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Damage accumulation and annihilation processes with low-energy boron implantation were studied by molecular dynamics (MD) simulation. The MD simulation of B atom accelerated with 500 eV iteratively implanted into Si(100) target showed that the number of interstitial Si atom saturates at about 1 times 1015/cm2 of B atomic dose. The results at several implant doses are annealed for about 4ns. When the B implanted dose is as low as 1 times or 2 times 1014/cm2, the annealing simulations showed the re-crystallization of surface damage at 1800 K and 2200 K. However, very slow re-crystallization ratio was observed at the implant dose of more than 1 times 1015/cm2.