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Dynamics in Biological Soft MaterialsHou, Jennifer Hsin-I 04 February 2015 (has links)
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
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Osmosis : a molecular dynamics computer simulation studyLion, Thomas January 2013 (has links)
Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modi cation to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modi cation on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures.
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Deformed Soft Matter under ConstraintsBertrand, Martin 13 January 2012 (has links)
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.
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Collective Behaviour of Confined Equilibrium And Non Equilibrium Soft Matter SystemsBanerjee, Rajarshi January 2016 (has links) (PDF)
Due to their diversity, soft matter systems provide a convenient platform to study a variety of physical phenomena like phase transitions and collective motion. Encompassing a wide range of equilibrium and non-equilibrium systems, they often provide significant insight into the statistical mechanics of different kinds of many-body systems. Though large scale properties of such systems are of fundamental interest in their own accord, since most experimental realizations of soft matter systems are finite sized, there is a growing need to understand the effects of confinement or boundary conditions on the collective behaviour of such systems. The primary purpose of this thesis is to study the effects of boundary conditions or confinement on both equilibrium and non-equilibrium soft matter systems via theoretical modelling. For equilibrium systems we have studied a system of colloidal particles in harmonic confinement, and for non-equilibrium systems we consider a system of self-propelled rods in both harmonic and hard wall confinement.
In Chapter 1 we first lay down some basic concepts of stochastic dynamics and Brownian motion, before discussing some of the recent results on confinement effects on colloidal systems, showing how the properties of a finite sized colloidal system can be very different from those of large, un confined systems. Thereafter turning to non-equilibrium active systems, we discuss various fundamental problems posed by these systems due to their unique ability to generate and dissipate energy on their own. We also point out some instances of observed confinement effects in such systems, such as boundary aggregation and transient hedgehog-like clusters near the boundary.
Chapter 2 deals with the effect of harmonic confinement on a finite sized colloidal assembly, where we show that such finite size effects coupled with a confining potential can give rise to special features like initial position dependent expulsion of dopant particles. First we model experimentally studied small two-dimensional colloidal assemblies trapped by a defocussed laser beam by Langevin dynamics simulations in the presence of harmonic confinement and demonstrate how the system shows a crossover from liquid state to crystalline state as a function of the stiffness of the confinement. We also show that in the crystalline state the system can be effectively modelled as a rigid body under small force perturbations. Notably, while studying the dynamics of a defect particle inside these crystallites, we found evidence for the occurrence of self purification by the crystallites.
In this process, a dopant is spontaneously expelled out of the crystallite. Surprisingly, this phenomena has a strong dependence on the initial position of the dopant, which turns out to be the consequence of the non monotonic spatial variation of the free energy of the system as a function of the dopant position. This is caused by a difference in the rate of change of internal energy and entropy with the dopant position, with the entropy decreasing faster when the dopant is closer to the centre. This can be attributed to the amount of disruption of crystalline order in the assembly due to the incommensurate dimensions of the defect particle. In order to put these results in a general perspective, we verify in the last part of this chapter that the presence of this free energy barrier is independent of the exact functional forms of the confining potential and the interaction of a defect particle with the host particles, as well as the shape and size of the defect particle.
Moving to non-equilibrium systems, we consider, in Chapter 3, the effect of harmonic and hard wall confinement on a two-dimensional system of self-propelled rods (SPRs). Though there have been very limited studies of confinement effects on such systems, existing studies are adequate to show that their behaviour near a boundary wall can be very different, e.g. formation of hedgehog like clusters near a boundary wall. First we show that for harmonic confinement small systems show polar order, which decays with system size, eventually going away for large systems. But the effect of hard wall confinement turns out to be rather different, where the system shows isotropic and clustered states depending on the values of activity and density. We construct a complete activity-density phase diagram showing four distinct phases. For high density and high activity, the rods spontaneously arrange themselves into a stable vortex structure in which the rods exhibit global radial polar order.
