• 정보과학회 컴퓨팅의 실제 논문지
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• 제20권10호
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• pp.534-542
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• 2014

멀티스케일 모델링은 시공간적으로 서로 다른 규모의 시스템을 다룰 수 있는 시뮬레이션 기법이다. 본 연구에서는 멀티스케일 모델링 연구의 일환으로 서로 다른 시뮬레이션 기법인 분자동역학과 확률회전동역학을 결합할 수 있는 방법을 제안한다. 분자동역학 프로그램 중 잘 알려진 오픈 소스인 LAMMPS를 기반으로 멀티스케일링 모델링을 구현하였으며 LAMMPS에서 정의한 제3자를 위한 표준 확장 방법을 따랐다. 제안된 방법에서는 확률회전동역학 모델을 기본으로 경계 영역은 분자동역학으로 해석 가능하게 하였고 심리스한 해석을 보장하기 위하여 중첩 영역과 정보 교환 영역을 함께 구현하였다. 예비실험을 수행한 결과, 제안된 멀티스케일 방법론이 기존 분자동역학 시뮬레이션 결과와 일치된 해석 결과를 보여주었으며 실행 시간 또한 단축시킬 수 있음을 확인하였다.

• 터널과지하공간
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• 제10권1호
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• pp.70-79
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• 2000

입자수, 압력, 온도일정의 앙상블(NPT-ensemble) 분자동력학(MD) 시뮬레이션을 이용하여 300$^{\circ}$K에서 $\alpha$-quartz의 결정축에 따른 일축압축강도를 계산하고, 자연산 $\alpha$-quartz 단결정 코아를 제작하여 일축압축강도시험을 실시하였다. $\alpha$-quartz 단결정 코아에 대한 일축압축시험에서 측정된 결과에 의하면 재하 방향이 c축에 평행한 경우가 수직인 경우보다 높은 강도를 나타내지만, MD 시뮬레이션에서 계산된 완전무결함 $\alpha$-quartz의 경우 이와 반대의 결과를 보이고 있다. 두 경우 모두 재하방향에 따른 강도 이방성을 보이고 있으나, 그 이유는 서로 다르다. MD 시뮬레이션에 의해 계산된 무결함 $\alpha$-quartz의 강도 이방성은 결정구조의 차이에 기인하는 것으로 사료된다. 이에 반해 일축압축시험을 통해 측정된 $\alpha$-quartz의 강도 이방성은 결정성장과정에서 생기는 주상 미세결함에 의해 영향을 받는다.

• 한국소성가공학회:학술대회논문집
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• 한국소성가공학회 2007년도 추계학술대회 논문집
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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.

• 한국환경과학회지
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• 제25권7호
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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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• 제32권1호
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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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• 제35권3호
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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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• 제31권4호
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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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• 제18권11호
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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.

• 광물과 암석
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• 제33권1호
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• pp.19-28
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• 2020

란시아이트(ranciéite)는 수화된 Ca²⁺ 양이온이 망간 원자 빈자리를 아래위로 덮고 층간을 채우고 있는 육방정계 층상형 산화망간광물(phyllomanganates)이다. 망간 원자 빈자리를 Mn²⁺ 양이온이 더 우세하게 채우는 경우, 다카네라이트(takanelite)라는 광물로 구분하며, 란시아이트와 다카네라이트는 서로 고용체를 이룬다. 이 광물들은 입자크기가 매우 작고 다른 광물과 함께 산출되기 때문에 실험만으로 정확한 결정구조를 규명하기 어렵다. 이번 연구에서는 층간 Mn²⁺/Ca²⁺ 양이온 비율에 따른 란시아이트-다카네라이트의 결정구조와 층간 구조를 규명하기 위해 고전분자동역학 시뮬레이션(molecular dynamics simulations; MD)을 수행하였다. 연구방법의 적합성을 판단하기 위해 결정구조가 잘 알려진 칼코파나이트 군(chalcophanite group) 광물들에 대해 시뮬레이션 계산을 수행 후 실험 결과와 비교하였다. 이후 층간 양이온 비율에 따른 란시아이트 및 다카네라이트 모델에 대한 MD 시뮬레이션을 수행하여 양이온 함량에 따른 양이온과 물 분자의 분포 및 (001)면간거리를 제시한다.

• 한국광물학회지
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• 제32권3호
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• pp.151-162
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• 2019

토도로카이트(todorokite)는 $3{\times}3$ 망간 팔면체로 이루어진 상대적으로 큰 나노공극(nanopore)을 가지는 터널구조의 산화망간광물로 나노공극에 다양한 양이온 함유가 가능하기 때문에 금속이온 거동에 큰 역할을 할 수 있다. 주로 결정도가 낮고 다른 산화망간광물들과 함께 집합체로 발견되어 나노 공극 내부 양이온의 배위(coordination)구조는 실험만으로 여전히 규명하기 매우 어렵다. 이번 논문에서는 고전분자동력학(classical molecular dynamics, MD) 시뮬레이션을 이용하여 토도로카이트 터널에 함유된 $Mg^{2+}$ 이온의 배위구조에 대한 연구결과를 처음으로 소개한다. 기존 실험에서는 토도로카이트 내부에 함유된 $Mg^{2+}$가 공극의 중앙에 우세하게 자리한다고 알려져 있다. MD 시뮬레이션 결과, $Mg^{2+}$ 이온의 약 60 %가 나노공극의 중앙에 위치하지만, 약 40 %의 $Mg^{2+}$는 광물의 표면에 해당하는 공극의 코너에 위치하였다. 공극 중앙의 $Mg^{2+}$는 수용액에서처럼 물 분자와 6배위수를 보였다. 공극 코너의 $Mg^{2+}$ 역시 6배위수를 보였는데, 물 분자 이외에도 망간 팔면체 표면 산소와 배위를 보였다. $Mg^{2+}$ 이온의 동적 거동을 파악하기 위해 계산한 평균 제곱 변위(mean squared displacement) 결과에서는, 수용액 벌크(bulk) 상태에서 갖는 물 분자와 양이온의 동적 성질이 토도로카이트 1D 나노공극에서는 유지되지 못하고 잃어버리는 것을 확인할 수 있었다.