  Healing of a hole in a carbon nanotube under electron irradiation in HRTEM at
room temperature is demonstrated using molecular dynamics simulations with the
CompuTEM algorithm. Formation of an amorphous patch is observed in all
simulation runs. The amorphous patch is formed in the absence of external
carbon adatoms only via reconstruction of the carbon bond network. It consists
mainly of 5-, 6- and 7-membered rings and causes a small bottleneck. In
addition, further growth of the initial amorphous patch under electron
irradiation takes place. Two-coordinated atoms are found to play a crucial role
in the latter process, analogous to autocatalisys of rearrangements of rings in
fullerenes. The principal rearrangements in the presence of two-coordinated
atoms can be described as generalized sp-defect migration: a bond is broken
between two three-coordinated atoms and one of them forms a new bond with a
nearby two-coordinated atom. If the new and former two-coordinated atoms are
not bonded, the reaction leads both to displacement of the sp defect and
changes in rings of the sp$^2$ carbon structure. Migration by hopping of
two-coordinated atoms and other reactions involving simultaneous breakage of
two bonds are also detected but much rarely. Long-living two-coordinated atoms
in the patch structure and related fast growth of the patch are observed in
more than half of the simulation runs. Since the amorphous patch and bottleneck
affect the electronic properties of the nanotube, such nanotubes can be
perspective for nanoelectronic applications.
