Publications

Refereed Journal

  • C.R.Sweet, B.J.Leimkuhler.
    The Canonical Ensemble via Symplectic
    Integrators using Nosé and Nose-Poincaré chains.
    J. Chem. Phys., 121, 108-126, 2004.

  • C.R.Sweet, B.J.Leimkuhler.
    A Hamiltonian Formulation for
    Recursive Multiple Thermostats in a Common Timescale.
    SIAM J. on Applied Dynamical Systems, 4, 187-216, 2005.

  • Paul Brenner, Christopher R. Sweet, Dustin VonHandorf, and Jesús A. Izaguirre.
    Accelerating the replica exchange method through an efficient all-pairs exchange.
    J. Chem. Phys., 126, 126-132, 2007.
  • Christopher R. Sweet, Paula Petrone, Vijay S. Pande and Jesús A. Izaguirre.
    Normal Mode Partitioning of Langevin Dynamics for Biomolecules.
    J. Chem. Phys., 128-11, 1-14, 2008
    [Supplementary Information]

  • Christopher R. Sweet, Scott S. Hampton, Robert D. Skeel and Jesús A. Izaguirre.
    Separable Shadow Hybrid Monte Carlo Method.
    J. Chem. Phys., 131, 174106 (2009)
    [Supplementary Information]

  • Trevor Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesús A. Izaguirre.
    MDLab: A Molecular Dynamics Simulation Prototyping Environment.
    J. Comp. Chem. 31(7):1345-1356, 2010. (DOI: 10.1002/jcc.21418)

Refereed Conference Proceedings

  • E.Barth, B.J.Leimkuhler, C.R.Sweet.
    Approach to Thermal
    Equilibrium in Biomolecular Simulation.
    New Algorithms for Macromolecular Simulation, Springer Berlin Heidelberg., 49, 125-140, 2006.
  • T. Cickovski, C. Sweet and J. A. Izaguirre.
    MDL, A Domain-Specific
    Language for Molecular Dynamics.
    In IEEE Proceedings of 40th Annual Simulation
    Symposium, Norfolk, VA. 256-266, 2007.  
  • Christopher R. Sweet and J. A. Izaguirre.
    Backward error analysis of multiscale symplectic integrators and propagators.
    Proc. Third International Conference Multiscale Materials Modelling MMM2006,
    Freiburg, Germany. September 2006.  
  • Jesús  A. Izaguirre, Chris R. Sweet, and Vijay S. Pande.
    Multiscale dynamics of macromolecules using Normal Mode Langevin.
    Pac. Symp. Biocomput. 2010:240-51.  
  • Jesús A. Izaguirre and Christopher R. Sweet.
    Adaptive dimensionality reduction of stochastic differential equations for protein dynamics
    Proc. Second International Workshop on Model Reduction in Reacting Flows, April 2009, Notre Dame, IN.

Papers Under Revision

  • C.R.Sweet, B.J.Leimkuhler.
    Higher Order Symmetric Variable Stepsize Methods.
    Submitted to Numerische Mathematik.
  • Christopher R. Sweet, Scott S. Hampton, Jesús A. Izaguirre.
    Optimal implementation of the Shadow hybrid Monte Carlo method.
    Submitted to SIAM J. on Scientific Computing.
  • Faruck Morcos, Santanu Chatterjee, Christopher L. McClendon, Paul R. Brenner, Roberto Lopez-Rendon, John Zintsmaster, Maria Ercsey-Ravasz, Chris R. Sweet, Matthew P. Jacobson, Jeffrey W. Peng, and Jesús A. Izaguirre.
    Modeling the conformational ensembles of NMR relaxation dispersion: molecular dynamics study of slow functional motions in the Pin1-WW domain.
    Submitted. 2009.
  • Santanu  Chatterjee, Christopher R. Sweet, and Jesús A. Izaguirre.
    String Method with Collective Variables from Normal Modes: Application to Alanine Dipeptide.
    Submitted. 2009.

Other