• Bulletin of the Korean Chemical Society
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• v.23 no.1
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• pp.107-111
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• 2002

The OSS2 (Oj？me-Shavitt-Singer 2)[L. Oj？me et al., J. Chem. Phys. 109, 5547 (1998)] model for the solvated proton in water is examined for $H_2O,\;H_3O^+,\;H_5O_2^+,\;H_7O_3^+,\;and\;H_9O_4^-$ by molecular dynamics (MD) simulations. The equilibrium molecular geometries and energies obtained from MD simulations at 5.0 and 298.15 K agree very well with the optimized calculations.

• Carbon letters
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• v.11 no.4
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• pp.316-324
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• 2010

The effects of geometrical parameters on mechanical properties of graphite-vinylester nanocomposites and their constituents (matrix, reinforcement and interface) are studied using molecular dynamics (MD) simulations. Young's modulii of 1.3 TPa and 1.16 TPa are obtained for graphene layer and for graphite layers respectively. Interfacial shear strength resulting from the molecular dynamic (MD) simulations for graphene-vinylester is found to be 256 MPa compared to 126 MPa for graphitevinylester. MD simulations prove that exfoliation improves mechanical properties of graphite nanoplatelet vinylester nanocomposites. Also, the effects of bromination on the mechanical properties of vinylester and interfacial strength of the graphene.brominated vinylester nanocomposites are investigated. MD simulation revealed that, although there is minimal effect of bromination on mechanical properties of pure vinylester, bromination tends to enhance interfacial shear strength between graphite-brominated vinylester/graphene-brominated vinylester in a considerable magnitude.

• Bulletin of the Korean Chemical Society
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• v.24 no.1
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• pp.95-98
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• 2003

Enantioselectivity of the propranolol on β-cyclodextrin was simulated by molecular modeling. Monte Carlo (MC) docking and molecular dynamics (MD) simulations were applied to investigate the molecular mechanism of enantioselective difference of both enantiomeric complexes. An energetic analysis of MC docking simulations coupled to the MD simulations successfully explains the experimental elution order of propranolol enantiomers. Molecular dynamics simulations indicate that average energy difference between the enantiomeric complexes, frequently used as a measure of chiral recognition, depends on the length of the simulation time. We found that, only in case of much longer MD simulations, noticeable chiral separation was observed.

• Bulletin of the Korean Chemical Society
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• v.29 no.8
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• pp.1505-1509
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• 2008

Comparative molecular simulations were performed to establish molecular interaction and inhibitory effect of flavonoid myricetin on formation of amyloid fibris. For computational comparison, the conformational stability of myricetin with amyloid $\beta$ -peptide (A$\beta$ ) and $\beta$ -amyloid fibrils (fA$\beta$) were traced with multiple molecular dynamics simulations (MD) using the CHARMM program from Monte Carlo docked structures. Simulations showed that the inhibition by myricetin involves binding of the flavonoid to fA$\beta$ rather than A$\beta$ . Even in MD simulations over 5 ns at 300 K, myricetin/fA$\beta$ complex remained stable in compact conformation for multiple trajectories. In contrast, myricetin/A$\beta$ complex mostly turned into the dissociated conformation during the MD simulations at 300 K. These multiple MD simulations provide a theoretical basis for the higher inhibitory effect of myricetin on fibrillogenesis of fA$\beta$ relative to A$\beta$ . Significant binding between myricetin and fA$\beta$ observed from the computational simulations clearly reflects the previous experimental results in which only fA$\beta$ had bound to the myricetin molecules.

• The Korean Journal of Ceramics
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• v.5 no.1
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• pp.40-43
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• 1999

In order to investigate Sn substitution sites and interstitial O atoms in tin-doped indium oxide, molecular dynamics (MD) simulations were carried out. There are two kinds of cation sites in $In_2O_3$, namely b-site and d-site. NTP-MD simulations under the condition of 300 K and 0 GPa were performed with two kinds of cells substituted by Sn atoms at each site. The excess oxygen atom accompanied with Sn doping was also taken into consideration. According to the calculations of Sn potential energies in each site, it was revealed that Sn atoms were substituted for b-sites rather than for d-sites. It was also revealed that the interstitial excess oxygen atoms tend to be connected with the Sn atoms substituted for the d-sites Sn rather than for the b-site. There MD simulation results well agreed with the experimental results.

