Les membranes biologiques sont le centre de nombreux phénomènes hors équilibres qui sont essentiels pour les cellules. Pour une description physique plus complète des biomembranes, nous avons étudié, théoriquement et expérimentalement, les effets de deux processus hors équilibres sur les propriétés de membranes artificielles. Premièrement, nous avons développé une théorie, complètement covariante, des membranes qui sont soumises à des échanges de matériels biologiques (i.e. lipides, enzymes et protéines membranaires). Avec cette description, l'étude des fluctuations de telles membranes nous a montré que, sous certaines conditions , celles-ci peuvent devenir instables en développant un long et fin tubule qui présente certaines similitudes morphologiques avec les membranes des organelles. Nous avons appliqué ce modèle avec succès pour décrire le phénomène de fusion observé expérimentalement entre de petites et de grosses vésicules chargées mimant le phénomène d'endocytose. Deuxièmement, nous avons étudié les effets de l'activité des protéines membranaires sur le spectre des fluctuations. Un modèle théorique qui prend en compte l'activité hors équilibre des protéines prévoit une amplification des fluctuations lorsqu'un bruit hors équilibre s'ajoute au bruit thermique. Pour tester expérimentalement ces prévisions, il a fallu reconstituer une pompe ATP-dépendante, l'ATPase-Calcium dans des vésicules géantes unilamellaires. Puis grâce à la technique d'aspiration par micropipette, nous avons mis en évidence à la fois une décroissance du module de courbure liée à la présence des protéines dans la membrane, et une augmentation des fluctuations dans les membranes actives.

Les défauts créés dans les polymères soumis aux rayonnements ionisants, en atmosphère inerte, suivent pratiquement tous la même évolution en fonction de la dose. Lorsque la dose augmente, leur concentration augmente puis se stabilise. L'hypothèse retenue pour expliquer ce comportement est la mise en place de transferts d'énergie vers les défauts macromoléculaires créés aux faibles doses. Ceux-ci agissent comme des pièges à énergie et conduisent donc à la radio-stabilisation du polymère. Au cours de cette thèse, nous nous sommes attachés à la quantification de l'apport de l'insaturation trans-vinylène dans le comportement sous rayonnements ionisants du polyéthylène. Avec le dihydrogène, ce groupement compte parmi les défauts majoritaires créés dans ce polymère. Du fait de la variété des défauts et de la simultanéité de leur création, nous avons choisi une méthodologie nouvelle consistant à insérer par voie de synthèse, de manière spécifique et à différentes concentrations, des insaturations de type trans-vinylène, dans les chaînes de polyéthylène. Les polymères résultants ont été irradiés, en atmosphère inerte, avec des rayonnements de faibles TEL (gamma, bêta) et de forts TEL (ions lourds). Tant les défauts macromoléculaires que l'émission de dihydrogène ont été quantifiés. Il apparaît, sur la base des résultats expérimentaux, que l'apport des groupements trans-vinylènes est prédominant dans la radio-stabilisation du polyéthylène en atmosphère inerte.

Dans cette thèse théorique, les propriétés élastiques et dynamiques d'un solide sont étudiées afin de mieux comprendre les étapes qui mènent d'un cristal parfait à un système vitreux. Les expérimentateurs observent au microscope confocal des couches de verre colloïdal, pour en étudier les propriétés élastiques locales. Il est prouvé analytiquement ici que, déjà pour un cristal, l'observation d'une couche bidimensionnelle conduit à des constantes élastiques et à une relation de dispersion différentes de celles du solide tridimensionnel. Des simulations de dynamique moléculaire d'un cristal de sphères dures confirment ce résultat. De plus, il est montré numériquement que l'ajout de polydispersité dans les rayons des sphères augmente les constantes élastiques du cristal et crée des modes élastiques localisés sur les particules de mobilité extrême. Parallèlement, les propriétés élastiques et dynamiques d'un solide surchauffé sont étudiées. Un modèle minimal, de type mécanisme réactionnel, est proposé pour décrire la dynamique de la fusion homogène. Ce modèle est utilisé pour établir une approche de champ moyen qui prédit les propriétés macroscopiques des états métastable et d'équilibre. Ces prédictions sont comparées avec succès à des résultats de dynamique moléculaire. Le mécanisme réactionnel sert également à concevoir des simulations de Monte-Carlo cinétique, qui rendent compte des fluctuations et reproduisent l'existence d'une goutte critique de liquide, analogue à celles identifiées en dynamique moléculaire, sans recourir à la description des vitesses et positions des particules.

