Dear Adel, I am indeed looking at the case where the Fermi energy is in the gap of the superconductor. Do you mean to say that the simulation with the superconductor in the scattering region is that same as a simulation with a superconductor as a lead and the scattering region's length increased by the penetration length?
I'm not quite I understand why there would be a difference at these energies. At least not in the nature I see them, where if you consider the case where the superconductor is in the scattering and you increase the superconducting region's length, yet the differences between these two simulations don't change. Regards, Henry