• The Journal of Engineering Geology
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• v.11 no.3
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• pp.269-278
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• 2001

We describe the calculation of thermal expansion coefficients of $\alpha$-quartz, muscovite and albite using a MD simulation method. The selection of interatomic potentials is important for the MD calculation, and we used the 2-body interatomic potential function. The coefficients are calculated using a differential operation of the temperature dependence of the lattice constant obtained from the NPT-ensemble molecular dynamics simulation. Reasonable agreement is found between the analytical results and measured data.

• 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.

• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.116-119
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• 2016

Chlorosulfolipids(CSLs)는 1960 년대에 해조류에서 발견되었다. 하지만 당시 기술력으로는 해조류에서 CSLs 를 추출해 내는 것이 불가능하여 연구가 중단 되었다. 그 후로 40 년 뒤 2009 년이 되어서야 CSLs 를 추출할 수 있게 되었다. CSLs 가 독성을 지니고 있다는 연구가 보고 되어 왔다. 하지만 이 CSL 가 형성하는 구조를 실험으로 알수가 없고 아직까지 학회에 보고 된 적이 없다. 따라서 본 연구원이 MD 시뮬레이션을 이용하여 CSLs 가 형성하는 세포막의 구조를 알아보기 위하여 Coarse-grain 모델을 이용한 CSLs 의 Self-Assembly 연구와 이 결과로 인해 얻은 정보로 atomistic 모델을 만들어서 MD 시뮬레이션을 수행하였다.

• Journal of the Mineralogical Society of Korea
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• v.26 no.2
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• pp.119-127
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• 2013

Borosilicate glass dissolution is an important chemical process that impacts the glass durability as nuclear waste form that may be used for high-level radioactive waste disposal. Experiments reported that the glass dissolution rates are strongly dependent on the bulk composition. Because some relationship exists between glass composition and molecular-structure distribution (e.g., non-bridging oxygen content of $SiO_4$ unit and averaged coordination number of B), the composition-dependent dissolution rates are attributed to the bulk structural changes corresponding to the compositional variation. We examined Na borosilicate glass structures by performing classical molecular dynamics (MD) simulations for four different chemical compositions ($xNa_2O{\cdot}B_2O_3{\cdot}ySiO_2$). Our MD simulations demonstrate that glass surfaces have significantly different chemical compositions and structures from the bulk glasses. Because glass surfaces forming an interface with solution are most likely the first dissolution-reaction occurring areas, the current MD result simply that composition-dependent glass dissolution behaviors should be understood by surface structural change upon the chemical composition change.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.27 no.3
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• pp.137-145
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• 2014

We present a design sensitivity analysis(DSA) method for multiscale problems based on bridging scale decomposition. In this paper, we utilize a bridging scale method for the coupled system analysis. Since the analysis of full MD systems requires huge amount of computational costs, a coupled system of MD-level and continuum-level simulation is usually preferred. The information exchange between the MD and continuum levels is taken place at the MD-continuum boundary. In the bridging scale method, a generalized Langevin equation(GLE) is introduced for the reduced MD system and the GLE force using a time history kernel is applied at the boundary atoms in the MD system. Therefore, we can separately analyze the MD and continuum level simulations, which can accelerate the computing process. Once the simulation of coupled problems is successful, the need for the DSA is naturally arising for the optimization of macro-scale design, where the macro scale performance of the system is maximized considering the micro scale effects. The finite difference sensitivity is impractical for the gradient based optimization of large scale problems due to the restriction of computing costs but the analytical sensitivity for the coupled system is always accurate. In this study, we derive the analytical design sensitivity to verify the accuracy and applicability to the design optimization of the coupled system.

• 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.30 no.4
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• pp.161-172
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• 2017

Clay minerals play a major role in the geochemical cycles of metals in the Critical Zone, the Earth surface-layer ranging from the groundwater bottom to the tree tops. Atomistic scale research of the very fine particles can help understand the fundamental mechanisms of the important geochemical processes and possibly apply to development of hybrid nanomaterials. Molecular dynamics (MD) simulations can provide atomistic level insights into the crystal structures of clay minerals and the chemical reactivity. Classical MD simulations use a force field which is a parameter set of interatomic pair potentials. The ClayFF force field has been widely used in the MD simulations of dioctahedral clay minerals as the force field was developed mainly based on dioctahedral phyllosilicates. The ClayFF is often used also for trioctahedral mineral simulations, but disagreement exits in selection of the interatomic potential parameters, particularly for Mg atom-types of the octahedral sheet. In this study, MD simulations were performed for trioctahedral clay minerals such as brucite, lizardite, and talc, to test how the two different Mg atom types (i.e., 'mgo' or 'mgh') affect the simulation results. The structural parameters such as lattice parameters and interatomic distances were relatively insensitive to the choice of the parameter, but the vibrational power spectra of hydroxyls were more sensitive to the choice of the parameter particularly for lizardite.

• Journal of the Korean Chemical Society
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• v.64 no.6
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• pp.345-349
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• 2020

In the self-assembled monolayer (SAM) of alkanethiol formed on a gold surface, some molecules fail to chemisorb with their terminal alkyl groups physisorbed. The previous molecular dynamics (MD) simulation showed that these defects can be cured by thermal annealing. Herein, we present a simple Ising model of alkanethiol. The Monte Carlo simulation based on the present model reproduced the essential features of the annealing of SAM observed in the MD simulation.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.14 no.11
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• pp.5338-5343
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• 2013

In a haptic system, a virtual wall is modeled as a virtual spring. The larger the stiffness of the virtual spring is, the more improved the reality of the virtual wall is, but the more unstable the haptic system becomes. This paper shows how to increase the stiffness of the virtual spring while the stability of the haptic system is guaranteed and shows the effects of a mass (Md) and a damper (Bd) of a haptic device on the stability when first-order hold method is applied and a virtual wall is modeled as a virtual spring (Kw). The simulation results show the boundary of the virtual spring is proportional to the square root of the mass (Md) and the damper (Bd) while maintaining the stability. The relation among the virtual spring (Kw), the mass (Md) and the damper (Bd) of the haptic device, and sampling time (T) is inferred as $K_w{\leq}{1.611M_d}^{0.50}{B_d}^{0.50}T^{-1.51}$, by using the simulation results. The maximum available stiffness of the virtual spring in first-order hold method is larger than in zero-order hold method. So the reality of the virtual wall can be improved.

• 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.