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

• Bulletin of the Korean Chemical Society
• /
• v.30 no.11
• /
• pp.2723-2728
• /
• 2009

The conformational properties of oligosaccharides are important to understand carbohydrate-protein interactions. A trimannoside, methyl 3,6-di-O-($\alpha$-D-Man)-$\alpha$-D-Man (TRIMAN) is a basic unit of N-linked oligosaccharides. This TRIMAN moiety was further modified by GlcNAc (BISECT), which is important to biological activity of N-glycan. To characterize the trimannoside and its bisecting one we performed a molecular dynamics simulation in water. The resulting models show the conformational transition with two major and minor conformations. The major conformational transition results from the $\omega$ angle transition; another minor transition is due to the $\psi$ angle transition of $\alpha$ (1 $\rightarrow$ 6) linkage. The introduction of bisecting GlcNAc on TRIMAN made the different population of the major and minor conformations of the TRIMAN moiety. Omega ($\omega$) angle distribution is largely changed and the population of gt conformation is increased in BISECT oligosaccharide. The inter-residue hydrogen bonds and water bridges via bisecting GlcNAc residue make alterations on the local and overall conformation of TRIMAN moiety. These changes of conformational distribution for TRIMAN moiety can affect the overall conformation of N-glycan and the biological activity of glycoprotein.

• Bulletin of the Korean Chemical Society
• /
• v.17 no.8
• /
• pp.700-706
• /
• 1996

We present the results of molecular dynamics simulations of monolayers of long-chain alkyl thiol [S(CH2)15CH3] molecules on an air-solid interface using the extended collapsed atom model for the chain-molecule and a gold surface for the solid surface. Several molecular dynamics simulations have been performed on monolayers with areas per molecule ranging from 18.30 to 32.10 Å2/molecule. It is found that there exist three possible transitions: a continuous transition characterized by a change in molecular configuration without change in lattice structure, a sudden transition characterized by the distinct lattice defects and perfect islands, and a third transition characterized by the appearance of a random, liquid-like state. The analysis of probability distributions of the segments shows that the structure of the chain-molecules at the air-solid interface is completely different from that at the air-water interface in the view of the degree of overlap of the probability distributions of the neighbor segments. The calculated diffusion coefficients of the chain-molecules on the monolayers seem to be not directly related to any one of the three transitions. However, the large diffusion of the molecules enhanced by the increment of the area per molecule may induce the second transition.

• Macromolecular Research
• /
• v.10 no.6
• /
• pp.297-303
• /
• 2002

We have investigated the microstructural properties of a weakly charged polyelectrolyte modeled with both Hookean spring and Debye-Huckel potential, by employing a novel hybrid scheme of molecular dynamics (MD) and Monte Carlo (MC) simulations. Although the off-lattice pivot step facilitates the earlier computations stage, it gives rise to oscillations and hinders the stable equilibrium state. In order to overcome this problem, we adopt the MC off-lattice pivot step in early stage only, and then switch the computation to a pure MD step. The result shows that the computational speed-up compared to the previous method is entirely above 10 to 50, without loss of the accuracy. We examined the conformations of polyelectrolyte in solvents in terms of the end-to-end distance, radius of gyration, and structure factor with variations of the screening effects of solvent and the monomer charges. The emphasis can favorably be given on the elongation behavior of a polyelectrolyte chain, with observing the simultaneous snapshots.

• Bulletin of the Korean Chemical Society
• /
• v.12 no.3
• /
• pp.315-322
• /
• 1991

In a recent $paper^1$ we reported equilibrium (EMD) and non-equilibrium (NEMD) molecular dynamics simulations of liquid argon using the Green-Kubo relations and NEMD algorithms to calculate the thermal transport coefficients-the self-diffusion coefficient, shear viscosity, and thermal conductivity. The overall agreement with experimental data is quite good. In this paper the same technique is applied to calculate the thermal transport coefficients of liquid water at 298.15 K and 1 atm using TIP4P model for the interaction between water molecules. The EMD results show difficulty to apply the Green-Kubo relations since the time-correlation functions of liquid water are oscillating and not decaying rapidly enough except the velocity auto-correlation function. The NEMD results are found to be within approximately ${\pm}$30-40% error bars, which makes it possible to apply the NEMD technique to other molecular liquids.

