• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.431-436
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• 2005

Living cells are sustained not by individual activities but rather by coordinated summative efforts of different biological functional modules. While recent research works have focused largely on finding individual functional modules, this paper attempts to explore the connections or relationships between different cellular functions through cross-function domain interaction maps. Exploring such a domain interaction map can help understand the underlying inter-function communication mechanisms. To construct a cross-function domain interaction map from existing genome-wide protein-protein interaction datasets, we propose a two-step procedure. First, we infer conserved domain-domain interactions from genome-wide protein-protein interactions of yeast, worm and fly. We then build a cross-function domain interaction map that shows the connections of different functions through various conserved domain interactions. The domain interaction maps reveal that conserved domain-domain interactions can be found in most detected cross-functional relationships and a f9w domains play pivotal roles in these relationships. Another important discovery in the paper is that conserved domains correspond to highly connected protein hubs that connect different functional modules together.

• Bioinformatics and Biosystems
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• 제1권2호
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• pp.128-133
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• 2006

This paper compares domain combination based protein-protein interaction prediction method with domain based protein-protein interaction method. The prediction accuracy and reliability of the methods are compared using the same prediction technique and interaction data. According to the comparison, domain combination based prediction method has showed superior prediction accuracy to domain based prediction method for protein pairs with fully overlapped domains with protein pairs in learning sets. When we consider that domain combination based method has the effects of assigning a weight to each domain interaction, it implies that we can improve the prediction accuracies of currently available domain or domain combination based protein interaction prediction methods further by developing more advanced weight assignment techniques. Several significant facts revealed from the comparative studies are also described in this paper.

• 한국정보과학회논문지:소프트웨어및응용
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• 제36권10호
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• pp.851-860
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• 2009

최근 계산을 통한 단백질 상호작용 예측 기법 중, 단백질 쌍이 포함하고 있는 도메인들 사이의 관계에 중점을 둔 도메인 정보 기반 예측 기법들이 다양하게 제안되고 있다. 하지만, 다수의 도메인 쌍들이 상호작용에 기여하는 정도를 정밀하게 반영하는 계산 기법은 드문 실정이다. 본 논문에서는 단백질 상호작용에 있어 도메인 조합 쌍의 상호작용 영향력을 수치화하여 반영한 상호작용 중요도 행렬을 고안하고 이를 기반으로 한 단백질 상호작용 예측 시스템을 구현한다. 일반적인 도메인 조합 기법과 달리, 상호작용 중요도 행렬에서는 상호작용을 위한 도메인간의 협업 확률이 고려된 Weighted 도메인 조합과, 다수의 Weighted 도메인 조합 중 실제 상호작용 주체가 될 확률을 도메인 조합 쌍의 힘(Domain Combination Pair Power, DCPPW)으로 수치화한다. DIP과 IntAct에서 얻어온 S. cerevisiae의 단백질 상호작용 데이터와 Pfam-A 도메인 정보를 사용한 정확도 검증 결과, 평균 63%의 민감도와 94%의 특이도를 확인하였으며, 학습집단의 증가에 따른 안정적인 예측 정확도 향상을 보였다. 본 논문에서 구현한 예측 시스템과 학습 데이터는 웹(http://code.google.com/p/prespi)을 통하여 내려 받을 수 있다.

• 한국광물학회지
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• 제10권2호
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• pp.97-104
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• 1997

