• Proceedings of the Korean Biophysical Society Conference
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• 2001.06a
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• pp.33-33
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• 2001

Bacterial Δ$\^$5/-3-ketosteroid isomerase (KSI) is one of the most proficient enzymes catalyzing the isomerization of a variety of Δ$\^$5/-ketosteroids to Δ$^4$-ketosteroids at a diffusion-controlled rate. Because of the simplicity of the reaction, the enzyme mechanism has been intensively studied as a prototype to understand enzyme-catalyzed C-H bond cleavage.(omitted)

• Bulletin of the Korean Chemical Society
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• v.14 no.2
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• pp.255-258
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• 1993

Molecular dynamics (MD) calculations were carried out in order to investigate the effect of MD cell size to predict the melting phenomena of A-type zeolite. We studied two model systems: a pseudocell of $(T_2O_4Na)_n$, (L= 12.264 $^{\AA}$, N= 84) and a true-cell of (SiAlO$_4Na)_n$. (L= 24.528 $^{\AA}$, N= 672), where T is Si or Al. The radial and bond angle distribution functions of T(Si, Al)-O-T(Si, Al) and diffusion coefficients of T and O were reported at various temperatures. For the true-cell model, the melting temperature is below 1500 K and probably around 1000 K, which is about 600-700 K lower than the pseudocell model. Although it took more time (about 30 times longer) to obtain the molecular trajectories of the true-cell model than those of the pseudocell model, the true-cell model gave more realistic structural transition for the A-type zeolite, which agrees with experiment.

• Bulletin of the Korean Chemical Society
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• v.12 no.3
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• pp.315-322
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• 1991

In a recent $paper^1$ we reported equilibrium (EMD) and non-equilibrium (NEMD) molecular dynamics simulations of liquid argon using the Green-Kubo relations and NEMD algorithms to calculate the thermal transport coefficients-the self-diffusion coefficient, shear viscosity, and thermal conductivity. The overall agreement with experimental data is quite good. In this paper the same technique is applied to calculate the thermal transport coefficients of liquid water at 298.15 K and 1 atm using TIP4P model for the interaction between water molecules. The EMD results show difficulty to apply the Green-Kubo relations since the time-correlation functions of liquid water are oscillating and not decaying rapidly enough except the velocity auto-correlation function. The NEMD results are found to be within approximately ${\pm}$30-40% error bars, which makes it possible to apply the NEMD technique to other molecular liquids.

• Journal of Soil and Groundwater Environment
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• v.11 no.6
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• pp.28-34
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• 2006

Laboratory column tests using $Cl^-$ tracer were conducted to study the correlation of soil particle distribution and hydrodynamic dispersion mechanism with three kinds of ununiformed soil samples, in which the ratio of gravel and sand versus silt and clay is 24.5 for S-1 soil, 4.48 for S-2 soil, and 0.4 for S-3 soil. Chloride breakthrough curves with time were fitted with gaussian functions. The relative concentrations of chloride were converged to 1.0 after 0.7 hours for S-1, 6.3 hours for S-2, and 389 hours for S-3. Average linear velocity, longitudinal dispersion coefficient, and longitudinal dispersivity were calculated by chloride breakthrough curves. Longitudinal dispersion coefficients were $1.20{\times}10^{-4}\;m^2/sec$ for S-1, $8.87{\times}10^{-7}\;m^2/sec$ for S-2, and $1.94{\times}10^{-9}\;m^2/sec$ for S-3. Peclet numbers calculated by the molecular diffusion coefficient of chloride and the mean grain diameters of soils were $2.59{\times}10^2$ for S-1, $6.27{\times}10^0$ for S-2, and $1.35{\times}10^{-4}$ for S-3. Mechanical dispersion was dominant for the hydrodynamic dispersion mechanism of S-1. Both mechanical dispersion and molecular diffusion were dominant for the hydrodynamic dispersion mechanism of S-2, but mechanical dispersion was ascendant over molecular diffusion. Hydrodynamic dispersion in S-3 was occurred mainly by molecular diffusion. When plotting three soils on the graph of $D_L/D_m$ versus Peclet number produced by Bijeljic and Blunt (2006), the values of $D_L/D_m$ for S-1 and S-2 were more than 2.0 order compared to their graph. S-3 was not plotted on their graph because the Peclet number was as small as $1.35{\times}10^{-4}$.

