Fig. 1: Computational framework for the dynamic analysis of structured DNA assemblies.

a Schematic representation of the framework. The proposed approach combines a structural model for DNA structures based on mechanical and electrostatic forces with a hydrodynamic model that considers the viscous effect and random force of the ionic solution. b Overview of modeling. Each base-pair was defined as a node with three translational and three rotational degrees of freedom, and the connections between nodes were modeled as finite elements. The internal force vector was obtained from the coordinates of the nodes and the geometry and properties of structural and electrostatic connections. The mass matrix was generated using the information on the mass of base sequences and the structural connection. The friction matrix was constructed using the generalized Rotne-Prager-Yamakawa mobility matrix²¹ to consider the effect of viscosity and random thermal force on the structure in the solvent. The dynamic trajectory was computed through a developed time-integrating scheme, allowing us to rapidly obtain trajectories of DNA structures with molecular-level precision.