We present a systematic study of the interaction between a silicon tip and a reconstructed Si(100)2×1 surface by means of total energy calculations using Density Functional Theory. We perform geometry optimisation to obtain the reconstructed Si surface using the Local Density Approximation and the Generalized Gradient Approximation methods and compare our results with those obtained experimentally. We then study the effects of the tip of a scanning probe of an Atomic Force Microscope (AFM) on the behaviour of atoms on the reconstructed surface when the tip translates at distances close to it. Our results show that at certain positions of the tip relative to the surface and depending on the direction of the scan, the Si dimer on the surface flips, resulting to a local reconstruction of the surface into p(2×2) or c(4×2) configurations. These configurations exhibit energy lower by 0.05 eV/dimer compared to the Si(100)2×1 structure
