• Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
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• 2002.10b
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• pp.59-60
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• 2002

In this digest, we briefly review our current molecular dynamics (MD) simulations that utilize both the reactive empirical bond order potential (REBO) and the adaptive intermolecular REBO (AIREBO) potential energy functions. The AIREBO potential includes intermolecular interactions, so that self·assembled monolayers, and liquids, can be modeled. We have examined the mechanical and tribological properties of model self assembled monolayers and amorphous carbon films. Self-assembled monolayers are modeled by covalently bonding hydrocarbon chains to diamond substrates. Because the REBO potentials can model chemical reactions, specific compression and sliding induced chemical reactions were identified.

• Proceedings of the KAIS Fall Conference
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• 2011.05a
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• pp.306-309
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• 2011

A lattice model based molecular clusters is presented to improve a classical equation of state(EOS) for volumetric properties in the critical region. The term is based on the two assumptions: (1) The Helmholtz energy is individually divided into classical and long-range density fluctuation contribution (2) All molecules form cluster near the critical region due to long-range density fluctuation. To formulate such molecular cluster, we extended the Veytsman statistics originally developed for the cluster due to hydrogen bonding. The probability function in the statistics is modified to represent the characteristics of long-range density fluctuation vanishing far from critical region. The proposed fluctuation contribution was incorporated into the Sanchez-Lacombe EOS and the combined model with 6 adjustable parameters has been tested against experimental VLE data for pure compounds. The combined model is found to well represent flatten critical isotherm for methane and top of the coexistence curve for the tested components.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.70-75
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• 2015

Fasciclin 1 (FAS1) is an extracellular protein whose aggregation in cornea leads to visual impairment. While a number of FAS1 mutants have been studied that exhibit enhanced/decreased aggregation propensity, no structural information has been provided so far that is associated with distinct aggregation potential. In this study, we have investigated the structural and thermodynamic characteristics of the wild-type FAS1 and its two mutants, R555Q and R555W, by using molecular dynamics simulations and three-dimensional reference interaction site model (3D-RISM) theory. We find that the hydrophobic solvent accessible surface area increases due to hydrophobic core repacking in the C-terminus caused by the mutation. We also find that the solvation free energy of the mutants increases due to the enhanced non-native H-bonding. These structural and thermodynamic changes upon mutation contribute to understand the aggregation of these mutants.

• Macromolecular Research
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• v.16 no.4
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• pp.320-328
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• 2008

We established a thermodynamic framework of group contribution method based on modified double lattice (MDL) model. The proposed model included the long-range interaction contribution caused by the Coulomb electrostatic forces, the middle-range interaction contribution from the indirect effects of the charge interactions and the short-range interaction from modified double lattice model. The group contribution method explained the combinatorial energy contribution responsible for the revised Flory-Huggins entropy of mixing, the van der Waals energy contribution from dispersion, the polar force, and the specific energy contribution from hydrogen bonding. We showed the solvent activities of various polymer solution systems in comparison with theoretical predictions based on experimental data. The proposed model gave a very good agreement with the experimental data.

• Journal of the Korean Chemical Society
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• v.67 no.4
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• pp.226-235
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• 2023

Chikungunya fever has a high morbidity rate in humans and is caused by chikungunya virus. There are no treatments available until now for this particular viral disease. The present study was carried out by selecting 19 flavonoids, which are available naturally in fruits, vegetables, tea, red wine and medicinal plants. The molecular docking of selected 19 flavonoids was carried out against the Chikungunya virus capsid protein using the Autodock4.2 software. Binding affinity analysis based on the Intermolecular interactions such as Hydrogen bonding and hydrophobic interactions and drug-likeness properties for all the 19 flavonoids have been carried out and it is found that the top four molecules are Chrysin, Fisetin, Naringenin and Biochanin A as they fit to the chikungunya protein and have binding energy of -8.09, -8.01, -7.6, and 7.3 kcal/mol respectively. This result opens up the possibility of applying these compounds in the inhibition of chikungunya viral protein.

• Bulletin of the Korean Chemical Society
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• v.34 no.6
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• pp.1814-1822
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• 2013

By using density functional theory calculations, we have performed a systemic study on the electronic structures and topological properties of interactions between N-butylpyridinium nitrate ($[BPY]^+[NO_3]^-$) and thiophene (TS), benzothiophene (BT), dibenzothiophene (DBT), naphthalene (NAP). The most stable structure of $[BPY]^+[NO_3]^-$ ion pair indicates that hydrogen bonding interactions between oxygen atoms on $[NO_3]^-$ anion and C2-H2 on pyridinium ring play a dominating role in the formation of ion pair. The occurrence of hydrogen bonding, ${\pi}{\cdots}$H-C, and ${\pi}{\cdots}{\pi}$ interactions between $[BPY]^+[NO_3]^-$ and TS, BT, DBT, NAP has been corroborated at the molecular level. But hydrogen bonding and ${\pi}{\cdots}{\pi}$ interactions between $[BPY]^+[NO_3]^-$ and NAP are weak in terms of structural properties and NBO, AIM analyses. DBT is prior to adsorption on N-butylpyridinium nitrate ionic liquid.

