• Bulletin of the Korean Chemical Society
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• v.27 no.8
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• pp.1154-1158
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• 2006

Anomalously high ionic mobilities of H+ and $OH^-$ are owing to the transfer of $H^+$ by the Grotthus chain mechanism. Molecular dynamics simulations for the system of 215 water including $OH^-$ ion at 298.15 K using the OSS2 model [J. Chem. Phys. 109, 5547 (1998)] as a dissociable water model with the use of Ewald summation were carried out in order to study the dynamics of $OH^-$ in water. The calculated ionic mobility of $OH^-$ is in good agreement with the experimental result and the Grotthus chain mechanism is fully understood.

• Bulletin of the Korean Chemical Society
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• v.32 no.2
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• pp.515-518
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• 2011

We investigated how temperature influences the structural and energetic dynamics of carbon nanotubes (CNTs) undergoing a high-speed impact with a Si (110) surface. By performing molecular dynamics simulations in the temperature range of 100 - 300 K, we found that a low temperature CNT ends up with a higher vibrational energy after collision than a high temperature CNT. The vibrational temperature of CNT increases by increasing the surface temperature. Overall, the structural and energy relaxation of low temperature CNTs are faster than those of high temperature CNTs.

• Journal of the Mineralogical Society of Korea
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• v.30 no.4
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• pp.161-172
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• 2017

Clay minerals play a major role in the geochemical cycles of metals in the Critical Zone, the Earth surface-layer ranging from the groundwater bottom to the tree tops. Atomistic scale research of the very fine particles can help understand the fundamental mechanisms of the important geochemical processes and possibly apply to development of hybrid nanomaterials. Molecular dynamics (MD) simulations can provide atomistic level insights into the crystal structures of clay minerals and the chemical reactivity. Classical MD simulations use a force field which is a parameter set of interatomic pair potentials. The ClayFF force field has been widely used in the MD simulations of dioctahedral clay minerals as the force field was developed mainly based on dioctahedral phyllosilicates. The ClayFF is often used also for trioctahedral mineral simulations, but disagreement exits in selection of the interatomic potential parameters, particularly for Mg atom-types of the octahedral sheet. In this study, MD simulations were performed for trioctahedral clay minerals such as brucite, lizardite, and talc, to test how the two different Mg atom types (i.e., 'mgo' or 'mgh') affect the simulation results. The structural parameters such as lattice parameters and interatomic distances were relatively insensitive to the choice of the parameter, but the vibrational power spectra of hydroxyls were more sensitive to the choice of the parameter particularly for lizardite.

• Bulletin of the Korean Chemical Society
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• v.30 no.9
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• pp.2087-2092
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• 2009

We performed molecular dynamics simulations on dimyristoylphosphatidylcholine lipid bilayer with 50 mol% halothane. The structural properties, electron density profile, segmental order parameter of acyl chains, headgroup orientation distribution, water dipole orientation distribution, have been examined. Overall the effects of the halothane molecules on structural properties of DMPC lipid bilayer were found to be small. The electron density profiles, the segmental order parameter, the headgroup orientation, the water dipole orientation were not affected significantly by the halothane molecules. Pressure tensor calculations shows that the lateral pressure increases at the hydrocarbon tail region and the headgroup region, and decreases at the water-headgroup interfacial region.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.49 no.6
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• pp.815-822
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• 2016

The cationic biopolymer chitosan has several applications in medicine. Chitosan is the deacetylated derivative of chitin, the second most abundant naturally occurring polymer. Recent studies have investigated the relationship between chitosan and antibacterial activity. However, the molecular interactions and mechanisms have not been detailed. This study used molecular dynamics simulations to study interactions between chitosan and anionic bacterial membranes (POPE-POPG) and electrically neutral non-bacterial membranes (POPC). We calculated the free energy using umbrella sampling to compare the interactions between membranes and chitosan in different protonation states. Fully protonated chitosan interacted most strongly with the bacterial membranes, but weakly with non-bacterial membranes. These results suggest that electrostatic interactions are the main mechanism of the antibacterial activity of chitosan, and they provide insights into the design of novel antibacterial and antimicrobial agents.

• Korean Journal of Materials Research
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• v.19 no.5
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• pp.276-280
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• 2009

The effect of the initial packing structure on the plasticity of amorphous alloys was investigated by tracing the structural evolution of the amorphous solid inside a shear band. According to the molecular dynamics simulations, the structural evolution of the amorphous solids inside the shear band was more abrupt in the alloy with a higher initial packing density. Such a difference in the structural evolution within the shear band observed from the amorphous alloys with different initial packing density is believed to cause different degrees of shear localization, providing an answer to the fundamental question of why amorphous alloys show different plasticity. We clarify the structural origin of the plasticity of bulk amorphous alloys by exploring the microstructural aspects in view of the structural disordering, disorder-induced softening, and shear localization using molecular dynamics simulations based on the recently developed MEAM (modified embedded atom method) potential.

