Zuckerman, Daniel M. - Department of Computational Biology, University of Pittsburgh

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Zuckerman, Daniel M. - Department of Computational Biology, University of Pittsburgh

Dynamic reaction paths and rates through importancesampled stochastic dynamics
On the structural convergence of biomolecular simulations
Simulation of an Ensemble of Conformational Transitions in a United-Residue Model of Daniel M. Zuckerman
Peptide Conformational Equilibria Computed via a Single-Stage Shifting Protocol F. Marty Ytreberg* and Daniel M. Zuckerman
A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange
Single-ensemble nonequilibrium path-sampling estimates of free energy differences
Vesiclevesicle adhesion by mobile lockandkey molecules: DebyeHu ckel theory and Monte Carlo simulation
Integrated library-based growth and Monte Carlo simulations allow for improved sampling and free
Resolution Exchange Simulation Edward Lyman,* F. Marty Ytreberg, and Daniel M. Zuckerman
Transition events in butane simulations: Similarities across models Daniel M. Zuckermana)
Erratum: "Single-ensemble nonequilibrium path-sampling estimates of free energy differences" [J. Chem. Phys. 120, 10876 (2004)]
Efficient Use of Nonequilibrium Measurement to Estimate Free Energy Differences for Molecular Systems
Efficient and verified simulation of a path ensemble for conformational change in a united-residue
A general library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic
Resampling improves the efficiency of a "fast-switch" equilibrium sampling protocol
A "black-box" re-weighting analysis can correct flawed
Supplementary material (Ytreberg and Zuckerman) Here we attempt to make precise the approximations made in applying black-box re-
A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation.
Resolution exchange simulation with incremental Edward Lyman
Transition-event durations in one-dimensional activated processes Bin W. Zhang and David Jasnowa
Journal of Molecular Graphics and Modelling 22 (2004) 359368 Tools for channels: moving towards molecular calculations of
Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model
Comparison of free energy methods for molecular systems F. Marty Ytreberga
Theory of a Systematic Computational Error in Free Energy Differences Daniel M. Zuckerman1,* and Thomas B. Woolf2,
Exact thermodynamic formulation of chemical association Michael E. Fisher and Daniel M. Zuckerman
Vesicle-vesicle adhesion by mobile lock-and-key molecules: Debye-Huckel theory and Monte Carlo simulation
Flexible-Planes Monte Carlo Code (Go-Flex) v.RC.1. Release Candidate 1 (Build 3.4.0.7.)
Confidence Intervals via Hypergeometric Distribution We have developed a method to analyze the convergence of a simulation trajectory which relies
Asymmetric primitive-model electrolytes: Debye-Huckel theory, criticality, and energy bounds Daniel M. Zuckerman,* Michael E. Fisher, and Stefan Bekiranov
Exact thermodynamic formulation of chemical association Michael E. Fisher and Daniel M. Zuckerman
arXiv:physics/0209098v127Sep2002 Rapid Determination of Multiple Reaction
Annealed importance sampling of peptides Edward Lyman
Simple estimation of absolute free energies for biomolecules F. Marty Ytreberga