Related papers: Estimating relaxation times from a single trajecto…
Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscles contraction. It is known that these biological molecular…
We show that time-correlation functions of arbitrary order for any random variable in a statistical dynamical system can be calculated as higher-order response functions of the mean history of the variable. The response is to a ``control…
Two-time correlations are a crucial tool to probe the dynamics of many-body systems. We use these correlation functions to study the dynamics of dissipative quantum systems. Extending the adiabatic elimination method, we show that the…
By means of molecular dynamics computer simulations we investigate the out of equilibrium relaxation dynamics of a simple glass former, a binary Lennard-Jones system, after a quench to low temperatures. We study both one time quantities and…
We study a stochastic model of protein dynamics that explicitly includes delay in the degradation. We rigorously derive the master equation for the processes and solve it exactly. We show that the equations for the mean values obtained…
A wide variety of nuclear magnetic resonance experiments rely on the prediction and analysis of relaxation processes. Recently, innovative approaches have been introduced where the sample travels through a broad range of magnetic fields in…
We use dynamic equations to derive a relation between correlation functions and response or relaxation functions in many-body systems. The relation is very general and holds both in equilibrium, when the usual fluctuation-dissipation…
An analytical prediction is established of how an isolated many-body quantum system relaxes towards its thermal long-time limit under the action of a time-independent perturbation, but still remaining sufficiently close to a reference case…
We propose a method to calculate the large deviations of current fluctuations in a class of stochastic particle systems with history-dependent rates. Long-range temporal correlations are seen to alter the speed of the large deviation…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
We study aging dynamics in two non-disordered spin models with multi-spin interactions, following a sudden quench to low temperature. The models are relevant to the physics of supercooled liquids. Their low temperature dynamics resemble…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
Slow relaxation occurs in many physical and biological systems. `Creep' is an example from everyday life: when stretching a rubber band, for example, the recovery to its equilibrium length is not, as one might think, exponential: the…
Melting of an ultrathin lubricant film confined between two atomically flat surfaces is we studied using the rheological model for viscoelastic matter approximation. Phase diagram with domains, corresponding to sliding, dry, and two types…
We have investigated the relaxational dynamics for a protein model at various temperatures. Theoretical analysis of this model in conjunction with numerical simulations suggests several relaxation regimes, including a single exponential, a…
Transition path sampling is a rare-event method that estimates state-to-state timecorrelation functions in many-body systems from samples of short trajectories. In this framework, it is proposed to bias the importance function using the…
Logarithmic oscillations superimposed on a power-law trend appear in the behavior of various complex hierarchical systems. In this paper, we study the logarithmic oscillations of relaxation curves in p-adic diffusion models that are used to…
Recovering properties of correlation functions is typically challenging. On one hand, experimentally, it requires measurements with a temporal resolution finer than the system's dynamics. On the other hand, analytical or numerical analysis…
Protein binding often involves conformational changes. Important questions are whether a conformational change occurs prior to a binding event ('conformational selection') or after a binding event ('induced fit'), and how conformational…
We study the probability distribution and the escape rate in systems with delayed dissipation that comes from the coupling to a thermal bath. To logarithmic accuracy in the fluctuation intensity, the problem is reduced to a variational…