In this paper, a developed three-dimensional model for AFM-based nanomachining is applied to study mechanical scratching at the nanoscale. The correlation between the scratching conditions, including applied force, scratching depth, and distant between any two scratched grooves, and the defect mechanism in the substrate/workpiece is investigated. The simulations of nanoscratching process are performed on different crystal orientations of single-crystal gold substrate, Au(100), Au(110), and Au(111). The material deformation and groove geometry are extracted from the final locations of atoms, which are displaced by the rigid indenter. The simulation also allows for the prediction of normal and friction forces at the interface between the indenter and substrate. An AFM is used to conduct actual scratching at the nanoscale, and provide measurements to which the MD simulation predictions are compared. The predicted forces obtained from MD simulation compares qualitatively with the experimental results.

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