• Journal of the Korean Chemical Society
• /
• v.42 no.1
• /
• pp.22-27
• /
• 1998

Fluorescence quenching of coumarin 153 and coumarin 481 with N,N-dimethylaniline in various solvents was investigated. Quenching rate constants are related to diffusion-limited rate constants to some extent. It is noted that smaller discrepancy was observed between the diffusion-limited rate constant and the experimental quenching rate constant when the stick boundary condition rather than the slip boundary condition was applied for estimating the diffusion coefficients. In nonpolar solvent like cyclohexane fluorescence quenching is adequately explained by the diffusion controlled process within the experimental error, but in acetonitrile the quenching rate constant was estimated to be consistently smaller than the diffusion limited rate constant. This may suggest that fluorescence quenching of coumarin dyes be affected not only by the molecular diffusion but also by the intramoleccular process such as charge separation.

• Proceedings of the Korean Ceranic Society Conference
• /
• 2000.10a
• /
• pp.109.1-109
• /
• 2000

• Mycobiology
• /
• v.46 no.4
• /
• pp.448-451
• /
• 2018

Fungal perylenequinones have photodynamic activity and are promising photosensitizers for photodynamic therapy (PDT). Here, we investigated the bactericidal and antitumor activities of phleichrome from the fungal perylenequinone family in vitro. Photodynamic bactericidal activity of phleichrome was analyzed by agar-well diffusion method under dark and illuminated conditions. The photodynamic antitumor activity of phleichrome was analyzed in MCF-7, HeLa, SW480, and HepG2 human cancer cell lines using in vitro cytotoxicity assays. Photodynamic bactericidal activities against Gram-negative and Gram-positive bacteria were species-specific. Antitumor activity against all tumor cell lines increased under the illuminated condition. Depending on the results of the analyses, Phleichrome has potential for further drug development related to its antibacterial and antitumor activities.

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

• Applied Chemistry for Engineering
• /
• v.9 no.3
• /
• pp.399-403
• /
• 1998

The gelation characteristics of chitosan of different molecular weight were investigated in terms of concentration and temperature of alkari aqueous solution. The average molecular weights and the degrees of deacetylation of the chitosan used were $2.0{\times}10^5$, $5.2{\times}10^5$, $8.2{\times}10^5$ and 85%, respectively. Sodium hydroxide solution was used as a gelation agent. A simple diffusion model was applied to study the gelation rate. The diffusion coefficients of the gelation agent in the chitosan gel increased with increasing its concentration, temperature of the casting solution, and molecular weight of the chitosan.

• Bulletin of the Korean Chemical Society
• /
• v.28 no.10
• /
• pp.1689-1696
• /
• 2007

Equilibrium molecular dynamics (EMD) simulations are used to evaluate the transport coefficients of argonkrypton mixtures at two liquid states (state A: 94.4 K and 1 atm; state B: 135 K and 39.5 atm) via modified Green-Kubo formulas. The composition dependency of the volume at state A obeys close to the linear model for ideal liquid mixture, while that at state B differs from the linear model probably due to the high pressure. The radial distribution functions for the Ar-Kr mixture (x = 2/3) show a mixing effect: the first peak of g11 is higher than that of g(r) for pure Ar and the first peak of g22 is lower than that of g(r) for pure Kr. An exponential model of engineering correlation for diffusion coefficient (D) and shear viscosity (η) is superior to the simple linear model for ideal liquid mixtures. All three components of thermal conductivity (λpm, λtm, and λti) at state A and hence the total thermal conductivity decrease with the increase of x. At state B, the change in λtm is dominant over those in λpm and λti, and hence the total thermal conductivity decrease with the increase of x.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2011.02a
• /
• pp.433-433
• /
• 2011