• Korean Journal of Crystallography
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• v.14 no.1
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• pp.16-23
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• 2003

The electronic structure and chemical bonding of β-MnO₂ were theoretically investigated by DV-X/sub α/ (the discrete variation X/sub α/) method. which is a sort of the first principle molecular orbital method using Hatre-Fock-Slater approximation. The calculations on several cluster models having different sizes were carried out for the determination of a model suited for analyzing bulk state. The Mn/sub 15/O/sub 56/ model was selected as a sufficiently suitable model for the calculation of electronic state and chemical bonding by the comparison of the calculated XPS (X-ray photo-electron spectrum) and experimentally measured XPS. By using this model, the electron energy level, the density of state, the bond overlap population, the charge density distribution, and the net ionic transfer between cations and anions were calculated and discussed.

• Macromolecular Research
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• v.16 no.5
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• pp.446-456
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• 2008

A recent theoretical approach based on the coupling of both the Flory-Huggins (FH) and the Association Equilibria thermodynamic (AET) theories was modified and adapted to study the miscibility properties of a multi-component system formed by two polymers (a proton-donor and a proton-acceptor) and a proton-acceptor solvent, named copolymer(A)/solvent(B)/polymer(C). Compatibility between polymers was mainly attained by hydrogen-bonding between the hydroxyl group on the phenol unit of the poly(styrene-co-vinyl phenol) (PSVPh) and the carbonyl group of the biodegradable and environmentally friendly poly(3-hydroxybutyrate) (PHB). However, the self-association of PSVPh and specific interactions between the PSVPh and the H-acceptor group (an ether oxygen atom) of the epichlorohydrin (ECH) solvent were also established in a lower extension, which competed with the polymer-polymer association. All the binary specific interactions and their dependence with the system composition as well as with the copolymer content were evaluated and quantified by means of two excess functions of the Gibbs tree energy, ${\Delta}g_{AB}$ and ${\Delta}g_{AC}$. Experimental results from fluorescence spectroscopy were consistent with the theoretical simulations derived with the model, which could also be applied and extended to predict the miscibility in solution of any polymer blend with specific interactions.

• Elastomers and Composites
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• v.57 no.4
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• pp.157-164
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• 2022

Representative bulletproof materials, such as aramid or ultra-high molecular weight polyethylene(UHMWPE), have excellent strength and modulus in the plane direction but are very vulnerable to forces applied in the thickness direction. This paper reports a study on the effects of reinforcement in the thickness direction when bulletproof composite fabrics are prepared to improve their performance. Aramid and UHMWPE fabrics were combined using the film-bonding, needle-punching, or stitching methods and then subjected to low-velocity projectile and ball-drop impact tests. The results of the low-velocity projectile test indicated that the backface signature(BFS) decreased by up to 29.2% in fabrics obtained via the film-bonding method. However, the weight of the film-bonded fabric increased by approximately 23% compared with that obtained by simple lamination, and the fabric stiffened on account of the binder. Flexibility, light weight for wearability, and excellent bulletproof performance are very important factors in the development of bulletproof materials. When the needle-punching method was used, the BFS increased as the fibers sustained damage by the needle. When the composite fabrics were combined by stitching, no significant difference in weight and thickness was observed, and the BFS showed similar results. When a diagonal stitching pattern was employed, the BFS decreased as the stitching density increased. By contrast, when a diamond stitching pattern was used, the fabric fibers were damaged and the BFS increased as the stitching density increased.

• Membrane Journal
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• v.27 no.4
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• pp.358-366
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• 2017

The most important factor in the performances of polymer electrolyte membranes for fuel cells is how fast hydrogen ions can be transported along the water channel formed inside the electrolyte membrane. Since the morphology of the water channel and the diffusivity of the protons are very important factors for the proton transport behavior, various molecular dynamics simulation studies are being carried out to clarify this. The force-field is an important variable parameterizing the movement and interaction of each atom in molecular dynamics simulation. In this study, proton diffusivities of the 3D models of polymer electrolyte membranes were calculated in order to analyze the effects of various types of force-fields on the molecular simulation. It has been found that the charge value determining the non-bonding interaction plays a very important role in the formation of the water channel morphology, and the COMPASS force-field can calculate the accurate proton diffusion behavior. Accordingly, for molecular dynamics simulation of polymer electrolyte membranes, the proper selection of the force-field is very important due to its great effect on the proton diffusion as well as the final molecular structure.