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Daniel M. Zuckerman

Identifiers

  • name variant Daniel M. Zuckerman 0.60 · backfill

Papers (41)

  1. Pathway Histogram Analysis of Trajectories: A general strategy for quantification of molecular mechanisms physics.chem-ph · 2018 · author #2
  2. Stochastic Simulation to Visualize Gene Expression and Error Correction in Living Cells q-bio.SC · 2018 · author #2
  3. Statistical uncertainty analysis for small-sample, high log-variance data: Cautions for bootstrapping and Bayesian bootstrapping stat.AP · 2018 · author #2
  4. Biophysical comparison of ATP-driven proton pumping mechanisms suggests a kinetic advantage for the rotary process depending on coupling ratio q-bio.SC · 2016 · author #2
  5. A proposal for regularly updated review/survey articles: "Perpetual Reviews" cs.DL · 2015 · author #2
  6. Efficient Stochastic Simulation of Chemical Kinetics Networks using a Weighted Ensemble of Trajectories q-bio.MN · 2013 · author #4
  7. Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories physics.bio-ph · 2012 · author #7
  8. Equilibrium Sampling in Biomolecular Simulation q-bio.BM · 2010 · author #1
  9. Extending fragment-based free energy calculations with library Monte Carlo simulation: Annealing in interaction space q-bio.QM · 2010 · author #3
  10. Automated sampling assessment for molecular simulations using the effective sample size physics.comp-ph · 2010 · author #3
  11. Symmetry of forward and reverse path populations physics.comp-ph · 2010 · author #2
  12. Steady-state simulations using weighted ensemble path sampling physics.bio-ph · 2009 · author #3
  13. Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Studied Using Well-Sampled Semi-Atomistic Simulations physics.bio-ph · 2009 · author #4
  14. Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo physics.bio-ph · 2009 · author #3
  15. Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase physics.bio-ph · 2009 · author #2
  16. Weighted Ensemble Path Sampling for Multiple Reaction Channels physics.bio-ph · 2009 · author #3
  17. Absolute free energies estimated by combining pre-calculated molecular fragment libraries physics.bio-ph · 2009 · author #3
  18. The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures physics.comp-ph · 2008 · author #2
  19. A library-based Monte Carlo technique enables rapid equilibrium sampling of a protein model with atomistic components physics.bio-ph · 2008 · author #4
  20. Annealed importance sampling of dileucine peptide q-bio.BM · 2007 · author #2
  21. Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model physics.bio-ph · 2007 · author #3
  22. Transition-Event Durations in One Dimensional Activated Processes cond-mat.stat-mech · 2006 · author #3
  23. A "black-box" re-weighting analysis can correct flawed simulation data, after the fact physics.comp-ph · 2006 · author #2
  24. The structural de-correlation time: A robust statistical measure of convergence of biomolecular simulations q-bio.QM · 2006 · author #2
  25. Comparison of free energy methods for molecular systems physics.bio-ph · 2006 · author #3
  26. A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation physics.bio-ph · 2006 · author #1
  27. Ensemble based convergence assessment of biomolecular trajectories physics.bio-ph · 2006 · author #2
  28. Resolution exchange simulation with incremental coarsening physics.bio-ph · 2006 · author #2
  29. Simple estimation of absolute free energies for biomolecules physics.bio-ph · 2005 · author #2
  30. Resolution exchange simulation q-bio.BM · 2005 · author #3
  31. Peptide Conformational Equilibria Computed via a Single-Stage Shifting Protocol physics.bio-ph · 2004 · author #2
  32. Single-ensemble nonequilibrium path-sampling estimates of free energy differences physics.comp-ph · 2004 · author #2
  33. Efficient use of non-equilibrium measurement to estimate free energy differences for molecular systems physics.comp-ph · 2004 · author #2
  34. Unbiased simulation of structural transitions in calmodulin physics.bio-ph · 2003 · author #1
  35. Rapid Determination of Multiple Reaction Pathways in Molecular Systems: The Soft-Ratcheting Algorithm physics.chem-ph · 2002 · author #1
  36. Systematic Finite-Sampling Inaccuracy in Free Energy Differences and Other Nonlinear Quantities physics.comp-ph · 2002 · author #1
  37. Theory of Systematic Computational Error in Free Energy Differences physics.comp-ph · 2002 · author #1
  38. Transition Events in Butane Simulations: Similarities Across Models physics.chem-ph · 2001 · author #1
  39. Extrapolative Analysis of Fast-Switching Free Energy Estimates in a Molecular System physics.chem-ph · 2001 · author #1
  40. Asymmetric Primitive-Model Electrolytes: Debye-Huckel Theory, Criticality and Energy Bounds cond-mat.stat-mech · 2001 · author #1
  41. Efficient Dynamic Importance Sampling of Rare Events in One Dimension physics.comp-ph · 2000 · author #1

Mentions

  • 1502.01329 #2 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 1303.5986 #4 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 1210.3094 #7 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 1009.2958 #1 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 1006.4111 #3 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 1002.3802 #3 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 1002.2402 #2 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 0910.5255 #3 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 0910.5136 #4 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 0910.2509 #3 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 0910.1582 #2 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 0902.2772 #3 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 0901.3944 #3 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 0810.1963 #2 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 0809.3809 #4 · backfill · confidence 0.70 Daniel M. Zuckerman
  • 0704.0464 #2 · backfill · confidence 0.70 Daniel M. Zuckerman

Frequent Coauthors