Tesis sobre el tema "Soft matters"

Informal intergovernmental organizations have become a prominent feature of the global landscape. Yet it remains unclear why states create informal organizations in some instances and formal organizations in others. Thus far, scholars have argued that states choose to create informal organizations when they offer an “efficient” solution to certain kinds of cross-border cooperation problems. However, such functionalist arguments are underspecified and rest on weak evidence at present. Existing research suggests that functionalist theories can indeed explain certain cases, but numerous anomalies arise when we look at others. This dissertation argues that this is because functionalists do not take into account how domestic politics, distributional conflict and state power can decisively influence the kinds of organizations that are likely to appear. It offers an alternative account of the emergence of informal organizations that incorporates these variables. The theory advanced emphasizes how domestic politics and institutions structure state preferences over organizational form, and how the distribution of preferences and state power then shape the organizations that subsequently emerge. Specifically, it argues that informal organizations arise when either a) policymakers in powerful states face significant domestic constraints, or b) autonomous bureaucrats are given responsibility for “leading” cooperation on the behalf of powerful states. In order to test this theory, a variety of methods are used. First, the theory is evaluated quantitatively through a statistical analysis of an original dataset of formal and informal organizations. Second, the theory is evaluated qualitatively through process tracing of the “emergence” of the International Monetary Fund, the General Agreement on Tariffs and Trade and the International Competition Network. Overall, the analysis provides powerful support for the central thesis of this dissertation: while certain aspects of the cooperation problems states face do play a role, domestic politics and state power are the most important determinants of organizational form. The dissertation’s findings are argued to have implications for theories of rational design in the field of International Relations, for our understanding of the overall rise of informal organizations in the global system, as well as for policy debates about the desirability of this new breed of international institution.
Arts, Faculty of
Political Science, Department of
Graduate

In the last few decades, an increasing number of physicists specialized in soft matter, including polymers, have turned their attention to biologically relevant materials. The properties of various molecules and fibres, such as DNA, RNA, proteins, and filaments of all sorts, are studied to better understand their behaviours and functions. Self-assembled biological membranes, or lipid bilayers, are also the focus of much attention as many life processes depend on these. Small lipid bilayers vesicles dubbed liposomes are also frequently used in the pharmaceutical and cosmetic industries. In this thesis, work is presented on both the elastic properties of polymers and the response of lipid bilayer vesicles to extrusion in narrow-channels. These two areas of research may seem disconnected but they both concern deformed soft materials. The thesis contains four articles: the first presenting a fundamental study of the entropic elasticity of circular chains; the second, a simple universal description of the effect of sequence on the elasticity of linear polymers such as DNA; the third, a model of the symmetric thermophoretic stretch of a nano-confined polymer; the fourth, a model that predicts the final sizes of vesicles obtained by pressure extrusion. These articles are preceded by an extensive introduction that covers all of the essential concepts and theories necessary to understand the work that has been done.

The term “soft matter” applies to a variety of physical systems, such as liquids, colloids, polymers, foams, gels, and granular materials. The most fascinating aspect of soft matter lies in the fact that they are not atomic or molecular in nature. They are instead macromolecular aggregates, whose spatial extent lies in the domain 1 nm to 1 ¹m. Some of the most important examples of soft matter are polymers, which exhibit intriguing and useful physical properties. In this work, the adsorption and self assembly of linear and star polymers on smooth surfaces are studied using coarse-grained, bead-springmolecular models and Langevin dynamics computer simulations. The aim is to gain insight on atomic-forcemicroscopy images of polymer films on mica surfaces, adsorbed from dilute solution following a good solvent-to-bad solvent quenching procedure. In the case of linear polymers, under certain experimental conditions, a bimodal cluster distribution is observed. It is demonstrated that this type of distribution can be reproduced in the simulations, and rationalized on the basis of the polymer structures prior to the quench. In addition to providing insight on experimental observations, the simulation results support a number of predicted scaling laws such as the decay of the monomer density as a function of distance from the surface, and the scaling of the filmheight with the strength of the polymer-surface interactions. Star polymers represent a special class of polymers, in which one end of each linear chain is tethered to a small central core to forma single particle. The discovery of these molecules led to the synthesis of a wide range of new materials. Their structures are effectively considered as intermediate between those of colloids and linear polymers. We explore the behaviour of the star polymers (which are like “soft colloids”) in the proximity of a surface, using Langevin dynamics simulations. A number of different measurements such as the height, radius of gyration, and asphericity of adsorbed stars with different number of arms, are shown to provide valuable insights on experimental findings. The simplest soft matter systems consist of spherical, rigid colloidal particles. Examples of such particles are chemically synthesized polystyrene or silica particles. We investigated the neighbour distribution in a two-dimensional polydisperse harddisk fluid, corresponding physically to a colloidal monolayer. The disk diameter distribution was defined by a power-law with the aim of realizing a scale-free nearneighbour network. Scale-free (power-law) behaviour is found in many important networks, for example, in transportation systems, biochemical reactions, scientific and movie-actor collaborations, and sexual contacts. We have provided the first example of a scale-free network in amodel condensed-matter system. Finally, we use genetic algorithms, a method for efficiently searching for minima on energy landscapes, to investigate the ordered equilibrium structures formed by binary mixtures of anisotropic dipolar particles confined on a plane, under the presence of an external magnetic field. The anisotropy of the interparticle forces is controlled by tilting the external magnetic field with respect to the plane. Initially, as the field is tilted the structures are only slightly perturbed, but once the anisotropy exceeds a critical value, completely new structures emerge.

La fracture des matériaux, omniprésente aussi bien en science des matériaux qu’en géologie, implique souvent des événements soudains et imprévisibles, sans précurseurs détectables macroscopiquement. Une compréhension approfondie des mécanismes microscopiques conduisant in fine à la rupture est requise, mais les expériences restent rares. La détection de la dynamique microscopique dans les échantillons cisaillés est expérimentalement très difficile, car elle nécessite de combiner sensibilité mécanique, qualité optique et exigences strictes sur l’encombrement. Dans ce travail, nous présentons l'une des premières tentatives réussies de mesure des précurseurs microscopiques de fracture dans des matériaux mous modèles, grâce à des mesures de la plasticité microscopique à l'aide d'un nouvel instrument, couplant une cellule de cisaillement à contrainte contrôlée à un appareil de diffusion de lumière statique et dynamique (DLS) à petits angles. Dans un premier temps, nous montrons théoriquement, numériquement et expérimentalement comment la DLS, une technique très puissante difficile à utiliser pour un échantillon sous cisaillement, peut être utilisée comme outil de mesure de la dynamique microscopique dans les systèmes mous sous cisaillement. Pour un solide parfait et un fluide visqueux simple, le champ de déplacement résultant d'une déformation de cisaillement est purement affine. Nous montrons comment les déplacements affines et non affines, qui sont présents dans de nombreuses situations d’intérêt (matériaux élastiquement hétérogènes ou en raison de réarrangements plastiques) peuvent être évalués séparément par DLS et discutons de l'effet des non-idéalités dans des expériences typiques.Ce travail est centré sur un gel colloïdal fractal modèle, dont nous caractérisons la rhéologie linéaire en loi de puissance. Nous montrons que celle-ci est décrite par un modèle phénoménologique Fractional Maxwell (FMM), et discutons la relation possible entre FMM et la structure microscopique du gel.Sous une contrainte de cisaillement constante (expérience de fluage), le gel colloïdal présente une déformation rapide élastique suivie d'un fluage lent en loi de puissance, puis, après plusieurs heures par une accélération du taux de cisaillement, entraînant la rupture retardée du gel. Nos expériences montrent que le premier régime en loi de puissance, bien décrit par la viscoélasticité linéaire, correspond à l'échelle microscopique à une dynamique partiellement nonaffine, mais entièrement réversible. Lorsque la viscoélasticité dévie de la linéarité, une accélération nette, localisée dans le temps de la dynamique non-affine, est observée. Ces réarrangements rapides précèdent la fracture macroscopique du gel de plusieurs heures: ce sont des précurseurs dynamiques de la fracture qui permettent de prédire l’évolution du gel bien avant toute mesure rhéologique.Pour obtenir une image plus complète de la fracture, nous étudions l'apparition de l'irréversibilité lors d’une perturbation cyclique répétée plusieurs fois (expérience de fatigue). En suivant l'évolution stroboscopique du système en fonction de la déformation cumulée, on constate que, au-delà du régime linéaire, le taux de relaxation augmente brusquement, signature de plasticité. Si la contrainte appliquée est suffisamment grande, le gel à long terme montre une rupture retardée, en analogie avec celle observée en fluage. Les différences et similitudes entre les deux mécanismes de fracture sont discutées.Enfin, la généralité des résultats obtenus sur les gels colloïdaux est vérifiée en étudiant comme second système modèle un verre colloïdal, dont la mise en écoulement sous contrainte oscillante est un processus progressif, pour lequel deux modes de relaxation contribuent à la dynamique observée. Les analogies qualitatives trouvées avec des systèmes similaires (par ex. des émulsions concentrées) suggèrent qu'une image unifiée pourrait être obtenue, motivant des recherches futures
Material failure is ubiquitous, with implications from geology to everyday life and material science. It often involves sudden, unpredictable events, with little or no macroscopically detectable precursors. A deeper understanding of the microscopic mechanisms eventually leading to failure is clearly required, but experiments remain scarce. The detection of microscopic dynamics in samples under shear is experimentally very challenging, because it requires to combine the highest mechanical sensitivity to strict requirements on the geometry of the whole setup and on the quality of the optical interfaces. In this work we present one of the first successful attempts to measure microscopic failure precursors in model soft solids. Here, microscopic plasticity under shear is observed using a novel setup, coupling a custom-made stress controlled shear cell to small angle static and dynamic light scattering (DLS).DLS is a very powerful technique, but its application to materials under shear is not trivial. In a first step we show a theoretical, numerical and experimental investigation of how DLS may be used as a tool to measure the microscopic dynamics in soft systems under shear. In ideal solids and simple viscous fluids, the displacement field resulting from an applied shear deformation is purely affine. Additional non-affine displacements arise in many situations of great interest, for example in elastically heterogeneous materials or due to plastic rearrangements. We show how affine and non-affine displacements can be separately resolved by DLS, and discuss the effect of several non-idealities in typical experiments.As a model system, this work mainly focuses on a fractal colloidal gel. We thoroughly characterize the linear power-law rheology of the gel, we show that it is very accurately described by the phenomenological Fractional Maxwell (FM) model, and we discuss the possible relationship between the FM model and the microscopic structure of the gel.Under a constant shear stress (creep experiment), the colloidal gel exhibits a fast, elastic deformation followed by a slow sublinear power-law creep, which is eventually interrupted after several hours by an upturn in the shear rate, leading to the delayed failure of the material. Our experiments show that the first power-law regime, nicely described by linear viscoelasticity, corresponds at the microscopic scale to partially nonaffine, yet fully reversible dynamics. Upon deviation from the linear viscoelasticity, a sharp acceleration, localized in time of the nonaffine dynamics is observed. These faster rearrangements precede the macroscopic failure of the gel by thousands of seconds: they thus are dynamic precursors of failure that allow one to predict the fate of the gel well before any rheological measurement.To obtain a more comprehensive picture of material failure, we next address the onset of irreversibility under a cyclic perturbation repeated many times (fatigue experiment). By following the stroboscopic evolution of the system as a function of the cumulated deformation, we observe that as soon as the shear amplitude is increased beyond the linear regime the relaxation rate increases abruptly, indicating that irreversible plasticity is at play. If a large enough stress amplitude is applied, the system on the long run displays delayed fatigue failure, with reminiscences of the one observed in creep. Differences and similarities between the two failure mechanisms are discussed.Finally, the generality of the results obtained on colloidal gels is checked by investigating as second model system a soft colloidal glass. In this case, our experiments indicate that oscillatory yielding is a gradual process, where two relaxation modes contribute to the observed dynamics. Qualitative analogies found with similar systems (e.g. concentrated emulsions) suggest that a general picture might be obtained with our study, which motivates ongoing and future investigations