Surprisingly this order does not decay with system size: the radial orientation of the rods exhibit strong spatial correlation even in large systems, ruling out the possibility that the radial order is a finite-size effect. Using other geometrical shapes of the hard wall boundary, we confirm this phase to be independent of the shape of the boundary. We also demonstrate how small modifications of the boundary conditions at the hard wall can collapse the clustered and vortex phases to a global flocking phase similar to that found in earlier studies of hydrodynamic active particles under confinement.
Based on these observations, we conclude that the bulk of the system is strongly affected by the subjected boundary condition, which is rather unusual for large systems.
In Chapter 4 this thesis concludes with a summary of the main results and suggestions for future work along similar lines
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Deformed Soft Matter under ConstraintsBertrand, Martin January 2012 (has links)
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.
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Droplets as model systems for investigating 2D crystals, glasses and the growth dynamics of granular aggregatesOno-dit-Biot, Jean-Christophe January 2021 (has links)
The research presented in this thesis focusses on the experimental study of two fundamental questions: the crystal-to-glass transition and how aggregates of adhesive droplets spread on a surface. Aggregates made of lightly adhesive oil droplets are used as models for crystals or amorphous glasses. The force applied on the aggregates can be directly measured as they are compressed.
A large portion of the work focusses on the crystal-to-glass transition and tries to answer the following question: how many defects are needed in a crystal for its mechanical response to be like a glass? To answer this question, the mechanical response of a perfect mono-crystal is measured. It is found that crystals deform elastically until they fail catastrophically in a single event once the force exceeds a critical value: the yield stress. The force measured during the compression of a crystal shows a well defined number of peaks which only depends on the initial geometry of the aggregate. As defects are added (the amount of disorder increased) the number of peaks in the force measurement increases rapidly before it saturates at a value obtained for model glasses. The magnitude of the force peaks also decreases as disorder is introduced. This work concludes that even a small amount of disorder in a crystal has a significant impact on its mechanical properties.
In the second project, the spreading of a monodisperse aggregate of oil droplets is studied. Droplets are added one-by-one to a growing aggregate and the area covered on the interface is measured. It is found that after an initial 3D growth, the height of the aggregate saturates and the growth only happens in 2D along the horizontal direction. The growth is analogous to a puddle of liquid. In analogy with the capillary length in liquids, the ``granular capillary length" is introduced to characterize the balance between buoyancy acting on the droplets and the adhesion strength. The height of the aggregates, in the later stage of the growth, is set by this length scale. A method was developed to characterize the adhesion between two droplets, a key parameter in this experiment, as a function of the relevant experimental parameters. / Thesis / Doctor of Philosophy (PhD)
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Fabrication and Characterization of Multifunctional Soft Composites for Hybrid Electronic SystemsPozarycki, Tyler Anthony 17 July 2023 (has links)
There has been an ever-increasing need for soft, functional materials within areas of research such as soft robotics, flexible electronics, and wearable devices. These materials must be stretchable and/or flexible, thermally and electrically conductive, and robustly adhesive to a wide variety of substrates and surfaces. Over the past several decades, soft composites consisting of functional solid particles within an elastic matrix have been developed with the aim of achieving these properties. However, solid particulate fillers in elastomeric materials have various limitations which hinders the ability to achieve the aforementioned properties simultaneously. In this work, two novel approaches to developing soft conductive adhesives are introduced in an effort to solve mechanical, thermal, electrical, and adhesive trade-offs.
The composites developed herein utilize liquid metal (LM) inclusions and a combination of LM with solid silver (Ag) flakes within deformable polymer matrices to maintain mechanical compliance while also achieving thermal and electrical functionality. Furthermore, adhesive properties of LM composites are enhanced through a chemical anchoring technique, while the composition and microstructure of LM-Ag composites are designed to control functional and adhesive properties. There are several demonstrations throughout which show the ability to robustly integrate the novel soft composites with rigid materials and electronic components for the creation of resilient and functional hybrid electronic systems. / Master of Science / There has been an ever-increasing need for soft, functional materials within areas of research such as soft robotics, flexible electronics, and wearable devices. These materials must be stretchable and/or flexible, thermally and electrically conductive, and robustly adhesive to a wide variety of substrates and surfaces. Over the past several decades, soft composites consisting of functional solid particles within an elastic matrix have been developed with the aim of achieving these properties. However, solid particulate fillers in elastomeric materials have various limitations which hinders the ability to achieve the aforementioned properties simultaneously. In this work, two novel approaches to developing soft conductive adhesives are introduced in an effort to solve mechanical, thermal, electrical, and adhesive trade-offs.
