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Here we report a new method combining strain and defect engineering for the periodic modulation of the graphene nanoscale rippling. First, gold nanoparticles of 16 nm in diameter were synthesized by seed-mediated, wet-chemical approach, and thiol-terminated polyethylene glycol (mPEG-SH) molecules were grafted onto their surface. High-density monolayers of the PEGylated gold nanoparticles were successfully prepared on Si substrates by the Langmuir-Blodgett technique. Graphene grown by chemical vapour deposition was transferred onto the nanoparticle monolayer, and characterized by atomic force microscopy, scanning tunneling microscopy, as well as Raman spectroscopy. The induced nanoscale rippling of graphene was fine-tuned by Ar+ ion irradiation.