Related papers: Exploring glassy dynamics with Markov state models…
Active glasses refer to a class of driven non-equilibrium systems that share remarkably similar dynamical behavior as conventional glass-formers in equilibrium. Glass-like dynamical characteristics have been observed in various biological…
We present an analytical and numerical study of a nonlinear diffusion model which describes density relaxation of loosely packed particles under gravity and weak random (thermal) vibration, and compare the results with Monte Carlo…
The topography of the free energy landscape in phase space of a dense hard sphere system characterized by a discretized free energy functional of the Ramakrishnan-Yussouff form is investigated numerically using a ``microcanonical'' Monte…
We use molecular dynamics simulation to study the relationship between structure and dynamics in supercooled binary Lennard--Jones nanoparticles over a range of particle sizes. The glass transition temperature of the nanoparticles is found…
The developing field of stochastic thermodynamics extends concepts of macroscopic thermodynamics such as entropy production and work to the microscopic level of individual trajectories taken by a system through phase space. The scheme…
We review the use of kinetically constrained models (KCMs) for the study of dynamics in glassy systems. The characteristic feature of KCMs is that they have trivial, often non-interacting, equilibrium behaviour but interesting slow dynamics…
An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this ``inherent…
The notion of complex energy landscape underpins the intriguing dynamical behaviors in many complex systems ranging from polymers, to brain activity, to social networks and glass transitions. The spin glass state found in dilute magnetic…
Markov State Models (MSM) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations, for example…
We study the Metropolis dynamics of the simplest mean-field spin glass model, the Random Energy Model. We show that this dynamics exhibits aging by showing that the properly rescaled time change process between the Metropolis dynamics and a…
The understanding of thermodynamic glass transition has been hindered by the lack of proper models beyond mean-field theories. Here, we propose a three-dimensional lattice glass model on a simple cubic lattice that exhibits the typical…
We present a simple model of a vibrated box of sand, and discuss its dynamics in terms of two parameters reflecting static and dynamic disorder respectively. The fluidised, intermediate and frozen (`glassy') dynamical regimes are…
Despite the use of glasses for thousands of years, the nature of the glass transition is still mysterious. On approaching the glass transition, the growth of dynamic heterogeneity has long been thought to play a key role in explaining the…
Dynamic heterogeneity has often been modeled by assuming that a single-particle observable, fluctuating at a molecular scale, is influenced by its coupling to environmental variables fluctuating on a second, perhaps slower, time scale.…
We report the combined results of molecular dynamics simulations and theoretical calculations concerning various dynamical arrest transitions in a model system representing a dipolar fluid, namely, N (softcore) rigid spheres interacting…
The well-established methodology for the estimation of hidden semi-Markov models (HSMMs) as hidden Markov models (HMMs) with extended state spaces is further developed to incorporate covariate influences across all aspects of the state…
Computer simulations of a model glass-forming system are presented, which are particularly sensitive to the correlation between the dynamics and the topography of the potential energy landscape. This analysis clearly reveals that in the…
The low-temperature quasi-universal behavior of amorphous solids has been attributed to the existence of spatially-localized tunneling defects found in the low-energy regions of the potential energy landscape. Computational models of…
We identify a link between the glass transition and percolation of mobile regions in configuration space. We find that many hallmarks of glassy dynamics, for example stretched-exponential response functions and a diverging structural…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…