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DNA nanotechnology has broad applications in biomedical drug delivery and pro- grammable materials. Characterization of the self-assembly of DNA origami and quan- tum dots (QDs) is necessary for the development of new DNA-based nanostructures. We use computation and experiment to show that the self-assembly of 3D hierarchi- cal nanostructures can be controlled by programming the binding site number and their positions on DNA origami. Using biotinylated pentagonal pyramid wireframe DNA origamis and streptavidin capped QDs, we demonstrate that DNA origami with 1 binding site at the outer vertex can assemble multi-meric origamis with up to 6 DNA origamis on 1 QD, and DNA origami with 1 binding site at the inner center can only assemble monomeric and dimeric origamis. Meanwhile, the yield percentages of differ- ent multi-meric origamis are controlled by the QD:DNA-origami stoichiometric mixing ratio. DNA origamis with 2 binding sites at the αγ positions (of the pentagon) make larger nanostructures than those with binding sites at the αβ positions. In general, increasing the number of binding sites leads to increases in the nanostructure size. At high DNA origami concentration, the QD number in each cluster becomes the limiting factor for the growth of nanostructures. We find that reducing the QD size can also affect the self-assembly because of the reduced access to the binding sites from more densely packed origamis. 

We address the challenge of representativity and dynamical consistency when un- bonded fine-grained particles are collected together into coarse-grained particles. We implement a hybrid procedure for identifying and tracking the underlying fine-grained particles—e.g., atoms or molecules—by exchanging them between the coarse-grained particles periodically at a characteristic time. The exchange involves a back-mapping of the coarse-grained particles into fine-grained particles, and a subsequent reassign- ment to coarse-grained particles conserving total mass and momentum. We find that an appropriate choice of the characteristic exchange time can lead to the correct effec- tive diffusion rate of the fine-grained particles when simulated in hybrid coarse-grained dynamics. In the compressed (supercritical) fluid regime, without the exchange term, fine-grained particles remain associated to a given coarse-grained particle, leading to substantially lower diffusion rates than seen in all-atom molecular dynamics of the fine- grained particles. Thus, this work confirms the need for addressing the representativity of fine-grained particles within coarse-grained particles, and offers a simple exchange mechanism so as to retain dynamical consistency between the fine- and coarse- grained scales.