The composites developed herein utilize liquid metal (LM) inclusions and a combination of LM with solid silver (Ag) flakes within deformable polymer matrices to maintain mechanical compliance while also achieving thermal and electrical functionality. Furthermore, adhesive properties of LM composites are enhanced through a chemical anchoring technique, while the composition and microstructure of LM-Ag composites are designed to control functional and adhesive properties. There are several demonstrations throughout which show the ability to robustly integrate the novel soft composites with rigid materials and electronic components for the creation of resilient and functional hybrid electronic systems.
Fabrication and Characterization of Multifunctional Soft Composites for Hybrid Electronic Systems Tyler A. Pozarycki (GENERAL AUDIENCE ABSTRACT) Composites are materials which are made up of two or more components with characteristics that exceed their counterparts. Steel reinforced concrete is a common example, where the steel helps to reinforce the concrete while the concrete itself gives shape to the structure. One cannot exist without the other, as the steel alone would create a meaningless skeleton and the concrete alone would not be able to withstand weights of heavier objects such as vehicles.
In recent years, soft composites have become an emerging paradigm. These materials are stretchable and flexible due to their main component typically being an elastomer, while their inner component can consist of various materials that give desired functionality. For example, iron particles can grant magnetic properties and carbon can allow the material to conduct heat and/or electricity. As a result, these materials have captured the interest of scientists and researchers in various fields such as robotics, electronics, and biomedicine.
However, there exists a unique challenge in developing such a material for applications in these areas. That is, the material needs to possess three critical properties simultaneously:
1) it must be compliant to various surfaces, meaning it must assume complex shapes such as those found on the human body, 2) it must be able to efficiently conduct electricity and heat, and 3) it must be able to adhere, or stick strongly to a variety of surfaces and materials for assembly. Typically, solving this problem has been attempted by fabricating soft composites with inner components consisting of metallic and ceramic particles, powders, or flakes. However, the use of these materials within elastomers, gels, and the like often create a composite which falls short of the aforementioned requirements, as the rigid inner structure and soft outer material are uncomplimentary to each other. Additionally, silicone elastomers and other similar materials typically do not adhere to a wide variety of surfaces, which further complicates the problem. In this work, two novel materials are produced in an effort to solve these long-standing issues. The first utilizes room-temperature liquid metal (LM) as the inner component to preserve overall material integrity while also using a chemical anchoring process to adhere the composites to several plastics and metals. The second consists of a flexible epoxy (naturally adhesive material) which incorporates both LM and silver flakes to create an as-prepared thermally and electrically conductive adhesive. Both soft composites are shown integrated with rigid electronic components and other materials to demonstrate the feasibility of using the composites to fabricate hybrid electronic systems.
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COMPUTATIONAL MULTISCALE INVESTIGATIONS OF BIOLOGICAL MOLECULESMattiotti, Giovanni 20 November 2023 (has links)
Introduction
Understanding the intricate workings of biological systems at the molecular level is crucial for unraveling the complex mechanisms that underlie Life itself. Proteins and RNA, two essential components of cellular structure and processes, exhibit remarkable structural and functional diversity. Traditional experimental techniques have provided valuable insights into their behaviors; however, they often fall short in capturing the dynamic nature of these biomolecules. Over the past few decades, multiscale molecular dynamics (MD) simulations have emerged as a powerful computational tool to bridge this gap, enabling the study of biological systems at an atomistic resolution.