• Membrane Journal
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• v.27 no.4
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• pp.358-366
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• 2017

The most important factor in the performances of polymer electrolyte membranes for fuel cells is how fast hydrogen ions can be transported along the water channel formed inside the electrolyte membrane. Since the morphology of the water channel and the diffusivity of the protons are very important factors for the proton transport behavior, various molecular dynamics simulation studies are being carried out to clarify this. The force-field is an important variable parameterizing the movement and interaction of each atom in molecular dynamics simulation. In this study, proton diffusivities of the 3D models of polymer electrolyte membranes were calculated in order to analyze the effects of various types of force-fields on the molecular simulation. It has been found that the charge value determining the non-bonding interaction plays a very important role in the formation of the water channel morphology, and the COMPASS force-field can calculate the accurate proton diffusion behavior. Accordingly, for molecular dynamics simulation of polymer electrolyte membranes, the proper selection of the force-field is very important due to its great effect on the proton diffusion as well as the final molecular structure.

• The Journal of Korea Institute of Information, Electronics, and Communication Technology
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• v.13 no.5
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• pp.338-343
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• 2020

In this paper, it was shown that the decoding method of Hamming codes using soft values can be applied to molecular communication channels. A soft value criterion that can be used for decoding of Hamming codes for a molecular communication channel was proposed, and it has been shown through simulation that the decoding method using these values can improve reliability even in the molecular communication channel. A diffusion-based molecular communication channel was assumed, and information symbols were transmitted using BCSK modulation. After demodulating the number of molecules absorbed by the receiver at each symbol interval with an appropriate threshold, the number of molecules is no longer used. In this paper, the BER performance of the decoder was improved by utilizing information on the number of molecules that are no longer used as soft values in the decoding process. Simulation was performed to confirm the improvement in BER performance. When the number of molecules per bit is 600, the error rate of the Hamming code (15,11) was improved about 5.0×10^-3 to the error rate of the BCSK system without the Hamming code. It can be seen that the error rate of (15,11) Hamming code with the soft values was improved to the same extent. In the case of (7,4) Hamming code, the result is similar to that of (15,11) Hamming code. Therefore, it can be seen that the BER performance of the Hamming code can be greatly improved even in the molecular communication channel by using the difference between the number of molecules absorbed by the receiver and the threshold value as a soft value.

• Bulletin of the Korean Chemical Society
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• v.19 no.5
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• pp.527-530
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• 1998

This paper presents the electrochemistry and molecular orbital (MO) picture of a series of conformationally-restricted thioxantone derivatives. A series of $C_2-substituted$ thioxanthones were examined to probe the electronic influence of the substituent on the electrooxidation and electroreduction sites (i.e., on the electron densities at the 10-and 9-positions), respectively. In the presence of "electrophoric" groups such as C=O and S, characteristic electrochemical reduction and oxidation responses are observed. The electrochemical reaction was diffusion-controlled, because the $I_p/{\upsilon}^{1/2}$ ratio was constant for the anodic and cathodic wave of thioxantone derivatives. These substituent effects are presented in terms of correlations of oxidation (or reduction) potentials with the highest occupied molecular orbital (HOMO), or lowest unoccupied molecular orbital (LUMO) energies, respectively. There is good correlation between energies of the HOMO vs. $E_{pa}^{(+)}$ and energies of the LUMO vs. $E_{pc}^{(-)}$. Frontier Molecular Orbital (FMO) is changed by the functional group of thioxanthones. FMO energy level was offered us the information about the electron transfer direction, and the coefficient of FMO was offered the information about the electron transfer position. Sulfur atom has an important effect on oxidation potential, $E_{pa}^{(+)}$ and the carbonyl carbon has an important effect on reduction potential, $E_{pc}^{(-)}$. Therefore we were appreciated that the contribution of sulfur atom for the $E_{pa}^{(+)}$ and HOMO energies is larger than the contribution of carbonyl group for the $E_{pc}^{(-)}$ and LUMO energies.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.499-499
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• 2011