In the search to understand the interaction between cells and their underlying substrates, life sciences are beginning to incorporate micro and nano-technology based tools to probe, measure and improve cellular behavior. In this frame, patterned surfaces provide a platform for highly defined cellular interactions and, in perspective, they offer unique advantages for artificial implants. For these reasons, functionalized materials have recently become a central topic in tissue engineering. Nanotechnology, with its rich toolbox of techniques, can be the leading actor in the materials patterning field. Laser assisted methods, conventional and un-conventional lithography and other patterning techniques, allow the fabrication of functional supports with tunable properties, either physically, or topographically and chemically. Among them, soft lithography provides an effective (and low cost) strategy for manufacturing micro and nanostructures. The main focus of this work is the use of different fabrication approaches aiming at a precise control of cell behavior, adhesion, proliferation and differentiation, through chemically and spatially designed surfaces.

In the search to understand the interaction between cells and their underlying substrates, life sciences are beginning to incorporate micro and nano-technology based tools to probe, measure and improve cellular behavior. In this frame, patterned surfaces provide a platform for highly defined cellular interactions and, in perspective, they offer unique advantages for artificial implants. For these reasons, functionalized materials have recently become a central topic in tissue engineering. Nanotechnology, with its rich toolbox of techniques, can be the leading actor in the materials patterning field. Laser assisted methods, conventional and un-conventional lithography and other patterning techniques, allow the fabrication of functional supports with tunable properties, either physically, or topographically and chemically. Among them, soft lithography provides an effective (and low cost) strategy for manufacturing micro and nanostructures. The main focus of this work is the use of different fabrication approaches aiming at a precise control of cell behavior, adhesion, proliferation and differentiation, through chemically and spatially designed surfaces.

Physical systems composed of a large number of reciprocally interacting constituents provide the natural context for the rise of emergent phenomena. Despite the intrinsic difficulty in providing a mathematical definition of what is meant for ‘emergence’ (see [Baas, in Langton, Alife III, Santa Fe Studies in the Sciences of Complexity, Proc. Volume XVII, Addison-Wesley, (1994)]), the intuitive notion of emergent property is that of a collection of interact- ing objects showing a novel collective behavior, qualitatively different from and not immediately attributable to the behaviors of the individual components. Non-linear interactions among elements of the system, or interactions between the system and the environment, or merely the large number of constituents are usually the motivations addressed to be responsible for emergent behavior. It is important to remark that emergent properties can only be inferred from a comprehension of the collective properties of the microscopic constituents [Kivelson et al, npj Quant. Mater. 1, 16024 (2016)]. In this regard, computer simulations provide a unique tool to support experimental observation, develop abstract models and investigate systems’ properties at a microscopic level. In general, condensed matter, particularly soft matter but also the complex systems studied in Physics, are necessarily described via simplified models, which include the key features of the corresponding real systems. On the one hand, this certainly represents a powerful approach when it finds its roots in the concept of universality, connected with critical phenomena, but this also turns into a limiting factor for the realistic description of the considered phenomena. On the other hand, it makes the properties of such abstract simulated systems calculable and investigable via computer simulations. As a consequence, the simulations assume a key role in complementing the comparison between experiments and theory [Frenkel and Smit, Understanding Molecular Simulations, Academic Press (2002); Allen and Tildesley, Computer simulation of liquids, Oxford University Press (2017)]. In this sense, simulations are often regarded as being computer experiments, in which materials properties and novel phases of matter can be investigated. The present PhD thesis is a collection of the main results coming from four different research lines which I have been involved into in the last 3 years. The topics could appear to be rather diverse but they are all connected by the presence of emergent phenomena which were studied via computer simulations (Molecular Dynamics and Monte Carlo methods, mainly). Three of these four research lines are related to collaborations with as many experimental groups. The first group I started collaborating with is led by dr. R. Grisenti, at the University of Frankfurt (https://www.atom. uni-frankfurt.de/hhng-grisenti/index.html). As reported in Chapter 1 and in a recent paper which I contributed to as first co-author [Schottelius, Mambretti et al., Nat. Mat. (2020)], we studied the crystal growth of supercooled Ar–Kr liquid mixtures by means of a micro–jet experiment, Molecular Dynamics simulation and thermodynamic analysis. The second ongoing collaboration is with the group of prof. P. Milani, which is the leader of the CIMaINa laboratories (http://cimaina.unimi.it/) at the Università degli Studi di Milano. We developed an abstract stochastic model of resistive switching devices that they are characterizing for neuromorphic applications (see Chapter 3). More recently, I started a collaboration with the group led by prof. T. Bellini at the Università degli Studi di Milano (https://sites.google.com/site/unimisoft/), in order to investigate the spinodal decomposition of mixtures of DNA nanostars via light scattering experiments and Monte Carlo simulations, as described in Chapter 4. I will now provide a brief overview of the contents of each Chapter, where each Chapter corresponds to a different research line. Crystal growth from a supercooled melt is of fundamental theoretical and practical importance in many fields, ranging from materials science to the production of phase–change memories. To date, the temperature dependence of the growth rates of many materials, including pure metals, metallic alloys, colloids and many others are still under intense scrutiny (see e.g. Tang et al., Nat. Mat. (2013) and Sun et al., Nat. Mat. (2018)). The majority of systems display a maximum growth rate at a temperature located between the melting point and the glass transition [Orava et al., J. Chem. Phys. (2014)]. Several materials are characterized by a range of many orders of magnitude between this maximum value and the crystal growth rates measured in other regimes. We still lack a deep comprehension of the mechanism underlying this phenomenology, which emerges from experiments and simulations both. Classical models of crystal growth from a melt hypothesize either a diffusion-limited process, or a collision–limited one, but for a lot of materials them both fail to fit the available data. This situation claims for further investigation about the key elements that tune the crystal growth rates from supercooled liquids, extending the current theoretical framework. Jointly with the experimental group of dr. Grisenti (which performed measurements at the EU-XFEL facility https://www.xfel.eu/), we studied the crystallization of supercooled mixtures of argon and krypton via Molecular Dynamics. Our results showed that their crystal growth rates (obtained from the analysis of simulated configurations exploiting Steinhardt angular order parameters) can be reconciled with existing crystal growth models only by explicitly accounting for the non–ideality of the mixtures. Our theoretical and computational contribution aided in highlighting the importance of thermodynamic aspects in describing the crystal growth kinetics, yielding a substantial step towards a more sophisticated theory of crystal growth. A second project concerns the study of soft matter systems in one dimension (1D), detailed in Chapter 2. Soft matter systems are made of particles which can overlap by paying a finite energy cost and they are renowned for being able to display complex emerging phenomena. Some of them, for example, are characterized by the presence of clustering phases [Prestipino, Phys. Rev. E (2014)]. Recently, a surprising quantum phase transition has been revealed in a 1D system composed of bosons interacting via a pairwise soft potential in the continuum. It was shown that the spatial coordinates undergoing two-particle clustering could be mapped into quantum spin variables of a 1D transverse Ising model [Rossotti et al., Phys. Rev. Lett. (2017)]. Extending the description and the results provided in a very recent paper I contributed to as first author [Mambretti et al., Phys. Rev. E (2020)], in the second Chapter we investigate the manifestation of an analogous critical phenomenon in 1D classical fluids of soft particles in the continuum. In particular, we studied the low–temperature behavior of three different classical models of 1D soft matter, whose inter–particle interactions allow for cluster- ing. The two–particle cluster phase is largely explored, by simulating the systems at the commensurate density via Monte Carlo and Simulated Annealing methods. The same string variables exploited in the aforementioned quantum case highlight that, at the right commensurate density, the peculiar pairing of neighboring soft particles can be nontrivially mapped onto a 1D discrete classical Ising model. We also observe a related phenomenon, i.e. the presence of an anomalous peak in the low–temperature specific heat, thus indicating the emergence of Schottky phenomenology in a non–magnetic fluid. The third Chapter presents the case of an electrical resistor network featuring novel emergent properties, such as memristivity and the possibility to be used as a self–assembled logic gate; an article on this topic is currently in preparation. The growing difficulties arising in the improvement of the performance of standard computing architectures encouraged the quest for different approaches aiming at reproducing the computational capability and energy efficiency of the human brain, by mimicking neurons and synapses as probabilistic computing units [Markovic et al., Nat. Rev. Phys. 2, 499–510 (2020)]. Networks based on the bottom–up assembling of nanoscale building blocks and characterized by resistive switching (RS) activities are becoming increasingly popular as possible solutions for a straightforward fabrication of complex architectures with neuromorphic features [Wang et al., Nat. Rev. Mat. 5, 173-195 (2020)]. Specifically, it has recently been demonstrated that metallic nanostructured Au films, under certain conditions show a non–ohmic electrical behavior and complex and reproducible resistive switching, which can be exploited for the innovative realization of logic gates. In these devices, the nonlinear dynamic switching behavior resulting from an applied input voltage can be exploited for developing hardware for reservoir computing applications. In Chapter 3, I show how it is possible to simulate a complex model (Stochastic Resistor Network Model, SRNM) able to imi- tate the phenomenology and give hints for the development of experiments ongoing at the CIMaINa research laboratories, regarding the electrical current passage through nanostructured cluster gold films [Mirigliano et al., Nanotechnology, 31, 23, (2020)]. To this purpose, I personally contributed to develop from scratch a C++ code, parallelized via the Armadillo library (http://arma.sourceforge.net/). To study the electrical transport properties of this system, we modeled the experimental sample as a network of interconnected resistors whose effective resistance under a given voltage can be determined using spectral graph theory. The network state evolves stochastically via random physically–inspired update moves, and its effective total resistance (and the related Power Spectral Density) has been analyzed. The structure and the topology of the network were studied via the investigation of the shortest path connecting the source and the sink of the system, thus exploring the possible paths in which the current could flow. Moreover, we also applied Information Theory entropy–based tools to investigate the time evolution of network resistance at a local, coarse–grained, scale. We observed that specific input signals corresponding to 2 logical ‘bits’ pro- duce rich outputs associable to a logical NAND gate, which posses functional completeness. Given that relevant differences could be detected between the behavior of the network at low voltage before and after the so called ‘writing’ step (where the system is under a high applied voltage), memristive effects naturally emerge in the study of network properties. These results encourage further investigations, both experimental and via the innovative SRNM approach we developed, in order to exploit these RS devices in hardware computing applications as self–assembled logic gates. Last, in Chapter 4 I focus on another soft matter system, that I have started to investigate during my PhD research activity, regarding Monte Carlo simulations of low valence DNA–based colloidal particles. This last Chapter is mainly devoted to the description of the simulation method I have been developing during my more recent PhD research activities, while the preliminary results presented obviously need to be confirmed and extended by further studies. Particles with a limited number of attractive spots (patches) on their surface are generally characterized by non–crystalline low energy states; they rather generate a disordered 3D network in which all the sticky sites are engaged in (mutually exclusive) patch–patch bonds [Bianchi et al., Phys. Rev. Lett. (2006)]. One of the most promising experimental realizations of such peculiar colloids is extremely recent: laboratory synthesized DNA nanostars (NS) with fixed valence [Bi et al., PNAS (2013)]. In this field the landmark is represented by our collaborators from the group led by prof. T. Bellini. Recently, they started to investigate the behavior of mixtures of nanostars with leftwise or rightwise chirality of the DNA strands, characterized by a merely repulsive interspecies interaction. To date, our contribution mainly consisted in the development of an abstract model of these DNA nanostars, schematized as limited valence soft patchy particles, whose equilibrium configurations are sampled via a canonical Monte Carlo program. Their different chirality is represented by a mixed interaction which only comprises excluded volume terms. Our goal in this project is twofold: on the one hand, we aim to reconstruct the temperature–density phase diagram of such mixtures, also depending on the mixing ratio. Experiments revealed a critical behavior and a phase separation processes for dilute mono–component DNA solutions; the properties of a mixture of two components, each found in critical conditions, are studied in this work. In this Chapter, after a detailed overview of the experimental, computational and theoretical studies regarding low valence particles, the simulation code is described and it is presented a comparison between the simulation results and the experimental measurements at equilibrium. The peculiar structures found in the patchy particles network claim for further analysis, as well as the interesting behavior near the critical point for mono–component and bi–component systems both. The second perspective of this research regards the unexplored aggregation and cluster growth process of such particles. In this concern, part of the future research effort will be devoted to the transformation of our custom code into a Brownian Monte Carlo in order to unveil the mechanisms underlying the dynamics of such particles during their aggregation stages. The conclusions and further perspectives concerning each of the four topics addressed in this work can be retrieved at the end of each Chapter.

