162 citations · 894 across the 45 of their papers we have counts for
46 papers
Weighted ensemble: Recent mathematical developments
D. Aristoff, J. Copperman, G. Simpson +2
The weighted ensemble (WE) method, an enhanced sampling approach based on periodically replicating and pruning trajectories in a set of parallel simulations, has grown increasingly…
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 (…
Key biology you should have learned in physics class: Using ideal-gas mixtures to understand biomolecular machines
Daniel M. Zuckerman
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, know…