• Journal of Microbiology and Biotechnology
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• 제26권7호
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• pp.1163-1172
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• 2016

The Ω-loop is a nonregular and flexible structure that plays an important role in molecular recognition, protein folding, and thermostability. In the present study, molecular dynamics simulation was carried out to assess the molecular stability and flexibility profile of the porcine trypsin structures. Two Ω-Loops (fragment 57-67 and fragment 78-91) were confirmed to represent the flexible region. Subsequently, glycosylation site-directed mutations (A73S, N84S, and R104S) were introduced within the Ω-loop region and its wing chain based on its potential N-glycosylation sites (Asn-Xaa-Ser/Thr consensus sequences) and structure information to improve the thermostability of trypsin. The result demonstrated that the half-life of the N84S mutant at 50℃ increased by 177.89 min when compared with that of the wild-type enzyme. Furthermore, the significant increase in the thermal stability of the N84S mutant has also been proven by an increase in the T_m values determined by circular dichroism. Additionally, the optimum temperatures of the wild-type enzyme and the N84S mutant were 75℃ and 80℃, respectively. In conclusion, we obtained the thermostability-improved enzyme N84S mutant, and the strategy used to design this mutant based on its structural information and N-linked glycosylation modification could be applied to engineer other enzymes to meet the needs of the biotechnological industry.

• EDISON SW 활용 경진대회 논문집
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• 제4회(2015년)
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• pp.14-23
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• 2015

Alzheimer's disease is one of the most common types of degenerative dementia. As a considerable cause of Alzheimer's disease, neurotoxic plaques composed of 39 to 42 residue-long amyloid beta($A{\beta}$) fibrils have been found in the patient's brain in large quantity. A previous study found that erythrosine B (ER), a red color food dye approved by FDA, inhibits the formation of amyloid beta fibril structures. Here, in an attempt to elucidate the inhibition mechanism, we performed molecular dynamics simulations to demonstrate the conformational change of $A{\beta}40$ induced by 2 ERs in atomistic detail. During the simulation, the ERs bound to the surfaces of both N-terminus and C-terminus regions of $A{\beta}40$ rapidly. The observed stacking of the ERs and the aromatic side chains near the N-terminus region suggests a possible inhibition mechanism in which disturbing the inter-chain stacking of PHEs destabilizes beta-sheet enriched in amyloid beta fibrils. The bound ERs block water molecules and thereby help stabilizing alpha helical structure at the main chain of C-terminus and interrupt the formation of the salt-bridge ASP23-LYS28 at the same time. Our findings can help better understanding of the current and upcoming treatment studies for Alzheimer's disease by suggesting inhibition mechanism of ER on the conformational transition of $A{\beta}40$ at the molecular level.

• Membrane and Water Treatment
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• 제10권3호
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• pp.207-212
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• 2019

Non-aqueous solvents (NASs) are generally known to be barely miscible, and reactive with polar compounds, such as water. However, water can interact with some NASs, which can be used as a new means for water recovery from saline water. This study explored the fate of water and salt in NAS, when saline water is mixed with NAS. Three amine solvents were selected as NAS. They had the same molecular formula, but were differentiated by their molecular structures, as follows: 1) NAS 'A' having the hydrophilic group ($NH_2$) at the end of the straight carbon chain, 2) NAS 'B' with symmetrical structure and having the hydrophilic group (NH) at the middle of the straight carbon chain, 3) NAS 'C' having the hydrophilic group ($NH_2$) at the end of the straight carbon chain but possessing a hydrophobic ethyl branch in the middle of the structure. In batch experiments, 0.5 M NaCl water was blended with NASs, and then water and salt content in the NAS were individually measured. Water absorption efficiencies by NAS 'B' and 'C' were 3.8 and 10.7%, respectively. However, salt rejection efficiency was 98.9% and 58.2%, respectively. NAS 'A' exhibited a higher water absorption efficiency of 35.6%, despite a worse salt rejection efficiency of 24.7%. Molecular dynamic (MD) simulation showed the different interactions of water and salts with each NAS. NAS 'A' formed lattice structured clusters, with the hydrophilic group located outside, and captured a large numbers of water molecules, together with salt ions, inside the cluster pockets. NAS 'B' formed a planar-shaped cluster, where only some water molecules, but no salt ions, migrated to the NAS cluster. NAS 'C', with an ethyl group branch, formed a cluster shaped similarly to that of 'B'; however, the boundary surface of the cluster looked higher than that of 'C', due to the branch structure in solvent. The MD simulation was helpful for understanding the experimental results for water absorption and salt rejection, by demonstrating the various interactions between water molecules and the salts, with the different NAS types.

• 한국추진공학회지
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• 제13권2호
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• pp.42-53
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• 2009

가스터빈 엔진을 모사하기 위한 프로그램을 2차원 CFD 코드를 기반으로 개발 하였다. 압축기와 터빈은 k-$\omega$ SST 난류 모델의 2차원 NS(Navier Stokes) 코드를 이용하였고, 연소기는 lumped method 화학 평형 코드를 바탕으로 완전 혼합 상태에서 연소효율 100%로 가정된 케로신 공기 반응의 생성물 중 대표적인 10종류를 몰분율을 계산, 당량비에 따른 연소기 온도를 예측하였다. 압축기, 터빈에서 로터의 회전에 의한 비정상 유동 현상은 mixing-plane 기법을 이용한 경계면 처리로 그 효과를 나타내었고, 압축기는 연소기로 온도 압력을 주고, 연소기는 터빈으로 온도와 질유량을 전달하나 압력의 변화가 없는 것으로 가정하였다. 이를 바탕으로 아음속 조건에서의 압축기 입구 조건과 터빈 출구 조건, 회전수, 연소기의 당량비를 주는 것만으로 엔진의 성능이 계산 될 수 있는 통합 코드를 구성하였다.

