The weighted ensemble (WE) methodology orchestrates quasi-independent parallel
simulations run with intermittent communication that can enhance sampling of rare events …

Rare events are processes that occur upon the emergence of unlikely fluctuations. Unlike
what their name suggests, rare events are fairly ubiquitous in nature, as the occurrence of …

Highlights•Advances, common features, and remaining challenges are presented for path
sampling approaches.•Key strengths are the efficient calculation of transition trajectories and …

Computational methodologies that couple the dynamical evolution of a set of replicated
copies of a system of interest offer powerful and flexible approaches to characterize complex …

We report simulations of full ligand exit pathways for the trypsin-benzamidine system,
generated using the sampling technique WExplore. WExplore is able to observe millisecond …

Conventional molecular dynamics simulations are incapable of sampling many important
interactions in biomolecular systems due to their high dimensionality and rough energy …

Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing
unbiased dynamics in which detailed balance is maintained on average. Non-equilibrium …

Many biological processes result from the effect of mechanical forces on macromolecular
structures and on their interactions. In particular, the cell shape, motion, and differentiation …

Transition path theory computes statistics from ensembles of reactive trajectories. A common
strategy for sampling reactive trajectories is to control the branching and pruning of …

The free energy of a process is the fundamental quantity that determines its spontaneity or
propensity at a given temperature. In particular, the binding free energy of a drug candidate …