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The effect of irradiation with He
+
, F
+
, and P
+
ions with various energies on photoluminescence and structure of Si nanocrystals is studied. It is established that, at low intensities of ion losses, quenching of photoluminescence is provided by individual atomic displacement. However, as this intensity is increased, quenching is accompanied by an increase in nuclear losses. It is believed that, in low-density displacement cascades, mobile defects predominantly drain to the surface, where they form the centers of nonradiative recombination. In contrast, mobile defects partially form stable structural defects within the nanocrystals in dense cascades. It is sufficient to accumulate ∼0.06 dpa for amorphization of Si nanocrystals at 20°C; dependence of this effect on the intensity of the ion energy loss was not observed. It was also noted that there is a low probability of annihilation of vacancies and interstitials within Si nanocrystals; this effect is attributed to the presence of an energy barrier.