• BMB Reports
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• v.39 no.3
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• pp.284-291
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• 2006

In this study, the cDNA of a new peptide from the venom of the scorpion, Buthotus saulcyi, was cloned and sequenced. It codes for a 64 residues peptide (Bsaul1) which shares high sequence similarity with depressant insect toxins of scorpions. The differences between them mainly appear in the loop1 which connects the $\beta$-strand1 to the $\alpha$-helix and seems to be functionally important in long chain scorpion neurotoxins. This loop is three amino acids longer in Bsaul1 compared to other depressant toxins. A comparative amino acid sequence analysis done on Bsaul1 and some of $\alpha$-, $\beta$-, excitatory and depressant toxins of scorpions showed that Bsaul1 contains all the residues which are highly conserved among long chain scorpion neurotoxins. Structural model of Bsaul1 was generated using Ts1 (a $\beta$-toxin that competes with the depressant insect toxins for binding to $Na^+$ channels) as template. According to the molecular model of Bsaul1, the folding of the polypeptide chain is being composed of an anti-parallel three-stranded $\beta$-sheet and a stretch of $\alpha$-helix, tightly bound by a set of four disulfide bridges. A striking similarity in the spatial arrangement of some critical residues was shown by superposition of the backbone conformation of Bsaul1 and Ts1.

• Composites Research
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• v.30 no.4
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• pp.247-253
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• 2017

In this study, the mechanical behavior and interface properties of boron nitride nanotube-poly(methyl methacrylate) nanocomposites are predicted using the molecular dynamics simulations and the double inclusion model. After modeling nanocomposite unit cell embedding single-walled nanotube and polymer, the stiffness matrix is determined from uniaxial tension and shear tests. Through the orientation average of the transversely isotropic stiffness matrix, the effective isotropic elastic constants of randomly dispersed microstructure of nanocomposites. Compared with the double inclusion model solution with a perfect interfacial condition, it is found that the interface between boron nitride nanotube and polymer matrix is weak in nature. To characterize the interphase surrounding the nanotube, the two step domain decomposition method incorporating a linear spring model at the interface is adopted. As a result, various combinations of the interfacial compliance and the interphase elastic constants are successfully determined from an inverse analysis.

• 한국정보디스플레이학회:학술대회논문집
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• 2008.10a
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• pp.1441-1444
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• 2008

We developed ultra-accelerated quantum chemical molecular dynamics and spectroscopic characterization simulators for development of PDP materials. By combination of these simulators, realistic structure of PDP materials is drawn on the computer. Furthermore, based on the structures, various properties such as cathode luminescence spectrum and secondary electron emission, is successfully evaluated. The strategy of "Experiment integrated Computational Chemistry" using developed simulators will presented that has the potential in being powerful tool for designing the PDP materials.

• Journal of Magnetics
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• v.20 no.3
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• pp.308-311
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• 2015

We design a crisscrossed double-layer birdcage (DLBC) coil by modifying the coil geometry of a standard single-layer BC (SLBC) coil to enhance the homogeneity of transmitting magnetic flux density ($B_1{^+}$) along the main magnetic field ($B_0$)-direction for small-animal magnetic resonance imaging (MRI) at 300 MHz. The performance assessment of the crisscrossed DLBC coil is conducted by computational analysis with the finite-difference time domain method (FDTD) and compared with SLBC coil in terms of the $B_1$ and the $B_1{^+}$ distribution. As per the computational calculation studies, the mean value in the two-dimensional $B_1{^+}$ map obtained at the mid-axial slice with the proposed DLBC coil is slightly lower than that obtained with the SLBC coil, but the $B_1{^+}$ value of the DLBC coil in the outermost plane (40 mm away from the central plane) shows improvements of 19.3% and 24.8% over the SLBC coil $B_1{^+}$ value when simulating a spherical phantom and realistic mouse body modeling. These simulation results indicate that, the $B_1{^+}$ homogeneity along the z-direction was improved by using DLBC configuration. Our approach enables $B_1{^+}$ homogeneity improvement along the zdirection, and it can also be applied to ultra-high field (UHF) MRI systems.

• Polymer(Korea)
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• v.25 no.1
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• pp.25-32
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• 2001

The kinetics of ester interchange reaction of dimethyl naphthalate(DMN) with ethylene glycol(EG) has been studied in the range of 180-200 $^{\circ}C$ using zinc and manganese catalysts. The reaction was performed in a semibatch reactor under nonisothermal condition and the degree of reaction was calculated from experimental data of methanol removal rate and reaction temperature. As a reaction model, both the functional group model and the molecular species model were applied and analysed. In case of zinc catalyst, the ratio of reaction rate of methyl hydroxyethyl naphthalate(MHEN) with EG on that of DMN with EG is about 1.4, whereas in case of manganese catalyst the ratio is about 4.3, which implies that the reaction rate is quite dependent on the type of catalyst. In case of zinc catalyst, the reaction order of catalyst concentration on either DMN or MHEN and EG is less than 1, whereas in case of manganese catalyst, the reaction order is larger than 1. The activation energy for zinc and manganese catalyst, irrespective of the type of molecular species, e.g., DMN and MHEN, were found to be 25000 and 28750 cal/mol, respectively. As a result of comparing two reaction model, the molecular species model fits well for the experimental data.