Biological matter is driven far from thermodynamic equilibrium by active processes on the molecular scale. These processes are usually driven by the chemical reaction of a fuel and generate spontaneous movements and mechanical stresses in the system, even in the absence of external forces or torques. Moreover these active stresses effectively fluidify the material. The cell cytoskeleton, suspensions of swimming microorganisms or tissues are prominent examples of active fluids. Active processes in biological systems often exhibit chiral asymmetries. Examples are the chirality of cytoskeletal filaments which interact with motor proteins, the chirality of the beat of cilia and flagella as well as the helical trajectories of many biological micro-swimmers. Moreover, large scale chiral flows have been observed in the cell cortex of C. elegans and Xenopus embryos. Active force generation induces force and torque dipoles in the material. If all forces are internal the total force and torque vanish as required by the conservation of momentum and angular momentum. The density of force dipoles is an active stress in the material. In addition, active chiral processes allow for the existence of active torque dipoles which enter the conservation of angular momentum and generate an active antisymmetric stress and active angular momentum fluxes. We developed a generic description of active fluids that takes into account active chiral processes and explicitly keeps track of spin and orbital angular momentum densities. We derived constitutive equations for an active chiral fluid based on identifying the entropy production rate from the rate of change of the free energy and linearly expanding thermodynamic fluxes in terms of thermodynamic forces. We identified four elementary chiral motors that correspond to localized distributions of chiral force and torque dipoles that differ by their symmetry and produce different chiral fluid flows and intrinsic rotation fields. We employ our theory to analyze different active chiral processes. We first show that chiral flows can occur spontaneously in an active fluid even in the absence of chiral processes. For this we investigate the Taylor-Couette motor, that is an active fluid confined between two concentric cylinders. For sufficiently high active stresses the fluid generates spontaneous rotations of the two cylinders with respect to each other thus breaking the chiral symmetry of the system spontaneously. We then investigate cases where active chiral processes on the molecular scale break the chiral symmetry of the whole system. We show that chiral flows occur in films of chiral motors and derive a generic theory for thin films of active fluids. We discuss our results in the context of carpets of beating cilia or E. coli swimming close to a surface. Finally, we discuss chiral flows that are observed in the cellular cortex of the nematode C. elegans at the one cell stage. Two distinct chiral flow events are observed. The first chiral flow event (i) is a screw like chiral rotation of the two cell halves with respect to each other and occurs around 15min after fertilization. This event coincides with the establishment of cortical cell polarity. The second chiral flow event (ii) is a chiral rotation of the entire cell cortex around the anterior posterior axis of the whole cell and occurs around 30min after fertilization. Measuring densities of molecular motors during episode (i) we fit the flow patterns observed using only two fit parameters: the hydrodynamic length and cortical chirality. The flows during (ii) can be understood assuming an increase of the hydrodynamic length. We hypothesize that the cell actively regulates the cortical viscosity and the friction of the cortex with the eggshell and cytosol. We show that active chiral processes in soft biological matter give rise to interesting new physics and are essential to understand the material properties of many biological systems, such as the cell cortex.

This thesis presents four investigations into mechanical aspects of soft thin structures, focusing on the effects of stochastic and thermal fluctuations and of material inhomogeneities. First, we study the self-organization of arrays of high-aspect ratio elastic micropillars into highly regular patterns via capillary forces. We develop a model of capillary mediated clustering of the micropillars, characterize the model using computer simulations, and quantitatively compare it to experimental realizations of the self-organized patterns. The extent of spatial regularity of the patterns depends on the interplay between cooperative enhancement and history-dependent stochastic disruption of order during the clustering process. Next, we investigate the influence of thermal fluctuations on the mechanics of homogeneous, elastic spherical shells. We show that thermal fluctuations give rise to temperature- and size-dependent corrections to shell theory predictions for the mechanical response of spherical shells. These corrections diverge as the ratio of shell radius to shell thickness becomes large, pointing to a drastic breakdown of classical shell theory due to thermal fluctuations for extremely thin shells. Finally, we present two studies of the mechanical properties of thin spherical shells with structural inhomogeneities in their walls. The first study investigates the effect of a localized reduction in shell thickness—a soft spot—whereas the second studies shells with a smoothly varying thickness. In both cases, the inhomogeneity significantly alters the response of the shell to a uniform external pressure, revealing new ways to control the strength and shape of initially spherical elastic capsules.
Engineering and Applied Sciences

Nanomaterials produced by molecular self-assembly has become one of the emerging technologies for the development of materials for the food, cosmetic and biotechnology industries. These materials exploit the unique properties of their molecular building blocks, which include natural molecules, such as peptides. Using the entire library of amino acids, consisting of 20 residues that are conserved across all life forms, a range of different materials can be created, such as hydrogels, emulsions, etc. However, such materials are normally found serendipitously or by complex molecular design and therefore the development of new systems has been challenging. In this thesis, a combination of computational and experimental techniques is used to predict, design, synthesize and apply a range of different tripeptides. Using design rules, a subset of tripeptides was chosen to examine their self-assembling ability. It was determined that peptides with cationic amino acids at the N-terminal position (KYF, KYW and KFF) promote the formation of nanofibers and hydrogelation whereas anionic amino acids form bilayer-like assemblies (DFF and FFD). Alteration of the peptides sequence disrupts the formation resulting in loss of ordered nanostructures. Exploiting this self-assembling process can result into different materials such as emulsions. Fibrous tripeptide assemblies have the ability to assemble at the water/oil interface stabilizing emulsions via interfacial nanofibrous networks, whereas anionic tripeptide assemblies form surfactant-like emulsifiers. These materials can be tuned to give different emulsion stabilities. The formation of tripeptides can be controlled using enzymatic methods where physiological conditions can be altered to selectively target different tripeptides. Conditions such as pH and temperature control peptide hydrolysis allowing for the retention of highly order peptide nanostructures. The promotion of highly order nanostructures is imperative and the presence of additive such as salts can influence the self-assembling structure formed. Different salts can interact with charged amino acids, which promote crosslinking between peptides creating new tripeptide nanomaterials.

