Decoupling Structure and Property in Discrete Protein Diffusion: Alignment Dynamics and Collapse Mechanisms
Junqi Wu, Liyan Dong, Nuo Jia, Longyu Li, Hao Zhang
This paper investigates the temporal dynamics of discrete protein diffusion models, revealing a decoupling between structural alignment and property optimization, and identifies a structural collapse regime due to Coulombic repulsion.
bioRxiv · Feb 8, 2026 · PreprintBioinformatics