Related papers: Estimating relaxation times from a single trajecto…
The objective of this work is to show that adiabatic processes can be very similar to isothermal ones. First, we show that the criteria for the compatibility of linear-response theory with the Second Law of Thermodynamics for thermally…
We use computer simulations to study the dynamics of a physical gel at high densities where gelation and the glass transition interfere. We report and provide detailed physical understanding of complex relaxation patterns for time…
Understanding how systems respond to external perturbations is a fundamental challenge in physics, particularly for non-equilibrium and non-stationary processes. The fluctuation-dissipation theorem provides a complete framework for…
In these lecture notes, the basic principles of stochastic thermodynamics are developed starting with a closed system in contact with a heat bath. A trajectory undergoes Markovian transitions between observable meso-states that correspond…
The classical fluctuation-dissipation theorem predicts the average response of a dynamical system to an external deterministic perturbation via time-lagged statistical correlation functions of the corresponding unperturbed system. In this…
When two isolated system are brought in contact, they relax to equilibrium via energy exchange. In another setting, when one of the systems is driven and the other is large, the first system reaches a steady-state which is not described by…
Extensive time-series encoding the position of particles such as viruses, vesicles, or individual proteins are routinely garnered in single-particle tracking experiments or supercomputing studies. They contain vital clues on how viruses…
We study the behavior of a moving wall in contact with a particle gas and subjected to an external force. We compare the fluctuations of the system observed in the microcanonical and canonical ensembles, at varying the number of particles.…
Understanding the dynamic behavior of proteins is critical to elucidating their functional mechanisms, yet generating realistic, temporally coherent trajectories of protein ensembles remains a significant challenge. In this work, we…
In systems of diffusing particles, we investigate large deviations of a time-averaged measure of clustering around one particle. We focus on biased ensembles of trajectories, which realise large-deviation events. The bias acts on a single…
We compare the spatial correlations of bond-breaking events and bond-orientational relaxation in a model two-dimensional liquid undergoing Newtonian dynamics. We find that the relaxation time of the bond-breaking correlation function is…
We investigate the dynamic relaxation of random walks on temporal networks by focusing in the recently proposed activity driven model [Perra \textit{et al.} Sci. Rep. srep00469 (2012)]. For realistic activity distributions with a power-law…
The hydrodynamic part of the velocity autocorrelation function of a granular fluid in the homogeneous cooling state has been calculated by using mode-coupling theory for a finite system with periodic boundary conditions. The existence of…
Stochastic processes are commonly used models to describe dynamics of a wide variety of nonequilibrium phenomena ranging from electrical transport to biological motion. The transition matrix describing a stochastic process can be regarded…
In this work, we provide a method which allows to compute exactly the multipoint and multi-time correlation functions of a one-dimensional stochastic model of dimer adsorption-evaporation with random (uncorrelated) initial states. In…
The dissipation function for a system is defined as the natural logarithm of the ratio between probabilities of a trajectory and its time-reversed trajectory, and its probability distribution follows a well-known relation called the…
The linear response to temperature changes is derived for systems with overdamped stochastic dynamics. Holding both in transient and steady state conditions, the results allow to compute nonequilibrium thermal susceptibilities from…
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…
Hydrated proteins undergo a transition in the deeply supercooled regime, which is attributed to rapid changes in hydration water and protein structural dynamics. Here, we investigate the nanoscale stress relaxation in hydrated lysozyme…
The relaxation time approximation (RTA) is a well known method of describing the time evolution of a statistical ensemble by linking distributions of the variables of interest at different stages of their temporal evolution. We show that if…