The aim of this work has been to make use of surface scattering techniques to study soft matter at interfaces. The work presented herein is composed of two distinct bodies of work. The first comprises a fundamental study of the physical and structural properties of Langmuir monolayers composed of sulfobetaine surfactants. Physiochemical properties of the films have been investigated through the use of Langmuir trough techniques. This has been used to support x-ray and neutron reflectometry data, from which structural parameters were derived. The second body of work involves attempts to find and/or characterize novel ways of aligning proteins at interfaces. Soluble proteins at lipid interfaces have been characterized in terms of their interactions with functionalized lipid monolayers. Specific interactions have been utilized to adsorb protein layers at the interface through interactions with His-tag chelating lipids within the monolayer. These have been characterized using neutron reflectometry and quartz crystal microbalance studies. Work has also been completed to design a suitable system for the adsorption of membrane proteins. This has involved aligning phospholipid bilayer nanodiscs at the lipid interface and subsequent characterization through neutron reflectometry.

Soft matter, here, liquids and polymers, have adaptability to a surrounding geometry. They intrinsically have advantageous characteristics from a mechanical perspective, such as flowing and wetting on surrounding surfaces, giving compliant, conformal and deformable behavior. From the behavior of soft matter for heterogeneous surfaces, compliant structures can be engineered as embedded liquid microstructures or patterned liquid microsystems for emerging compliant microsystems. Recently, skin electronics and soft robotics have been initiated as potential applications that can provide soft interfaces and interactions for a human-machine interface. To meet the design parameters, developing soft material engineering aimed at tuning material properties and smart processing techniques proper to them are to be highly encouraged. As promising candidates, Ga-based liquid alloys and silicone-based elastomers have been widely applied to proof-of-concept compliant structures. In this thesis, the liquid alloy was employed as a soft and stretchable electrical and thermal conductor (resistor), interconnect and filler in an elastomer structure. Printing-based liquid alloy patterning techniques have been developed with a batch-type, parallel processing scheme. As a simple solution, tape transfer masking was combined with a liquid alloy spraying technique, which provides robust processability. Silicone elastomers could be tunable for multi-functional building blocks by liquid or liquid-like soft solid inclusions. The liquid alloy and a polymer additive were introduced to the silicone elastomer by a simple mixing process. Heterogeneous material microstructures in elastomer networks successfully changed mechanical, thermal and surface properties. To realize a compliant microsystem, these ideas have in practice been useful in designing and fabricating soft and stretchable systems. Many different designs of the microsystems have been fabricated with the developed techniques and materials, and successfully evaluated under dynamic conditions. The compliant microsystems work as basic components to build up a whole system with soft materials and a processing technology for our emerging society.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2019
Cataloged from PDF version of thesis.
Includes bibliographical references.
This thesis describes the systematic development of methods to perform large scale dynamic simulations of hydrodynamically interacting colloidal particles undergoing Brownian motion. Approximations to the hydrodynamic interactions between particles are built from the periodic fundamental solution for flow at zero Reynolds number and are methodically improved by introducing the multipole expansion and constraints on particle dynamics. Ewald sum splitting, which decomposes the sum of slowly decaying interactions into two rapidly decaying sums evaluated indepently in real space and Fourier space, is used to accelerate the calculation and serves as the basis for a new technique to sample the Brownian displacements that is orders of magnitude faster than prior approaches. The simulation method is first developed using the ubiquitous Rotne-Prager approximation for the hydrodynamic interactions.
Extension of the Rotne-Prager approximation is achieved via the multipole expansion, which introduces the notion of induced force moments whose value is determined from the solution of constraint problems (for example, rigid particles cannot deform in flow), and methods for handling these multipole-based constraints are illustrated. The multipole expansion converges slowly when particles are nearly touching, a problem which is functionally solved for dynamic simulations by including divergent lubrication interactions, in the style of Stokesian Dynamics. The lubrication interactions effectively introduce an additional constraint on the relative motion of closely separated particle pairs. This constraint is combined with the multipole constraints by developing a general method to handle nearly arbitrary dynamic constraints using saddle point matrices. Finally, the methods developed herein are applied to study sedimentation in suspensions of attractive colloidal particles.
The simulation results are used to develop a predictive model for the hindered/promoted settling function that describes the mean sedimentation rate as a function of particle concentration and attraction strength.
"The research in this thesis was supported by the MIT Energy Initiative Shell Seed Fund and NSF Career Award CBET-1 554398"
by Andrew M. Fiore.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Chemical Engineering

A new method, probability distribution of diffusivities (time scaled square displacements between succeeding video frames), was developed to analyze single molecule tracking (SMT) experiments. This method was then applied to SMT experiments on ultrathin liquid tetrakis(2-ethylhexoxy)silane (TEHOS) films on Si wafer with 100 nm thermally grown oxide, and on thin semectic liquid crystal films. Spatial maps of diffusivities from SMT experiments on 220 nm thick semectic liquid crystal films reveal structure related dynamics. The SMT experiments on ultrathin TEHOS films were complemented by fluorescence correlation spectroscopy (FCS). The observed strongly heterogeneous single molecule dynamics within those films can be explained by a three-layer model consisting of (i) dye molecules adsorbed to the substrate, (ii) slowly diffusing molecules in the laterally heterogeneous near-surface region of 1 - 2 molecular diameters, and (iii) freely diffusing dye molecules in the upper region of the film. FCS and SMT experiments reveal a strong influence of substrate heterogeneity on SM dynamics. Thereby chemisorption to substrate surface silanols plays an important role. Vertical mean first passage times (mfpt) in those films are below 1 µs. This appears as fast component in FCS autocorrelation curves, which further contain a contribution from lateral diffusion and from adsorption events. Therefore, the FCS curves are approximated by a tri-component function, which contains an exponential term related to the mfpt, the correlation function for translational diffusion and a stretched exponential term for the broad distribution of adsorption events. Lateral diffusion coefficients obtained by FCS on 10 nm thick TEHOS films, thereby, are effective diffusion coefficients from dye transients in the focal area. They strongly depend on the substrate heterogeneity. Variation of the frame times for the acquisition of SMT experiments in steps of 20 ms from 20 ms to 200 ms revealed a strong dependence of the corresponding probability distributions of diffusivities on time, in particular in the range between 20 ms and 100 ms. This points to average dwell times of the dye molecules in at least one type of the heterogeneous regions (e.g. on and above silanol clusters) in the range of few tens of milliseconds. Furthermore, time series of SM spectra from Nile Red in 25 nm thick poly-n-alkyl-methacrylate (PnAMA) films were studied. In analogy to translational diffusion, spectral diffusion (shifts in energetic positions of SM spectra) can be studied by probability distributions of spectral diffusivities, i.e. time scaled square energetic displacements. Simulations were run and analyzed to study contributions from noise and fitting uncertainty to spectral diffusion. Furthermore the effect of spectral jumps during acquisition of a SM spectrum was investigated. Probability distributions of spectral diffusivites of Nile Red probing vitreous PnAMA films reveal a two-level system. In contrast, such probability distributions obtained from Nile Red within a 25 nm thick poly-n-butylmethacrylate film around glass transition and in the melt state, display larger spectral jumps. Moreover, for longer alkyl side chains a solvent shift to higher energies is observed, which supports the idea of nanophase separation within those polymers.

