• 통합자연과학논문집
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• 제3권1호
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• pp.49-53
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• 2010

Molecular docking is a critical event which mostly forms Van der waals complex in molecular recognition. Since the majority of developed drugs are small molecules, docking them into proteins has been a prime concern in drug discovery community. Since the binding pose space is too vast to cover completely, many search algorithms such as genetic algorithm, Monte Carlo, simulated annealing, distance geometry have been developed. Proper evaluation of the quality of binding is an essential problem. Scoring functions derived from force fields handle the ligand binding prediction with the use of potential energies and sometimes in combination with solvation and entropy contributions. Knowledge-based scoring functions are based on atom pair potentials derived from structural databases. Forces and potentials are collected from known protein-ligand complexes to get a score for their binding affinities (e.g. PME). Empirical scoring functions are derived from training sets of protein-ligand complexes with determined affinity data. Because non of any single scoring function performs generally better than others, some other approaches have been tried. Although numerous scoring functions have been developed to locate the correct binding poses, it still remains a major hurdle to derive an accurate scoring function for general targets. Recently, consensus scoring functions and target specific scoring functions have been studied to overcome the current limitations.

• 한국전기전자재료학회논문지
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• 제26권11호
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• pp.821-825
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• 2013

Effect of multi-stacked layer (MSL), 0.1 mol (M) and 0.3 mol (M) hafnium oxide ($HfO_2$) alignment layers were fabricated via a solution-process for LCs orientation. The solutions were spin-coated and annealed in a furnace. MSL consists of three sub-layers using 0.1 M solution, mono-layer (ML) is composed of 0.3 M $HfO_2$ solution. Then ion-beam irradiation was treated with 1.8 keV for 2 min. $HfO_2$-based LC cells were investigated through photographs, pre-tilt angle using crystal rotation method, X-ray photoelectron spectroscopy (XPS) measurement, and surface roughness using atomic force microscopy(AFM) for their characteristic research. Good LC orientation characteristics were observed on MSL $HfO_2$ surface. The LC alignment mechanism on MSL $HfO_2$ and ML $HfO_2$ surfaces was attributed to van der Waals (VDW) interaction between the LC molecular and substrate surface.

• 한국콘크리트학회:학술대회논문집
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• 한국콘크리트학회 2006년도 추계 학술발표회 논문집
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• pp.537-540
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• 2006

Over the past few decades, a considerable number of studies on the durability of concrete have been carried out extensively. A lot of improvements have been achieved especially in modeling of ionic flows. However, the majority of these researches have not dealt with the chloride binding isotherm based on the mechanism, although chloride binding capacity can significantly impact on the total service life of concrete under marine environment. The purpose of this study is to develop the model of chloride binding isotherm based on the individual mechanism. It is well known that chlorides ions in concrete can be present; free chlorides dissolved in the pore solution, chemical bound chlorides reacted with the hydration compounds of cement, and physical bound attracted to the surface of C-S-H grains. First, sub-model for water soluble chloride content is suggested as a function of pore solution and degree of saturation. Second, chemical model is suggested separately to estimate the response of binding capacity due to C-S-H and Friedel's salt. Finally, physical bound chloride content is estimated to consider a surface area of C-S-H nano-grains and the distance limited by the Van der Waals force. The new model of chloride binding isotherm suggested in this study is based on their intrinsic binding mechanisms and hydration reaction of concrete. Accordingly, it is possible to characterize chloride binding isotherm at the arbitrary stage of hydration time and arbitrary location from the surface of concrete. Comparative study with experimental data of published literature is accomplished to validity this model.

• 한국전산구조공학회논문집
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• 제23권4호
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• pp.403-407
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• 2010

게코 접착 시스템은 보(beam)의 형상을 가지는 seta와 접착패드 역할을 하는 spatula로 구성된다. 본 논문에서는 보 접착 모델(ahhesive beam contact model)을 사용하여 게코(gecko) 접착 시스템의 접착 메커니즘의 해석을 수행한다. 보 접착 모델은 접촉면에서 불균일한 응력 분포를 가지는 특징이 있으며, 접촉면에서의 최대 인장 응력(tensile stress)에 의하여 접착/분리 메커니즘이 결정된다. 접착패드 역할을 하는 spatula는 최대 인장응력을 감소시키는 역할을 하며, 이로 인해 접착력이 증가한다. 역방향 하중에 대해서는 spatula에 의하여 최대 압축 응력(compressive stress)이 감소하며, 이러한 현상에 의하여 접착력과 분리력의 비대칭성이 발생한다. 본 연구에서는 보 접착 모델의 해석을 위해 유한요소법(Finite Element Method)을 사용되며, spatula effect를 위한 해석 결과가 제시된다.

