Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems. - F. Marty Ytreberg; Daniel M. Zuckerman (J. Comput. Chem., 2004)

Absolute free energies estimated by combining precalculated molecular fragment libraries. - Xin Zhang 011; Artem B. Mamonov; Daniel M. Zuckerman (J. Comput. Chem., 2009)

Extending fragment-based free energy calculations with library monte carlo simulation: Annealing in interaction space. - Steven Lettieri; Artem B. Mamonov; Daniel M. Zuckerman (J. Comput. Chem., 2011)

Rapid sampling of all-atom peptides using a library-based polymer-growth approach. - Artem B. Mamonov; Xin Zhang 011; Daniel M. Zuckerman (J. Comput. Chem., 2011)

Accelerating molecular monte carlo simulations using distance and orientation-dependent energy tables: Tuning from atomistic accuracy to smoothed "coarse-grained" models. - Steven Lettieri; Daniel M. Zuckerman (J. Comput. Chem., 2012)

A proposal for regularly updated review/survey articles: "Perpetual Reviews". - David L. Mobley; Daniel M. Zuckerman (CoRR, 2015)

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. - Rory M. Donovan; José Juan Tapia; Devin P. Sullivan; James R. Faeder; Robert F. Murphy; Markus Dittrich; Daniel M. Zuckerman (PLoS Comput. Biol., 2016)

Optimizing Weighted Ensemble Sampling of Steady States. - David Aristoff; Daniel M. Zuckerman (Multiscale Model. Simul., 2020)

A kinetic mechanism for enhanced selectivity of membrane transport. - Paola Bisignano; Michael A. Lee; August George; Daniel M. Zuckerman; Michael Grabe; John M. Rosenberg (PLoS Comput. Biol., 2020)

A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms. - August George; Paola Bisignano; John M. Rosenberg; Michael Grabe; Daniel M. Zuckerman (PLoS Comput. Biol., 2020)

Weighted ensemble: Recent mathematical developments. - David Aristoff; J. Copperman; Gideon Simpson; Robert J. Webber; Daniel M. Zuckerman (CoRR, 2022)

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. - Abigail C. Dommer; Lorenzo Casalino; Fiona L. Kearns; Mia A. Rosenfeld; Nicholas Wauer; Surl-Hee Ahn; John Russo 003; A. Sofia F. Oliveira; Clare Morris; Anthony T. Bogetti; Anda Trifan; Alexander Brace; et al. (Int. J. High Perform. Comput. Appl., 2023)

Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference. - Aidan B. Estelle; August George; Elisar J. Barbar; Daniel M. Zuckerman (PLoS Comput. Biol., 2023)