• 한국자동차공학회논문집
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• 제7권9호
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• pp.165-171
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• 1999

An oil layer fuel absorption /desorption modeling was developed. Multi-component fuel model has showed more reasonable condition than single component model. Henry's constant which is related to solubility is the most important variable in the oil layer absorption/desorption mechanism. The oil segments close to the top of the cylinder liner have more significant contribution to the fuel absorption and desorption process than other oil segments. At the warmed-up condition, the effect of the engine speed on the precent fuel absorbed/desorbed is minimal. But at low il film temperature, percent of fuel abosrbed/desorbed is decreased with increasing the engine speed because of low value of molecular diffusion coefficient of fuel. The amount of fuel trapped in the piston crevice is from 2 to 2.3 times larger than that of fuel in the oil fim. However, fuel form oil film slowly desorbs into the combustion chamber compared with fuel from the piston crevices when the engines is cold.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.348-353
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• 2005

In this paper we discuss the formulation and the analysis of a signaling pathway by Petri nets. In order to explicitly and formally describe the molecular mechanisms and pathological characteristics of signaling pathways, we propose a new modeling method to construct signaling pathways on the basis of formal representation of Petri net. Our proposed extended algorithm effectively finds basic enzymic components of signaling pathways by employing T-invariants of Petri nets with considering the origination leading to an occurrence of inhibition functions than existing methods. An application of the proposed algorithm is given with the example of Interleukin-1 and Interleukin-6 signaling pathways.

• Fibers and Polymers
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• 제1권1호
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• pp.18-24
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• 2000

The phase transformation of poly(trimethylene terephthalate) in crystalline state was simulated by atomistic modeling using molecular mechanics technique. The crystalline structure of PTT was successfully prepared using the well-defined unit cell structure of PTT and was satisfactorily verified by comparing that with the structure obtained from the x-ray diffraction experiments. The basic elastic properties were predicted in this study, showing that the crystalline structure of PTT is very pliable to the deformation at small strain. When the crystalline structure of PTT was stepwise deformed up to 50% of strain in chain direction under uniaxial extension condition, the change in dihedral angle of trimethylene unit from gg to tt conformation was accompanied with a large increase of stress, indicating that the phase transformation of PTT in crystalline state is difficult to occur.

• Molecules and Cells
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• 제25권3호
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• pp.397-406
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• 2008

Computational modeling of signal transduction is currently attracting much attention as it can promote the understanding of complex signal transduction mechanisms. Although several mathematical models have been used to examine signaling pathways, little attention has been given to crosstalk mechanisms. In this study, an attempt was made to develop a computational model for the pathways involving growth-factor-mediated mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3'-kinase/protein kinase B (PI3K/Akt). In addition, the dynamics of the protein activities were analyzed based on a set of kinetic data. The simulation approach integrates the information on several levels and predicts systems behavior. The in-silico analysis conducted revealed that the Raf and Akt pathways act independently.

• Journal of Microbiology and Biotechnology
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• 제22권6호
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• pp.788-792
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• 2012

We report the computational structural simulation of the Cry1Ab19 toxin molecule from B. thuringiensis BtX-2 based on the structure of Cry1Aa1 deduced by x-ray diffraction. Validation results showed that 93.5% of modeled residues are folded in a favorable orientation with a total energy Z-score of -8.32, and the constructed model has an RMSD of only $1.13{\AA}$. The major differences in the presented model are longer loop lengths and shortened sheet components. The overall result supports the hierarchical three-domain structural hypothesis of Cry toxins and will help in better understanding the structural variation within the Cry toxin family along with facilitating the design of domain-swapping experiments aimed at improving the toxicity of native toxins.

• Journal of Microbiology and Biotechnology
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• 제24권7호
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• pp.954-958
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• 2014

Succinic semialdehyde dehydrogenase (SSADH) catalyzes the oxidation of succinic semialdehyde (SSA) into succinic acid in the final step of ${\gamma}$-aminobutyric acid degradation. Here, we characterized Bacillus subtilis SSADH (BsSSADH) regarding its cofactor discrimination and substrate inhibition. BsSSADH showed similar values of the catalytic efficiency ($k_{ca}t/K_m$) in both $NAD^+$ and $NADP^+$ as cofactors, and exhibited complete uncompetitive substrate inhibition at higher SSA concentrations. Further analyses of the sequence alignment and homology modeling indicated that the residues of catalytic and cofactor-binding sites in other SSADHs were highly conserved in BsSSADH.

