Related papers: Transition path dynamics of a nanoparticle in a bi…
Interacting many-particle systems can self-organize into a rich variety of crystalline structures. While symmetry provides a powerful framework for predicting whether transitions between crystal states are continuous or discontinuous,…
A semiclassical method of complex trajectories for the calculation of the tunneling exponent in systems with many degrees of freedom is further developed. It is supplemented with an easily implementable technique, which enables one to…
Transport of nanoscale objects in complex, structured environments plays a key role in a wide range of processes, from biomolecular dynamics in extracellular spaces to transport in porous materials such as filters and catalysts. While…
We present a method to study rare nonadiabatic dynamics in open quantum systems using transition path sampling and quantum jump trajectories. As with applications of transition path sampling to classical dynamics, the method does not rely…
The transport of particles through channels holds immense significance in physics, chemistry, and biological sciences. For instance, the motion of solutes through biological channels is facilitated by specialized proteins that create…
Mobile microscopic bodies, such as motile cells, can be modelled phenomenologically as ``active particles'' which can move against external forces by depleting an internal energy depot. The microscopic mechanisms underlying such ``active''…
We explore the thermodynamic geometry of a simple system that models the bistable dynamics of nucleic acid hairpins in single molecule force-extension experiments. Near equilibrium, optimal (minimum-dissipation) driving protocols are…
The ability to control and understand the phase transitions of individual nanoscale building blocks is key to advancing the next generation of low-power reconfigurable nanophotonic devices. To address this critical challenge, molecular…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
We investigate the appearance of trapping states in pedestrian flows through bottlenecks as a result of the interplay between the geometry of the system and the microscopic stochastic dynamics. We model the flow trough a bottleneck via a…
Target search by active agents in rugged energy landscapes has remained a challenge because standard enhanced sampling methods do not apply to irreversible dynamics. We overcome this non-equilibrium rare-event problem by developing an…
Single-electron escape from a metastable state over an oscillating barrier is experimentally investigated in silicon-based ratchet transfer. When the barrier is oscillating on a time scale characteristic of the single-electron escape,…
We perform molecular dynamics simulation of a small number of particles in a box with periodic boundary conditions from a view point of chaotic dynamical systems. There is a transition at a critical energy E_c that each particle is confined…
Interacting particle systems with many degrees of freedom may undergo phase transitions to sustain atypical fluctuations of dynamical observables such as the current or the activity. This leads in some cases to symmetry-broken space-time…
Based on the general form of the master equation for open quantum systems the tunneling is considered. Using the path integral technique a simple closed form expression for the tunneling rate through a parabolic barrier is obtained. The…
We study the transition time distribution for a particle moving between two wells of a multidimensional potential in the low-noise limit of overdamped Langevin dynamics. Possible transition paths are restricted to a thin tube surrounding…
Many biological, chemical, and physical systems are underpinned by stochastic transitions between equilibrium states in a potential energy. Here, we consider such transitions in a minimal model with two possible competing pathways, both…
We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state…
A study of the dynamics of a tunneling particle in a driven bistable potential which is moderately-to-strongly coupled to a bath is presented. Upon restricting the system dynamics to the Hilbert space spanned by the M lowest energy…
The properties of a particle diffusing on a one-dimensional lattice where at each site a random barrier and a random trap act simultaneously on the particle are investigated by numerical and analytical techniques. The combined effect of…