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Saccharide Insertion in Carbon Nanotube: Molecular Dynamics Simulation Studies
이정민,장락우 대한화학회 2020 Bulletin of the Korean Chemical Society Vol.41 No.4
We have investigated the insertion process of saccharides into nanopores using atomistic molecular dynamic (MD) simulations of the model systems, which consist of three different saccharides (α-d-glucose, sucrose, and ?-cyclodextrin) and carbon nanotubes (CNTs) with various diameters (13.6?21.7 Å). We have observed that unlike small saccharides such as α-d-glucose and sucrose, ?-cyclodextrin shows a nonmonotonic behavior in the absorption free energy with the minimum at the CNT pore of about 16?Å in diameter. In addition, we have decomposed the system energy into several components to understand the driving force of the saccharide insertion into nanopores and found that the nonmonotonic insertion free energy is attributed to several contributions such as the dehydration and the conformational change of saccharides, van der Waals interactions among saccharides, CNT and water molecules, and the entropic effects of water molecules.
Effect of Pore Geometry on Gas Adsorption: Grand Canonical Monte Carlo Simulation Studies
이은지,장락우,한지형,정택동 대한화학회 2012 Bulletin of the Korean Chemical Society Vol.33 No.3
In this study, we investigated the pure geometrical effect of porous materials in gas adsorption using the grand canonical Monte Carlo simulations of primitive gas-pore models with various pore geometries such as planar, cylindrical, and random pore geometries. Although the model does not possess atomistic level details of porous materials, our simulation results provided many insightful information in the effect of pore geometry on the adsorption behavior of gas molecules. First, the surface curvature of porous materials plays a significant role in the amount of adsorbed gas molecules: the concave surface such as in cylindrical pores induces more attraction between gas molecules and pore, which results in the enhanced gas adsorption. On the contrary, the convex surface of random pores gives the opposite effect. Second, this geometrical effect shows a nonmonotonic dependence on the gas-pore interaction strength and length. Third, as the external gas pressure is increased, the change in the gas adsorption due to pore geometry is reduced. Finally, the pore geometry also affects the collision dynamics of gas molecules. Since our model is based on primitive description of fluid molecules, our conclusion can be applied to any fluidic systems including reactant-electrode systems.
Plasma‐induced Water Pore Formation in Model Cell Membranes: Molecular Dynamics Simulation
김성한,이준열,장락우 대한화학회 2018 Bulletin of the Korean Chemical Society Vol.39 No.4
We have investigated the mechanism of plasma‐induced water pore formation in model 1,2‐dioleoyl‐sn‐glycero‐3‐phosphocholine (DOPC) bilayer membrane systems using atomistic molecular dynamics (MD) simulations. Oxidized by reactive oxygen species generated upon the plasma treatment, unsaturated hydrocarbon tails of DOPC lipids are converted into shortened hydrocarbon tails with terminal groups such as peroxide or aldehyde. Among them, the lipids with both hydrocarbon tails oxidized into aldehyde groups are particularly susceptible to the stable water pore formation. By analyzing the water pore formation dynamics, lipid escape, and lipid clustering for the plasma‐damaged DOPC membrane systems, we have found that a stable water pore is formed in the membrane region where the plasma‐damaged lipids are highly concentrated or locally clustered. In the plasma‐damaged lipid‐rich region, a continuous water channel through the membrane is easily established with the help of the terminal aldehyde groups in the tails of damaged lipids, and it continuously grows with time to form a stable water pore. The rapid local clustering or domain formation of the plasma‐damaged lipids is due to both the hydrophobic mismatch between normal and oxidized DOPC lipids and enhanced lateral diffusion of the oxidized lipids in the membrane. We have also observed that the onset concentration of oxidized lipids for the stable water pore formation is approximately 30% in the model DOPC membrane systems.
Seonghan Kim,장락우 대한화학회 2016 Bulletin of the Korean Chemical Society Vol.37 No.7
Full atomistic molecular dynamics simulations have been performed for model mixture bilayer membrane systems consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) phospholipids to understand the effects of two essential parameters such as lipid composition and temperature on the structural, dynamical, and phase behavior of mixture membrane systems. Although pure DSPC membranes are in the gel-like (Lβ ′ or P β ′) phase at 323 K, raising the temperature by only 10 K or replacing 20% of DSPC lipids by DOPC lipids can change the gel-like phase into the completely liquid-crystalline phase (L α ). This phase change is accompanied by dramatic change in both structural properties such as area per lipid, membrane thickness, deuterium order parameter, and tail angle distribution, and dynamics properties such as mobility map. We also observe that the full width at half-maximum (FWHM) data of tail angle distribution as well as area per lipid (or membrane thickness) can be used as order parameters for the membrane phase transition.
Biochemical and Molecular Modeling Studies of the Interaction between Human CEP55 and TEX14
김희정,Hyunook Kim,장락우,유연규,이형호 대한화학회 2016 Bulletin of the Korean Chemical Society Vol.37 No.6
To arrest the normal cell abscission in mammalian cells, testis-expressed gene 14 (TEX14) competitively binds to the midbody protein centrosomal protein 55 kDa (CEP55). To gain further insights into the interactions between CEP55 and TEX14 (or ALIX), we performed molecular modeling studies. Molecular dynamics simulation indicated that CEP55-EABR (ESCRT and ALIX-binding region) formed a stable coiled coil in the absence of TEX14 (or ALIX) peptides. We also identified interaction sites between CEP55-EABR and TEX14 (or ALIX) responsible for the stability of the complex by calculating H-bonding and van der Waals interaction maps. Biochemical studies also suggested that CEP55 (residues 230–464) forms an elongated coiled coil. The overall architecture of CEP55 and detailed analyses of the interactions between CEP55-EABR and TEX14 (or ALIX) gives more specific atomistic details about interactions between CEP55 and TEX14 (or ALIX), which is not easy to identify in experiments.