162 citations · 894 across the 45 of their papers we have counts for
6 papers · 1 filter
Pathway Histogram Analysis of Trajectories: A general strategy for quantification of molecular mechanisms
Ernesto Suárez, Daniel M. Zuckerman
A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions an…
Learning from history: Non-Markovian analyses of complex trajectories for extracting long-time behavior
Ernesto Suarez, Daniel Zuckerman
A number of modern sampling methods probe long time behavior in complex biomolecules using a set of relatively short trajectory segments. Markov state models (MSMs) can be useful i…
Rapid Determination of Multiple Reaction Pathways in Molecular Systems: The Soft-Ratcheting Algorithm
Daniel M. Zuckerman, Thomas B. Woolf
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure,…
Transition Events in Butane Simulations: Similarities Across Models
Daniel M. Zuckerman, Thomas B. Woolf
From a variety of long simulations of all-atom butane using both stochastic and fully-solved molecular dynamics, we have uncovered striking generic behavior which also occurs in on…
Extrapolative Analysis of Fast-Switching Free Energy Estimates in a Molecular System
Daniel M. Zuckerman, Thomas B. Woolf
We perform an extrapolative analysis of "fast-growth" free-energy-difference (DF) estimates of a computer-modeled, fully-solvated ethane<->methanol transformation. The results sugg…
Chemical Association via Exact Thermodynamic Formulations
Michael E. Fisher, Daniel M. Zuckerman
It can be fruitful to view two-component physical systems of attractive monomers, A and B, ``chemically'' in terms of a reaction A + B <-> C, where C = AB is an associated pair or…