• Coupled systems mechanics
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• v.6 no.1
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• pp.41-54
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• 2017

Shape-memory alloys (SMA) have interesting behaviors and important mechanical properties due to the solid-solid phase transformation. These phenomena are dominated by the evolution of microstructures. In recent years, the microstructures in SMAs have been studied extensively and modeled using molecular dynamics (MD) simulations. However, it remains difficult to identify the crystal variants in the simulation results, which consist of large numbers of atoms. In the present work, a method is developed to identify the austenite phase and the monoclinic martensite crystal variants in MD results. The transformation matrix of each lattice is calculated to determine the corresponding crystal variant. Evolution of the volume fraction of the crystal variants and the microstructure in Ni-Ti SMAs under thermal and mechanical boundary conditions are examined. The method is validated by comparing MD-simulated interface normals with theoretical solutions. In addition, the results show that, in certain cases, the interatomic potential used in the current study leads to inconsistent monoclinic lattices compared with crystallographic theory. Thus, a specific modification is applied and the applicability of the potential is discussed.

• Journal of the Korean Society of Manufacturing Process Engineers
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• v.18 no.5
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• pp.60-65
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• 2019

Since nanofluids (NFs), which are a mixture of a small amount of nanoparticles and a bulk liquid solvent, were first proposed by Stephen Choi at the Argonne National Lab in 1995, they have been considered for use in many technical studies of power cooling systems and their practical application due to their high thermal conductivity and heat transfer coefficients compared to conventional coolants. Although nanofluids are a well-known form of engineering fluid that show great promise for use in future cooling systems, their underlying physics as demonstrated in experiments remain unclear. One proven method of determining the heat transfer performance of nanofluids is measuring the concentration of nanoparticles in a mixture. However, it is experimentally inefficient to build testbeds to systematically observe particle distributions on a nanoscale. In this paper, we demonstrate the distribution of nanoparticles under a temperature gradient in a solution using molecular dynamics simulations. First, temperature profiles based on substrate temperature are introduced. Following this, the radial pair distribution functions of pairs of nanoparticles, solvents, and substrates are calculated. Finally, the distribution of nanoparticles in different heating regions is determined.

• Current Optics and Photonics
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• v.8 no.1
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• pp.86-96
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• 2024

This research investigation employs a terahertz (THz) time-domain spectroscopy system to study the terahertz spectral characteristics of five different citrates in both solution and solid state. The citrates under examination are lithium citrate, monosodium citrate, disodium citrate, trisodium citrate, and potassium citrate. The results show that the THz absorption coefficients of the first four citrate solutions exhibit a decreasing trend with increasing concentration. However, the potassium citrate solution shows an opposite phenomenon. At the same time, the absorption coefficients of lithium citrate, trisodium citrate, and potassium citrate solutions are compared at the same concentration. The results indicate that the absorption coefficient of citrate solution increases in proportion to the increase of metal cation radius, which is explained from the perspective of the influence of metal cations on hydrogen bonds. In addition, we also study the absorption peaks of solid citrates, and characterize the formation mechanism of the absorption peaks by molecular dynamics simulations. This methodology can be further extended to the study of multitudinous salts, presenting theoretical foundations for the detection in food and medicine industries.

• Bulletin of the Korean Chemical Society
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• v.34 no.3
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• pp.753-758
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• 2013

Molecular dynamics (MD) simulations have been used to study the diffusion behavior of small gas molecules ($CO_2$) in polyethylene terephthalate (PET)/polylactide (PLA) blends. The Flory-Huggins interaction parameters (${\chi}$) determined from the cohesive energy densities are smaller than the critical value of Flory-Huggins interaction parameters (${\chi}_{critical}$), and that indicates the good compatibility of PET/PLA blends. The diffusion coefficients of $CO_2$ are determined via MD simulations at 298 K. That the order of diffusion coefficients is correlated with the availably fractional free volume (FFV) of $CO_2$ in the PET/PLA blends means that the FFV plays a vital role in the diffusion behavior of $CO_2$ molecules in PET/PLA blends. The slopes of the log (MSD) as a function of log (t) are close to unity over the entire composition range of PET/PLA blends, which confirmes the feasibility of MD approach reaches the normal diffusion regime of $CO_2$ in PET/PLA blends.