• ALGAE
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• v.38 no.4
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• pp.295-306
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• 2023

Human coronavirus diseases, particularly severe acute respiratory syndrome coronavirus 2, still remain a persistent public health issue, and many recent studies are focusing on the quest for new leads against coronaviruses. To contribute to this growing pool of knowledge and explore the available marine natural products against coronaviruses, this study investigated the antiviral effects of fucoxanthin isolated from Sargassum siliquastrum-a brown alga found on Jeju Island, South Korea. The antiviral effects of fucoxanthin were confirmed in severe acute respiratory syndrome coronavirus 2-infected Vero cells, and its structural characteristics were verified in silico using molecular docking and molecular dynamic simulations and in vitro colorimetric method. Fucoxanthin inhibited the infection in a concentration-dependent manner, without showing cytotoxicity. Molecular docking simulations revealed that fucoxanthin binds to the angiotensinconverting enzyme 2-spike protein (binding energy -318.306 kcal mol^-1) and main protease (binding energy -205.118 kcal mol^-1). Moreover, molecular dynamic simulations showed that fucoxanthin remains docked to angiotensin-converting enzyme 2-spike protein for 20 ns, whereas it breaks away from main protease after 3 ns. Also, the in silico prediction of the fucoxanthin was verified through the in vitro colorimetric method by inhibiting the binding between angiotensinconverting enzyme 2 and spike protein in a concentration-dependent manner. These results indicate that fucoxanthin exhibits antiviral effects against severe acute respiratory syndrome coronavirus 2 by blocking the entry of the virus. Therefore, fucoxanthin from S. siliquastrum can be a potential candidate for treating coronavirus infection.

• Journal of the Korean Society of Propulsion Engineers
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• v.19 no.6
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• pp.54-63
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• 2015

We present a microscopic understanding of the chemical erosion due to combustion product on the nozzle throat using molecular dynamics simulations. The present erosion process consists of molecule-addition step and equilibrium step. First, either $CO_2$ or $H_2O$ are introduced into the system with high velocity to provoke the collision with graphite surface. Then, the equilibrium simulation is followed. The collision-included dissociation and its influence on the erosion is emphasized and the present molecular observations are compared with the macroscopic chemical reaction model.

• Bulletin of the Korean Chemical Society
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• v.25 no.7
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• pp.1061-1064
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• 2004

Molecular visualization software has the common objective of manipulation and interpretation of data from numerical simulations. They visualize many complicated molecular structures with personal computer and workstation, to help analyze a large quantity of data produced by various computational methods. However, users are often discouraged from using these tools for visualization and analysis due to the difficult and complicated user interface. In this regard, we have developed an easy-to-use three-dimensional molecular visualization and analysis program named POSMOL. This has been developed on the Microsoft Windows platform for the easy and convenient user environment, as a compact program which reads outputs from various computational chemistry software without editing or changing data. The program animates vibration modes which are needed for locating minima and transition states in computational chemistry, draws two and three dimensional (2D and 3D) views of molecular orbitals (including their atomic orbital components and these partial sums) together with molecular systems, measures various geometrical parameters, and edits molecules and molecular structures.

• Korean Journal of Materials Research
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• v.20 no.9
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• pp.478-482
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• 2010

A series of molecular dynamic (MD), finite element (FE) and ab initio simulations are carried out to establish suitable modeling schemes for the continuum-based analysis of aluminum matrix nanocomposites reinforced with carbon nanotubes (CNTs). From a comparison of the MD with FE models and inferences based on bond structures and electron distributions, we propose that the effective thickness of a CNT wall for its continuum representation should be related to the graphitic inter-planar spacing of 3.4${\AA}$. We also show that shell element representation of a CNT structure in the FE models properly simulated the carbon-carbon covalent bonding and long-range interactions in terms of the load-displacement behaviors. Estimation of the effective interfacial elastic properties by ab initio simulations showed that the in-plane interfacial bond strength is negligibly weaker than the normal counterpart due to the nature of the weak secondary bonding at the CNT-Al interface. Therefore, we suggest that a third-phase solid element representation of the CNT-Al interface in nanocomposites is not physically meaningful and that spring or bar element representation of the weak interfacial bonding would be more appropriate as in the cases of polymer matrix counterparts. The possibility of treating the interface as a simply contacted phase boundary is also discussed.

• The Bulletin of The Korean Astronomical Society
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• v.36 no.2
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• pp.142.2-142.2
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• 2011

Hydrodynamic simulations of gas clouds in the central hundred parsecs region of the Milky Way that is modeled with a three-dimensional bar potential are presented. Our simulations consider realistic gas cooling and heating, star formation, and supernova feedback. A ring of dense gas clouds forms as a result of $X_1-X_2$ orbit transfer, and our potential model results in a ring radius of ~200 pc, which coincides with the extraordinary reservoir of dense molecular clouds in the inner bulge, the Central Molecular Zone (CMZ). The gas clouds accumulated in the CMZ can reach high enough densities to form stars, and with an appropriate choice of simulation parameters, we successfully reproduce the observed gas mass and the star formation rate (SFR) in the CMZ, ${\sim}2{\times}10^7\;M_{\odot}$ and ${\sim}0.1\;M_{\odot}/yr$. Star formation in our simulations takes place mostly in the outermost $X_2$ orbits, and the SFR per unit surface area outside the CMZ is much lower. These facts suggest that the inner Galactic bulge may harbor a mild version of the nuclear star-forming rings seen in some external disk galaxies. We also find that the stellar population resulting from sustained star formation in the CMZ would be enlogated perpendicularly to the main bar, and this "inner bar" can migrate the gas in the CMZ further down to the central parsecs region.

