• Bulletin of the Korean Chemical Society
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• v.34 no.9
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• pp.2711-2719
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• 2013

Hydrogen bonding interaction between alcohols and water molecules is an important characteristic in the aqueous solutions of alcohols. In this paper, a series of molecular dynamics simulations have been performed to investigate the aqueous solutions of low molecular weight alcohols (methanol, ethylene glycol and glycerol) at the concentrations covering a broad range from 1 to 90 mol %. The work focuses on studying the effect of the alcohols molecules on the hydrogen bonding of water molecules in binary mixtures. By analyzing the hydrogen bonding ability of the hydroxyl (-OH) groups for the three alcohols, it is found that the hydroxyl group of methanol prefers to form more hydrogen bonds than that of ethylene glycol and glycerol due to the intra-and intermolecular effects. It is also shown that concentration has significant effect on the ability of alcohol molecule to hydrogen bond water molecules. Understanding the hydrogen bonding characteristics of the aqueous solutions is helpful to reveal the cryoprotective mechanisms of methanol, ethylene glycol and glycerol in aqueous solutions.

• Bulletin of the Korean Chemical Society
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• v.24 no.8
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• pp.1126-1134
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• 2003

The signals obtained from the $5^{th}$-order (two-dimensional) Raman spectrum of a liquid can depend dramatically on the polarizations of the various light beams, but to date there has been no evidence presented that different polarization conditions probe any fundamentally different aspects of liquid dynamics. In order to explore the molecular significance of polarization we have carried out a molecular dynamics simulation of the $5^{th}$-order spectrum of a dilute solution of CS₂ in liquid Xe, perhaps the simplest system capable of displaying a full range of polarization dependencies. By focusing on the 5 distinct rotational invariants revealed by the different polarizations and by comparing our results with those from liquid Xe, a liquid whose spectrum has no significant polarization dependence, we discovered that the polarization experiments do, in fact, yield valuable microscopic information. With different linear combinations of the experimental response functions one can separate the part of the signal derived from the purely interaction-induced part of the many-body polarizability from the portion with the largest contributions from single-molecule polarizabilities. This division does not directly address the underlying liquid dynamics, but it significantly simplifies the interpretation of the theoretical calculations which do address this issue. We find that the different linear combinations differ as well in whether they exhibit nodal lines. Despite the absence of nodes with the atomic liquid Xe, observing the resilience of our solution's nodes when we artificially remove the anisotropy of our solute leads us to conclude that there is no direct connection between nodes and specifically molecular degrees of freedom.

• Journal of the Korean Vacuum Society
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• v.14 no.1
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• pp.40-48
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• 2005

Bucky shuttle memory systems were investigated by the classical molecular dynamics(MD) simulations. Energetics and operating response of the shuttle-memory-elements u?ere examined by MD simulations of the C/sub 60/ shuttle in the nanomemory systems under various external force fields. Single-nanopeapod type was consisting of three fullerenes encapsulated in (10, 10) boron-nitride nanotube and filled Cu electrode. Studied systems could be applied to nonvolatile memory. MD simulation results showed that the stable bit flops could be achieved from the external force fields of 0.1 eV/Å for single-nanopeapod type.

• Journal of the HCI Society of Korea
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• v.4 no.1
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• pp.17-27
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• 2009

A computer supported cooperative work(CSCW) system is a collaboration system, which enables cooperative works among various participants through the Internet. A collaborative virtual reality environment(CRVE) can be used in scientific research and cultural research because it can provide users with virtual experiences of three dimensional molecular models in cyberspace. However, general CVRE systems are only focused on synchronous collaborations. We propose a remote collaboration system, which provides synchronous and asynchronous cooperation in collaborative virtual reality environment. The proposed system can be applied to bioscience experiments such as molecular docking process, and crystallography simulation. The proposed system is evaluated in performance comparison with previous approaches.