This thesis uses theory and simulation to elucidate the principles and mechanisms that govern the thermodynamics, material science, and rheology of biological anisotropic soft matter that are involved in growth/self-assembly/material processing in plant cell walls, a multi-functional biological fibrous composite. The plant cell wall can be considered as a reinforced biological membrane consisting of cellulose microfibrils (CMFs) of high tensile strength embedded in a polysaccharide matrix. These CMFs in the extracellular matrix are oriented instrategic directions and generate commonly observed textures such as line, ring, helix, crossed helix and helicoids. The orientation of CMFs governs the physical properties of wood, controls the shape of the cell and contributes to themorphology at the tissue and organ level. Two models are used in this thesis, depending on the concentration of CMFs.At concentration of CMFs below Onsager critical limit, we develop an integrated mechanical model that describes nematic liquid crystalline self-assembly of rigid fibers on an arbitrarily curved 2D fluid membrane to demonstrate the possibility of the CMF orientation imparted by the interaction between membrane curvature and embedded fiber order. This curvature driven planar self assembly model can predict and explain the observed line, ring and helical cell wall textures. These predictions are partially validated through available experimental observations. An integrated shape and nematic order equation developed in this thesis gives a complete model whose solution describes the coupled membraneshape and fiber order state. The validated model is then used to analyze the structure and mechanics of biological and biomimetic fiber-laden membranes of variable curvature. The statics of anisotropic fiber-laden membranes developed inthis model is integrated with the planar nematodynamics of fibers and the dynamics of isotropic membranes to formulate a viscoelastic model to study dynamic remodeling of plant cell wall during growth and morphogenesis. The novel coupling between in-plane fiber orientation and order and membrane curvature formulated this thesis has the potential to open up a novel venue to control two dimensional anisotropic soft matter with tailored functionalities. When the concentration of the CMFs exceeds Onsager's critical fiber concentration threshold, the interaction between these CMFs results in theiralignment in a specific direction as an attempt to minimize the excluded volume of the CMFs. A mathematical model based on the Landau–de Gennes theory of liquid crystals is used to simulate defect textures arising in the domain of chiralself-assembly due to the presence of secondary phases such as pit canal and cell lumens. In addition to providing information on material properties and length scales that cannot be experimentally measured in vivo, the simulated transient defect pattern confirms for first time the long postulated formation mechanism of helicoidal plywoods through liquid crystalline self-assembly. The model is further extended to investigate defect textures and liquid crystalline (LC) phases observed in polygonal arrangement of cylindrical particles embedded in a cholesteric liquid crystal matrix. These validated findings provide a comprehensive set of trends and mechanisms that contribute to the evolving understanding of biological plywoods and serve as a platform for future biomimetic applications.The integration of soft matter physics theories and models with actual biological data for plant cell walls provides a foundation for understanding growth, form, and function and a platform for biomimetic innovation.
Cette thèse utilise la théorie et la simulation pour élucider les principes et mécanismes qui gouverne la hermodynamique, la science des matériaux, et la rhéologie de la matière biologique molle anisotropique qui est impliquée dans ledéveloppement/auto-assemblage/la transformation des parois cellulaires de plantes, un composite biologique fibreux multifonctionnel. Les parois cellulaires de plantes peuvent être considérées comme des membranes biologiques renforcées consistant en des microfibres de cellulose (CMFs) de hautes ténacités contenues dans une matrice de polysaccaride. Ces CMFs dans la matrice extracellulaire sont orientés dans une direction stratégique hélices et des hélicoïdes. L'orientation des CMFs gouverne les propriétés physiques du bois et contrôle la forme des cellules. Deux modèles sont employés dans cette thèse dépendamment de la concentration en CMFs. A la concentration de CMFs dessous la limite critique de Onsager, nous développons un modèle mécanique intégré qui décrit un auto-assemblage de fibres rigides de type cristal liquide nématique sur une membrane courbée bidimensionnelle arbitraire afin de démontrer la possibilité de l'orientation des CMFs indue par les interactions entre la courbature de la membrane et l'organisation fibrillaire intrinsèque. Cette auto-assemblage planaire indus par la courbature peut prédire et expliquer les lignes, annaux et textures hélicoïdales observées dans les parois cellulaires. Ces prédictions sont partiellement validées au travers d'observations expérimentales publiés. Une équation décrivant l'ordre nématique et la forme intégrée qui a été développé dans cette thèse fournis un modèle complet dont la solution décrit le couplage entre l'alignement des fibres et la forme de la membrane. Le model validé est par la suite utilisé à fin d'analyser la structure et la mécanique de membrane fibreuses biologiques et biomimétiques de courbatures variables. La statique des membranes fibreuses anisotropes développés dans ce modèle est intégrée avec la némato-dynamique planaire des fibres et la dynamique des membranes isotropes afin de formuler un modèle viscoélastique pour étudier le remodelage dynamique des CMF durant leur développement et morphogénèse. Le nouveau couplage entre l'orientation fibrillaire planaire et l'ordre ainsi que la courbature de la membrane formulé dans cette thèse à le potentiel d'ouvrir de nouvelles avenues pour contrôler l'ordre bidimensionnel de matière molle selon des propriétés bien définies. Quand la concentration en CMFs excède la limite critique en fibre de Onsager, l'interaction entre les CMFs résulte en un alignement dans une direction spécifique qui tente de minimiser le volume exclu de CMFs. Un modèle mathématique basé sur la théorie de Landau de Gennes des cristaux liquides est utilisé pour simuler les textures de défauts survenant dans un chirale d'auto assemblage du à la présence de phases secondaires tel que les lumens cellulaires. En plus de fournir de l'information sur les propriétés matériels et les ordres de grandeurs qui ne peuvent être mesuré expérimentalement in vivo, les motifs des défauts transitoires simulés confirment pour la première fois le mécanisme de formation des assemblages hélicoïdaux. Le modèle est de plus étendu pour investiguer les textures de défauts et les phases liquides cristallines (LC) observées dans les arrangements polygonaux de particules cylindriques inclus dans des matrices de cristaux liquide cholestériques. Ces découvertes validées fournissent un ensemble de mécanismes qui contribues à faire évoluer la compréhension des assemblages lamellaires biologiques et servent de plateforme pour de futur développement d'applications biomimétiques. L'intégration des théories et des modèles de la matière molle avec des données biologique concrète pour les parois cellulaires fournissent des fondement pour la compréhension du développement, de formation et fonctionnalité ainsi qu'une plateforme pour l'innovation biomimétique

Life is soft. From the fluid-like structure of lipid bilayers to the flexible folding of proteins, the realm of nanoscale soft matter is a complex and vibrant area of research. The lure of personalized medicine, advanced sensing technology, and understanding life at a fundamental level pushes research forward. This work considers to areas: (1) lipid bilayer dynamics in the presence of substrate defects and (2) the inverse temperature transition of elastic proteins. Molecular dynamics simulations as well as umbrella sampling were employed. The behavior of the bilayers discussed in the work provides evidence that small defects on confining surfaces can promote nucleation of lipid tethers. Results the second part of this work indicate elastin-like peptides experiencing inverse temperature transitions may be capable of performing amounts of work similar to RNA polymerase; additionally, resilin's inverse temperature transition may be closely linked to the molecule's ability to efficiently transmit energy through the similar coil-β secondary structure transition seen in both cases. These insights into the inverse transition temperature are relevant for the design of bio-inspired sensors and energy storage devices.
Master of Science

Polymer science is rapidly advancing towards the precise construction of synthetic macromolecules of formidable complexity. The impressive advances in control over polymer composition, topology and uniformity, enabled by the living polymerisation revolution, now permit the introduction of compartmentalisation within macromolecules. Despite the straightforward and versatile synthetic approaches to produce block copolymer, nanostructures built-up from these linear building-blocks rarely reaches dimensions beyond the 5–50 nm range and can be sensitive to their environment. The development of robust controlled polymerisation techniques has enabled the synthesis of covalently-bond polymer architectures that can be used as nano-scale building-blocks. One of these architectures are molecular polymer brushes (also known as bottlebrush polymers or cylindrical polymer brushes). Molecular polymer brushes (MPBs) are unique materials that possess astonishing properties arising from their densely grafted and extended chain structure. The field of MPBs, especially as compartmentalised entities, is rapidly growing. Recent efforts have focussed on achieving MPBs with programmed complexity and the introduction of orthogonal chemical functionality. Compartmentalised brushes can elevate their functionality beyond that of their linear constituent parts, thus offering immense potential in self-assembly and template chemistry. The aim of this thesis is to demonstrate how the compartmentalisation in MPBs can be used for the construction of complex, yet precise, polymer nano- and microstructures with the scope to develop advanced functional materials.

The present thesis deals with the development and implementation of models for problems in soft condensed matter, at the interface between biology and material science. In particular, two projects have been carried out. The first focuses on the molecular origin of chirality in liquid crystalline solutions of semiflexible polyelectrolytes like DNA, columnar aggregates of deoxyguanosine tetramers (G-wires) and filamentous becteriophages. The second project deals with the integration between theoretical and experimental methods for the study of membrane-proteins systems, starting from the analysis of ESR spectra of spin labelled proteins. Both projects have been carried out in collaboration with experimental groups. This thesis is organised in two parts. In the first part, from chapter 1 to chapter 4, the work on chiral amplification in liquid crystalline solutions of polyelectrolytes is presented. In chapter 1, the phenomenon of chiral amplification is introduced and the main properties of liquid crystals are summarised. In chapters 2 and 3 the theoretical model which has been developed to connect the molecular and phase chirality of rigid polyelectrolytes is presented, together with its application to solutions of B-DNA and colloidal suspensions of M13 virus. In chapter 4, this model is extended to semiflexible polymers. The second part, from chapter 5 to chapter 9, deals with the theoretical and computational methods used to analyse ESR experiments on spin labeled proteins. Chapter 5 is a short introduction to peripheral proteins, the Site-Directed Spin Labelling (SDSL) technique and ESR lineshape simulations. In chapters 6 and 7, a method for the analysis of the ESR spectra of spin labeled proteins is proposed, based on the structural and motional characteristics of typical spin labels in their environment. In chapter 9, the model is applied to the investigation of controversial aspects of ?-Synuclein binding to lipid bilayers. Chapter 8 reports on Molecular Dynamics simulations of a fragment ?-Synuclein, in the presence of a POPC bilayer. Finally, chapter 10 presents a summary of the two projects, with some highlights on the relevant results obtained in this thesis.

This practice-led research examines how the emerging role of the ‘material designer’ can enrich the design process in Human Computer Interaction. It advocates embodiment as a design methodology by employing tacit knowledge; focusing on a subjective, affective and visceral engagement with computational materials. This theoretical premise is explored by drawing on the fields of soft robotics, as well as transitive and programmable materials. With the advancement and democratisation of physical computing and digital fabrication, it is now possible for designers to process, or even invent and composite new programmable materials, merging both their physical and digital capabilities. This study questions how the notion of soft can develop a distinct space for the design of novel user interfaces. This premise is applied through a phenomenological understanding of technology development—as opposed to generating data which is solely reliant on observable and measurable evidence. Bio-engineered technologies such as electroactive polymer, pneumatic and hydraulic actuator systems are deployed to explore a new type of responsive, sensual and organic materiality. Here, traditional medical diagnostic applications such as microfluidics are transferred into the experimental contexts of textiles and wearable technology. Therefore, by thinking through physical prototyping, a bodily engagement with materials and the interpretation of the elements of water, air and steam; a designer can create a fertile ground for a polyvalent imagination. Together, this methodology is used as a qualitative system for collecting and evaluating data on the significance of design-led thinking in soft robotic materials. This research concludes that there are insights to be gained from the creative practice and exploratory methods of material-led thinking in HCI that can contribute to the commercial research and development fields of wearable technology. Outputs include a prototype box of ‘Invention Tools’ for textile designers and the identification and creation of the role 04 of embodied making in relation to the imagination. Further, soft composite hybrids, incorporating elastomers, have potential applications in colour, texture and shape changing surfaces. Thus, this thesis argues that it is within the creative soft sciences that the next advancements in soft robotics may emerge.

