• Asia-pacific Journal of Multimedia Services Convergent with Art, Humanities, and Sociology
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• v.8 no.6
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• pp.939-946
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• 2018

In this work, we present simple schematics for a three-terminal graphene-based nanoelectromechanical switch with the vertical electrode, and we investigated their operational dynamics via classical molecular dynamics simulations. The main structure is both the vertical pin electrode grown in the center of the square hole and the graphene covering on the hole. The potential difference between the bottom gate of the hole and the graphene of the top cover is applied to deflect the graphene. By performing classical molecular dynamic simulations, we investigate the nanoelectromechanical properties of a three-terminal graphene-based nanoelectromechanical switch with vertical pin electrode, which can be switched by the externally applied force. The elastostatic energy of the deflected graphene is also very important factor to analyze the three-terminal graphene-based nanoelectromechanical switch. This simulation work explicitly demonstrated that such devices are applicable to nanoscale sensors and quantum computing, as well as ultra-fast-response switching devices.

• Proceedings of the KSME Conference
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• 2003.04a
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• pp.1366-1371
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• 2003

Molecular dynamics (MD) simulations are conducted to investigate the thermophysical characteristics and the stability of liquid threads for various conditions. A cylindrical thread in the simulation domain is made of Lennard-Jones molecules. The surface tension of liquid threads can be determined from local densities, local normal and transverse components of the pressure force. In order to understand the effects of thread radii on surface tensions, the Tolman equation is modified on the basis of the cylindrical coordinates for prediction of surface tensions. Surface tensions calculated from the MD simulation agree with the prediction from the modified Tolman equation. In addition, surface tensions decrease linearly with increasing system temperature. For a binary system, the surface tension decreased linearly compared to that for a pure system with increasing binary ratio of solute molecules which have relatively large value of the affinity coefficient. For a fixed binary ratio, the surface tension increased slightly with the affinity coefficient and the maximum value appear around where the affinity coefficient is 1.5 and decreased rapidly for upper value of 1.5. In addition, the critical wavelengths of perturbations are proven to be directly proportional to the equimolar dividing radii of the liquid threads.

• Membrane Journal
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• v.25 no.2
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• pp.162-170
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• 2015

In this study, gas permeability of polyimide materials having a various amine group was measured and molecular dynamics was used to analyze the dynamic characteristics of the gas molecules in the polyimide by calculating the position and velocity of the gas molecules with change of the time. The gas permeability of polyimide membrane having substitution site which increase free volume in the polymer was increased. However, polyimide with rigid structure showed decreased gas permeability. As a result of analyzing the change in the gas permeation behavior using molecular dynamics simulations, we confirmed that the results show the same tendency with actual measurements of the gas permeability.

• Bulletin of the Korean Chemical Society
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• v.31 no.2
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• pp.453-456
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• 2010

The structural and energetic preferences of thiacalix[4]biscrown-5 with and without alkali metal ions ($Na^+$, $K^+$, $Rb^+$, and $Cs^+$) have been theoretically investigated for the first time using molecular dynamic (MD) simulations and density functional theory (MPWB1K/6-31G(d)//B3LYP/6-31G(d)) methods. The formation of the metal ion complex by the host is mainly driven by the electrostatic attraction between crown-5 oxygens and a cation together with the minor contribution of the cation-$\pi$ interaction between two facing phenyl rings around the cation. The computed binding energies and the atomic charge distribution analysis for the metal binding complexes indicate the selectivity toward a potassium ion. The theoretical results herein explain the experimentally observed extractability order by this host towards various alkali metal ions. The physical nature and the driving forces for cation recognition by this host are discussed in detail.

• Bulletin of the Korean Chemical Society
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• v.31 no.11
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• pp.3195-3200
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• 2010

We have performed molecular dynamics simulations of atomistic models of $C_{60}$ molecules and DMPC bilayer membranes to study the static and dynamic effects of carbon nanoparticles on biological membranes. All four $C_{60}$-membrane systems were investigated representing dilute and concentrated solutions of $C_{60}$ residing either inside or outside the membrane. The concentrated $C_{60}$ molecules in water phase start forming an aggregated cluster. Due to its heavy mass, the cluster tends to adhere on the surface of the bilayer membrane, hindering both translational and rotational diffusion of individual $C_{60}$. On the other hand, once $C_{60}$ molecules accumulate inside the membrane, they are well dispersed in the central region of the bilayer membrane. Because of the homogeneous dispersion of $C_{60}$ inside the membrane, each leaflet is pushed away from the center, making the bilayer membrane thicker. This thickening of the membrane provides more room for both translational and rotational motions of $C_{60}$ inside the membrane compared to that in the water region. As a result, the dynamics of $C_{60}$ inside the membrane becomes faster with increasing its concentration.