The structure and dynamics of the smectic-A liquid crystal 8CB (4 cyano-4 octylbiphenyl) when sheared and confined to mesoscale gaps (with crossed cylindrical geometry and mica confining surfaces) were studied using a Surface Forces Apparatus (SFA). Triangular shear patterns with frequencies of 0.01, 0.1, 1.0 and 10 Hz, and amplitudes of 62.5 nm, 625 nm and 6.25 m were applied to samples at gap sizes of 0.5 and 5.0 m. The study was performed at room temperature (20.5C) and at two higher temperatures (22C and 27C). In order to minimize the thermal fluctuations within the test chamber and hence to allow for the rapid re-initialization of test runs, the SFA was modified to allow for quick, precise and remote control of the confining surfaces. The procedure maximized the number of tests that could be undertaken with a single pair of surfaces so that a single gap geometry could be maintained for the duration of the test run. In order to run the SFA remotely, scripts written with a commercial software package, LabVIEW, were used to control of the SFA components, its FECO-monitoring camera and all its peripheral electronic equipment as well. Samples were agitated to disrupt any shear-induced liquid crystal domain alignment from previous testing following each shear test, and methodologies were developed to ascertain the extent of confinement quickly and remotely following agitation. Separate methods were developed for gap sizes at each extreme of the mesoscale regime, where the transition from bulklike structure and dynamics to nano-confinement occurs (between 1 and 10 microns for smectic-A 8CB). The results revealed that the greater amplitude-gap aspect ratio and surface-to-domain contact associated with smaller gaps facilitated reorientation of the domains in the shear direction. Evidence was also presented of domains at the higher end or outside of the mesoscale regime that, while straining and accreting, were unable to reorient and thereby led to an overall increase of viscoelastic response. The effective viscosity was found to obey a simple power law with respect to shear rate, , and the flow behaviour indices, n, slightly in excess of unity indicate shear thickening occurs with large enough shear amplitude, and that the viscosity reached a plateau near unity over shear rates of 0.005 to 500 s-1 within the mesoscale regime. Different K and n values were observed depending on the shear amplitude used. Unlike bulk smectic 8CB, whose domains do not align well in the shear direction with large shear-strain amplitude, at mesoscale levels of confinement large amplitude shearing (up to 12.5 shear strain amplitude) was found to be very effective at aligning domains. In general domain reorientation is found to be much more rapid within the mesoscale regime than has been reported in bulk. Aggressive shearing was found to result in a complete drop in viscoelastic response within seconds, while gentler shearing is found to produce a very gradual increase that persists for more than six hours, with individual shear periods exhibiting frequent and significant deviations from the expected smooth shear path that may be a product of discrete domain reorientations. From these findings, certain traits of the smectic 8CB domain structures under mesoscale confinement were deduced, including how they respond to shear depending on the level of confinement, and how their reorientation due to shear varies not only with shear rate but also independently with shear amplitude. An equation describing the viscosity change as a function of both shear rate and shear amplitude is proposed. The shear amplitude dependence introduces the notion of shearing beyond the proposed smectic 8CB “viscoelastic limit”, which was shown to exhibit behaviour in accordance with Large Amplitude Oscillatory Shear (LAOS) techniques developed for Fourier Transform rheology. The findings provided an understanding of the behavioural changes that occur as one reduces the level of confinement of smectic materials from bulk to nanoconfinement.

Active matter refers to systems driven out of thermal equilibrium by the uptake and dissipation of energy directly at the level of the individual constituents, which then undergo systematic movement in a direction decided by their own internal state. This category of nonequilibrium systems was defined as the physical model of motile, metabolizing matter, but the definition has a wider application. In this thesis we work with monolayer of macro-scopic granular particles lying on a vibrated surface and show that it provides a faithful realisation of active matter. The vibration feeds energy into the tilting vertical motion of the particles, which transduces it into a horizontal movement via frictional contact with the base in a direction determined by its orientation in the plane. We show that the dynamics of the particles can be easily controlled by manipulating their geometrical shapes. In the second part of the thesis, not addressing active matter, we do experiments on a soft condensed mat-ter system of viscoelastic surfactant gel formed of an entangled network of wormlike micelles and shows shear-thinning and is therefore non-Newtonian. These systems have relaxation times of the order of seconds and we have studied their non-equilibrium response properties when driven out of equilibrium externally by the gravitational sedimentation of objects and rising air-bubbles. Chapter 1 gives a general introduction to the term active matter and emphasize particularly on how these systems are internally driven and work far away from the equilibrium. We then explain in detail how a system of granular particles lying on a vibrating surface acts as active matter. We later give a brief introduction to the field of soft condensed matter and discuss the viscoelastic properties of surfactant solutions and their phase behaviour. We end this chapter by giving a brief introduction to flocking and non-equilibrium fluctuation relations which act as prerequisite to the following chapters. In Chapter 2 we discuss the experimental techniques used by us. We will first describe the shapes and dimensions of the granular particles used in the experiments. Next we introduce the shaker set-up and describe the experimental cell in which the particles are confined and variation in cell’s boundary. We show the dynamics of the particles in a quasi one-dimensional channel and then in two-dimensions. We give a brief account of image analysis and tracking algorithms employed and other data analyses techniques. In Chapter 3, we study the non-equilibrium fluctuations of a self-propelled polar particle moving through a background of non-motile spherical beads in the context of the Gallavotti-Cohen Fluctuation Relation (GCFR), which generalizes the second law of thermodynamics by quantifying the relative probabilities of the instantaneous events of entropy consumption and production. We find a fluctuation relation for a non-thermodynamic quantity, the velocity component along the long axis of the particle. We calculate the Large Deviation Function (LDF) of the velocity fluctuations and find the first experimental evidence for its theoretically predicted slope singularity at zero. We also propose an independent way to estimate the mean phase-space contraction rate. In Chapter 4 we expand the analysis