• Journal of the Korean Crystal Growth and Crystal Technology
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• v.15 no.4
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• pp.162-167
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• 2005

As the properties of porous materials during the drying process relate to the atomistic defects of heterogeneous materials such as dislocation, grain, grain boundary, pore, etc., the knowledge of nano-scale analysis is needed in order to accurately analyze the drying process for porous materials. In this study, the atomic behavior of porous materials Is statically predicted by using the molecular dynamics simulation and the nano-scale material properties are computed. The elastic modulus, thermal expansion coefficient, and volumetric heat capacity numerically found from the molecular dynamics simulation are compared with those of experiment and theory and proved the accuracy.

• Transactions on Electrical and Electronic Materials
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• v.5 no.6
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• pp.227-232
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• 2004

We investigated a nonvolatile nanomemory element based on boron nitride nanopeapods using molecular dynamics simulations. The studied system was composed of two boron-nitride nanotubes filled Cu electrodes and fully ionized endo-fullerenes. The two boron-nitride nanotubes were placed face to face and the endo-fullerenes came and went between the two boron-nitride nanotubes under alternatively applied force fields. Since the endo-fullerenes encapsulated in the boron-nitride nanotubes hardly escape from the boron-nitride nanotubes, the studied system can be considered to be a nonvolatile memory device. The minimum potential energies of the memory element were found near the fullerenes attached copper electrodes and the activation energy barrier was $3{\cdot}579 eV$. Several switching processes were investigated for external force fields using molecular dynamics simulations. The bit flips were achieved from the external force field of above $3.579 eV/{\AA}$.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.35 no.6
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• pp.325-331
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• 2022

Hydrogen embrittlement in metals has been a serious issue with regard to structural safety. In this study, molecular dynamics simulations revealed that the aggregation of hydrogen atoms at the crack tips suppresses the dislocation emission and thus results in cleavage fracture. A series of molecular dynamics simulations were performed considering factors such as the concentration of hydrogen atoms, loading rate, and diffusion coefficient. We investigated the conditions that minimize hydrogen embrittlement. The simulation results were consistent with the experimental results and used to quantify hydrogen embrittlement.

• Bulletin of the Korean Chemical Society
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• v.26 no.12
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• pp.2001-2006
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• 2005

Glycoproteins and glycolipids play key roles in intracellular reactions between cells and their environments at the membrane surface. For better understanding of the nature of these events, it is necessary to know threedimensional structures of those carbohydrates, involved in them. Since carbohydrates contain many hydroxyl groups which can serve both as hydrogen bond donors and acceptors, hydrogen bond is an important factor stabilizing the structure of carbohydrate. DMSO is an aprotic solvent frequently used for the study of carbohydrates because it gives detailed insight into the intramolecular hydrogen bond network. In this study, conformational properties and the hydrogen bonds in $\beta$-lactose in DMSO are investigated by NMR spectroscopy and molecular dynamics simulations. NOEs, temperature coefficients, deuterium isotope effect, and molecular dynamics simulations proved that there is a strong intramolecular hydrogen bond between O3 and HO2' in $\beta$-lactose and also OH3 in $\beta$-lactose may form an intermolecular hydrogen bond with DMSO.

• Journal of Microbiology and Biotechnology
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• v.17 no.7
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• pp.1098-1105
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• 2007

Quantum mechanical and molecular dynamics simulation analysis has been performed on the model system for CALB (Candida antarctica lipase B) with esters to study the reaction mechanism and conformational preference of catalytic hydrolysis and the esterification reaction. Using quantum mechanical analysis, the ping-pong bi-bi mechanism was applied and energies and 3-dimensional binding configurations of the whole reaction pathways were calculated. Further molecular dynamics simulation analysis was performed on the basis of the transition state obtained from quantum mechanical study to observe the effect of structures of the substrates. Calculation results using substrates of different chain length and chiral configurations were compared for conformational preference. The calculated results showed very small influence on chain length, whereas chiral conformation showed big differences. Calculated results from molecular modeling studies have been compared qualitatively with the experimental data using racemic mixtures of (${\pm}$)-cis-4-acetamido-cyclopent-2-ene-1-ethyl acetate as substrates.

