Part of developing new strategies for fabrications of nanowire structures involves in many cases the aid of metal nanoparticles (NPs). It is highly beneficial if one can define both diameter and position of the initial NPs and make well-defined nanowire arrays. This sets additional requirement on the NPs with respect to being able to withstand a pre-growth annealing process (i.e. de- oxidation of the III-V semiconductor surface) in an epitaxy system. Recently, it has been demonstrated that Ag may be an alternative to using Au NPs as seeds for particle-seeded nanowire fabrication. This work brings light onto the effect of annealing of Au, Ag and Au-Ag alloy NP arrays in two commonly used epitaxial systems, the Molecular Beam Epitaxy (MBE) and the Metalorganic Vapor Phase Epitaxy (MOVPE). The NP arrays are fabricated with the aid of Electron Beam Lithography on GaAs 100 and 111B wafers and the evolution of the NPs with respect to shape, size and position on the surfaces are studied after annealing using Scanning Electron Microscopy (SEM). We find that while the Au NP arrays are found to be stable when annealed up to 600 $^{circ}$C in a MOVPE system, a diameter and pitch dependent splitting of the particles are seen for annealing in a MBE system. The Ag NP arrays are less stable, with smaller diameters ($leq$ 50 nm) dissolving during annealing in both epitaxial systems. In general, the mobility of the NPs is observed to differ between the two the GaAs 100 and 111B surfaces. While the initial pattern is found be intact on the GaAs 111B surface for a particular annealing process and particle type, the increased mobility of the NP on the 100 may influence the initial pre-defined positions at higher annealing temperatures. The effect of annealing on Au-Ag alloy NP arrays suggests that these NP can withstand necessary annealing conditions for a complete de-oxidation of GaAs surfaces.
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