• Journal of the Korean Chemical Society
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• v.63 no.4
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• pp.237-245
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• 2019

Hydrogen bihalide anions, $XHX^-$ (X = F, Cl, and Br) have been studied by high level ab initio methods to determine the molecular structure, vibrational frequencies, and energetics of the anions. All bihalide anions are found to be of linear and symmetric structures, and the calculated bond lengths are consistent with experimental data. The harmonic frequencies exhibit large deviations from the experimental frequencies, suggesting the vibrations of these anions are very anharmonic. Two different approaches, the VSCF and VPT2 methods, are employed to calculate the anharmonic frequencies, and the results are compared with the experimental frequencies. While the ${\nu}_1$ and ${\nu}_2$ frequencies are in reasonable agreement with the experimental values, the ${\nu}_3$ and ${\nu}_1+{\nu}_3$ frequencies still exhibit large deviations. The hydrogen-bond energies and enthalpies are calculated at various levels including the W1BD and G4 composite methods. The hydrogen-bond enthalpies calculated are in good agreement with the experimental values.

• Advances in nano research
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• v.6 no.4
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• pp.357-375
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• 2018

Two dimensional (2D) atomic layered nanomaterials exhibit some of the most striking phenomena in modern materials research and hold promise for a wide range of applications including energy and biomedical technologies. Graphene has received much attention for having extremely high surface area to mass ratio and excellent electric conductivity. Graphene has also been shown to maximize the activity of surface-assembled metal nanoparticle catalysts due to its unique characteristics of enhancing mass transport of reactants to catalysts. This paper specifically investigates the strategy of pre-formed nanoparticle self-assembly used for the formation of various metal nanoparticles supported on graphene families such as graphene, graphene oxide, and reduced graphene oxide and aims at understanding the interactions between ligand-capped metal nanoparticles and 2D nanomaterials. By varying the functional groups on the ligands between alkyl, aromatic, amine, and alcohol groups, different interactions such as van der Waals, ${\pi}-{\pi}$ stacking, dipole-dipole, and hydrogen bonding are formed as the 2D hybrids produced.

• Journal of the Korean Society of Clothing and Textiles
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• v.45 no.5
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• pp.866-880
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• 2021

This study aimed to ex situ colorize laccase-entrapped bacterial cellulose (BC) with natural phenolic dyes, namely,madder, turmeric, and cochineal, and to determine the effect of laccase entrapment on the dyeability of BC using color strength (K/S) analysis. Results showed that laccase entrapment improved the dyeability of BC and that pre-entrapment was the most effective method, compared with meta-entrapment and post-entrapment methods. In addition, surface characterizations confirmed the successful entrapment of laccase inside the BC nanostructure and retention of the cellulosic and crystalline structures of BC. The washing durability test confirmed that the K/S value of BC had improved after laccase entrapment. Furthermore, laccase-entrapped BC colorized with cochineal dye had the highest washing durability due to the high molecular weight of cochineal dyerelative to the other dyes. This study suggests a novel method for enhancing the dyeability and washing durability of BC colorized ex situ with natural phenolic dyes by laccase entrapment.

• Korean Journal of Metals and Materials
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• v.47 no.11
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• pp.759-772
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• 2009

Amorphous alloys, in addition to being promising materials for a variety of practical applications, provide an excellent test bed for evaluating our understanding of the underlying physics on deformation in amorphous solids. Like many amorphous materials, amorphous alloys can exhibit either homogeneous or inhomogeneous deformation depending on the stress level. The mode of deformation has a strong influence on whether the material behavior is classified as ductile or brittle. It was observed that the characteristics of these deformations are largely dependent on the atomic-scale structures of the alloys and determine the amount of the plastic deformation prior to failure. In this study, the structural features that control the homogeneous deformation of amorphous alloys are outlined on the basis on experiments and molecular dynamics simulations.

• Steel and Composite Structures
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• v.39 no.5
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• pp.565-581
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• 2021

In this paper the buckling analysis of the nanoplate made of arbitrary bi-directional functionally graded (BDFG) materials with small scale effects are investigated. To study the small-scale effects on buckling load, the Eringen's nonlocal theory is applied. Employing the principle of minimum potential energy, the governing equations are obtained. Generalize differential quadrature method (GDQM) is used to solve the governing equations for various boundary conditions to obtain the buckling load of BDFG nanoplates. These models can degenerate into the classical models if the material length scale parameter is taken to be zero. Comparison between the results of GDQ method and other papers for buckling analysis of a simply supported rectangular nano FGM plate reveals the accuracy of GDQ method. At the end some numerical results are presented to study the effects of material length scale parameter, plate thickness, aspect ratio, Poisson's ratio boundary condition and side to thickness ratio on size dependent Frequency.

