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In order to study nanoscale contact mechanics behavior, taking the rigid hemispherical surface contacted on and pressed in the silicon surface as the research object, the molecular dynamics model of nanoscale contact process was established. State changing of microscopic contact area and variation law of contact force was acquired. Results showed that the adhesion force caused the hemispherical surface and monocrystalline silicon surface to jump-to-contact when the hemispherical surface has not fully contact with monocrystalline silicon substrate surface. With the increase of contact depth, dislocations and sliding of matrix atoms appeared successively. The initial stage of contact was mainly elastic deformation with some dislocations. The later stage of contact was plastic deformation with lots of dislocation accumulation. In the process of disengagement, the substrate material generated some extent elastic recovery. When the hemispherical surface and the matrix surface were completely out of touch, the contact surface still contacted with some matrix atoms due to adhesion phenomenon. Finally, atomic force microscopy was used to finish comparative analysis of the experiment according to the parameter conditions and the contact process of molecular dynamics. The experimental results showed that molecular dynamics simulation was practicable and effective for analysis of the nanoscale contact mechanics behavior. Moreover, molecular dynamics simulation could acquire the microscopic details that not be observed through the experiment.