• Journal of the Mineralogical Society of Korea
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• v.31 no.1
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• pp.13-22
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• 2018

Aluminum silicates ($Al_2SiO_5$) undergo phase transitions among kyanite, andalusite, and sillimanite depending on temperature and pressure conditions. The minerals are often used as an important indicator of the degree of metamorphism for certain metamorphic rocks. In this study, we have applied classical molecular dynamics (MD) simulations and density functional theory (DFT) to the aluminum silicates. We examined the crystal structures as a function of applied pressure and the corresponding stabilities based on calculated enthalpies at each pressure. In terms of the lattice parameters, both methods showed that the volume decreases as the pressure increases as observed in the experiment. In particular, DFT results differed from experimental results by much less than 1%. As to the relative stability, however, both methods showed different levels of accuracy. In the MD simulations, a transition pressure at which the relative stability between two minerals reverse could not be determined because the enthalpies were insensitive to the applied pressure. On the other hand, in DFT calculations, the relative stability relation among the three minerals was consistent with experiment, although the transition pressure was strongly dependent on the choice of the electronic exchange-correlation functional.

• Journal of the Korean Society for Precision Engineering
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• v.29 no.4
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• pp.479-486
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• 2012

Two of fundamental approaches that can be used to understand ion-solid interaction are Monte Carlo (MC) and Molecular Dynamic (MD) simulations. For the simplicity of simulation Monte Carlo simulation method is widely preferred. In this paper, basic consideration and algorithm of Monte Carlo simulation will be presented as well as simulation results. Sputtering caused by incident ion beam will be discussed with distribution of sputtered particles and their energy distributions. Redeposition of sputtered particles that are experienced refraction at the substrate-vacuum interface additionally presented. In addition, reflection of incident ions with reflection coefficient will be presented together with spatial and energy distributions. This Monte Carlo simulation will be useful in simulating and describing ion beam related processes such as Ion beam induced deposition/etching process, local nano-scale distribution of focused ion beam implanted ions, and ion microscope imaging process etc.

• Journal of the Korean Society for Aeronautical & Space Sciences
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• v.32 no.7
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• pp.60-68
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• 2004

High velocity impacts are accompanied with large deformations, which generate a large amount of heat due to plastic works, resulting in a significant temperature rise of the material. Because the elevated temperature affects the dynamic properties of materials, it is important to predict the temperature rise during high-stram-rate deformations. Both existing vacancies and excess vacancies are credited to the stored energy, yet it is difficult to distinguish one from another in contribution to the stored energy using macroscopic level materials models. In this study, an atomistic material model for fee materials such as copper is set up to calculate the stored energy using molecular dynamics (MD) simulations. It is concluded that excess vacancies play an important role for the stored energy during a high-strain-rate deformation.

• Biomolecules & Therapeutics
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• v.29 no.5
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• pp.506-518
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• 2021

The imprinted tumour suppressor NOEY2 is downregulated in various cancer types, including ovarian cancers. Recent data suggest that NOEY2 plays an essential role in regulating the cell cycle, angiogenesis and autophagy in tumorigenesis. However, its detailed molecular function and mechanisms in ovarian tumours remain unclear. In this report, we initially demonstrated the inhibitory effect of NOEY2 on tumour growth by utilising a xenograft tumour model. NOEY2 attenuated the cell growth approximately fourfold and significantly reduced tumour vascularity. NOEY2 inhibited the phosphorylation of the signalling components downstream of phosphatidylinositol-3'-kinase (PI3K), including phosphoinositide-dependent protein kinase 1 (PDK-1), tuberous sclerosis complex 2 (TSC-2) and p70 ribosomal protein S6 kinase (p70S6K), during ovarian tumour progression via direct binding to vascular endothelial growth factor receptor-2 (VEGFR-2). Particularly, the N-terminal domain of NOEY2 (NOEY2-N) had a potent anti-angiogenic activity and dramatically downregulated VEGF and hypoxia-inducible factor-1α (HIF-1α), key regulators of angiogenesis. Since no X-ray or nuclear magnetic resonance structures is available for NOEY2, we constructed the three-dimensional structure of this protein via molecular modelling methods, such as homology modelling and molecular dynamic simulations. Thereby, Lys15 and Arg16 appeared as key residues in the N-terminal domain. We also found that NOEY2-N acts as a potent inhibitor of tumorigenesis and angiogenesis. These findings provide convincing evidence that NOEY2-N regulates endothelial cell function and angiogenesis by interrupting the VEGFR-2/PDK-1/GSK-3β signal transduction and thus strongly suggest that NOEY2-N might serve as a novel anti-tumour and anti-angiogenic agent against many diseases, including ovarian cancer.

• Nuclear Engineering and Technology
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• v.38 no.3
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• pp.201-210
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• 2006

This article presents a brief overview of an important area of neutron scattering: the general principles and techniques of elastic, quasielastic and inelastic scattering from a system composed predominately of incoherent scatterers. The methodology is then applied to the study of water, specifically when it is confined in nanometer-scale environments. The confined water exhibits uniquely anomalous properties in the supercooled state. It also nourishes biological functions, and supports essential chemical reactions in living systems. We focus on recent investigations of water encapsulated in nanoporous silica and carbon nanotubes, hydrated water in proteins and water or hydroxyl species incorporated in nanostructured minerals. Through these scientific examples, we demonstrate the advantages derived from the high sensitivity of incoherent neutron spectroscopy to hydrogen atom motions and hydrogen-bond dynamics, aided by rigorous data interpretation method using molecular dynamics simulations or theoretical modelling. This enables us to probe the inter-/intramolecular vibrations and relaxation/diffusion processes of water molecules in a complex environment.