• Bulletin of the Korean Chemical Society
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• 제32권7호
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• pp.2237-2242
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• 2011

Anomalous scaling behaviors such as significantly large growth exponent (${\beta}$) and small reciprocal of dynamic exponent (1/z) values for many molecular crystalline thin films have been reported. In this study, the variation of scaling exponent values and consequent growth behaviors of molecular thin films were more quantitatively analysed using a (1+1)-dimensional surface lateral diffusion model. From these simulations, influence of step edge barriers and grain boundaries of molecular thin films on the various scaling exponent values were elucidated. The simulation results for the scaling exponents were also well consistent with the experimental data for previously reported molecular thin film systems.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2010년도 제39회 하계학술대회 초록집
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• pp.93-93
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• 2010

In this talk, I will introduce a reactive force field (ReaxFF) molecular dynamics (MD) simulation. In contrast to common MD simulations with empirical FFs, we can predict chemical reactions (bond breaking and formation) in large scale systems with the ReaxFF simulation where all of the ReaxFF parameters are from quantum mechanical calculations such as density functional theory to provide high accuracy. Accordingly, the ReaxFF simulation provides both accuracy of quantum mechanical calculations and description of large scale systems of atomistic simulations at the same time. Here, I will first discuss a theory in the ReaxFF including the differences from other empirical FFs, and then show several applications for studying chemical reactions of SiHx radicals on Si surfaces, which is an important issue in Si process.

• Bulletin of the Korean Chemical Society
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• 제19권10호
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• pp.1068-1072
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• 1998

We present results of molecular dynamic (MD) simulations for the segmental motion of liquid n-butane as the base case for a consistent study for conformational transition from one rotational isomeric state to another in long chains of liquid n-alkanes. The behavior of the hazard plots for n-butane obtained from our MD simulations are compared with that for n-butane of Brownian dynamics study. The MD results for the conformational transition of n-butane by a Poisson process form the total first passage times are different from those from the separate t-g and g-t first passage times. This poor agreement is probably due to the failure of the detailed balance between the fractions of trans and gauche. The enhancement of the transitions t-g and g-t at short time regions are also discussed.

• Bulletin of the Korean Chemical Society
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• 제19권11호
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• pp.1217-1221
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• 1998

We present results of molecular dynamic (MD) simulations for the segmental motion of liquid n-heptadecane in order to investigate conformational transitions from one rotational isomeric state to another. The behavior of the hazard plots for n-heptadecane obtained from our MD simulations are compared with that for polymer of Brownian dynamics (BD) study. The transition rate at the ending dihedrals of the n-heptadecane chain is much higher than that at the central dihedrals. In the study of correlation between transitions of neighboring dihedrals, the large value of c2 implies that some 30% of the transitions of the second neighbors can be regarded as following transitions two bonds away in a correlated fashion. Finally the analysis of multiple transitions and the number of times occurred in the initial 0.005 ns are discussed.

• Structural Engineering and Mechanics
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• 제30권2호
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• pp.177-190
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• 2008

Material failure behavior is generally dependent on loading rate. Especially in brittle and quasi-brittle materials, rate dependent material behavior can be significant. Empirical formulations are often used to predict the rate dependency, but such methods depend on extensive experimental works and are limited by practical constraints of physical testing. Numerical simulation can be an effective means for extracting knowledge about rate dependent behavior and for complementing the results obtained by testing. In this paper, the failure behavior of a brittle material under different loading rates is simulated by molecular dynamics analysis. A notched specimen is modeled by sub-million particles with a normalization scheme. Lennard-Jones potential is used to describe the interparticle force. Numerical simulations are performed with six different loading rates in a direct tensile test, where the loading velocity is normalized to the ratio of the pseudo-sonic speed. As a consequence, dynamic features are achieved from the numerical experiments. Remarkable failure characteristics, such as crack surface interaction/crack arrest, branching, and void nucleation, vary in case of the six loading cases. These characteristics are interpreted by the energy concept approach. This study provides insight into the change in dynamic failure mechanism under different loading rates.

• Tribology and Lubricants
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• 제36권5호
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• pp.290-296
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• 2020

When two layers of carbon nanotube (CNT) arrays are loaded to mate, the free ends of individual CNTs come into contact at the interface of the two layers. This leads to a higher contact resistance due to a smaller contact region. However, when the free CNT ends of one array penetrate into the mating array, the contact region increases, effectively lowering the contact resistance. To explore the penetration of mating CNTs, we perform molecular dynamic simulations of a simple unit cell model, incorporating four CNTs in the lower array layer coupled with a single moving CNT on the upper layer. The interaction with neighboring CNTs is modelled by long-range carbon bond order potential (LCBOP I). The model structure is optimized by energy minimization through the conjugate gradient method. A NVT ensemble is used for maintain a room temperature during simulation. The time integration is performed through the velocity-Verlet algorithm. A significant vibrational motion of CNTs is captured when penetration is not available, resulting in a specific vibration mode with a high frequency. Due to this vibrational behavior, the random behaviors of CNT motion for predicting the penetration are confirmed under the specific gap distances between CNTs. Thus, the probability of penetration is examined according to the gap distance between CNTs in the lower array and the aspect ratio of CNTs. The penetration is significantly affected by the vibration mode due to the van der Waals forces between CNTs.

