• Journal of the Korean Chemical Society
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• v.57 no.5
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• pp.554-559
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• 2013

In this study, we have investigated potential energy of ${\beta}$-D-glucopyranose in vacuum and implicit water condition. By Comparing two conditions we find that how solvation energy influence ${\beta}$-D-glucopyranose structure. We use AMBER package program and GLYCAM_06 force field. Solvation model was used for the generalized Born model with Hawkins, Cramer, Truhlar has been proposed. We conclude that difference of contour map of two conditions is caused by solvation effect by reducing hydrogen bonding interaction.

• Nuclear Engineering and Technology
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• v.47 no.6
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• pp.662-668
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• 2015

A suspension of titanium nanoparticles (Ti NPs) in liquid sodium (Na) has been proposed as a method to mitigate the violent sodium-water reaction (SWR). The interparticle potential between Ti NPs in liquid Na may play a significant role in the agglomeration of NPs on the reaction surface and in the bulk liquid Na, since the potential contributes to a reduction in the long-term dispersion stability. For the effective control of the SWR with NPs, a physical understanding of the molecular dynamics of NPs in liquid Na is key. Therefore in this study, the nonretarded Van der Waals model and the solvation potential model are employed to analyze the interparticle potential. The ab initio calculation reveals that a strong repulsive force driven by the solvation potential exceeds the interparticle attraction and predicts the agglomeration energy required for two 10-nm Ti NPs to be $4{\times}10^{-17}J$. The collision theory suggests that Ti NPs can be effective suppressors of the SWR due to the high energy barrier that prevents significant agglomeration of Ti NPs in quiescent liquid Na.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.237-249
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• 2014

Deposition of amyloid-${\beta}$ ($A{\beta}$) proteins is the conventional pathological hallmark of Alzheimer's disease (AD). The $A{\beta}$ protein formed from the amyloid precursor protein is predominated by the 40 residue protein ($A{\beta}40$) and by the 42 residue protein ($A{\beta}42$). While $A{\beta}40$ and $A{\beta}42$ differ in only two amino acid residues at the C-terminal end, $A{\beta}42$ is much more prone to aggregate and exhibits more neurotoxicity than $A{\beta}40$. Here, we investigate the molecular origin of the difference in the aggregation propensity of these two proteins by performing fully atomistic, explicit-water molecular dynamics simulations. Then, it is followed by the solvation thermodynamic analysis based on the integral-equation theory of liquids. We find that $A{\beta}42$ displays higher tendency to adopt ${\beta}$-sheet conformations than $A{\beta}40$, which would consequently facilitate the conversion to the ${\beta}$-sheet rich fibril structure. Furthermore, the solvation thermodynamic analysis on the simulated protein conformations indicates that $A{\beta}42$ is more hydrophobic than $A{\beta}40$, implying that the surrounding water imparts a larger thermodynamic driving force for the self-assembly of $A{\beta}42$. Taken together, our results provide structural and thermodynamic grounds on why $A{\beta}42$ is more aggregation-prone than $A{\beta}40$ in aqueous environments.

• Tribology and Lubricants
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• v.14 no.1
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• pp.54-63
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• 1998

In many practical lubricated contacts such as a rough concentrated contact on the sliding of nominally flat surfaces, the fluid may be of molecular (nanometer) scale owing to the asperity interactions on the surfaces. Under this condition, there is insufficient lubricant on the concentrated contact spot to maintain a realistic continuum. Rheological behavior for this kind of concentrated contact has been studied extensively to know whether the application of viscous fluid model is appropriate. The interaction of two rough surfaces is simplified as perfectly flat-rough surfaces contact under certain conditions by "composite topography" and for a nanometer scale fluid film, three kinds of rheological fluid behavior are analyzed in elastohydrodynamic asperity point contact.t contact.

• Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
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• 1997.10a
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• pp.173-182
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• 1997

In many practical lubricated contacts such as a rough concentrated contact on the sliding of nominally flat surfaces, the fluid may be of molecular (nanometer) scale owing to the asperity interactions on the surfaces. Under this condition, there is insufficient lubricant on the concentrated contact spot to maintain a realistic continuum. Rheological behavior for this kind of concentrated contact was studied to know whether the application of viscous fluid model is appropriate. The interaction of two rough surfaces is simplified as perfectly flat-rough surfaces contact under certain conditions by "composite topography" and for a nanometer scale fluid film, three kinds of rheological fluid behavior are analyzed in elastohydrodynamic asperity point contact.t contact.