done in Chapter 3 and study the two-dimensional velocity vector of the particle in the context of Isometric Fluctuation Relation (IFR) which measures the relative probability of current fluctuations in different directions in space of dimension >1. We first show that the dynamics of the particle is not isotropic and present a minimal model for its dynamics as a biased random walker, driven by a noise with anisotropic strength and construct an Anisotropic IFR (AIFR). We then show that the velocity statistics of the polar particle agree with the AIFR. We also confirm that the GCFR can be obtained as a special case of AIFR when the velocity vectors point in opposite directions. We calculate the LDF of particle’s velocity vector and find an extended kink in the velocity plane. In Chapter 5 we study the flocking phenomenon of a collection of polar particles when moving through a background of non-motile beads. We show that in the presence of bead medium, polar particles can flock at much lower concentrations, in contrast to the Vicsek model which predicts flocking at high concentrations. We show that the moving rods lead to a bead flow which in turn helps them to communicate their orientations and velocities at much greater distances. We provide a phase diagram in the parameter space of concentrations of beads and polar particles and show power-law spatial correlations as we approach the phase boundary. We also discuss the numerical simulations and theoretical model presented which support the experiments results. In Chapter 6 we experimentally study the angle dependence of the trapping of collection of active granular rods in a chevron shaped geometry. We show the particles undergo a trapping-detrapping transition at θ = 1150. On the contrary, this angle value is θ = 700 for a single rod. We find a substantial decrease in rotational noise for a collection of particles inside a trap as compared to a single rod which explains the increased value of θ for the trapping-detrapping transition. We also show that polar active particles which tend to change their direction of motion do not show the trapping phenomenon. In Chapter 7 we conduct experiments on falling balls and rising air bubbles through a non-Newtonian solution of surfactant CTAT in water, which forms a viscoelastic wormlike micellar gel. We show that the motion of the ball undergoes a transition from a steady state to oscillatory as the diameter of the ball is increased. The oscillations in velocity of the ball are non-sinusoidal, consisting of high-frequency bursts occurring periodically at intervals long compared to the period within the bursts. We present a theoretical model based on a slow relaxation mechanism owing to structural instabilities in the constituent micelles of the viscoelastic gel. For the case of air bubbles, we show that an air bubble rising in the viscoelastic gel shows a discontinuous jump in the velocity beyond a critical volume followed by a drastic change in its shape from a teardrop to almost spherical. We also observe shape oscillations for bigger bubbles with the tail swapping in and out periodically.

Depuis son invention en 1986, les microscopes à force atomique (AFM) ont été des puissants outils pour la caractérisation des matériaux et des propriétés des matériaux à l'échelle nanométrique. Cette thèse est entièrement dédiée à la mesure de l'interaction entre une sonde AFM et une surface avec une nouvelle technique AFM appelée Force Feedback Microscopy (FFM). La technique a été développée et utilisée pour l'étude d'échantillons biologiques. Le principe central de la technologie FFM est que la force totale moyenne appliquée à la pointe est égal à zéro. En conséquence, en présence d'une interaction pointe-échantillon, une force égale et contraire doit être appliqué à la pointe par une boucle de rétroaction . La force de réaction est ici appliquée à la pointe à travers le déplacement d'un petit élément piézoélectrique positionné à la base du levier AFM. La boucle de rétroaction permet d'éviter instabilités mécaniques tels que le saut au contact, permettant la mesure complète de la courbe d'interaction. En plus, il donne la possibilité de mesurer simultanément les parties élastique et inélastique de l'interaction.La technique a été appliquée à l'étude des interactions à l'interface solide/gaz, avec un intérêt particulier pour l'observation de la formation et de la rupture des ponts capillaires entre pointe et échantillon. Ensuite, on a focalisé notre attention aux interfaces solide/liquide. Dans ce contexte, courbes complètes de type DLVO sont caractérisées d'un point de vue élastique et dissipatif.Nous avons développé des nouveaux modes d'imagerie AFM pour l'étude des biomolécules. Images de phospholipides et de l'ADN à force constante ont été réalisées et certaines propriétés mécaniques comme le module de Young des échantillons ont été évaluées. En plus, nous avons réalisé une étude spectroscopique de l'élasticité et du coefficient d'amortissement de l'interaction entre des cellules vivantes de type PC-12 et une pointe AFM en silicium. L'étude montre que le FFM est un instrument capable de mesurer l'interaction à des fréquences qui ne sont pas nécessairement liées aux résonances caractéristiques du levier. L'étude spectroscopique pourrait avoir dans le futur des applications importantes pour l'étude des bio-molécules et des polymères. / Since its invention in 1986, the atomic force microscopes (AFMs) have been powerful tools for the characterization of materials and material properties at the nanoscale. The present thesis focuses on the measurement of the interaction between an AFM probe and a surface. A new AFM technique called Force Feedback Microscopy (FFM) has been developed and applied to the study of biological specimens. The central principle of the FFM is that the average total force acting on the tip is maintained equal to zero. It means that, in presence of a tip-sample interaction, a counteracting force has to be applied to the tip by a feedback loop. We apply a counteracting force to the tip by displacing the cantilever base with a small piezoelectric element. The feedback loop avoids mechanical instabilities such as jump to contact allowing the complete measurement of the interaction force. Moreover it is possible to simultaneously measure the elastic and inelasticcomponents of the interaction.The technique has been applied to the study of interactions at the solid/gas interface with a particular interest to the observation of the nucleation and rupture of capillary condensates between the tip and the sample. At the solid/liquid interface, complete DLVO force curves are characterized elastically and inelastically.We developed new AFM imaging modes for the study of biomolecules. Images of phospholipids and DNA at constant force have been acquired and the mechanical Young modulus of the samples has been evaluated when possible. In addition, a spectroscopic study of the elasticity and the damping factor of the interaction between living cells and the tip has been carried out. The study reveals that the FFM is an instrument capable of measuring the interaction at frequencies which are not necessarily linked to the cantilever eigenmodes. The spectroscopy study could have in the future important applications on the study of biomolecules and polymers.

