66 research outputs found
Microstructural Rearrangements and their Rheological Implications in a Model Thixotropic Elastoviscoplastic Fluid
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
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
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
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
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
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
Molecular Dynamics Simulations of Claudin Paracellular Channel
Physics of the Liquid and Supercritical States of Matter.
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
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)]
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
- …