• Journal of the Mineralogical Society of Korea
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• v.28 no.1
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• pp.61-69
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• 2015

While the macroscopic properties and eruption style of basaltic and phonolitic melts are different, the microscopic origins including atomic structures are not well understood. Here we report the atomic structure differences of glass in diopside-anorthite eutectic composition (basaltic glass) and phonolitic glass using high-resolution 1D and 2D solid-state Nuclear Magnetic Resonance (NMR). The $^{27}Al$ MAS NMR spectra for basaltic glass and phonolitic glass show that the full width at half maximum (FWHM) of Al for basaltic glass is about twice than phonolitic glass, suggesting the topological disorder of basaltic magma is larger than that of phonolitic magma. The $^{27}Al$ 3QMAS NMR spectra for basaltic glass and phonolite glass show much improved resolution than the 1D MAS NMR, resolving Al and Al. Approximately 3.3% of Al is observed for basaltic glass, demonstrating the configurational disorder of basaltic magma is larger than phonolitic magma. This result confirms that the topological disorder of Al in basaltic glass is larger than that of phonolitic glass. The observed structural differences between basaltic glass and phonolitic glass can provide an atomistic origin for change of the macroscopic properties with composition including viscosity.

• Journal of the Mineralogical Society of Korea
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• v.27 no.4
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• pp.271-281
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• 2014

The physicochemical properties of clay minerals have been investigated at the atomistic to nano scale. The microscopic studies are often challenging to perform by using experimental approaches alone. In particular, hydroxyl groups of octahedral sheets in 2:1 clay minerals have been hypothesized to impact the sorption process of metal cations; however, X-ray based techniques alone, a common tool for mineral structure examination, cannot properly test the hypothesis. The current study has examined whether computational mineralogy techniques can be applied to examine the hydroxyl structures of clay minerals. Based on quantum-mechanics and molecular-mechanics computational methods, geometry optimizations were carried out for representative dioctahedral and trioctahedral phyllosilicate minerals. Both methods well reproduced the experimental lattice parameters; however, for structural distortion occurring in the tetrahedral or octahedral sheets, molecular mechanics showed significant deviations from experimental data. The orientation angle of the hydroxyl with respect to (001) basal plane is determined by the balance of repulsion between the hydroxyl proton and Si cations of tetrahedral sites; the quantum-mechanics method predicted $25-26^{\circ}$ for the angle, whereas the angle predicted by the molecular-mechanics method was much higher by $10^{\circ}$ (i.e., $35^{\circ}$). These results demonstrate that computational mineralogy techniques are a reliable tool for clay mineral studies and can be used to further elucidate the roles of hydroxyls in metal sorption process.

• Journal of the Institute of Electronics Engineers of Korea SD
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• v.41 no.6
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• pp.25-31
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• 2004

In this paper, we introduce kinetic Monte Carlo (kMC) methods for simulating diffusion process in nano-scale device fabrication. At first, we review kMC theory and backgrounds and give a simple point defect diffusion process modeling in thermal annealing after ion (electron) implantation into Si crystalline substrate to help understand kinetic Monte Carlo methods. kMC is a kind of Monte Carlo but can simulate time evolution of diffusion process through Poisson probabilistic process. In kMC diffusion process, instead of. solving differential reaction-diffusion equations via conventional finite difference or element methods, it is based on a series of chemical reaction (between atoms and/or defects) or diffusion events according to event rates of all possible events. Every event has its own event rate and time evolution of semiconductor diffusion process is directly simulated. Those event rates can be derived either directly from molecular dynamics (MD) or first-principles (ab-initio) calculations, or from experimental data.

• Journal of the Mineralogical Society of Korea
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• v.23 no.4
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• pp.403-411
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• 2010

Essentials of understanding the geochemical evolution and geophysical processes in Earth's system are macroscopic properties and atomistic (and electronic) structures of Earth materials. Recent advances in quantum calculations based on the density functional theory allow us to unveil the previously unknown details of local atomic structures in diverse silicates in Earth's interior. Here, we report the O K-edge ELNES (energy-loss near-edge structure; ELNES) spectra and PLDOS (partial local density of states) for oxygen atoms in ${\alpha}$-quartz and stishovite using the quantum calculations based on FP-LAPW (full potential linearized augmented plane wave). The calculated O K-edge ELNES spectrum of ${\alpha}$-quartz shows a strong peak at ~538 eV due to comer-sharing oxygen linking two $SiO_4$ tetrahedra and that for stishovite shows two distinct peaks at ~537 and ~543 eV corresponding to edge-sharing oxygen linking $SiO_6$ octahedra. The significant differences in spectral features of O K-edge ELNES spectra suggest that the O K-edge features can be useful indicator to distinguish various oxygen sites in diverse crystal and amorphous silicates in the Earth's interior.

• 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.

• Journal of the Mineralogical Society of Korea
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• v.27 no.1
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• pp.1-15
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• 2014

Probing the electronic structures of crystalline Mg-silicates at high pressure is essential for understanding the various macroscopic properties of mantle materials in Earth's interior. Quantum chemical calculations based on the density functional theory are used to explore the atomic configuration and electronic structures of Earth materials at high pressure. Here, we calculate the partial density of states (PDOS) and O K-edge energy-loss near-edge structure (ELNES) spectra for $MgSiO_3$ perovskite at 25 GPa and 120 GPa using the WIEN2k program based on the full-potential linearized projected augmented wave (FP-LPAW) method. The calculated PDOS and O K-edge ELNES spectra for $MgSiO_3$ Pv show significant pressure-induced changes in their characteristic spectral features and relative peak intensity. These changes in spectral features of $MgSiO_3$ Pv indicate that the pressure-induced changes in local atomic configuration around O atoms such as Si-O, O-O, and Mg-O length can induce the significant changes on the local electronic structures around O atoms. The result also indicates that the significant changes in O K-edge features can results from the topological densification at constant Si coordination number. This study can provide a unique opportunity to understand the atomistic origins of pressure-induced changes in local electronic structures of crystalline and amorphous $MgSiO_3$ at high pressure more systematically.