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Physical unclonable functions (PUFs) are hardware structures in a physical system (e.g. semiconductor, crystals etc.) that are used to enable unique identification of the semiconductor or to secure keys for cryptographic processes. A PUF thus generates a noisy secret reproducible at runtime. This secret can either be used to authenticate the chip, or it is available as a cryptographic key after removing the noise. Latest advancements in the field of quantum hardware, in some cases claiming to achieve quantum supremacy, highly target the fragility of current RSA type classical cryptosystems. As a solution, one would like to develop Quantum PUFs to mitigate such problem. There are several approaches for this technology. In our work we compare these different approaches and introduce the requirements for QTOKSim, a quantum token based authentication simulator testing its performance on a multi-factor authentication protocol.