My Ph.D. thesis aims to delve into the realm of multiscale MD simulations to unravel the dynamic landscape of proteins and RNA, shedding light on their folding mechanisms, conformational transitions, and functional dynamics. By integrating the principles of classical, atomistic MD and more advanced modelling techniques, such as coarse-grained models, this research endeavors to highlight and possibly propose ways to overcome the limitations of conventional simulations and offer a comprehensive understanding of the complex dynamics governing these biomolecules.
Chapter 1
The first chapter of the thesis provides a comprehensive overview of the theoretical foundations and practical aspects of classical all-atom molecular dynamics (MD) simulations. It begins with a schematic derivation of the all-atom MD equations, emphasizing the integration of electronic degrees of freedom and their contribution to the potential energy. The chapter then focuses on the energy terms utilized in all-atom force fields, highlighting their significance in accurately representing the interactions among atoms. The discussion extends to the theoretical underpinnings of thermostats, drawing from statistical mechanics principles to elucidate their role in controlling temperature during simulations. Furthermore, the use of periodic boundary conditions and the particle mesh Ewald method are discussed, highlighting their importance in simulating (or at least mimicking) large systems and accounting for long-range electrostatic interactions. By delving into these foundational concepts and techniques, this chapter establishes the groundwork for subsequent investigations in multiscale molecular dynamics simulations.
Chapter 2
The second chapter focuses on the characterization of the conformational space of the Shwachman-Bodian-Diamond syndrome (SBDS) protein, a critical component involved in cellular processes. Specifically, this research employs all-atom molecular dynamics simulations to study the wild-type SBDS and 12 missense mutations of clinical relevance. The simulations are initiated with two distinct NMR structures representing an open and a closed conformation, respectively, to capture a wide range of conformational variability. Each starting conformation is simulated for the wild type and all 12 mutations, resulting in a total of 26 simulations with a cumulative sampling time of 13$\mu s$.
The analyses of these extensive simulations provide valuable insights into the effects of missense mutations on SBDS dynamics and function. The investigation reveals a common trend among all mutations, characterized by increased residue fluctuations in the hinge I-II region. This observation suggests potential interference with the conformational changes involving the reorientation of domains II-III and the detachment of eIF6 from the 60S subunit. Furthermore, the study highlights the structural similarity of the K67E mutation to the wild type, despite a lower exposed positive charge. This finding, supported by free energy analysis, suggests that the pathological mechanism associated with this mutation may be linked more closely to a decrease in binding affinity rather than structural deformation. Additionally, the simulations of R19Q and C84R exhibit lower binding affinity specifically in closed trajectories, corroborating experimental observations regarding their potential impact on RNA binding. Moreover, K151 and R218 reveal importance in stabilizing the conformation assumed by SBDS upon binding with the 60S subunit. Notably, the dynamics-based clustering and free energy analysis highlight the distinct behavior of the K151N mutation, both in open and closed simulations, suggesting that compromised dynamics may hinder the protein's ability to stabilize a functional conformation for effective cooperation with EFL1. Collectively, this chapter contributes to our understanding of SBDS dynamics and the effects of missense mutations, paving the way for further investigations into the molecular mechanisms underlying Shwachman-Diamond syndrome.
Chapter 3
The third chapter explores the principles and applications of coarse-graining (CG) and multiscale modeling techniques in computational biophysics. After providing a theoretical foundation for CG, the chapter presents several examples of CG models employed in the research. This includes the implementation of Elastic Network Models (ENMs), which capture the essential dynamics of proteins by simplifying their atomistic representation. Additionally, the oxRNA model, designed specifically for RNA molecules, and the CANVAS multi-resolution model for proteins are introduced, showcasing their ability to capture the key features of the molecular system while significantly reducing computational complexity. Furthermore, the chapter delves into the theory of implicit solvation, as it plays a crucial role in some of the aforementioned models. Implicit solvation methods enable the efficient treatment of solvent effects without explicitly simulating water molecules, thereby reducing computational costs. Notably, the chapter sets the stage for the subsequent chapter by introducing the concept of implicit solvation, as chapter 5 presents a novel technique for implicit solvation based on Artificial Neural Networks. By providing an in-depth exploration of CG and multiscale modeling techniques, along with their associated solvation models, this chapter equips readers with the necessary tools to understand the methods developed to effectively study large-scale biological systems with reduced computational demands.