• Nuclear Engineering and Technology
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• v.41 no.1
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• pp.11-20
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• 2009

Radiation effects on materials are inherently multiscale phenomena in view of the fact that various processes spanning a broad range of time and length scales are involved. A multiscale modeling approach to embrittlement of pressure vessel steels is presented here. The approach includes an investigation of the mechanisms of defect accumulation, microstructure evolution and the corresponding effects on mechanical properties. An understanding of these phenomena is required to predict the behavior of structural materials under irradiation. We used molecular dynamics (MD) simulations at an atomic scale to study the evolution of high-energy displacement cascade reactions. The MD simulations yield quantitative information on primary damage. Using a database of displacement cascades generated by the MD simulations, we can estimate the accumulation of defects over diffusional length and time scales by applying kinetic Monte Carlo simulations. The evolution of the local microstructure under irradiation is responsible for changes in the physical and mechanical properties of materials. Mechanical property changes in irradiated materials are modeled by dislocation dynamics simulations, which simulate a collective motion of dislocations that interact with the defects. In this paper, we present a multi scale modeling methodology that describes reactor pressure vessel embrittlement in a light water reactor environment.

• Proceedings of the KSME Conference
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• 2001.11a
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• pp.252-257
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• 2001

With the help of newly arrived technology such as PC clustering, molecular dynamics (MD) seems to be promising for large-scale materials simulations. A cost-effective cluster is set up using commodity PCs connected over Ethernet with fast switching devices and free software Linux. Executing MD simulations in the parallel sessions makes it possible to carry out large-scale materials simulations at acceptable computation time and costs. In this study, the MD computer code for fracture simulation is modified to comply with MPI (Message Passing Interface) specification, and runs on the PC cluster in parallel mode flawlessly. It is noted that PC clusters can provide a rather inexpensive high-performance computing environment comparing to supercomputers, if properly arranged.

• Journal of the Korean Ceramic Society
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• v.53 no.3
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• pp.295-300
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• 2016

To investigate the thermal conductivity and the structural properties of naturally cooled excimer-laser annealed Si, molecular-dynamics (MD) simulations have been performed. The thermal conductivity of crystalline Si (c-Si) was measured by direct method at 1000 K. Steady-state heat flow was measured using a stationary temperature profile; significant deviations from Fourier's law were not observed. Reliable processes for measuring the thermal conductivity of c-Si were presented. A natural cooling process to admit heat flow from molten Si (l-Si) to c-Si was performed using an MD cell with a size of $48.9{\times}48.9{\times}97.8{\AA}^3$. During the cooling process, the temperature of the bottom $10{\AA}$ of the MD cell was controlled at 300 K. The results suggest that the natural cooling system described the static structural property of amorphous Si (a-Si) well.

• Membrane Journal
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• v.26 no.5
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• pp.329-336
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• 2016

Proton exchange membrane (PEM) is one of the key components of membrane-electrode assembly (MEA), which plays important role in fuel cell performance together with catalysts. It is widely accepted that water channel morphology inside PEMs as a proton pathway significantly affects the PEM performance. Molecular dynamics (MD) simulations are a very useful tool to understand molecular and atomic structures of materials, so that many related researches are currently being studied. In this paper, we summarize the current research trend in MD simulations, present which properties can be characterized, and finally introduce the usefulness of MD simulations to the researchers for proton exchange membranes.

• Bulletin of the Korean Chemical Society
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• v.18 no.5
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• pp.501-509
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• 1997

In recent papers[Bull. Kor. Chem. Soc. 1996, 17, 735; ibid 1997, 18, 478] we reported results of molecular dynamics (MD) simulations for the thermodynamic, structural, and dynamic properties of liquid normal alkanes, from n-butane to n-heptadecane, using three different models. Two of the three classes of models are collapsed atomic models while the third class is an atomistically detailed model. In the present paper we present results of MD simulations for the corresponding properties of liquid branched-chain alkanes using the same models. The thermodynamic property reflects that the intermolecular interactions become weaker as the shape of the molecule tends to approach that of a sphere and the surface area decreases with branching. Not like observed in the straight-chain alkanes, the structural properties of model Ⅲ from the site-site radial distribution function, the distribution functions of the average end-to-end distance and the root-mean-squared radii of gyration are not much different from those of models Ⅰ and Ⅱ. The branching effect on the self diffusion of liquid alkanes is well predicted from our MD simulation results but not on the viscosity and thermal conductivity.