Daniel M Zuckerman, Associate Professor      

 

Publications
PAPERS AND PREPRINTS

   Papers are divided into the following categories (with some repeats)

   Canonical Sampling of Biomolecules

  • "A general library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models" Artem B. Mamonov, Divesh Bhatt, Derek J. Cashman, Ying Ding, Daniel M. Zuckerman (J. Phys. Chem. B, in press) (PDF)
  • "Resampling improves the efficiency of a “fast-switch” equilibrium sampling protocol,” E. Lyman and D.M. Zuckerman (J. Chem. Phys., 130:081102, 2009) (PDF).
  • "A black-box re-weighting analysis can correct flawed simulation data," F.M. Ytreberg, and D.M. Zuckerman,(Proc. Nat. Acad. Sci. USA 105:7982-7987 (2008).) (click here for PDF); (Supplementary Material PDF)
  • "Annealed importance sampling of peptides," E. Lyman and D.M. Zuckerman, J. Chem. Phys., 127:065101 (2007). (click here for PDF)
  • "A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation," Daniel M. Zuckerman and Edward Lyman, J. Chem. Theory Comput. 2:1200-1202 (2006). (click here for PDF); (Erratum PDF)
  • "Resolution Exchange Simulation with Incremental Coarsening," E. Lyman and D. M. Zuckerman, J. Chem. Theory Comp., 2:656-666 (2006). (click here for PDF);
  • "Resolution Exchange Simulation," E. Lyman, F. M. Ytreberg, and D. M. Zuckerman, Physical Review Letters, Phys. Rev. Lett. 96:028105 (2006). (click here for PDF)
  • "Ensemble based convergence analysis of biomolecular trajectories," E. Lyman and D.M. Zuckerman, Biophysical Journal, 91:164-172(2006). (click here for PDF)

   Conformational Transitions and Reaction Path Sampling

  • "Efficient and verified simulation of a path-ensemble for conformational change in a united-residue model of calmodulin," Bin W. Zhang, David Jasnow, and Daniel M. Zuckerman (Proc. Nat. Acad. Sci. USA, 104:18043-18048 (2007).) (click here for PDF)
  • Transition-event durations in one-dimensional activated processes, Bin W. Zhang, David Jasnow, and Daniel M. Zuckerman, J. Chem. Phys. 126:074504 (2007). (PDF)
  • "Fast Simulation Protocol for Protein Structural Transitions: Modeling of the Relationship of Structure and Function", Arun K. Setty and D.M. Zuckerman in Proteins as Materials, edited by V.P. Conticello, A. Chilkoti, E. Atkins, and D.G. Lynn (Mater. Res. Soc. Symp. Proc. 826E, Warrendale, PA , 2004).
  • "Simulation of an ensemble of conformational transitions in a united-residue model of calmodulin," D. M. Zuckerman J. Phys. Chem. B 108:5127-5137 (2004). PDF Version
  • Transition events in butane simulations: Similarities across models [Journal of Chemical Physics, vol. 116, pp. 2586-2591 (2002)] PDF Versionor Postscript Version
  • Efficient dynamic importance sampling of rare events in one dimension [Physical Review E, vol. 63, No. 016702 (2001)]
    PDF Version or Postscript Version
  • Dynamic reaction paths and rates through importance-sampled stochastic dynamics
    [Journal of Chemical Physics, vol. 111, pp. 9475-9484 (1999)] PDF Version or Postscript Version
  • "Tools for channels: moving towards molecular calculations of gating and permeation in ion channel biophysics" Thomas B. Woolf, Daniel M. Zuckerman, Nandou Lu, Hyunbum Jang, J. Molec. Graph. Model. 22:359-368 (2004).
    PDF Version
  • Rapid Determination of Multiple Reaction Pathways in Molecular Systems: The Soft-Ratcheting Algorithm [www.arXiv.org:physics/0209098]
    PDF Version or Postscript Version
  • Dynamic reaction paths and rates through importance-sampled stochastic dynamics
    [Journal of Chemical Physics, vol. 111, pp. 9475-9484 (1999)] PDF Version or Postscript Version

   Coarse-grained Modeling of Proteins

  • "A general library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models" Artem B. Mamonov, Divesh Bhatt, Derek J. Cashman, Ying Ding, Daniel M. Zuckerman (J. Phys. Chem. B, in press) (PDF).
  • "Efficient and verified simulation of a path-ensemble for conformational change in a united-residue model of calmodulin," Bin W. Zhang, David Jasnow, and Daniel M. Zuckerman (Proc. Nat. Acad. Sci. USA, 104:18043-18048 (2007).) (click here for PDF)
  • "Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model" F.M. Ytreberg, S.Kh. Aroutiounian and D.M. Zuckerman (J. Chem. Theory Comp., 3:1860-1866 (2007).) (click here for PDF)
  • "Fast Simulation Protocol for Protein Structural Transitions: Modeling of the Relationship of Structure and Function", Arun K. Setty and D.M. Zuckerman in Proteins as Materials, edited by V.P. Conticello, A. Chilkoti, E. Atkins, and D.G. Lynn (Mater. Res. Soc. Symp. Proc. 826E, Warrendale, PA , 2004).
  • "Simulation of an ensemble of conformational transitions in a united-residue model of calmodulin," D. M. Zuckerman J. Phys. Chem. B 108:5127-5137 (2004). PDF Version

