Related papers: Reactive path ensembles within nonequilibrium stea…
In this review we consider those processes in condensed matter that involve the irreversible flow of energy between electrons and nuclei that follows from a system being taken out of equilibrium. We survey some of the more important…
Molecular systems often remain trapped for long times around some local minimum of the potential energy function, before switching to another one -- a behavior known as metastability. Simulating transition paths linking one metastable state…
Non-linear dynamical systems represent a compact, flexible, and robust tool for reactive motion generation. The effectiveness of dynamical systems relies on their ability to accurately represent stable motions. Several approaches have been…
The transport phenomena of a nonequilibrium lattice gas system are investigated. We consider a simple system that consists of two particles interacting repulsively and the potential forces acting on these particles. Under an external…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
Stochastic resetting breaks detailed balance and drives the formation of nonequilibrium steady states . Here, we consider a chain of diffusive processes $x_i(t)$ that interact unilaterally: at random time intervals, the process $x_n$…
Many interesting phenomena in nature are described by stochastic processes with irreversible dynamics. To model these phenomena, we focus on a master equation or a Fokker-Planck equation with rates which violate detailed balance. When the…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component systems which are well-studied experimentally as well…
We report the complete statistical treatment of a system of particles interacting via Newtonian forces in continuous boundary-driven flow, far from equilibrium. By numerically time-stepping the force-balance equations of a model fluid we…
Dynamical symmetries are of considerable importance in elucidating the complex behaviour of strongly interacting systems with many degrees of freedom. Paradigmatic examples are cooperative phenomena as they arise in phase transitions, where…
First-order nonequilibrium phase transitions observed in active matter, fluid dynamics, biology, climate science, and other systems with irreversible dynamics are challenging to analyze because they cannot be inferred from a simple free…
We discuss entropy production in nonequilibrium steady states by focusing on paths obtained by sampling at regular (small) intervals, instead of sampling on each change of the system's state. This allows us to study directly entropy…
Numerous aqueous systems host elements in multiple redox states, with wide ranging implications such as their influence on the formation/dissolution of minerals, water toxicity, and nutrient cycling. To uncover governing mechanisms and…
Non-typical transport phenomena may arise when randomly driven particles remain in an active relationship with the environment instead of being passive. If we attribute to Brownian particles an ability to induce alterations of the…
Anomalous kinetics of infective (e.g., autocatalytic) reactions in open, nonhyperbolic chaotic flows are important for many applications in biological, chemical, and environmental sciences. We present a scaling theory for the singular…
We introduce a class of continuum mechanical models aimed at describing the behaviour of viscoelastic fluids by incorporating concepts originated in the theory of solid plasticity. Within this class, even a simple model with constant…
We study the dynamics of a parametrically and externally driven Rayleigh-Lienard hybrid model and report the emergence of extreme bursting events due to a novel pulse-shaped explosion mechanism. The system exhibits complex periodic and…
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
Understanding transition pathways between two meta-stable states of a molecular system is crucial to advance drug discovery and material design. However, unbiased molecular dynamics (MD) simulations are computationally infeasible because of…