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Multiscale Modeling & Simulation : a SIAM Interdisciplinary Journal|August 23, 2021
OPTIMIZING WEIGHTED ENSEMBLE SAMPLING OF STEADY STATESDavid Aristoff, Daniel M ZuckermanJournal of Chemical Theory and Computation|December 3, 2015
Resolution Exchange Simulation with Incremental CoarseningEdward Lyman, Daniel M ZuckermanJournal of Chemical Theory and Computation|April 11, 2024
Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte CarloDaniel M Zuckerman, August GeorgeBiophysical Journal|May 5, 2011
Direct observations of shifts in the β-sheet register of a protein-peptide complex using explicit solvent simulationsMaria T Panteva, Reza Salari, Monica Bhattacharjee, et al.Journal of Chemical Information and Modeling|December 4, 2023
LPATH: A Semiautomated Python Tool for Clustering Molecular PathwaysAnthony T Bogetti, Jeremy M G Leung, Lillian T ChongBiorxiv : the Preprint Server for Biology|August 30, 2023
LPATH: A semi-automated Python tool for clustering molecular pathwaysAnthony T Bogetti, Jeremy M G Leung, Lillian T ChongJournal of Chemical Theory and Computation|September 23, 2015
WESTPA: an interoperable, highly scalable software package for weighted ensemble simulation and analysisMatthew C Zwier, Joshua L Adelman, Joseph W Kaus, et al.Journal of Computational Chemistry|September 14, 2004
Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systemsF Marty Ytreberg, Daniel M ZuckermanThe Journal of Physical Chemistry. B|July 21, 2006
Peptide conformational equilibria computed via a single-stage shifting protocolF Marty Ytreberg, Daniel M ZuckermanAmerican Journal of Physics|May 9, 2022
A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applicationsDaniel M Zuckerman, John D RussoPageof 15