We explore two distinct domains in the field of soft matter. The first three experimental chapters concern the synthesis, characterisation and application of Janus particles fabricated by heterogeneous polymerisation techniques. Initially in Chapter 2 we describe an optimised one pot seeded emulsion polymerisation strategy to render submicron amphiphilic Janus particles exhibiting surface active behaviour which can be tuned by the variation of hydrophilic to hydrophobic lobe volume ratios. These particles have been shown to inhibit ice recrystallisation in aqueous systems. In Chapter 3 we explore the synthesis of hard-soft Janus particles comprising of respective high and low glass transition temperature lobes. Although the rate of polymerisation is unaffected by available seed particle surface area, particles with multiple soft lobes and secondary nucleation occur below a seed surface area threshold. We additionally demonstrate the ability to fabricate sub-micron hard-soft Janus particles. Chapter 4 utilises the particles made in the previous chapter as building blocks to fabricate ‘colloidal molecules’ and colloidosomes. In the former case, cluster morphology of particles is shown to be governed by surface area minimisation of the central soft domain. The final two experimental chapters explore two different strategies to emulsify water into chocolate whilst retaining the desirable physical characteristics of the confectionery. In Chapter 5 we utilise colloidal silica and a cationic polyelectrolyte to generate highly stable quiescent Pickering emulsions, allowing up to 50% of the fat content in chocolate to be replaced with water and fruit juice. Chapter 6 improves upon this work by allowing the replacement of up to 80% of the fat content in chocolate by the dispersion of aqueous hydrogels within the chocolate fat matrix. In both chapters we characterise the physical properties of the formulations and demonstrate their suitability for use in chocolate confectionery.

In this thesis we explore two different theories for modelling soft matter systems. We start by discussing density functional theory (DFT) and dynamical density functional theory (DDFT) and consider the thermodynamics underpinning these theories as well as showing how the main results may be derived from the microscopic properties of soft matter. We use this theory to set up a model for the evaporation of the solvent from a thin film of a colloidal suspension. The general background for such systems is discussed and we display some of the striking nanostructures which self-assemble during the evaporation process. We show that our theory successfully reproduces some of these patterns and deduce the various mechanisms and transport processes behind the formation of the different structures. In the second part of this thesis we discuss results for a second model; the phase field crystal (PFC) model. The model equations are discussed, showing how they may be derived from DDFT as well as discussing the general background of PFC models. We present some results for the PFC model in its most commonly used form before going on to introduce a modified PFC model. We show how the changes in the model equations are reflected in the thermodynamics of the model. We then proceed by demonstrating how this modified PFC model may be used to qualitatively describe colloidal systems. A two component generalisation of the modified PFC model is introduced and used to investigate the transition between hexagonal and square ordering in crystalline structures. We conclude by discussing the similarities and connections between the two models presented in the thesis.

The collective motion of organisms such as flights of birds, swimming of school of fish, migration of bacteria and movement of herds across long distances is a fascinating phenomenon that has intrigued man for centuries. Long and details observations have resulted in numerous abstract hypothesis and theories regarding the collective motion animals and organisms. In recent years the developments in supercomputers and general computational power along with highly refined mathematical theories and equations have enabled the collective motion of particles to be investigated in a logical and systematic manner. Hence, this study is focused mathematical principles are harnessed along with computational programmes in order to obtain a better understanding of collective behaviour of particles. Two types of systems have been considered namely homogeneous and heterogeneous systems, which represent collective motion with and without obstacles respectively. The Vicsek model has been used to investigate the collective behaviour of the particles in 2D and 3D systems. Based on this, a new model was developed: the obstacle avoidance model. This showed the interaction of particles with fixed and moving obstacles. It was established using this model that the collective motion of the particles was very low when higher noise was involved in the system and the collective motion of the particles was higher when lower noise and interaction radius existed. Very little is known about the collective motion of self-propelled particles in heterogeneous mediums, especially when noise is added to the system, and when the interaction radius between particles and obstacles is changed. In the presence of moving obstacles, particles exhibited a greater collective motion than with the fixed obstacles. Collective motion showed non-monotonic behaviour and the existence of optimal noise maximised the collective motion. In the presence of moving obstacles there were fluctuations in the value of the order parameter. Collective systems studies are highly useful in order to produce artificial swarms of autonomous vehicles, to develop effective fishing strategies and to understand human interactions in crowds for devising and implementing efficient and safe crowd control policies. These will help to avoid fatalities in highly crowded situations such as music concerts and sports and entertainment events with large audiences, as well as crowded shopping centres. In this study, a new model termed the obstacle avoidance model is presented which investigates the collective motion of self-propelled particles in the heterogeneous medium. In future work this model can be extended to include a combination of a number of motionless and moving obstacles hence bringing the modelling closer to reality.

In recent years, the study of stimulated emission from and by biological systems has gained wide spread attention as a promising technology platform for novel biointegrated laser. However, the photonic properties and the associated physics of many biological laser systems are not yet fully understood and many promising resonator architectures and laser classes have not yet transitioned into the biological world. In this thesis, we investigate the fundamental photonic properties of lasers based on single biological cells and explore the potential of distributed feedback (DFB) gratings as novel biointegrated laser resonators. We show how the easy and flexible fabrication of DFB resonators helps to realize optofluidic and solid-state biological lasers. Lasing characteristics, such as tunable and single mode emission, are investigated and different applications are explored. Fourier-space emission studies on different biological lasers give insight in to the photonic dispersion relation of the system and the fundamental creation of lasing modes and their confinement in living systems. The first purely water based optofluidic DFB laser is demonstrated and novel sensing applications are suggested. This device shows low threshold lasing due to an optimized mode shape, which is achieved by a low refractive index substrate and the use of a mixed-order grating. Next, by integrating a high refractive index interlayer on a DFB resonator, a laser device incorporating the novel solid-state biological gain material green fluorescent protein (GFP) is realized. Lastly, we show how the thickness of organic polymer lasers can be reduced to its fundamental limit (< 500 nm) and the resulting membrane like laser devices can be applied to and operated on various body parts to potentially complement biometric identification.

Thesis (Ph. D.)--University of Oregon, 2000.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 100-104). Also available for download via the World Wide Web; free to University of Oregon users. Address: http://wwwlib.umi.com/cr/uoregon/fullcit?p9957568.

The fullerene cage provides an ideal, isolated environment for trapping spin active atoms such as nitrogen or phosphorous. Alignment of these endohedral fullerenes in linear arrays would have applications in quantum computing as the interactions between spin-active molecules can be easily controlled. Self-assembled molecular networks such as block copolymers, Langmuir-Blodgett films, and self-assembled monolayers are ideal for this purpose as the spacing and geometry can be easily tuned. This dissertation will discuss using each of these methods to achieve alignment or orientation of fullerenes for application in quantum information processing.

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 appliquée 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 coeffcient d'amortissement de l'interaction entre des cellules vivantes de type PC12 et une pointe AFM en nitrure de 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 biomolécules et des polymères.

Surface patterning is important for a range of engineering applications, including controlled wetting and spreading of liquids, adhesion and assembly of smart coatings. There is therefore a need of simple, cost-effective and scalable techniques for pattern formation over a wide range of scales. Conventional methods fail to comply with these requirements, as costs and complexity increase in the attempt to impress nm to µm scale features. By contrast, wrinkling of bi-(multi- )layers is inherently inexpensive, scalable and robust, and has the potential for soft matter patterning from the nano- to the macro-scale. This work investigates the controlled multi-layer generation of polydimethylsiloxane (PDMS) glassy skins via surface oxidation using plasma exposure and/or ultraviolet ozonolysis (UVO). Uniaxial mechanical compression is then employed to induce pattern formation via a well-known wrinkling instability. Topographies with wavelengths down to 45 nm are achieved, for the first time, as well as features with characteristic lengthscales of ∼ 10s µm. Moreover, simple design routes for double frequency nested pattern formation, imposed by compression of tri-layer laminate films, are established. The work concludes by exploiting wrinkling as a method for the mechanical characterisation of thin drying films. A time-resolved wrinkling interrogation during film drying is established as a simple and reliable approach to determining evolving mechanical properties of films, overcoming the difficulties associated with handling very thin free-standing films and the limited sensitivity of conventional methods, with potential applications extending to coatings, personal care items, and foods.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior
Nesta tese estudamos a influÃncia de potenciais de confinamento externos nas propriedades dinÃmicas de sistemas de matÃria condensada mole. Analisamos as propriedades difusivas de dois sistemas especÃficos utilizando simulaÃÃes computacionais (DinÃmica Molecular de Langevin e DinÃmica Browniana). No CapÃtulo 1, introduzimos o tÃpico sobre matÃria condensada mole. Mostramos vÃrios aspectos teÃricos e experimentais neste tipo de sistema. Fazemos uma breve introduÃÃo ao tÃpico de difusÃo, onde discutimos os principais aspectos do movimento Browniano. Introduzimos o problema de difusÃo em linha (SFD, do inglÃs "single-file diffusion") e o discutimos, teorica e experimentalmente, no contexto de sistemas de matÃria condensada mole. No CapÃtulo 2, introduzimos os mÃtodos computacionais utilizados nesta tese. Discutimos os mÃtodos de DinÃmica Molecular e suas variantes, o mÃtodo de DinÃmica de Langevin e DinÃmica Browniana. TambÃm introduzimos algoritmos de integraÃÃo utilizados nos capÃtulos posteriores. Nos Caps. 3, 4 e 5, analisamos dois sistemas distintos, (i) um sistema de partÃculas de Yukawa confinadas em um canal parabÃlico quasi-unidimensional (q1D) e (ii) um sistema de colÃides magnÃticos sob a influÃncia de um potencial parabÃlico e uma modulaÃÃo periÃdica externa ao longo da direÃÃo nÃo confinada. No primeiro sistema, estudamos a transiÃÃo do regime de difusÃo em linha (SFD) para o regime de difusÃo normal (2D). No segundo sistema, estudamos os efeitos de vÃrios parÃmetros que caracterizam o sistema (e.g., a magnitude do campo magnÃtico externo e a presenÃa da modulaÃÃo periÃdica externa) em suas propriedades dinÃmicas. Finalmente, apresentamos um sumÃrio dos principais resultados obtidos nesta tese e mostramos algumas questÃes em aberto como perspectivas para pesquisas futuras na Ãrea de difusÃo em sistemas de matÃria condensada mole.
In this thesis we study the influence of external confinement potentials on the dynamical properties of soft condensed matter systems. We analyze the diffusive properties of two specific systems by means of Langevin and Brownian Dynamics simulations. In Chapter 1, we introduce the subject of soft condensed matter. We show several theoretical and experimental aspects of these type of systems. We make a brief introduction to the topic of diffusion, where we discuss main aspects of Brownian motion. We introduce the single-file diffusion (SFD) problem and discuss it in the context of soft condensed matter systems, both theoretically and experimentally. In Chapter 2, we introduce the computational method used in this thesis. We discuss Molecular Dynamics (MD) and its variants, Langevin and Brownian Dynamics simulations. We also introduce numerical algorithms used in the following chapters. In Chapters 3, 4 and 5, we analyze two different systems, namely (i) a system of interacting Yukawa particles confined in a parabolic quasi-one-dimensional (q1D) channel and (ii) a system of magnetic colloidal particles under the influence of both a parabolic confinement potential and a periodic external modulation along the unconfined direction. In the former, we study the transition from the single-file diffusion (SFD) regime to the two-dimensional (2D) diffusion regime. In the latter, we study the influence of several parameters that characterizes the system, e.g., the strength of an external magnetic field and the periodic modulation along the unconfined direction, on its dynamical properties. Finally, we present the summary of the main findings reported in this thesis and we show some open questions as perspectives for future research in the field of diffusion in soft condensed matter systems.

