Gold nanoparticles functionalized with anionic 11-mercapto-undecane-sulphonate (MUS) and hydrophobic octane-thiol (OT) ligands are promising theranostic platforms, as they have spontaneous, stable interactions with biological membranes. The amphiphilic shell serves, by design, two purposes. The presence of the hydrophobic OT ligand provides hydrophobicity to the NPs, allowing them to penetrate their biological target (the lipid bilayer) spontaneously . The negatively charged MUS ligands instead provide colloidal stability to the NPs in solution. However, recent experimental and theoretical works have shown that MUS:OT nanoparticles can aggregate, in aqueous solution, into oligomers or larger (tens of nm) aggregates. As expected, the aggregation is promoted by increasing salt concentrations . Which are the main driving forces controlling the extent and shape of the aggregates? With atomistic and coarse-grained molecular dynamics simulations, our group and the group of S.