• International Journal of Control, Automation, and Systems
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• 제4권3호
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• pp.382-393
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• 2006

Mechanical system dynamics plays an important role in the area of computational structural biology. Elastic network models (ENMs) for macromolecules (e.g., polymers, proteins, and nucleic acids such as DNA and RNA) have been developed to understand the relationship between their structure and biological function. For example. a protein, which is basically a folded polypeptide chain, can be simply modeled as a mass-spring system from the mechanical viewpoint. Since the conformational flexibility of a protein is dominantly subject to its chemical bond interactions (e.g., covalent bonds, salt bridges, and hydrogen bonds), these constraints can be modeled as linear spring connections between spatially proximal representatives in a variety of coarse-grained ENMs. Coarse-graining approaches enable one to simulate harmonic and anharmonic motions of large macromolecules in a PC, while all-atom based molecular dynamics (MD) simulation has been conventionally performed with an aid of supercomputer. A harmonic analysis of a macroscopic mechanical system, called normal mode analysis, has been adopted to analyze thermal fluctuations of a microscopic biological system around its equilibrium state. Furthermore, a structure-based system optimization, called elastic network interpolation, has been developed to predict nonlinear transition (or folding) pathways between two different functional states of a same macromolecule. The good agreement of simulation and experiment allows the employment of coarse-grained ENMs as a versatile tool for the study of macromolecular dynamics.

• 한국콘텐츠학회논문지
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• 제13권7호
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• pp.24-37
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• 2013

본 연구는, 픽사의 와 에 나타난 부모와 자녀 캐릭터 사이의 갈등구도를, MBTI의 유형역동이라는 관점에서 비교 분석하고자 했다. 이에, 캐릭터의 성격유형과 심리기능의 위계를 추론하고, 유형역동에 의한 갈등과 화해의 구조를 분석하였다. 작품 분석을 통해 도출된 결론은: (1) 부모의 사고기능이 자녀의 직관기능을 구속하는 구조로, '현실과 가능성의 충돌'로 은유됨. (2) 보완 역할 캐릭터의 외향적 심리기능이, 결핍 캐릭터의 미발달된 3차기능을 보완하면서, 유형발달에 기여함. (3) 에서는, 갈등주체에 의한 직접적 단방향의 보완을 이루며, (4) 에서는, 갈등주체가 아닌 거울캐릭터에 의한 간접적 쌍방향의 상호보완을 이루는 방법론의 차이를 보인다.

• BMB Reports
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• 제34권1호
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• pp.1-7
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• 2001

Structural and physical properties of type wild type and various selected mutants of the vnd/NK-2 homeodomain, the protein product of the homeobox, and the implication in genetic disease are reviewed. The structure, dynamics and thermodynamics have been Investigated by NMR and by calorimetry. The interactions responsible for the nucleotide sequence-specific binding of the homeodomain to its consensus DNA binding site have been identified. There is a strong correlation between significant structural alterations within the homeodomain or its DNA complex and the appearance of genetic disease. Mutations in positions known to be important in genetic disease have been examined carefully For example, mutation of position 52 of vnd/NK-2 results in a significant structural modification and mutation of position 54 alters the DNA binding specificity and amity The $^{15}N$ relaxation behavior and heteronuclear Overhauser effect data was used to characterize and describe the protein backbone dynamics. These studies were carried out on the wild type and the double mutant proteins both in the free and in the DNA bound states. Finally, the thermodynamic properties associated with DNA binding are described for the vnd/NK-2 homeodomain. These thermodynamic measurements reinforce the hypothesis that water structure around a protein and around DNA significantly contribute to the protein-DNA binding behavior. The results, taken together, demonstrate that structure and dynamic studies of proteins combined with thermodynamic measurements provide a significantly more complete picture of the solution behavior than the individual studies.

• 한국시스템다이내믹스연구
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• 제13권3호
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• pp.5-22
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• 2012

Although many system dynamists point out the close relationship between institutional economics and system dynamics, the relationship between institutional political theory and system dynamics approach is not explicitly appreciated yet. We developed a system dynamics model to investigate theoretical propositions of institutional politics. Our system dynamics model showed how the endogenous mechanism can explain the political changes as well as orders. Although simple in the causal structure, our model could show a complex behavior of political competition. Several simulation results imply that some unexpected changes in election and power competition may come from the endogenous system rather than from exogenous factors such as economic and environmental shocks.

