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Daniel M. Zuckerman
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2020 – today
- 2023
- [j11]Abigail C. Dommer, Lorenzo Casalino
, Fiona L. Kearns, Mia Rosenfeld
, Nicholas Wauer, Surl-Hee Ahn
, John Russo
, A. Sofia F. Oliveira
, Clare Morris
, Anthony T. Bogetti, Anda Trifan, Alexander Brace
, Terra Sztain, Austin Clyde, Heng Ma, S. Chakra Chennubhotla, Hyungro Lee
, Matteo Turilli
, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders S. Christensen, Daniel G. A. Smith, Zhuoran Qiao
, Sai K. Sirumalla
, Michael O'Connor, Frederick R. Manby, Anima Anandkumar
, David J. Hardy, James C. Phillips
, Abraham C. Stern, Josh Romero, David Clark, Mitchell Dorrell
, Tom Maiden, Lei Huang, John D. McCalpin
, Christopher J. Woods
, Alan Gray, Matt Williams
, Bryan Barker, Harinda Rajapaksha, Richard Pitts
, Tom Gibbs, John E. Stone
, Daniel M. Zuckerman
, Adrian J. Mulholland
, Thomas F. Miller III, Shantenu Jha
, Arvind Ramanathan
, Lillian T. Chong
, Rommie E. Amaro
:
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. Int. J. High Perform. Comput. Appl. 37(1): 28-44 (2023) - [j10]Aidan B. Estelle
, August George, Elisar J. Barbar, Daniel M. Zuckerman
:
Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference. PLoS Comput. Biol. 19(4) (2023) - 2022
- [i2]David Aristoff, J. Copperman, Gideon Simpson, Robert J. Webber, Daniel M. Zuckerman:
Weighted ensemble: Recent mathematical developments. CoRR abs/2206.14943 (2022) - 2020
- [j9]David Aristoff, Daniel M. Zuckerman:
Optimizing Weighted Ensemble Sampling of Steady States. Multiscale Model. Simul. 18(2): 646-673 (2020) - [j8]Paola Bisignano
, Michael A. Lee, August George
, Daniel M. Zuckerman, Michael Grabe, John M. Rosenberg
:
A kinetic mechanism for enhanced selectivity of membrane transport. PLoS Comput. Biol. 16(7) (2020) - [j7]August George
, Paola Bisignano
, John M. Rosenberg
, Michael Grabe, Daniel M. Zuckerman
:
A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms. PLoS Comput. Biol. 16(7) (2020)
2010 – 2019
- 2016
- [j6]Rory M. Donovan
, José Juan Tapia, Devin P. Sullivan
, James R. Faeder
, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman:
Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. PLoS Comput. Biol. 12(2) (2016) - 2015
- [i1]David L. Mobley, Daniel M. Zuckerman:
A proposal for regularly updated review/survey articles: "Perpetual Reviews". CoRR abs/1502.01329 (2015) - 2012
- [j5]Steven Lettieri, Daniel M. Zuckerman
:
Accelerating molecular monte carlo simulations using distance and orientation-dependent energy tables: Tuning from atomistic accuracy to smoothed "coarse-grained" models. J. Comput. Chem. 33(3): 268-275 (2012) - 2011
- [j4]Artem B. Mamonov, Xin Zhang, Daniel M. Zuckerman
:
Rapid sampling of all-atom peptides using a library-based polymer-growth approach. J. Comput. Chem. 32(3): 396-405 (2011) - [j3]Steven Lettieri, Artem B. Mamonov, Daniel M. Zuckerman
:
Extending fragment-based free energy calculations with library monte carlo simulation: Annealing in interaction space. J. Comput. Chem. 32(6): 1135-1143 (2011)
2000 – 2009
- 2009
- [j2]Xin Zhang, Artem B. Mamonov, Daniel M. Zuckerman
:
Absolute free energies estimated by combining precalculated molecular fragment libraries. J. Comput. Chem. 30(11): 1680-1691 (2009) - 2004
- [j1]F. Marty Ytreberg, Daniel M. Zuckerman
:
Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems. J. Comput. Chem. 25(14): 1749-1759 (2004)
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