• 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.

• Tribology and Lubricants
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• v.39 no.5
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• pp.167-172
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• 2023

Titanium alloys are widely recognized among engineering materials owing to their impressive mechanical properties, including high strength-to-weight ratios, fracture toughness, resistance to fatigue, and corrosion resistance. Consequently, applications involving titanium alloys are more susceptible to damage from unforeseen events, such as scratches. Nevertheless, the impact of microscopic damage remains an area that requires further investigation. This study delves into the microscopic wear behavior of α-titanium crystal structures when subjected to linear scratch-induced damage conditions, utilizing molecular dynamics simulations as the primary methodology. The configuration of crystal lattice structures plays a crucial role in influencing material properties such as slip, which pertains to the movement of dislocations within the crystal structure. The molecular dynamics technique surpasses the constraints of observing microscopic phenomena over brief intervals, such as sub-nano- or pico-second intervals. First, we demonstrate the localized transformation of lattice structures at the end of initialization, indentation, and wear processes. In addition, we obtain the exerted force on a rigid sphere during scratching under linear movement. Furthermore, we investigate the effect of the relaxation period between indentation and scratch deformation. Finally, we conduct a comparison study of nanoindentation between crystal and amorphous Ti substrates. Thus, this study reveals the underlying physics of the microscopic transformation of the α-titanium crystal structure under wear-like accidental events.

• Biomolecules & Therapeutics
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• v.24 no.2
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• pp.191-198
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• 2016

The vitamin D receptor (VDR) is a member of the nuclear receptor (NR) superfamily. The VDR binds to active vitamin $D_3$ metabolites, which stimulates downstream transduction signaling involved in various physiological activities such as calcium homeostasis, bone mineralization, and cell differentiation. Quercetin is a widely distributed flavonoid in nature that is known to enhance transactivation of VDR target genes. However, the detailed molecular mechanism underlying VDR activation by quercetin is not well understood. We first demonstrated the interaction between quercetin and the VDR at the molecular level by using fluorescence quenching and saturation transfer difference (STD) NMR experiments. The dissociation constant ($K_d$) of quercetin and the VDR was $21.15{\pm}4.31{\mu}M$, and the mapping of quercetin subsites for VDR binding was performed using STD-NMR. The binding mode of quercetin was investigated by a docking study combined with molecular dynamics (MD) simulation. Quercetin might serve as a scaffold for the development of VDR modulators with selective biological activities.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.02a
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• pp.654-654
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• 2013

One of the most important yet unresolved problems in molecular electronics is the controversy over the number and nature of multiple conductance peaks in single-molecule junctions. Currently, there are three competing explanations of this observation: (1) manifestation of different molecule-electrode contact geometries, (2) formation of gauche defects within the molecular core, (3) involvement of different electrode surface orientations [1]. However, the exact origin of multiple conductance peaks is not yet fully understood, which indicates our incomplete understanding of the scientifically as well as techno-logically important organic-metal contacts. To theoretically resolve this problem, we previously applied a multiscale computational approach that combines force fields molecular dynamics (FF MD), density functional theory (DFT), and matrix Green's function (MGF) calculations [2] to a thermally fluctuating haxanedithiol (C6DT) molecule stretched between flat Au(111) electrodes, but could observe only a single conductance peak [3]. In this presentation, using DFT geometry optimizations and MGF calculations, we consider molecular junctions with more realistic molecule-metal contact conformations and Au(111) electrode surface directions. We also conduct DFT-based molecular dynamics for the highly stretched junction models to confirm our conclusion. We conclude that the S-Au coordination number should be the more dominant factor than the electrode surface orientation.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1519-1526
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• 2010

The behavior of peptide or protein solutes in saline aqueous solution is a fundamental topic in physical chemistry. Addition of ions can strongly alter the thermodynamic and physical properties of peptide molecules in solution. In order to study the effects of added ionic salts on protein conformation and dynamics, we have used the molecular dynamics (MD) simulations to investigate the behavior of Staphylococcus aureus Hfq protein under two different ionic concentrations: 0.1 M NaCl and 1.0 M NaCl in presence and absence of RNA (a hepta-oligoribonucleotide AU5G). Hfq, a global regulator of gene expression is highly conserved and abundant RNA-binding protein. It is already reported that in vivo the increase of ionic strength results in a drastic reduction of Hfq affinity for $Q{\beta}$ RNA and reduces the tendency of aggregation of Escherichia coli host factor hexamers. Our results revealed the crucial role of 0.1 M NaCl Hfq system on the bases with strong hydrogen bonding interactions and by stabilizing the aromatic stacking of Tyr42 residue of the adjacent subunits/monomers with the adenine and uridine nucleobases. An increase in RNA pore diameter and weakened compactness of the Hfq-RNA complex was clearly observed in 1.0 M NaCl Hfq system with bound RNA. Aggregation of monomers in Hfq and the interaction of Hfq with RNA are greatly affected due to the presence of high ionic strength. Higher the ionic concentration, weaker is the aggregation and interaction. Our results were compatible with the experimental data and this is the first theoretical report for the experimental study done in 1980 by Uhlenbeck group for the present system.

