Nanochannels are essential features of many microelectronic and biomedical devices. To date, the most commonly employed method to fabricate these nanochannels is atomic force microscopy (AFM). However, there is presently a very poor understanding on the fundamental principles underlying this process, which limits its reliability and controllability. In this study, we present a comprehensive multiscale model by incorporating strain gradient plasticity and strain gradient elasticity theories, which can predict nanochannel depths during AFM-based nanofabrication. The modeling results are directly verified with experiments performed on Cu and Pt substrates. As this model can also be extended to include many additional conditions, it has broad applicability in a wide range of AFM-based nanofabrication applications.

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