• Journal of the Computational Structural Engineering Institute of Korea
• /
• v.26 no.5
• /
• pp.393-399
• /
• 2013

In this paper, a novel approach to estimate cohesive laws for the mode I fracture of the graphene is presented by combining molecular dynamic simulations and an inverse algorithm based on field projection method and finite element method. The determination of crack-tip cohesive laws of the graphene based on continuum mechanics is a non-trivial inverse problem of finding unknown tractions and separations from atomic simulations. The displacements of molecular dynamic simulations in a region far away from the crack tip are transferred to finite element nodes by using moving least square approximation. Inverse analyses for extracting unknown cohesive tractions and separation behind the crack tip can be carried out by using conservation nature of the interaction J- and M-integrals with numerical auxiliary fields which are generated by systematically imposing uniform surface tractions element-by-element along the crack surfaces in finite element models. The preset method can be a very successful approach to extract crack-tip cohesive laws from molecular dynamic simulations as a scale bridging method.

• Proceedings of the KSME Conference
• /
• 2004.11a
• /
• pp.410-415
• /
• 2004

Molecular dynamics simulations of nanoimprint lithography in which a stamp with patterns is pressed onto amorphous poly-(methylmethacrylate) (PMMA) surface are performed to study the deformation of polymer. Force fields including bond, angle, torsion, inversion, van der Waals and electrostatic potential are used to describe the intermolecular and intramolecular force of PMMA molecules and stamp. Periodic boundary condition is used in horizontal direction and $Nos\acute{e}$-Hoover thermostat is used to control the system temperature. As the simulation results, the adhesion forces between stamp and polymer are calculated and the mechanism of deformation are investigated. The effects of the adhesion force and friction force on the polymer deformation are also studied to analyze the pattern transfer in nanoimprint lithography. The mechanism of polymer deformation is investigated by means of inspecting the indentation process, molecular configurational properties, and molecular configurational energies.

• Transactions of the Korean Society of Mechanical Engineers A
• /
• v.29 no.6 s.237
• /
• pp.852-859
• /
• 2005

Molecular dynamics simulations of nanoimprint lithography in which a stamp with patterns is pressed onto amorphous poly-(methylmethacrylate) (PMMA) surface are performed to study the deformation of polymer. Force fields including bond, angle, torsion, inversion, van der Waals and electrostatic potential are used to describe the intermolecular and intramolecular force of PMMA molecules and stamp. Periodic boundary condition is used in horizontal direction and Nose-Hoover thermostat is used to control the system temperature. As the simulation results, the adhesion forces between stamp and polymer are calculated and the mechanism of deformation are investigated. The effects of the adhesion and friction forces on the polymer deformation are also studied to analyze the pattern transfer in nanoimprint lithography. The mechanism of polymer deformation is investigated by means of inspecting the indentation process, molecular configurational properties, and molecular configurational energies.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2002.06a
• /
• pp.106-106
• /
• 2002

• Proceedings of the Korean Society for Technology of Plasticity Conference
• /
• 2003.10a
• /
• pp.347-354
• /
• 2003

The dynamics of fluid flow through nanomachines is completely different from that of continuum. In this study, molecular dynamics simulations were performed for the flow of helium, neon, argon inside carbon(graphite) nanotubes of several sizes. The fluid was introduced into the nanotube at a given initial velocity according to given temperature. Diffusion coefficients were evaluated by Green-Kubo equation derived from Einstein relationship. The behaviour of the fluid was strongly dependent on the density of fluid and tube diameter, not on the tube length. It was found that the diffusion Coefficients increased With decreasing the density of molecules and increasing the diameter and temperature.