• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.24-31
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• 2015

효소는 생명 현상을 구현하는 단백질 촉매인데 그 동안 효소의 촉매 반응 속도는 Michaelis-Menten(MM) 모델로 대부분 설명되어 왔다. 그러나 MM 모델은 실험으로 측정된 단일 효소 반응시간의 확률분포 모양을 설명할 수 없다. MM 모델에 반응계수의 정적 무질서 개념을 도입한 효소 반응 모델도 기질 농도에 따라 변화하는 효소 반응시간의 통계적 요동을 설명하지 못한다. 우리는 단일 효소 반응시간의 통계적 요동이 기질에 따라 변화하는 양상을 설명하기 위해 효소 반응을 구성하는 개별 화학반응을 단순히 푸아송 과정이 아닌 갱신과정(renewal process)으로 확장한 효소 반응 모델을 제안한다. 우리는 이 단일 효소 반응 모델과 기질에 따른 효소 반응시간 분산 변화 데이터를 비교하여 효소-기질 복합체의 지속시간 분포를 간단한 형태로 얻어내었다. 또한, 이 정보를 토대로 전산모사를 수행하여 효소 반응시간의 확률분포를 얻어내고, 실제 실험 결과 및 기존 이론들과 비교하였다. 뿐만 아니라 단일 효소 반응시간의 확률분포를 연속 시간 임의의 보행자(continuous time random walker)의 대기시간 확률분포(waiting time distribution)로 대응하면, 평균 제곱 변위가 시간에 따라 단순히 증가 하지 않는 고분자의 특이 수송(anomalous diffusion) 현상도 정량적으로 설명할 수 있었다.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.177-183
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• 2015

$\text\tiny{D}$-Psicose 3-Epimerase (DPE)는 $\text\tiny{D}$-Fructose의 C3 Epimerase로써 $\text\tiny{D}$-Fructose를 $\text\tiny{D}$-Psicose로 전환해 주는 효소이다. $\text\tiny{D}$-Psicose는 설탕 대신 사용하는 감미료로 몸에 흡수되지 않아 칼로리가 없다고 알려져 있고 자연에서는 오로지 DPE에 의해서만 생산되는 희귀당이다. 이에 따라 DPE를 통한 $\text\tiny{D}$-Psicose 대량생산의 필요성이 대두되고 있는 등 이 분야에 대한 관심이 뜨거운 실정이다. 본 연구팀은 이 당과 관련된 작용기작 연구를 수행하기 위하여 아직 단백질 3차구조가 알려지지 않은 Clostridium hylemonae DPE (chDPE) 단백질의 3차 구조예측 연구를 수행 하였다. 우리는 HHsearch를 이용하여 agrobacterium tumefaciens의 DPE 외 2개의 구조를 호몰로지 모델링 연구를 위한 주형으로 선정하였다. 다음으로 PROMALS3D를 이용하여 주형들과 chDPE의 multiple sequence alignment를 수행하였고 이를 바탕으로 3차구조 예측 연구를 수행 하였다. 예측된 구조를 검증하기 위하여 ProSA와 Ramachandran plot분석을 이용하였고 Ramachandran plot에서 단백질의 94.8%에 해당하는 잔기들이 favoured regions에 위치하였다. ProSA에서는 Z-score값이 -9.3으로 X-선 결정학이나 핵자기 공명법으로 밝혀진 구조들에서 관측되는 범위 내에 위치하였다. 나아가 예측된 구조에 $\text\tiny{D}$-Psicose와 $\text\tiny{D}$-Fructose의 결합모드를 규명하기 위하여 도킹을 시도하였다. 이번 연구를 통하여 chDPE의 구조를 예측 할 수 있었고 이를 바탕으로 이 단백질의 기능을 이해하는데 도움을 줄 것으로 기대된다.

• Journal of Korean Tunnelling and Underground Space Association
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• v.14 no.1
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• pp.37-53
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• 2012

There is considerable uncertainty in ground properties used in tunnel designs. In this study, a back analysis was performed to find optimal ground properties based on the artificial neural network facility of MATLAB program of using tunnel monitoring data. Total 81 data were constructed by changing elastic modulus and coefficient of lateral pressure which have great influence on tunnel convergence. A sensitivity analysis was conducted to establish an optimal training model by varying the number of hidden layers, the number of nodes, learning rate, and momentum. Meanwhile, the optimal training model was selected by comparing MSE (Mean Squared Error) and coefficient of determination ($R^2$) and was used to find the correct elastic moduli of layers and the coefficient of lateral pressure. In future, it is expected that the suggested method of this study can be applied to determine the optimum tunnel support pattern under given ground conditions.

• Korean Chemical Engineering Research
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• v.47 no.2
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• pp.179-184
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• 2009

Recent evolution of computer technology enhances the effectiveness of CFD(Computational Fluid Dynamics) analysis for the 3-dimensional complex transport phenomena including turbulent flows. Cheaper and easier than laser and ultra-sonic methods, the windows simulator name by CAMSI(Computer-Aided Management of Stereo Images) has been developed in order to implement the 3-dimensional image using a disparity histogram extracted from left and right stereo images. In our program using the area-based method, the matching pixel finding methods consist of SSD(Sum of Squared Distance), SAD(Sum of Absolute Distance), NCC(Normalized Correlation Coefficient) and MPC(Matching Pixel Count). On performing the program, stereo images on different window sizes for various matching pixel finding methods are compared reasonably. When the image has a small noise, SSD on small window size is more effective. Whereas there is much noise, NCC or MPC is more effective than SSD. CAMSI from the present study will be much helpful to implement the complex objects and to analyze 3-dimensional CFD around them.

