• Proceedings of the Korean Society for Noise and Vibration Engineering Conference
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• 2008.11a
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• pp.668-669
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• 2008

In this paper, we introduce various coarse-grained elastic network modeling (ENM) techniques as a novel computational method for simulating atomic scale dynamics in macromolecules including DNA, RNA, protein, and polymer. In ENM, a system is modeled as a spring network among representative atoms in which each linear elastic spring is well designed to replace both bonded and nonbonded interactions among atoms in the sense of quantum mechanics. Based on this simplified system, a harmonic Hookean potential is defined and used for not only calculating intrinsic vibration modes of a given system, but also predicting its anharmonic conformational change, both of which are strongly related with its functional features. Various nano and bio applications of ENM such as fracture mechanics of nanocomposite and protein dynamics show that ENM is one of promising tools for simulating atomic scale dynamics in a more effective and efficient way comparing to the traditional molecular dynamics simulation.

• Bulletin of the Korean Chemical Society
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• v.32 no.6
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• pp.1849-1850
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• 2011

• Bulletin of the Korean Chemical Society
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• v.30 no.2
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• pp.499-501
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• 2009

• Proceedings of the KSME Conference
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• 2007.05b
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• pp.1912-1915
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• 2007

The disjoining pressure is critical in modeling the transport phenomena in small scales. They are very useful in characterizing the non-continuum effects that are not negligible in heat and mass transports in the film of less than submicro-scales. We present he disjoining pressure of thin film absorbed on solid substrate using Molecular Dynamics Simulation (MD). The disjoining pressure with respect to the film thickness is accurately calculated in the resolution of a molecular scale. The characteristics of the pressure are discussed regarding the molecular nature of the fluid system like molecular diameter and intermolecular interaction. Also, the MD results are compared with those based on the macroscopic approximation of the slab-like density profile. Significant discrepancy is observed when the effective film thickness is less than several molecular diameter

• Journal of Advanced Marine Engineering and Technology
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• v.29 no.1
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• pp.34-41
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• 2005

An experimental study of molecular motions on a liquid-vapor interface is limited due to micro-scale characteristics of a system with an angstrom or a nanometer size Therefore, in recent, many studies for micro-scale systems have been conducted by a computer simulation because it is free from experimental limitations. In this study, through the molecular dynamic (MD) method. molecular behavior was clarified on a liquid-vapor interface and a criterion to distinguish between liquid and vapor was suggested by a potential energy and the number of neighboring molecules. At an interface. the potential energy of a molecule was increased but the number of neighboring molecules was decreased when the molecule moved into a vapor region from a liquid region, and vice versa.

• Transactions of the Korean Society of Mechanical Engineers B
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• v.33 no.2
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• pp.101-106
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• 2009

The disjoining pressure is an important physical property in modeling the small-scale transport phenomena on thin film. It is a very useful definition in characterizing the non-continuum effects that are not negligible in heat and mass transport of the film thinner than submicro-scales. We present the calculated values of disjoining pressure of He, Kr and Xe thin films absorbed on graphite substrate using Molecular Dynamics Simulation (MD). The disjoining pressure is accurately calculated in the resolution of a molecular scale of the film thickness. The characteristics of the pressure are discussed regarding the molecular nature of the fluid system such as molecular diameter and intermolecular interaction parameters. The MD results are also compared with those based on the continuum approximation of the slab-like density profile and the results on other novel gases in the previous study. The discrepancies of the continuum model with MD results are shown in all three configurations and discussed in the view point of molecular features.

• Bulletin of the Korean Chemical Society
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• v.29 no.3
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• pp.641-646
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• 2008

Equilibrium molecular dynamics simulations in a canonical ensemble are performed to evaluate the transport coefficients of several Lennard-Jones (LJ) mixtures at a liquid argon states of 94.4 K and 1 atm via modified Green-Kubo formulas. Two component mixture of A and B is built by considering the interaction between A and A as the attractive (A) potential, that between A and B as the attractive potential (A), and that between B and B as the repulsive potential (R), labelled as AAR mixture. Three more mixtures - ARA, ARR, and RAR are created in the same way. The behavior of the LJ energy and the transport properties for all the mixtures is easily understood in terms of the portion of attractive potential (A %). The behavior of the thermal conductivities by the translational energy transport due to molecular motion exactly coincides with that of diffusion constant while that of the thermal conductivities by the potential energy transport due to molecular motion is easily understood from the fact that the LJ energy of AAR, ARR, and RAR mixtures increases negatively with the increase of A % from that of the pure repulsive system while that of ARA changes rarely.

• Bulletin of the Korean Chemical Society
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• v.26 no.8
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• pp.1203-1208
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• 2005

A computational study based on molecular dynamics (MD) simulations was performed in order to explain the difference in aqueous solubilities of two flavonoid/$\beta$-cyclodextrin ($\beta$-CD) complexes, hesperetin/$\beta$-CD and naringenin/$\beta$-CD. The aqueous solubility of each flavonoid/$\beta$-CD complex could be characterized by complexwater interaction not by flavonoid-CD interaction. The radial distribution of water around each inclusion complex elucidated the difference of an experimentally observed solubility of each flavonoid/$\beta$-CD complex. The analyzed results suggested that a bulky hydrophobic moiety (-$OCH_3$) of B-ring of hesperetin nearby primary rim of $\beta$-CD was responsible for lower aqueous solubility of the hesperetin/$\beta$-CD complex.

• Journal of Integrative Natural Science
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• v.13 no.4
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• pp.170-180
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• 2020

Abnormal regulation, hyperphosphorylation, and aggregation of the tau protein are the hallmark of several types of dementia, including Alzheimer's Disease. Increased activity of Glycogen Synthase Kinase-3β (GSK-3β) in the Central Nervous System (CNS), increased the tau hyperphosphorylation and caused the neurofibrillary tangles (NFTs) formation in the brain cells. Over the last two decades, numerous adenosine triphosphate (ATP) competitive inhibitors have been discovered that show inhibitory activity against GSK-3β. But these compounds exhibited off-target effects which motivated researchers to find new GSK-3β inhibitors. In the present study, we have collected the dataset of 31 C-Glycosylflavones derivatives that showed inhibitory activity against GSK-3β. Among the dataset, the most active compound was docked with the GSK-3β and molecular dynamics (MD) simulation was performed for 50 ns. Based on the 50 ns MD pose of the most active compound, the other dataset compounds were sketched, minimized, and aligned. The 3D-QSAR based Comparative Molecular Field Analysis (CoMFA) model was developed, which showed a reasonable value of q2=0.664 and r2=0.920. The contour maps generated based on the CoMFA model elaborated on the favorable substitutions at the R2 position. This study could assist in the future development of new GSK-3β inhibitors.

• Bulletin of the Korean Chemical Society
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• v.27 no.2
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• pp.325-328
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• 2006