The overall simulation was a three-compartment model in which the laws of mass transfer kinetics were used.

Medium compartment. This compartment included the medium environment from which cells receive their respective NM dose. The initial dose condition was taken as the 10 nM applied in the fluorescence assay. The medium compartment NM dose evolution with time was then described asd[Med]dt=kads*[Med]+kdes*[Mem](10)where [Med] was the concentration (nM) of NM in medium, [Mem] was the concentration (nM) of NM adhered to the cell membrane, and kads and kdes were the first-order rate constants for adsorption and desorption to and from the cell membrane, respectively.

Cell membrane compartment. The cell membrane compartment was defined as the outer boundary of the cell with which the NM reversibly binds. This compartment separated the medium from the internal space of the cell. NMs that were internalized by the cell first adsorbed to this compartment through the adsorption rate constant, kads. Once adsorbed, NMs (i) left this compartment through desorption, kdes, or (ii) entered the cell via kint as expressed byd[Mem]dt=kads*[Med]kdes*[Mem]kint*[Mem](11)with parameters described above.

Cell space compartment. The cell space compartment received NMs that have transported inside the cell via the first-order rate constant for internalization (kint). Here, NMs can become degraded if the process occurs (determined through the fluorescence assay). The cell space compartment NM dose evolution as a function of time was then described asd[Cell]dt=kint*[Mem]kdeg*[Cell](12)where [Cell] was the concentration (nM) of NM in cell interior at time t and kdeg was the first-order rate constant for degradation of QD obtained from optimization to raw datasets (see below). The degradation rate constant was used to track quantities of NM degraded over the course of the experiment.

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