Based on the method of determination for relative stability of each phase from the difference among the interaction parameters of the phases consisting the mixed layer, the types of interactions between layers were specified and interaction parameter between layers in ordered domain was analytically derived as a function parameter between layers in ordered domain was analytically derived as a function of not only temperature and mole fraction of layers but also ordering parameter. Interaction parameter between the different layers in ordered phase, L is as follows:{{{{ {L }_{1 } (X,Q,T)= { C} over { Q} -4(1-2Q) { L}^{2 } - { RT} over {2} ln { 1} over {2 } - { 2RT} over { { X}_{ s} } ln { { 4QX}`_{s } ^{2 } } over {(1- { X}_{s }- { QX}_{s })( { X}_{s }- {QX }_{s } ) } }}}}L2 is the interaction parameter between ordered and disordered phase in domain and is the mole fraction of the domain which represent the infinite length of mixed layer mineral and Q and C are the reaction progress parameter and arbitrary constant, respectively. This equation was used for the I/S mixed layer clay minerals to infer the relative stability of R1 type I/S mixed layer in the temperature range from 373K to 450K. The result of calculation suggest that, owing to the decrease in interaction parameter with increasing temperature. The interaction parameter decreases more rapidly with decreasing mole fraction of smectite in domain, which is consistent with the fact that the probability of finding the series smectite layer is lo in the domain with small mole fraction of smectite layers in natural system.

• Structural Engineering and Mechanics
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• 제15권6호
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• pp.717-733
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• 2003

A time domain method is presented for soil-structure interaction analysis under seismic excitations. It is based on the finite element formulation incorporating infinite elements for the far field soil region. Equivalent earthquake input forces are calculated based on the free field responses along the interface between the near and far field soil regions utilizing the fixed exterior boundary method in the frequency domain. Then, the input forces are transformed into the time domain by using inverse Fourier transform. The dynamic stiffness matrices of the far field soil region formulated using the analytical frequency-dependent infinite elements in the frequency domain can be easily transformed into the corresponding matrices in the time domain. Hence, the response can be analytically computed in the time domain. A recursive procedure is proposed to compute the interaction forces along the interface and the responses of the soil-structure system in the time domain. Earthquake response analyses have been carried out on a multi-layered half-space and a tunnel embedded in a layered half-space with the assumption of the linearity of the near and far field soil region, and results are compared with those obtained by the conventional method in the frequency domain.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2002년도 제1차워크샵
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• pp.5-23
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• 2002

Motivation: Protein-protein interaction plays a critical role in the biological processes. The identification of interacting proteins by bioinformatical methods can provide new lead In the functional studies of uncharacterized proteins without performing extensive experiments. Results: Protein-protein interactions are predicted by a computational algorithm based on the weighted scoring system for domain interactions between interacting protein pairs. Here we propose potential interaction domain (PID) pairs can be extracted from a data set of experimentally identified interacting protein pairs. where one protein contains a domain and its interacting protein contains the other. Every combinations of PID are summarized in a matrix table termed the PID matrix, and this matrix has proposed to be used for prediction of interactions. The database of interacting proteins (DIP) has used as a source of interacting protein pairs and InterPro, an integrated database of protein families, domains and functional sites, has used for defining domains in interacting pairs. A statistical scoring system. named "PID matrix score" has designed and applied as a measure of interaction probability between domains. Cross-validation has been performed with subsets of DIP data to evaluate the prediction accuracy of PID matrix. The prediction system gives about 50% of sensitivity and 98% of specificity, Based on the PID matrix, we develop a system providing several interaction information-finding services in the Internet. The system, named PreDIN (Prediction-oriented Database of Interaction Network) provides interacting domain finding services and interacting protein finding services. It is demonstrated that mapping of the genome-wide interaction network can be achieved by using the PreDIN system. This system can be also used as a new tool for functional prediction of unknown proteins.

• 한국과학교육학회지
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• 제32권4호
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• pp.760-774
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• 2012

