As we know, there are two distinct Dirac points for the free electrons in graphene. Which means that the energy spectrum of the 2$\times$2 Hermitian matrix $H(k_x,k_y)$ has two degenerate points $K$ and $K^{'}$ in BZ.
According to the von Neumann-Wigner theorem (no-crossing theorem): To make two eigenvalues of a Hermitian matrix (depending on some independent real parameters) cross, generally speaking, we need to change at least 3 parameters. But in the 2D graphene case, the variation of only 2 parameters $k_x,k_y$ can cause the energy levels cross.
So I want to know whether there are some physical or mathematical reasons for the existence of Dirac points in graphene.
Answer
Your use of the no-crossing idea is correct - we do not expect level crossings in two dimension to appear unless protected by symmetry. The symmetries in this case are the symmetries of the honeycomb lattice and time reversal. The protection of level crossings by symmetry is ubiquitous in solid-state.
I should add that the existence of these Dirac point is actually slightly more robust than would be implied by simple symmetry arguments. The band structure will still have Dirac cones if one applies any perturbation that does not violate parity, time reversal and is not extremely strong[1]. This is because of the interplay of the Berry's curvature and the Dirac point, which I could find a reference for if you would like.
[1] Extremely strong means that if I imagined increasing the strength of this perturbation up from zero it would drag the Dirac cones from the $K$, $K'$ points into each other. This would mean a perturbation of energy about the bandwidth, which is several electron-volts.
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