• Proceedings of the KSME Conference
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• 2007.05a
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• pp.337-342
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• 2007

In this study, molecular dynamics simulation of nano imprint lithography in which patterned stamp is pressed onto amorphous polyethylene(PE) surface are performed to study the behaviour of polymer. Force fields including bond, angle, torsion, and Lennard Jones potential are used to describe the inter-molecular and intra-molecular force of PE molecules and stamp, substrate. Periodic boundary condition is used in horizontal direction and canonical NVT ensemble is used to control the system temperature. As the simulation results, the behaviour of polymer is investigated during the imprinting process. The mechanism of polymer deformation is studied by means of inspecting the surface shape, volume, density, atom distribution. Deformation of the polymer resist was found for various of the stamp geometry and the alignment state of the polymer molecules.

• Bulletin of the Korean Chemical Society
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• v.15 no.10
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• pp.852-856
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• 1994

A series of aliphatic hydrocarbons, methane to hexane in the liquid state, are modeled with the molecular mechanical potential parameters treating all hydrogen degrees of freedom explicitly. Thermodynamic properties (heat capacities and heats of vaporization) are calculated from relatively short (20ps) molecular dynamics trajectories. The liquid state structures are also examined through various radial distribution functions. Molecular dynamics simulations reproduce experimentally measured properties within a few percent errors, thus indicate that the present set of all-hydrogen parameters is suitable for simulating macromolecular systems in bulk.

• Advances in nano research
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• v.15 no.2
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• pp.105-111
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• 2023

Integrin αvβ3 is one of the receptors expressed in cancer cells. RGD peptides have the potential to target integrin αvβ3 (receptor), which can increase drug delivery efficiency. In this study, 55 different RGD dimer motifs were investigated. At first, the binding energy between RGD peptides and the receptor was calculated using molecular docking. Then, three RGD peptides with the strongest binding energy with the receptor were selected, and their dynamic adsorption on the receptor was simulated by molecular dynamics (MD). The obtained results showed that a sequence that has RGD at the beginning and end with tryptophan (TRP) has strong Lennard-Jones (LJ) and electrostatic interactions with Integrin αvβ3 and has changed the conformation of receptor significantly, which analyzed by root mean square deviation (RMSD) and radius of gyration.

• Journal of the Korean institute of surface engineering
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• v.39 no.2
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• pp.76-81
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• 2006

Molecular dynamics simulations were carried out to investigate physical sputtering of Fe(100) substrate due to energetic ion bombardments. Repulsive interatomic potentials at short internuclear distances were determined with ab initio calculations using the density functional theory. Bohr potentials were fitted to the ab initio results on diatomic pairs (Ar-Fe, Fe-Fe) and used as repulsive screened Coulombic potentials in sputtering simulations. The fitted-Bohr potentials improve the accuracy of the sputtering yields predicted by molecular dynamics for sputtering of Fe(100), whereas Moliere and ZBL potentials were found to be too repulsive and gave relatively high sputtering yields. In spite of assumptions and limitations in this simulation work, the sputtering yields predicted by the molecular dynamics method were in fairly good accordance with the obtainable experimental data in absolute values as well as in manner of the variation according to the Incident energy. Threshold energy for sputtering of Fe(100) substrate was found to be about 40 eV. Additionally, distributions of kinetic energies of sputtered atoms and their original depths could be obtained.

• 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.

• 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.

• Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
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• 2002.10b
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• pp.61-62
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• 2002

In order to clarify the contact mechanism between specimen surface and probe tip in the surface observation by the AFM (atomic force microscope) or the FFM (friction force microscope), several molecular dynamics simulations have been performed. In the simulation, a 3-dimensional simulation model is proposed where the specimen and the probe are assumed to consist of mono-crystal line copper and a carbon atom respectively and the effect of cantilever stiffness is also taken into considered. The surface observation process on a well-defined Cu{100} is simulated. The influences of cantilever stiffness on the reactive force images and the behavior of probe tip were evaluated. As a resuIt, several phenomena similar to those observed by the actual surface observation experiment, such as double-slip behavior and dispersion in the stick-slip wave period were observed.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.343-348
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• 2007

Molecular dynamics study of thermal NIL (Nano Imprint Lithography) process is performed to examine stamp-resist interactions. A layered structure consists of Ni stamp, poly-(methylmethacrylate) thin film resist and Si substrate was constructed for isothermal ensemble simulations. Imposing confined periodicity to the layered unit-cell, sequential movement of stamp followed by NVT simulation was implemented in accordance with the real NIL process. Both vdW and electrostatic potentials were considered in all non-bond interactions and resultant interaction energy between stamp and PMMA resist was monitored during stamping and releasing procedures. As a result, the stamp-resist interaction energy shows repulsive and adhesive characteristics in indentation and release respectively and irregular atomic concentration near the patterned layer were observed. Also, the spring back and rearrangement of PMMA molecules were analyzed in releasing process.

• Tribology and Lubricants
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• v.20 no.2
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• pp.102-108
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• 2004

In this paper, friction and wear behaviors between monocrystalline, defect-free copper and carbon on the atomic scale are investigated by using 2-dimensional molecular dynamics simulation. It is assumed that all interatomic forces are given by Morse potential. The deformation of carbon is assumed to be neglected and vacuum condition is also assumed. Average friction and normal forces for various surface conditions, various scratch speeds and scratch depths are obtained from simulations. Changes of wear behaviors for various scratch speeds and surface conditions are investigated by observing snapshots in scratch process. The effects of surface conditions, scratch speeds, and scratch depths on the friction force, normal force, and friction coefficient are also investigated.

• Transactions of the Society of Information Storage Systems
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• v.9 no.2
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• pp.36-41
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• 2013

Frictional behavior of a single carbon nanotube(CNT) was investigated using molecular dynamics simulation. A single CNT aligned horizontally on silver or graphene substrate was modeled to evaluate its frictional behavior such as frictional force and rolling/sliding motion with respect to potential parameter and lattice structure of the substrate. As a result, it was found that friction and rolling was affected by adhesion between two surfaces and period of the rolling depended on lattice distance of the substrate.