We include here a pair of examples of molecular dynamics simulation trajectories that
reflect the general trends highlighted in Figure 5. The sequences of the nucleic acid
constructs shown here correspond to Sequence 1 (the one used in Figure 5). These
trajectories have been stripped of waters and monatomic ions, and they have been
downsampled to 1 frame per nanosecond (such that each PDB file represents the state of the
system one 1 nanosecond after the previous file).
In the author's notes, the "3prime_boundary" trajectory included here corresponds to
"V-like Trajectory #3".
In the author's notes, the "5prime_boundary" trajectory included here corresponds to
"II-like Trajectory #1".