Silicon nanowires (Si NWs) have been extensively studied for nanoelectronics owing to their unique optical and electrical properties different from those of bulk silicon. For the development of Si NW devices, better understanding of oxidation behavior in Si NWs would be an important issue. For example, it is widely known that atomic scale roughness at the dielectric (SiOx)/channel (Si) interface can significantly affect the device performance in the nano-scale devices. However, the oxidation process at the atomic-scale is still unknown because of its complexity. In the present work, we investigated the oxidation behavior of Si NW in atomic scale by simulating the dry oxidation process using a reactive molecular dynamics simulation technique. We focused on the residual stress evolution during oxidation to understand the stress effect on oxidation behavior of Si NWs having two different diameters, 5 nm and 10 nm. We calculated the charge distribution according to the oxidation time for 5 and 10 nm Si NWs. Judging from this data, it was observed that the surface oxide layer started to form before it is fully oxidized, i.e., the active diffusion of oxygen in the surface oxide layer. However, it is well-known that the oxide layer formation on the Si NWs results in a compressive stress on the surface which may retard the oxygen diffusion. We focused on the stress evolution of Si NWs during the oxidation process. Since the surface oxidation results in the volume expansion of the outer shell, it shows a compressive stress along the oxide layer. Interestingly, the stress for the 10 nm Si NW exhibits larger compressive stress than that of 5 nm Si NW. The difference of stress level between 5 an 10 anm Si NWs is approximately 1 or 2 GPa. Consequently, the diameter of Si NWs could be a significant factor to determine the self-limiting oxidation behavior of Si NWs when the diameter was very small.

• Transactions of the Korean Society of Mechanical Engineers B
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• v.34 no.2
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• pp.99-103
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• 2010

A new analytic solution was derived for the diffusion into or from an immobile zone of a rectangular 2-D pore. For a long time, the new solution converges to a traditional mobile-immobile zone (MIM) model, but only if the latter is used with an apparent initial concentration that is smaller by almost 20% than the true one. This is the tradeoff for using a simple MIM model instead of an exact model based on the diffusion equation. The mass-transfer coefficient was found to be constant for a sufficiently long time; it was proportional to the molecular diffusion and inversely proportional to the square of the pore depth. The mass-transfer coefficient was time-dependent for a sufficiently short time and may be significantly larger than its asymptotic value.

• The Korean Journal of Pharmacology
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• v.29 no.1
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• pp.157-163
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• 1993

Intramolecular excimer formation with the fluorescent probe 1,3-di(1-pyrenyl)propane (Py-3-Py) was used to investigate the effects of methanol, ethanol, 1-propanol, 1-butanol, 1-pentanol, 1-hexanol, 1-heptanol, 1-octanol, 1-nonanol and 1-decanol on the lateral diffusion of synaptosomal plasma membrane vesicles isolated from bovine cerebral cortex (SPMV). The n-alkanols increased the excimer to monomer fluorescence intensity ratio (I'/I) of Py-3-Py in the SPMV. In a dose-dependent manner, n-alkanols increased lateral diffusion of hydrocarbon region of bulk (inner+outer monolayers) SPMV lipid bilayers, and the potencies of n-alkanols up to l-nonanol increased with carbon chain length. It appears that the potencies in bilayer fluidization due to the lateral diffusion increase by 1 order of magnitude as the carbon chain length increases by two carbon atoms. The cut-off phenomenon was reached at 1-decanol, where further increase in hydrocarbon length resulted in a decrease in pharmacological activity.