This thesis deals with the non-equilibrium phenomena under shear observed mainly in bilayer forming liquid crystalline phases of mixed surfactant systems, anisotropic colloidal dispersions as well as Langmuir monolayers of membrane peptides. To correlate the structural transitions under shear with the mechanical properties or flow behaviour, the rheological measurements are combined with different techniques such as optical imaging (bright field, polarizing or confocal), small angle light scattering as well as small angle x-ray scattering (Rheo-SAXS) measurements. The bilayer forming phases that have been studied consist of mixed surfactant system formed by a mixture of ionic amphiphiles with strong binding organic counter ions. The propensity of the hydrophobic counterion to modify the spontaneous curvature at the micelle-water interface gives rise to a rich equilibrium phase behaviour consisting of different bilayer forming liquid crystalline mesophases in between the hexagonal and lamellar phases. The liquid crystalline mesophases presently examined under shear are the weakly swollen isotropic and lamellar phases as well as the random and rhombohedral mesh phases. The main motivation of the thesis was to examine the stability of these phases under shear since all the existing studies so far on shear induced structural transitions are mainly confined to highly swollen isotropic sponge phase of interconnecting bilayers that can transform to a lamellar phase consisting of a stack of bilayers with 1D quasi long range order or a dilute lamellar phase is shear transformed to a collapsed surfactant rich lamellar phase coexisting with excess solvent at Peclet Number greater than 1. The present study revealed for the first time a shear reversible crystallization above the equilibrium crystallization temperature in the weakly swollen isotropic and lamellar phases formed in the SDS-PTHC-water system where the structural transition is feasible through a shear induced segregation/microphase separation of the hydrophobic counterions to tune the curvature of the bilayer-water interface. These results incited us to examine the role of shear on another class of mesophases that are structurally similar to lamellar phase but with a non-uniform interfacial curvature of the bilayers identified as the intermediate mesh phases. Mesh phases are formed by a 1D stack of perforated bilayers with quasi-long range order where the water filled pores or curvature defects can have a liquid-like ordering in the plane of the bilayers as in a random mesh phase or the pores can have a square or hexagonal ordering locking into a three dimensional lattice with either tetragonal or rhombohedral symmetry to form Tα or R3m ordered mesh phases. Two characteristic features of the mesh phases that is noteworthy are i) the non-uniform mean curvature for the bilayers formed by 3-coordinated hexagonal mesh or the 4-coordinated square mesh; ii) the elasticity of the bilayers forming the hexagonal or square ordered mesh in R3m or Tα phases as opposed to the fluid-like bilayers with zero surface shear modulus in the random mesh or classical lamellar phases (Lα). Hence the structural similarity as well as differences of the mesh phases with the lamellar phase raises some pertinent questions regarding the stability of surfactant mesh phases under shear. Two striking consequences of shear flow on the random and ordered mesh phases of a cationic-anionic mixed surfactant system were revealed: a shear-induced 3D ordering of the curvature defects in LDα phase as well as a hydrodynamic instability wherein a sequence of structural rearrangements leading to buckling instability gives rise to unstable flows in the R3m phase. These studies on shear induced structural transitions on partially ordered mesophases is juxtaposed with the study on another class of systems that were examined under shear comprising dispersion of anisotropic colloidal rods. We demonstrate that these suspensions shear thicken at low concentrations (≥ 25 %) and origin of shear thickening is formation of stress bearing hydrodynamic clusters rather than order-disorder transition. Finally we also examine the rheological properties of a monolayer of membrane peptide Alamethicin where the coexistence of solid-like domains in a backround of liquid expanded phase at high surface concetrations gives rise to a dense anisotropic suspension in 2D. The rheological properties of these jammed fluid/fluid interfaces formed by membrane proteins is well explained by the soft glassy rheology model proposed earlier in the context of 3D soft glasses, comprising emulsions, foams, colloidal glasses and gels. Chapter 1 starts with a general introduction of soft condensed matter systems and then we proceed to describe surfactant systems, their phase behaviour and self assembly. The formation of liquid crystalline phases in pure surfactant systems and in presence of additives such as salt or counterions are discussed. A brief introduction to colloids is explained further. This is followed by the discussion on the inter-macromolecular forces governing soft matter systems such as van der Waals interaction, the screened Coulomb repulsion, hydrogen bond, depletion, peristaltic, hydrophobic and hydration forces and steric repulsion. We further explain the systems studied and their phase behaviour at different concentrations formed by SDS-PTHC-water, CTAB-SHN-water system in detail. In the next section we describe the characterization of different liquid crystalline phases viz. nematic, hexagonal, isotropic, lamellar, intermediate mesh and ribbon phases using cross polarizing optical microscopy, small angle x-ray and rheology. Then, a theoretical background