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The invention relates to methods of making optical waveguide structures by way of molecular beam epitaxy (MBE). The method comprises the steps of : (1) providing a single crystal substrate in an ultra-high vacuum (UHV) environment, wherein the single crystal substrate has a first index of refraction; (2) heating the single crystal substrate; (3) depositing an epitaxial oxide layer having a rare-earth dopant and a second index of refraction on the single crystal substrate, wherein the epitaxial oxide layer is deposited by way of at least first, second, and third molecular beam fluxes; and (4) depositing a cladding layer on the single crystal oxide layer, wherein the cladding layer has a third index of refraction that is the same or about the same as the first index of refraction of the single crystal substrate, and wherein the second index of refraction is greater than the first and third indexes of refraction.