• Bulletin of the Korean Chemical Society
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• v.32 no.11
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• pp.4027-4034
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• 2011

$CaCO_3$ crystalline structures having novel assemblies were in situ fabricated as analogs of naturally occurring proteins and polysaccharides for biomineralization. The calcite crystal was mineralized in a poly(vinyl alcohol)-$Ca^{2+}$ complex film immersed in a $Na_2CO_3$ solution containing poly(aspartic acid). The morphology and size of the $CaCO_3$ crystals were tuned by varying the concentration of poly(aspartic acid). The mechanisms of their nucleation orientation and formation were investigated experimentally and through molecular dynamics (MD) simulations in order to obtain a better understanding of the interactions between the polymers and the crystal at the molecular level. Both the MD results and experimental results indicate that the interaction between PVA and calcite mainly depends on the concentration of the polymer. The novel approach proposed herein for the fabrication of inorganic crystalline assembly structures can be used to fabricate precise crystalline structures.

• 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.

• 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.

• Interaction and multiscale mechanics
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• v.6 no.4
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• pp.395-409
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• 2013

Molecular dynamics (MD) systems are highly nonlinear and nonlocal, and the conventional model order reduction methods are ineffective for MD systems. The RBF-POD method (Lee and Chen, 2013) employed a radial basis function (RBF) approximated potential energies and inter-atomic forces of MD systems under the framework of the proper orthogonal decomposition (POD) method for the reduced-order modeling of MD systems. In this work, we focus on the numerical procedures of the RBF-POD method and demonstrate how to apply this approach to the modeling of ds-DNA molecules under stretching and bending conditions.

• The Korean Journal of Ceramics
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• v.5 no.1
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• pp.40-43
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• 1999

In order to investigate Sn substitution sites and interstitial O atoms in tin-doped indium oxide, molecular dynamics (MD) simulations were carried out. There are two kinds of cation sites in $In_2O_3$, namely b-site and d-site. NTP-MD simulations under the condition of 300 K and 0 GPa were performed with two kinds of cells substituted by Sn atoms at each site. The excess oxygen atom accompanied with Sn doping was also taken into consideration. According to the calculations of Sn potential energies in each site, it was revealed that Sn atoms were substituted for b-sites rather than for d-sites. It was also revealed that the interstitial excess oxygen atoms tend to be connected with the Sn atoms substituted for the d-sites Sn rather than for the b-site. There MD simulation results well agreed with the experimental results.

• Journal of Powder Materials
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• v.5 no.4
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• pp.324-328
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• 1998

This paper is aimed to study the computer simulation of sintering process for ceramics by Monte Carlo and molecular dynamics methods. Plural mechanisms of mass transfer were designed in the MC simulation of sintering process for micron size particles; the transfer of pore lattices for shrinkage and the transfer of solid lattices for grain growth ran in the calculation arrays. The MD simulation was performed in the case of nano size particles of ionic ceramics and showed the characteristic features in sintering process at atomic levels. The MC and MD simulations for sintering process are useful for microstructural design for ceramics.

• Nuclear Engineering and Technology
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• v.52 no.2
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• pp.337-343
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• 2020

Oxide dispersed strengthened (ODS) steel is an important candidate for Gen-IV reactors. Oxide embedded in Fe can help to trap irradiation defects and enhances the strength of steel. It was observed in this study that the size of oxide has a profound impact on the depinning mechanism. For smaller sizes, the oxide acts as a void; thus, letting the dislocation bypass without any shear. On the other hand, oxides larger than 2 nm generate new dislocation segments around themselves. The depinning is similar to that of Orowan mechanism and the strengthening effect is likely to be greater for larger oxides. It was found that higher shear deformation rates produce more fine-tuned stress-strain curve. Both molecular dynamics (MD) simulations and BKS (Bacon-Knocks-Scattergood) model display similar characteristics whereby establishing an inverse relation between the depinning stress and the obstacle distance. It was found that (110)_oxide || (111)_Fe (oriented oxide) also had similar characteristics as that of (100)_oxide || (111)_Fe but resulted in an increased depinning stress thereby providing greater resistance to dislocation bypass. Our simulation results concluded that critical depinning stress depends significantly on the size and orientation of the oxide.

• Transactions of the Korean Society of Mechanical Engineers B
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• v.36 no.8
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• pp.873-876
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• 2012

Ionic liquids (ILs) existing in the liquid ion form under standard conditions show a unique properties. 1-10-Alkyl-3-methyl-imidazolium bromide ([C10mim][Br]) is one of the ILs that shows amphiphilic characteristics under specific conditions. This property enables it to function as a surfactant, and therefore, it finds applications in a wide range of areas. In this study, we tried to predict the behavior, especially the aggregation aspect, of [C10mim][Br] in an aqueous solution using molecular dynamics (MD) simulations. The canonical (NVT) ensemble was used to relax the system and trace the trajectory of atoms. Several case studies were simulated and the interaction among [C10mim]+, [Br]-, and water was analyzed using the radial distribution function of each atom. The density distribution function was also used for the structural analysis of the entire system. We used the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code for the present MD simulations.

• Bulletin of the Korean Chemical Society
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• v.26 no.8
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• pp.1203-1208
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• 2005

A computational study based on molecular dynamics (MD) simulations was performed in order to explain the difference in aqueous solubilities of two flavonoid/$\beta$-cyclodextrin ($\beta$-CD) complexes, hesperetin/$\beta$-CD and naringenin/$\beta$-CD. The aqueous solubility of each flavonoid/$\beta$-CD complex could be characterized by complexwater interaction not by flavonoid-CD interaction. The radial distribution of water around each inclusion complex elucidated the difference of an experimentally observed solubility of each flavonoid/$\beta$-CD complex. The analyzed results suggested that a bulky hydrophobic moiety (-$OCH_3$) of B-ring of hesperetin nearby primary rim of $\beta$-CD was responsible for lower aqueous solubility of the hesperetin/$\beta$-CD complex.

• Advances in nano research
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• v.15 no.1
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• pp.59-65
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• 2023

In this present article, the mechanical behavior of single-walled black phosphorene nanotubes (SW-αPNTs) is simulated using molecular dynamics (MD). The proposed model is subjected to the axial loading and the effects of morphological parameters, such as the mono-vacancy defect and strain rate on the tensile behavior of the zigzag and armchair SW-αPNTs are studied as a pioneering work. In order to assess the accuracy of the MD simulations, the stress-strain response of the current MD model is successfully verified with the efficient quantum mechanical approach of the density functional theory (DFT). Along with reproducing the DFT results, the accurate MD simulations successfully anticipate a significant variation in the stress-strain curve of the zigzag SW-αPNTs, namely the knick point. Predicting such mechanical behavior of SW-αPNTs may be an important design factor for lithium-ion batteries, supercapacitors, and energy storage devices. The simulations show that the ultimate stress is increased by increasing the diameter of the pristine SW-αPNTs. The trend is identical for the ultimate strain and stress-strain slope as the diameter of the pristine zigzag SW-αPNTs enlarges. The obtained results denote that by increasing the strain rate, the ultimate stress/ultimate strain are respectively increased/declined. The stress-strain slope keeps increasing as the strain rate grows. It is worth noting that the existence of mono-atomic vacancy defects in the (12,0) zigzag and (0,10) armchair SW-αPNT structures leads to a drop in the tensile strength by amounts of 11.1% and 12.5%, respectively. Also, the ultimate strain is considerably altered by mono-atomic vacancy defects.