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Graphene has a 4x4 Pauli matix due to a special property of graphene known as psuedospin, due to the fact that there is a "chirality" associated with the K points of the brillion zone in momentum space, that results from its unusual linear energy dispersion at the Fermi point. This is related to geometric Berrry phase. I don't know if this helps you?

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Q: Why graphene hamiltonian is a 4x4 matrix?
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