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High quality single Josephson junctions and junction arrays with 10 junctions in series have been fabricated using masked proton beam irradiation damage technology. Monte Carlo simulation of the irradiation damage profile underneath the metal mask has been carried out systematically to guide the metal mask structure design. A high resolution and high aspect ratio metal mask opening was fabricated by focused 30 keV Ga ion beam milling. Various nonconducting oxide buffer layers have been investigated for a Ga contamination free mask fabrication. A contamination free irradiation process and subsequent removal of metal mask after ion irradiation are the keys for the improved properties of junctions fabricated with YBCO.