• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.862-868
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• 2012

Based on the recently derived general expression for the rates of diffusion-controlled reactions, we calculate the rates of dismutation of the superoxide anion radical catalyzed by Cu/Zn superoxide dismutases (SOD). This is the first attempt to calculate the absolute rates of diffusion-controlled enzyme reactions based on the atomiclevel molecular dynamics simulations. All solvent molecules are included explicitly and the effects of the structural flexibility of enzyme, especially those of side chain motions near the active site, are included in the present calculation. In addition, the actual mobility of the substrate molecule is taken into account, which may change as the molecule approaches the active site of enzyme from the bulk solution. The absolute value of the rate constant for the wild type SOD reaction obtained from MD simulation is shown to be in good agreement with the experimental value. The calculated reactivity of a mutant SOD is also in agreement with the experimental result.

• Journal of Environmental Science International
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• v.25 no.7
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• pp.927-935
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• 2016

Dissolved oxygen is necessary for many biological processes as well as many industrial practices. Dissolved oxygen released from water in dissolved air flotation (DAF) systems can be have many different applications. However, DAF systems are very costly to operate. To develop more efficient DAF systems, a deeper understanding of the process of oxygen being released from water is required. In this study, molecular dynamics (MD) simulations were used to simulate 100 oxygen molecules surrounded by 31002 water molecules at temperatures ranging from $0^{\circ}C$ to $100^{\circ}C$. Simulations were carried out for 10 ns, during which, in most cases, all the oxygen molecules were released from the water droplet. With MD simulations, visualization of the molecules escaping the water droplet was possible, which aided the understanding of the interactions between molecules at the nano-scale. The results showed that as the oxygen molecules moved near the edge of the water droplet that the oxygen molecules hesitated before escaping the water droplet or returned to the interior of the water droplet. This was because of the attractive forces between the water and oxygen molecules. Moreover, after most of the oxygen molecules were released from the droplet, some were found to return to the droplet's edge or even the interior of the droplet. It was also confirmed that oxygen molecules were released at a faster rate at higher temperatures.

• 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.

• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.783-792
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• 2014

The binding interaction between a hemolytic peptide ${\delta}$-lysin and a zwitterionic lipid bilayer POPC was investigated through a series of molecular dynamics (MD) simulations. ${\delta}$-Lysin is a 26-residue, amphipathic, ${\alpha}$-helical peptide toxin secreted by Staphylococcus aureus. Unlike typical antimicrobial peptides, ${\delta}$-lysin has no net charge and it is often found in aggregated forms in solution even at low concentration. Our study showed that only the monomer, not dimer, inserts into the bilayer interior. The monomer is preferentially attracted toward the membrane with its hydrophilic side facing the bilayer surface. However, peptide insertion requires the opposite orientation where the hydrophobic side of peptide points toward the membrane interior. Such orientation allows the charged residues, Lys and Asp, to have stable salt bridges with the lipid head-group while the hydrophobic residues are buried deeper in the hydrophobic lipid interior. Our simulations suggest that breaking these salt bridges is the key step for the monomer to be fully inserted into the center of lipid bilayer and, possibly, to translocate across the membrane.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.18 no.5
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• pp.414-422
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• 2005

This paper shows the results of atomistic modeling for the Interaction between spherical nano abrasive and substrate In chemical mechanical polishing processes. Atomistic modeling was achieved from 2-dimensional molecular dynamics simulations using the Lennard-jones 12-6 potentials. We proposed and investigated three mechanical models: (1) Constant Force Model; (2) Constant Depth Model, (3) Variable Force Model, and three chemical models, such as (1) Chemically Reactive Surface Model, (2) Chemically Passivating Surface Model, and (3) Chemically Passivating-reactive Surface Model. From the results obtained from classical molecular dynamics simulations for these models, we concluded that atomistic chemical mechanical polishing model based on both Variable Force Model and Chemically Passivating-reactive Surface Model were the most suitable for realistic simulation of chemical mechanical polishing in the atomic scale. The proposed model can be extended to investigate the 3-dimensional chemical mechanical polishing processes in the atomic scale.

• Bulletin of the Korean Chemical Society
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• v.24 no.11
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• pp.1590-1598
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• 2003

In this paper we have presented the results for viscosity and self-diffusion constants of model systems for four liquid n-alkanes ($C_{12}, C_{20}, C_{32}, and C_{44}$) in a canonical ensemble at several temperatures using molecular dynamics (MD) simulations. The small chains of these n-alkanes are clearly $<{R_{ee}}^2>/6<{R_g}^2>>1$, which leads to the conclusion that the liquid n-alkanes over the whole temperatures considered are far away from the Rouse regime. Calculated viscosity ${\eta}$ and self-diffusion constants D are comparable with experimental results and the temperature dependence of both ${\eta}$ and D is suitably described by the Arrhenius plot. The behavior of both activation energies, $E_{\eta}$ and $E_D$, with increasing chain length indicates that the activation energies approach asymptotic values as n increases to the higher value, which is experimentally observed. Two calculated monomeric friction constants ${\zeta}$ and ${\zeta}_D$ give a correct qualitative trend: decrease with increasing temperature and increase with increasing chain length n. Comparison of the time auto-correlation functions of the end-to-end vector calculated from the Rouse model for n-dodecane ($C_{12}$) at 273 K and for n-tetratetracontane ($C_{44}$) at 473 K with those extracted directly from our MD simulations confirms that the short chain n-alkanes considered in this study are far away from the Rouse regime.

