• Journal of the Korean Ceramic Society
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• v.34 no.7
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• pp.713-721
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• 1997

Molecular dynamic (MD) simulations with new interatomic potential function including the covalent bond were performed on the phase transition of $\alpha$-quartz-type GeO2 under high pressure. The optimized crystal structure and the pressure dependence of the lattice constant showed higher reproducibility than the previous models and were in very good agreement with the experimental data. A phase transition of $\alpha$-quartz and $\alpha$-quartz-type GeO2 by simulation was found approximately 24 GPa and 6-7 GPa, respectively. This phase transition involved an abrupt volume shrinkage and showed 4-6 coordination mixed structure with the increasing in the coordination number of cation.

• Journal of the Korean Magnetic Resonance Society
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• v.3 no.2
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• pp.71-83
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• 1999

The dynamics of the dipolar demagnetizing field is investigated by numerical simulation. The effects of radiation damping, molecular diffusion, and relaxation processes on the dipolar demagnetizing field are examined in terms of the modulation pattern of the z-magnetization and the signal intensity variation. Simulations for multi-components suggest applications for sensitivity enhancement in favorable conditions.

• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2233-2236
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• 2011

We evaluate quantum-mechanical velocity autocorrelation functions from classical molecular dynamics simulations using quantum correction approaches. We apply recently developed approaches to supercritical argon and liquid neon. The results show that the methods provide a solution more efficient than previous methods to investigate quantum-mechanical dynamic behavior in condensed phases. Our numerical results are found to be in excellent agreement with the previous quantum-mechanical results.

• Korea-Australia Rheology Journal
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• v.18 no.2
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• pp.99-102
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• 2006

Primitive chain network model for block copolymers is used here to simulate molecular dynamics in the entangled state with acceptable computational cost. It was found that i) the hooking procedure rearranging the topology of the entangled network is critical for the equilibrium structure of the system, and ii) simulations accounting for the different chemistry, i.e., with a biased hooking probability based on interaction parameter ${\chi}$ for selection of the hooked partner, generates a reasonable phase diagram.

• Korean Journal of Mineralogy and Petrology
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• v.33 no.3
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• pp.143-152
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• 2020

Birnessite is a layered manganese oxide mineral with ~7 Å of d-spacing. Because of its high cation exchange capacity, birnessite greatly impacts the chemical compositions of ground water and fluids in sediment pores. Understanding the cation exchange mechanisms requires atomistic investigations of the crystal structures and coordination environments of hydrated cations in the interlayer. In this study, we conducted classical molecular dynamics (MD) simulations, an atomistic simulation method of computational mineralogy, for triclinic Na-birnessite and K-birnessite whose chemical formula are from previous experiments. We report our MD simulation results of the crystal structures, coordination environments of Na⁺ and K⁺, and the polytypes of birnessite and compare them with available experimental results. The simulation results well reproduced experimental lattice parameters and provided atomic level information for the interlayer cation and water molecule sites that are difficult to distinguish in X-ray experiments. We also report that the polytype of the Mn octahedral sheets is identical between Na- and K-birnessite, but the cation positions differ from each other, demonstrating a correlation between the coordination environment of the interlayer cations and the crystal lattice parameters. This study shows that MD simulations are very promising in elucidating ion exchange reactions of birnessite.

• Proceedings of the Korea Crystallographic Association Conference
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• 2000.05a
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• pp.26-26
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• 2000

• Bulletin of the Korean Chemical Society
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• v.29 no.8
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• pp.1554-1560
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• 2008

The probe diffusion and friction constants of methyl yellow (MY) in liquid n-alkanes of increasing chain length were calculated by equilibrium molecular dynamics (MD) simulations at temperatures of 318, 418, 518 and 618 K. Lennard-Jones particles with masses of 225 and 114 g/mol are modeled for MY. We observed that the diffusion constant of the probe molecule follows a power law dependence on the molecular weight of nalkanes, DMY${\sim}M^{-\gamma}$ well. As the molecular weight of n-alkanes increases, the exponent $\gamma$ shows sharp transitions near n-dotriacontane ($C_{32}$) for the large probe molecule (MY2) at low temperatures of 318 and 418 K. For the small probe molecule (MY1) $D_{MY1}$ in $C_{12}$ to C80 at all the temperatures are always larger than Dself of n-alkanes and longer chain n-alkanes offer a reduced friction relative to the shorter chain n-alkanes, but this reduction in the microscopic friction for MY1 is not large enough to cause a transition in the power law exponent in the log-log plot of DMY1 vs M of n-alkane. For the large probe molecule (MY2) at high temperatures, the situation is very similar to that for MY1. At low temperatures and at low molecular weights of n-alkanes, $D_{MY2}$ are smaller than $D_{self}$ of n-alkanes due to the relatively large molecular size of MY2, and MY2 experiences the full shear viscosity of the medium. As the molecular weight of n-alkane increases, $D_{self}$ of n-alkanes decreases much faster than $D_{MY2}$ and at the higher molecular weights of n-alkane, MY2 diffuses faster than the solvent fluctuations. Therefore there is a large reduction of friction in longer chains compared to the shorter chains, which enhances the diffusion of MY2. The calculated friction constants of MY1 and MY2 in liquid n-alkanes supported these observations. We deem that this is the origin of the so-called“solventoligomer”transition.