• 한국시스템다이내믹스연구
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• 제17권3호
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• pp.31-50
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• 2016

This study examines the basic conditions of joint authorship research activities in the Korean System Dynamics Review and points out the structural co-author network characteristics among co-authored papers based on the social network analysis(SNA) techniques. In specific, this study identifies the cooperative relationship of research papers in the Korean System Dynamics Review, knowledge formation, and knowledge propagation paths. The study results imply that Korean System Dynamics Review has exhibited the typical 'Steven's power law,' which is repeatedly observed among complex systems, and that knowledge structure centered upon and propagated around couples of researchers. Additionally, the study results present that there have been active personal exchanges among major researchers. In contrast, personal contacts among research groups and within groups seem relatively weak.

• 대한금속재료학회지
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• 제47권8호
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• pp.461-465
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• 2009

We study the diffusion of Ag based bimetallic nanoclusters supported on graphite. Using a molecular dynamics simulation, we reveal that the Ag clusters show rapid diffusion because of their hexagonal bottom layer. In order to decrease the rate of diffusion, we added Pt and Ni to distort the structure of the alloy cluster (i.e., the alloying method). We expected Pt to provide a stronger force on Ag atoms, and Ni to shorten the bond length and thereby change the structure of Ag cluster. However, the attempt was unsuccessful, because Pt and Ni atoms formed cores inside the Ag clusters. We therefore designed a collision system where large Ag clusters collide with small Pt or Ni clusters. Upon collision with Pt clusters, the diffusion showed little change, because Pt atoms are substituted at the Ag atomic site and form a perfectly ordered structure. The collision with Ni, however, deforms the bottom layer as well as the overall cluster structure and decreases diffusion. This outcome appoints toward the possibility of further application to the manufacture of durable nanocatalysts.

• 한국시스템다이내믹스연구
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• 제15권1호
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• pp.75-96
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• 2014

This research primarily aims at analyzing major crises originating from marginalizing population, especially in counties. In addition, based on the system dynamics approaches, it pays attention to divulging causal loop structure which has been rather strengthened by diverse interactions among key variables. Judging from simulation works, even though Korea is exposed to unprecedented aging trends over decades, its counter response seems inadequate and insufficient, mostly dismissing a series of impact embedded in the aging dynamics. This research statistically confirms that demographic marginalization trends have already begun in the villages within Eup and Myon counties. Furthermore, this research pinpoints out the fact that it would be almost impossible for majority of villages within Eup and Myon counties to escape from going out of existence in the course of time, as they tend to be entrapped vicious cycle of marginalization or extinction.

• 한국소음진동공학회:학술대회논문집
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• 한국소음진동공학회 2005년도 춘계학술대회논문집
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• pp.128-131
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• 2005

Structural Dynamics Modification (SDM) is a very effective technique to improve structure's dynamic characteristics by adding or removing auxiliary structures. changing material properties and shape of structure. Among those of SDM technique, the method to change shape of structure has been mostly relied on engineer's experience and trial-and-error process which are very time consuming. In order to develop a systematic method to change structure shape, surface grooving technique is studied and successfully applied to HDD cover model. To check the effectiveness of this surface grooving technique, the grooved HDD cover design was manufactured using rapid prototyping and experimentally tested to prove the effectiveness of the grooving method as one of SDM techniques. And the modal strain energy and eigenvalue sensitivity method for choosing the initial starting point are compared.

• 한국소음진동공학회:학술대회논문집
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• 한국소음진동공학회 2005년도 추계학술대회논문집
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• pp.834-837
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• 2005

Structural Dynamics Modification (SDM) is a very effective technique to improve structure's dynamic characteristics by adding or removing auxiliary structures, changing material properties and shape of structure. Among those of SDM technique, the method to change shape of structure has been mostly relied on engineer's experience and trial-and-error process which are very time consuming. In order to develop a systematic method to change structure shape, surface grooving technique is studied and successfully applied to HDD cover model. At first, to check the effect of mesh size, surface grooving technique was tested to the fine HDD cover FEmodel. And fur the more efficient method, the algorithm is modified. Removing the low-valued modal strain energy element among the target domain, computational effort can be greatly reduced and the result of simulation is similar with the other simulation result.

• Smart Structures and Systems
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• 제13권2호
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• pp.305-318
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• 2014

This paper numerically investigates the feasibility of an active mass damper (AMD) system using the time delay control (TDC) algorithm, which is one of the robust and adaptive control algorithms, for effectively suppressing the excessive vibration of a building structure under wind loading. Because of its several attractive features such as the simplicity and the excellent robustness to unknown system dynamics and disturbance, the TDC algorithm has the potential to be an effective control system for mitigating the vibration of civil engineering structures such as buildings and bridges. However, it has not been used for structural response reduction yet. In this study, therefore, the active control method combining an AMD system with the TDC algorithm is first proposed in order to reduce the wind-induced vibration of a building structure and its effectiveness is numerically examined. To this end, its stability analysis is first performed; and then, a series of numerical simulations are conducted. It is demonstrated that the proposed active structural control system can effectively reduce the acceleration response of the building structure.