Accurate transition state generation with an object-aware equivariant elementary reaction diffusion model. - Chenru Duan; Yuanqi Du; Haojun Jia; Heather J. Kulik (Nat. Comput. Sci., 2023)

React-OT: Optimal Transport for Generating Transition State in Chemical Reactions. - Chenru Duan; Guan-Horng Liu; Yuanqi Du; Tianrong Chen; Qiyuan Zhao; Haojun Jia; Carla P. Gomes; Evangelos A. Theodorou; Heather J. Kulik (CoRR, 2024)

Generative Design of Functional Metal Complexes Utilizing the Internal Knowledge of Large Language Models. - Jieyu Lu; Zhangde Song; Qiyuan Zhao; Yuanqi Du; Yirui Cao; Haojun Jia; Chenru Duan (CoRR, 2024)

Optimal transport for generating transition states in chemical reactions. - Chenru Duan; Guan-Horng Liu; Yuanqi Du; Tianrong Chen; Qiyuan Zhao; Haojun Jia; Carla P. Gomes; Evangelos A. Theodorou; Heather J. Kulik (Nat. Mac. Intell., 2025)

AlphaNet: Scaling Up Local Frame-based Atomistic Foundation Model. - Bangchen Yin; Jiaao Wang; Weitao Du; Pengbo Wang; Penghua Ying; Haojun Jia; Zisheng Zhang; Yuanqi Du; Carla P. Gomes; Chenru Duan; Hai Xiao; Graeme Henkelman (CoRR, 2025)

Building-Block Aware Generative Modeling for 3D Crystals of Metal Organic Frameworks. - Chenru Duan; Aditya Nandy; Sizhan Liu; Yuanqi Du; Liu He; Yi Qu; Haojun Jia; Jin-Hu Dou (CoRR, 2025)