• 한국자기공명학회논문지
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• 제17권1호
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• pp.11-18
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• 2013

Rapid advances of computational power and method have made it practical to apply the time-consuming calculations with all-atom force fields and sophisticated potential energies into refining NMR structure. Added to the all-atom force field, generalized-Born implicit solvent model (GBIS) contributes substantially to improving the qualities of the resulting NMR structures. GBIS approximates the effects that explicit solvents bring about even with fairly reduced computational times. Although GBIS is employed in the final stage of NMR structure calculation with experimental restraints, the effects by GBIS on structures have been reported notable. However, the detailed effect is little studied in a quantitative way. In this study, we report GBIS refinements of ubiquitin and GB1 structures by six GBIS models of AMBER package with experimental distance and backbone torsion angle restraints. Of GBIS models tested, the calculations with igb=7 option generated the closest structures to those determined by X-ray both in ubiquitin and GB1 from the viewpoints of root-mean-square deviations. Those with igb=5 yielded the second best results. Our data suggest that the degrees of improvements vary under different GBIS models and the proper selection of GBIS model can lead to better results.

• 한국자기공명학회논문지
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• 제19권1호
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• pp.1-10
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• 2015

Refinements with atomistic molecular dynamics (MD) simulation have contributed to improving the qualities of NMR structures. In most cases, the calculations with atomistic MD simulation for NMR structures employ generalized-Born implicit solvent model (GBIS) to take into accounts solvation effects. Developments in algorithms and computational capacities have ameliorated GBIS to approximate solvation effects that explicit solvents bring about. However, the quantitative comparison of NMR structures in the latest GBIS and explicit solvents is lacking. In this study, we report the direct comparison of NMR structures that atomistic MD simulation coupled with GBIS and water molecules refined. Two model proteins, GB1 and ubiquitin, were recalculated with experimental distance and torsion angle restraints, under a series of simulated annealing time steps. Whereas the root mean square deviations of the resulting structures were apparently similar, AMBER energies, the most favored regions in Ramachandran plot, and MolProbity clash scores witnessed that GBIS-refined structures had the better geometries. The outperformance by GBIS was distinct in the structure calculations with sparse experimental restraints. We show that the superiority stemmed, at least in parts, from the inclusion of all the pairs of non-bonded interactions. The shorter computational times with GBIS than those for explicit solvents makes GBIS a powerful method for improving structural qualities particularly under the conditions that experimental restraints are insufficient. We also propose a method to separate the native-like folds from non-violating diverged structures.

• Bulletin of the Korean Chemical Society
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• 제35권7호
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• pp.1944-1950
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• 2014

Employment of a time consuming, sophisticated calculation using the all-atom force field and generalized-Born implicit solvent model (GBIS) for refinement of NMR structures has become practical through advances in computational methods and capacities. GBIS refinement improves the qualities of the resulting NMR structures with reduced computational times. However, the contribution of GBIS to NMR structures has not been sufficiently studied in a quantitative way. In this paper, we report the effects of GBIS on the refined NMR structures of ubiquitin (UBQ) and GB1 with subsets of distance restraints derived from experimental data. Random omission prepared a series of distance restraints 0.05, 0.1, 0.3, 0.5, and 0.7 times smaller. For each number, we produced five different restraints for statistical analysis. We then recalculated the NMR structures using CYANA software, followed by GBIS refinements using the AMBER package. GBIS improved both the precision and accuracy of all the structures, but to varied levels. The degrees of improvement were significant when the input restraints were insufficient. In particular, GBIS enabled GB1 to form an accurate structure even with distance restraints of 5%, revealing that the root-mean-square deviation was less than 1 ${\AA}$ from the X-ray backbone structure. We also showed that the efficiency of searching the conformational space was more important for finding accurate structures with the calculation of UBQ with 5% distance restraints than the number of conformations generated. Our data will provide a meaningful guideline to judge and compare the structural improvements by GBIS.

• 한국자기공명학회논문지
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• 제18권1호
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• pp.24-29
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• 2014

Atomistic molecular dynamics (MD) simulation has become mature enabling close approximation of the real behaviors of biomolecules. In biomolecular NMR field, atomistic MD simulation coupled with generalized implicit solvent model (GBIS) has contributed to improving the qualities of NMR structures in the refinement stage with experimental restraints. Here all-atom force fields play important roles in defining the optimal positions between atoms and angles, resulting in more precise and accurate structures. Despite successful applications in refining NMR structure, however, the research that has studied the influence of force fields in GBIS is limited. In this study, we compared the qualities of NMR structures of two model proteins, ubiquitin and GB1, under a series of AMBER force fields-ff99SB, ff99SB-ILDN, ff99SB-NMR, ff12SB, and ff13-with experimental restraints. The root mean square deviations of backbone atoms and packing scores that reflect the apparent structural qualities were almost indistinguishable except ff13. Qualitative comparison of parameters, however, indicates that ff99SB-ILDN is more recommendable, at least in the cases of ubiquitin and GB1.

