The coarse-grained (CG) models for the TMA-Au NPs and for the citrate ions studied herein were reported in our previous work. As described in detail in Ref. 31, these models were developed based on the results of all-atom (AA) simulations of interacting TMA-Au NP sub-sections in citrate-rich water solvent. Explicit and implicit solvent representations of the system were proposed, based on the MARTINI force-field, where a CG bead accounts for 3-4 heavy atoms (resolution of ∼ 5 Å). In particular, we considered the implicit solvent model, based on the "dry" MARTINI force-field. This level of resolution is sufficient to explore the submolecular dynamics of complex supramolecular aggregates, while being able to reach the relevant sizes and timescales that characterize their collective, macroscopic behavior (see, e.g., Refs. 31,82,83). It is worth noting that the information extracted from such approximated models should be considered qualitative. However, the results obtained from the proposed simulations can be still reliably used to compare the dynamics of the system subjected to different external conditions, and to draw indicative trends of the resulting dynamic behavior, as shown in our previous work and in the present article.