66 research outputs found

    Microstructural Rearrangements and their Rheological Implications in a Model Thixotropic Elastoviscoplastic Fluid

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    We identify the sequence of microstructural changes that characterize the evolution of an attractive particulate gel under flow and discuss their implications on macroscopic rheology. Dissipative particle dynamics is used to monitor shear-driven evolution of a fabric tensor constructed from the ensemble spatial configuration of individual attractive constituents within the gel. By decomposing this tensor into isotropic and nonisotropic components we show that the average coordination number correlates directly with the flow curve of the shear stress versus shear rate, consistent with theoretical predictions for attractive systems. We show that the evolution in nonisotropic local particle rearrangements are primarily responsible for stress overshoots (strain-hardening) at the inception of steady shear flow and also lead, at larger times and longer scales, to microstructural localization phenomena such as shear banding flow-induced structure formation in the vorticity direction

    Temperature in and out of equilibrium: a review of concepts, tools and attempts

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    We review the general aspects of the concept of temperature in equilibrium and non-equilibrium statistical mechanics. Although temperature is an old and well-established notion, it still presents controversial facets. After a short historical survey of the key role of temperature in thermodynamics and statistical mechanics, we tackle a series of issues which have been recently reconsidered. In particular, we discuss different definitions and their relevance for energy fluctuations. The interest in such a topic has been triggered by the recent observation of negative temperatures in condensed matter experiments. Moreover, the ability to manipulate systems at the micro and nano-scale urges to understand and clarify some aspects related to the statistical properties of small systems (as the issue of temperature's "fluctuations"). We also discuss the notion of temperature in a dynamical context, within the theory of linear response for Hamiltonian systems at equilibrium and stochastic models with detailed balance, and the generalised fluctuation-response relations, which provide a hint for an extension of the definition of temperature in far-from-equilibrium systems. To conclude we consider non-Hamiltonian systems, such as granular materials, turbulence and active matter, where a general theoretical framework is still lacking.Comment: Review article, 137 pages, 12 figure

    Extended stochastic dynamics: theory, algorithms, and applications in multiscale modelling and data science

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    This thesis addresses the sampling problem in a high-dimensional space, i.e., the computation of averages with respect to a defined probability density that is a function of many variables. Such sampling problems arise in many application areas, including molecular dynamics, multiscale models, and Bayesian sampling techniques used in emerging machine learning applications. Of particular interest are thermostat techniques, in the setting of a stochastic-dynamical system, that preserve the canonical Gibbs ensemble defined by an exponentiated energy function. In this thesis we explore theory, algorithms, and numerous applications in this setting. We begin by comparing numerical methods for particle-based models. The class of methods considered includes dissipative particle dynamics (DPD) as well as a newly proposed stochastic pairwise Nosé-Hoover-Langevin (PNHL) method. Splitting methods are developed and studied in terms of their thermodynamic accuracy, two-point correlation functions, and convergence. When computational efficiency is measured by the ratio of thermodynamic accuracy to CPU time, we report significant advantages in simulation for the PNHL method compared to popular alternative schemes in the low-friction regime, without degradation of convergence rate. We propose a pairwise adaptive Langevin (PAdL) thermostat that fully captures the dynamics of DPD and thus can be directly applied in the setting of momentum-conserving simulation. These methods are potentially valuable for nonequilibrium simulation of physical systems. We again report substantial improvements in both equilibrium and nonequilibrium simulations compared to popular schemes in the literature. We also discuss the proper treatment of the Lees-Edwards boundary conditions, an essential part of modelling shear flow. We also study numerical methods for sampling probability measures in high dimension where the underlying model is only approximately identified with a gradient system. These methods are important in multiscale modelling and in the design of new machine learning algorithms for inference and parameterization for large datasets, challenges which are increasingly important in "big data" applications. In addition to providing a more comprehensive discussion of the foundations of these methods, we propose a new numerical method for the adaptive Langevin/stochastic gradient Nosé-Hoover thermostat that achieves a dramatic improvement in numerical efficiency over the most popular stochastic gradient methods reported in the literature. We demonstrate that the newly established method inherits a superconvergence property (fourth order convergence to the invariant measure for configurational quantities) recently demonstrated in the setting of Langevin dynamics. Furthermore, we propose a covariance-controlled adaptive Langevin (CCAdL) thermostat that can effectively dissipate parameter-dependent noise while maintaining a desired target distribution. The proposed method achieves a substantial speedup over popular alternative schemes for large-scale machine learning applications

    Time-Rate-Transformation framework for targeted assembly of short-range attractive colloidal suspensions

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    The aggregation of attractive colloids has been extensively studied from both theoretical and experimental perspectives as the fraction of solid particles is changed, and the range, type and strength of attractive or repulsive forces between particles varies. The resulting gels consisting of disordered assemblies of attractive colloidal particles, have also been investigated with regards to percolation, phase separation, and the mechanical characteristics of the resulting fractal networks. Despite tremendous progress in our understanding of the gelation process, and the exploration of different routes for arresting the dynamics of attractive colloids, the complex interplay between convective transport processes and many-body effects in such systems has limited our ability to drive the system towards a specific configuration. Here we study a model attractive colloidal system over a wide range of particle characteristics and flow conditions undergoing aggregation far from equilibrium. The complex multiscale dynamics of the system can be understood using a Time-Rate-Transformation diagram adapted from understanding of materials processing in block copolymers, supercooled liquids and much stiffer glassy metals to direct targeted assembly of attractive colloidal particles

