• Bulletin of the Korean Chemical Society
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• v.22 no.3
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• pp.253-254
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• 2001

• Molecules and Cells
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• v.27 no.6
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• pp.651-656
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• 2009

The formation of ${\beta}$-amyloid peptide ($A{\beta}$) is initiated from cleavage of amyloid precursor protein (APP) by a family of protease, ${\alpha}$-, ${\beta}$-, and ${\gamma}$-secretase. Sub W, a substrate peptide, consists of 10 amino acids, which are adjacent to the ${\beta}$-cleavage site of wild-type APP, and Sub M is Swedish mutant with double mutations on the left side of the ${\beta}$-cleavage site of APP. Sub W is a normal product of the metabolism of APP in the secretary pathway. Sub M is known to increase the efficiency of ${\beta}$-secretase activity, resulting in a more specific binding model compared to Sub W. Three-dimensional structures of Sub W and Sub M were studied by CD and NMR spectroscopy in water solution. On the basis of these structures, interaction models of ${\beta}$-secretase and substrate peptides were determined by molecular dynamics simulation. Four hydrogen bonds and one water-mediated interaction were formed in the docking models. In particular, the hydrogen bonding network of Sub M-BACE formed spread over the broad region of the active site of ${\beta}$-secretase (P5-P3'), and the side chain of P2- Asn formed a hydrogen bond specifically with the side chain of Arg235. These are more favorable to the cleavage of Sub M by ${\beta}$-secretase than Sub W. The two substrate peptides showed different tendency to bind to ${\beta}$-secretase and this information may useful for drug development to treat and prevent Alzheimer's disease.

• Journal of KIISE:Computer Systems and Theory
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• v.33 no.7
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• pp.380-389
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• 2006

In this paper, we present the MGrid system and its application for the construction of the Glycoconjugates simulation database called e-Glycoconjugates. The MGrid system is an integrated molecular simulation grid system for computing, databases, and analyses. For e-Glycoconjugates, we have been constructing the simulation database for 2,000 glycan chains and 100 glycoproteins until 2008. In this paper, we present the goal, architecture, and current implementation status of the MGrid system, and e-Glycoconjugates.

• Proceedings of the KSME Conference
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• 2007.05b
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• pp.2702-2707
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• 2007

The purpose of this study is to calculate the behavior of molecules for the generation of homogeneous thin-films in the process of spray deposition. The calculation system was composed of a suface molecular region and droplet molecular region. The thin-film was generated when droplet molecules fell to surface molecules. Lennard-Jones potential had been used as intermolecular potential, and only attraction 때 d repulsion had been used for the behavior of the droplet on the solid surface. As results, the behavior of the droplet was so much influenced by the surface temperature in the spray deposition process. High temperature of surface has higher porosity and larger spread area. It was found that simulation results generally agreed well with previous the experimental results. This simulation result will be the foundation for the deposition processes of industry.

• Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
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• 2002.10b
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• pp.61-62
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• 2002

In order to clarify the contact mechanism between specimen surface and probe tip in the surface observation by the AFM (atomic force microscope) or the FFM (friction force microscope), several molecular dynamics simulations have been performed. In the simulation, a 3-dimensional simulation model is proposed where the specimen and the probe are assumed to consist of mono-crystal line copper and a carbon atom respectively and the effect of cantilever stiffness is also taken into considered. The surface observation process on a well-defined Cu{100} is simulated. The influences of cantilever stiffness on the reactive force images and the behavior of probe tip were evaluated. As a resuIt, several phenomena similar to those observed by the actual surface observation experiment, such as double-slip behavior and dispersion in the stick-slip wave period were observed.

• Bulletin of the Korean Chemical Society
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• v.33 no.8
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• pp.2553-2559
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• 2012

The adsorption properties of benzene, toluene, p-xylene in MCM-41 with heterogeneous and cylindrical pore were studied using grand canonical ensemble Monte Carlo simulation. The simulated isotherms were compared with experimental ones, and the different adsorption behaviors in MCM-41 with pore diameters of 2.2 and 3.2 nm were investigated. The simulated adsorption amounts above the capillary-condensation pressure agreed with the experimental ones. The simulation results showed that most molecular planes were nearly parallel to the pore axis. This orientation was not affected by the molecular position in the pore. The molecular planes were nearly parallel to the pore surface for the adsorbate molecules close to the pore wall, and the molecules in the MCM-41 with the pore diameter of 3.2 nm were ordered along the pore axis.

• 한국정보디스플레이학회:학술대회논문집
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• 2004.08a
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• pp.1151-1154
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• 2004

In this study, we presented a novel method to calculate unknown voltages on the floating electrodes introduced in a unit pixel of TFT-LCDs using three-dimensional molecular director simulation. For the simulation of the potential distribution profiles generated under the influence of the floating electrodes, we used the floating boundary condition on the surface enclosing the floating electrodes. The constraint for the floating boundary condition was derived from the charge neutrality condition about the floating electrodes disconnected from voltage sources. For the pixel with the floating electrodes patterned between the pixel and the data electrodes, we simulated the molecular director and the potential distribution in three-dimension, and then observed the location of the disclination lines around the edge of the pixel electrode. As a result, it was revealed that the floating electrodes significantly affect the electro-optical characteristics such as the location of the disclination line.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.343-348
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• 2007

Molecular dynamics study of thermal NIL (Nano Imprint Lithography) process is performed to examine stamp-resist interactions. A layered structure consists of Ni stamp, poly-(methylmethacrylate) thin film resist and Si substrate was constructed for isothermal ensemble simulations. Imposing confined periodicity to the layered unit-cell, sequential movement of stamp followed by NVT simulation was implemented in accordance with the real NIL process. Both vdW and electrostatic potentials were considered in all non-bond interactions and resultant interaction energy between stamp and PMMA resist was monitored during stamping and releasing procedures. As a result, the stamp-resist interaction energy shows repulsive and adhesive characteristics in indentation and release respectively and irregular atomic concentration near the patterned layer were observed. Also, the spring back and rearrangement of PMMA molecules were analyzed in releasing process.

• Macromolecular Research
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• v.15 no.6
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• pp.491-497
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• 2007

NPT Monte Carlo simulations were performed to calculate the molecular properties of syndiotactic poly(vinyl chloride) (PVC) and syndiotactic poly(vinyl alcohol) (PVA) melts using the configurational bias Monte Carlo move, concerted rotation, reptation, and volume fluctuation. The density, mean square backbone end-to-end distance, mean square radius of gyration, fractional free-volume distribution, distribution of torsional angles, small molecule solubility constant, and radial distribution function of PVC at 0.1 MPa and above the glass transition temperature were calculated/measured, and those of PVA were calculated. The calculated results were compared with the corresponding experimental data and discussed. The calculated densities of PVC and PVA were smaller than the experimental values, probably due to the very low molecular weight of the model polymer used in the simulation. The fractional free-volume distribution and radial distribution function for PVC and PVA were nearly independent of temperature.

• Tribology and Lubricants
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• v.20 no.2
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• pp.102-108
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• 2004

In this paper, friction and wear behaviors between monocrystalline, defect-free copper and carbon on the atomic scale are investigated by using 2-dimensional molecular dynamics simulation. It is assumed that all interatomic forces are given by Morse potential. The deformation of carbon is assumed to be neglected and vacuum condition is also assumed. Average friction and normal forces for various surface conditions, various scratch speeds and scratch depths are obtained from simulations. Changes of wear behaviors for various scratch speeds and surface conditions are investigated by observing snapshots in scratch process. The effects of surface conditions, scratch speeds, and scratch depths on the friction force, normal force, and friction coefficient are also investigated.