Global Optimization of Morse Clusters by Potential Energy Transformations. - Jonathan P. K. Doye; Robert H. Leary; Marco Locatelli 001; Fabio Schoen (INFORMS J. Comput., 2004)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model. - Petr Sulc; Thomas E. Ouldridge; Flavio Romano; Jonathan P. K. Doye; Ard A. Louis (Nat. Comput., 2014)

TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami. - Antonio Suma; Erik Poppleton; Michael Matthies; Petr Sulc; Flavio Romano; Ard A. Louis; Jonathan P. K. Doye; Cristian Micheletti; Lorenzo Rovigatti (J. Comput. Chem., 2019)

Simulation of reversible molecular mechanical logic gates and circuits. - Ian Seet; Thomas E. Ouldridge; Jonathan P. K. Doye (CoRR, 2022)

Reconfigurable nanomaterials folded from multicomponent chains of DNA origami voxels. - Minh Tri Luu; Jonathan F. Berengut; Jiahe Li 014; Jing-Bing Chen; Jasleen Kaur Daljit Singh; Kanako Coffi Dit Glieze; Matthew Turner; Karuna Skipper; Sreelakshmi Meppat; Hannah Fowler; William Close; Jonathan P. K. Doye; et al. (Sci. Robotics, 2024)