• Journal of the Semiconductor & Display Technology
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• v.21 no.4
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• pp.6-13
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• 2022

The electrostatic phenomenon seriously issued in extreme ultraviolet semiconductor cleaning was studied in junction with molecular dynamic aspect. It was understood that two lone pairs of electrons in water molecule were subtly different each other in molecular orbital symmetry, existed as two states of large energy difference, and became basis for water clustering through hydron bonds. It was deduced that when hydrogen bond formed by lone pair of higher energy state was broken, two types of [H₂O]⁺ and [H₂O]^- ions would be instantaneously generated, or that lone pair of higher energy state experiencing reactions such as friction with Teflon surface could cause electrostatic generation. It was specifically observed that, in case of electrolyzed cathode water, negative electrostatic charges by electrons were overlapped with negative oxidation reduction potentials without mutual reaction. Therefore, it seemed that negative electrostatic development could be minimized in cathode water by mutual repulsion of electrons and [OH]^- ions, which would be providing excellences on extreme ultraviolet cleaning and electrostatic control as well.

• 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.

• Journal of the Korean Vacuum Society
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• v.12 no.1
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• pp.25-34
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• 2003

Deposition behavior of hard amorphous carbon film was investigated by molecular dynamic simulation using Tersoff potential which was suggested for the interaction potential between carbon atoms. When high energy carbon atoms were collided on diamond (100) surface, dense amorphous carbon film could be obtained. Physical properties of the simulated carbon film were compared with those of the film deposited by filtered cathodic arc process. As in the experimental result, the most diamond-like film was obtained at an optimum kinetic energy of the incident carbon atoms. The optimum kinetic energy was 50 eV, which is comparable to the experimental observation. The simulated film was amorphous with short range order of diamond lattice. At the optimum kinetic energy condition, we found that significant amount of carbon atom were placed at a metastable site of distance 2.1 $\AA$. By melting and quenching simulation of diamond lattice, it was shown that this metastatic peak is Proportional to the quenching rate. These results show that the hard and dense diamond-like film could be obtained when the localized thermal spike due to the collision of high energy carbon atom can be effectively dissipated to the lattice.

• Bulletin of the Korean Chemical Society
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• v.23 no.3
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• pp.447-453
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• 2002

In this paper we have presented the results of thermodynamic, structural, and dynamic properties of model systems for liquid benzene, toluene and p-xylene in an isobaric-isothermal (NpT) ensemble at 283.15, 303.15, 323.15, and 343.15 K using molecular dynamics (MD) simulation. This work is initiated to compensate for our previous canonical (NVT) ensemble MD simulations [Bull. Kor. Chem. Soc. 2001, 23, 441] for the same systems in which the calculated pressures were too low. The calculated pressures in the NpT ensemble MD simulations are close to 1 atm and the volume of each system increases with increasing temperature. The first and second peaks in the center of mass g(r) diminish gradually and the minima increase as usual for the three liquids as the temperature increases. The three peaks of the site-site gC-C(r) at 283.15 K support the perpendicular structure of nearest neighbors in liquid benzene. Two self-diffusion coefficients of liquid benzene via the Einstein equation and via the Green-Kubo relation are in excellent agreement with the experimental measures. The self-diffusion coefficients of liquid toluene and p-xylene are in accord with the trend that the self-diffusion coefficient decreases with increasing number of methyl group. The friction constants calculated from the force auto-correlation (FAC) function with the assumption that the fast random force correlation ends at time which the FAC has the first negative value give a correct qualitative trends: decrease with increase of temperature and increase with the number of methyl group. The friction constants calculated from the FAC's are always less than those obtained from the friction-diffusion relation which reflects that the random FAC decays slower than the total FAC as described by Kubo [Rep. Prog. Phys. 1966, 29, 255].

• Molecules and Cells
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• v.43 no.9
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• pp.763-773
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• 2020

Recently, tumor microenvironment (TME) and its stromal constituents have provided profound insights into understanding alterations in tumor behavior. After each identification regarding the unique roles of TME compartments, non-malignant stromal cells are found to provide a sufficient tumorigenic niche for cancer cells. Of these TME constituents, adipocytes represent a dynamic population mediating endocrine effects to facilitate the crosstalk between cancer cells and distant organs, as well as the interplay with nearby tumor cells. To date, the prevalence of obesity has emphasized the significance of metabolic homeostasis along with adipose tissue (AT) inflammation, cancer incidence, and multiple pathological disorders. In this review, we summarized distinct characteristics of hypertrophic adipocytes and cancer to highlight the importance of an individual's metabolic health during cancer therapy. As AT undergoes inflammatory alterations inducing tissue remodeling, immune cell infiltration, and vascularization, these features directly influence the TME by favoring tumor progression. A comparison between inflammatory AT and progressing cancer could potentially provide crucial insights into delineating the complex communication network between uncontrolled hyperplastic tumors and their microenvironmental components. In turn, the comparison will unravel the underlying properties of dynamic tumor behavior, advocating possible therapeutic targets within TME constituents.

