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D

Daniel M. Zuckerman

Oregon Health and Science University

45H-index
307Paper Count
6.4KCitation Count
Published Papers 94
Publication Date
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Weighted Ensemble Simulation: Advances in Methods, Software, and Applications
errWIREs Computational Molecular Science
IF0
err2025-11-14
err0
PREAI
errLillian T. Chong; Daniel M. Zuckerman
errShare
errSave
Design of facilitated dissociation enables timing of cytokine signalling
errNature
IF48.5
err2025-09-24
err0
errOAAI
errAdam J. Broerman; Christoph Pollmann; Yang Zhao; Mauriz A. Lichtenstein; Mark D. Jackson; Maxx H. Tessmer; Won Hee Ryu; Masato Ogishi; Mohamad H. Abedi; Danny D. Sahtoe; Aza Allen; Alex Kang; Joshmyn De La Cruz; Evans Brackenbrough; Banumathi Sankaran; Asim K. Bera; Daniel M. Zuckerman; Stefan Stoll; K. Christopher Garcia; Florian Praetorius; Jacob Piehler; David Baker
errShare
errSave
Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte Carlo
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2024-04-11
err3
PREAI
errZuckerman, Daniel M.; George, August
errShare
errSave
Morphodynamical cell state description via live-cell imaging trajectory embedding
errCOMMUNICATIONS BIOLOGY
IF5.1
err2023-05-04
err7
errOAAI
errCopperman, Jeremy; Gross, Sean M.; Chang, Young Hwan; Heiser, Laura M.; Zuckerman, Daniel M.
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errSave
Weighted ensemble: Recent mathematical developments
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2023-01-05
err11
errOAAI
errAristoff, D.; Copperman, J.; Simpson, G.; Webber, R. J.; Zuckerman, D. M.
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errSave
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol
errINTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS
IF2.5
err2022-10-02
err36
errOAAI
errDommer, Abigail; Casalino, Lorenzo; Kearns, Fiona; Rosenfeld, Mia; Wauer, Nicholas; Ahn, Surl-Hee; Russo, John; Oliveira, Sofia; Morris, Clare; Bogetti, Anthony; Trifan, Anda; Brace, Alexander; Sztain, Terra; Clyde, Austin; Ma, Heng; Chennubhotla, Chakra; Lee, Hyungro; Turilli, Matteo; Khalid, Syma; Tamayo-Mendoza, Teresa; Welborn, Matthew; Christensen, Anders; Smith, Daniel Ga; Qiao, Zhuoran; Sirumalla, Sai K.; O'Connor, Michael; Manby, Frederick; Anandkumar, Anima; Hardy, David; Phillips, James; Stern, Abraham; Romero, Josh; Clark, David; Dorrell, Mitchell; Maiden, Tom; Huang, Lei; McCalpin, John; Woods, Christopher; Gray, Alan; Williams, Matt; Barker, Bryan; Rajapaksha, Harinda; Pitts, Richard; Gibbs, Tom; Stone, John; Zuckerman, Daniel M.; Mulholland, Adrian J.; Miller, Thomas, III; Jha, Shantenu; Ramanathan, Arvind; Chong, Lillian; Amaro, Rommie E.
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errSave
WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2022-01-19
err41
errOAAI
errRusso, John D.; Zhang, She; Leung, Jeremy M. G.; Bogetti, Anthony T.; Thompson, Jeff P.; DeGrave, Alex J.; Torrillo, Paul A.; Pratt, A. J.; Wong, Kim F.; Xia, Junchao; Copperman, Jeremy; Adelman, Joshua L.; Zwier, Matthew C.; LeBard, David N.; Zuckerman, Daniel M.; Chong, Lillian T.
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errSave
Vascular KATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2021-10-28
err33
errOAAI
errSung, Min Woo; Yang, Zhongying; Driggers, Camden M.; Patton, Bruce L.; Mostofian, Barmak; Russo, John D.; Zuckerman, Daniel M.; Shyng, Show-Ling
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errSave
Computational Estimation of Microsecond to Second Atomistic Folding Times (vol 141, pg 6519, 2019)
