24 citations · 48 across the 15 of their papers we have counts for
4 papers · 1 filter
Pathway Histogram Analysis of Trajectories: A general strategy for quantification of molecular mechanisms
Ernesto Suárez, Daniel M. Zuckerman
A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions an…
Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture
Jeremy Copperman, David Aristoff, Dmitrii E. Makarov +2
Probability currents are fundamental in characterizing the kinetics of non-equilibrium processes. Notably, the steady-state current for a source-sink system can provide th…
Stochastic Simulation to Visualize Gene Expression and Error Correction in Living Cells
Kevin Y. Chen, Daniel M. Zuckerman, Philip C. Nelson
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories ins…
Statistical uncertainty analysis for small-sample, high log-variance data: Cautions for bootstrapping and Bayesian bootstrapping
Barmak Mostofian, Daniel M. Zuckerman
Recent advances in molecular simulations allow the evaluation of previously unattainable observables, such as rate constants for protein folding. However, these calculations are us…