Copernicus: a new paradigm for parallel adaptive molecular dynamics. - Sander Pronk; Per Larsson; Iman Pouya; Gregory R. Bowman; Imran S. Haque; Kyle Beauchamp; Berk Hess; Vijay S. Pande; Peter M. Kasson; Erik Lindahl (SC, 2011)

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale. - Daniel L. Parton; Patrick B. Grinaway; Sonya M. Hanson; Kyle Beauchamp; John D. Chodera (PLoS Comput. Biol., 2016)

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. - Peter K. Eastman; Jason M. Swails; John D. Chodera; Robert McGibbon; Yutong Zhao; Kyle Beauchamp; Lee-Ping Wang; Andrew C. Simmonett; Matthew P. Harrigan; Chaya D. Stern; Rafal P. Wiewiora; Bernard R. Brooks; et al. (PLoS Comput. Biol., 2017)

Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems. - Josh Fass; David A. Sivak; Gavin E. Crooks; Kyle Beauchamp; Benedict J. Leimkuhler; John D. Chodera (Entropy, 2018)