• Bulletin of the Korean Chemical Society
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• v.30 no.8
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• pp.1845-1850
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• 2009

We have performed replica-exchange molecular dynamics (REMD) simulations on the dimer formation of fibrilforming segments of $\alpha$-Synuclein (residues 71 - 82) using implicit solvation models with two kinds of force fields- AMBER parm99SB and parm96. We observed spontaneous formation of dimers from the extensive simulations, demonstrating the self-aggregating and fibril forming properties of the peptides. Secondary structure profile and clustering analysis showed that dimers with antiparallel $\beta$-sheet conformations, stabilized by well-defined hydrogen boding, are major species corresponding to global free energy minimum. Parallel dimers with partial $\beta$-sheets are found to be off-pathway intermediates. The relative instability of the parallel arrangements is due to the repulsive interactions between bulky and polar side chains as well as weaker backbone hydrogen bonds.

• Journal of Integrative Natural Science
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• v.3 no.1
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• pp.49-53
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• 2010

Molecular docking is a critical event which mostly forms Van der waals complex in molecular recognition. Since the majority of developed drugs are small molecules, docking them into proteins has been a prime concern in drug discovery community. Since the binding pose space is too vast to cover completely, many search algorithms such as genetic algorithm, Monte Carlo, simulated annealing, distance geometry have been developed. Proper evaluation of the quality of binding is an essential problem. Scoring functions derived from force fields handle the ligand binding prediction with the use of potential energies and sometimes in combination with solvation and entropy contributions. Knowledge-based scoring functions are based on atom pair potentials derived from structural databases. Forces and potentials are collected from known protein-ligand complexes to get a score for their binding affinities (e.g. PME). Empirical scoring functions are derived from training sets of protein-ligand complexes with determined affinity data. Because non of any single scoring function performs generally better than others, some other approaches have been tried. Although numerous scoring functions have been developed to locate the correct binding poses, it still remains a major hurdle to derive an accurate scoring function for general targets. Recently, consensus scoring functions and target specific scoring functions have been studied to overcome the current limitations.

• Journal of the Korean Chemical Society
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• v.18 no.5
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• pp.320-328
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• 1974

It is unable to derive the standard emf ($E^{\circ}$) of the cell at high pressure from the conventional method. However, when the concept of the complete equilibrium constant($K{\circ})$) is available to the conventional Nernst equation, it is possible to get the standard emf of the cell at high pressure(complete Nernst equation). Moreover, the other thermodynamic properties, such as the net change of solvation number(k), the compressibility of solvent(${\beta}$), ionization constant(K), the standard free energy change(${\Delta}G^{\circ}$), the standard enthalpy change(${\Delta}H^{\circ}$) and the standard entropy change (${\Delta}S^{\circ}$) of the cell reaction at equilibrium state have been also obtained. In this experiment, the emf of the cell; 12.5 % Cd(Hg)│$CdSO_4(3.105{\times}10^{-3}M),\;Hg_2SO_4│Hg$ have bee measured at temperature from 20 to $35^{\circ}C$ and at pressures from 1 to 2500 atms. The emf of the cell increased with increasing pressure at constant temperature, and did with increasing temperature at constant pressure. The net change of solvation number(k) of the cell reaction was 41.96 at $25^{\circ}C$, and kept constant value with pressure, while, K and ${\Delta}S^{\circ}$ increased with pressure, but whereas ${\Delta}G^{\circ}$ and ${\Delta}H^{\circ}$ decreased. Since the standard emf of the cell at high pressure can be calculated from the complete Nernst equation, the theory of chemical equilibrium could be developed with at high pressure as well as at the atmosphere.

• Journal of the Korean Chemical Society
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• v.24 no.6
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• pp.444-451
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• 1980

In order to further elucidate the process of electron solvation in liquids, the medium effect, as the difference between the free energy of $H^+$ in aqueous and non-aqueous states (${\Delta}{\Delta}G_0$), of THF-water mixtures has been investigated. (${\Delta}{\Delta}G_0$) were determined by electromotive force masurements of the cell Pt$H_2Q$, Q, HCI, THF, $H_2O$|KC1 | $Hg_2Cl_2$|Hg(Pt), where $H_2Q$ and Q are hydroquinone and quinone respectively. The effect of dielectric constant on the difference of free energy and the absorption energy of solvated electrons have been studied. For the consideration of these effect the polymerization of water in THF has been studied. Near infrared spectrum of O-H stetching energy has been used to measure the extent of water aggregates. The expermental results indicate that at least in some composition of binary mixtures the electrons or other ions are solvated preferentially with one component of solvents.