• Journal of Korean Society of Coastal and Ocean Engineers
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• v.22 no.1
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• pp.10-17
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• 2010

The interaction of oblique incident waves with a porous dual semi-cylindrical structure is investigated under the assumption of linear potential theory. The porous dual semi-cylindrical structure consists of two concentric bottom-mounted cylindrical structures that are porous in front half and transparent in back half. By changing porosity, gap, and wave characteristics(wave frequencies, incidence angle), the wave blocking performance as well as the wave loads and the wave run-up are obtained. As a convenient measure of overall wave blocking performance, the root mean square(R.M.S.) of the wave elevation in a sheltered region is used. It is found that the porous semi-cylindrical structure may significantly reduce the wave response in a sheltered region and the wave forces decrease largely compared to the impermeable structure. The dual structure is more effective in reducing the wave response in a sheltered region than the mono type in the region of high frequencies.

• Journal of KIISE:Software and Applications
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• v.32 no.7
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• pp.612-624
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• 2005

In this paper, we propose a surface-based registration using a gaussian weighted distance map for PET-CT brain image fusion. Our method is composed of three main steps: the extraction of feature points, the generation of gaussian weighted distance map, and the measure of similarities based on weight. First, we segment head using the inverse region growing and remove noise segmented with head using region growing-based labeling in PET and CT images, respectively. And then, we extract the feature points of the head using sharpening filter. Second, a gaussian weighted distance map is generated from the feature points in CT images. Thus it leads feature points to robustly converge on the optimal location in a large geometrical displacement. Third, weight-based cross-correlation searches for the optimal location using a gaussian weighted distance map of CT images corresponding to the feature points extracted from PET images. In our experiment, we generate software phantom dataset for evaluating accuracy and robustness of our method, and use clinical dataset for computation time and visual inspection. The accuracy test is performed by evaluating root-mean-square-error using arbitrary transformed software phantom dataset. The robustness test is evaluated whether weight-based cross-correlation achieves maximum at optimal location in software phantom dataset with a large geometrical displacement and noise. Experimental results showed that our method gives more accuracy and robust convergence than the conventional surface-based registration.

• Journal of the Korea institute for structural maintenance and inspection
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• v.21 no.6
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• pp.113-125
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• 2017

In spite of bulk literature about the tuning of TMD, the effectiveness of TMD in reducing the seismic response of engineering structures is still in a row. This paper deals with the optimum tuning parameters of a passive TMD and simulated on MATLAB with a ten-story numerical shear building. A weighted multi-objective optimization method based on computer experiment consisting of coupled with central composite design(CCD) central composite design and response surface methodology(RSM) was applied to find out the optimum tuning parameters of TMD. After the optimization, the so-conceived TMD turns out to be optimal with respect to the specific seismic event, hence allowing for an optimum reduction in seismic response. The method was employed on above structure by assuming first the El Centro seismic input as a sort of benchmark excitation, and then additional recent strong-motion earthquakes. It is found that the RSM based weighted multi-objective optimized damper improves frequency responses and root mean square displacements of the structure without TMD by 31.6% and 82.3% under El Centro earthquake, respectively, and has an equal or higher performance than the conventionally designed dampers with respect to frequency responses and root mean square displacements and when applied to earthquakes.

• Journal of the Mineralogical Society of Korea
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• v.32 no.3
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• pp.151-162
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• 2019

Todorokite, a tunnel-structured manganese oxide, can contain cations within the relatively large nanopores created by the $3{\times}3$ Mn octahedra. Because todorokite is poorly crystalline and found as aggregates mixed with other phases of Mn oxides in nature, the coordination structure of cations in the nanopores is challenging to fully characterize in experiment. In the current article, we report the atomistic coordination structures of $Mg^{2+}$ ions in todorokite tunnel nanopores using the classical molecular dynamics (MD) simulations. In experiment, $Mg^{2+}$ is known to occupy the center of the nanopores. In our MD simulations, 60 % of $Mg^{2+}$ ions were located at the center of the nanopores; 40 % of the ions were found at the corners. All $Mg^{2+}$ located at the center formed the six-fold coordination with water molecules, just as the ion in bulk aqueous solution. $Mg^{2+}$ ions at the corners also formed the six-fold coordination with not only water molecules but also Mn octahedral surface oxygens. The mean squared displacements were calculated to examine the dynamic features of $Mg^{2+}$ ions in the one-dimensional (1D) nanopores. Our MD simulations indicate that the dynamic features of water molecules and the cations observed in bulk aqueous solution are lost in the 1D nanopores of todorokite.

• Korean Journal of Mineralogy and Petrology
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• v.36 no.4
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• pp.221-232
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• 2023

Carbon neutrality requires carbon dioxide reduction technology and alternative green energy sources. Palygorskite is a clay mineral with a ribbon structure and possess a large surface area due to the nanoscale pore size. The clay mineral has been proposed as a potential material to capture carbon dioxide (CO₂) and possibly to store eco-friendly hydrogen gas (H2). We report our preliminary results of grand canonical Monte Carlo (GCMC) simulations that investigated the adsorption isotherms and mechanisms of CO₂ and H₂ into palygorskite nanopores at room temperature. As the chemical potential of gas increased, the adsorbed amount of CO₂ or H₂ within the palygorskite nanopores increased. Compared to CO₂, injection of H₂ into palygorskite required higher energy. The mean squared displacement within palygorskite nanopores was much higher for H₂ than for CO₂, which is consistent with experiments. Our simulations found that CO₂ molecules were arranged in a row in the nanopores, while H₂ molecules showed highly disordered arrangement. This simulation method is promising for finding Earth materials suitable for CO₂ capture and H₂ storage and also expected to contribute to fundamental understanding of fluid-mineral interactions in the geological underground.