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Cadmium selenide nanocrystal quantum dots (NC-QDs) are site-selectively synthesized by sequential ion beam implantation of selenium and cadmium ions in a SiO2 matrix through sub-micron apertures followed by a rapid thermal annealing step. The size, areal density and optical emission energy of the NC-QDs are controlled by the ion fluence during implantation and the diameter of implantation aperture. For low fluences and small apertures the emission of these optically active emitters is blue-shifted compared to that of the bulk material by due to quantum confinement. The emission exhibits spectral diffusion and blinking on a second timescales as established also for solution synthesized NC-QDs.

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