Related papers: Time-Varying Energy Landscapes and Temperature pat…
We examine the structural relaxation of glassy materials at finite temperatures, considering the effect of activated rearrangements and long-range elastic interactions. Our three-dimensional mesoscopic relaxation model shows how the…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
Under certain conditions, the dynamics of coarse-grained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in…
We combine the swap Monte Carlo algorithm to long multi-CPU molecular dynamics simulations to analyse the equilibrium relaxation dynamics of model supercooled liquids over a time window covering ten orders of magnitude for temperatures down…
This work extends the results of the recently developed theory of a rather complete thermodynamic formalism for discrete-state, continuous-time Markov processes with and without detailed balance. We aim at investigating the question that…
We employ the Distance Matrix method to investigate metabasin dynamics in supercooled water. We find that the motion of the system consists in the exploration of a finite region of configuration space (enclosing several distinct local…
In this article we introduce the ultrametric networks which are p-adic continuous analogues of the standard Markov state models constructed using master equations. A p-adic transition network (or an ultrametric network) is a model of a…
We present a mean-field theory of a coarse-grained model of a super-cooled liquid in which relaxation occurs via local plastic rearrangements. Local relaxation can be induced by thermal fluctuations or by the long-range elastic consequences…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
In this work we revisit the description of dynamics based on the concepts of metabasins and activation in mildly supercooled liquids via the analysis of the dynamics of a paradigmatic glass former between its onset temperature $T_{o}$ and…
To solve a long-standing problem of condensed matter physics with determining a proper description of the thermodynamic evolution of the time scale of molecular dynamics near the glass transition, we extend the well-known Adam-Gibbs model…
Strong changes in bulk properties, such as modulus and viscosity, are observed near the glass transition temperature, T_{g}, of amorphous materials. For more than a century, intense efforts have been made to define a microscopic origin for…
As shown by early studies on mean-field models of the glass transition, the geometrical features of the energy landscape provide fundamental information on the dynamical transition at the Mode-Coupling temperature $T_d$. We show that active…
A master equation describing the evolution of averaged molecular state occupancies in molecular systems where alternation of molecular energy levels is caused by discrete dichotomous and trichotomous stochastic fields, is derived. This…
In this Letter, we investigate how changes in the system entropy influence the characteristic time scale of the system molecular dynamics near the glass transition. Independently of any model of thermodynamic evolution of the time scale,…
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…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
The Adam-Gibbs view of the glass transition relates the relaxation time to the configurational entropy, which goes continuously to zero at the so-called Kauzmann temperature. We examine this scenario in the context of a dimer model with an…
Elastic models of the glass transition relate the relaxation dynamics and the elastic properties of structural glasses. They are based on the assumption that the relaxation dynamics occurs through activated events in the energy landscape…
Understanding the realization of thermal equilibrium through the thermalization process in a many-body system is a fundamental and complex scientific question, bridging thermodynamics and classical dynamics and connecting to a host of…