• BMB Reports
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• v.38 no.1
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• pp.104-110
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• 2005

We extended the measurable time scale of DNA dynamics to microsecond using $[Ru(phen)_2(dppz)]^{2+}$ (phen = 1,10-phenanthroline, dppz = dipyrido[3,2-a:2',3'-c]phenazine) (RuPD), which displays a mean lifetime near 500 ns. To evaluate the usefulness of this luminophore (RuPD) for probing nucleic acid dynamics, its intensity and anisotropy decays when intercalated into supercoiled and linear pBluescript (pBS) II SK(+) phagemids were examined using frequency-domain fluorometry with a blue light-emitting diode (LED) as the modulated light source. The mean lifetime for the supercoiled phagemids (< $\tau$ > = 489.7 ns) was somewhat shorter than that for the linear phagemids (< $\tau$ > = 506.4 ns), suggesting a more efficient shielding from water by the linear phagemids. The anisotropy decay data also showed somewhat shorter slow rotational correlation times for supercoiled phagemids (997.2 ns) than for the linear phagemids (1175.6 ns). The slow and fast rotational correlation times appear to be consistent with the bending and torsional motions of the phagemids, respectively. These results indicate that RuPD can have applications in studies of both bending and torsional dynamics of nucleic acids.

• Journal of Photoscience
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• v.11 no.1
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• pp.35-40
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• 2004

[Ru(2,2'-bipyridine)$_2$(4,4'-dicarboxy-2,2'-bipyridine)]$^{2+}$(RuBDc) is a very photostable probe that possesses favorable photophysical properties including long lifetime, high quantum yield, large Stokes' shift, and highly polarized emission. To evaluate the usefulness of this luminophore (RuBDc) for studying macromolecular dynamics, its intensity and anisotropy decays when conjugated to RNA bacteriophage MS2 were examined using frequency-domain fluorometry with a high-intensity, blue light-emitting diode (LED) as the modulated light source. The intensity decays were best fit by a sum of two exponentials, and the mean intensity decay time was 442.2 ns. The anisotropy decay data showed a single rotational correlation time (2334.9 ns), which is typical for a spherical molecule. The use of RuBDc enabled us to measure the rotational correlation time up to several microseconds. These results indicate that RuBDc can be useful for studying rotational diffusion of biological macromolecules.s.

• Bulletin of the Korean Chemical Society
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• v.25 no.4
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• pp.533-538
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• 2004

Canonical sampling method has been presented to generate the initial conditions for reactive flux studies of organic reactions in water. Velocity Verlet version of Nose-Hoover chain dynamics algorithm has been employed to sample the initial conditions according to canonical distribution. The unstable normal mode of a transition state has been introduced to define a dividing plane separating reactant and product regions in reaction processes. This method has been implemented and tested for the case iels-Alder reaction of methyl vinyl ketone (MVK) and cyclopentadiene (CPD) in water, providing a reliable tool for further reactive flux molecular dynamics studies in condensed media.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 1993.10a
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• pp.83-88
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• 1993

Recently, the analysis of microcutting with submicrometer depth of cut is tried to get a more high quality surface product, but to get a valuable result another method instead of conventional finite element method must be considered because finite elment method is impossible for a very small focused region and mesh size. As the altermative method, Molecular Dynamics or Statics is suggested and acceoted in the field of microcutting, indentation and crack propagation. In this paper using Molecuar Dynamics simulation, the phenomena of microcutting with subnanometer chip thickness is studied and the cutting mechanism for tool edge configuration is evaluated. As the result of simulation the atomistic chip formation is achieved.

• 한국전산유체공학회:학술대회논문집
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• 2010.05a
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• pp.575-580
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• 2010

In this work, the electrophoretic motion of dsDNA molecule represented by a polymer through an artificial nano-pore in a membrane is simulated using the numerical method combining the lattice Boltzmann and Langevin molecular dynamic method. The polymer motion is represented by Langevin molecular dynamics technique while the fluid flow is taken into account by fluctuating lattice-Boltzmann method. The hydrodynamic interactions between the polymer and solvent in a confined space with a membrane having a hole are considered explicitly through the frictional and the random forces. The electric field intensity over the space is obtained from a finite difference method. Initially, the polymer is placed at one side of the space, and an electric field is applied to drive the polymer to the other side of the space through the nano-pore. In future, we plan to study the effect of the polymer size and the electric field on the electrophoretic velocity.