Papers

A complete list of my publications. For a broader overview of my research interests, check out the research section of the front page.

  1. Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics
    Matthew P. Harrigan; Diwakar Shukla; Vijay S. Pande
    February 12, 2015
    J. Chem. Theory Comput., 2015, 11 (3), pp 1094--1101. doi:10.1021/ct5010017 [pdf]
  2. MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
    Robert T. McGibbon; Kyle A. Beauchamp; Matthew P. Harrigan; Christoph Klein; Jason M. Swails; Carlos X. Hernández; Christian R. Schwantes; Lee-Ping Wang; Thomas J. Lane; Vijay S. Pande
    October 20, 2015
    Biophys. J., 109, 8, pp 1528--1532. doi:10.1016/j.bpj.2015.08.015 [bioRxiv] [pdf]
  3. Osprey: Hyperparameter Optimization for Machine Learning
    Robert T. McGibbon; Carlos X. Hernández; Matthew P. Harrigan; Steven Kearnes; Mohammad M. Sultan; Stanislaw Jastrzebski; Brooke E. Husic; Vijay S. Pande
    September 07, 2016
    JOSS, 1, 5. doi:10.21105/joss.00034
  4. MSMBuilder: Statistical Models for Biomolecular Dynamics
    Matthew P. Harrigan; Mohammad M. Sultan; Carlos Xavier Hernandez; Brooke E. Husic; Peter Eastman; Christian R. Schwantes; Kyle A. Beauchamp; Robert T. McGibbon; Vijay S. Pande
    January 10, 2017
    Biophys. J., 112, 10--15. doi:10.1016/j.bpj.2016.10.042 [bioRxiv]
  5. OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics
    Peter Eastman; Jason Swails; John D. Chodera; Robert T. McGibbon; Yutong Zhao; Kyle A. Beauchamp; Lee-Ping Wang; Andrew C. Simmonett; Matthew P. Harrigan; Bernard R. Brooks; Vijay S. Pande
    July 26, 2017
    PLOS Comp. Bio. 13(7): e1005659. doi:10.1371/journal.pcbi.1005659 [bioRxiv]
  6. Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter
    Matthew P. Harrigan; Keri A. McKiernan; Veerabahu Shanmugasundaram; Rajiah Aldrin Denny; Vijay S. Pande
    April 04, 2017
    Scientific Reports, 7, 632. doi:10.1038/s41598-017-00256-y [bioRxiv] [medium]
  7. Landmark Kernel tICA For Conformational Dynamics
    Matthew P. Harrigan; Vijay S. Pande
    April 04, 2017
    bioRxiv. doi:10.1101/123752