• Journal of the Korean Society for Aeronautical & Space Sciences
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• v.32 no.7
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• pp.60-68
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• 2004

High velocity impacts are accompanied with large deformations, which generate a large amount of heat due to plastic works, resulting in a significant temperature rise of the material. Because the elevated temperature affects the dynamic properties of materials, it is important to predict the temperature rise during high-stram-rate deformations. Both existing vacancies and excess vacancies are credited to the stored energy, yet it is difficult to distinguish one from another in contribution to the stored energy using macroscopic level materials models. In this study, an atomistic material model for fee materials such as copper is set up to calculate the stored energy using molecular dynamics (MD) simulations. It is concluded that excess vacancies play an important role for the stored energy during a high-strain-rate deformation.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.14-23
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• 2015

Alzheimer's disease is one of the most common types of degenerative dementia. As a considerable cause of Alzheimer's disease, neurotoxic plaques composed of 39 to 42 residue-long amyloid beta($A{\beta}$) fibrils have been found in the patient's brain in large quantity. A previous study found that erythrosine B (ER), a red color food dye approved by FDA, inhibits the formation of amyloid beta fibril structures. Here, in an attempt to elucidate the inhibition mechanism, we performed molecular dynamics simulations to demonstrate the conformational change of $A{\beta}40$ induced by 2 ERs in atomistic detail. During the simulation, the ERs bound to the surfaces of both N-terminus and C-terminus regions of $A{\beta}40$ rapidly. The observed stacking of the ERs and the aromatic side chains near the N-terminus region suggests a possible inhibition mechanism in which disturbing the inter-chain stacking of PHEs destabilizes beta-sheet enriched in amyloid beta fibrils. The bound ERs block water molecules and thereby help stabilizing alpha helical structure at the main chain of C-terminus and interrupt the formation of the salt-bridge ASP23-LYS28 at the same time. Our findings can help better understanding of the current and upcoming treatment studies for Alzheimer's disease by suggesting inhibition mechanism of ER on the conformational transition of $A{\beta}40$ at the molecular level.

• Journal of the Korean Chemical Society
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• v.54 no.4
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• pp.363-373
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• 2010

Computational studies were carried out on the opiates morphine, heroin, codeine, pentazocine, and buprenorphine, under the density functional theory. The geometric parameters of the pharmacophore and substituents were evaluated at the B3LYP/6-31+G(d) level of theory. The electronic structure calculations were performed using the same hybrid functional at the B3LYP/6-311++G (d,p) level of theory. The atomic charges were obtained by Mulliken population analysis. Given the reported biological activity, calculated partition coefficients, and electronic and geometric analysis, pentazocine and buprenorphine were chosen as models for proposed analogues. These analogues were then studied and compared with the model molecules. The study reveals that the geometry and electronic structure of the pharmacophore remains consistent in the presence of different substituents. Because the proposed analogues preserve the studied properties of the model molecules, it is likely that these analogues display biological activity.

• Membrane Journal
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• v.30 no.4
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• pp.242-251
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• 2020

Computer simulation tools mainly used for polymer materials and polymeric membranes are divided into various fields depending on the size of the object to be simulated and the time to be simulated. The computer simulations introduced in this review are classified into three categories: Quantum mechanics (QM), molecular dynamics (MD), and mesoscale modeling, which are mainly used in computational material chemistry. The computer simulation used in polymer research has different research target for each kind of computational simulation. Quantum mechanics deals with microscopic phenomena such as molecules, atoms, and electrons to study small-sized phenomena, molecular dynamics calculates the movement of atoms and molecules calculated by Newton's equation of motion when a potential or force of is given, and mesoscale simulation is a study to determine macroscopically by reducing the computation time with large molecules by forming beads by grouping atoms together. In this review, various computer simulation programs mainly used for polymers and polymeric membranes divided into the three types classified above will be introduced according to each feature and field of use.

• Journal of Ginseng Research
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• v.44 no.5
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• pp.690-696
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• 2020

Background: As the main metabolites of ginsenosides, 20(S, R)-protopanaxadiol [PPD(S, R)] and 20(S, R)-protopanaxatriol [PPT(S, R)] are the structural basis response to a series of pharmacological effects of their parent components. Although the estrogenicity of several ginsenosides has been confirmed, however, the underlying mechanisms of their estrogenic effects are still largely unclear. In this work, PPD(S, R) and PPT(S, R) were assessed for their ability to bind and activate human estrogen receptor α (hERα) by a combination of in vitro and in silico analysis. Methods: The recombinant hERα ligand-binding domain (hERα-LBD) was expressed in E. coli strain. The direct binding interactions of ginsenosides with hERα-LBD and their ERα agonistic potency were investigated by fluorescence polarization and reporter gene assays, respectively. Then, molecular dynamics simulations were carried out to simulate the binding modes between ginsenosides and hERα-LBD to reveal the structural basis for their agonist activities toward receptor. Results: Fluorescence polarization assay revealed that PPD(S, R) and PPT(S, R) could bind to hERα-LBD with moderate affinities. In the dual luciferase reporter assay using transiently transfected MCF-7 cells, PPD(S, R) and PPT(S, R) acted as agonists of hERα. Molecular docking results showed that these ginsenosides adopted an agonist conformation in the flexible hydrophobic ligand-binding pocket. The stereostructure of C-20 hydroxyl group and the presence of C-6 hydroxyl group exerted significant influence on the hydrogen bond network and steric hindrance, respectively. Conclusion: This work may provide insight into the chemical and pharmacological screening of novel therapeutic agents from ginsenosides.