of linear and nonlinear rheology, optical/confocal microscopy and x-ray scattering techniques are given. This is followed by discussion on flow properties of colloidal suspensions in dilute and semi-dilute regime and finally shear thickening phenomena observed in concentrated suspensions. We discuss shear thickening phenomena observed in anisotropic precipitated calcium carbonate (PCC) colloids. We have also discussed shear induced phase and structural transitions observed in different liquid crystalline phases. Chapter 2 discusses the experimental apparatus and techniques used in our studies. We have discussed the different components of the MCR-300 and 101 stress-controlled rheometer (Paar Physica, Germany). The cross polarizing optical microscopy in transmission and reflection mode using a home-made shear cell and in built set-up respectively, and small angle light scattering set-up are discussed. Next, we discuss in-situ small angle x-ray rheology setup, a home made Couette cell installed at RRI Bangalore, Couette installed at SWING beamline Soleil, Paris, France and parallel plate setup at PETRA III, Germany. This is followed by discussion on sample preparation and synthesis technique of silica colloidal rods and modification of surface potential using a thermo-responsive polymer. Further, we explain the algorithm to track rods and analysis of SAXS 2D diffraction pattern. Flow behaviour of different phases formed in SDS-PTHC-water system are described in Chapter 3. This chapter has been divided into four sections. In section I, we describe the phase behaviour and rheology of micellar solution at different surfactant concentrations (ϕ) and molar ratios (α = [PTHC]/[SDS]) of two components. At ϕ = 0.3, a transition from viscous to visco-elastic behaviour is observed with increasing α from 0 to 0.3. Zero shear viscosity shows a non-monotonic behaviour with increasing α and reveals a maxima at α = 0.15. At low α, we observe a Newtonian behaviour which changes to shear thinning behaviour with increasing α and finally again retains the Newtonian behaviour. Dynamic light scattering studies in conjunction with presence of nematic phase made up of disks (confirmed by cross-polarizing optical microscopy) at higher α > 0.325, suggest that the drop in zero shear viscosity is due to decrease in length of the micelles from rods to disks. A similar behaviour is observed with increasing ϕ at constant α = 0.2, 0.25, 0.6. A change in the morphology of micellar aggregates with increase in α is expected in mixed surfactant systems with strongly binding counterions. However the change in morphology of micellar aggregates with surfactant content in surprising which is witnessed for the first time in mixed surfactant systems. In section II of this chapter we discuss the phase behaviour and rehological properties of different liquid crystalline phases formed in SDS-PTHC-water system at ϕ = 0.4, and varying α from 0 to 0.4. Using deutrium nuclear magnetic resonance (NMR) studies we show that the transition from hexagonal phase at α = 0, to lamellar phase at α = 0.4 occurs through a nemtaic phase of rods at α = 0.05 and nemtaic phase of disks at α = 0.2 through an isotropic phase of rods at α = 0.15. NMR studies reveal a decrease in variation of the quadrupole splitting across the transition from NC to ND. The visco-elastic and flow behaviour of the different phases were examined. A decrease in the steady shear viscosity across the different phases with increasing α suggests a decrease in the aspect ratio of the micellar aggregates. From the transient shear stress response of the NC and ND nematic phases in step shear experiments, they were characterized to be tumbling and flow aligning, respectively. Our studies reveal that by tuning the morphology of the surfactant micelles, strongly binding counterions modify the phase behaviour and rheological properties of concentrated surfactant solutions. In section III, we discuss shear induced phase transition in SDS-PTHC-water system using in-situ rheo-optical imaging and in-situ rheo-SAXS. Bilayer forming liquid crystalline phases namely isotropic (Li - optically isotropic) and lamellar (Lα - optically birefringence) are formed at α = 1.5, ϕ = 0.4 and α = 1, ϕ = 0.5. Both phases co-exist with excess solvent and remain fully swollen at temperature T > 50 oC. We have constructed a dynamic phase diagram in the parameter space of shear rate and temperature which demonstrate a novel shear induced phase transition to a crystalline phase (Lc) above a critical shear rate. At constant shear rate, the increase in viscosity is accompanied by presence of birefringent texture of Lα phase after a waiting time (t) which decreases with increasing shear rate. The Lc phase is stable under shear and melts back to equilibrium Li phase once shear is stopped. At higher temperature a transition from Li → Lα is observed. In-situ small angle x-ray scattering reveals an evolution of additional peaks in small as well as wide angle region which does not evolve any further once the viscosity reaches a maxima. The Lc phase obtained under shear at different shear rates can be indexed to a triclinic lattice with the lattice parameters depending on shear rates. We propose that the possible origin of phase transition is re-distribution of counterions under shear which results in counterion-rich and counterion-poor region. This counterion rich region results in crystalline Lc phase. In addition to revealing a unique class of non-equilibrium phase transition, the present study urges a unique approach toward understanding shear-induced phenomena in concentrated meso-phases of mixed amphiphilic systems In section IV we propose a shear induced nucleation