Related papers: Exploring glassy dynamics with Markov state models…
Non-equilibrium Markov State Modeling (MSM) has recently been proposed [Phys. Rev. E 94, 053001 (2016)] as a possible route to construct a physical theory of sliding friction from a long steady state atomistic simulation: the approach…
We study slow dynamics of particles moving in a matrix of immobile obstacles using molecular dynamics simulations. The glass transition point decreases drastically as the obstacle density increases. At higher obstacle densities, the…
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
We develop a transferable machine learning model which predicts structural relaxation from amorphous supercooled liquid structures. The trained networks are able to predict dynamic heterogeneity across a broad range of temperatures and time…
In a recent publication we established an analogy between the free energy of a hard sphere system and the energy of an elastic network [1]. This result enables one to study the free energy landscape of hard spheres, in particular to define…
Markov state models (MSMs) have been widely used to analyze computer simulations of various biomolecular systems. They can capture conformational transitions much slower than an average or maximal length of a single molecular dynamics (MD)…
Markov state models (MSMs) have been demonstrated to be a powerful method for computationally studying intramolecular processes such as protein folding and macromolecular conformational changes. In this article, we present a new approach to…
Markov state models (MSMs) are a powerful tool to analyze and coarse-grain complex dynamical data into interpretable kinetic processes. This capability is particularly important in heterogeneous catalysis, where a medley of reactants and…
Measuring, characterizing and modelling the slow dynamics of glassy soft matter is a great challenge, with an impact that ranges from industrial applications to fundamental issues in modern statistical physics, such as the glass transition…
When clustering molecular dynamics (MD) trajectories into a few metastable conformational states, the Markov state models (MSMs) assumption of timescale separation between fast intrastate fluctuations and rarely occurring interstate…
We study the dynamics of a glassy model with infinite range interactions externally driven by an oscillatory force. We find a well-defined transition in the (Temperature-Amplitude-Frequency) phase diagram between (i) a `glassy' state…
The relationship between short and long time relaxation dynamics is obtained for a simple solvable two-level energy landscape model of a glass. This is done through means of the Kramers transition theory, which arises in very natural manner…
The time evolution of the pore size distributions and mechanical properties of amorphous solids at constant pressure is studied using molecular dynamics simulations. The porous glasses were initially prepared at constant volume conditions…
We provide a theoretical perspective on the glass transition in molecular liquids at thermal equilibrium, on the spatially heterogeneous and aging dynamics of disordered materials, and on the rheology of soft glassy materials. We start with…
The understanding of glassy dynamics above the devitrification temperature of a glass remains poorly understood. Here, we use real-time AFM imaging to build a spatio-temporal map of the relaxation dynamics of a highly stable glass into its…
Adopting a $300 \, \mu$s-long molecular dynamics (MD) trajectory of the reversible folding of villin headpiece (HP35) published by D. E. Shaw Research, we recently constructed a Markov state model (MSM) of the folding process based on…
The dynamical glass transition is typically taken to be the temperature at which a glassy liquid is no longer able to equilibrate on experimental timescales. Consequently, the physical properties of these systems just above or below the…
The origins of rapid dynamical slow down in glass forming liquids in the growth of static length scales, possibly associated with identifiable structural ordering, is a much debated issue. Growth of medium range crystalline order (MRCO) has…
The existence of multiple amorphous states, or polyamorphism, remains one of the most debated phenomena in disordered matter, particularly regarding its microscopic origin and impact on glassy dynamics. Profiting of the enhanced data…
We describe our perspective on the Structural Glass Transition (SGT) problem built on the premise that a viable theory must provide a consistent picture of the dynamics and statics, which are manifested by large increase in shear viscosity…