• BMB Reports
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• v.55 no.3
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• pp.125-135
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• 2022

Continuously renewing the proteome, translation is exquisitely controlled by a number of dedicated factors that interact with the ribosome. The RNA helicase DDX3 belonging to the DEAD box family has emerged as one of the critical regulators of translation, the failure of which is frequently observed in a wide range of proliferative, degenerative, and infectious diseases in humans. DDX3 unwinds double-stranded RNA molecules with coupled ATP hydrolysis and thereby remodels complex RNA structures present in various protein-coding and noncoding RNAs. By interacting with specific features on messenger RNAs (mRNAs) and 18S ribosomal RNA (rRNA), DDX3 facilitates translation, while repressing it under certain conditions. We review recent findings underlying these properties of DDX3 in diverse modes of translation, such as cap-dependent and cap-independent translation initiation, usage of upstream open reading frames, and stress-induced ribonucleoprotein granule formation. We further discuss how disease-associated DDX3 variants alter the translation landscape in the cell.

• Journal of Species Research
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• v.11 no.1
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• pp.10-21
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• 2022

Two strains of cyanobacteria were isolated from the soil of Seodaemun-gu, Seoul and from the gravel of the Ansung Stream, Gyeonggi Province, Korea, respectively. They were identified as Pantanalinema rosaneae and Alkalinema pantanalense under the Leptolyngbyaceae through the morphological, ecological, and molecular analyses and first reported in Korea. Belonging to the Leptolyngbya morphotypes, they are thin filamentous cyanobacteria and morphologically indistinguishable cryptic species. The strains of P. rosaneae and A. pantanalense isolated in Korea revealed the same cluster as their type species in the phylogenetic analysis using the 16S rRNA gene sequences, and similarities in the secondary structures of 16S-23S ITS sequences. Although both P. rosaneae and A. pantanalense were collected from water samples in the Pantanal wetland of Brazil, the P. rosaneae obtained in Korea, was soil-dwelling subaerophytic species whereas A. pantanalense was epilithic species living on gravel in the freshwater. Therefore, they are considered to have an extensive habitat.

• Molecules and Cells
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• v.45 no.1
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• pp.33-40
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• 2022

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

• BMB Reports
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• v.55 no.7
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• pp.316-322
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• 2022

Ubiquitin is relatively modest in size but involves almost entire cellular signaling pathways. The primary role of ubiquitin is maintaining cellular protein homeostasis. Ubiquitination regulates the fate of target proteins using the proteasome- or autophagy-mediated degradation of ubiquitinated substrates, which can be either intracellular or foreign proteins from invading pathogens. Legionella, a gram-negative intracellular pathogen, hinders the host-ubiquitin system by translocating hundreds of effector proteins into the host cell's cytoplasm. In this review, we describe the current understanding of ubiquitin machinery from Legionella. We summarize structural and biochemical differences between the host-ubiquitin system and ubiquitin-related effectors of Legionella. Some of these effectors act much like canonical host-ubiquitin machinery, whereas others have distinctive structures and accomplish non-canonical ubiquitination via novel biochemical mechanisms.

• Molecules and Cells
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• v.45 no.1
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• pp.16-25
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• 2022

Mechanical forces play pivotal roles in regulating cell shape, function, and fate. Key players that govern the mechanobiological interplay are the mechanosensitive proteins found on cell membranes and in cytoskeleton. Their unique nanomechanics can be interrogated using single-molecule tweezers, which can apply controlled forces to the proteins and simultaneously measure the ensuing structural changes. Breakthroughs in high-resolution tweezers have enabled the routine monitoring of nanometer-scale, millisecond dynamics as a function of force. Undoubtedly, the advancement of structural biology will be further fueled by integrating static atomic-resolution structures and their dynamic changes and interactions observed with the force application techniques. In this minireview, we will introduce the general principles of single-molecule tweezers and their recent applications to the studies of force-bearing proteins, including the synaptic proteins that need to be categorized as mechanosensitive in a broad sense. We anticipate that the impact of nano-precision approaches in mechanobiology research will continue to grow in the future.