• 한국소음진동공학회:학술대회논문집
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• 한국소음진동공학회 2008년도 추계학술대회논문집
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• pp.668-669
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• 2008

In this paper, we introduce various coarse-grained elastic network modeling (ENM) techniques as a novel computational method for simulating atomic scale dynamics in macromolecules including DNA, RNA, protein, and polymer. In ENM, a system is modeled as a spring network among representative atoms in which each linear elastic spring is well designed to replace both bonded and nonbonded interactions among atoms in the sense of quantum mechanics. Based on this simplified system, a harmonic Hookean potential is defined and used for not only calculating intrinsic vibration modes of a given system, but also predicting its anharmonic conformational change, both of which are strongly related with its functional features. Various nano and bio applications of ENM such as fracture mechanics of nanocomposite and protein dynamics show that ENM is one of promising tools for simulating atomic scale dynamics in a more effective and efficient way comparing to the traditional molecular dynamics simulation.

• Natural Product Sciences
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• 제10권5호
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• pp.197-206
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• 2004

Cytochrome P4501A2 (CYP1A2) is responsible for the metabolic activation of a number of aromatic amines and amides to mutagenic and carcinogenic moieties. Considerable variations in the level of CYP1A2 expression in humans have been reported. Thus, the level of human CYP1A2 may determine an individuals susceptibility to these chemicals. Given its importance, the molecular mechanisms of CYP1A2 regulation have been studied by many groups. Direct interactions between transcription factors with the promoters of the gene represent one of the primary means by which the expression of CYP1A2 is controlled. In this review, several important cis elements, transcription factors and the effects of deacetylation/methylation of promoter regions that play an important role in the induction by PAHs as well as constitutive expression of human CYP1A2 are discussed.

• 한국전산유체공학회:학술대회논문집
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• 한국전산유체공학회 2010년 춘계학술대회논문집
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• pp.575-580
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• 2010

In this work, the electrophoretic motion of dsDNA molecule represented by a polymer through an artificial nano-pore in a membrane is simulated using the numerical method combining the lattice Boltzmann and Langevin molecular dynamic method. The polymer motion is represented by Langevin molecular dynamics technique while the fluid flow is taken into account by fluctuating lattice-Boltzmann method. The hydrodynamic interactions between the polymer and solvent in a confined space with a membrane having a hole are considered explicitly through the frictional and the random forces. The electric field intensity over the space is obtained from a finite difference method. Initially, the polymer is placed at one side of the space, and an electric field is applied to drive the polymer to the other side of the space through the nano-pore. In future, we plan to study the effect of the polymer size and the electric field on the electrophoretic velocity.

• Toxicological Research
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• 제15권1호
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• pp.89-93
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• 1999

2,3,7,8-Tetrachlorodibenzo-p-dioxin(TCDD) is known to induce cytochrome p450 1A1 and to activate c-Src kinase and p21 Ras. This study examined the molecular interactions of adaptor proteins including Shc, Grb2, and Sos in rat primary hepatocytes and their relationship to the induction of CYP1A1 by TCDD. TCDD induced CYP1A1 level and EROD activity in a dose-dependent mode. Sos/Grb2 association isincreased by TCDDㅑㅜ a dose dependent mode. Tyrosine phosphorylated Shc, mainly p152, onloads to Grb2/Sos complex upon TCDD stimulation. The electrophoretic mobility shift of Sos is showed by TCDD. These results indicate that TCDD modulated the molecular interaction features of adaptor compoes proteins including Shc, Grb2, and Cnl in early signaling pathway of TCDD-mediated CYP 1A1 induction of rat primary hepatocyte.

• 대한핵의학회지
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• 제38권2호
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• pp.143-151
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• 2004

Recent progress in the development of non-invasive imaging technologies continues to strengthen the role of molecular imaging biological research. These tools have been validated recently in variety of research models, and have been shown to provide continuous quantitative monitoring of the location(s), magnitude, and time-variation of gene expression. This article reviews the principles, characteristics, categories and the use of radionuclide reporter gene imaging technologies as they have been used in imaging cell trafficking, imaging gene therapy, imaging endogenous gene expression and imaging molecular interactions. The studios published to date demonstrate that reporter gene imaging technologies will help to accelerate pre-clinical model validation as well as allow for clinical monitoring of human diseases.

