Publications

R. T. McGibbon and V. S. Pande, "Identification of simple reaction coordinates from complex dynamics" arXiv:1602.08776 (2016) [arXiv]

L.-P. Wang, R. T. McGibbon, V. S. Pande and T. J. Martinez, "Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways" J. Chem. Theory Comput. (2015) [doi] [pdf]

R. T. McGibbon and V. S. Pande, "Efficient maximum likelihood parameterization of continuous-time Markov processes" J. Chem. Phys. (2015) [doi] [pdf]

R. T. McGibbon, K. A. Beauchamp, M. P. Harrigan, C. Klein, J. M. Swails, C. X. Hernandez, C. R. Schwantes, L.-P. Wang, T. J. Lane and V. S. Pande, "MDTraj: a modern, open library for the analysis of molecular dynamics trajectories" Biophys J. (2015) [doi] [pdf]

L.-P. Wang, A. Titov, R. T. McGibbon, F. Liu, V. S. Pande, and T. J. Martinez, "Discovering chemistry with an ab initio nanoreactor" Nature Chem. (2014) [doi] [pdf]

R. T. McGibbon and V. S. Pande, "Variational cross-validation of slow dynamical modes in molecular kinetics" J. Chem. Phys. (2015) [doi] [pdf]

C. R. Schwantes, R. T. McGibbon, and V. S. Pande, "Perspective: Markov Models for Long-Timescale Biomolecular Dynamics" J. Chem. Phys. (2014) [doi] [pdf]

R. T. McGibbon, B. Ramsundar, M. M. Sultan, G. Kiss and V. S. Pande, "Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models" ICML (2014) [jmlr] [arXiv]

R. T. McGibbon, C. R. Schwantes, and V. S. Pande, "Statistical Model Selection for Markov Models of Biomolecular Dynamics" J. Phys. Chem B (2014) [doi] [pdf]

R. T. McGibbon and V. S. Pande, "Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics" J. Chem. Theory Comput. (2013) [doi] [pdf]

K. A. Beauchamp, R. T. McGibbon, Y. S. Lin and V. S. Pande, "Simple few-state models reveal hidden complexity in protein folding," Proc. Natl. Acad. Sci. U. S. A. (2012) [doi] [pdf]

A. J. Morris, R. T. McGibbon and A. B. Bocarsly, "Electrocatalytic Carbon Dioxide Activation: The Rate-Determining Step of Pyridinium-Catalyzed CO2 Reduction," ChemSusChem (2011) [doi] [pdf]