errJOURNAL OF THE AMERICAN CHEMICAL SOCIETY
IF15.6
err2021-05-07
err0
PREAI
errAdhikari, Upendra; Mostofian, Barmak; Copperman, Jeremy; Subramanian, Sundar Raman; Petersen, Andrew A.; Zuckerman, Daniel M.
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errSave
What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2021-04-27
err44
errOAAI
errSuarez, Ernesto; Wiewiora, Rafal P.; Wehmeyer, Chris; Noe, Frank; Chodera, John D.; Zuckerman, Daniel M.
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errSave
Should Virus Capsids Assemble Perfectly? Theory and Observation of Defects
errBIOPHYSICAL JOURNAL
IF3.1
err2020-11-01
err6
errOAAI
errSpiriti, Justin; Conway, James F.; Zuckerman, Daniel M.
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errSave
Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian Microbin Analysis
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2020-09-29
err30
errOAAI
errCopperman, Jeremy; Zuckerman, Daniel M.
errShare
errSave
Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å
errNATURE COMMUNICATIONS
IF15.7
err2020-08-28
err66
errOAAI
errFlores, Jonathan A.; Haddad, Bassam G.; Dolan, Kimberly A.; Myers, Janette B.; Yoshioka, Craig C.; Copperman, Jeremy; Zuckerman, Daniel M.; Reichow, Steve L.
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errSave
A kinetic mechanism for enhanced selectivity of membrane transport
errplos biology
IF3.6
err2020-07-02
err17
errOAAI
errBisignano, Paola; Lee, Michael A.; George, August; Zuckerman, Daniel M.; Grabe, Michael; Rosenberg, John M.
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errSave
EmrE reminds us to expect the unexpected in membrane transport
errJOURNAL OF GENERAL PHYSIOLOGY
IF2.9
err2019-12-09
err7
errOAAI
errGrabe, Michael; Zuckerman, Daniel M.; Rosenberg, John M.
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errSave
Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture
errJOURNAL OF CHEMICAL PHYSICS
IF3.1
err2019-11-05
err3
errOAAI
errCopperman, Jeremy; Aristoff, David; Makarov, Dmitrii E.; Simpson, Gideon; Zuckerman, Daniel M.
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errSave
High-throughput, single-particle tracking reveals nested membrane domains that dictate KRasG12D diffusion and trafficking
errELIFE
IF0
err2019-11-01
err39
errOAAI
errLee, Yerim; Phelps, Carey; Huang, Tao; Mostofian, Barmak; Wu, Lei; Zhang, Ying; Tao, Kai; Chang, Young Hwan; Stork, Philip J. S.; Gray, Joe W.; Zuckerman, Daniel M.; Nan, Xiaolin
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errSave
Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2019-04-19
err26
errOAAI
errMostofian, Barmak; Zuckerman, Daniel M.
errShare
errSave
Computational Estimation of Microsecond to Second Atomistic Folding Times
errJOURNAL OF THE AMERICAN CHEMICAL SOCIETY
IF15.6
err2019-03-20
err48
errOAAI
errAdhikari, Upendra; Mostofian, Barmak; Copperman, Jeremy; Subramanian, Sundar Raman; Petersen, Andrew A.; Zuckerman, Daniel M.
errShare
errSave
Should Virus Capsids Assemble Perfectly? A Simple Equilibrium Model for Defects
errBIOPHYSICAL JOURNAL
IF3.1
err2019-02-01
err0
errOAAI
errSpiriti, Justin M.; Conway, James F.; Zuckerman, Daniel M.
errShare
errSave

Research Directions

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Co-authors
Cooperation Journals
J
Joe W. Gray
H-index: 130 · Papers: 1.2K
K
K. Christopher García
H-index: 119 · Papers: 545
M
Michael E. Fisher
H-index: 111 · Papers: 516
A
Athanassios Z. Panagiotopoulos
H-index: 80 · Papers: 417
J
J. C. Phillips
H-index: 73 · Papers: 330
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