• Journal of the Korean Magnetic Resonance Society
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• v.17 no.1
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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.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.1
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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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• v.35 no.7
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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.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.1
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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.

• Journal of Nuclear Fuel Cycle and Waste Technology(JNFCWT)
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• v.6 no.2
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• pp.73-100
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• 2008

For the purpose of evaluating dose rate to individual due to long-term release of nuclides from the HLW repository, a biosphere assessment model and the implemented code, ACBIO, based on BIOMASS methodology have been developed by utilizing AMBER, a general compartment modeling tool. To show its practicability and usability as well as to see the sensitivity of compartment scheme or parametric variation to concentration and activity in compartments as well as annual flux between compartments at their peak values, some calculations are made and investigated: For each case when changing the structure of compartments and GBIs as well as varying selected input Kd values, all of which seem very important among others, dose rate per nuclide release rate is separately calculated and analyzed. From the maximum dose rates (Bq/y), flux-to-dose conversion factors (Sv/Bq) for each nuclide were derived, which are to be used for converting the nuclide release rate appearing from the geosphere through various GBIs to dose rate (Sv/y) for individual in critical group. It has been also observed that compartment scheme, identification of possible exposure group and GBIs could be all highly sensitive to the final consequences in biosphere modeling.

• Journal of Nuclear Fuel Cycle and Waste Technology(JNFCWT)
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• v.21 no.1
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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.

• The Journal of the Korea Contents Association
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• v.8 no.3
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• pp.8-17
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• 2008

A new algorithm for automatic extraction of interesting objects is proposed in this paper. The proposed algorithm can be summarized in two steps. First, segmentation of color image that split interesting objects and backgrounds is performed. According to the research stating, 'Humans perceive things by contracting color into three to four essential colors,' a color image is segmented into three regions utilizing k-mean algorithm, followed by annexing the regions when the similarities of them exceeds the critical value based on the calculation of degrees in the histogram similarity, Second, identifying the interesting objects out of the segmented image, partitioned by the image composition theory, is performed. To have a good picture, it is important to adjust positions of interesting objects according to picture composition. Extracting objects is a retro-deduction process using a weighted mask designed upon the triangular composition of picture. To prove the quality of the proposed method, experiments are performed over four hundreds images as well as comparison with recently proposed KMCC and GBIS methods.

• Journal of Nuclear Fuel Cycle and Waste Technology(JNFCWT)
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• v.3 no.3
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• pp.213-229
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• 2005

Nuclides in radioactive wastes are assumed to be transported in the geosphere by groundwater and probably discharged into the biosphere. Quantitative evaluation of doses to human beings due to nuclide transport in the geosphere and through the various pathways in the biosphere is the final step of safety assessment of the radioactive waste repository. To calculate the flux to dose conversion factors (DCFs) for nuclides appearing at GBIs with their decay chains, a template ACBIO which is an AMBER case file based on mathematical model for the mass transfer coefficients between the compartments has been developed considering material balance among the compartments in biosphere and then implementing to AMBER, a general and flexible software tool that allows to build dynamic compartment models. An illustrative calculation with ACBIO is shown.

• The Journal of Korean Institute of Electromagnetic Engineering and Science
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• v.14 no.8
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• pp.863-870
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• 2003

The digital transmission system entered in a RF region as digital system use IC chips of the speeder edge rate and clock speed nowadays. Optical path really was used in order to obtain the more capacity. In this paper, we described importance of electrical interconnect to get the signal integrity in optical module by simulation and experiment. 12 channel${\times}$2.5 G/ps optical parallel transmitter modules were manufactured by two different method ; access lines with microstrip and stripline type. We have clearly shown that the optical module adopting microstrip type with S$\sub$11/ $\geq$ -10 dB presents distortion but the optical module adopting stripline type with S$\sub$11/ $\leq$ : 15 dB obtains eye opening in 2.5 Gbis optical eye pattern response.