• Genomics & Informatics
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• v.15 no.4
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• pp.142-146
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• 2017

More effective production of human insulin is important, because insulin is the main medication that is used to treat multiple types of diabetes and because many people are suffering from diabetes. The current system of insulin production is based on recombinant DNA technology, and the expression vector is composed of a preproinsulin sequence that is a fused form of an artificial leader peptide and the native proinsulin. It has been reported that the sequence of the leader peptide affects the production of insulin. To analyze how the leader peptide affects the maturation of insulin structurally, we adapted several in silico simulations using 13 artificial proinsulin sequences. Three-dimensional structures of models were predicted and compared. Although their sequences had few differences, the predicted structures were somewhat different. The structures were refined by molecular dynamics simulation, and the energy of each model was estimated. Then, protein-protein docking between the models and trypsin was carried out to compare how efficiently the protease could access the cleavage sites of the proinsulin models. The results showed some concordance with experimental results that have been reported; so, we expect our analysis will be used to predict the optimized sequence of artificial proinsulin for more effective production.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.24-25
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• 2011

Molecular self-assembly has several advantages over other nanofabrication methods. Molecular building blocks ensure ultrafine pattern precision, parallel structure formation allows for mass production and a variety of three-dimensional structures are available for fabricating complex structures. Nevertheless, the molecular interaction for self-assembly generally relies on weak forces such as van der Waals force, hydrogen bonding, or hydrophobic interaction. Due to the weak interaction, the structure formation is usually slow and the degree of ordering is low in a self-assembled structure. To promote self-assembly, directed assembly methods employing prepatterned substrates or external fields have been developed and gathered a great deal of technological attention as a next generation nanofabrication process. In this presentation a variety of directed assembly methods for soft nanomaterials including block copolymers, peptides and carbon nanomaterials will be introduced. Block copolymers are representative self-assembling materials extensively utilized in nanofabrication. In contrast to colloid assembly or anodized metal oxides, various shapes of nanostructures, including lines or interconnected networks, can be generated with a precise tunability over their shape and size. Applying prepatterned substrates$^{1,2}$ or introducing thickness modulation$^3$ to block copolymer thin films allowed for the control over the orientational and positional orderings of self-assembled structures. The nanofabrication processes for metals, semiconductors$^4$, carbon nanotubes$^{5,6}$, and graphene$^{6,7}$ templating block copolymer self-assembly will be presented.

• Proceedings of the KSME Conference
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• 2003.11a
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• pp.228-232
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• 2003

It has recently been shown that the instability of thin film of a nanoscale can be used in the processes of building nano-size structures, which have potential practical importance in nanotechnology. Molecular dynamics simulation is conducted to probe the thin fluid film of a nano-size and its dynamic behavior during destabilization and structure formation. Non-continuum characteristics are shown in the properties like pressure tensor, viscosity, and thermal conductivity. The thermocapillary force induces a slow growth of long waves in the scale considered. A long-range interaction with the solid wall induces vertical structures, whose formation time and space between neighbors are proportional to the strength of the interaction.

• Macromolecular Research
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• v.8 no.3
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• pp.125-130
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• 2000

Resorcinol formaldehyde resins are synthesized by polycondensation of resorcinol with formal-dehyde and have various structures by the condensation type. The influence of polycondensation type on the stability and structure of the resorcinol formaldehyde resin was studied by molecular mechanics and molecular dynamics. The resins formed by 2,6-polycondensation and 4,6-polycondensationwith head-to-tail orientations have structures of intramolecular hydrogen bonds between 1-hydroxyl groups and between outer hydroxyl groups of the adjacent resorcinols, respectively. The resin formed by 2,6-polycon-densation with head-to-head orientation has a structure that inner hydroxyl groups cluster in the center of the molecule. Energetical stability of the resin is affected by both the intramolecular hydrogen bonds and the steric' hindrance by phenyl group.

