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Modification of the classical Zeldovich nucleation theory for nonstationary conditions is presented. It is applied to the recently discovered repeating nucleation events in point contact reactions between metal and silicon nanowires to form epitaxial silicides; the nucleation provides the reproducible quasi-stationary conditions satisfying the fundamental suppositions of the modified theory. The modified theory enables us to predict the rate of repeating nucleation at nanoscale level by developing a theory of the incubation time. The understanding is extremely important for the design and applications of nanoheterostructures.