Chapter 4
The fourth chapter, extracted from the paper \textit{``In search of a dynamical vocabulary: a pipeline to construct a basis of shared traits in large-scale motions of proteins'', published in Applied Sciences, introduces a structure-based pipeline for capturing the main features of large-scale protein motions. The pipeline aims to provide a general description of protein motion, not only for those proteins whose structures are used as input but also for structurally similar proteins that were not included in the initial dataset. To demonstrate the effectiveness of the pipeline, the research applied it to a set of 116 chymotrypsin-related proteases. By employing the presented workflow, the study successfully captured dynamical features of proteins that are structurally similar to, but not part of, the input structures used to build the basis set of the dynamical space of the proteins. This allows a comprehensive understanding of the shared traits in large-scale motions, facilitating the characterization of protein dynamics beyond the limitations of specific protein structures. Overall, this chapter highlights the development and application of a structure-based pipeline that enables the extraction of essential dynamic features from proteins, contributing to the establishment of a comprehensive dynamical vocabulary in the study of protein motion.
Chapter 5
The fifth chapter introduces a novel method for implicit solvation of biomolecules in molecular dynamics simulations, leveraging the power of artificial neural networks (ANN). The chapter begins by formally describing the methodology, starting with the architecture of ANN. The latter are trained to predict the free energy of solvation for each atom in the system at every time step of the simulation. The inputs to the network are derived from special symmetry functions, which capture the local environment of each atom. The output of the ANN provides the necessary information to extract forces, which are subsequently integrated into the equations of motion. Moreover, the chapter presents the algorithmic implementation of the method into the LAMMPS molecular dynamics software package, enabling its practical application to a wide range of molecular systems. To assess the performance and accuracy of the method, three test cases are examined: the alanine dipeptide, the icosalanine (a polymer composed of 20 alanine amino acids), and a small RNA fragment containing approximately 1000 atoms. The results of the tests indicate that the method performs well in describing general macroscopic features of the molecules. However, it exhibits limitations in accurately predicting high-resolution properties, such as specific minima in the Ramachandran space of dihedral angles for the alanine dipeptide or the precise hydrogen bond network among the bases in the RNA fragment. Despite these limitations, the method demonstrates promising computational performance and scalability, making it a valuable tool for efficient implicit solvation simulations. Overall, this chapter presents a new approach to implicit solvation using artificial neural networks, showcasing its potential for accurately describing general molecular features while highlighting areas for further refinement. The method holds promise for enabling large-scale simulations with reduced computational costs, thereby expanding the scope of molecular dynamics studies.
Chapter 6
The sixth chapter presents the results of a comprehensive and multi-resolution molecular dynamics study focusing on a virion particle of the Chlorotic Cowpea Mottle Virus (CCMV) and its constituent molecules. The chapter encompasses various MD simulations, each offering unique insights into the dynamics and behavior of the viral components. The first set of simulations investigates the coarse-grained folding and relaxation of the RNA2 viral single-stranded RNA (ssRNA) fragment. The simulations start with a free, rod-like polymer chain configuration, and the subsequent folding and relaxation processes are examined. Furthermore, non-equilibrium squeezing of the folded RNA structure into a spherical region of space, mimicking the confinement within the capsid, is explored. These simulations are aimed at shedding light on the structural and dynamic aspects of viral RNA during the self-assembly process of the virus. The chapter then proceeds to present multi-resolution equilibrium simulations of a trimer, which consists of three capsid molecules. The trimer is studied using five different approaches: all-atom representation in explicit solvent, all-atom representation in implicit solvent employing Debye-Huckel electrostatics, and three different applications of the CANVAS model. The latter is a model multi-resolution for proteins, developed in my group, which combines atomistic force fields together with an elastic network model to describe protein dynamics with manually deployed levels of resolution. These simulations allow for a comprehensive analysis of the trimer's dynamics and interactions, highlighting the influence of different models on the observed behavior, as well as testing the applicability of the CANVAS model to this kind of system. Additionally, all-atom simulations are performed for both the capsid and the virion, which includes the RNA2 fragment within the capsid, in explicit solvent. These simulations provide detailed information about the structural and dynamic properties of the viral capsid and the interactions between the capsid and the encapsulated RNA2 fragment. By leveraging multi-resolution approaches and conducting various simulations at different levels of detail, this chapter offers a comprehensive understanding of the RNA dynamics, folding, relaxation, and interactions within the virion particle of CCMV. These findings contribute to our knowledge of viral assembly and the behavior of viral constituents, facilitating further insights into the functioning and stability of viral systems.
