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Annual Review of Biophysics|March 17, 2017
Weighted Ensemble Simulation: Review of Methodology, Applications, and SoftwareDaniel M Zuckerman, Lillian T ChongJournal 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 RussoThe Journal of Chemical Physics|July 23, 2004
Single-ensemble nonequilibrium path-sampling estimates of free energy differencesF Marty Ytreberg, Daniel M ZuckermanWiley Interdisciplinary Reviews. Computational Molecular Science|December 8, 2025
Weighted Ensemble Simulation: Advances in methods, software, and applicationsLillian T Chong, Daniel M ZuckermanPhysical Review Letters|October 26, 2002
Theory of a systematic computational error in free energy differencesDaniel M Zuckerman, Thomas B WoolfThe Journal of Chemical Physics|March 18, 2006
Simple estimation of absolute free energies for biomoleculesF Marty Ytreberg, Daniel M ZuckermanProceedings of the National Academy of Sciences of the United States of America|June 12, 2008
A black-box re-weighting analysis can correct flawed simulation dataF Marty Ytreberg, Daniel M ZuckermanBiophysical Journal|August 5, 2018
From Dynamics to Membrane Organization: Experimental Breakthroughs Occasion a "Modeling Manifesto"Edward Lyman, Chia-Lung Hsieh, Christian EggelingPageof 15