• KIISE Transactions on Computing Practices
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• v.20 no.10
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• pp.534-542
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• 2014

Multiscale modeling is a new simulation approach which can manage different spatial and temporal scales of system. In this study, as part of multiscale modeling research, we propose the way of combining two different simulation methods, molecular dynamics(MD) and stochastic rotation dynamics(SRD). Our conceptual implementations are based on LAMMPS, one of the well-known molecular dynamics programs. Our prototype of multiscale modeling follows the form of the third party implementation of LAMMPS. It added MD to SRD in order to simulate the boundary area of the simulation box. Because it is important to guarantee the seamless simulation, we also designed the overlap zones and communication zones. The preliminary experimental results showed that our proposed scheme is properly worked out and the execution time is also reduced.

• Tunnel and Underground Space
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• v.10 no.1
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• pp.70-79
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• 2000

We carried out NPT-ensemble (constant-number of particles, pressure, and temperature) Molecular Dynamics (MD) simulations for measuring strength anisotropy under uniaxial compressive stress rotated to the crystallographic axes in $\alpha$-quartz. Uniaxial compressive strengths of a single quartz crystal were measured in directions of the a- and c-axis. Measured uniaxial strength of a single quartz crystal was higher in the direction parallel to the c-axis than that measured in the direction normal to the c-axis. However the reverse was found in calculated uniaxial strengths by MD simulation. The contradictive result of strengths was observed in both cases but was found to be different in origin. Strength anisotropy of defectless $\alpha$-quartz crystal in MD simulation is basically caused by structural difference of quartz. By contrast, anisotropy of measured strength in the uniaxial compression test is related to oriented micro-defects developed during crystal growth.

• Proceedings of the Korean Society for Technology of Plasticity Conference
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• 2007.10a
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• pp.348-351
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• 2007

Simulations of the buckling behavior of a single wall carbon nanotube(SWCNT) was carried out using molecular dynamics simulation. Molecular dynamics simulations were done with 1fs of time step. Tersoff's potential function was used as the interatomic potential function since it has been proved to be reliable to describe the C-C bonds in carbon nanotubes. Compressive force was applied by moving the top end of the nanotube at a constant velocity. Buckling behavior under compressive load was observed for (15,15) armchair SWCNTs with 2nm of diameter and 24.9nm of length. Buckling load and critical strain is obtained from the MD simulation. Deformation occurred on the top region of the CNT because of fast downward velocity.

• Journal of Environmental Science International
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• v.25 no.7
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• pp.927-935
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• 2016

Dissolved oxygen is necessary for many biological processes as well as many industrial practices. Dissolved oxygen released from water in dissolved air flotation (DAF) systems can be have many different applications. However, DAF systems are very costly to operate. To develop more efficient DAF systems, a deeper understanding of the process of oxygen being released from water is required. In this study, molecular dynamics (MD) simulations were used to simulate 100 oxygen molecules surrounded by 31002 water molecules at temperatures ranging from $0^{\circ}C$ to $100^{\circ}C$. Simulations were carried out for 10 ns, during which, in most cases, all the oxygen molecules were released from the water droplet. With MD simulations, visualization of the molecules escaping the water droplet was possible, which aided the understanding of the interactions between molecules at the nano-scale. The results showed that as the oxygen molecules moved near the edge of the water droplet that the oxygen molecules hesitated before escaping the water droplet or returned to the interior of the water droplet. This was because of the attractive forces between the water and oxygen molecules. Moreover, after most of the oxygen molecules were released from the droplet, some were found to return to the droplet's edge or even the interior of the droplet. It was also confirmed that oxygen molecules were released at a faster rate at higher temperatures.

• Tribology and Lubricants
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• v.32 no.1
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• pp.9-17
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• 2016

Contact between solid surfaces is one of the most important factors that influence dynamic behavior in micro/nanoscale. Although numerous theories and experimental results on contact behavior have been proposed, a thorough investigation for nanomaterials is still not available owing to technical difficulties. Therefore, molecular dynamics simulation was performed to investigate the contact behavior of nanomaterials, and the application of conventional contact theories to nanoscale was assessed in this work. Particularly, the contact characteristics of cylindrical nanowires were examined via simulation and contact theories. For theoretical analysis, various contact models were utilized and work of adhesion, Hamaker constant and elastic modulus those are required for calculation of the models were obtained from both indentation simulation and tensile simulation. The contact area of the cylindrical nanowire was assessed directly through molecular dynamics simulation and compared with the results obtained from the theories. Determination of the contact area of the nanowires was carried out via simulation by counting each atom, which is within the equilibrium length. The results of the simulation and theoretical calculations were compared, and it was estimated that the discrepancy in the results calculated between the simulation and the theories was less than 10 except in the case of the smallest nanowires. As the result, it was revealed that contact models can be effectively utilized to assess the contact area of nanomaterials.

• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.783-792
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• 2014

The binding interaction between a hemolytic peptide ${\delta}$-lysin and a zwitterionic lipid bilayer POPC was investigated through a series of molecular dynamics (MD) simulations. ${\delta}$-Lysin is a 26-residue, amphipathic, ${\alpha}$-helical peptide toxin secreted by Staphylococcus aureus. Unlike typical antimicrobial peptides, ${\delta}$-lysin has no net charge and it is often found in aggregated forms in solution even at low concentration. Our study showed that only the monomer, not dimer, inserts into the bilayer interior. The monomer is preferentially attracted toward the membrane with its hydrophilic side facing the bilayer surface. However, peptide insertion requires the opposite orientation where the hydrophobic side of peptide points toward the membrane interior. Such orientation allows the charged residues, Lys and Asp, to have stable salt bridges with the lipid head-group while the hydrophobic residues are buried deeper in the hydrophobic lipid interior. Our simulations suggest that breaking these salt bridges is the key step for the monomer to be fully inserted into the center of lipid bilayer and, possibly, to translocate across the membrane.

• Bulletin of the Korean Chemical Society
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• v.31 no.4
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• pp.959-964
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• 2010

In this work, equilibrium molecular dynamics (MD) simulations in a microcanonical ensemble are performed to evaluate the friction coefficient of a Brownian particle (BP) in a Lennard-Jones (LJ) solvent. The friction coefficients are determined from the time dependent friction coefficients and the momentum autocorrelation functions of the BP with its infinite mass at various ratios of LJ size parameters of the BP and solvent, ${\sigma}_B/{\sigma}_s$. The determination of the friction coefficients from the decay rates of the momentum autocorrelation functions and from the slopes of the time dependent friction coefficients is difficult due to the fast decay rates of the correlation functions in the momentum-conserved MD simulation and due to the scaling of the slope as 1/N (N: the number of the solvent particle), respectively. On the other hand, the friction coefficient can be determined correctly from the time dependent friction coefficient by measuring the extrapolation of its long time decay to t=0 and also from the decay rate of the momentum autocorrelation function, which is obtained by time integration of the time dependent friction coefficient. It is found that while the friction coefficient increases quadratically with the ratio of ${\sigma}_B/{\sigma}_s$ for all ${\sigma}_B$, for a given ${\sigma}_s$ the friction coefficient increases linearly with ${\sigma}_B$.

• Current Applied Physics
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• v.18 no.11
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• pp.1313-1319
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• 2018

The coil-to-globule behavior of poly{${\gamma}$-2-[2-(2methoxyethoxy)ethoxy]ethoxy-3-caprolactone} (PMEEECL) as a ${\gamma}$-substituted poly (${\varepsilon}$-caprolactone) was investigated via atomistic molecular dynamics (MD) simulation. For this purpose, radius of gyration, end-to-end distance and radial distribution function of the chain in the presence of water were calculated. Consequently, the lower critical solution temperature (LCST) of PMEEECL chain at which the coil-to-globule transition takes place, was determined in each calculated parameter curve. The simulation results indicated that the LCST of PMEEECL was occurred at close to 320 K, which is in a good agreement with previous experimental results. Additionally, the appearance of sudden change in both Flory-Huggins interaction parameter (${\chi}$) and interaction energy between the PMEEECL chain and water molecules at about 320 K confirmed the calculated LCST result. The radial distribution function (RDF) results showed that the affinity of the PMEEECL side chain to water molecules is lower than its backbone.

• Korean Journal of Mineralogy and Petrology
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• v.33 no.1
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• pp.19-28
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• 2020

Ranciéte is a hexagonal phyllomanganate mineral containing random Mn(IV) vacancies with hydrated Ca²⁺ cations charged balanced as interlayer cations. Its Mn²⁺ analogue is called takanelite, and ranciéite and takanelite are regarded as end-members of a solid solution series of (Ca²⁺,Mn²⁺)Mn₄O₉·nH₂O. Because the minerals are found as very small particles associated with other minerals, the crystal structures of the solid solution series have yet to be defined. In this research, we conducted classical molecular dynamics (MD) simulations of ranciéite and takanelite by varying the Mn²⁺/Ca²⁺ interlayer cation ratio to find relations between the interlayer cations and mineral structures. MD simulation results of chalcophanite group minerals are compared with experimental results to verify our method applied. Then, lattice parameters of ranciéite and takanelite models are presented along with detailed interlayer structures as to the distribution and coordination of cations and water molecules. This study shows the potentials of MD simulations in entangling complicated phyllomanganates structures.

• Journal of the Mineralogical Society of Korea
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• v.32 no.3
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• pp.151-162
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• 2019

Todorokite, a tunnel-structured manganese oxide, can contain cations within the relatively large nanopores created by the $3{\times}3$ Mn octahedra. Because todorokite is poorly crystalline and found as aggregates mixed with other phases of Mn oxides in nature, the coordination structure of cations in the nanopores is challenging to fully characterize in experiment. In the current article, we report the atomistic coordination structures of $Mg^{2+}$ ions in todorokite tunnel nanopores using the classical molecular dynamics (MD) simulations. In experiment, $Mg^{2+}$ is known to occupy the center of the nanopores. In our MD simulations, 60 % of $Mg^{2+}$ ions were located at the center of the nanopores; 40 % of the ions were found at the corners. All $Mg^{2+}$ located at the center formed the six-fold coordination with water molecules, just as the ion in bulk aqueous solution. $Mg^{2+}$ ions at the corners also formed the six-fold coordination with not only water molecules but also Mn octahedral surface oxygens. The mean squared displacements were calculated to examine the dynamic features of $Mg^{2+}$ ions in the one-dimensional (1D) nanopores. Our MD simulations indicate that the dynamic features of water molecules and the cations observed in bulk aqueous solution are lost in the 1D nanopores of todorokite.