In each case, the NPs form a single cluster within the first few microseconds. All the final aggregates appear to be stable but relatively flexible in shape. Interestingly, the aggregate topology strongly depends on the composition of the ligand shell, as detailed in the following paragraphs. All-MUS NPs aggregate as clusters of dumbbells. Figure shows two representative aggregates obtained from the simulations of all-MUS NPs. Snapshots of all the aggregates can be found in Figure . The aggregates appear quite spherical, but at closer inspection, they are composed of dimers loosely bound to each other. We thus analyzed the structure of the all-MUS aggregates in more detail, as shown in Figure . We calculated the NP-NP radial distribution function g(r) in the last 3 µs of the simulations (when the aggregates were formed and stable). The g(r) presented in Figure , obtained as an average over the 5 independent simulations, shows two primary peaks, one at 2.1 nm, which corresponds to the hydrophobic bond, and one at about 4.7 nm, which corresponds to the ionbridged contact. We designed a tailored analysis of the aggregates to appreciate the network of NP-NP connections and obtain the precise aggregate topology. We assigned each NP to the node of an undirected graph, in which the edges represent the hydrophobic bonds or ion-bridged contacts. The operational definition of these two different connections is described in the SI. Figure shows, as a representative example, the network graph we obtained for the aggregate shown in Figure . The connection between the NPs within the dimers is hydrophobic, while the connection among different dimers is ion-bridged. . In some cases, like in the aggregate of Figure , the ribbons fold on themselves. In the average g(r) of MUS:OT 1:1 NPs, shown in Figure , the hydrophobic connection region is broader and has two peaks: the second, smaller one represent the second neighbors; the third peak accounts for both third neighbors and ion-bridged contacts, which are less relevant in this case. The graph in Figure shows an example in which all NP-NP connections are hydrophobic contacts.