Publications








  1. Adelene YL. Sim, Peter Minary, Michael Levitt
    Modeling nucleic acids
    Current Opinion in Structural Biology , 22(3), 273-278 (2012).
  1. Junjie Zhang, Peter Minary, Michael Levitt
    Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images
    Proceedings of the National Academy of Sciences , 109(25), 9845-9850 (2012).
  1. Adelene YL. Sim, Michael Levitt, Peter Minary
    Modeling and design by hierarchical natural moves
    Proceedings of the National Academy of Sciences , 109(8), 2890-2895 (2012).
  1. Peter Minary, Michael Levitt
    Conformational Optimization with Natural Degrees of Freedom: A Novel Chain Breakage/Closure Algorithm
    Journal of Computational Biology , 17(8), 993-1010 (2010).
  1. Peter Minary, Mark E. Tuckerman, Glenn J. Martyna
    Dynamical Spacial Warping: A Novel Method for the Conformational Sampling of Biophysical Structure
    SIAM Journal of Scientific Computing , 30, 2055-2083 (2008).
  1. Peter Minary, Michael Levitt
    Probing Protein Fold Space with a Simplified Model
    Journal of Molecular Biology , 375, 920 (2008).
  1. Peter Minary, Michael Levitt
    Discussion of the Equi-Energy Monte Carlo Method
    Annals of Statistics , 34, 1636 (2006).
  1. Radu Iftimie, Peter Minary, Mark E. Tuckerman
    Ab initio molecular dynamics: Concepts, recent developments, and future trends
    Proceedings of the National Academy of Science , 102, 6654 (2005).
  1. Peter Minary, Mark E. Tuckerman, Glenn J. Martyna
    Long time molecular dynamics for enhanced conformational sampling in biomolecular systems
    Physical Review Letters , 93, 150201 (2004).
  1. Peter Minary, Mark E. Tuckerman
    Reaction pathway leading to the [4+2] Diels-Alder adduct on Si(100)-2x1
    Journal of the American Chemical Society;(Communication), 126, 13920 (2004)
  1. Peter Minary, Joseph A. Morrone, Dawn A. Yarne, Mark E. Tuckerman, Glenn J. Martyna
    Long range interactions on wires: A reciprocal space based formalism
    Journal of Chemical Physics, 121, 11949 (2004)
  1. Peter Minary, Mark E. Tuckerman
    Reaction chemistry between 1,3-butadiene and the Si(100)-2x1 surface
    Journal of the American Chemical Society;(Communication), 127, 1110 (2005)
  1. Peter Minary, Glenn J. Martyna, Mark E. Tuckerman
    Algorithms and novel Applications based on the isokinetic ensemble II: Ab initio molecular dynamics.
    Journal of Chemical Physics,118,2527 (2003).
  1. Peter Minary, Glenn J. Martyna, Mark E. Tuckerman
    Algorithms and novel Applications based on the isokinetic ensemble I: Biophysical and path integral molecular dynamics.
    Journal of Chemical Physics,118,2510 (2003).
    This article was selected in the 2003 February issue of the
    Virtual Journal of Biological Physics Research.
  1. Mark E. Tuckerman, Peter Minary, Katianna A. Pihakari, Glenn J. Martyna
    A New Reciprocal Space Based Method for Treating Long Range Interactions In Ab Initio and Force-Field Based Calculations for Surfaces, Wires, and Clusters.
    Computational Methods for Macromolecules: Challenges and Applications.
    H. H. Gan, T. Schlick eds.,Lecture Notes in Computational Science and Engineering,Vol. 24, Springer, New York (2002).
  1. Peter Minary, Mark E. Tuckerman, Katianna A. Pihakari, Glenn J. Martyna
    A new reciprocal space based treatment of long range interactions on surfaces.
    Journal of Chemical Physics,116,5351 (2002).
  1. Lula Rosso, Peter Minary, Zhongwei Zhu, Mark E. Tuckerman
    On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles.
    Journal of Chemical Physics,116,4389 (2002).
  1. Peter Minary, Pal Jedlovszky, Mihaly Mezei, Laszlo Turi
    A Comprehensive Liquid Simulation Study of Neat Formic Acid.
    Journal of Physical ChemistryB,104,8287 (2000).
  1. Laszlo Turi, Peter Minary, Peter J. Rossky
    Non-linear response and hydrogen bond dynamics for electron solvation in methanol.
    Chemical Physics Letters,316,465 (2000).
  1. Peter Minary, Laszlo Turi, Peter J. Rossky
    Non-adiabatic molecular dynamics simulation of photo-excitation experiments for the solvated electron in methanol.
    Journal of Chemical Physics,100,10953 (1999).