Weighted Ensemble Simulation: Advances in methods, software, and applications.

For more than two decades, weighted ensemble (WE) path sampling strategies have enabled the simulation of pathways for rare events-or barrier-crossing processes-with significantly less computing cost than conventional simulations, all while preserving rigorous kinetics. This review highlights recent advances in WE methods and software, including tools for mechanistic analysis of path ensembles and efficient estimation of rates. We showcase successful weighted ensemble applications across a wide range of condensed-phase processes, such as hybrid quantum mechanics/molecular mechanics (QM/MM) simulations of microsecond-timescale chemical reactions, and atomistic simulations of slower processes on the millisecond to seconds timescale. These applications span drug membrane permeation, ligand unbinding, and the large-scale opening of the SARS-CoV-2 spike protein. We also discuss the current limitations and key challenges facing WE strategies, which have yet to reach their full potential.