Quantum-dot Cellular Automata: Computation with Real-world Molecules. - Alessandro P. Bramanti; Alejandro Santana-Bonilla; Ross Rinaldi (Int. J. Unconv. Comput., 2015)

Nanoscale Molecular Automata: From Materials to Architectures. - Ross Rinaldi; Rafael Gutierrez; Alejandro Santana-Bonilla; Gianaurelio Cuniberti; Alessandro P. Bramanti (Computational Matter, 2018)

Modular Software for Generating and Modeling Diverse Polymer Databases. - Alejandro Santana-Bonilla; Raquel Lopez-Rios de Castro; Peike Sun; Robert M. Ziolek; Christian D. Lorenz (J. Chem. Inf. Model., 2023)

Automated Analysis of Soft Matter Interfaces, Interactions, and Self-Assembly with PySoftK. - Raquel Lopez-Rios de Castro; Alejandro Santana-Bonilla; Robert M. Ziolek; Christian D. Lorenz (J. Chem. Inf. Model., 2025)

PUCHIK: A Python Package To Analyze Molecular Dynamics Simulations of Aspherical Nanoparticles. - Hrachya Ishkhanyan; Alejandro Santana-Bonilla; Christian D. Lorenz (J. Chem. Inf. Model., 2025)