We report on the isolation of single SiV$^-$ centers in nanodiamonds. We observe the fine-structure of single SiV$^-$ center with improved inhomogeneous ensemble linewidth below the excited state splitting, stable optical transitions, good polarization contrast and excellent spectral stability under resonant excitation. Based on our experimental results we elaborate an analytical strain model where we extract the ratio between strain coefficients of excited and ground states as well the intrinsic zero-strain spin-orbit splittings. The observed strain values are as low as best values in low-strain bulk diamond. We achieve our results by means of H-plasma treatment of the diamond surface and in combination with resonant and off-resonant excitation. Our work paves the way for indistinguishable, single photon emission. Furthermore, we demonstrate controlled nano-manipulation via atomic force microscope cantilever of 1D- and 2D-alignments with a so-far unreached accuracy of about 10nm, as well as new tools including dipole rotation and cluster decomposition. Combined, our results show the potential to utilize SiV$^-$ centers in nanodiamonds for the controlled interfacing via optical coupling of individually well-isolated atoms for bottom-up assemblies of complex quantum systems.
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