Related papers: Transition in relaxation paths in allosteric molec…
In these four lectures I describe basic ideas and methods applicable to both classical and quantum systems displaying slow relaxation and non-equilibrium dynamics. The first half of these notes considers classical systems, and the second…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
The dramatic dynamic slowing down associated with the glass transition is considered by many to be related to the existence of a static length scale that grows when temperature decreases. Defining, identifying and measuring such a length is…
The glass transition is considered within two toys models, a mean field spin glass and a directed polymer in a correlated random potential. In the spin glass model there occurs a dynamical transition, where the system condenses in a state…
Allostery is a fundamental mechanism of protein regulation and is commonly interpreted as modulating enzymatic activity or product abundance. Here we show that this view is incomplete. Using a stochastic model of allosteric regulation…
A theoretical analysis [Angelani et al., Phys. Rev. Lett. 96, 065702 (2006)] predicts glassy behaviour of light in a nonlinear random medium. This implies slow dynamics related to the presence of many metastable states. We consider very…
The glass transition, extensively studied in dense fluids, polymers, or colloids, corresponds to a dramatic evolution of equilibrium transport coefficients upon a modest change of control parameter, like temperature or pressure. A similar…
In spin glass models one can remove minimization of free energy by some order parameter. One can consider hierarchy of order parameters. It is possible to divide energy among these parts. We can consider relaxation process in glass system…
We simulate the dynamics of a disordered interacting spin chain subject to a quasi-periodic time-dependent drive, corresponding to a stroboscopic Fibonacci sequence of two distinct Hamiltonians. Exploiting the recursive drive structure, we…
We consider the non-equilibrium dynamics of the East model, a linear chain of 0-1 spins evolving under a simple Glauber dynamics in the presence of a kinetic constraint which forbids flips of those spins whose left neighbor is 1. We focus…
The nature of polyamorphism and amorphous-to-amorphous transition is investigated by means of an exactly solvable model with quenched disorder, the spherical s+p multi-spin interaction model. The analysis is carried out in the framework of…
We describe a phase transition that gives rise to structurally non-trivial states in a two-dimensional ordered network of particles connected by harmonic bonds. Monte Carlo simulations reveal that the network supports, apart from the…
Slow dynamics in disordered materials prohibits direct simulation of their rich nonequilibrium behavior at large scales. "Patchwork dynamics" is introduced to mimic relaxation over a very broad range of time scales by equilibrating or…
We apply a generalized Kibble-Zurek out-of-equilibrium scaling ansatz to simulated annealing when approaching the spin-glass transition at temperature $T=0$ of the two-dimensional Ising model with random $J= \pm 1$ couplings. Analyzing the…
We use large scale computer simulations of a glass-forming liquid in which a fraction c of the particles has been permanently pinned. We find that the relaxation dynamics shows an exponential dependence on c. This result can be rationalized…
We consider the quench dynamics of a two-dimensional quantum dimer model and determine the role of its kinematic constraints. We interpret the non-equilibrium dynamics in terms of the underlying equilibrium phase transitions consisting of a…
From molecular, cellular, to ecological systems, the modeling of biological processes often stands on the assumption that fast components immediately reach the equilibrium at each moment (quasi-steady state) and only slow components govern…
For several atomistic models of glass formers, at conditions below their glassy dynamics onset temperatures, ${T_\mathrm{o}}$, we use importance sampling of trajectory space to study the structure, statistics and dynamics of excitations…
We study the problem of glassy relaxations in the presence of an external field in the highly controlled context of a spin-glass simulation. We consider a small spin glass in three dimensions (specifically, a lattice of size L=8, small…
Spatiotemporal pattern formation in a product-activated enzymic reaction at high enzyme concentrations is investigated. Stochastic simulations show that catalytic turnover cycles of individual enzymes can become coherent and that complex…