• Bulletin of the Korean Chemical Society
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• v.19 no.11
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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.

• Transactions of the Korean Society of Mechanical Engineers B
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• v.26 no.2
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• pp.227-237
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• 2002

A numerical technique for simulating the aggregation of charged particles was presented with a Brownian dynamic simulation in the free molecular regime. The Langevin equation was used for tracking each particle making up an aggregate. A periodic boundary condition was used for calculation of the aggregation process in each cell with 500 primary particles of 16 nm in diameter. We considered the thermal force and the electrostatic force for the calculation of the particle motion. The electrostatic force on a particle in the simulation cell was considered as a sum of electrostatic forces from other particles in the original cell and its replicate cells. We assumed that the electric charges accumulated on an aggregate were located on its center of mass, and aggregates were only charged with pre-charged primary particles. The morphological shape of aggregates was described in terms of the fractal dimension. In the simulation, the fractal dimension for the uncharged aggregate was D$\_$f/ = 1.761. The fractal dimension changed slightly for the various amounts of bipolar charge. However, in case of unipolar charge, the fractal dimension decreased from 1.641 to 1.537 with the increase of the average number of charges on the particles from 0.2 to 0.3 in initial states. In the bipolar charge state, the average sizes of aggregates were larger than that of the uncharged state in the early and middle stages of aggregation process, but were almost the same as the case of the uncharged state in the final stage. On the other hand, in the unipolar charge state, the average size of aggregates and the dispersion of particle volume decreased with the increasing of the charge quantities.

• Composites Research
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• v.32 no.3
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• pp.163-169
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• 2019

In this paper, we constructed a molecular dynamics (MD) polymer model of PMMA with 95% of conversion by using dynamic polymerization algorithm of a thermoplastic polymer based on free radical polymerization. In this algorithm, we introduced a united-atom level coarse-grained force field that combines the non-bonded terms from the TraPPE-UA force field and the bonded terms from the PCFF force field to alleviate the computation efforts. The molecular weight distribution and the average molecular weight of the polymer were calculated by investigating each chain generated from the free radical polymerization simulation. The molecular weight of the polymer was controlled by the number of initiator radicals presented in the initial state and molecular weight effect to the density, the glass transition temperature, and the mechanical properties were studied.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.28 no.9
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• pp.1306-1313
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• 2004

This paper addresses a theoretical approach to calculate the amount of the stored energy during high strain-rate deformations using atomistic level simulation. The dynamic behavior of materials at high strain-rate deformation are of great interest. At high strain-rates deformations, materials generate heat due to plastic work and the temperature rise can be significant, affecting various properties of the material. It is well known that a small percent of the energy input is stored in the material, and most of input energy is converted into heat. However, microscopic analysis has not been completed without construction of a material model, which can simulate the movement of dislocations and vacancies. A major cause of the temperature rise within materials is traditionally credited to dislocations, vacancies and other defects. In this study, an atomistic material model for FCC such as copper is used to calculate the stored energy.

• Proceedings of the IEEK Conference
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• 1999.11a
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• pp.913-916
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• 1999

Recent developments of carbon nanotubes are reviewed［1,2,3,4］. We use Tersoff carbon potential for bonded interactions［5］ and Lennard-Jones 12-6 potential for non bonding interactions［6］to describe mechanical properties of the temperature-dependent armchair single wall carbon nanotube. At first we report that through defect number and bonding energy calculation, how single wall carbon nanutube is capped in the constant temperature. (300K, 2000K, 3000K, 4000K) At second, we perform MD simulation, which are performed on the energy optimized structure of carbon nanotube.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.141-155
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• 2014

Peptide bond hydrolysis는 세포 내외의 생화학반응에 있어서 핵심이다. 하지만 amide Hydrolysis Mechanism은 아직 명확하게 규명되지 않았다. pH가 중성인 물에서의 비 촉매 가수분해가 발생하는 몇몇 실험적 증거가 있지만, 해당 반응 매커니즘은 4 가지(non-assisted concerted, non-assisted step-wise, assisted concerted, assisted step-wise)로 여전히 논란이 있다. 이번 연구에서는, Formamide의 가능한 Hydrolysis Mechanism을 자세히 연구해보고자 한다. 먼저, Ab-initio 계산을 통해 4가지 반응 메커니즘의 다시 한번 확인하고, quantum chemical calculations과 quantum mechanical molecular dynamic이 결합된 (QMMD) simulation을 통하여 water solvent에서의 반응 메커니즘의 에너지관계를 규명하였다. 결론적으로 아직 계산이 끝나지 않은 supported concerted mechanism을 제외한 모든 계산에서 non-supported, supported 두 system 모두에서 step-wise가 일어나기 쉬웠고, non-supported 보다 supported mechanism이 선호됨을 보였다. Intermediate인 amino-gem-diol의 수용액 상에서 안정화 또한 나타났다. 이는 Ab-initio 계산만 통해서는 정확하게 산출할 수 없는 엔트로피의 영향을 잘 보여준다.

