• Genomics & Informatics
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• v.20 no.1
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• pp.11.1-11.20
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• 2022

Vibrio harveyi belongs to the Vibrio genus that causes vibriosis in marine and aquatic fish species through double-stranded DNA virus replication. In humans, around 12 Vibrio species can cause gastroenteritis (gastrointestinal illness). A large amount of virus particles can be found in the cytoplasm of infected cells, which may cause death. Despite these devastating complications, there is still no cure or vaccine for the virus. As a result, we used an immunoinformatics approach to develop a multi-epitope vaccine against most pathogenic hemolysin gene of V. harveyi. The immunodominant T- and B-cell epitopes were identified using the hemolysin protein. We developed a vaccine employing three possible epitopes: cytotoxic T-lymphocytes, helper T-lymphocytes, and linear B-lymphocyte epitopes, after thorough testing. The vaccine was developed to be antigenic, immunogenic, and non-allergenic, as well as having a better solubility. Molecular dynamics simulation revealed significant structural stiffness and binding stability. In addition, the immunological simulation generated by computer revealed that the vaccination might elicit immune reactions in the actual life after injection. Finally, using Escherichia coli K12 as a model, codon optimization yielded ideal GC content and a higher codon adaptation index value, which was then included in the cloning vector pET2+ (a). Altogether, our experiment implies that the proposed peptide vaccine might be a good option for vibriosis prophylaxis.

• Macromolecular Research
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• v.12 no.2
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• pp.178-188
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• 2004

We performed molecular dynamics (MD) simulations at 300 K on a series of poly(benzyl ether) (PBE) dendrimers having a different core functionalities. We used the rotational isomeric state Metropolis Monte Carlo (RMMC) method to construct the initial configuration in a periodic boundary cell (PBC) before the MD simulations were undertaken. To elucidate the effects that the structural features have on the chain dimension, the overall internal structure, and the morphology, we monitored the radii of gyration, R$\sub$g/ and the conformational changes during the simulations. The PBE dendrimers in a glassy state adopted less-extended structures when compared with the conformations obtained from the RMMC calculations. We found that R$\sub$g/ of the PBE dendrimer depends on the molecular weight, M, according to the relation, R$\sub$g/∼M$\^$0.22/. The radial distributions of the dendrimers were developed identically in the PBC, irrespective of the core functionality. A gradual decrease in radial density resulted from the fact that the terminal branch ends are distributed all over the molecule, except for the core region.

• Smart Structures and Systems
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• v.13 no.4
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• pp.685-709
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• 2014

Carbon nanotubes are due to their outstanding mechanical properties destined for a wide range of possible applications. Since the knowledge of the material behavior is vital regarding the possible applications, experimental and theoretical studies have been conducted to investigate the properties of this promising material. The aim of the present research is the calculation of mechanical properties and of the mechanical behavior of single wall carbon nanotubes (SWCNTs). The numerical simulation was performed on basis of a molecular mechanics approach. Within this approach two different issues were taken into account: (i) the nanotube geometry and (ii) the modeling of the covalent bond. The nanotube geometry is captured by two different approaches, the roll-up and the exact polyhedral model. The covalent bond is modeled by a structural molecular mechanics approach according to Li and Chou. After a short introduction in the applied modeling techniques, the results for the Young's modulus for several SWCNTs are presented and are discussed extensively. The obtained numerical results are compared to results available in literature and show an excellent agreement. Furthermore, deviations in the geometry stemming from the different models are given and the resulting differences in the numerical findings are shown. Within the investigation of the deformation mechanisms occurring in SWCNTs, the basic contributions of each individual covalent bond are considered. The presented results of this decomposition provide a deeper understanding of the governing deformation mechanisms in SWCNTs.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.32-34
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• 2000

Computational chemistry is a discipline using computational methods for the calculation of molecular structure, properties, and reaction or for the simulation of molecular behavior. Relating and turning the complexity of data from genomics, high-throughput screening, combinatorial chemical synthesis, gene-expression investigations, pharmacogenomics, and proteomics into useful information and knowledge is the primary goal of bioinformatics. In particular, the structure-based molecular design is one of essential fields in bioinformatics and it can be called as structural bioinformatics. Therefore, the conformational analysis for proteins and peptides using the techniques of computational chemistry is expected to play a role in structural bioinformatics. There are two major computational methods for conformational analysis of proteins and peptides; one is the molecular orbital (MO) method and the other is the force field (or empirical potential function) method. The MO method can be classified into ab initio and semiempirical methods, which have been applied to relatively small and large molecules, respectively. However, the improvement in computer hardwares and softwares enables us to use the ab initio MO method for relatively larger biomolecules with up to v100 atoms or ∼800 basis functions. In order to show how computational chemistry can be used in structural bioinformatics, 1 will present on (1) cis-trans isomerization of proline dipeptide and its derivatives, (2) positional preference of proline in ${\alpha}$-helices, and (3) conformations and activities of Arg-Gly-Asp-containing tetrapeptides.