• Genomics & Informatics
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• v.20 no.3
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• pp.33.1-33.17
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• 2022

Nervous necrosis virus (NNV) is a deadly infectious disease that affects several fish species. It has been found that the NNV utilizes grouper heat shock cognate protein 70 (GHSC70) to enter the host cell. Thus, blocking the virus entry by targeting the responsible protein can protect the fishes from disease. The main objective of the study was to evaluate the inhibitory potentiality of 70 compounds of Azadirachta indica (Neem plant) which has been reported to show potential antiviral activity against various pathogens, but activity against the NNV has not yet been reported. The binding affinity of 70 compounds was calculated against the GHSC70 with the docking and molecular dynamics (MD) simulation approaches. Both the docking and MD methods predict 4 (PubChem CID: 14492795, 10134, 5280863, and 11119228) inhibitory compounds that bind strongly with the GHSC70 protein with a binding affinity of -9.7, -9.5, -9.1, and -9.0 kcal/mol, respectively. Also, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the compounds confirmed the drug-likeness properties. As a result of the investigation, it may be inferred that Neem plant compounds may act as significant inhibitors of viral entry into the host cell. More in-vitro testing is needed to establish their effectiveness.

• Journal of the Korean Vacuum Society
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• v.15 no.4
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• pp.410-420
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• 2006

The dynamic effects, such as the steering and the screening effects during deposition on an epitaxial growth is studied by kinetic Monte Carlo simulation. In the simulation, we incorporates molecular dynamic simulation to rigorously take the interaction of the deposited atom with the substrate atoms into account, We find three characteristic features of the surface morphology developed by grazing angle deposition: (1) enhanced surface roughness, (2) asymmetric mound, and (3) asymmetric slopes of mound sides, Regarding their dependence on both deposition angle and substrate temperature, a reasonable agreement of the simulated results with the previous experimental ones is found. The characteristic growth features by grazing angle deposition are mainly caused by the inhomogeneous deposition flux due to the steering and screening effects, where the steering effects play the major role rather than the screening effects. Newly observed in the present simulation is that the side of mound in each direction is composed of various facets instead of all being in one selected mound angle even if the slope selection is attained, and that the slope selection does not necessarily mean the facet selection.

• Bulletin of the Korean Chemical Society
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• v.34 no.11
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• pp.3429-3443
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• 2013

Chemokine receptor (CCR2) is a G protein-coupled receptor that contains seven transmembrane helices. Recent pharmaceutical research has focused on the antagonism of CCR2 and candidate drugs are currently undergoing clinical studies for the treatment of diseases like arthritis, multiple sclerosis, and type 2 diabetes. In this study, we analyzed the time dependent behavior of CCR2 docked with a potent 4-azetidinyl-1-aryl-cyclohexane (4AAC) derivative using molecular dynamics simulations (MDS) for 20 nanoseconds (ns). Homology modeling of CCR2 was performed and the 4AAC derivative was docked into this binding site. The docked model of selected conformations was then utilized to study the dynamic behavior of the 4AAC enzyme complexes inside lipid membrane. MDS of CCR2-16b of 4AAC complexes allowed us to refine the system since binding of an inhibitor to a receptor is a dynamic process and identify stable structures and better binding modes. Structure activity relationships (SAR) for 4AAC derivatives were investigated and reasons for the activities were determined. Probable binding pose for some CCR2 antagonists were determined from the perspectives of binding site. Initial modeling showed that Tyr49, Trp98, Ser101, Glu291, and additional residues are crucial for 4AAC binding, but MDS analysis showed that Ser101 may not be vital. 4AAC moved away from Ser101 and the hydrogen bonding between 4AAC and Ser101 vanished. The results of this study provide useful information regarding the structure-based drug design of CCR2 antagonists and additionally suggest key residues for further study by mutagenesis.

• Journal of the Korean Society of Food Science and Nutrition
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• v.46 no.5
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• pp.653-658
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• 2017

To evaluate the effects of amylose content and dissolution media on the molecular structure of maize starch, changes in the hydrodynamic diameter of starch molecules were assessed via dynamic light scattering depending on amylose content and dissolution media. As the amylose content of starch increased, the hydrodynamic diameter of starch molecules proportionally decreased from 204 to 92 nm. To alter ionic strength, hydrogen bonding, or polarity of dissolution media, various contents of NaCl (1, 2, or 3 M), urea (1, 2, or 3 M), or 1-butanol (0.1, 0.5, or 1.0%) were added to media, respectively, resulting in increased hydrodynamic diameter of starch. However, the degree of expansion was dependent on amylose content and the concentration and/or type of additive. The hydrodynamic diameter of starch molecules exhibited significant correlation with amylose content obtained by size exclusion chromatography, regardless of dissolution conditions.

• Macromolecular Research
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• v.17 no.10
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• pp.785-790
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• 2009

In this paper, the relaxation behavior of the regenerated silk fibroin (SF) films was investigated using dielectric thermal analysis (DETA), and compared with the dynamic mechanical behavior obtained from dynamic mechanical thermal analysis (DMTA), in order to gain a better understanding of the characteristics of dielectric behavior of SF film and identify the differences between the two analyses. Compared to DMTA, DETA exhibited a higher sensitivity on the molecular relaxation behaviors at low temperature ranges that showed a high $\gamma$-relaxation peak intensity without noise. However, it was not effective to examine the relaxation behaviors at high temperatures such as $\alpha-$ and ${\alpha}_c$-relaxations that showed a shoulder peak shape. On the contrary, DMTA provided more information regarding the relaxation behaviors at high temperatures, by exhibiting the changes in width, intensity and temperature shift of the $\alpha$-relaxation peak according to various crystallinities. Conclusively, DETA and DMTA can be utilized in a complementary manner to study the relaxation behavior of SF over a wide temperature range, due to the different sensitivity of each technique at different temperatures.