• Proceedings of the Korean Vacuum Society Conference
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• 2004.02a
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• pp.93-93
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• 2004

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.1059-1062
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• 2012

• Bulletin of the Korean Chemical Society
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• v.34 no.8
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• pp.2515-2518
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• 2013

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.771-776
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• 2003

The structural and dynamic properties of small n-alkane clusters embedded in a mesoscopic solvent are investigated. The solvent interactions are taken into account through a multi-particle collision operator that conserves mass, momentum and energy and the solvent dynamics is updated at discrete time intervals. The cluster molecules interact among themselves and with the solvent molecules through intermolecular forces. The properties of n-heptane and n-decane clusters interacting with the mesoscopic solvent molecules through repulsive Lennard-Jones interactions are studied as a function of the number of the mesoscopic solvent molecules. Modifications of both the cluster and solvent structure as a result of cluster-solvent interactions are considered. The cluster-solvent interactions also affect the dynamics of the small n-alkane clusters.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.16 no.12S
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• pp.1157-1164
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• 2003

This paper shows the results of atomistic modeling for the interaction between spherical nano abrasive and substrate in chemical mechanical polishing processes. Atomistic modeling was achieved from 2-dimensional molecular dynamics simulations using the Lennard-Jones 12-6 potentials. The abrasive dynamics was modeled by three cases, such as slipping, rolling, and rotating. Simulation results showed that the different dynamics of the abrasive results the different features of surfaces. This model can be extended to investigate the 3-dimensional chemical mechanical polishing processes.

• Journal of the Korea Institute of Military Science and Technology
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• v.14 no.1
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• pp.147-153
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• 2011

A series of nonequilibrium molecular dynamics(NEMD) simulations are performed to investigate the kinetic energy and velocity distributions of molecules in shock waves. In the simulations, argon molecules are used as a medium gas through which shock waves are propagating. The kinetic energy distribution profiles reveals that as a strong shock wave whose Mach number is 27.1 is applied, 39.6% of argon molecules inside the shock wave have larger kinetic energy than molecular ionization energy. This indicates that an application of a strong shock wave to argon gas can give rise to an intense light. The velocity distribution profiles in z direction along which shock waves propagate clearly represent two Maxwell-Boltzmann distributions of molecular velocities in two equilibrium regions and one bimodal velocity distribution profile that is attributed to a nonequilibrium region. The peak appearing in the directional temperature in z direction is discussed on a basis of the bimodal velocity distribution in the nonequilibrium region.

• 한국신재생에너지학회:학술대회논문집
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• 2011.11a
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• pp.122.2-122.2
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• 2011

Sulfur hexafluoride ($SF_6$), one of the most potent greenhouse gases, is known as a hydrate former and has been studied at the high pressure up to 1.3 GPa with gas mixtures and with aqueous surfactant. Since we regard $SF_6$ as a potential promoter molecule that can stabilize hydrate structure more effectively compare to the other promoters, further investigation is required to verify the stabilizing ability of $SF_6$ in the hydrate structure. However, the insoluble nature of $SF_6$ in water or gases hinders fine scale analyses. This work discusses the data obtained by using molecular dynamics simulations of structure II (sII) clathrate hydrates containing $SF_6$ and $H_2$. The simulations were performed using the TIP4P/Ice model for water molecule and a previously reported $SF_6$ molecular model (optimized at the pure $SF_6$ single phase system (Olivet and Vega, 2007)), and a $H_2$ molecular model (adapted from the THF+$H_2$ hydrate system (Alavi et al., 2006)). The simulations are performed to observe the stability of $SF_6$ and $H_2$ in the sII clathrate hydrate system with varying temperature and pressure conditions and occupancies of $SF_6$ and $H_2$, which cannot be easily tuned experimentally. We observe that stability of H2 enclathrated in the hydrate structure more affected by the occupancy of $SF_6$ molecules and temperature than pressure, which ranges from 1 to 100 bar.

• 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.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.21-21
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• 2011

A series of Quasi-Elastic Neutron Scattering (QENS) experiments helps us to understand the single-particle (hydrogen atom) dynamics of a globular protein and its hydration water and strong coupling between them. We also performed Molecular Dynamics (MD) simulations on a realistic model of the hydrated hen-egg Lysozyme powder having two proteins in the periodic box. We found the existence of a Fragile-to-Strong dynamic Crossover (FSC) phenomenon in hydration water around a protein occurring at TL=$225{\pm}5K$ by analyzing Intermediate Scattering Function (ISF). On lowering of the temperature toward FSC, the structure of hydration water makes a transition from predominantly the High Density Liquid (HDL) form, a more fluid state, to predominantly the Low Density Liquid (LDL) form, a less fluid state, derived from the existence of a liquid?liquid critical point at an elevated pressure. We showed experimentally and confirmed theoretically that this sudden switch in the mobility of the hydration water around a protein triggers the dynamic transition (so-called glass transition) of the protein, at a temperature TD=220 K. Mean Square Displacement (MSD) is the important factor to show that the FSC is the key to the strong coupling between a protein and its hydration water by suggesting TL${\fallingdotseq}$TD. MD simulations with TIP4P force field for water were performed to understand hydration level dependency of the FSC temperature. We added water molecules to increase hydration level of the protein hydration water, from 0.30, 0.45, 0.60 and 1.00 (1.00 is the bulk water). These confirm the existence of the FSC and the hydration level dependence of the FSC temperature: FSC temperature is decreased upon increasing hydration level. We compared the hydration water around Lysozyme, B-DNA and RNA. Similarity among those suggests that the FSC and this coupling be universal for globular proteins, biopolymers.