• Journal of Photoscience
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• v.3 no.3
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• pp.147-151
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• 1996

Dynamics of contact ion-pair between 1, 2, 4, 5-tetracyanobenzene anion and cation of biphenyl derivatives was investigated on the picosecond time scale. Solvent effect on the electron transfer was observed and electron transfer rates were examined using Marcus equation which contains distance dependence of the electron transfer rate in the frequency factor, along with the consideration of molecular shape. From the discussion based on disk model for molecular shape, contribution of interring torsional motion of biphenyl to the inner-sphere reorganization energy is strongly suggested, which leads to the physical explanation for the observed solvent effect on the rate of electron transfer.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.41 no.7
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• pp.621-627
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• 2017

The understanding of the mechanical properties of amyloid fibers, which induce various neurodegenerative diseases, is directly related to the amyloid growth mechanism. Diverse studies have been performed on amyloid fibers from the viewpoint of disease epidemiology. Recently, attempts have been made to use amyloid fibers as new materials because of their notable mechanical properties and self-aggregation abilities. In this study, the mechanical properties of transthyretin (TTR105-115), which induces cardiovascular disease, were evaluated using a molecular dynamics (MD) simulation. In particular, the effect of the end-terminal capping on the structural stability of TTR105-115 was evaluated. The mechanical behavior and properties of TTR105-115 were measured by steered molecular dynamics (SMD). We clarified the factors affecting the mechanical properties of these materials and suggested the possibility of utilizing them as nature inspired materials.

• Membrane Journal
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• v.25 no.2
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• pp.162-170
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• 2015

In this study, gas permeability of polyimide materials having a various amine group was measured and molecular dynamics was used to analyze the dynamic characteristics of the gas molecules in the polyimide by calculating the position and velocity of the gas molecules with change of the time. The gas permeability of polyimide membrane having substitution site which increase free volume in the polymer was increased. However, polyimide with rigid structure showed decreased gas permeability. As a result of analyzing the change in the gas permeation behavior using molecular dynamics simulations, we confirmed that the results show the same tendency with actual measurements of the gas permeability.

• Journal of the Korean Society of Manufacturing Process Engineers
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• v.17 no.5
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• pp.117-122
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• 2018

3D printing technology and its applications have grown rapidly in academia and industry. We consider a 3D printing system designed for the selective laser sintering (SLS) method, which is one of the powder bed fusion (PBF) techniques to build up the final product by layering sintered powder slices. Thermal distortion of printing products is a critical challenge in 3D printing. This study investigates temperature-dependent conformational behaviors of 3D printed samples of sintered poly-ether-ether-ketone (PEEK) powders using molecular dynamics simulations. The wear and chemical resistance properties of PEEK are understood, as it is a well-known biocompatible material used for implants. However, studies on physical phenomena at nanoscale in PEEK are rarely published in public. We simulate dissipative particle dynamics to elucidate how a cavity regime forms in PEEK at different system temperatures. We demonstrate how PEEK structures deform subject to the system temperature distribution.

• KIISE Transactions on Computing Practices
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• v.20 no.10
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• pp.534-542
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• 2014

Multiscale modeling is a new simulation approach which can manage different spatial and temporal scales of system. In this study, as part of multiscale modeling research, we propose the way of combining two different simulation methods, molecular dynamics(MD) and stochastic rotation dynamics(SRD). Our conceptual implementations are based on LAMMPS, one of the well-known molecular dynamics programs. Our prototype of multiscale modeling follows the form of the third party implementation of LAMMPS. It added MD to SRD in order to simulate the boundary area of the simulation box. Because it is important to guarantee the seamless simulation, we also designed the overlap zones and communication zones. The preliminary experimental results showed that our proposed scheme is properly worked out and the execution time is also reduced.