Fig. 3: MD simulation of mechanical loading.
From: Realizing mechanical frustration at the nanoscale using DNA origami
a Snapshots of oxDNA configurations under mechanical loading from (i) initial to (xi) adaptable states. Each snapshot represents the conformation in the intervals of 5 × 106 steps. The edges being pulled are highlighted using black arrows in (i). The structure returns to the initial state after removal of external forces (xii). b Snapshots of DNA conformations during deformation from (i) initial to (xi) inadaptable states. The inadaptable mode bounces back to the initial state (xii), with the buckled edge completely recovered. All the edges in the structures are colored based on normalized strain calculated using the local tangent vector \(\overrightarrow{{t}_{{{{\rm{n}}}}}}\) at each location. We use the tangent vector 10-nt upstream (n-10) and downstream (n + 10) to obtain the strain at nt no. n as \({strain}=1-{\left(\overrightarrow{{t}_{n-10}}.\overrightarrow{{t}_{n+10}}\right)}^{2}\) which ranges from 0 to 1. The buckled edge shows the highest local strain in (b) and small kinks also have relatively high strain in (a).
