If your structure is periodic in the direction transverse to the transport direction, then in principle you are simulating an infinite system (interface). In this case you have an infinite number of eigenstates, and according to bloch's theorem they can be characterized with psi_k(r) = u(r) exp(ikr), where u(r) is a periodic function, and k is parallel to the transport direction.
k-parallel is conserved during transport, so it is a good quantum number, and we calculate transmission as function of k. To describe the contribution for all states, we must integrate over k.