• Asian Pacific Journal of Cancer Prevention
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• 제14권12호
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• pp.7095-7100
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• 2013

Histone deacetylase (HDAC) inhibitors of cyclic peptide have been proved to be the most complex but the most stable and relative efficient inhibitors because of their large cap region. In this paper, a series of studies were carried out to evaluate the efficacy of synthetic bicyclic tetrapeptide inhibitors 1-5 containing hydroxamic acid referring molecular docking, anti-proliferation, morphology and apoptosis. Docking analysis, together with enzyme inhibitory results, verified the selective capability of inhibitor 4 to HDAC4, which might closely related to haematological tumorigenesis, with Phe227, Asp115, Pro32, His198 and Ser114 participating into hydrophobic interactions and Van der Waals force which was familiar with former study. Moreover, inhibitor 4 inhibited K562 cell line at the $IC_{50}$ value of 1.22 ${\mu}M$ which was 51-67 times more efficient than that for U937 and HL60 cell lines. Inhibitor 4 exhibited the cell cycle-arrested capability to leukemia at S phase or G2/M phase as well as apoptosis-induced ability in different degrees. Finally, we considered that bicyclic tetrapeptide inhibitors were promising inhibitors used in cancer treatment and inhibitor 4 could prevent K562 cell line well from proliferation, arrest cell cycle and induce K562 towards apoptosis to achieve the goals of reversing cancer cells which could become a potential leukemia therapeutic agent in the future.

• Composites Research
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• 제33권1호
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• pp.19-24
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• 2020

본 연구에서는 Poly(vinylidene fluoride) (PVDF) 필름 제작 과정 중 마이크로웨이브 처리 과정을 도입하여 β 결정성 향상에 어떠한 영향을 미치는지 분석하였다. 또한, 나노 입자 보강제로써 금속산화물인 TiO₂를 혼합하여 PVDF 복합재료 필름을 만들어, 전기적 음성도 차이로 인한 반데르발스 힘을 통해 β 결정 형성을 추가적으로 향상시키려고하였다. FTIR과 XRD 분석을통하여해당필름시편들에대해결정화도(Crystallinity) 및결정성(Crystalline)을 분석하였다. 이러한 분석 결과를 바탕으로, 용매 증발 과정 중 마이크로웨이브 처리 과정이 PVDF 필름의 결정화도를 높여주는 것을 확인하였고, 추가적인 연신(Stretching) 공정을 통해 α 결정에서 β 결정 변화(Crystalline phase change)가 발생함으로써 결과적으로 더 많은 β 결정성을 나타내었다. 그리고 금속산화물을 넣은 PVDF 복합재료 필름이 Neat PVDF 필름보다 상대적으로 더 높은 β 결정성을 나타내는 것을 확인하였다.

• Journal of Microbiology and Biotechnology
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• 제24권4호
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• pp.483-488
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• 2014

In order to improve the expression of heat-resistant xylanase XYNB from Aspergillus niger SCTCC 400264, XynB has been cloned into Pichia pastoris secretary vector pPIC9K. The XynB production of recombinant P. pastoris was four times that of E. coli, and the $V_{max}$ and specific activity of XynB reached $2,547.7{\mu}mol/mg$ and 4,757 U/mg, respectively. XynB still had 74% residual enzyme activity after 30 min of heat treatment at $80^{\circ}C$. From the van der Waals force analysis of XYNB (ACN89393 and AAS67299), there is one more oxygen radical in AAS67299 in their catalytic site, indicating that the local cavity is much more free, and it is more optimal for substrate binding, affinity reaction, and proton transfer, etc, and eventually increasing enzyme activity. The H-bonds analysis of XYNB indicated that there are two more H-bonds in the 33rd Ser of XYNB (AAS67299) than in the 33rd Ala(ACN89393 ), and two H-bonds between Ser70 and Asp67.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2009년도 제38회 동계학술대회 초록집
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• pp.358-358
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• 2010

