Daniel M. Zuckerman
Title
Cited by
Cited by
Year
Coarse-graining of condensed phase and biomolecular systems
GA Voth
CRC press, 2008
6492008
Quantifying uncertainty and sampling quality in biomolecular simulations
A Grossfield, DM Zuckerman
Annual reports in computational chemistry 5, 23-48, 2009
2712009
Resolution exchange simulation
E Lyman, FM Ytreberg, DM Zuckerman
Physical review letters 96 (2), 028105, 2006
2172006
Equilibrium sampling in biomolecular simulations
DM Zuckerman
Annual review of biophysics 40, 41-62, 2011
2152011
Theory of a systematic computational error in free energy differences
DM Zuckerman, TB Woolf
Physical Review Letters 89 (18), 180602, 2002
1802002
The “weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures
BW Zhang, D Jasnow, DM Zuckerman
The Journal of chemical physics 132 (5), 054107, 2010
1462010
Comparison of free energy methods for molecular systems
FM Ytreberg, RH Swendsen, DM Zuckerman
The Journal of chemical physics 125 (18), 184114, 2006
1452006
Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin
BW Zhang, D Jasnow, DM Zuckerman
Proceedings of the National Academy of sciences 104 (46), 18043-18048, 2007
1312007
Ensemble-based convergence analysis of biomolecular trajectories
E Lyman, DM Zuckerman
Biophysical journal 91 (1), 164-172, 2006
1192006
Single-ensemble nonequilibrium path-sampling estimates of free energy differences
FM Ytreberg, DM Zuckerman
The Journal of chemical physics 120 (23), 10876-10879, 2004
1172004
A second look at canonical sampling of biomolecules using replica exchange simulation
DM Zuckerman, E Lyman
Journal of chemical theory and computation 2 (4), 1200-1202, 2006
1132006
Dynamic reaction paths and rates through importance-sampled stochastic dynamics
DM Zuckerman, TB Woolf
The Journal of chemical physics 111 (21), 9475-9484, 1999
971999
Simulation of an ensemble of conformational transitions in a united-residue model of calmodulin
DM Zuckerman
The Journal of Physical Chemistry B 108 (16), 5127-5137, 2004
962004
Hydrophobic matching mechanism investigated by molecular dynamics simulations
HI Petrache, DM Zuckerman, JN Sachs, JA Killian, RE Koeppe, TB Woolf
Langmuir 18 (4), 1340-1351, 2002
962002
Weighted ensemble simulation: review of methodology, applications, and software
DM Zuckerman, LT Chong
Annual review of biophysics 46, 43-57, 2017
932017
Statistical physics of biomolecules: an introduction
DM Zuckerman
CRC Press, 2010
902010
Resolution exchange simulation with incremental coarsening
E Lyman, DM Zuckerman
Journal of chemical theory and computation 2 (3), 656-666, 2006
872006
WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis
MC Zwier, JL Adelman, JW Kaus, AJ Pratt, KF Wong, NB Rego, E Suárez, ...
Journal of chemical theory and computation 11 (2), 800-809, 2015
862015
Transition-event durations in one-dimensional activated processes
BW Zhang, D Jasnow, DM Zuckerman
The Journal of chemical physics 126 (7), 074504, 2007
852007
Steady-state simulations using weighted ensemble path sampling
D Bhatt, BW Zhang, DM Zuckerman
The Journal of chemical physics 133 (1), 014110, 2010
832010
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Articles 1–20