Related papers: Dominant Reaction Pathways in High Dimensional Sys…
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…
Transition pathways of stochastic dynamical systems are typically approximated by instantons. Here we show, using a dynamical system containing two competing pathways, that at low-to-intermediate temperatures, instantons can fail to capture…
A theory for chemical reaction dynamics in condensed phase systems based on the generalized Langevin formalism of Grote and Hynes is presented. A microscopic approach to calculate the dynamic friction is developed within the framework of a…
Transition of a system between two states is an important but difficult problem in natural science. In this article we study the transition problem in the framework of transition path ensemble. Using the overdamped Langevin method, we…
We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where…
Searching for reaction pathways describing rare events in large systems presents a long-standing challenge in chemistry and physics. Incorrectly computed reaction pathways result in the degeneracy of microscopic configurations and inability…
We propose an efficient method to compute reaction rate constants of thermally activated processes occurring in many-body systems at finite temperature. The method consists in two steps: first, paths are sampled using a transition path…
A new asymptotic method is presented for the analysis of the traveling waves in the one-dimensional reaction-diffusion system with the diffusion with a finite velocity and Kolmogorov-Petrovskii-Piskunov kinetics. The analysis makes use of…
We introduce a framework to investigate ab-initio the dynamics of rare thermally activated reactions. The electronic degrees of freedom are described at the quantum-mechanical level in the Born-Oppenheimer approximation, while the nuclear…
Ring-polymer instanton theory has been developed to simulate the quantum dynamics of molecular systems at low temperatures. Chemical reaction rates can be obtained by locating the dominant tunneling pathway and analyzing fluctuations around…
Overdamped Langevin dynamics are reversible stochastic differential equations which are commonly used to sample probability measures in high-dimensional spaces, such as the ones appearing in computational statistical physics and Bayesian…
Reaction-diffusion models have been used over decades to study biological systems. In this context, evolution equations for probability distribution functions and the associated stochastic differential equations have nowadays become…
The main motivation of this work is to assess the validity of a LWR traffic flow model to model measurements obtained from trajectory data, and propose extensions of this model to improve it. A formulation for a discrete dynamical system is…
We introduce a general procedure for directly ascertaining how many independent stochastic sources exist in a complex system modeled through a set of coupled Langevin equations of arbitrary dimension. The procedure is based on the…
Thermodynamics of trajectories promises to make possible the thorough analysis of the dynamical properties of an open quantum system, a sought-after goal in modern physics. Unfortunately, calculation of the relevant quantities presents…
We study general linear transport-reaction systems on an arbitrary dimensional hypercube with periodic boundary conditions. Transport-reaction systems are often used to model the finite speed movement and interaction of particles, bacteria…
We discuss dynamical response theory of driven-dissipative quantum systems described by Markovian Master Equations generating semi-groups of maps. In this setting thermal equilibrium states are replaced by non-equilibrium steady states and…
The inherent complexity of biological agents often leads to motility behavior that appears to have random components. Robust stochastic inference methods are therefore required to understand and predict the motion patterns from time…
Sampled structure sequences obtained, for instance, from real-time reactivity explorations or first-principles molecular dynamics simulations contain valuable information about chemical reactivity. Eventually, such sequences allow for the…
For sampling multiple pathways in a rugged energy landscape, we propose a novel action-based path sampling method using the Onsager-Machlup action functional. Inspired by the Fourier-path integral simulation of a quantum mechanical system,…