• Nuclear Engineering and Technology
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• v.50 no.6
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• pp.907-914
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• 2018

In this article, we conducted molecular dynamics simulations to investigate the effect of applied strain and temperature on irradiation-induced damage in alpha-zirconium. Cascade simulations were performed with primary knock-on atom energies ranging between 1 and 20 KeV, hydrostatic and uniaxial strain values ranging from -2% (compression) to 2% (tensile), and temperatures ranging from 100 to 1000 K. Results demonstrated that the number of defects increased when the displacement cascade proceeded under tensile uniaxial hydrostatic strain. In contrast, compressive strain states tended to decrease the defect production rate as compared with the reference no-strain condition. The proportions of vacancy and interstitial clustering increased by approximately 45% and 55% and 25% and 32% for 2% hydrostatic and uniaxial strain systems, respectively, as compared with the unstrained system, whereas both strain fields resulted in a 15-30% decrease in vacancy and interstitial clustering under compressive conditions. Tensile strains, specifically hydrostatic strain, tended to produce larger sized vacancy and interstitial clusters, whereas compressive strain systems did not significantly affect the size of defect clusters as compared with the reference no-strain condition. The influence of the strain system on radiation damage became more significant at lower temperatures because of less annealing than in higher temperature systems.

• Korean Chemical Engineering Research
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• v.49 no.3
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• pp.361-366
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• 2011

By using Monte Carlo simulation method we developed a new molecular simulation software which can be used to predict the thermodynamic properties of organic compounds. Starting from molecular structure and intermolecular potential function, rigorous statistical mechanical principles give a probability distribution for the behavior of a system containing many molecules, which enables us to calculate macroscopic thermodynamic properties of the system. The software developed in this work, cheMC, is based on Windows platform providing with easy access. One can efficiently administrate simulations by using an intuitive interface equipped with visualization tool and chart generation. It is expected that molecular simulations supplement the equation of state approach and will play a more important role in the study of thermodynamic properties.

• BMB Reports
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• v.33 no.1
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• pp.54-58
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• 2000

Recent research results regarding the very long chain transmembrane ${\alpha},{\omega}-dicarboxylic$ components in the membrane of extremophilic eubacteria, such as Sarcina ventriculi, Thennotoga maritima, and Thermoanaerobacter ethanolicus have raised interesting questions concerning the physical and biochemical function on these components in the membrane. In order to understand the dynamic characteristics of these acids which reside in the bilayer membrane, 580 ps molecular dynamic simulations at 300 K were performed for two model systems. These systems were the bilayer with regular chain (C16:0 or C18:1) fatty acid methyl esters and the fatty acid bilayer containing very long chain transmembrane dicarboxylic acid methyl esters (${\alpha},{\omega}-15,16-dimethyltriacotane-dioate$ dimethyl ester; C32:0). Our analyses indicate that very long chain transmembrane dicarboxylic acids have a noticeable influence on the bilayer dynamics at a sub-nanosecond time scale. The center-ofmass mean-squared-displacement (MSD) of regular chain fatty acids adjacent to the very long chain transmembrane dicarboxylic acids decreased, the long-axis order parameter increased, and the reorientational motions of methylene groups were slowed along the hydrocarbon chains. These results indicate that the very long chain transmembrane dicarboxylic acids reduce the molecular order of the whole bilayer membrane.

• 한국신재생에너지학회:학술대회논문집
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• 2011.11a
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• pp.122.2-122.2
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• 2011

Sulfur hexafluoride ($SF_6$), one of the most potent greenhouse gases, is known as a hydrate former and has been studied at the high pressure up to 1.3 GPa with gas mixtures and with aqueous surfactant. Since we regard $SF_6$ as a potential promoter molecule that can stabilize hydrate structure more effectively compare to the other promoters, further investigation is required to verify the stabilizing ability of $SF_6$ in the hydrate structure. However, the insoluble nature of $SF_6$ in water or gases hinders fine scale analyses. This work discusses the data obtained by using molecular dynamics simulations of structure II (sII) clathrate hydrates containing $SF_6$ and $H_2$. The simulations were performed using the TIP4P/Ice model for water molecule and a previously reported $SF_6$ molecular model (optimized at the pure $SF_6$ single phase system (Olivet and Vega, 2007)), and a $H_2$ molecular model (adapted from the THF+$H_2$ hydrate system (Alavi et al., 2006)). The simulations are performed to observe the stability of $SF_6$ and $H_2$ in the sII clathrate hydrate system with varying temperature and pressure conditions and occupancies of $SF_6$ and $H_2$, which cannot be easily tuned experimentally. We observe that stability of H2 enclathrated in the hydrate structure more affected by the occupancy of $SF_6$ molecules and temperature than pressure, which ranges from 1 to 100 bar.