Related papers: A multiple replica approach to simulate reactive t…

We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are considerably different, for instance, because the replicas run on different type…

Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is difficult to design Monte Carlo moves with high acceptance probabilities that also…

Metastable structures in macromolecular and colloidal systems are non-equilibrium states that often have long lifetimes and cause difficulties in simulating equilibrium. In order to escape from the long-lived metastable states, we propose a…

Markov chain Monte Carlo methods are a powerful tool for sampling equilibrium configurations in complex systems. One problem these methods often face is slow convergence over large energy barriers. In this work, we propose a novel method…

Understanding kinetics including reaction pathways and associated transition rates is an important yet difficult problem in numerous chemical and biological systems especially in situations with multiple competing pathways. When these…

Transition state theory is a standard framework for predicting the rate of a chemical reaction. Although the transition state theory has been successfully applied to numerous chemical reaction analyses, many experimental and theoretical…

The usual identification of reactive trajectories for the calculation of reaction rates requires very time-consuming simulations, particularly if the environment presents memory effects. In this paper, we develop a new method that permits…

Stochastic modeling of reaction networks is a framework used to describe the time evolution of many natural and artificial systems, including, biochemical reactive systems at the molecular level, viral kinetics, the spread of epidemic…

Within a fully microscopic setting, we derive a variational principle for the non-equilibrium steady states of chemical reaction networks, valid for time-scales over which chemical potentials can be taken to be slowly varying: at…

In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding, and chemical reactions. For these…

In conventional molecular simulation, metastable structures often survive over considerable computational time, resulting in difficulties in simulating equilibrium states. In order to overcome this difficulty, here we propose a newly…

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…

We present an elementary and self-contained account of the analogies existing between classical diffusion and the imaginary-time evolution of quantum systems. These analogies are used to develop a new quantum simulation method which allows…

We consider large-dimensional dynamical systems involving a linear force and a random force comprising both potential and non-conservative contributions. Such systems are known to exhibit a topological trivialization phase transition as the…

We consider the problem of state selection for a stochastic system, initially in an unstable stationary state, when multiple metastable states compete for occupation. Using path-integral techniques we derive remarkably simple and accurate…

We extend the weighted ensemble (WE) path sampling method to perform rigorous statistical sampling for systems at steady state. The straightforward steady-state implementation of WE is directly practical for simple landscapes, but not when…

In the framework of time series analysis with recurrence networks, we introduce a self-adaptive method that determines the elusive recurrence threshold and identifies metastable states in complex real-world time series. As initial step, we…

A system of replicators with Hebbian random couplings is studied using dynamical methods. The self-reproducing species are here characterized by a set of binary traits and interact based on complementarity. In the case of an extensive…

We present a time dependent variational method to learn the mechanisms of equilibrium reactive processes and efficiently evaluate their rates within a transition path ensemble. This approach builds off variational path sampling methodology…

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…