Related papers: Reactive trajectories and the transition path proc…
Continuous-time random walks combining diffusive scattering and ballistic propagation on lattices model a class of L\'evy walks. The assumption that transitions in the scattering phase occur with exponentially-distributed waiting times…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
The trajectories of diffusion processes are continuous but non-differentiable, and each occurs with vanishing probability. This introduces a gap between theory, where path probabilities are used in many contexts, and experiment, where only…
In this paper we compute and analyse the transition rates and duration of reactive trajectories of the stochastic 1-D Allen-Cahn equations for both the Freidlin-Wentzell regime (weak noise or temperature limit) and finite-amplitude white…
An idea for evaluating transition probabilities in chemical reaction systems is proposed, which is efficient for repeated calculations with various rate constants. The idea is based on duality relations; instead of direct time-evolutions of…
We study reaction diffusion equations with a deterministic reaction term as well as two random reaction terms, one that acts on the interior of the domain, and another that acts only on the boundary of the domain. We are interested in the…
This study address the computational determination of catalytic reaction rates by moving beyond traditional Transition State Theory (TST), addressing its limitations in complex systems. The Hill relation framework, integrated with Adaptive…
We used transition path theory (TPT) to infer "reactive" pathways of floating marine debris trajectories. The TPT analysis was applied on a pollution-aware time-homogeneous Markov chain model constructed from trajectories produced by…
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 $x_n$…
We study planar random motions with finite velocities, of norm $c>0$, along orthogonal directions and changing at the instants of occurrence of a non-homogeneous Poisson process with rate function $\lambda(t),\ t\ge0$. We focus on the…
Classical chemical kinetics use rate-equation models to describe how a reaction proceeds in time. Such models are sufficient for describing state transitions in a reaction where coherences between different states do not arise, or in other…
Atypical, rare trajectories of dynamical systems are important: they are often the paths for chemical reactions, the haven of (relative) stability of planetary systems, the rogue waves that are detected in oil platforms, the structures that…
The thermal ratchets model toggles a spatially periodic asymmetric potential to rectify random walks and achieve transport of diffusing particles. We numerically solve the governing equation for the full dynamics of an infinite 1D ratchet…
Systems switching between different dynamical phases is an ubiquitous phenomenon. The general understanding of such a process is limited. To this end, we present a general expression that captures fluctuations of a system exhibiting a…
We consider a one-dimensional run-and-tumble particle, or persistent random walk, in the presence of an absorbing boundary located at the origin. After each tumbling event, which occurs at a constant rate $\gamma$, the (new) velocity of the…
The stochastic trajectories of molecules in living cells, as well as the dynamics in many other complex systems, often exhibit memory in their path over long periods of time. In addition, these systems can show dynamic heterogeneities due…
We study stochastic differential equations (SDEs) whose drift and diffusion coefficients are path-dependent and controlled. We construct a value process on the canonical path space, considered simultaneously under a family of singular…
Using a theory of large amplitude collective motion, the adiabatic self-consistent collective coordinate method, we derive reaction path for the fusion process at sub-barrier energies. The collective Hamiltonian to describe the fusion…
As computational chemistry methods evolve, dynamic effects have been increasingly recognized to govern chemical reaction pathways in both organic and inorganic systems. Here, we introduce a committor-based workflow that integrates a…
In this paper we show that a path-wise solution to the following integral equation $$ Y_t = \int_0^t f(Y_t) dX_t \qquad Y_0=a \in \R^d $$ exists under the assumption that X_t is a L\'evy process of finite p-variation for some $p \geq1$ and…