• Bulletin of the Korean Chemical Society
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• 제23권1호
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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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• 제11권4호
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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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• 제24권1호
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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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• 제29권8호
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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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• 제5권1호
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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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• 제41권1호
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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.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2001년도 추계학술대회논문집A
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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.

• 한국세라믹학회지
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• 제53권3호
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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.

• 멤브레인
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• 제26권5호
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• pp.329-336
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• 2016

수소이온 교환막(PEM; Proton Exchange Membrane)은 연료전지 막-전극 복합체(MEA; Membrane-electrode Assembly)를 구성하는 핵심 소재 중 하나로서, 촉매와 함께 연료전지 성능을 결정하는 중요한 역할을 한다. 이러한 수소이온교환막의 성능은 내부에 존재하는 수소이온 전달 통로인 수화 채널의 구조에 큰 영향을 받는 것으로 알려져 있다. 분자 동역학(MD; Molecular Dynamics) 전산모사 기술은 이러한 소재 내부의 분자 및 원자구조를 파악하기 위한 유용한 도구로서, 수소이온 교환막의 구조 및 특성에 관한 많은 관련 연구가 진행되고 있다. 본 총설에서는 분자동역학 전산모사 관련 연구에 대한 동향을 정리하고, 이를 통해 어떤 구조적 특징들을 분석할 수 있는지 제시하여, 수소이온 교환막 연구자들과 분리막 연구자들에게 분자동역학 전산모사 기술의 유용성에 대하여 소개하고자 한다.

• Bulletin of the Korean Chemical Society
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• 제18권5호
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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.