• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.268-274
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• 2003

Most currently known molecular structures were determined by X-ray crystallography or Nuclear Magnetic Resonance (NMR). These methods generate a large amount of structure data, even far small molecules, and consist mainly of three-dimensional atomic coordinates. These are useful for analyzing molecular structure, but structure elements at higher level are also needed for a complete understanding of structure, and especially for structure prediction. Computational approaches exist for identifying secondary structural elements in proteins from atomic coordinates. However, similar methods have not been developed for RNA due in part to the very small amount of structure data so far available, and extracting the structural elements of RNA requires substantial manual work. Since the number of three-dimensional RNA structures is increasing, a more systematic and automated method is needed. We have developed a set of algorithms for recognizing secondary and tertiary structural elements in RNA molecules and in the protein-RNA structures in protein data banks (PDB). The present work represents the first attempt at extracting RNA structure elements from atomic coordinates in structure databases. The regularities in the structure elements revealed by the algorithms should provide useful information for predicting the structure of RNA molecules bound to proteins.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.02a
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• pp.280-280
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• 2013

Using both experimentaland theoretical methods, we have investigated the structural and electronic properties of self-assembled two-dimensional organic molecule (hexaaza-triphenylene-hexacarbonitrile, HATCN), which is used as an efficient OLED hole injection material, on Au(111) surfaces. Low-temperature scanning tunneling microscope (STM) measurements revealed that self-assembled linear and hexagonal porous structures are formed at atomic steps and terraces of Au(111), respectively. We also found that the hexagonal porous structure have chirality and forms only small (＜1,000 nm2) phase-separated chiral domains that can easily change their chiral phase in subsequence STM images at 80 K. To explain these observations, we calculated the molecular-molecular and molecule-surface interaction energies by using first-principles density functional theory method. We found that the change of their chiral phase resulted from the competition between the two energies. These results have not only verified our experimental observations, but also revealed the delicate balance between different interactions that caused the self-assembed structures at the surface.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.28 no.1
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• pp.31-41
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• 2002

Proline-rich proteins (PRPs) are major components of human saliva. In order to know the biological roles of PRPs, we explored the expression pattern and functional protein structures of PRPs by the immunohistochemical and various molecular biological methods. Polyclonal antibody against human gPRP was generated from rabbit by the injection of oral exfoliated cells specially treated by urea and SDS buffer. The PRPs began to be expressed both in the acinar cells and ductal cells from the EIDS (Early Intermediate Developmental Stage) of fetal salivary glands and became intense in the salivary epithelium in the LDS (Late Developmental Stage) and adult salivary glands. The polyclonal antibody against the gPRP showed the cross-reactivity with aPRP and bPRP, these results were relevant to the high homology among subtypes of PRP. However, the simulated protein structures of PRPs showed the characteristic repetitive whorling domains except the N-terminal signal peptide. The whorling domains were also contained the multiple amino acids of glutamine and glycine, which may provide the receptor binding or cross-linking sites of PRPs.

• Korean Membrane Journal
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• v.6 no.1
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• pp.16-23
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• 2004

The silica containing carbon (C-SiO$_2$) membranes were fabricated using poly(imide siloxane) (PIS) having -CO- swivel group. The characteristics of porous C-SiO$_2$ structures prepared by the pyrolysis of poly(imide siloxane) were related with the micro-phase separation between the imide block and the siloxane block. Furthermore, the nitrogen adsorption isotherms of the CMS and the C-SiO$_2$ membranes were investigated to define the characteristics of porous structures. The C-SiO$_2$ membranes derived from PIS showed the type IV isotherm and possessed the hysteresis loop, which was associated with the mesoporous carbon structures, while the CMS membranes derived from PI showed the type I isotherm. For the molecular sieving probe, the C-SiO$_2$ membranes pyrolyzed at 550, 600, and 700$^{\circ}C$ showed the O$_2$ permeability of 924, 1076, and 367 Barrer (1 ${\times}$ 10$\^$-10/㎤(STP)cm/$\textrm{cm}^2$$.$s$.$cmHg) and O$_2$/N$_2$ selectivity of 9, 8, and 12.

