ada (DT-Ada), les microgels pNIPAm/bCDN ont pu être associés pour produire des hydrogels 3D hiérarchiques (10wt %). Leur température de transition sol-gel est décalée vers le bas pour atteindre la gamme des températures physiologiques (37-41°C) par rapport à celle observée dans un hydrogel hôte-invité uniforme bCDN/DT-Ada (51°C) / This PhD work is based on the development of new architectures of polysaccharide-based host and guest polymers and their application in the design of hierarchically structured soft nanoparticles and supramolecular hydrogels with interesting drug delivery profiles. In the first section of the manuscript we describe a synthetic pathway to host and guest polymers with hydrophilic poly(ethylene glycol) PEG spacer between the dextran backbone and either b-cyclodextrin (bCD) host or adamantane (Ada) guest grafted groups. The presence of the PEG spacer led to a substantial improvement of the availability of Ada groups of the guest polymer as compared to its counterpart, where Ada are linked to the backbone with a short hydrophobic spacer. This was followed by the study of nanoassemblies formation between the different types of host and guest polymers. Once again, PEG spacer had a significant impact on the size and internal structure of the resulting nanoassemblies. The second part of this work describes synthesis of a series of new (PEG, Ada)-grafted dextrans prepared by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The degrees of substitution (DS) by PEG grafts (5000 g/mole) are close to 20 mol% while the DS by Ada-groups are varied from 0 to 10 mol.%. The affinity of these polymers to monomeric bCD, as well as their ability to form superficial layers with b-cyclodextrin polymers (pbCD, pbCDN+), are strongly dependent on the DS by Ada, giving an indication of cooperativity effects between them. In the last part we described a strategy to a non-covalent modification of thermoresponsive poly(N-isopropylacrylamide) (pNIPAm)-based microgels with a pbCDN+ host polymer shell. It uses on electrostatic self-assembly between pbCDN+ and negatively charged poly(acrylic acid) (pAAc) chains grafted to the surface of microgels. The resulting pNIPAm/bCDN microgels with neutral overall charge could be colloidally stabilized with (PEG, Ada)-grafted dextrans via a hierarchical self-assembly procedure. Finally, using Ada-modified dextrans (DT-Ada), pNIPAm/bCDN microgels could be physically cross-linked to yield hierarchical 3D hydrogels (at 10 wt%). Their gel-sol transition temperature is shifted down to the physiological temperature range (37-41°C) as compared to uniform pbCDN/DT-Ada host-guest hydrogels (51°C

<div>Advances in modern research have unveiled numerous fundamental and practical benefits of studying the hydrodynamics of microorganisms. Many microorganisms, especially bacteria, actively search for nutrients via a process called chemotaxis. The physical constraints posed by hydrodynamics in the locomotion of microorganisms can combine with their chemotactic ability to significantly affect functions like colonization of nutrient sources. In this thesis, we investigate the interplay between hydrodynamics and chemotaxis toward dictating bacterial distribution around fluid-fluid interfaces, which often act as a source of nutrition. We approach our problem statements using mathematical models and numerical and/or semi-analytical tools. Our studies are particularly relevant in the context of hydrocarbon degradation after oil-spills.</div><div><br></div><div>We begin by showing that the flow generated by rising oil drops delocalizes dissolved nutrient patches in the ocean, and aids chemotactic bacteria in improving their nutrition (over non-chemotactic bacteria) by 45%. We then move from studying colonization of soluble nutrient patches to colonization around nutrient sources, e.g., oil drops, marine snow. Towards this, we first demonstrate the phenomenon of hydrodynamics-mediated 'trapping' of bacteria around oil drops and show that a surfactant-laden drop can retain an approaching bacterium on its surface for approximately 35% longer times than a clean drop. We also analyze hydrodynamic trapping of bacteria around settling marine snow particles and show how bacteria can collide with and colonize the marine snow, even when the latter moves 10 times faster than the former. In all the cases above, we show how the hydrodynamic interactions are complemented by chemotaxis to enable extremely effective bacterial foraging. We next explore how propulsion mechanisms of microorganisms affect their ability to form biofilms on fluid-fluid interfaces and unveil the hydrodynamic origins behind the tendency of flagellated bacteria to swim parallel to plane surfactant-laden interfaces. Finally, we summarize our results, identify further avenues of research and propose problem statements related to them.</div>