2 citations · 4 across the 5 of their papers we have counts for
5 papers
Reducing Weighted Ensemble Variance With Optimal Trajectory Management
Won Hee Ryu, John D. Russo, Mats S. Johnson +7
Weighted ensemble (WE) is an enhanced path-sampling method that is conceptually simple, widely applicable, and statistically exact. In a WE simulation, an ensemble of trajectories…
Simple synthetic molecular dynamics for efficient trajectory generation
John D. Russo, Daniel M. Zuckerman
Synthetic molecular dynamics (synMD) trajectories from learned generative models have been proposed as a useful addition to the biomolecular simulation toolbox. The computational e…
Unbiased estimation of equilibrium, rates, and committors from Markov state model analysis
John D. Russo, Jeremy Copperman, David Aristoff +2
Markov state models (MSMs) have been broadly adopted for analyzing molecular dynamics trajectories, but the approximate nature of the models that results from coarse-graining into…
A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications
Daniel M. Zuckerman, John D. Russo
Despite the importance of non-equilibrium statistical mechanics in modern physics and related fields, the topic is often omitted from undergraduate and core-graduate curricula. Key…
Iterative trajectory reweighting for estimation of equilibrium and non-equilibrium observables
John D. Russo, Jeremy Copperman, Daniel M. Zuckerman
We present two algorithms by which a set of short, unbiased trajectories can be iteratively reweighted to obtain various observables. The first algorithm estimates the stationary (…