Publications by authors named "DM Zuckerman"

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Design of facilitated dissociation enables timing of cytokine signalling.
Adam J Broerman, Christoph Pollmann, Yang Zhao, Mauriz A Lichtenstein, Mark D Jackson, Daniel M Zuckerman

Nature· November 2025

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Weighted Ensemble Simulation: Advances in methods, software, and applications.
Lillian T Chong, Daniel M Zuckerman

Wiley Interdiscip Rev Comput Mol Sci· November 2025

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Secretins of type-two secretion systems are necessary for exopolymeric slime secretion in cyanobacteria and myxobacteria.
David M Zuckerman, Jeffery Man To So, Egbert Hoiczyk

Nat Commun· September 2025

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Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.
Jeremy Copperman, Ian C Mclean, Sean M Gross, Jalim Singh, Vaibhav Murthy, Daniel M Zuckerman

bioRxiv· July 2025

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Improving parameter inference by resolving Bayesian prior ambiguity via multi-dataset analysis: Application to isothermal titration calorimetry.
Lisa Otten, Douglas R Walker, Elisar J Barbar, Daniel M Zuckerman

bioRxiv· July 2025

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Design of facilitated dissociation enables control over cytokine signaling duration.
Adam J Broerman, Christoph Pollmann, Mauriz A Lichtenstein, Mark D Jackson, Maxx H Tessmer, Daniel M Zuckerman

bioRxiv· November 2024

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Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte Carlo.
Daniel M Zuckerman, August George

J Chem Theory Comput· April 2024

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From Average Transient Transporter Currents to Microscopic Mechanism─A Bayesian Analysis.
August George, Daniel M Zuckerman

J Phys Chem B· February 2024

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The Regulatory Repercussions of Approving Muscular Dystrophy Medications on the Basis of Limited Evidence.
Liam Bendicksen, Diana M Zuckerman, Jerry Avorn, Sophia Phillips, Aaron S Kesselheim

Ann Intern Med· September 2023

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Morphodynamical cell state description via live-cell imaging trajectory embedding.
Jeremy Copperman, Sean M Gross, Young Hwan Chang, Laura M Heiser, Daniel M Zuckerman

Commun Biol· May 2023

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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· April 2023

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Weighted ensemble: Recent mathematical developments.
D Aristoff, J Copperman, G Simpson, R J Webber, D M Zuckerman

J Chem Phys· January 2023

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#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia Rosenfeld, Nicholas Wauer, Daniel M Zuckerman

Int J High Perform Comput Appl· January 2023

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A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0].
Anthony T Bogetti, Jeremy M G Leung, John D Russo, She Zhang, Jeff P Thompson, Daniel M Zuckerman

Living J Comput Mol Sci· January 2023

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Ligand-mediated Structural Dynamics of a Mammalian Pancreatic K Channel.
Min Woo Sung, Camden M Driggers, Barmak Mostofian, John D Russo, Bruce L Patton, Daniel M Zuckerman

J Mol Biol· October 2022

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Continuum dynamics and statistical correction of compositional heterogeneity in multivalent IDP oligomers resolved by single-particle EM.
Barmak Mostofian, Russell McFarland, Aidan Estelle, Jesse Howe, Elisar Barbar, Daniel M Zuckerman

J Mol Biol· May 2022

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WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.
John D Russo, She Zhang, Jeremy M G Leung, Anthony T Bogetti, Jeff P Thompson, Daniel M Zuckerman

J Chem Theory Comput· February 2022

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Vascular K channel structural dynamics reveal regulatory mechanism by Mg-nucleotides.
Min Woo Sung, Zhongying Yang, Camden M Driggers, Bruce L Patton, Barmak Mostofian, Daniel M Zuckerman

Proc Natl Acad Sci U S A· November 2021

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A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications.
Daniel M Zuckerman, John D Russo

Am J Phys· November 2021

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Connexin 46 and connexin 50 gap junction channel properties are shaped by structural and dynamic features of their N-terminal domains.
Benny Yue, Bassam G Haddad, Umair Khan, Honghong Chen, Mena Atalla, Daniel M Zuckerman

J Physiol· July 2021

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Emergency Use Authorizations (EUAs) Versus FDA Approval: Implications for COVID-19 and Public Health.
Diana M Zuckerman

Am J Public Health· June 2021

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What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models.
Ernesto Suárez, Rafal P Wiewiora, Chris Wehmeyer, Frank Noé, John D Chodera, Daniel M Zuckerman

J Chem Theory Comput· May 2021

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Correction to "Computational Estimation of Microsecond to Second Atomistic Folding Times".
Upendra Adhikari, Barmak Mostofian, Jeremy Copperman, Sundar Raman Subramanian, Andrew A Petersen, Daniel M Zuckerman

J Am Chem Soc· May 2021

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Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian "Microbin" Analysis.
Jeremy Copperman, Daniel M Zuckerman

J Chem Theory Comput· November 2020

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Should Virus Capsids Assemble Perfectly? Theory and Observation of Defects.
Justin Spiriti, James F Conway, Daniel M Zuckerman

Biophys J· November 2020

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