Ion beam bombardment at low energy forms nanosize patterns such as ripples, dots or wrinkles on the surface of polymers in ambient temperature and pressure. It has been known that the ion beam can alter the polymer surface that induces skins stiffer or the density higher by higher compressive stress or strain energies associated with chain scissions and crosslinks of the polymer. Atomic scale structure evolution in polymers is essential to understand a stress generation mechanism during the ion beam bombardment, which governs the nanoscale surface structure evolution. In this work, Molecular Dynamics (MD) simulations are employed to characterize the phenomenon occurred in bombardment between the ion beam and polymers that forms nanosize patterns. We investigate the structure evolution of Low Density Polyethylene (LDPE) at 300 K as the polymer is bombarded with Argon ions having various kinetic energies ranging from 100 eV to 1 KeV with 50 eV intervals having the fluence of $1.45\;{\times}\;1014 #/cm2$. These simulations use the Reactive Force Field (ReaxFF), which can mimic chemical covalent bonds and includes van der Waals potentials for describing the intermolecular interactions. The results show the details of the structural evolution of LDPE by the low energy Ar ion bombardment. Analyses through kinetic and potential energy, number of crosslinks and chain scissions, level of local densification and motions of atoms support that the residual strain energies on the surface is strongly associated with the number of crosslinks or scissored chains. Also, we could find an optimal Ar ion beam energy to make crosslinks well.

• Bulletin of the Korean Chemical Society
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• 제12권6호
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• pp.686-691
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• 1991

Emission quenching of photoexcited tris(${\alpha},{\alpha} '$-diimine)-ruthenium(II) complex cations, $RuL_3^{2+}$ (L: 2,2'-bipyridine, 4,4'-dimethyl-2,2'-bipyridine; 4,4'-diphenyl-2,2'-bipyridine; 1,10-phenanthroline; 5-methyl-1,10-phenanthroline; 5,6-dimethyl-1,10-phenanthroline or 4,7-diphenyl-1,10-phenanthroline) by $Cu^{2+}$, dimethylviologen $(MV^{2+})$, nitrobenzene (NB), and oxygen was studied in aqueous homogeneous and sodium dodecyl sulfate (SDS) micellar solutions. The apparent bimolecular quenching rate constants $k_q$ were determined from the quenching data and life-times of $^{\ast}RuL_3^{2+}$. In homogeneous media, the quenching rate was considerably slower than that for the diffusion-controlled reaction. The decreasing order of quenching activity of quenchers was $NB>O_2>MV^{2+}>Cu^{2+}$. The rate with $Cu^{2+}$ was faster as the reducing power of $^{\ast}RuL_3^{2+}$ is greater. On the other hand, the rates with NB and $O_2$ were faster as the ligand is more hydrophobic. This was attributed to the stabilization of encounter pair by van der Waals force. The presence of SDS enhanced the rate of quenching reactions with $Cu^{2+}$ and $MV^{2+}$, whereas it attenuated the quenching activity of NB and $O_2$ toward $RuL_3^{2+}$. The binding affinity of quenchers to SDS micelle and binding sites of the quenchers and $RuL_3^{2+}$ in micelle appear to be important factors controlling the micellar effect on the quenching reactions.

• 대한화학회지
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• 제34권6호
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• pp.517-526
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• 1990

D-glucitol hexaacetate 와 xylitol pentaacetate의 결정구조를 단결정 X-선 회절법으로 연구하였다. D-glucitol hexaacetate 는 공간군 P2$_1$, 단위세포 상수는 a = 10.275 (2), b = 8.363 (1), c = 12.560 (5) $\AA$, $\beta$= 95.97 $(2)^{\circ}$; Z = 2이고, xylitol pentaacetate는 공간군이 P2$_1$/C이고, a = 18.126 (1), b = 11.422 (2), c = 8.649 (1) $\AA$, $\beta$ = 95.03 $(1)^{\circ}$이며 Z = 4이다. 회절세기는 diffractomerer로 얻었고, 분자구조는 직접법으로 밝혔으며, 최소자승법으로 정밀화하였다. 두 분자에 결쳐 결합의 평균길이는 C($sp^3)-C(sp^3$)가 1.514 (10), C($sp^3)-O: 1.444 (6),\; C(sp^2)-O: 1.347 (9),\; C(sp^2)=O: 1.197 (6),\; C(sp^2)-C(sp^3): 1.479(9){\AA}$이고, 평균 결합각도는 C($sp^3)-C(sp^3)-C(sp^3): 114.6 (17),\; O-C(sp^3)-C(sp^3): 109.4 (23),\; C(sp^2)-O-C(sp^3): 117.4 (6),\; O=C(sp^2)-O: 122.6 (6),\; C(sp^3)-C(sp^2)-O: 111.8 (7), C(sp^3)-C(sp^2)=O: 125.5 (4)${\circ}$이다. 두 분자내의 탄소 사슬들은 extended zigzag chain으로 되어 있어 D-glucitol과 xylitol 분자들의 conformation과는 다르다. Acetate group들의 각 원자들은 모두 한 평편상에 놓여있다.