• Nuclear Engineering and Technology
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• v.34 no.3
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• pp.202-210
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• 2002

The details of the electronic structure of the perfect crystal provides a critically important foundation for understanding the various defect states in uranium dioxide. In order to understand the local defect and impurity mechanism, the calculation of electronic structure of UO$_2$ in the one-electron approximation was carried out, using a semi-empirical tight-binding formalism(LCAO) with and without f-orbitals. The energy band, local and total density of states for both spin states are calculated from the spectral representation of Green’s function. The bonding mechanism in Perfect lattice of UO$_2$ is discussed based upon the calculations of band structure, local and total density of states.

• Current Applied Physics
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• v.18 no.11
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• pp.1393-1398
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• 2018

We have investigated Bernal-stacked tetralayer graphene as a function of interlayer distance and perpendicular electric field by using density functional theory calculations. The low-energy band structure was found to be very sensitive to the interlayer distance, undergoing a metal-insulator transition. It can be attributed to the nearest-layer coupling that is more sensitive to the interlayer distance than are the next-nearest-layer couplings. Under a perpendicular electric field above a critical field, six electric-field-induced Dirac cones with mass gaps predicted in tight-binding models were confirmed, however, our density functional theory calculations demonstrate a phase transition to a quantum valley Hall insulator, contrasting to the tight-binding model prediction of an ordinary insulator.

• Advances in nano research
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• v.2 no.3
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• pp.157-172
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• 2014

The three-dimensional Nano-Electronic Modeling toolkit (NEMO 3-D) is an open source software package that allows the atomistic calculation of single-particle electronic states and optical response of various semiconductor structures including bulk materials, quantum dots, impurities, quantum wires, quantum wells and nanocrystals containing millions of atoms. This paper, first, describes a software module introduced in the NEMO 3-D toolkit for the calculation of electronic bandstructure and interband optical transitions in nanowires having wurtzite crystal symmetry. The energetics (Hamiltonian) of the quantum system under study is described via the tight-binding (TB) formalism (including $sp^3$, $sp^3s^*$ and $sp^3d^5s^*$ models as appropriate). Emphasis has been given in the treatment of surface atoms that, if left unpassivated, can lead to the creation of energy states within the bandgap of the sample. Furthermore, the developed software has been validated via the calculation of: a) modulation of the energy bandgap and the effective masses in [0001] oriented wurtzite nanowires as compared to the experimentally reported values in bulk structures, and b) the localization of wavefunctions and the optical anisotropy in GaN/AlN disk-in-wire nanowires.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.340-340
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• 2010

Various structures of vacancy defects in graphene layers and carbon nanotubes have been reported by high resolution transmission electron microscope (HR-TEM) and those arouse an interest of reconstruction processes of vacancy defects. In this talk, we present reconstruction processes of vacancy defects in a graphene and a carbon nanotube by tight-binding molecular dynamics (TBMD) simulations and by first principles total energy calculations. We found that a structure of a dislocation defect with two pentagon-heptagon (5-7) pairs in graphene becomes more stable than other structures when the number of vacancy units is ten and over. The simulation study of scanning tunneling microscopy reveals that the pentagon-heptagon pair defects perturb the wavefunction of electrons near Fermi level to produce the $\sqrt{3}\;{\times}\;\sqrt{3}$ superlattice pattern, which is in excellent agreement with experiment. It is also observed in our tight-binding molecular dynamics simulation that 5-7 pair defects play a very important role in vacancy reconstruction in a graphene layer and carbon nanotubes.

• Bulletin of the Korean Chemical Society
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• v.16 no.2
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• pp.164-168
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• 1995

The band structure of nickel monoxide having a cation defect rock salt structure is calculated by means of the tight-binding extended Huckel method. The calculation is also made for the net charge, the DOS, the COOP, the electron density of the constituent atoms, and the O 1s binding energy shift when one of the adjacent nickel atoms is defected. It is found that the band gap near the Γ direction on the Brillouin zone is about 0.2 eV, and that all of the properties calculated including the electronic structure of the oxygen atom are more effectively affected by the surface defect than the inside one. The core O 1s binding energy shift is calculated by the use of valence potential method and the results are very satisfactory in comparison with the XPS experimental findings.