• Korean Chemical Engineering Research
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• 제57권4호
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• pp.475-483
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• 2019

화학적 무기 중 혈액작용제는 전자전달계 내 효소의 철 이온과 반응하고 세포호흡을 정지시켜 사망을 초래한다. 혈액작용제는 활성탄의 미세공보다 분자크기가 작아 화학적 흡착이 유일한 제독방법이다. 본 연구는 SG 생활안전에서 개발한 SG-1 가스 여과기를 이용하여 혈액작용제 시아노겐 클로라이드(CK) 가스의 유입에 따른 유동해석을 수행하였다. 구리, 은, 아연 및 몰리브데늄 이온이 첨착된 ASZM TEDA 활성탄을 적용하여 가스 여과기 제작 시험 규정에 따라 화학적 흡착 모사를 수행하였으며 흡착 Kinetic을 적용하기 위해 선 수행된 흡착 베드에서 CK 가스 흡착 실험 결과를 분석하였다. 화학적 흡착을 통해 발생되는 가스 여과기 내부 압력강하 및 가스 흡착 질량 등 주요 변수의 동적거동을 예측하였다. CFD에서 다공성 물질을 적용할 때 사용하는 Ergun 방정식 대신 Granular와 Packed bed를 사용하여 활성탄 적용 가능 결과를 확인하였으며 시간에 따른 흡착 및 유속에 따른 흡착의 유동 해석에 대한 동적 모사를 수행하였다.

• 멤브레인
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• 제23권6호
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• pp.393-408
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• 2013

고분자 분리막을 이용한 기체 분리막은 높은 에너지 효율, 경제적인 장점으로 최근 수년간 지속적으로 개발되어 왔다. 최적화된 경제적 성능을 얻기 위하여 기체 분리막은 높은 투과도와 선택도를 가져야 한다. 따라서 기체분리 분리막용으로 다양한 고분자를 시험한 연구 결과들이 보고되어 왔다. 다양한 소재 중, 폴리이미드는 다양한 기체인자에 대하여 높은 투과 선택도와 높은 화학적 열적 안정성, 그리고 물리적 안정성으로 많은 주목을 받아왔다. 따라서 본고에서는 기체분리용 폴리이미드 소재의 개발동향과 분리막의 제조방법, 기체 분리의 원리에 대하여 다루었다.

• Bulletin of the Korean Chemical Society
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• 제34권12호
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• pp.3703-3708
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• 2013

The scaling relationship of the longest relaxation time of a single chain of semiflexible biological polyelectrolyte has been investigated by performing well-established coarse-grained Brownian dynamics simulations. Two kinds of longest relaxation times were estimated from time-sequences of chain trajectories, and their behaviors were interpreted by applying the scaling law for different molecular weights of polyelectrolyte and Debye lengths. The scaling exponents for longest stress relaxation and rotational relaxation are found in the ranges of 1.67-1.79 and 1.65-1.81, respectively, depending on the physicochemical interaction of electrostatic Debye screening. The scaling exponent increases with decreasing screening effect, which is a special feature of polyelectrolytes differing from neutral polymers. It revealed that the weak screening allows a polyelectrolyte chain to follow the behavior in good solvent due to the strong electrostatic repulsion between beads.

• 한국정보디스플레이학회:학술대회논문집
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• 한국정보디스플레이학회 2006년도 6th International Meeting on Information Display
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• pp.121-124
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• 2006

A novel quantum chemical molecular dynamics program, 'Colors' was developed to simulate the electronic structure of rare earth-doped phosphor materials as well as the destruction processes of MgO protecting layer in plasma display panel (PDP). We have also developed a quantitative prediction method based on Monte Carlo simulation technique to evaluate the electrical conductivity of insulators, semiconductors, and metals as well as the spatial distribution of electron density by Colors code. All these original simulators enable us to study theoretically a variety of materials related to PDP.

• 한국전기전자재료학회:학술대회논문집
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• 한국전기전자재료학회 2008년도 추계학술대회 논문집 Vol.21
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• pp.241-242
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• 2008

The Velocity Autocorrelation Function (VAF) of the sodium ions is calculated for a range of temperature from 250K to 1000K and converted into the linear ac-conductivity and ac-susceptibility response via Fourier transformation. A peak is found in the conductivity around $6\times10^{12}$ Hz that has some of the character of a Poley absorption. Here it is shown to be due to an harmonically coupled site vibrations of the sodium atoms, which extend only over a limited range. At frequencies below the peak the conductivity tends towards a constant i.e. dc value corresponding to a constant flow of ions through the simulation cell. At high temperatures the conductivity due to this ion transport process behaves like a metal with an insulator to metal transition occurring around a specific temperature.

• 한국전산유체공학회지
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• 제21권1호
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• pp.43-49
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• 2016

Thermal cracking is commonly modeled as plug flow reaction, neglecting the lateral gradients present. In this paper, 2-dimensional computational fluid dynamics including turbulence model and molecular reaction scheme are carried out. This simulation is solved by means of coupled implicit scheme for stable convergence of solution. The reactor is modeled as an isothermal tube, whose length is 1.2 m and radius is 0.01 m, respectively. At first, The radial profile of velocity and temperature at each point are predicted in its condition. Then the bulk temperature and conversion curve along the axial direction are compared with other published data to identify the reason why discussed variations of properties are important to product yield. Finally, defining a new non-dimensional number, Effect of interaction with turbulence, heat transfer and chemical reaction are discussed for design of thermal cracking furnace.