We report on the electron beam-induced segregation of alloyed Ni-Au clusters into a Ni and Au rich phase at temperatures above the miscibility gap of a binary system. The nanoparticles, with diameters less than 10 nm, are grown fully inert in superfluid helium droplets with a Ni-Au core-shell morphology. Upon heating, the clusters are alloyed and subsequently transformed to a Janus-type morphology under irradiation with swift electrons. The underlying mechanisms are studied experimentally via in situ scanning transmission electron microscopy and theoretically via atomistic simulation techniques under consideration of elastic electron interactions. We find that the segregation kinetics is highly temperature-dependent and attribute this behavior to diffusive relaxation processes. The presented results shed light on radiation induced phenomena using clusters as a model system and suggest new routes for the synthesis of structures in nonequilibrium configurations.

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