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Rare transitions between long-lived metastable states underlie a great variety of physical, chemical and biological processes. Our quantitative understanding of reactive mechanisms has been driven forward by the insights of transition state…
A major impediment to a more complete understanding of barrier crossing and other single-molecule processes is the inability to directly visualize the trajectories and dynamics of atoms and molecules in reactions. Rather, the kinetics are…
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the…
Nonlinear dynamical systems may be exposed to tipping points, critical thresholds at which small changes in the external inputs or in the systems parameters abruptly shift the system to an alternative state with a contrasting dynamical…
The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…
Reaction dynamics involving subdiffusive species is an interesting topic with only few known results, especially when the motion of different species is characterized by different anomalous diffusion exponents. Here we study the reaction…
We explore the classical dynamics of atoms in an optical dipole trap formed by two identical Gaussian beams propagating in perpendicular directions. The phase space is a mixture of regular and chaotic orbits, the later becoming dominant as…
Stochastic systems often exhibit multiple viable metastable states that are long-lived. Over very long timescales, fluctuations may push the system to transition between them, drastically changing its macroscopic configuration. In realistic…
Transition State Theory is a central cornerstone in reaction dynamics. Its key step is the identification of a dividing surface that is crossed only once by all reactive trajectories. This assumption is often badly violated, especially when…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
The thermal decay of linear chains from a metastable state is investigated. A crossover from rigid to elastic decay occurs when the number of particles, the single particle energy barrier or the coupling strength between the particles is…
We explore the dynamical large-deviations of a lattice heteropolymer model of a protein by means of path sampling of trajectories. We uncover the existence of non-equilibrium dynamical phase-transitions in ensembles of trajectories between…
A simple model of oscillator chain with dynamical traps and additive white noise is considered. Its dynamics was studied numerically. As demonstrated, when the trap effect is pronounced nonequilibrium phase transitions of a new type arise.…
We analyze the dynamics of a paramagnetic, dipolar molecule in a generic "magneto-electrostatic'' trap where both magnetic and electric fields may be present. The potential energy that governs the dynamics of the molecules is found using a…
We study metastability and nucleation for the Blume-Capel model: a ferromagnetic nearest neighbour two-dimensional lattice system with spin variables taking values in -1,0,+1. We consider large but finite volume, small fixed magnetic field…
We study the time-averaged flow in a model of particles that randomly hop on a finite directed graph. In the limit as the number of particles and the time window go to infinity but the graph remains finite, the large-deviation rate…
We report optical trapping and transport of nanoparticles in a moving interference pattern in hollow-core photonic crystal fiber at atmospheric pressure, when competition between trapping and drag forces causes the particle velocity to…
A general system of particles (of one or several species) on a one dimensional lattice with boundaries is considered. Two general behaviors of such systems are investigated. The stationary behavior of the system, and the dominant way of the…
This work is devoted to the investigation of the most probable transition time between metastable states for stochastic dynamical systems. Such a system is modeled by a stochastic differential equation with non-vanishing Brownian noise, and…
We study various models of independent particles hopping between energy `traps' with a density of energy barriers $\rho(E)$, on a $d$ dimensional lattice or on a fully connected lattice. If $\rho(E)$ decays exponentially, a true dynamical…