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Recent progress in nanotechnology enables the production of atomically abrupt interfaces in multilayered junctions, allowing to increase the number of transistors in a processor, as known as Moore’s law, for example. However, uniform electron transport has never been achieved across the entire interfacial area in junctions due to the existence of local defects, causing local heating and reduction in transport efficiency. To date, junction uniformity has been predominantly assessed by cross-sectional transmission electron microscopy, which requires slicing and milling processes with potentially introducing additional damage and deformation. It is therefore essential to develop an alternative non-destructive method. Here we show a non-destructive technique using scanning electron microscopy to map buried junction properties. By controlling the electron-beam energy, we demonstrate the contrast imaging of local junction resistances at a controlled depth. This technique can be applied to any buried junctions, from conventional semiconductor and metal devices to organic devices.