Ermod: Fast and versatile computation software for solvation free energy with approximate theory of solutions. - Shun Sakuraba; Nobuyuki Matubayasi (J. Comput. Chem., 2014)

Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points. - Robert C. Harris; Nan-Jie Deng; Ronald M. Levy; Ryosuke Ishizuka; Nobuyuki Matubayasi (J. Comput. Chem., 2017)

Effective charges of ionic liquid determined self-consistently through combination of molecular dynamics simulation and density-functional theory. - Ryosuke Ishizuka; Nobuyuki Matubayasi (J. Comput. Chem., 2017)

Prediction of Water Diffusion in Wide Varieties of Polymers with All-Atom Molecular Dynamics Simulations and Deep Generative Models. - Ryo Kawada; Katsuhiro Endo; Kenji Yasuoka; Hidekazu Kojima; Nobuyuki Matubayasi (J. Chem. Inf. Model., 2023)