and growth of crystalline phase in metastable bilayer forming Li and Lα phases. Nucleation and growth of crystalline phase ac-celerated by shear exhibits a power law dependence on time. The time of nucleation strongly depends on the shear rate with different exponents for different phase compositions. The crystalline phase formed under the influence of shear is stable and irreversible for tempera-ture < 28 oC. The crystal structure obtained under shear can be indexed to a triclinic unit cell with different lattice parameters depending on the shear rate and concentration probed. In Chapter 4, we discuss shear induced transitions observed in mesh phases formed in cationic surfactant system CTAB in the presence of strongly binding counterions SHN formed at different surfactant concentration (ϕ) and molar ratio (α). Random mesh phase (LDα) formed at ϕ = 0.3, 0.4, 0.5 and α = 1 are identified as stack of bilayers having curvature defects in form of water filled pores in the plane of bilayers . These pores do not have any long range correlation either in-plane or across the plane. A 3D ordered mesh phase (R3m) is formed at α = 1 and ϕ = 0.6, where these pores have in-plane and out of plane positional correlation and locked into a 3D lattice with rhombohedral symmetry. These phases are easily identified from small angle x-ray scattering studies wherein LDα a diffuse peak corresponding to in-plane defect spacing (ddef ) is observed along with lamellar d-spacing (d). However several additional peaks along with lamellar peak are observed for R3m phase revealing a long range correlation of pores. By shearing different LDα phases formed at different ϕ′s, we D phases formed probe the effect of shear far and near to the R3m phase boundary. When Lα at ϕ = 0.3 and 0.4 are sheared at constant shear rate, we observe a structural transition to an onion phase which is accompanied by increase in viscosity at the onset of the transition. D When Lα phase formed near R3m phase at ϕ = 0.5 is sheared, we observe a decrease in viscosity which is accompanied by the presence of a sharp peak near the diffuse peak corresponding to ddef along with several other small as well as wide angle peaks. All these D phase. We propose that peaks can be indexed to R3m phase co-existing with equilibrium Lα the locking of the defects into a 3D lattice occurs when the in-plane correlation length (ddef ) is larger than the bilayer periodicity (d). Prior to appearance of sharp peak near ddef , we observe an a-orientation of lamellae i.e. bilayers align along the shear-gradient plane where shear is likely to increase the length of cylindrical arrays or rods. A shear driven increase in the length of the rods implies a larger radius of this in-plane circle forming the pores, leading to a lower curvature and consequently a lower curvature energy. This increase in average size of the pores under shear favored by the lower curvature energy is expected to increase the in-plane as well as the trans-bilayer correlation length of the defects. The Lα → R3m phase transition is also observed in another system cetylpyridinium chloride (CPCl)-SHN-water. Thus this type of transition is general feature of random mesh phases when sheared near R3m phase in the equilibrium phase diagram. A thixotropic behaviour with yield stress (σy = 500 Pa, is observed when equilibrium R3m phase is sheared. When the shear stress crosses a threshold value of 1000 Pa, we observe an avalanche behaviour with drop in viscosity of more than 4 orders of magnitude. This drop is accompanied by appearance of several sharp peaks which can be indexed to two or three R3m phases. The similar transition is observed under shear in R3m phase formed in CPCl-SHN-water system. We propose that shearing a 3D ordered lattice of defects as in the R3m phase leads to additional structural transitions, though the rhombohedral symmentry is retained. In Chapter 5, we discuss shear thickening observed in colloidal rods. Using rheology combined with microscopy, we demonstrate that origin of shear thickening in colloidal rods is the formation of hydroclusters and not order-disorder transition. We observe continuous (CST) as well as discontinuous shear thickening (DST) at volume fractions of colloidal sus-pension at 25 % and > 30 % respectively. In DST, in controlled stress measurements, flow curve exhibits an S-shaped flow curve (stress vs. shear rate) where we observe a negative slope in shear thickening regime. By combining fast confocal microscopy with rheometer (parallel plate geometry), we investigate the possible mechanism for shear thickening in our suspension and rule out order-disorder transition. This indicates that the shear thickening might be a consequence of formation of hydroclusters which is confirmed by modifying sur-face properties of these colloids where a thermo responsive microgel PNIPAM was used as a shell to the silica core. The advantage of using PNIPAM is that the polymer brush remains fully swollen below the lower critical solution temperature (LCST) and shrinks above the LCST (34 oC) acting as hard particles. Thus by controlling the temperature, the interparticle separation can be tuned. We observe a pure shear thinning and shear thickening behaviour below and above LCST respectively. We show that by changing the interparticle separation we can avoid hydrocluster formation arsing due to the hydrodynamic lubrication forces re-sponsible for the shear thickening. The calculation the order parameter and measurements on core-shell particles illustrate that microscopic origin of shear thickening is the formation of hydroclusters and not order-disorder transition. Chapter 6 deals with the 2D interfacial rheology of antibiotic alamethecin