Subdividing space through interfaces leads to many space partitions that are relevant to soft matter self-assembly. Prominent examples include cellular media, e.g. soap froths, which are bubbles of air separated by interfaces of soap and water, but also more complex partitions such as bicontinuous minimal surfaces. Using computer simulations, this thesis analyses soft matter systems in terms of the relationship between the physical forces between the system’s constituents and the structure of the resulting interfaces or partitions. The focus is on two systems, copolymeric self-assembly and the so-called Quantizer problem, where the driving force of structure formation, the minimisation of the free-energy, is an interplay of surface area minimisation and stretching contributions, favouring cells of uniform thickness. In the first part of the thesis we address copolymeric phase formation with sharp interfaces. We analyse a columnar copolymer system “forced” to assemble on a spherical surface, where the perfect solution, the hexagonal tiling, is topologically prohibited. For a system of three-armed copolymers, the resulting structure is described by solutions of the so-called Thomson problem, the search of minimal energy configurations of repelling charges on a sphere. We find three intertwined Thomson problem solutions on a single sphere, occurring at a probability depending on the radius of the substrate. We then investigate the formation of amorphous and crystalline structures in the Quantizer system, a particulate model with an energy functional without surface tension that favours spherical cells of equal size. We find that quasi-static equilibrium cooling allows the Quantizer system to crystallise into a BCC ground state, whereas quenching and non-equilibrium cooling, i.e. cooling at slower rates then quenching, leads to an approximately hyperuniform, amorphous state. The assumed universality of the latter, i.e. independence of energy minimisation method or initial configuration, is strengthened by our results. We expand the Quantizer system by introducing interface tension, creating a model that we find to mimic polymeric micelle systems: An order-disorder phase transition is observed with a stable Frank-Caspar phase. The second part considers bicontinuous partitions of space into two network-like domains, and introduces an open-source tool for the identification of structures in electron microscopy images. We expand a method of matching experimentally accessible projections with computed projections of potential structures, introduced by Deng and Mieczkowski (1998). The computed structures are modelled using nodal representations of constant-mean-curvature surfaces. A case study conducted on etioplast cell membranes in chloroplast precursors establishes the double Diamond surface structure to be dominant in these plant cells. We automate the matching process employing deep-learning methods, which manage to identify structures with excellent accuracy.

CAMARÃO, Diego de Lucena. Diffusive properties of soft condensed matter systems under external confinement. 2014. 142 f. Tese (Doutorado em Física) - Programa de Pós-Graduação em Física, Departamento de Física, Centro de Ciências, Universidade Federal do Ceará, Fortaleza, 2014.
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In this thesis we study the influence of external confinement potentials on the dynamical properties of soft condensed matter systems. We analyze the diffusive properties of two specific systems by means of Langevin and Brownian Dynamics simulations. In Chapter 1, we introduce the subject of soft condensed matter. We show several theoretical and experimental aspects of these type of systems. We make a brief introduction to the topic of diffusion, where we discuss main aspects of Brownian motion. We introduce the single-file diffusion (SFD) problem and discuss it in the context of soft condensed matter systems, both theoretically and experimentally. In Chapter 2, we introduce the computational method used in this thesis. We discuss Molecular Dynamics (MD) and its variants, Langevin and Brownian Dynamics simulations. We also introduce numerical algorithms used in the following chapters. In Chapters 3, 4 and 5, we analyze two different systems, namely (i) a system of interacting Yukawa particles confined in a parabolic quasi-one-dimensional (q1D) channel and (ii) a system of magnetic colloidal particles under the influence of both a parabolic confinement potential and a periodic external modulation along the unconfined direction. In the former, we study the transition from the single-file diffusion (SFD) regime to the two-dimensional (2D) diffusion regime. In the latter, we study the influence of several parameters that characterizes the system, e.g., the strength of an external magnetic field and the periodic modulation along the unconfined direction, on its dynamical properties. Finally, we present the summary of the main findings reported in this thesis and we show some open questions as perspectives for future research in the field of diffusion in soft condensed matter systems.
Nesta tese estudamos a influência de potenciais de confinamento externos nas propriedades dinâmicas de sistemas de matéria condensada mole. Analisamos as propriedades difusivas de dois sistemas específicos utilizando simulações computacionais (Dinâmica Molecular de Langevin e Dinâmica Browniana). No Capítulo 1, introduzimos o tópico sobre matéria condensada mole. Mostramos vários aspectos teóricos e experimentais neste tipo de sistema. Fazemos uma breve introdução ao tópico de difusão, onde discutimos os principais aspectos do movimento Browniano. Introduzimos o problema de difusão em linha (SFD, do inglês "single-file diffusion") e o discutimos, teorica e experimentalmente, no contexto de sistemas de matéria condensada mole. No Capítulo 2, introduzimos os métodos computacionais utilizados nesta tese. Discutimos os métodos de Dinâmica Molecular e suas variantes, o método de Dinâmica de Langevin e Dinâmica Browniana. Também introduzimos algoritmos de integração utilizados nos capítulos posteriores. Nos Caps. 3, 4 e 5, analisamos dois sistemas distintos, (i) um sistema de partículas de Yukawa confinadas em um canal parabólico quasi-unidimensional (q1D) e (ii) um sistema de colóides magnéticos sob a influência de um potencial parabólico e uma modulação periódica externa ao longo da direção não confinada. No primeiro sistema, estudamos a transição do regime de difusão em linha (SFD) para o regime de difusão normal (2D). No segundo sistema, estudamos os efeitos de vários parâmetros que caracterizam o sistema (e.g., a magnitude do campo magnético externo e a presença da modulação periódica externa) em suas propriedades dinâmicas. Finalmente, apresentamos um sumário dos principais resultados obtidos nesta tese e mostramos algumas questões em aberto como perspectivas para pesquisas futuras na área de difusão em sistemas de matéria condensada mole.

I present applications of imaging and spectroscopy to understand mechanical, chemical, and electrical dynamics in biological materials. The first part describes the development and characterization of a protein-based fluorescent calcium and voltage indicator (CaViar). The far-red fluorescence of CaViar faithfully tracks the cardiac action potential in cardiomyocytes. CaViar's green fluorescence reports the resulting calcium transients. I demonstrated the applicability of CaViar in vivo with transgenic zebrafish designed to express CaViar in their hearts. Spinning disk confocal imaging allowed detailed three-dimensional mapping of simultaneous voltage and calcium dynamics throughout the heart of zebrafish embryos, in vivo, as a function of developmental stage. I tested the effect of channel blockers on voltage and calcium dynamics and discovered a chamber-specific transition from a calcium-dependent to a sodium-dependent action potential. I also describe a new measurement technique using a fluorescent voltage indicator to report absolute voltage via the indicator's temporal response.
Physics

Soft magnetic $ rm Ni sb{ it x}Co sb{ it 100-x}$/Cu multilayers in the range x = 20 to 80 have been prepared by DC-magnetron sputtering. NiCo alloys were chosen because of their small magnetoelastic parameters around the range x = 70-80 and very small lattice mismatch between NiCo and Cu. This combination of parameters should lead to good giant magnetoresistance (GMR) with a small saturation field. Structural characterization reveals that high quality layered structures were obtained. Quantitative interpretation of the superlattice structure parameters, such as interface roughness, interfacial mixing profiles and layer-thickness disorders, have been carried out by modelling the X-ray diffraction data.
GMR was found to be largest at x = 80 with well-defined oscillations as a function of the thickness of the Cu layer, mirroring the interlayer magnetic coupling. In particular, GMR with small saturation fields around Cu thickness near the second MR maximum (t$ sb{Cu}$ = 20A) will be technologically important because of the very high magnetic field sensitivity. Correlating the multilayer structure to the GMR allow us to optimize the structural parameters by enhancing the spin-dependent interfacial scattering in a high quality layered structure. Direct observation of the simple antiferromagnetic order has been achieved by the presence of the (0,0,${1 over2})$ wavevector in small angle neutron scattering experiments. A near-perfect antiferromagnetic spin arrangement is found for a Cu thickness t$ sb{Cu}$ = 20 A, that can be readily aligned ferromagnetically in a small external field of less than 200 Oe.
A complementary system, FM/Ag (FM = $ rm Ni sb{81}Fe sb{19}, Ni sb{80}Co sb{20}$ and $ rm Ni sb{66}Co sb{18}Fe sb{16})$ granular multilayer prepared by annealing multilayers, has also been studied. Enhanced magnetoresistance observed in these systems is shown to be controlled by the size, concentration and thermal stability of the magnetic precipitates in a nonmagnetic matrix. For a particular multilayer structure with a magnetic layer of 20 A, annealed at around 325$ sp circ$C, a GMR of $ sim$4% with a characteristic saturation field of 10 Oe was found, leading to a high magnetoresistive sensitivity of $ sim$0.4%/Oe at room temperature.

