The quest for a microscopic foundation of thermodynamics is addressed within the Nonunitary Newtonian Gravity model through the study of a specific closed system, namely a three-dimensional harmonic nanocrystal. A numerical calculation of the nanocrystal von Neumann entropy as a function of time is performed, showing a sharp monotonic increase, followed by a stabilization at late times. This behavior is consistent with the emergence of a micro-canonical ensemble within the initial energy levels, signaling, in this way, the establishment of a nonunitary gravity-induced thermal equilibrium.