• Bulletin of the Korean Chemical Society
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• v.32 no.10
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• pp.3675-3681
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• 2011

Fusarium oxysporum, an important pathogen that mainly causes vascular or fusarium wilt disease which leads to economic loss. Disruption of gene encoding a heterotrimeric G-protein-${\beta}$-subunit (FGB1), led to decreased intracellular cAMP levels, reduced pathogenicity, colony morphology, and germination. The plant defense protein, Nicotiana alata defensin (NaD1) displays potent antifungal activity against a variety of agronomically important filamentous fungi. In this paper, we performed a molecular modeling and docking studies to find vital amino acids which can interact with various antifungal compounds using Discovery Studio v2.5 and GRAMMX, respectively. The docking results from FGB1-NaD1 and FGB1-antifungal complexes, revealed the vital amino acids such as His64, Trp65, Ser194, Leu195, Gln237, Phe238, Val324 and Asn326, and suggested that the anidulafungin is a the good antifungal compound.The predicted interaction can greatly assist in understanding structural insights for studying the pathogen and host-component interactions.

• Asia-pacific Journal of Multimedia Services Convergent with Art, Humanities, and Sociology
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• v.8 no.1
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• pp.887-894
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• 2018

We investigated the position controlling C60 fullerene encapsulated into a graphene-nanoribbon trench via classical molecular dynamics simulations. The graphene-nanoribbon trench can provide nanoscale empty spaces, and a C60 encapsulated therein can be considered as media for a nanoelectromechanical shuttle device. The classical molecular dynamics simulations presented here provide information on the potential application of a graphene-nanoribbon trench in a C60 shuttle device. Driving forces applied to C60 resulted in its motion toward the edges of the graphene-nanoribbon trench, the suction forces induced at both edges were balanced with the driving forces, and finally, the C60 fullerene gradually settled on the edges of the graphene-nanoribbon trench after several oscillations. The results of the present simulation suggest the importance of graphene-nanoribbon trenches encapsulating fullerenes in a wide range of applications in the field of nanotechnology.

• Journal of the Semiconductor & Display Technology
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• v.6 no.4
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• pp.1-4
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• 2007

Carbon nanotube oscillators encapsulating copper nanowire were investigated by molecular dynamics simulations. The excess forces due to the carbon-carbon van der Waals interactions are higher than the excess force due to carbon-copper interactions. And the masses of copper atoms are higher than those of carbon atoms. So, the carbon atoms are easier accelerated than the copper atoms. When the encapsulated copper nanowire deforms the encapsulating nanotube, the frequency can not be estimated by the mass-frequency dependence in classical oscillation theory.

• Journal of the Korean Magnetic Resonance Society
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• v.3 no.2
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• pp.71-83
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• 1999

The dynamics of the dipolar demagnetizing field is investigated by numerical simulation. The effects of radiation damping, molecular diffusion, and relaxation processes on the dipolar demagnetizing field are examined in terms of the modulation pattern of the z-magnetization and the signal intensity variation. Simulations for multi-components suggest applications for sensitivity enhancement in favorable conditions.

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.356.3-357
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• 2002

Metoprolol (MT) is one kinds of adrenergic beta-blockers. Its (S)-enantiomer is known to be more active than the (R). Recently. the x-ray structure of beta-blocker. (S)-propranolol (a-naphthyl analogue), complexed in a mould fungal cellulase. Cel7A. was reported and the (R)-form did not build any complex. And in our previous study the conformation and stability of MT in carboxymethylated beta-cyclodextrin (BCD) complex was determined by NMR. HPLC, UV and electrophoresis measurement. (omitted)

• Proceedings of the KIEE Conference
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• 1989.11a
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• pp.505-508
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• 1989

A computer simulation code of UV preionized discharge KrF laser is developed, including time dependent circuit equations, boltzmann equations, and plasma kinetic equations for various atomic and molecular species. Rate constants for electron collision processes are calculated with a boltzmann equations as a function of E/N. In this study, we studied mainly the $KrF^*$ formation process, relaxation process, and the 248nm absorption process as a function of charging voltage.