• Proceedings of the Computational Structural Engineering Institute Conference
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• 2007.04a
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• pp.427-432
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• 2007

In general, the response of bulk material is independent of its size when it comes to considering classical elasticity theory. Because the surface to bulk ratio of the large solids is very small, the influence of surface can be negligible. But the surface effect plays important role as the surface to bulk ratio becomes larger, that is, the contribution of the surface effect must be considered in nano-size elements such as thin film or beam structure. Molecular dynamics computation has been a conventional way to analyze these ultra-thin structures but this method is limited to simulate on the order of $10^6-10^8$ atoms for a few nanoseconds, and besides, very time consuming. Analysis of structures in submicro to micro range(thin-film, wire etc.) is difficult with classical molecular dynamics due to the restriction of computing resources and time. Therefore, in this paper, the continuum-based method is considered to simulate the overall physical and mechanical properties of the structures in nano-scale, especially, for the thin-film.

• Nuclear Engineering and Technology
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• v.55 no.6
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• pp.2147-2157
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• 2023

The aggregate-forming minerals in concrete undergo volume swelling and microstructure change under neutron irradiation, leading to degradation of physical and mechanical properties of the aggregates and concrete. A comprehensive investigation of volume change and elastic property variation of major aggregate-forming minerals is still lacking, so molecular dynamics simulations have been employed in this paper to improve the understanding of the degradation mechanisms. The results demonstrated that the densities of the selected aggregate-forming minerals of similar atomic structure and chemical composition vary in a similar trend with deposited energy due to the similar amorphization mechanism. The elastic tensors of all silicate minerals are almost isotropic after saturated irradiation, while those of irradiated carbonate minerals remain anisotropic. Moreover, the elastic modulus ratio versus density ratio of irradiated minerals is roughly following the density-modulus scaling relationship. These findings could further provide basis for predicting the volume and elastic properties of irradiated concrete aggregates in nuclear facilities.

• BMB Reports
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• v.37 no.2
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• pp.177-184
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• 2004

The Crustacean hyperglycemic hormone (CHH) has been shown to exist as multiple molecular forms in several crustacean species. In Penaeus monodon, a gene encoding CHH (so-called Pem-CHH1) was recently described. In this study, the molecular structures of two other CHH genes (Pem-CHH2 and Pem-CHH3) are reported. Both the Pem-CHH2 and Pem-CHH3 genes contain three exons that are separated by two introns that are similar to the structure of other genes in the same family. An analysis of the upstream nucleotide sequences of each Pem-CHH gene has identified the putative promoter element (TATA box) and putative binding sites for several transcription factors. The binding sites for CREB, Pit-1, and AP-1 were found upstream of all three Pem-CHH genes. A Southern blot analysis showed that at least one copy of each Pem-CHH gene was located within the same 10 kb genomic DNA fragment. These results suggest that the CHH genes are arranged in a cluster in the genome of P. monodon, and that their expression may be modulated by similar mechanisms.

• Journal of the Korean Vacuum Society
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• v.11 no.1
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• pp.59-67
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• 2002

The structures and properties of Cu nanowires have been investigated using molecular dynamics simulations. Cylindrical multi-shell Cu nanowires maintain their structures at room temperature and their structural properties are different from the structural properties of nanowires with face-centered-cubic structure. The results from nanopillar and tensile testing of cylindrical multi-shell Cu nanowire showed structures related to pentagonal needle-like crystal structures. Since the subunits of pentagonal nanowire with needle-like crystal are face-centered-cubic structure, pentagonal multi-shell nanowires are stable one-dimensional structures in nanostructured materials.

• BMB Reports
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• v.54 no.10
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• pp.489-496
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• 2021

Chromatin has highly organized structures in the nucleus, and these higher-order structures are proposed to regulate gene activities and cellular processes. Sequencing-based techniques, such as Hi-C, and fluorescent in situ hybridization (FISH) have revealed a spatial segregation of active and inactive compartments of chromatin, as well as the non-random positioning of chromosomes in the nucleus, respectively. However, regardless of their efficiency in capturing target genomic sites, these techniques are limited to fixed cells. Since chromatin has dynamic structures, live cell imaging techniques are highlighted for their ability to detect conformational changes in chromatin at a specific time point, or to track various arrangements of chromatin through long-term imaging. Given that the imaging approaches to study live cells are dramatically advanced, we recapitulate methods that are widely used to visualize the dynamics of higher-order chromatin structures.

• Electrical & Electronic Materials
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• v.7 no.4
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• pp.341-346
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• 1994