• 방사성폐기물학회지
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• 제6권2호
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• pp.73-100
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• 2008

고준위 방사성폐기물 처분장으로부터 유출된 핵종에 의한 선량률을 계산하기 위한 생태계평가 코드 ACBIO를 일반적인 구획모델링도구인 AMBER를 이용하여 BIOMASS 방법론을 적용하여 개발하였다. ACBIO의 유용성을 보이고, 구획의 변화나 일부 파라미터값의 변화에 따른 구획 내 농도와 방사능, 그리고 구획간의 플럭스의 민감도도 검토하였다. 지하매질-생태계 경계(GBI)를 통해 넘어오는 핵종의 유출플럭스에 따른 선량환산인자를 각 핵종별로 구하여 결정집단내 개인의 최대피폭선량율을 선량환산인자로 얻는 계산을 수행하였다. 또한 생태계 요소의 구획모델링이나 가능한 피폭집단의 설정, 그리고 GBI의 인지 등이 생태계평가에 중요한 요소가 되는 것을 확인하였다.

• 방사성폐기물학회지
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• 제21권1호
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• pp.149-164
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• 2023

As part of the safety case development for generic disposal sites in Korea, it is necessary to develop generic assessment models using various geosphere-biosphere interfaces (GBIs) and potentially exposed groups (PEGs) that reflect the natural environmental characteristics and the lifestyles of people in Korea. In this study, a unique modeling strategy was developed to systematically construct and select Korean generic biosphere assessment models. The strategy includes three process steps (combination, screening, and experts' scoring) for the biosphere system conditions. First, various conditions, such as climate, topography, GBIs, and PEGs, were combined in the biosphere system. Second, the combined calculation cases were configured into interrelation matrices to screen out some calculation cases that were highly unlikely or less significant in terms of the exposure dose. Finally, the selected calculation cases were prioritized based on expert judgment by scoring the knowledge, probability, and importance. The results of this study can be implemented in the development of biosphere assessment models for Korean generic sites. It is believed that this systematic methodology for selecting the candidate calculation cases can contribute to increasing the confidence of future site-specific biosphere assessment models.

• 한국콘텐츠학회논문지
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• 제8권3호
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• pp.8-17
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• 2008

본 논문에서는 새로운 주요객체 자동추출 알고리즘을 제안한다. 제안된 알고리즘은 크게 2단계 과정으로 요약될 수 있다. 1단계로 객체와 배경을 분리하는 영상분할 작업을 수행한다. 우선적으로 '인간은 3또는 4개의 주요 색상으로 축약하여 사물을 인식한다'는 연구 결과에 따라 K-means 알고리즘을 이용하여 3구역으로 분할하고, 분할된 영상 간 히스토그램 유사도를 계산하여 임계값 이상으로 유사하면 병합하는 과정을 수행한다. 2단계로 영상구도에 근거해 분할된 영상 중에 객체라고 지정하는 작업을 수행한다. 사람이 사진을 잘 찍기 위해서는 '주요객체의 위치를 영상구도에 맞추어 촬영하는 것이 바람직하다는 사실'에 근거하여 삼각구도를 바탕으로 가중치 마스크를 설계하여 객체위치를 역 추정하였다. 제안된 방법의 우수성을 보이기 위해 약 400개의 영상에 대해 실험하였으며, 최근에 발표된 KMCC, GBIS방법과도 비교하였다.

• 방사성폐기물학회지
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• 제3권3호
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• pp.213-229
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• 2005

심부 및 천부 지질 환경을 갖는 지하 모암 내의 방사성 폐기물 처분장으로부터 유출된 핵종은 다양한 인공 및 지하 매질을 거쳐 궁극적으로 인간 생태환경으로 도달하게 된다. 그 결과로 인간에게 주는 피폭선량률을 정량적으로 계산하는 것은 처분안전성 평가의 최종 단계가 된다. 방사성폐기물에 포함된 핵종에 대해 붕괴사슬을 고려하고 방사성폐기물처분 시스템의 주요한 부분을 이루는 생태계를 구획으로 모델링 한 후 이들 구획간의 핵종이동에 대한 전이계수를 적용하여 동적 구획모델을 기반으로 하는 AMBER를 이용한 케이스화일로서 ACBIO템플릿을 개발하고 이를 이용하여 각 핵종별 선량환산인자를 평가해 보았다.

• 한국전자파학회논문지
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• 제14권8호
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• pp.863-870
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• 2003

디지털시스템이 더 빠른 edge rate와 클럭 속도를 갖는 소자를 사용함으로 디지털 정보를 전송하는 시스템은 이제 초고주파 영역으로 진입하였으며, 더 많은 전송량을 얻기 위해 광경로를 활용하는 실정이다. 따라서 본 논문에서는 시스템 설계의 가장 중요한 변수가 되고 있는 디지털 신호의 무결성(Signal Integrity)을 확보하기 위한 병렬 광송수신 모듈에 전기 접속부의 중요성에 관한 시뮬레이션 및 실험적 분석을 수행하였다. 칩 구동을 위한 Access Line 및 Evaluation Board를 다른 두 경우로 모듈을 제작하였으며, S$_{11}$이 -10dB 이상인 마이크로 스트립의 경우, 2.5 Gb/s 광 신호의 왜곡이 많이 형성됨을 확인할 수 있었으며, 반면 S$_{11}$이 -15 dB 이하의 특성을 갖는 스트립라인에서는 완전한 Eye Opening신호를 확인할 수 있었다.