   Assessment of Sampling Quality

  • "On the structural convergence of biomolecular simulations by determination of the effective sample size," E. Lyman and D.M. Zuckerman (J. Phys. Chem. B, 111:12876-12882 (2007).) (click here for PDF)
  • "Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model" F.M. Ytreberg, S.Kh. Aroutiounian and D.M. Zuckerman (J. Chem. Theory Comp., 3:1860-1866 (2007).) (click here for PDF)
  • "A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation," Daniel M. Zuckerman and Edward Lyman, J. Chem. Theory Comput. 2:1200-1202 (2006). (click here for PDF); (Erratum PDF)
  • "Ensemble based convergence analysis of biomolecular trajectories," E. Lyman and D.M. Zuckerman, Biophysical Journal, 91:164-172(2006). (click here for PDF)

   Free Energy Computations

  • "Absolute free energies estimated by combining pre-calculated molecular fragment libraries,” by X. Zhang, A.B. Mamonov, and D.M. Zuckerman (J. Comp. Chem., in press) (PDF).
  • "Comparison of free energy methods for molecular systems," F.M. Ytreberg, R.H. Swendsen, and D.M. Zuckerman, J. Chem. Phys 125:184114 (2006). (click here for PDF)
  • "Simple estimation of absolute free energies for biomolecules," F. Marty Ytreberg and Daniel M. Zuckerman, J. Chem. Phys. 124:104105 (2006) (click here for PDF)
  • "Peptide conformational equilibria studied via a single-stage shifting protocol," F. Marty Ytreberg and Daniel M. Zuckerman, J. Phys. Chem. B, 109:9096-9103 (2005) (click here for PDF)
  • "Single-ensemble nonequilibrium path-sampling estimates of free energy differences," F.M. Ytreberg and D.M. Zuckerman, J. Chem. Phys. (Communication), 120:10876-10879 (2004). (PDF Version); Erratum (PDF).
  • "Efficient Use of Non-Equilibrium Measurement to Estimate Free Energy Differences for Molecular Systems" F. Marty Ytreberg and Daniel M. Zuckerman J. Comp. Chem. 25:1749-1759 (2004). (PDF Version) (Download Scripts To Perform Extrapolation Analysis)
  • "Systematic Finite-Sampling Inaccuracy in Free Energy Differences and Other Nonlinear Quantities," D. M. Zuckerman and T. B. Woolf  J. Stat. Phys. 114:1303-1323 (2004). (PDF Version)
  • "Theory of a Systematic Computational Error in Free Energy Differences," D. M. Zuckerman and T. B. Woolf, Phys. Rev. Lett, 89:180602 (2002). (PDF Version)
  • Overcoming finite-sample-size errors in fast-switching free energy estimates: Extrapolative analysis of a molecular system [Chemical Physics Letters, vol. 351, pp. 445-453 (2002)]
    PDF Version or Postscript Version

   Ionic Systems and Chemical Association (with M. E. Fisher)

  • Asymmetric Primitive Model Electrolytes: Debye-Huckel Theory, Criticality and Energy Bounds
    [Physical Review E, vol. 64, No. 011206 (2001)] PDF Version or Postscript Version
  • Exact Thermodynamic Formulation of Chemical Association [Journal of Chemical Physics, vol. 109, pp. 7961-7981 (1998)]
    PDF Version or Postscript Version
  • Chemical Association via Exact Thermodynamic Formulations [Chemical Physics Letters, vol. 293, pp. 461-468 (1998)]
  • Critique of Primitive Model Electrolyte Theories [Physical Review E, vol. 56, pp. 6569-6580 (1997)]
    PDF Version or Postscript Version

   Simple Models of Vesicle Adhesion and a Polymer Problem (with R. Bruinsma)

  • Vesicle-Vesicle Adhesion by Mobile Lock-and-Key Molecules: Debye-Huckel Theory and Monte Carlo Simulation
    [Physical Review E., vol. 57, pp. 964-977 (1998)] PDF Version or Poscript Version
  • Forces between Surfaces with Weakly End-Adsorbed Polymers [Journal de Physique II (France), vol. 7, pp. 1111-1121 (1997)]
  • Statistical Mechanics of Membrane Adhesion by Reversible Molecular Bonds [Physical Review Letters, vol. 74, pp. 3900-3903 (1995)]
University of Pittsburgh Department of Computational Biology