• Proceedings of the Korean Vacuum Society Conference
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• 2012.02a
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• pp.129-129
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• 2012

Covalently bonded halogen ligands possess unusual charge distributions, attracting both electrophilic and nucleophilic molecular ligands to form halogen bonds. In many biochemical systems, halogen bonds coexist with hydrogen bonds, being complementary to them due to their similar bond strength and dissimilardirectionality. In this study, we directly visualize the individual molecular configuration of chlorinated 1,5-dichloroanthraquinone and brominated 1,5-dibromoanthraquinone molecules on Au(111) using scanning tunneling microscopy. The precise arrangements of observed molecular structures were explained in the context of halogen and hydrogen bonds. We discuss the distances and the strengths of the observed halogen and hydrogen bonds, which are consistent with previous bulk data.

• Bulletin of the Korean Chemical Society
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• v.30 no.4
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• pp.857-862
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• 2009

We model lattice-mismatched group III-V semiconductor $In_{x}Ga_{1-x}$ alloys with the three-parameter anharmonic Kirkwood-Keating potential, which includes realistic distortion effect by introducing anharmonicity. Although the potential parameters were determined based on optical properties of the binary parent alloys InAs and GaAs, simulated dielectric functions, reflectance, and Raman spectra of alloys agree excellently with experimental data for any arbitrary atomic composition. For a wide range of atomic composition, InAs- and GaAs-bond retain their respective properties of binary parent crystals despite lattice and charge mismatch. It implies that use of the anharmonic Kirkwood-Keating potential may provide an optimal model system to investigate diverse and unique optical properties of quantum dot heterostructures by circumventing potential parameter searches for particular local structures.

• Bulletin of the Korean Chemical Society
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• v.17 no.12
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• pp.1112-1117
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• 1996

The electronic structures of twenty-seven isomers of a macrocyclic fulleropyrrolidine are investigated with semi-empirical extended Huckel (EH) molecular orbital method. The geometry of each isomer is determined by the molecular mechanics and dynamics methods based on UFF (universal force field) empirical force field. The calculated geometries, such as the carbon-carbon distances of the fullerene moiety, are in good agreement with those of related fullerene derivatives. The EH calculation shows that the formation of macrocyclic pyrrolidine ring on fullerene moiety results in the reduction of the HOMO-LUMO energy gap. From the graphical analysis of the DOS (density of states), PDOS (projected DOS), and MOOP (molecular orbital overlap population) curves, we can find that this reduction is due to splitting of the HOMO of fullerene moiety, which results from the symmetry-breaking and the distortion of the buckminsterfullerene framework from its ideal icosahedral structure.

• Nuclear Engineering and Technology
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• v.54 no.8
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• pp.2783-2791
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• 2022

Molecular dynamics simulations were performed to predict the behavior of graphite atoms under neutron irradiation using large-scale atomic/molecular massively parallel simulator (LAMMPS) package with adaptive intermolecular reactive empirical bond order (AIREBOM) potential. Defect structures of graphite were compared with results from previous studies by means of density functional theory (DFT) calculations. The quantitative relation between primary knock-on atom (PKA) energy and irradiation damage on graphite was calculated. and the effect of PKA direction on the amount of defects is estimated by counting displaced atoms. Defects are classified into four groups: structural defects, energy defects, vacancies, and near-defect structures, where a structural defect is further subdivided into six types by decision tree method which is one of the supervised machine learning techniques.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.303-303
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• 2011

Orderings and electronic structures of organic molecules on metal substrates have been studied due to possible applications in electronic devices. In molecular systems, delocalized pi-electrons play important roles in the adsorption behaviors and electronic structures. We studied the adsorption and electronic structures of Co-Porphyrin molecules on Au(111) using scanning tunneling microscopy (STM) and spectroscopy (STS) at low temperature. Molecules form closely packed two-dimensional islands on Au(111) surface with two different types, having different shape evolutions in our energy-dependent STM observations. The Kondo resonance state, occurred by spin exchange interaction between the Co center atom and conduction electrons in the metal substrate, was observed in one type, while it was absent in the other type in scanning tunneling spectroscopy measurements. Possible origins of two molecular shapes will be discussed.