film at air-water interface. Fluorescence microscopy of alamethicin monolayers revealed a coexistence of liquid expanded (LE) and solid phases at the surface concentrations studied. Interfa-cial oscillatory shear measurements on alamethicin monolayers indicate that its viscoelastic properties are determined by the area fraction of the solid domains. The role of zwitterionic phospholipids dioleoylphosphatidyl choline (DOPC) and dioleoylphosphatidyl ethanolamine (DOPE) on the peptide aggregation behaviour was investigated. Fluorescence microscopy of alamethicin/phospholipid monolayers revealed an intermediate phase (I) in addition to the solid and LE phase. In mixed monolayers of phospholipid (L)/alamethicin (P), with increase in L/P, the monolayer transforms from a viscoelastic to a viscous fluid with the increase in area fraction of the intermediate phase. Further, a homogeneous mixing of alamethicin/lipid molecules is observed at L/P>4. Our studies also confirm that the visco-elasticity of alame-thicin/phospholipid monolayers is closely related to the alamethicin/phospholipid interac-tions at the air-water interface.

Due to their diversity, soft matter systems provide a convenient platform to study a variety of physical phenomena like phase transitions and collective motion. Encompassing a wide range of equilibrium and non-equilibrium systems, they often provide significant insight into the statistical mechanics of different kinds of many-body systems. Though large scale properties of such systems are of fundamental interest in their own accord, since most experimental realizations of soft matter systems are finite sized, there is a growing need to understand the effects of confinement or boundary conditions on the collective behaviour of such systems. The primary purpose of this thesis is to study the effects of boundary conditions or confinement on both equilibrium and non-equilibrium soft matter systems via theoretical modelling. For equilibrium systems we have studied a system of colloidal particles in harmonic confinement, and for non-equilibrium systems we consider a system of self-propelled rods in both harmonic and hard wall confinement. In Chapter 1 we first lay down some basic concepts of stochastic dynamics and Brownian motion, before discussing some of the recent results on confinement effects on colloidal systems, showing how the properties of a finite sized colloidal system can be very different from those of large, un confined systems. Thereafter turning to non-equilibrium active systems, we discuss various fundamental problems posed by these systems due to their unique ability to generate and dissipate energy on their own. We also point out some instances of observed confinement effects in such systems, such as boundary aggregation and transient hedgehog-like clusters near the boundary. Chapter 2 deals with the effect of harmonic confinement on a finite sized colloidal assembly, where we show that such finite size effects coupled with a confining potential can give rise to special features like initial position dependent expulsion of dopant particles. First we model experimentally studied small two-dimensional colloidal assemblies trapped by a defocussed laser beam by Langevin dynamics simulations in the presence of harmonic confinement and demonstrate how the system shows a crossover from liquid state to crystalline state as a function of the stiffness of the confinement. We also show that in the crystalline state the system can be effectively modelled as a rigid body under small force perturbations. Notably, while studying the dynamics of a defect particle inside these crystallites, we found evidence for the occurrence of self purification by the crystallites. In this process, a dopant is spontaneously expelled out of the crystallite. Surprisingly, this phenomena has a strong dependence on the initial position of the dopant, which turns out to be the consequence of the non monotonic spatial variation of the free energy of the system as a function of the dopant position. This is caused by a difference in the rate of change of internal energy and entropy with the dopant position, with the entropy decreasing faster when the dopant is closer to the centre. This can be attributed to the amount of disruption of crystalline order in the assembly due to the incommensurate dimensions of the defect particle. In order to put these results in a general perspective, we verify in the last part of this chapter that the presence of this free energy barrier is independent of the exact functional forms of the confining potential and the interaction of a defect particle with the host particles, as well as the shape and size of the defect particle. Moving to non-equilibrium systems, we consider, in Chapter 3, the effect of harmonic and hard wall confinement on a two-dimensional system of self-propelled rods (SPRs). Though there have been very limited studies of confinement effects on such systems, existing studies are adequate to show that their behaviour near a boundary wall can be very different, e.g. formation of hedgehog like clusters near a boundary wall. First we show that for harmonic confinement small systems show polar order, which decays with system size, eventually going away for large systems. But the effect of hard wall confinement turns out to be rather different, where the system shows isotropic and clustered states depending on the values of activity and density. We construct a complete activity-density phase diagram showing four distinct phases. For high density and high activity, the rods spontaneously arrange themselves into a stable vortex structure in which the rods exhibit global radial polar order. Surprisingly