Molecular dynamics simulations of tetrahedra. (a,b) Superposition of molecular dynamics snapshots of FV (a) and MV (b) tetrahedra of 42-bp edge length at 0, 100, and 200 ns. Initial atomic models were generated by TALOS. (c) Total RMSD of all nucleic acid atoms based on the ground-state atomic model generated by TALOS. The FV and DX tetrahedra of 42-bp edge lengths show additional dynamical motion due to vertex fluctuations compared with the MV design. (d) All-atom RMSFs were calculated for the FV, MV, and DX tetrahedra over the 200 ns simulation and mapped as a white-to-red color gradient on each of the structures.