Entanglement in massive coupled oscillators. - Nathan L. Harshman; William F. Flynn (Quantum Inf. Comput., 2011)

Asynchronous replica exchange software for grid and heterogeneous computing. - Emilio Gallicchio; Junchao Xia; William F. Flynn; Baofeng Zhang; Sade Samlalsingh; Ahmet Mentes; Ronald M. Levy (Comput. Phys. Commun., 2015)

Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. - Junchao Xia; William F. Flynn; Emilio Gallicchio; Bin W. Zhang; Peng He; Zhiqiang Tan; Ronald M. Levy (J. Comput. Chem., 2015)

Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease. - William F. Flynn; Max W. Chang; Zhiqiang Tan; Glenn Oliveira; Jinyun Yuan; Jason F. Okulicz; Bruce E. Torbett; Ronald M. Levy (PLoS Comput. Biol., 2015)

Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015. - Nan-Jie Deng; William F. Flynn; Junchao Xia; R. S. K. Vijayan; Baofeng Zhang; Peng He; Ahmet Mentes; Emilio Gallicchio; Ronald M. Levy (J. Comput. Aided Mol. Des., 2016)

A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. - Rajat Kumar Pal; Kamran Haider; Divya Kaur; William F. Flynn; Junchao Xia; Ronald M. Levy; Tetiana Taran; Lauren Wickstrom; Tom Kurtzman; Emilio Gallicchio (J. Comput. Aided Mol. Des., 2017)

Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. - Rajat Kumar Pal; Kamran Haider; Divya Kaur; William F. Flynn; Junchao Xia; Ronald M. Levy; Tetiana Taran; Lauren Wickstrom; Tom Kurtzman; Emilio Gallicchio (J. Comput. Aided Mol. Des., 2017)

Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials. - Junchao Xia; William F. Flynn; Ronald M. Levy (J. Chem. Inf. Model., 2018)

Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. - Junchao Xia; William F. Flynn; Emilio Gallicchio; Keith Uplinger; Jonathan D. Armstrong; Stefano Forli; Arthur J. Olson; Ronald M. Levy (J. Chem. Inf. Model., 2019)