Trapped Either Way: Lose–Lose Diffusion in Ordered Porous Environments

Understanding diffusion through complex environments is crucial for a wide range of pharmaceutical and biomedical applications. Recently, highly ordered arrays of DNA nanocages have been synthesized with tunable site-specific interactions between nanocages (NCs) and diffusing nanoparticles (NPs), potentially allowing for diffusion control through porous DNA networks[1]. In this work, we simulate the diffusion of NPs through a network of NCs to elucidate the dependence of NP–NC interactions on NP diffusion. We find that both attractive and repulsive interactions decrease the diffusion coefficient of particles in these lattices—a “lose–lose” situation. Through particle tracking, we show that the diffusing particles spend more time inside the cages as we increase the NP–NC attraction. With increasing NP–NC repulsion, the diffusing particles spend increased time in cage-adjacent sites, which are geometrically identical to the cages but lack site-specific attraction or repulsion; this effect also decreases the overall diffusion coefficient. Finally, we show that the diffusion coefficient in these systems can be predicted via a coarse-grained master equation.



[1] Tian, Y. et al. Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels. Nat. Mater. 1–8 (2020) doi:10.1038/s41563-019-0550-x.