• 대한기계학회논문집A
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• 제31권8호
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• pp.862-869
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• 2007

The compressive and torsional buckling behavior of carbon nanotube bundles at room temperature is examined with classical molecular dynamics simulation. The critical compressive load and stiffness of a single carbon nanotube in the bundle are found to be similar to those of individual carbon nanotubes. However, the critical torsional moment and stiffness of a single carbon nanotube in the bundle are found to be higher than those of individual carbon nanotubes. In addition, this study demonstrates that van der Waals interactions between the nanotubes in the bundle significantly affect the critical compressive load of the nanotube bundle.

• Journal of Microbiology and Biotechnology
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• 제14권1호
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• pp.162-166
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• 2004

Phage P22 tailspike is a thermostable homotrimeric protein, and temperature-sensitive folding (tsf) and global suppressor mutations affect its folding yields at elevated temperatures. We earlier suggested that the folding of the tailspike protein in Escherichia coli requires an unidentified molecular chaperone. Accordingly, in the present study, the interactions of purified DnaK, DnaJ, and GrpE heat-shock proteins with the tailspike protein were investigated during the translation and folding of the protein. The cotranslational addition of DnaJ to the tailspike protein resulted in the arrest of folding, when Dnak and GrpE were missing. However, the presence of DnaK, DnaJ, and GrpE had no effect on the folding yield of the tails pike protein, thus, providing evidence for the binding of the nascent tailspike protein with DnaJ protein, a member of DnaK chaperoning cycle.

• Molecular & Cellular Toxicology
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• 제3권2호
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• pp.145-149
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• 2007

Studies of relationship between structure and toxicity of azo dyes have been performed with comparative molecular field analysis (CoMFA) techniques. 3D QSTR analyses indicate that the steric and electrostatic interactions are important. The steric field based model gives strong correlation ($q^2$=0.57, $r^2$= 0.92). The steric field in conjunction with electrostatic field give more strong correlation ($q^2$=0.57, $r^2$=0.95). All study indicates that a bulky and electronegative group at benzene ring and a small group at position 3 of aniline ring might be significant to reduce the mutagenicity.

• Nuclear Engineering and Technology
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• 제36권3호
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• pp.229-236
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• 2004

Radiation hardening is a multiscale phenomenon involving various processes over a wide range of time and length. We present a multiscale model for estimating the amount of radiation hardening in pressure vessel steel in the environment of a light water reactor. The model comprises two main parts: molecular dynamics (MD) simulation and a point defect cluster (PDC) model. The MD simulation was used to investigate the primary damage caused by displacement cascades. The PDC model mathematically formulates interactions between point defects and their clusters, which explains the evolution of microstructures. We then used a dislocation barrier model to calculate the hardening due to the PDCs. The key input for this multiscale model is a neutron spectrum at the inner surface of reactor pressure vessel steel of the Younggwang Nuclear Power Plant No.5. A combined calculation from the MD simulation and the PDC model provides a convenient tool for estimating the amount of radiation hardening.

• Bulletin of the Korean Chemical Society
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• 제31권11호
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• pp.3291-3296
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• 2010

A gelastatins (1), natural MMP inhibitors, and their hydroxamate analogues (2) in TACE enzyme evaluated for discovery of potent TACE inhibitors. We have employed molecular dynamics simulations to compute the relative free energy of hydration and binding to TACE for gelastatin (1) and its hydroxamate analogue (2). The relative free energy difference is directly described in this article using the free energy perturbation approach as a means to accurately predict the TACE inhibitor of gelastatin analogues. The results show that the good agreement between the experimental and theoretical relative free energies of binding, gelastatin hydroxamate (2) binds stronger to TACE by -3.37 kcal/mol. The desolvation energy costs significantly reduced binding affinity, hydroxamate group associated with high desolvation energy formed strong favorable interactions with TACE with more than compensated for the solvation costs and therefore led to an improvement in relative binding affinity.