    Nonequilibrium and irreversibility

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    The booklet contain an overview on selected recent developments in nonequilibrium statistical mechanics and chaos theory: SRB distributions, chaotic hypothesis, fluctuation theorem, proposals for tests and applications to granular materials, fluidodynamics, irreversibility of quasi static processes. In appendices examples of the kind of technical work necessary for actual construction of nonequilibrium stationary states.Comment: XI+247 pages, latex, V.2 with new references and typos eliminated V.3 references added, further typos eliminated, style adjustment

    Molecular Dynamics Simulation

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    Condensed matter systems, ranging from simple fluids and solids to complex multicomponent materials and even biological matter, are governed by well understood laws of physics, within the formal theoretical framework of quantum theory and statistical mechanics. On the relevant scales of length and time, the appropriate ‘first-principles’ description needs only the Schroedinger equation together with Gibbs averaging over the relevant statistical ensemble. However, this program cannot be carried out straightforwardly—dealing with electron correlations is still a challenge for the methods of quantum chemistry. Similarly, standard statistical mechanics makes precise explicit statements only on the properties of systems for which the many-body problem can be effectively reduced to one of independent particles or quasi-particles. [...

    Targeting Tight Junctions in Nanomedicine: a Molecular Modeling Perspective

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    Molecular Dynamics Simulations of Claudin Paracellular Channel

    Physics of the Liquid and Supercritical States of Matter.

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    PhD Theses.The liquid and supercritical states of matter are respectively the least understood and most misunderstood states of ordinary matter, from a theoretical view. The work exposited in this thesis aims to elucidate the nature of the supercritical state and its relationship to the liquid and gas states which ank it on the phase diagram. Contrary to the belief of the supercritical state as lacking transitions, these works present several transitions to be found in this state. This is done with molecular dynamics simulations data. We begin with structural crossovers discovered in the two most important supercritical uids from an industrial point of view: water and carbon dioxide. These crossovers coincide with calculations of the dynamical crossover called the Frenkel line, which marks termination of oscillatory molecular motion, giving way to purely di usive motion. These structural crossovers across the Frenkel line demonstrate the universal applicability of the Frenkel picture of uids. I then perform simulations of argon to calculate the dynamical instability of its supercritical state. Using tools from chaos theory, I show that the dynamical instability undergoes a crossover at the Frenkel line, which demonstrates that the supercritical state sports a transition in the fundamental geometry of phase space. The \c"-transition is presented next. This is a universal interrelation between the dynamics and thermodynamics across the supercritical state and a transition which provides an unambiguous separation of liquidlike and gaslike states in several di erent supercritical uids. This discovery was completely unanticipated and is like nothing else ever seen in the supercritical state. The \c"-transition is suggestive of a phase transition, and the thesis concludes with the beginnings of a search for it. The heat capacity is calculated from molecular dynamics simulations of argon with unprecedented precision, and other methods used to nd a phase transition are discussed

    Exoteric effects at nanoscopic interfaces - Uncommon negative compressibility of nanoporous materials and unexpected cavitation at liquid/liquid interfaces

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    This PhD thesis is devoted to the investigation of some peculiar effects happening at nanoscopic interfaces between immiscible liquids or liquids and solids via molecular dynamics simulations. The study of the properties of interfaces at a nanoscopic scale is driven by the promise of many interesting technological applications, including: a novel technology for developing both eco-friendly energy storage devices in the form of mechanical batteries, as well as energy dissipation systems and, in particular, shock absorbers for the automotive market; biomedical applications related to cavitation, such as High-Intensity Focused Ultrasound (HIFU) ablation of cancer tissues and localised drug delivery, and many more. The kinetics of phenomena taking places at these scales is typically determined by large free-energy barriers separating the initial and final states, and even intermediate metastable states, when they are present. Because of such barriers, the phenomena we are interested in are "rare events", i.e. the system attempts the crossing of the barrier(s) many times before finally succeeding when an energy fluctuation makes it possible. At the same time, the magnitude of the barrier is determined by the energetics and dynamics of atoms, which forces us to model the system by taking into account both the femtosecond atomistic timescale and the timescale of the relevant phenomena, typically exceeding the former by several orders of magnitude. These longer timescales are inaccessible to standard molecular dynamics, so, in order to tackle this issue, advanced MD techniques need to be employed. The thesis is divided into two parts, corresponding to the main lines of research investigated, which are (I) the interfaces between water and complex nanoporous solids, and (II) planar solid-liquid and liquid-liquid interfaces. Anticipating some results, atomistic simulations helped uncovering the microscopic mechanism behind the (incredibly rare!) giant negative compressibility exhibited by the ZIF-8 metal organic framework (MOF) upon water intrusion. Molecular dynamics simulations also supported experimental results showing how it is possible to change the intermediate intrusion-extrusion performance of ZIF-8 by changing its grain morphology and arrangement, from a fine powder to compact monolith. Free-energy MD calculations allowed to explain the exceptional stability of surface nanobubbles in water, at undersaturated conditions, on a surprisingly wide variety of substrates, characterized by disparate hydrophobicities and gas affinities; and yet, how they catastrophically destabilize in organic solvents. Finally, through simulations, some light was shed upon the working mechanism behind the novelly discovered phenomenon of how the interface between two immiscible liquids can act as a nucleation site for cavitation

    Complexity, Emergent Systems and Complex Biological Systems:\ud Complex Systems Theory and Biodynamics. [Edited book by I.C. Baianu, with listed contributors (2011)]

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    An overview is presented of System dynamics, the study of the behaviour of complex systems, Dynamical system in mathematics Dynamic programming in computer science and control theory, Complex systems biology, Neurodynamics and Psychodynamics.\u
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