• Bulletin of the Korean Chemical Society
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• v.17 no.8
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• pp.735-744
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• 1996

We present results of molecular dynamic (MD) simulations for the thermodynamic and structural properties of liquid n-alkanes, from n-butane to n-heptadecane, using three different models Ⅰ-Ⅲ. Two of the three classes of models are collapsed atomic models while the third class is an atomistically detailed model. Model Ⅰ is the original Ryckaert and Bellemans' collapsed atomic model [Discuss. Faraday Soc. 1978, 66, 95] and model Ⅱ is the expanded collapsed model which includes C-C bond stretching and C-C-C bond angle bending potentials in addition to Lennard-Jones and torsional potentials of model Ⅰ. In model Ⅲ all the carbon and hydrogen atoms in the monomeric units are represented explicitly for the alkane molecules. Excellent agreement of the results of our MD simulations of model Ⅰ for n-butane with those of Edberg et al.[J. Chem. Phys. 1986, 84, 6933], who used a different algorithm confirms the validity of our algorithms for MD simulations of model Ⅱ for 14 liquid n-alkanes and of models Ⅰ and Ⅲ for liquid n-butane, n-decane, and n-heptadecane. The thermodynamic and structural properties of models Ⅰ and Ⅱ are very similar to each other and the thermodynamic properties of model Ⅲ for the three n-alkanes are not much different from those of models Ⅰ and Ⅱ. However, the structural properties of model Ⅲ are very different from those of models Ⅰ and Ⅱ as observed by comparing the radial distribution functions, the average end-to-end distances and the root-mean-squared radii of gyrations.

• Bulletin of the Korean Chemical Society
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• v.23 no.1
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• pp.48-52
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• 2002

Using several molecular modeling programs we have performed computer simulations to investigate the complexation behaviors of an ester derivative of p-tert-butylcalix[5]arene (1e) toward a variety of butylammonium ions. Semi-empirical AM1 method was used for calculating the binding energies and the formation enthalpies. MM and CVFF forcefields for molecular mechanics calculations were adapted to express the complexation energies of the host. Molecular dynamics were performed to the calculated complex systems to simulate the ionophoric behavior of the host-guest complexes. The absolute Gibbs free energies of the host (1e) complexed with four kinds of butylammonium ions have been calculated using the Finite Difference Thermodynamic Integration (FDTI) method in Discover. Calculation results show that the trend in complex formation is n-$BuNH_3^+$ > iso-$BuNH_3^+$ >> sec-$BuNH_3^+$ > tert-$BuNH_3^+$, which is in good agreement with the experimental results.

• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2237-2242
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• 2011

Anomalous scaling behaviors such as significantly large growth exponent (${\beta}$) and small reciprocal of dynamic exponent (1/z) values for many molecular crystalline thin films have been reported. In this study, the variation of scaling exponent values and consequent growth behaviors of molecular thin films were more quantitatively analysed using a (1+1)-dimensional surface lateral diffusion model. From these simulations, influence of step edge barriers and grain boundaries of molecular thin films on the various scaling exponent values were elucidated. The simulation results for the scaling exponents were also well consistent with the experimental data for previously reported molecular thin film systems.

• Journal of Integrative Natural Science
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• v.7 no.2
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• pp.75-78
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• 2014

Computer-aided drug design uses computational chemistry to discover, enhance, or study drugs and related biologically active molecules. It is now proved to be effective in reducing costs and speeding up drug discovery. In this short review, we discussed on the importance of combining molecular docking and molecular dynamics simulation methodologies. We also reviewed the importance of protein flexibility, refinement of docked complexes using molecular dynamics and the use of free energy calculations for the calculation of accurate binding energies has been reviewed.

• Journal of the Korean Ceramic Society
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• v.53 no.3
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• pp.295-300
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• 2016

To investigate the thermal conductivity and the structural properties of naturally cooled excimer-laser annealed Si, molecular-dynamics (MD) simulations have been performed. The thermal conductivity of crystalline Si (c-Si) was measured by direct method at 1000 K. Steady-state heat flow was measured using a stationary temperature profile; significant deviations from Fourier's law were not observed. Reliable processes for measuring the thermal conductivity of c-Si were presented. A natural cooling process to admit heat flow from molten Si (l-Si) to c-Si was performed using an MD cell with a size of $48.9{\times}48.9{\times}97.8{\AA}^3$. During the cooling process, the temperature of the bottom $10{\AA}$ of the MD cell was controlled at 300 K. The results suggest that the natural cooling system described the static structural property of amorphous Si (a-Si) well.