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Nanometer-sized noble metallic particles embedded in dielectric matrices are of wide interest. To exploit their plasmonic properties, efforts have been made to vary their size and shape by various methods during or after fabrication. Energetic ion irradiation has been found to be very useful in this objective. In the present work, we have studied the effect of inter-particle separation using atomistic simulations to gain a better understanding of the pathway in the modification of size of nanoparticles which are smaller than the ion track size in the matrix. It is found that the size of nanoparticles can be varied depending on the initial inter-particle separation and the temperature in the spike generated by the passed energetic ion. The results agree with the model proposed by our group, based on inter-particle separation, to explain experimental results on the swift heavy ion-induced modification of the size of embedded nanoparticles. [ABSTRACT FROM AUTHOR]