From the standpoint of simulations, a quantum dot would be more like a smallish 3D system. Depending on the number of atoms in the qdot, it could be simulated directly. You would simply need set up an isolated arrangement of atoms. Some DFT programs allow you to turn off periodic boundary conditions (PBC), otherwise, you might simply leave the PBC on, but make the box big enough that the interactions between neighboring qdots can be neglected.
It might be more challenging to simulate a large quantum dot, one with too many atoms to directly solve using methods like DFT. These so-called mesoscale systems are challenging because they aren't well described by infinite-size approximations (like PBC), but they are too big to study as finite-size systems.
I am not very familiar with any of the details of specific DFT codes (like Quantum ESPRESSO), so hopefully someone more knowledgeable can answer with the specific considerations for how to set this up.