The AFM can be used to image and manipulate atoms and structures on a variety of surfaces.  The atom at the apex of the tip "senses" individual atoms on the underlying surface when it forms incipient chemical bonds with each atom.  Because these chemical interactions subtly alter the tips vibration frequency, they can be detected and mapped. This principle was used to distinguish between atoms of silicon, tin and lead on an alloy surface, by comparing these "atomic fingerprints" with values obtained from density functional theory (DFT) simulations.
The trick is to first measure these forces precisely for each type of atom expected in the sample, and then to compare with forces given by DFT simulations. The team found that the tip interacted most strongly with silicon atoms, and interacted 24% and 41% less strongly with tin and lead atoms, respectively.  Thus, each different type of atom can be identified in the matrix as the tip is moved across the surface.