162 citations · 894 across the 45 of their papers we have counts for
12 papers · 1 filter
Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories
Ernesto Suarez, Steven Lettieri, Matthew C. Zwier +4
Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing unbiased dynamics in which detailed balance is maintained. Many non-equilibrium processes can…
Steady-state simulations using weighted ensemble path sampling
Divesh Bhatt, Bin W. Zhang, Daniel M. Zuckerman
We extend the weighted ensemble (WE) path sampling method to perform rigorous statistical sampling for systems at steady state. The straightforward steady-state implementation of W…
Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo
Ying Ding, Artem B. Mamonov, Daniel M. Zuckerman
We applied our previously developed library-based Monte Carlo (LBMC) to equilibrium sampling of several implicitly solvated all-atom peptides. LBMC can perform equilibrium sampling…
Rapid sampling of all-atom peptides using a library-based polymer-growth approach
A. B. Mamonov, X. Zhang, D. M. Zuckerman
We adapted existing polymer growth strategies for equilibrium sampling of peptides described by modern atomistic forcefields with implicit solvent. The main novel feature of our ap…
Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase
Divesh Bhatt, Daniel M. Zuckerman
We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semi-atomistic protein models. Our study investigated both the biophysics of conformat…
Weighted Ensemble Path Sampling for Multiple Reaction Channels
Bin W. Zhang, David Jasnow, Daniel M. Zuckerman
Finding and sampling multiple reaction channels for molecular transitions remains an important challenge in physical chemistry. Here we show that the weighted ensemble (WE) path sa…