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We present a fabrication scheme and testing results for epitaxial sub-micrometer Josephson junctions. The junctions are made using a high-temperature (1170 K) 'via process' yielding junctions as small as 0.8 µm in diameter by use of optical lithography. Sapphire (Al2O3) tunnel-barriers are grown on an epitaxial Re/Ti multilayer base-electrode. We have fabricated devices with both Re and Al top-electrodes. While room temperature (295 K) resistance versus area data are favorable for both types of top-electrodes, the low-temperature (50 mK) data show that junctions with the Al top-electrode have a much higher subgap resistance. The microwave loss properties of the junctions have been measured by use of superconducting Josephson junction qubits. The results show that high subgap resistance correlates with improved qubit performance.