• Journal of Life Science
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• v.8 no.2
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• pp.119-125
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• 1998

Column-purified double-stranded RNA binding factor (RBF) protein was tested for its binding affinity for the different forms of nucleic acids structure such as single-stranded(ss) and double-stranded(ds)RNA and ss- and dsDNA. The RBF protein was incubated with each of these nucleic acid structures in separate reactions and its comparative binding affnity was visualized by SDS-polyacrylamide gel electrophoresis. The RBF protein bound to the dsRNA molecule to form a tight RNA:protein complex in agreement with previous studies, but not to the other nucleic acid molecules confirming its distinctive affinity for the dsRNA structure. In phosphorylation assay in vito, the purified RBF protein significantly inhibited the autophosphorylation of the PKR derived from not only human but mouse source in the presence of poly(I):poly(C). It is suggesting that PKR vs. RBF is similarly under a competitive interaction among different eukaryotic organisms during protein synthesis.

• BMB Reports
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• v.41 no.7
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• pp.555-560
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• 2008

The interaction of the rod GTP binding protein, Transducin ($G_t$), with bleached Rhodopsin ($R^*$) was investigated by measuring radiolabeled guanine nucleotide binding to and release from soluble and/or membrane-bound Gt by reconstituting $G_t$ containing bound GDP ($G_t$-GDP) or the hydrolysis-resistant GTP analog guanylyl imidodiphosphate ($G_t$-p[NH]ppG) with $R^*$ under physiological conditions. Release of GDP and p[NH]ppG from $G_t$ occurred to the same extent and with the same light sensitivity both in the presence and absence of added GTP. Significant amounts of $G_t$ without bound nucleotide ($G_{t^-}$) were generated. When ROS containing bleached rhodopsin ($R^*$) were centrifuged in low ionic strength buffer, $G_{t^-}$ remained associated with the membrane fraction, whereas $G_t$-GDP remained in the soluble fraction. These results suggest that $G_t$-GDP and $G_t$-p[NH]ppG have similar affinities for $R^*$. The results also suggest that $G_{t^-}$, rather than $G_t$-GDP, is the moiety which exhibits tight, "light-induced" binding to rhodopsin.

• Genomics & Informatics
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• v.3 no.3
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• pp.53-62
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• 2005

MicroRNAs play an important role in regulating gene expression, but their target identification is a difficult task due to their short length and imperfect complementarity. Burge and coworkers developed a program called TargetScan that allowed imperfect complementarity and established a procedure favoring targets with multiple binding sites conserved in multiple organisms. We improved their algorithm in two major aspects - (i) using well-defined UTR (untranslated region) database, (ii) examining the extent of conservation inside the 3' UTR specifically. Average length in our UTR database, based on the ECgene annotation, is more than twice longer than the Ensembl. Then, TargetScan was used to identify putative binding sites. The extent of conservation varies significantly inside the 3' UTR. We used the 'tight' tracks in the UCSC genome browser to select the conserved binding sites in multiple species. By combining the longer 3' UTR data, TargetScan, and tightly conserved blocks of genomic DNA, we identified 107 putative target genes with multiple binding sites conserved in multiple species, of which 85 putative targets are novel.

• Journal of Microbiology and Biotechnology
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• v.26 no.4
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• pp.659-665
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• 2016

The oligosaccharides in human milk constitute a major innate immunological mechanism by which breastfed infants gain protection against infectious diarrhea. Clostridium difficile is the most important cause of nosocomial diarrhea, and the C-terminus of toxin A with its carbohydrate binding site, TcdA-f2, demonstrates specific abolishment of cytotoxicity and receptor binding activity upon diethylpyrocarbonate modification of the histidine residues in TcdA. TcdA-f2 was cloned and expressed in E. coli BL21 (DE3). A human milk oligosaccharide (HMO) mixture displayed binding with TcdA-f2 at 38.2 respond units (RU) at the concentration of 20 μg/ml, whereas the eight purified HMOs showed binding with the carbohydrate binding site of TcdA-f2 at 3.3 to 14 RU depending on their structures via a surface plasma resonance biosensor. Among them, Lacto-N-fucopentaose V (LNFPV) and Lacto-N-neohexaose (LNnH) demonstrated tight binding to TcdA-f2 with docking energy of −9.48 kcal/mol and −12.81 kcal/mol, respectively. It displayed numerous hydrogen bonding and hydrophobic interactions with amino acid residues of TcdA-f2.

• Proceedings of the IEEK Conference
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• 2001.06b
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• pp.169-172
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• 2001

We have investigated the mechanical deformation of carbon nanotube using TBMD(tight-binding molecular dynamics) simulation. We have studied four carbon nanotubes, armchair (6, 6), (7, 7), (8, 8), and (9, 9) carbon nanotubes whose length were same. As a result of study, we have known that the nanotube's yield force increases with incresing their diameter. It is similar between (6, 6) and (8, 8) CNT's force-strain curves. Also force-strain curve between (7,7) and (9, 9) CNTs are nearly same.