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We propose a scar model to reproduce how double-strand breaks occur in the telomeric DNA damaged by the effect of the $\beta$-decay of tritium to helium. In this scar model, the two hydrogens bonded to the 5$^\prime$ carbon connecting the pent saccharides and phosphate are removed. Molecular dynamics simulations using the reactive force field are carried out for 10 cases for the telomeric DNA consisting of 16 base pairs (32 nucleotides). It results in double-strand breaks (DSBs) being observed for structures with more than 24 scars. For 16 scar cases, only single-strand breaks (SSB) are observed. Moreover, in the case of $\left\{16, 0 \right\}$ and $\left\{ 0, 16 \right\},$ where only one of the strands had scars, SSB occurs only in the scarred strand. Secondly, in the $\left\{16, 8 \right\}$ and $\left\{ 8, 16 \right\}$ cases, DSBs occurs. Therefore, we conclude that the following conditions are necessary for DSBs:(i) Scars must occur on both the L and R strands. (ii) A large number of scars (24 or more) must occur in close proximity to each other.

We performed molecular dynamics simulations of coalescence of two vacancies in a tungsten (W) crystal to elucidate the effect of temperature and hydrogen atoms. Simulations were performed for two types of vacancy structures, $\mathrm{V}_9 + \mathrm{W}_1 + \mathrm{V}_9$ and $\mathrm{V}_{10} + \mathrm{W}_4 + \mathrm{V}_{10}$ ($\mathrm{V}_{n}$ means that a vacancy corresponds to the absence of $n$ W atoms, and $\mathrm{W}_{m}$ indicates that there are $m$ W atoms between two vacancies) in various cases of temperature and hydrogen atom concentration. Under the vacancy structure $\mathrm{V}_9 + \mathrm{W}_1 + \mathrm{V}_9$, we observed vacancy coalescence for all the cases of the temperature and the number of hydrogen atoms. Evaluating the potential energy required for removing one of the W atoms between two vacancies, we found that high temperature and existing hydrogen atoms in the vacancies facilitate vacancy coalescence, and that under the structure $\mathrm{V}_{10} + \mathrm{W}_4 + \mathrm{V}_{10}$, hydrogen atoms facilitate vacancy coalescence most strongly when the number is around 45 to 54 in each vacancy., Comment: 12 pages, 5 figures

By using molecular dynamics simulation, formation mechanisms of amorphous carbon in particular sp${}^3$ rich structure was researched. The problem that reactive empirical bond order potential cannot represent amorphous carbon properly was cleared in the transition process from graphite to diamond by high pressure and the deposition process of amorphous carbon thin films. Moreover, the new potential model which is based on electron distribution simplified as a point charge was developed by using downfolding method. As a result, the molecular dynamics simulation with the new potential could demonstrate the transition from graphite to diamond at the pressure of 15 GPa corresponding to experiment and the deposition of sp${}^3$ rich amorphous carbon., Comment: International Symposium ISPlasma 2012, submitted to Jpn. J. Appl. Phys

By molecular dynamics simulation, the chemical vapor deposition of amorphous carbon onto graphite and diamond surfaces was studied. In particular, we investigated the effect of source H/C ratio, which is the ratio of the number of hydrogen atoms to the number of carbon atoms in a source gas, on the deposition process. In the present simulation, the following two source gas conditions were tested: one was that the source gas was injected as isolated carbon and hydrogen atoms, and the other was that the source gas was injected as hydrocarbon molecules. Under the former condition, we found that as the source H/C ratio increases, the deposition rate of carbon atoms decreases exponentially. This exponential decrease in the deposition rate with increasing source H/C ratio agrees with experimental data. However, under the latter molecular source condition, the deposition rate did not decrease exponentially because of a chemical reaction peculiar to the type of hydrocarbon in the source gas., Comment: accepted by Jpn. J. Appl. Phys. (2008)

Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's size is less than several nm for the performance of a computer. To extend the size of the MD simulation, we develop a hybrid simulation code between MD code using REBO potential and binary collision approximation (BCA) code. Using the BCA code instead of computing all particles with a high kinetic energy for every step in the MD simulation, considerable computation time is saved. By demonstrating a hydrogen atom injection on a graphite by the hybrid simulation code, it is found that the hybrid simulation code works efficiently in a large simulation box., Comment: 5 pages, 5 figures

We have investigated plasma-surface interactions with molecular dynamics (MD) simulations. It, however, is high cost computation and is limited to simulations for materials of nanometer order. In order to overcome the limitation, a complementary model based on binary collision approximation (BCA) can be established. We employed a BCA-based simulation code ACAT and extended to handle any structure involving crystalline and amorphous. The extended code, named "ACaT", stores all positions of projectile and target atoms and velocities of recoil atoms, so it can be combined with the MD code. It also holds the potential to reproduce channeling phenomena. Thus it is expected to be useful for evaluation of channeling effects.

Incident angle dependence of reactions between graphene and hydrogen atoms are obtained qualitatively by classical molecular dynamics simulation under the NVE condition with modified Brenner reactive empirical bond order (REBO) potential. Chemical reaction depends on two parameters, i.e., polar angle $\theta$ and azimuthal angle $\phi$ of the incident hydrogen. From the simulation results, it is found that the reaction rates strongly depend on polar angle $\theta$. Reflection rate becomes larger with increasing $\theta$, and the $\theta$ dependence of adsorption rate is also found. The $\theta$ dependence is caused by three dimensional structure of the small potential barrier which covers adsorption sites. $\phi$ dependence of penetration rate is also found for large $\theta$., Comment: 4 pages, 7 figures