• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2005.09a
• /
• pp.431-436
• /
• 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
• /
• v.1 no.2
• /
• pp.128-133
• /
• 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.

• Journal of KIISE:Software and Applications
• /
• v.36 no.10
• /
• pp.851-860
• /
• 2009

Recently, among the computational methods of protein-protein interaction prediction, vast amounts of domain based methods originated from domain-domain relation consideration have been developed. However, it is true that multi domains collaboration is avowedly ignored because of computational complexity. In this paper, we implemented a protein interaction prediction system based the Interaction Significance matrix, which quantified an influence of domain combination pair on a protein interaction. Unlike conventional domain combination methods, IS matrix contains weighted domain combinations and domain combination pair power, which mean possibilities of domain collaboration and being the main body on a protein interaction. About 63% of sensitivity and 94% of specificity were measured when we use interaction data from DIP, IntAct and Pfam-A as a domain database. In addition, prediction accuracy gradually increased by growth of learning set size, The prediction software and learning data are currently available on the web site.

• Journal of the Mineralogical Society of Korea
• /
• v.10 no.2
• /
• pp.97-104
• /
• 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
• /
• v.15 no.6
• /
• pp.717-733
• /
• 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.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2002.06a
• /
• pp.5-23
• /
• 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.

• Journal of The Korean Association For Science Education
• /
• v.32 no.4
• /
• pp.760-774
• /
• 2012

The purpose of this study was to analyze the characteristic of the linguistic interaction according to leadership type of the leader in the scientific inquiry activity groups and examine how leadership factors affect the linguistic interaction within a group. In this investigation, leaders among 12 elementary school students were chosen by considering results of the leadership diagnosis that tested 3 leadership factors: vision and promotion, assignment responsibility, and decision-making. The members of the groups were organized according to scientific inquiry ability and academic achievement; the groups were assigned to perform scientific inquiry activities. The linguistic interaction was largely divided into the cognitive domain and the affective domain for analysis. According to the results, the frequency of linguistic interaction within a group sorted by leadership type is more influenced by the cognitive domain than the affective domain. The highest frequency of linguistic interaction appeared within the group that had vision and promotion type leader. Assumedly, the vision and confidence of the vision and promotion type leader produced such an outcome. While solving the assignments, linguistic interaction in all three groups had more cognitive domain than affected domain. Linguistic interaction in cognitive domain displayed only low level of linguistic interaction in relation to the experiment itself: high level of linguistic interaction barely occurred. In the case of affected domain, active participation appeared more frequently than maintaining the mood: Interactions related to restricting the group members actions to solve the assignment appeared more frequently than those for maintaining the mood.

• Proceedings of the Computational Structural Engineering Institute Conference
• /
• 1999.04a
• /
• pp.121-128
• /
• 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.

• Proceedings of the Korean Society for Noise and Vibration Engineering Conference
• /
• 2005.11a
• /
• pp.812-817
• /
• 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.

• Proceedings of the Computational Structural Engineering Institute Conference
• /
• 1997.10a
• /
• pp.42-49
• /
• 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.