• 공업화학전망
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• 제24권3호
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• pp.1-13
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• 2021

유리 소재는 뛰어난 기계적, 화학적, 광학 특성으로 인해 다양한 영역에서 광범위하게 활용되어 왔으며, 최근에는 특정 물성이 강화된 기능성 유리 수요가 다양한 산업 영역에서 급속히 증가하고 있다. 유리 소재 분야에서의 연구 개발은 유리 특유의 비정질 구조 및 다원소 조성 특성에 의한 복합성 때문에 전통적으로 경험에 기반한 실험 기법에 의존하여 왔다. 그러나 적용 분야에 따른 맞춤형 물성 강화에 대한 필요성이 증대됨에 따라, 핵심 물성 발현 원리 등을 원자 단위에서 이해하고 이를 바탕으로 기능성 유리 소재를 설계하는 접근법이 주목받고 있다. 원자단위 시뮬레이션 및 이론 기반 모델링은 유리 소재의 다양한 물성과 조성 변화에 따른 원자 구조의 상관관계를 매우 효율적으로 분석할 수 있는 기법이다. 본 기고문 에서는 밀도범함수이론, 분자동역학 및 위상속박이론을 활용한 기능성 유리 소재 개발 및 연구 동향에 대해서 소개하고자 한다.

• Molecules and Cells
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• 제45권2호
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• pp.53-64
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• 2022

Three-dimensional cultures of human neural tissue/organlike structures in vitro can be achieved by mimicking the developmental processes occurring in vivo. Rapid progress in the field of neural organoids has fueled the hope (and hype) for improved understanding of brain development and functions, modeling of neural diseases, discovery of new drugs, and supply of surrogate sources of transplantation. In this short review, we summarize the state-of-the-art applications of this fascinating tool in various research fields and discuss the reality of the technique hoping that the current limitations will soon be overcome by the efforts of ingenious researchers.

• Bulletin of the Korean Chemical Society
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• 제27권7호
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• pp.1025-1030
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• 2006

A 3D-CoMFA model with pranlukast analogues was constructed, which could be applied to predict the antagonistic activity of aryl benzyl ether analogues against LTD4. Molecular modeling and 3D-CoMFA studies were performed on 78 pranlukast analogues and 14 aryl benzyl ethers to evaluate the antagonistic behavior of aryl benzyl ethers and provide information for further modification of this kind of compounds. The aryl benzyl ether core was found to be in excellent three dimensional match with the central planar moiety of pranlukast analogues, and the pranlukast 3D-CoMFA model could be successfully applied to predict the biological activity of aryl benzyl ether analogues.

• Bulletin of the Korean Chemical Society
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• 제35권5호
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• pp.1440-1448
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• 2014

Co(II)-tetrasulfonated phthalocyanine (CoTSP) is known to be aggregated to dimer at high concentration levels in water. A study on the aggregation of CoTSP using multivariate curve resolution analysis of the visible absorbance spectra over a concentration range of 30, 40 and 50 ${\mu}M$ in the presence of dimethyl sulfoxide (DMSO), dimethyl formamide (DMF), acetonitrile (AN) and ethanol (EtOH) in the concentration range of 0 to 3.57 M is conducted. A hard modeling-based multivariate curve resolution method was applied to determine the dissociation constants of the CoTSP aggregates at various temperatures ranging from 25, 45 and $65^{\circ}C$ and in the presence of various co-solvents. Dissociation constant for aggregation was increased and then decrease by temperature and concentration of phthalocyanine, respectively. Utilizing the vant Hoff relation, the enthalpy and entropy of the dissociation equilibriums were calculated. For the dissociation of both aggregates, the enthalpy and entropy changes were positive and negative, respectively. Molecular dynamics simulation of cosolvent effect on CoTSP aggregation was done to confirm spectroscopy results. Results of radial distribution function (RDF), root mean square deviation (RMSD) and distance curves confirmed more effect of polar solvent to decrease monomer formation.