• Advances in nano research
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• 제11권6호
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• pp.607-620
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• 2021

In this paper, the vibrations of boron nitride nanotubes (BNNTs) are investigated by considering the electric field. To consider the size effect at nanoscale dimensions, the surface elasticity theory is exploited. The equations of motion of the BNNTs are obtained by applying Hamilton's principle, and the clamped-guided boundary conditions are also considered. The governing equations and boundary conditions are discretized using the differential quadrature method (DQM), and the natural frequency is obtained by using the eigenvalue problem solution. The results are compared with the molecular dynamic simulation in order to validate the accurate values of the surface effects. In the molecular dynamics (MD) simulation, the potential between boron and nitride atoms is considered as the Tersoff type. The Timoshenko beam model is adopted to model BNNT. The vibrations of two types of zigzag and armchair BNNTs are considered. In the result section, the effects of chirality, surface elasticity modulus, surface residual tension, surface density, electric field, length, and thickness of BNNT on natural frequency are investigated. According to the results, it should be noted that, as an efficient non-classical continuum mechanic approach, the surface elasticity theory can be used in scrutinizing the dynamic behavior of BNNTs.

• Bulletin of the Korean Chemical Society
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• 제32권11호
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• pp.4016-4020
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• 2011

A number of mimetic peptides of apolipoprotein A-I, a major component for high density lipoproteins (HDL), were screened from the phase-displayed random peptide library by utilizing monoclonal antibodies (A12). A mimetic peptide for A12 epitope against apolipoprotein A-I was selected as FVLVRDTFPSSVCCP(pA2) exhibiting 45% homology with Apo A-I in the BLAST search. Solution structure determination of this mimotope was made by using 2D-NMR data and NMR-based distance geometry (DG)/molecular dynamic calculations. The resulting DG structures had low penalty value of 0.4-0.6 ${\AA}^2$ and the total RMSD of 0.7-1.7 ${\AA}$. The mimotope pA2 exhibited a characteristic ${\beta}$-turn conformation from Val[2] to Phe[8] near Pro[9] residue.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2007년도 춘계학술대회A
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• pp.326-331
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• 2007

Large-scale molecular dynamics simulations are performed to verify the deformation characteristics of grain boundaries in nanolithography process. The copper substrate made of 200,000 atoms is constructed by two grains in different crystal orientations using dynamic relaxation method. The grain boundary is located in the middle of the substrate with $45\sim135$ degree angles. The plowing tip is made of diamond-like-carbon atoms in a variety of shapes. In the simulations, the generation, propagation, and accumulation of dislocations are observed inside the substrate. From the numerical results, we address the dynamic behavior of the grain boundaries as well as the frictional characteristics in terms of the morphology of initial grain boundaries.

• 한국정보디스플레이학회:학술대회논문집
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• 한국정보디스플레이학회 2003년도 International Meeting on Information Display
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• pp.482-483
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• 2003

We have synthesized a new material of polyoxetane based liquid crystalline polymer/liquid crystal (LCP/LC) for flexible memory or dynamic mode device and characterized the electro-optics behavior of this system. The microscopic dynamic behavior of main chain, side chain, and the low molecular weight LC were characterized by X-ray scattering and time resolved FTIR..

• BMB Reports
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• 제49권4호
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• pp.201-207
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• 2016

The CRISPR-Cas system has emerged as a fascinating and important genome editing tool. It is now widely used in biology, biotechnology, and biomedical research in both academic and industrial settings. To improve the specificity and efficiency of Cas nucleases and to extend the applications of these systems for other areas of research, an understanding of their precise working mechanisms is crucial. In this review, we summarize current studies on the molecular structures and dynamic functions of type I and type II Cas nucleases, with a focus on target DNA searching and cleavage processes as revealed by single-molecule observations.

• Tribology and Lubricants
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• 제25권4호
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• pp.236-242
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• 2009

Oil viscosity is one of the important parameters for machinery condition monitoring. Basically, it is expressed as kinematic viscosity measured by capillary flow and dynamic or absolute viscosity measured by rotary shear viscometry. Recently, acoustic wave techniques appear in the market, measuring viscosity as the product of dynamic viscosity and density. For Newtonian fluids, knowledge of density allows conversion from one viscosity parameter to the other at a specific shear rate and temperature. In this work, oil samples with different chain lengths of viscosity index (VI) improvers and concentrations were examined by different viscometric techniques. Results showed that acoustic viscosity measurements give misleading results for oil samples with high molecular weight VI improvers and at low temperatures ${\leq}40^{\circ}C$.

