Minimizing variance of reaction rate estimation in weighted ensemble simulation using synthetic molecular dynamics von Hee Ryu, Won, Russo, John, Johnson, Mats S., Thompson, Jeffrey P., LeBard, David N., Simpson, Gideon, Aristoff, David, Webber, Robert J., Copperman, Jeremy T., Zuckerman, Daniel M.

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Accelerated Estimation of Long-timescale Kinetics by Combining Weighted Ensemble Simulation with Markov Model “Microstates” using Non-Markovian Theory von Copperman, Jeremy T., Zuckerman, Daniel M.

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A near-continuum model of morphodynamic single-cell states quantifying gene expression during epithelial-mesenchymal transitions von Singh, Jalim, Copperman, Jeremy T., McLean, Ian, Heiser, Laura M., Zuckerman, Daniel M.

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Iterative steady state restarting to accelerate weighted ensemble convergence von Russo, John, Copperman, Jeremy T., Aristoff, David, Simpson, Gideon, Zuckerman, Daniel M.

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Exploring Optimal Resource Allocation for Weighted Ensemble Resampling of Rare Events von Copperman, Jeremy T., Aristoff, David, Zuckerman, Daniel M.

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Data-driven variance reduction in weighted ensemble simulations von Ryu, Won Hee, Russo, John D., Johnson, Mats S., Thompson, Jeffrey P., LeBard, David N., Simpson, Gideon, Aristoff, David, Webber, Robert J., Copperman, Jeremy T., Zuckerman, Daniel M.

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Unbiased Trajectory-Based Estimation of Stationary Distributions and Splitting Probabilities von Russo, John D., Aristoff, David, Simpson, Gideon, Copperman, Jeremy T., Zuckerman, Daniel M.

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Mode Localization in the Cooperative Dynamics of Protein Recognition von Copperman, Jeremy T., Guenza, Marina G.

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A Coarse-Grained Langevin Equation for Protein Dynamics: Global Anisotropy and a Mode Approach to Local Complexity von Copperman, Jeremy T., Guenza, Marina G.

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In Silico Insight into Transitional Structures and Barrier-Crossing Dynamics of DNA and RNA Oligomers von Copperman, Jeremy T., Guenza, Marina G.

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Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å von Flores, 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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Computational Estimation of Microsecond to Second Atomistic Folding Times von Adhikari, Upendra, Mostofian, Barmak, Copperman, Jeremy, Subramanian, Sundar Raman, Petersen, Andrew A, Zuckerman, Daniel M

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

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Featurizing Koopman mode decomposition for robust forecasting von Aristoff, David, Copperman, Jeremy, Mankovich, Nathan, Davies, Alexander

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Conformational landscape of a virus by single-particle X-ray scattering von Hosseinizadeh, Ahmad, Mashayekhi, Ghoncheh, Copperman, Jeremy, Schwander, Peter, Dashti, Ali, Sepehr, Reyhaneh, Fung, Russell, Schmidt, Marius, Yoon, Chun Hong, Hogue, Brenda G, Williams, Garth J, Aquila, Andrew, Ourmazd, Abbas

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Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility von deLorimier, Elaine, Hinman, Melissa N., Copperman, Jeremy, Datta, Kausiki, Guenza, Marina, Berglund, J. Andrew

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Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 angstrom von Flores, 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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Morphodynamical cell-state description via live-cell imaging trajectory embedding von Copperman, Jeremy, Gross, Sean M., Hwan Chang, Young, Heiser, Laura M., Zuckerman, Daniel M.

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Recovering hidden information from live-cell trajectories to predict the biological pathway activity underlying cell state change decisions von Copperman, Jeremy, Hwan Chang, Young, McLean, Ian, Heiser, Laura M., Zuckerman, Daniel M.

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Computational Estimation of Microsecond to Second Atomistic Folding Times (vol 141, pg 6519, 2019) von Adhikari, Upendra, Mostofian, Barmak, Copperman, Jeremy, Subramanian, Sundar Raman, Petersen, Andrew A., Zuckerman, Daniel M.

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