Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. - Nandou Lu; David A. Kofke; Thomas B. Woolf (J. Comput. Chem., 2004)

Multiple pathways in conformational transitions of the alanine dipeptide: An application of dynamic importance sampling. - Hyunbum Jang; Thomas B. Woolf (J. Comput. Chem., 2006)

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. - Naveen Michaud-Agrawal; Elizabeth J. Denning; Thomas B. Woolf; Oliver Beckstein (J. Comput. Chem., 2011)

Computing ensembles of transitions from stable states: Dynamic importance sampling. - Juan R. Perilla; Oliver Beckstein; Elizabeth J. Denning; Thomas B. Woolf (J. Comput. Chem., 2011)

Adaptive exploration for large-scale protein analysis in the molecular dynamics database. - Sarana Nutanong; Nick Carey; Yanif Ahmad; Alexander S. Szalay; Thomas B. Woolf (SSDBM, 2013)

Controlling Collective Motions of Self-Propelled Particles by Mean Field Couplings Defined by Topology. - Thomas B. Woolf; Justin Tervala; Ian Carter (CISS, 2021)