• Molecules and Cells
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• 제41권9호
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• pp.809-817
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• 2018

Discovery of the naturally evolved fluorescent proteins and their genetically engineered biosensors have enormously contributed to current bio-imaging techniques. These reporters to trace dynamic changes of intracellular protein activities have continuously transformed according to the various demands in biological studies. Along with that, light-inducible optogenetic technologies have offered scientists to perturb, control and analyze the function of intracellular machineries in spatiotemporal manner. In this review, we present an overview of the molecular strategies that have been exploited for producing genetically encoded protein reporters and various optogenetic modules. Finally, in particular, we discuss the current efforts for combined use of these reporters and optogenetic modules as a powerful tactic for the control and imaging of signaling events in cells and tissues.

• Bulletin of the Korean Chemical Society
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• 제4권2호
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• pp.87-91
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• 1983

Molecular dynamic method has been applied to a single polymer chain immersed in a solvent. The interactions for the pairs, of two solvent molecules (SS), of a chain element and a solvent molecules (CS), and of two non-neighbor chain elements (CC) are given by the Lennard-Jones potential, and the interaction between two bonded chain elements is given by a harmonic potential. We changed the CS interaction parameter ${\varepsilon}_{CS}$ to 0.5, 1.0 and 2.0 times of the SS interaction ${\varepsilon}_{SS}$. We calculated the pair correlation functions for the SS, CS, and CC pairs, end-to-end distance and radius of gyration with the varying ${\varepsilon}_{CS}$ parameters. The results showed that a phase separation occurs between the polymer and solvent in the 0.5 system where ${\varepsilon}_{CS}$ = 0.5 {\varepsilon}_{SS}$. The autocorrelation functions for end-to-end distance and radius of gyration were also calculated.

• Bulletin of the Korean Chemical Society
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• 제18권5호
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• pp.501-509
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• 1997

In recent papers[Bull. Kor. Chem. Soc. 1996, 17, 735; ibid 1997, 18, 478] we reported results of molecular dynamics (MD) simulations for the thermodynamic, structural, and dynamic properties of liquid normal alkanes, from n-butane to n-heptadecane, using three different models. Two of the three classes of models are collapsed atomic models while the third class is an atomistically detailed model. In the present paper we present results of MD simulations for the corresponding properties of liquid branched-chain alkanes using the same models. The thermodynamic property reflects that the intermolecular interactions become weaker as the shape of the molecule tends to approach that of a sphere and the surface area decreases with branching. Not like observed in the straight-chain alkanes, the structural properties of model Ⅲ from the site-site radial distribution function, the distribution functions of the average end-to-end distance and the root-mean-squared radii of gyration are not much different from those of models Ⅰ and Ⅱ. The branching effect on the self diffusion of liquid alkanes is well predicted from our MD simulation results but not on the viscosity and thermal conductivity.

• 한국자기공명학회논문지
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• 제25권4호
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• pp.58-63
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• 2021

Apolipoprotein B-100 (apo B-100), the main protein component that makes up LDL (Low density lipoprotein), consists of 4,536 amino acids and serves to combine with the LDL receptor. The oxidized LDL peptides by malondialdehyde (MDA) or acetylation in vivo act as immunoglobulin (Ig) antigens and peptide groups were classified into 7 peptide groups with subsequent 20 amino acids (P1-P302). The biomimetic peptide P143 (IALDD AKINF NEKLS QLQTY) out of C-group peptides carrying the highest value of IgG antigens were selected for structural studies that may provide antigen specificity. Experimental results show that P143 has β-sheet in Ile[1]-Asn[9] and α-helice in Gln[16]-Tyr[20] structure. Homonuclear 2D-NMR (COSY, TOCSY, NOESY) experiments were carried out for NMR signal assignments and structure determination for P143. On the basis of these completely assigned NMR spectra and proton distance information, distance geometry (DG) and molecular dynamic (MD) were carried out to determine the structures of P143. The proposed structure was selected by comparisons between experimental NOE spectra and back-calculated 2D NOE results from determined structure showing acceptable agreement. The total Root-Mean-Square-Deviation (RMSD) value of P143 obtained upon superposition of all atoms were in the set range. The solution state P143 has a mixed structure of pseudo α-helix and β-turn(Phe[10] to Glu[12]). These results are well consistent with calculated structure from experimental data of NOE spectra. Structural studies based on NMR may contribute to the prevent oxidation studies of atherosclerosis and observed conformational characteristics of apo B-100 in LDL using monoclonal antibodies.