Since the concept of graphene was established, it has been intensively investigated by researchers. The unique characteristics of graphene have been reported, the graphene attracted a lot of attention for material overcomes the limitations of existing semiconductor materials. Because of these trends, economical fabrication technique is becoming more and more important topic. Especially, the epitaxial growth method by sublimating the silicon atoms on Silicon carbide (SiC) substrate have been reported on the mass production of high quality graphene sheets. Although SiC exists in a variety of polytypes, the 3C-SiC polytypes is the only polytype that grows directly on Si substrate. To practical use of graphene for electronic devices, the technique, forming the graphene on 3C-SiC(111)/Si structure, is much helpful technique. In this paper, we report on the growth of graphene on 3C-SiC(111) surface. To investigate the morphology of formed graphene on the 3C-SiC(111) surface, the radial distribution function (RDF) was calculated using molecular dynamics (MD) simulation. Through the comparison between the kinetic energies and the diffusion energy barrier of surface carbon atoms, we successfully determined that the graphitization strongly depends on temperature. This graphitization occurs above the annealing temperature of 1500K, and is also closely related to the behavior of carbon atoms on SiC surface. By analyzing the results, we found that the diffusion energy barrier is the key parameter of graphene growth on SiC surface.

• Korean Journal of Materials Research
• /
• v.16 no.2
• /
• pp.92-98
• /
• 2006

Molecular dynamics simulations were performed to study interface structures between an $Al_2O_3$ crystalline phase and a interface phase of $CaAl_2Si_2O_8$. We calculated atomic structures and excess interface energies in systems with different thicknesses of the interface film. It was found that excess interface energies at first readily decreased with increasing film thickness, but increased for larger thicknesses of more than 2 nm. The excess energies of $Al_2O_3/CaAl_2Si_2O_8$ interfaces exhibit a minimum at a thickness around 1 nm. In this range of film thicknesses, the atoms in the interface film show a short-range ordered structure and slow diffusion rather than the random structure and rapid diffusion expected to an observation of an equilibrium thickness for interface films in ceramics.

• Bulletin of the Korean Chemical Society
• /
• v.12 no.3
• /
• pp.309-315
• /
• 1991

The thermal transport coefficients-the self-diffusion coefficient, shear viscosity, and thermal conductivity-of liquid argon at 94.4 K and 1 atm are calculated by non-equilibrium molecular dynamics (NEMD) simulations of a Lennard-Jones potential and compared with those obtained from Green-Kubo relations using equilibrium molecular dynamics (EMD) simulations and with experimental data. The time-correlation functions-the velocity, pressure, and heat flux auto-correlation functions-of liquid argon obtained from the EMD simulations show well-behaved smooth curves which are not oscillating and decaying fast around 1.5 ps. The calculated self-diffusion coefficient from our NEMD simulation is found to be approximately 40% higher than the experimental result. The Lagrange extrapolated shear viscosity is in good agreement with the experimental result and the asymptotic formula of the calculated shear viscosities seems to be an exponential form rather than the square-root form predicted by other NEMD studies of shear viscosity. The agreement for thermal conductivity between the simulation results (NEMD and EMD) and the experimental result is within statistical error. In conclusion, through our NEMD and EMD simulations, the overall agreement is quite good, which means that the Green-Kubo relations and the NEMD algorithms of thermal transport coefficients for simple liquids are valid.

• BMB Reports
• /
• v.54 no.3
• /
• pp.157-163
• /
• 2021

The transient interactions between cellular components, particularly on membrane surfaces, are critical in the proper function of many biochemical reactions. For example, many signaling pathways involve dimerization, oligomerization, or other types of clustering of signaling proteins as a key step in the signaling cascade. However, it is often experimentally challenging to directly observe and characterize the molecular mechanisms such interactions-the greatest difficulty lies in the fact that living cells have an unknown number of background processes that may or may not participate in the molecular process of interest, and as a consequence, it is usually impossible to definitively correlate an observation to a well-defined cellular mechanism. One of the experimental methods that can quantitatively capture these interactions is through membrane reconstitution, whereby a lipid bilayer is fabricated to mimic the membrane environment, and the biological components of interest are systematically introduced, without unknown background processes. This configuration allows the extensive use of fluorescence techniques, particularly fluorescence fluctuation spectroscopy and single-molecule fluorescence microscopy. In this review, we describe how the equilibrium diffusion of two proteins, K-Ras4B and the PH domain of Bruton's tyrosine kinase (Btk), on fluid lipid membranes can be used to determine the kinetics of homodimerization reactions.