Related papers: Exploring glassy dynamics with Markov state models…
Using two extremely different models of glass formers in two and three dimensions we demonstrate how to encode the subtle changes in the geometric rearrangement of particles during the scenario of the glass transition. We construct a…
We prepare metastable glassy states in a model glass-former made of Lennard-Jones particles by sampling biased ensembles of trajectories with low dynamical activity. These trajectories form an inactive dynamical phase whose `fast'…
We consider two systems of Ising spins with plaquette interactions. They are simple models of glasses which have dual representations as kinetically constrained systems. These models allow an explicit analysis using the mosaic, or entropic…
We numerically study the potential energy landscape of a fragile glassy system and find that the dynamic crossover corresponding to the glass transition is actually the effect of an underlying geometric transition caused by a qualitative…
When a liquid melt is cooled, a glass or phase transition can be obtained depending on the cooling rate. Yet, this behavior has not been clearly captured in energy landscape models. Here a model is provided in which two key ingredients are…
Many systems, including polymers and molecular liquids, when adequately cooled and/or compressed, solidify into a disordered solid, i.e., a glass. The~transition is not abrupt, featuring progressive decrease of the microscopic mobility and…
We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a non-equilibrium steady state. We apply this method to study the globule-stretch transition of a single…
Cell motion inside dense tissues governs many biological processes, including embryonic development and cancer metastasis, and recent experiments suggest that these tissues exhibit collective glassy behavior. To make quantitative…
In this note we discuss metastability in a long-but-finite range disordered model for the glass transition. We show that relaxation is dominated by configuration belonging to metastable states and associate an in principle computable…
Apart from not having crystallized, supercooled liquids can be considered as being properly equilibrated and thus can be described by a few thermodynamic control variables. In contrast, glasses and other amorphous solids can be arbitrarily…
Molecular dynamics simulations are performed to investigate heterogeneous dynamics in amorphous glassy materials under oscillatory shear strain. We consider three-dimensional binary Lennard-Jones mixture well below the glass transition…
A simple monatomic system in two dimensions with a double-well interaction potential is investigated in a wide range of temperature by molecular dynamics simulation. The system is melted and equilibrated well above the melting temperature,…
Molecular Dynamics (MD) is a powerful computational microscope for probing protein functions. However, the need for fine-grained integration and the long timescales of biomolecular events make MD computationally expensive. To address this,…
We present results from molecular dynamics simulations exploring the supercooled dynamics of the Gaussian Core Model in the low- and intermediate-density regimes. In particular, we discuss the transition from the low-density…
We consider damage spreading transitions in the framework of mode-coupling theory. This theory describes relaxation processes in glasses in the mean-field approximation which are known to be characterized by the presence of an exponentially…
It is now possible to routinely perform atomistic simulations at the microsecond timescale. In the present work, we exploit this for a model binary Lennard-Jones glass to study structural relaxation at a timescale spanning up to 80…
We explore the glassy dynamics of soft colloids using microgels and charged particles interacting by steric and screened Coulomb interactions, respectively. In the supercooled regime, the structural relaxation time $\tau_\alpha$ of both…
Soft Glassy Materials (SGM) consist in dense amorphous assemblies of colloidal particles of multiple shapes, elasticity, and interactions, which confer upon them solid-like properties at rest. They are ubiquitously encountered in modern…
We study the viscoelastic response of amorphous polymers using theory and simulations. By accounting for internal stresses and considering instantaneous normal modes (INMs) within athermal non-affine theory, we make parameter-free…
Many state of the art methods for the thermodynamic and kinetic characterization of large and complex biomolecular systems by simulation rely on ensemble approaches, where data from large numbers of relatively short trajectories are…