• Journal of Korean Society for Atmospheric Environment
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• v.27 no.6
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• pp.681-691
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• 2011

The size distributions of smoke particles from fire are prerequisite for the studies on fire detection and adverse health effects. Above the flame of the fire, coagulation dominates and the smoke particles grow from 1 to 50 nm up to 100 to 3,000 nm, sizes ranging from the free-molecular regime to the continuum regime. The characteristics of the agglomeration of the smoke particles are well known, independently for each of the free-molecular and continuum regimes. However, there are not many systematic studies in the entire regime by the complexity of the mechanisms. The purpose of this work is to find the characteristics of the development of the size distribution of smoke particles by agglomeration in the entire size range covering the free-molecular regime, via transition regime, to the near-continuum and continuum regime for each variation of parameters such as fractal dimension, primary particle size and dimensionless coagulation time. In this work, the dynamic equation for the discrete-size spectrum of the particles was solved using a nodal method based on the modification of a sectional method. In the calculation, the collision frequency function for the entire regime, which is derived by using the concept of collision volume and general enhancement function, was applied. The self-preserving size distribution for the entire regime is compared with the ones for the free-molecular or continuum regimes for each variation of the parameters.

• Bulletin of the Korean Chemical Society
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• v.29 no.3
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• pp.590-594
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• 2008

The inclusion complexes of cyclodextrins (CDs) with flavones in aqueous solution were investigated by phase solubility measurements. The effect of b -cyclodextrin (b -CD), heptakis (2,6-di-O-methyl) b -cyclodextrin (DM-b -CD) and 2-hydroxypropyl-b -cyclodextrin (HP-b -CD) on the aqueous solubility of three flavones, namely, chrysin, apigenin and luteolin was investigated, respectively. Solubility enhancements of all flavones obtained with three CDs followed the rank order: HP-b -CD > DM-b -CD > b -CD, and besides, CDs show higher stability constant on luteolin than that on others flavones. 1H-nuclear magnetic resonance (NMR) spectroscopy and molecular modeling was used to help establish the model of interaction of the CDs with luteolin. NMR spectroscopic analysis suggested that A-C ring, and part of the B ring of luteolin display favorable interaction with the CDs, which was also confirmed by docking studies based on the molecular simulation. The observed augmentation of solubility of luteolin by three CDs was explained by the difference of electrostatic interaction of each complex, especially hydrogen bonding.

• Transactions on Electrical and Electronic Materials
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• v.5 no.6
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• pp.227-232
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• 2004

We investigated a nonvolatile nanomemory element based on boron nitride nanopeapods using molecular dynamics simulations. The studied system was composed of two boron-nitride nanotubes filled Cu electrodes and fully ionized endo-fullerenes. The two boron-nitride nanotubes were placed face to face and the endo-fullerenes came and went between the two boron-nitride nanotubes under alternatively applied force fields. Since the endo-fullerenes encapsulated in the boron-nitride nanotubes hardly escape from the boron-nitride nanotubes, the studied system can be considered to be a nonvolatile memory device. The minimum potential energies of the memory element were found near the fullerenes attached copper electrodes and the activation energy barrier was $3{\cdot}579 eV$. Several switching processes were investigated for external force fields using molecular dynamics simulations. The bit flips were achieved from the external force field of above $3.579 eV/{\AA}$.

• Bulletin of the Korean Chemical Society
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• v.30 no.11
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• pp.2723-2728
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• 2009

The conformational properties of oligosaccharides are important to understand carbohydrate-protein interactions. A trimannoside, methyl 3,6-di-O-($\alpha$-D-Man)-$\alpha$-D-Man (TRIMAN) is a basic unit of N-linked oligosaccharides. This TRIMAN moiety was further modified by GlcNAc (BISECT), which is important to biological activity of N-glycan. To characterize the trimannoside and its bisecting one we performed a molecular dynamics simulation in water. The resulting models show the conformational transition with two major and minor conformations. The major conformational transition results from the $\omega$ angle transition; another minor transition is due to the $\psi$ angle transition of $\alpha$ (1 $\rightarrow$ 6) linkage. The introduction of bisecting GlcNAc on TRIMAN made the different population of the major and minor conformations of the TRIMAN moiety. Omega ($\omega$) angle distribution is largely changed and the population of gt conformation is increased in BISECT oligosaccharide. The inter-residue hydrogen bonds and water bridges via bisecting GlcNAc residue make alterations on the local and overall conformation of TRIMAN moiety. These changes of conformational distribution for TRIMAN moiety can affect the overall conformation of N-glycan and the biological activity of glycoprotein.

• Bulletin of the Korean Chemical Society
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• v.17 no.8
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• pp.700-706
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• 1996

We present the results of molecular dynamics simulations of monolayers of long-chain alkyl thiol [S(CH2)15CH3] molecules on an air-solid interface using the extended collapsed atom model for the chain-molecule and a gold surface for the solid surface. Several molecular dynamics simulations have been performed on monolayers with areas per molecule ranging from 18.30 to 32.10 Å2/molecule. It is found that there exist three possible transitions: a continuous transition characterized by a change in molecular configuration without change in lattice structure, a sudden transition characterized by the distinct lattice defects and perfect islands, and a third transition characterized by the appearance of a random, liquid-like state. The analysis of probability distributions of the segments shows that the structure of the chain-molecules at the air-solid interface is completely different from that at the air-water interface in the view of the degree of overlap of the probability distributions of the neighbor segments. The calculated diffusion coefficients of the chain-molecules on the monolayers seem to be not directly related to any one of the three transitions. However, the large diffusion of the molecules enhanced by the increment of the area per molecule may induce the second transition.

• Proceedings of the KSME Conference
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• 2005.11a
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• pp.231.2-231.2
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• 2005