이 연구의 목적은 과학 탐구활동에서 모둠 리더의 리더십 유형에 따른 언어적 상호작용의 특징과 리더가 지니고 있는 리더십 요소가 모둠의 언어적 상호작용에 어떠한 영향을 미치는 지에 대하여 알아보는 것이다. 비전과 추진, 과제책임, 의사결정 세 가지 리더십 요소별로 모둠의 리더를 선정하여 과학탐구능력, 학업성취도평가의 항목으로 모둠원을 구성하여 과학탐구활동을 실시하면서 언어적 상호 작용을 분석하였다. 비전과 추진 모둠이 상대적으로 가장 많은 언어적 상호작용의 빈도수를 보였는데, 이는 리더 속에 내재되어있는 비전과 추진 리더십의 '비전'과 '자신감'의 요소가 영향을 주었기 때문이다. 세 모둠 모두 과제해결과 관련하여 인지적 측면이 정의적 측면 언어적 상호작용보다 많았다. 인지적 측면의 언어적 상호작용에서는 실험 현상과 관련하여 낮은 수준의 언어적 상호작용이 대다수였고, 상위수준의 언어적 상호작용은 적은 빈도수로 일어났다. 정의적 측면에서는 행동참여가 분위기조절보다 더 많은 빈도수를 보였다. 이는 모둠에서 분위기 조절보다는 과제 해결을 위한 모둠원의 행동 제어와 관련된 상호작용이 많았기 때문이다.

• 한국전산구조공학회:학술대회논문집
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• 한국전산구조공학회 1999년도 봄 학술발표회 논문집
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• pp.121-128
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• 1999

This paper presents a time domain method for soil-structure interaction analysis for seismic loadings. It is based on the finite element formulation incorporating analytical frequency-dependent infinite elements for the far field soil. The dynamic stiffness matrices of the far field region formulated using the present method in frequency domain can be easily transformed into the corresponding matrices in time domain. At first, the equivalent earthquake forces are evaluated along the interface between the near and the far fields from the free-field response analysis carried out in frequency domain, and the results are transformed into the time domain. An efficient procedure is developed for the convolution integrals to evaluate the interaction force along the interface, which depends on the response on the interface at the past time instances as well as the concurrent instance. Then, the dynamic responses are obtained for the equivalent earthquake force and the interaction force using Newmark direct integration technique. Since the response analysis is carried out in time domain, it can be easily extended to the nonlinear analysis. Example analysis has been carried out to verify the present method in a multi-layered half-space.

• 한국소음진동공학회:학술대회논문집
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• 한국소음진동공학회 2005년도 추계학술대회논문집
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• pp.812-817
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• 2005

The objective of the present work is to develop a time-domain numerical method of broadband noise in a cascade of airfoils. This paper focuses on dipole broadband noise sources, resulting from the interaction of turbulent inflows with the flat-plate airfoil cascade. The turbulence response of a two-dimensional cascade is studied by solving both of the linearised and full nonlinear Euler equations employing accurate higher order spatial differencing, time stepping techniques and non-reflecting inflow/outflow boundary condition. The time-domain result using the linearised Euler equations shows good agreement with the analytical solution using the modified LINSUB code. Through the comparison of the nonlinear time-domain result using the full nonlinear Euler equations with the linear, it is found that the acoustic mode amplitude of the nonlinear response is less than that of the linear response due to the energy cascade from low frequency components to the high frequency ones. Considering the merits of the time-domain methods over the typical time-linearised frequency-domain analysis, the current method is expected to be promising tools for analyzing the effects of the airfoil shapes, non-uniform background flow, linear-nonliear regimes on the broadband noise due to gust-cascade interaction.

• 한국전산구조공학회:학술대회논문집
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• 한국전산구조공학회 1997년도 가을 학술발표회 논문집
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• pp.42-49
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• 1997

In this paper, the method for soil-structure interaction analyses in the time domain is proposed. The far field soil region which is the outside of the artificial boundary is modeled by using explicit frequency-dependent two dimensional infinite elements which can include multiple wave components propagating into the unbounded medium. Since the dynamic stiffness matrix of the far field soil region using the proposed infinite elements is obtained explicitly in terms of exciting frequencies and constants in the frequency domain, the matrix can be easily transformed into the displacement unit-impulse response matrix, which corresponds to a convolution integral of it in the time domain. To verify the proposed method for soil-structure interaction analyses in the time domain, the displacement responses due to an impulse load on the surface of a soil layer with the rigid bed rock are compared with those obtained by the method in the frequency domain and those by models with extend finite element meshes. Good agreements have been found between them.