• The Journal of Korea Institute of Information, Electronics, and Communication Technology
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• v.13 no.5
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• pp.397-402
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• 2020

Collagen type I is the most abundant protein in the human body. It shows viscoelastic behavior, which is what confers tendons with their viscoelastic properties. There are two different temperature setting methods in molecular dynamics simulations, namely rescaling and reassignment. The rescaling method maintains the temperature by scaling the given temperature, while the reassignment method sets the temperature according to a Maxwell distribution at the target temperature. We observed time-dependent behavior when the reassignment method was applied in tensile simulation, but not when the rescaling method was applied. Time-dependent behavior was observed only when the reassignment method was applied or when one side of the collagen molecule was stretched to a greater extent than the other side. As result, the collagen is elongated to 80nm, 100nm, 130nm, and 180nm, respectively, when the collagen is pulled by different velocities, 0.5, 1, 2, and 5 Å/ps, up to 40 Å. The results do not provide a detailed physical explanation, but the phenomena illustrated in this result are important for caution when further simulations are performed.

• Asia-pacific Journal of Multimedia Services Convergent with Art, Humanities, and Sociology
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• v.8 no.6
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• pp.939-946
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• 2018

In this work, we present simple schematics for a three-terminal graphene-based nanoelectromechanical switch with the vertical electrode, and we investigated their operational dynamics via classical molecular dynamics simulations. The main structure is both the vertical pin electrode grown in the center of the square hole and the graphene covering on the hole. The potential difference between the bottom gate of the hole and the graphene of the top cover is applied to deflect the graphene. By performing classical molecular dynamic simulations, we investigate the nanoelectromechanical properties of a three-terminal graphene-based nanoelectromechanical switch with vertical pin electrode, which can be switched by the externally applied force. The elastostatic energy of the deflected graphene is also very important factor to analyze the three-terminal graphene-based nanoelectromechanical switch. This simulation work explicitly demonstrated that such devices are applicable to nanoscale sensors and quantum computing, as well as ultra-fast-response switching devices.

• Journal of Integrative Natural Science
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• v.16 no.3
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• pp.81-95
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• 2023

Colorectal cancer is one of the most common types of cancer worldwide, ranking third after lung and breast cancer in terms of global prevalence. With an expected 1.93 million new cases and 935,000 deaths in 2020, it is more prevalent in males than in women. Evidence has shown that during the later stages of colon cancer, STAT1 promotes tumor progression by promoting cell survival and resistance to chemotherapy. Recent studies have shown that inhibiting STAT1 pathway leads to a reduction in tumor cell proliferation and growth, and can also promote apoptosis in colon cancer cells. One of the recent approaches in the field of drug discovery is drug repurposing. In drug repurposing approach we have virtually screened FDA database against STAT1 protein and their interactions have been studied through Molecular docking. Cross docking was performed with the top 10 compounds to be more specific with STAT1 comparing the affinity with STAT2, STAT3, STAT4, STAT5a, STAT5b and STAT6. The drugs that showed higher affinity were subjected to Conceptual - Density functional theory. Besides, the Molecular dynamic simulation was also carried out for the selected leads. We also validated in-vitro against colon cancer cell lines. The results showed mainly Acetyldigitoxin has shown better binding to the target. From this study, we can predict that the drug Acetyldigitoxin has shown noticeable inhibitory efficiency against STAT1, which in turn can also lead to the reduction of tumor cell growth in colon cancer.

• Journal of the Korean Vacuum Society
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• v.21 no.2
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• pp.86-92
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• 2012

We have studied the effect of speed of deposited atom on morphology evolution during Glancing Angle Deposition (GLAD). Using Kinetic Monte Carlo simulation that incorporate molecular dynamics simulations, we have shown that the rough surface morphology became smoother as the speed of deposited atom is increased. The growth exponent ${\beta}$ change from 0.97 to 0.67 as the speed increase from ${\upsilon}_0$ to $10{\upsilon}_0$ in the case of GLAD. We also examined the effect of speed of deposited atom for the case of chemical vapor deposition (CVD) simulation. Compared to GLAD, the variation in scaling exponent ${\beta}$ is small but the speed of deposited atom also have considerable effect on growth morpholgy in the case of CVD.