  Important recent advances in transmission electron microscopy instrumentation
and capabilities have made it indispensable for atomic-scale materials
characterization. At the same time, the availability of two-dimensional
materials has provided ideal samples where each atom or vacancy can be
resolved. Recent studies have also revealed new possibilities for a different
application of focused electron irradiation: the controlled manipulation of
structures and even individual atoms. Evaluating the full range of future
possibilities for this method requires a precise physical understanding of the
interactions of electrons with energies as low as 15 keV now used in (scanning)
transmission electron microscopy, becoming feasible due to advances both in
experimental techniques and in theoretical models. We summarize the state of
current knowledge of the underlying physical processes based on the latest
results on two-dimensional materials, with a focus on the physical principles
of the electron-matter interaction, rather than the material-specific
irradiation-induced defects it causes.