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Rearrangement of 2D clusters of droplets under compression: from crystal to glassOno-dit-Biot, Jean-Christophe January 2017 (has links)
Emulsions and colloidal suspensions have various industrial applications but are also used in laboratories as model systems for studying the different phases of matter. They are versatile as their nature, size and inter-particle interactions are easily tuneable. These systems are perfect for studying questions such as the phase transition. In this thesis, we investigate the transition from an ordered crystal to a disordered glass. Perfectly ordered crystals are modeled by clusters of highly monodisperse droplets. We study the transition toward a glassy system by mixing two monodisperse populations of droplets in different proportions. The clusters are compressed between two thin glass rods, one of which is a force transducer. The forces within the clusters are directly measured and used as an indicator of the composition of the cluster. Upon introduction of disorder, the number of peaks in the force measurement increases drastically. We find that the way the energy is dissipated in the cluster is valuable information to characterize the crystal-to-glass transition.
In addition to the experimental study of the crystal-to-glass transition, we have developed an analytical model that is in full agreement with the experimental observations. A crystal is modeled as an assembly of Hookean springs that will store elastic energy until it reaches a fracture point. We are able to predict the number of peaks in the force measurements when defects are introduced using simple geometric arguments. From this prediction, the way the work is dissipated in a given transition can be predicted. / Thesis / Master of Science (MSc)
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Elastocapillary interactions between liquids and thin solid films under tensionSchulman, Rafael D January 2018 (has links)
PhD Thesis / In this thesis, experiments are described which study the elastocapillary interactions between liquids and taut solid films. The research employs contact angle measurements to elucidate how capillary forces deform compliant solid structures, but also to attain fundamental insight into the energy of interfaces involving amorphous solids.
The majority of the work focuses on how capillary deformations of compliant elastic membranes introduce modifications to descriptions of common wetting phenomena. Particular focus is given to studying partial wetting in the presence of compliant membranes in various geometries: droplet on a free-standing membrane, droplet capped by a membrane but sessile on a rigid substrate, and droplet pressed between two free-standing membranes. The mechanical tension in these membranes is found to play an equivalent role as the interfacial tensions. As such, the mechanical tension is incorporated into Young-Dupre's law (capped droplet on a rigid substrate) or Neumann's triangle (droplet on free-standing membrane), leading to departures from the classical wetting descriptions. In addition, one study is conducted investigating how viscous dewetting is affected by the liquid film being capped by an elastic film. The results of this study show that the dewetting rate and rim morphology are dictated by the elastic tension.
Another important aspect of the work is demonstrating the utility of anisotropic membrane tension for liquid patterning. A biaxial tension is shown to produce droplets and dewetting holes which are elongated along the high tension direction. The compliant membrane geometry can also be designed to produce droplets and holes with square morphology.
In the final project, the surface energy of strained glassy and elastomeric solids is studied. Glassy solids are shown to have strain-dependent surface energies, which implies that surface energy (energy per unit area) and surface stress (force per unit length) are not equivalent for this class of materials by virtue of the Shuttleworth equation. On the other hand, this study provides strong evidence that surface energy and surface stress are equivalent for elastomeric interfaces. / Thesis / Doctor of Philosophy (PhD)
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