65 research outputs found
Hybrid Simulation between Molecular Dynamics and Binary Collision Approximation Codes for Hydrogen injection onto Carbon Materials
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 figure
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The hybrid Monte Carlo simulation code ACAT-DIFFUSE have been applied to the investigation of the preferential sputtering and the depth profile near the surface at high temperature where the 3keV Ne ions are bonbarded on a Cu_Ni_ alloy. At 100â the stationary Cu surface concentration is nearly equal to its bulk concentration and at high temperature (400â) the Cu surface concentration is larger than the bulk concentration due to surface Gibbsian segregation. There simulated results are in good agreement with the Lam\u27s results of experiment
Molecular dynamics study on DNA damage by tritium disintegration
Using molecular dynamics (MD) simulation, we simulate the structural change of a telomeric DNA by β-decay of substituted tritium to helium-3. The configuration of the telomeric DNA is obtained by removing TRF2 protein from the TRF2-Dbd-DNA complex (Protein Data Bank ID is 3SJM). We assume that hydrogens (H) of guanines in the telomeric DNA are replaced to helium-3. Since this replacement of the H atoms to the 3He atoms changes the charge distribution significantly, the charge distribution used in the MD simulation for the modified guanine is obtained by the density functional theory calculations. We adopt, as the MD simulation, nanoscale molecular dynamics code with CHARMM36 force field using Langevin thermostat and NoséâHoover Langevin piston to control the temperature and pressure of the system, respectively. Moreover, changing both the number of replaced guanine N and the temperature of the system T, we calculate the root mean square deviation RMSD to quantify the dependence of the durability of the telomeric DNA on the β-decays. From the MD simulation, it is found that as N or T becomes larger, the RMSD of the DNA becomes also larger. Namely, it denotes that as the intensity of the β-decays becomes larger or as the temperature is increased, the DNA structure becomes more fragile
Unified Analytic Formula for Physical Sputtering Yield at Normal Ion Incidence
A new analytic representation of the physical sputtering yield at normal ion incidence is derived providing a unified description of the sputtering data at all impact energies and for all ion-monoatomic-solid-target combinations. The reduced sputtering yield Y is expressed in terms of only one energy parameter eta. The function ilde{Y}(eta) has a simple analytic form and describes all the available experimental and calculated data with an rms deviation of 32%. Tables of the parameters entering the analytic formula for ilde{Y}(eta) are provided for a number of ions and monoatomic solids of interest in fusion and other research fields
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