• Bulletin of the Korean Chemical Society
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• v.23 no.11
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• pp.1595-1603
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• 2002

In this paper we have presented the results of diffusion behavior of model systems for eight liquid n-alkanes ($C_{12}$-$C_{44}$) in a canonical (NVT) ensemble at several temperatures using molecular dynamics simulations. For these n-alkanes of small chain length n, the chains are clearly <$R_{ee}^2$>/6<$R_g^2$>>1 and non-Gaussian. This result implies that the liquid n-alkanes over the whole temperatures considered are far away from the Rouse regime, though the ratio becomes close to the unity as n increases. Calculated self-diffusion constants $D_{self}$ are comparable with experimental results and the Arrhenius plot of self-diffusion constants versus inverse temperature shows a different temperature dependence of diffusion on the chain length. The global rotational motion of n-alkanes is examined by characterizing the orientation relaxation of the end-to-end vector and it is found that the ratio ${\tau}1/{\tau}2$ is less than 3, the value expected for a isotropically diffusive rotational process. The friction constants ${\xi}$of the whole molecules of n-alkanes are calculated directly from the force auto-correlation (FAC) functions and compared with the monomeric friction constants ${\xi}_D$ extracted from $D_{self}$. Both the friction constants give a correct qualitative trends: decrease with increasing temperature and increase with increasing chain length. The friction constant calculated from the FAC's decreases very slowly with increasing temperature, while the monomeric friction constant varies rapidly with temperature. By considering the orientation relaxation of local vectors and diffusion of each site, it is found that rotational and translational diffusions of the ends are faster than those of the center.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.48 no.1
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• pp.71-75
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• 2015

Nicotinic acetylcholine receptors (nAChRs) are essential for neurotransmission and important therapeutic targets of diseases related to neurotransmission. A recent experimental study identified three residues (Lys185, Asp187, and Ile188) of the ${\alpha}6$ nAChR subunit as determinants of ${\alpha}$-conotoxin BuIA selectivity, yet how these residues confer toxin selectivity remains unclear. In this study, we performed all-atom molecular dynamics simulations with two toxin-bound ${\alpha}4{\beta}2$ nAChR systems: the wild-type ${\alpha}4{\beta}2$ and one in which we replaced the three ${\alpha}4$ subunit residues with three ${\alpha}6$ subunit residues identified in an experimental study (Tyr185Lys, Thr187Asp, and Arg188Ile). After mutation, Asp199 lost the salt bridge formed with Arg188 in the wild type located around loop C. Then, the loop C conformation changed and became more flexible than that of the wild type. We also detected reduced space between the toxin and the binding site in the mutant simulation, resulting in increased binding affinity to the toxin. Therefore, we propose a new Asp199 mutation that breaks the salt bridge and may produce similar selectivity to that of the Arg188 mutation.

• Bulletin of the Korean Chemical Society
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• v.23 no.3
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• pp.447-453
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• 2002

In this paper we have presented the results of thermodynamic, structural, and dynamic properties of model systems for liquid benzene, toluene and p-xylene in an isobaric-isothermal (NpT) ensemble at 283.15, 303.15, 323.15, and 343.15 K using molecular dynamics (MD) simulation. This work is initiated to compensate for our previous canonical (NVT) ensemble MD simulations [Bull. Kor. Chem. Soc. 2001, 23, 441] for the same systems in which the calculated pressures were too low. The calculated pressures in the NpT ensemble MD simulations are close to 1 atm and the volume of each system increases with increasing temperature. The first and second peaks in the center of mass g(r) diminish gradually and the minima increase as usual for the three liquids as the temperature increases. The three peaks of the site-site gC-C(r) at 283.15 K support the perpendicular structure of nearest neighbors in liquid benzene. Two self-diffusion coefficients of liquid benzene via the Einstein equation and via the Green-Kubo relation are in excellent agreement with the experimental measures. The self-diffusion coefficients of liquid toluene and p-xylene are in accord with the trend that the self-diffusion coefficient decreases with increasing number of methyl group. The friction constants calculated from the force auto-correlation (FAC) function with the assumption that the fast random force correlation ends at time which the FAC has the first negative value give a correct qualitative trends: decrease with increase of temperature and increase with the number of methyl group. The friction constants calculated from the FAC's are always less than those obtained from the friction-diffusion relation which reflects that the random FAC decays slower than the total FAC as described by Kubo [Rep. Prog. Phys. 1966, 29, 255].