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.
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