Materials where thermal energy is comparable to the interaction energy between molecules are called soft materials. Soft materials are everywhere in our life: food, rubber, polymer diaper, our own body, etc. The thermal fluctuation endows soft materials with fundamentally different behavior comparing to hard materials like metals and ceramics. This dissertation studies three aspects of the mechanics and physics of soft materials, as is reviewed below. First, soft materials are generally swellable and viscous. The combination of diffusion and viscous flow gives rise to a length scale we called poroviscous length. The emergence of a length scale results in size dependent relaxation. We show that the coupling between diffusion and viscous flow explains the Brownian motion in supercooled liquids, where the classical result of Stokes-Einstein relation generally fails. The concurrent diffusion and viscous flow cannot be described by the classical hydrodynamics, where all the material transport is lumped into velocity field. We formulated a continuum theory to modify the classical hydrodynamics. In particular, the new theory predicts a new bulk viscosity that could exist in incompressible material. We generalize this idea of bulk viscosity to binary systems and study the mixing of materials that is limited by local structural rearrangement instead of diffusion. This model develops formulation of non-equilibrium thermodynamics by removing the common assumption of local equilibrium. Second, capillarity has strong influence on the morphology of soft materials. The competition between capillarity and elasticity gives rise to the elastocapillary length, which is defined as surface tension over the shear modulus. We show that elastocapillary effect explains the complex nucleation of crease, a widely observed surface instability in soft elastic materials. We also explore the possible competition between capillarity and osmosis in gels, which defines the osmocapillary length, the surface tension divided by osmotic pressure. We show that at small enough length scale or for a gel that is nearly fully swollen, surface tension can pull liquid solvent out from the gel phase, a phenomenon we termed osmocapillary phase separation. Third, soft materials are nearly incompressible. The incompressibility and softness makes elastomers ideal for the design of seals. Although the failure of seals has been studies for decades, existing studies mainly focus on the damage and degradation of materials. Here we study the leak of a seal due to elastic deformation without any damage. We call such a failure mode the elastic leak. We point out that elastic leak is involved in any leak event no matter whether material is damaged or not. We also show that the reversible nature of the elastic leak enable seal series to achieve higher sealing capability.
Engineering and Applied Sciences - Engineering Sciences

Many different physical systems, such as granular materials, colloids, foams and emulsions exhibit a jamming transition where the system changes from a liquid-like flowing state to a solid jammed state as the packing fraction increases. These systems are often modeled using soft-core particles with repulsive contact forces. In this thesis we explore several different dynamical models for these kinds of systems, and see how they affect the behavior around the jamming transition. We investigate the effect of different types of dissipative forces on the rheology, and study how different methods of preparing a particle configuration affect their probability to jam when quenched. We study the rheology of sheared systems close to the jamming transition. It has been proposed that the athermal jamming transition is controlled by a critical point, point J, with certain scaling properties. We investigate this using multivariable scaling analysis based on renormalization group theory to explore the scaling properties of the transition and determine the position of point J and some of the critical exponents.

In this thesis we asses the phenomena of arising interactions in soft matter in coexistence with soft active matter. As a non-equilibrium bath we introduce ensembles of self-propelled particles, granular shaken beds, and photo active catalytic particles. We start the thesis with a detailed study of the widely used Active Brownian Particle (ABP) model. This model exhibits a non-equilibrium phase transition which has been intensively studied in recent years, we have finally reported that this transition satisfies all features of equilibrium first order phase transitions. Then, we introduce aligning interactions in ABP and characterize the emergent collective phenomena. In parallel, we explore the emergent forces, from mechanical contact forces, in probe particles in suspensions of aligning active particles and horizontally shaken granular beds. We characterize the forces and identify the emergence of long range interactions in both systems, in aligning active particles long range attractive interactions appear as alignment is increased, and in granular shaken media when the pair of particles align in the shaking direction. Finally, we conclude this thesis with the study of emergent interactions in spherically symmetric systems of catalytic active particles. Symmetry does not permit such particles to propell but the symmetry is broken with the addition of neighboring particles. We model the pair interaction in terms of the relative velocity between particles, and proceed to explore the emergent structures in mixtures of catalytic magnetic particles, and passive particles. We have unveiled the formation of clusters of passive particles. The addition of magnetic interactions between active particles leads to the formation of ramified gel-like structures for dense configurations of active particles. In this case, experimentalists have checked the formation of structures with the same morphologies in experiments in the laboratory.
En aquesta tesi abordem el fenomen de les interaccions emergents en matèria tova en coexistència amb matèria tova activa. Com a sistemes de matèria tova activa introduïm col·lectius de partícules autopropulsades, col·loides amb capacitat de catalitzar productes químics i medis granulars agitats. Primer de tot estudiem en detall un model molt estès per a partícules actives, el model de les partícules actives brownianes (ABP). D'aquest model estudiem amb detall una transició de fase de no equilibri i comprovem que la transició satisfà amb les característiques d'una transició en equilibri de primer ordre. Seguidament incorporem interaccions d'alineació en el model de partícules actives i procedim a estudiar les propietats col·lectives de les suspensions de partícules actives amb alineació. Per tal d'abordar l'objectiu de la tesi introduïm partícules de prova en suspensions de partícules actives, i en medis granulars amb forçament periòdic horitzontal, amb diferents paràmetres d'activitat per tal d'estudiar les forces, des d'un punt de vista mecànic, que emergeixen entre les parelles. Hem caracteritzat les forces i hem identificat l'aparició d'interaccions de llarg abast per sistemes de partícules amb alineació i en sistemes granulars en la direcció del forçament. Finalment, tanquem la tesi amb l'estudi i modelització d'interaccions emergents per a partícules catalítiques amb simetria esfèrica. La simetria no permet a les partícules d'autopropulsar-se però la presència de partícules al seu entorn sí que dóna lloc a interaccions, en forma de velocitats induïdes. Amb un model raonable de la interacció a distància hem calibrat la magnitud de la interacció amb sistemes experimentals i procedit a caracteritzar les estructures emergents per a mescles de partícules actives i passives que van des de la formació d'agregats en forma de clústers. L'addició d'interaccions magnètiques entre partícules actives permet la formació d'estructures ramificades de tipus gel. En aquest cas l'equip experimental ha pogut comparar l'aparició d'estructures amb les mateixes característiques al laboratori.

The soft matter field considers a wide class of objects such as liquids, polymers, gels, colloids, liquid crystals and biological macromolecules, which have complex internal structure and conformational flexibility leading to phenomena and properties having multiple spacial and time scales. Existing computer simulation methods are able to cover these scales, but with different resolutions, and ability to link them together performing a multiscale simulation is highly desirable. The present work addresses systematic multiscaling approach for soft matter studies, using structure-based coarse-graining (CG) methods such as iterative Boltzmann inversion and inverse Monte Carlo. A new software package MagiC implementing these methods is introduced. The software developed for the purpose of effective CG potential derivation is applied for ionic water solution and for water solution of DMPC lipids. A thermodynamic transferability of the obtained potentials is studied. The effective inter-ionic solvent mediated potentials derived for NaCl successfully reproduce structural properties obtained in explicit solvent simulation, which indicates the perspectives of using the structure-based coarse-graining for studies of ion-DNA and other polyelectrolytes systems. The potentials have temperature dependence, dominated mostly by the electrostatic long-range part which can be described by temperature dependent effective dielectric permittivity, leaving the short-range part of the potential thermodynamically transferable. For CG simulations of lipids a 10-bead water-free model of dimyristoylphosphatidylcholine is introduced. Four atomistic reference systems, having different lipid/water ratio are used to derive the effective bead-bead potentials, which are used for subsequent coarse-grained simulations of lipid bilayer. A significant influence of lipid/water ratio in the reference system on the properties of the simulated bilayers is noted, however it can be softened by additional angle-bending interactions. At the same time the obtained bilayers have stable structure with correct density profiles. The model provides acceptable agreement between properties of coarse-grained and atomistic bilayer, liquid crystal - gel phase transition with temperature change, as well as realistic self-aggregation behavior, which results in formation of bilayer, bicell or vesicle from a dispersed lipid solution in a large-scale simulation.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Submitted. 

 

In this paper we demonstrate and discuss the potentials of pulsed field gradient nuclear magnetic resonance (PFG NMR) at high magnetic field and high magnetic field gradients for uncovering the relationship between the structural and transport properties of soft matter systems. The reported diffusion studies are focused on room temperature ionic liquids and their mixtures with carbon dioxide or water as well as on multicomponent lipid bilayers. Both types of systems exhibit a well-defined structural organization on various length scales. Our experimental approach allows correlating this structural organization with the transport properties. The diffusion data were obtained by proton and carbon-13 PFG NMR. The experimental studies were in some cases complemented by dynamic Monte Carlo simulations.

In this paper we demonstrate and discuss the potentials of pulsed field gradient nuclear magnetic resonance (PFG NMR) at high magnetic field and high magnetic field gradients for uncovering the relationship between the structural and transport properties of soft matter systems. The reported diffusion studies are focused on room temperature ionic liquids and their mixtures with carbon dioxide or water as well as on multicomponent lipid bilayers. Both types of systems exhibit a well-defined structural organization on various length scales. Our experimental approach allows correlating this structural organization with the transport properties. The diffusion data were obtained by proton and carbon-13 PFG NMR. The experimental studies were in some cases complemented by dynamic Monte Carlo simulations.