• Bulletin of the Korean Chemical Society
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• 제32권12호
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• pp.4397-4402
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• 2011

The NF-${\kappa}B$ system of transcription factors plays a crucial role in inflammatory diseases, making it an important drug target. We combined quantitative structure activity relationships for predicting the activity of new compounds and quantitative dynamic models for the NF-${\kappa}B$ network with intracellular concentration models. GFA-MLR QSAR analysis was employed to determine the optimal QSAR equation. To validate the predictability of the $IKK{\beta}$ QSAR model for an external set of inhibitors, a set of ordinary differential equations and mass action kinetics were used for modeling the NF-${\kappa}B$ dynamic system. The reaction parameters were obtained from previously reported research. In the IKKb QSAR model, good cross-validated $q^2$ (0.782) and conventional $r^2$ (0.808) values demonstrated the correlation between the descriptors and each of their activities and reliably predicted the $IKK{\beta}$ activities. Using a developed simulation model of the NF-${\kappa}B$ signaling pathway, we demonstrated differences in $I{\kappa}B$ mRNA expression between normal and different inhibitory states. When the inhibition efficiency increased, inhibitor 1 (PS-1145) led to long-term oscillations. The combined computational modeling and NF-${\kappa}B$ dynamic simulations can be used to understand the inhibition mechanisms and thereby result in the design of mechanism-based inhibitors.

• Bulletin of the Korean Chemical Society
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• 제17권8호
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• pp.735-744
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• 1996

We present results of molecular dynamic (MD) simulations for the thermodynamic and structural properties of liquid n-alkanes, from n-butane to n-heptadecane, using three different models Ⅰ-Ⅲ. Two of the three classes of models are collapsed atomic models while the third class is an atomistically detailed model. Model Ⅰ is the original Ryckaert and Bellemans' collapsed atomic model [Discuss. Faraday Soc. 1978, 66, 95] and model Ⅱ is the expanded collapsed model which includes C-C bond stretching and C-C-C bond angle bending potentials in addition to Lennard-Jones and torsional potentials of model Ⅰ. In model Ⅲ all the carbon and hydrogen atoms in the monomeric units are represented explicitly for the alkane molecules. Excellent agreement of the results of our MD simulations of model Ⅰ for n-butane with those of Edberg et al.[J. Chem. Phys. 1986, 84, 6933], who used a different algorithm confirms the validity of our algorithms for MD simulations of model Ⅱ for 14 liquid n-alkanes and of models Ⅰ and Ⅲ for liquid n-butane, n-decane, and n-heptadecane. The thermodynamic and structural properties of models Ⅰ and Ⅱ are very similar to each other and the thermodynamic properties of model Ⅲ for the three n-alkanes are not much different from those of models Ⅰ and Ⅱ. However, the structural properties of model Ⅲ are very different from those of models Ⅰ and Ⅱ as observed by comparing the radial distribution functions, the average end-to-end distances and the root-mean-squared radii of gyrations.

• 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.

• Bulletin of the Korean Chemical Society
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• 제18권4호
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• pp.415-424
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• 1997

Conformational flexibilities of the GlcNAc(β1,3)Gal(β)OMe are investigated through NMR spectroscopy and molecular modeling. Adiabatic energy map generated with a dielectric constant of 50 contains three local minima. All of the molecular dynamics simulations on three local minimum energy structures show fluctuations between two low energy structures, N2 at φ=80° and ψ=60° and N3 at φ=60° and ψ=-40°. We have presented adequate evidences to state that GlcNAc(β1,3)Gal(β)OMe exists in two conformationally discrete forms. Two state model of N2 and N3 conformers with a population ratio of 40:60 is used to calculate the effective cross relaxation rate and reproduces the experimental NOEs very well. Molecular dynamics simulation in conjunction with two state model proves successfully the dynamic equilibrium existed in GlcNAc(β1,3)Gal(β)OMe and can be considered as a powerful method to analyze the motional properties in the structure of carbohydrate. This observation also cautions against the indiscriminate use of a rigid model to analyze NMR data.