SNUPI framework (static analysis): Rapid computational analysis of DNA origami assemblies at near-atomic resolution, ACS Nano (2021)  [Link]

Improved model of single-stranded DNA: Characterizing and harnessing the mechanical properties of short single-stranded DNA in structured assemblies, ACS Nano (2021)  [Link]

Partition and relocation framework (free-form structures): Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint, ACS Nano (2022)  [Link]

Langevin dynamics simulations: A computational model for structural dynamics and reconfiguration of DNA assemblies, Nature Communications (2023)  [Link]

EtBr-binding simulations: Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies, Nature Communications (2024)  [Link]

Graph neural network: Prediction of DNA origami shape using graph neural network, Nature Materials (2024)  [Link]