Related papers: Understanding Reaction Mechanisms from Start to Fi…
The discovery of transition pathways to unravel distinct reaction mechanisms and, in general, rare events that occur in molecular systems is still a challenge. Recent advances have focused on analyzing the transition path ensemble using the…
The probability that a configuration of a physical system reacts, or transitions from one metastable state to another, is quantified by the committor function. This function contains richly detailed mechanistic information about transition…
We propose an efficient novel path sampling-based framework designed to accelerate the investigation of rare events in complex molecular systems. A key innovation is the shift from sampling restricted path ensemble distributions, as in…
The reaction coordinate describing a transition between reactant and product is a fundamental concept in the theory of chemical reactions. Within transition-path theory, a quantitative definition of the reaction coordinate is found in the…
As an optimal one-dimensional reaction coordinate, the committor function not only describes the probability of a trajectory initiated at a phase space point first reaching the product state before reaching the reactant state, but also…
The committor constitutes the primary quantity of interest within chemical kinetics as it is understood to encode the ideal reaction coordinate for a rare reactive event. We show the generative utility of the committor, in that it can be…
In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the…
The committor function is a central object for quantifying the transitions between metastable states of dynamical systems. Recently, a number of computational methods based on deep neural networks have been developed for computing the…
We extend the non-parametric framework of reaction coordinate optimization to non-equilibrium ensembles of (short) trajectories. For example, we show how, starting from such an ensemble, one can obtain an equilibrium free energy profile…
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…
This contribution introduces a neural-network-based approach to discover meaningful transition pathways underlying complex biomolecular transformations in coherence with the committor function. The proposed path-committor-consistent…
Determining the kinetic bottlenecks that make transitions between metastable states difficult is key to understanding important physical problems like crystallization, chemical reactions, or protein folding. In all these phenomena, the…
The committor function is a central object of study in understanding transitions between metastable states in complex systems. However, computing the committor function for realistic systems at low temperatures is a challenging task, due to…
We propose a reinforcement learning based method to identify important configurations that connect reactant and product states along chemical reaction paths. By shooting multiple trajectories from these configurations, we can generate an…
Many processes in nature such as conformal changes in biomolecules and clusters of interacting particles, genetic switches, mechanical or electromechanical oscillators with added noise, and many others are modeled using stochastic…
The problem of studying rare events is central to many areas of computer simulations. In a recent paper [Kang, P., et al., Nat. Comput. Sci. 4, 451-460, 2024], we have shown that a powerful way of solving this problem passes through the…
The study of rare events is one of the major challenges in atomistic simulations, and several enhanced sampling methods towards its solution have been proposed. Recently, it has been suggested that the use of the committor, which provides a…
Computing long-timescale kinetics of biomolecular processes remains a major challenge for atomistic simulations. A way out is to exploit local kinetic information to construct the global stationary flux across the reaction space. The…
Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems,…
We introduce a general definition of a quantum committor in order to clarify reaction mechanisms and facilitate control in processes where coherent effects are important. With a quantum committor, we generalize the notion of a transition…