this order does not decay with system size: the radial orientation of the rods exhibit strong spatial correlation even in large systems, ruling out the possibility that the radial order is a finite-size effect. Using other geometrical shapes of the hard wall boundary, we confirm this phase to be independent of the shape of the boundary. We also demonstrate how small modifications of the boundary conditions at the hard wall can collapse the clustered and vortex phases to a global flocking phase similar to that found in earlier studies of hydrodynamic active particles under confinement. Based on these observations, we conclude that the bulk of the system is strongly affected by the subjected boundary condition, which is rather unusual for large systems. In Chapter 4 this thesis concludes with a summary of the main results and suggestions for future work along similar lines

This thesis describes the development and applications of an extension of DWS which enables the recovery of ‘localized’ mechanical properties, in a specified region of a complex jelly-like object which is inhomogeneous, marked out by the focal volume of an ultrasound transducer, also called the region-of-interest (ROI). Introduction of the sinusoidal forcing creates a sinusoidal phase variation in the detected light in a DWS experiment which modulates the measured intensity autocorrelation, g2 (τ ). Decay in the modulation depth with τ is used to recover the visco-elastic spectrum of the material in the ROI. En route to this, growth of the mean-squared dis- placement (MSD) with time is extracted from the modulation depth decay, which was verified first by the usual DWS experimental data from an homogeneous object with properties matching those in the ROI of the inhomogeneous object and then those obtained by solving the generalized Langevin equation (GLE) modelling the dynamics of a typical scattering centre in the ROI. A region-specific visco-elastic spectral map was obtained by scanning the inhomogeneous object by the ultrasound focal volume. Further, the resonant modes of the vibrating ROI were measured by locating the peaks of the modulation depth variation in g2(τ ) with respect to the ultrasound frequency. These resonant modes were made use of to recover elasticity of the material of the object in the ROI. Using a similar strategy, it was also shown that flow in pipe can be detected and flow rate computed by ‘tagging’ the photons passing through the pipe with a focussed ultrasound beam. It is demonstrated, both through experiments and simulations that the ultrasound-assisted technique devel- oped is better suited to both detect and quantitatively assess flow in a background of Brownian dynamics than the usual DWS. In particular, the MSD of particles in the flow, which shows forth a super-diffusive dynamics with MSD growing following τ α with α < 2, is captured over larger intervals of τ than was possible using existing methods. On the theoretical front, the main contribution is the derivation of the GLE, with multiplicative noise modulating the interaction ‘spring constant’. The noise is derived as an average effect of the micropolar rotations suffered by the ‘bath’ particles on the ‘system’ particle modelled. It has been shown that the ‘local’ dynamics of the system particle is nontrivially influenced by the dynamics, both translation and rotation, of ‘nonlocal’ bath particles.

Microorganisms and drops are ubiquitous in nature: while drops can be found in sneezes, ink-jet printers, oceans etc, microorganisms are present in our stomach, intestine, soil, oceans etc. In most situations they are present in complex conditions: drop spreading on a rigid or soft substrate, drop covered with impurities that act as surfactants, marine microbe approaching a surfactant laden drop in density stratified oceanic waters in the event of an oil spill etc. In this thesis, we extract the physics underlying the influence of two such complicated effects (surfactant redistribution and density-stratification) on the motion of drops and swimming microorganisms when they are in isolation or in the vicinity of each other. This thesis is relevant in understanding the bioremediation of oil spill by marine microbes.<div><br></div><div>We divide this thesis into two themes. In the first theme, we analyze the motion of motile microorganisms near a surfactant-laden interface in homogeneous fluids. We begin by calculating the translational and angular velocities of a swimming microorganism outside a surfactant-laden drop by assuming the surfactant is insoluble, incompressible, and non-diffusing, as such system is relevant in the context of bioremediation of oil spill. We then study the motion of swimming microorganism lying inside a surfactant-laden drop by assuming the surfactant is insoluble, compressible, and has large surface diffusivity. This system is ideal for exploring the nonlinearities associated with the surfactant transport phenomena and is relevant in the context of targeted drug delivery systems wherein one uses synthetic swimmers to transport the drops containing drug. We then analyze the motion of a swimming organism in a liquid film covered with surfactant without making any assumptions about the surfactant and this system is relevant in the case of free-standing films containing swimming organisms as well as in the initial stages of the biofilm formation. In the second theme, we consider a density-stratified background fluid without any surfactants. In this theme, we examine separately a towed drop and a swimming microorganism, and find the drag acting on the drop, drop deformation, and the drift volume induced by the drop as well as the motility of the swimming microorganism.</div>