• Nuclear Engineering and Technology
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• v.36 no.3
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• pp.229-236
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• 2004

Radiation hardening is a multiscale phenomenon involving various processes over a wide range of time and length. We present a multiscale model for estimating the amount of radiation hardening in pressure vessel steel in the environment of a light water reactor. The model comprises two main parts: molecular dynamics (MD) simulation and a point defect cluster (PDC) model. The MD simulation was used to investigate the primary damage caused by displacement cascades. The PDC model mathematically formulates interactions between point defects and their clusters, which explains the evolution of microstructures. We then used a dislocation barrier model to calculate the hardening due to the PDCs. The key input for this multiscale model is a neutron spectrum at the inner surface of reactor pressure vessel steel of the Younggwang Nuclear Power Plant No.5. A combined calculation from the MD simulation and the PDC model provides a convenient tool for estimating the amount of radiation hardening.

• Bulletin of the Korean Chemical Society
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• v.30 no.5
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• pp.1139-1142
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• 2009

Refinement of NMR structures by molecular dynamics (MD) simulations with a solvent model has improved the structural quality. In this study, we applied MD refinement with the generalized Born (GB) implicit solvent model to protein structure determined under membrane-like environments. Despite popularity of the GB model, its applications to the refinement of NMR structures of hydrophobic proteins, in which detergents or organic solvents enclose proteins, are limited, and there is little information on the use of another GB parameter for these cases. We carried out MD refinement of crambin NMR structure in dodecylphosphocholine (DPC) micelles (Ahn et al., J. Am. Chem. Soc. 2006, 128, 4398-4404) with GB/Surface area model and two different surface tension coefficients, one for aquatic and the other for hydrophobic conditions. Our data show that, of two structures by MD refinement with GB model, the one refined with the parameter to consider hydrophobic condition had the better qualities in terms of precision and solvent accessibility.

• Proceedings of the KSME Conference
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• 2007.05b
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• pp.1912-1915
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• 2007

The disjoining pressure is critical in modeling the transport phenomena in small scales. They are very useful in characterizing the non-continuum effects that are not negligible in heat and mass transports in the film of less than submicro-scales. We present he disjoining pressure of thin film absorbed on solid substrate using Molecular Dynamics Simulation (MD). The disjoining pressure with respect to the film thickness is accurately calculated in the resolution of a molecular scale. The characteristics of the pressure are discussed regarding the molecular nature of the fluid system like molecular diameter and intermolecular interaction. Also, the MD results are compared with those based on the macroscopic approximation of the slab-like density profile. Significant discrepancy is observed when the effective film thickness is less than several molecular diameter

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.4
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• pp.139-143
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• 2018

Short antimicrobial peptide, A4W, have been studied by molecular dynamics (MD) simulation in an explicit dodecylphosphocholine (DPC) micelle. Peptide was aligned with DPC micelle and transferred new peptide-micelle coordinates within the same solvent box using specific micelle topology parameters. After initial energy minimization and equilibration, the conformation and orientation of the peptide were analyzed from trajectories obtained from the RMD (restrained molecular dynamics) or the subsequent free MD. Also, the information of solvation in the backbone and the side chain of the peptide, hydrogen bonding, and the properties of the dynamics were obtained. The results showed that the backbone residues of peptide are either solvated using water or in other case, they relate to hydrogen bonding. These properties could be a critical factor against the insertion mode of interaction. Most of the peptide-micelle interactions come from the hydrophobic interaction between the side chains of peptide and the structural interior of micelle system. The interaction of peptide-micelle, electrostatic potential and hydrogen bonding, between the terminal residues of peptide and the headgroups in micelle were observed. These interactions could be effect on the structure and flexibility of the peptide terminus.

• Interaction and multiscale mechanics
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• v.1 no.2
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• pp.303-315
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• 2008

In this paper, thermodynamical properties of crystalline silicon under strain are calculated using classical molecular dynamics (MD) simulations based on the Tersoff interatomic potential. The Helmholtz free energy of the silicon crystal under strain is calculated by using the ensemble method developed by Frenkel and Ladd (1984). To account for quantum corrections under strain in the classical MD simulations, we propose an approach where the quantum corrections to the internal energy and the Helmholtz free energy are obtained by using the corresponding energy deviation between the classical and quantum harmonic oscillators. We calculate the variation of thermodynamic properties with temperature and strain and compare them with results obtained by using the quasi-harmonic model in the reciprocal space.

• Proceedings of the IEEK Conference
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• 2003.07b
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• pp.735-738
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• 2003

In this paper, we report a molecular dynamics (MD) simulation of the ion implantation for nano-scale devices with ultra-shallow junctions. In order to model the profile of ion distribution in nanometer scale, the molecular dynamics with a damage model has been employed. As an exemplary case, we calculate the dopant profile during the ion implantation of B, As, and Ge.

• Journal of Advanced Marine Engineering and Technology
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• v.28 no.3
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• pp.441-450
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• 2004

The velocity distribution of gas molecules from the experimental results was confirmed as the same with the Maxwell-Boltzmann's theoretical results within the experimental error. This study is on the realization of the Maxwell-Boltzmann's velocity distribution of gas molecules by the molecular dynamics(MD) method. The Maxwell-Boltzmann's velocity distribution of gas molecules is extremely important to confirm the equilibrium state because the properties of a thermodynamic system shall be obtained from the system's equilibrium configuration in the MD method. This study is the first trial in the successive researches to calculate the properties of a thermodynamic system by the computer simulations. We confirmed that the maxwell-boltzmann's velocity distribution is developed in some transient time after starting a simulation and dependent on the size of a system. Also it is found that the velocity distribution has no relation with an initial configuration of gas molecules.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.32 no.12
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• pp.1047-1054
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• 2008

In this paper, the molecular dynamics (MD) simulations are performed with single-crystal copper blocks under simple shear and simple tension to investigate the effect of size and crystal orientation. There are many variances to give influences such as deformation path, temperature, specimen size and crystal orientation. Among them, the crystal orientation has a primary influence on the volume averaged stress. The numerical results show that the volume averaged shear stress decreases as the specimen size increases and as the crystal orientation changes from single to octal. Furthermore, the Schmid factor and yield stress for crystal orientation are evaluated by using the MD simulation on the standard triangle of stereographic projection.

• Interaction and multiscale mechanics
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• v.4 no.3
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• pp.219-237
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• 2011

Recent advances in scientific computing enable the full atomistic simulation of DNA molecules. However, there exists length and time scale limitations in molecular dynamics (MD) simulation for large DNA molecules. In this work, a two-level homogenization of DNA molecules is proposed. A wavelet projection method is first introduced to form a coarse-grained DNA molecule represented with superatoms. The coarsened MD model offers a simplified molecular structure for the continuum description of DNA molecules. The coarsened DNA molecular structure is then homogenized into a three-dimensional beam with embedded molecular properties. The methods to determine the elasticity constants in the continuum model are also presented. The proposed continuum model is adopted for the study of mechanical behavior of DNA loop.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 2011.06a
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• pp.597-598
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• 2011