• 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.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.383-383
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• 2010

Gas-phase hydrogen atoms create a variety of chemical and physical phenomena on Si surfaces: adsorption, abstraction of pre-adsorbed H, Si etching, Si amorphization, and penetration into the bulk lattice. Thermal desorption/evolution analyses exhibited three distinct peaks, including one from the crystalline bulk. It was previously found that thermal-energy gaseous H(g) atoms penetrate into the Si(100) crystalline bulk within a narrow substrate temperature window(centered at ~460K) and remain trapped in the bulk lattice before evolving out at a temperature as high as ~900K. Developing and sustaining atomic-scale surface roughness, by H-induced silicon etching, is a prerequisite for H absorption and determines the $T_s$ windows. Issues on the H(g) absorption to be further clarified are: (1) the role of the detailed atomic surface structure, together with other experimental conditions, (2) the particular physical lattice sites occupied by, and (3) the chemical nature of, absorbed H(g) atoms. This work has investigated and compared the thermal H(g) atom absorptivity of Si(100), Si(111) and Si(110) samples in detail by using the temperature programmed desorption mass spectrometry (TPD-MS). Due to the differences in the atomic structures of, and in the facility of creating atom-scale etch pits on, Si(100), (100) and (110) surfaces, the H-absorption efficiency was found to be larger in the order of Si(100) > Si(111) > Si(110) with a relative ratio of 1 : 0.22 : 0.045. This intriguing result was interpreted in terms of the atomic-scale surface roughening and kinetic competition among H(g) adsorption, H(a)-by-H(g) abstraction, $SiH_3(a)$-by-H(g) etching, and H(g) penetraion into the crystalline silicon bulk.

• Applied Chemistry for Engineering
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• v.16 no.2
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• pp.187-193
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• 2005

The photocatalyst $TiO_2$ thin film was made from titanium (IV) isopropoxide, ethanol, and HCl by sol-gel method. The surface observation by SEM showed the sample that was coated 5 times at $500^{\circ}C$ had good properties. The component ratio, in atom% of O : Ti by EDX analysis, of 61 : 39 by spin coating was superior than dip coating. It was found that crystal structure changed from anatase phase to rutile phase as a function of the temperature of thin film fabrication, and this was measured by XRD. The photolysis efficiency of total organic compounds (TOC) by lighting UV beam on $TiO_2$ thin film showed 20%~65% within 1 h, and decreased slowly thereafter.

• Journal of Internet Computing and Services
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• v.5 no.2
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• pp.97-105
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• 2004

The reason that an intelligent agent cannot understand the representation of its own perception or activity is caused by the traditional syntactic approach that translates a semantic feature into a simulated string, To implement an autonomously learning intelligent agent, Cohen introduces a experimentally semantic approach that the system learns a contentful representation of physical schema from physically interacting with environment using its own sensors and effectors. We propose that negation is a meta-level schema that enables an agent to recognize its own physical schema, To improve the planner's efficiency, Graphplan introduces the control rule that manipulates the inconsistency between planning operators, but it cannot cognitively understand negation and suffers from redundancy problem. By introducing a negative function not, IPP solves the problem, but its approach is still syntactic and is inefficient in terms of time and space. In this paper, we propose that, to represent a negative fact, a positive atom, which is called opposite concept, is a very efficient technique for implementing an cognitive agent, and demonstrate some empirical results supporting the hypothesis.

• Bulletin of the Korean Chemical Society
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• v.28 no.12
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• pp.2153-2161
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• 2007

The transition metal-induced in situ generation of carbene complexes from alkynes having a carbonyl or imino group as a nucleophilic functionality has been investigated. These reactive carbenoid species are generated with high atom efficiency through a 6-endo-dig cyclization mode based on the electrocyclization of vinylidene complexes or a 5-exo-dig cyclization mode in π-alkyne complexes, and have been found to serve as versatile intermediates in catalytic carbene transfer reactions. Highlighted and reviewed in this account are the generation and preparation of pyranylidene, furylcarbene, pyrrolylcarbene, and vinylcarbene complexes and their application to [3,3]sigmatropic rearrangement of acylcyclopropylvinylidenes, catalytic cyclopropanation reactions, [2,3]sigmatropic rearrangement or condensation reactions via ylides, ring-opening and substitution reactions with heteroaromatic compounds, and catalytic isomerization of oligoynes.

• The Transactions of The Korean Institute of Electrical Engineers
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• v.59 no.5
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• pp.932-938
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• 2010

This paper proposed the effective treatment method for organic substances using the barrier discharge plasma process and catalytic chemical reaction followed from ozone decomposition. The decomposition by the plasma process of organic substances such as trichloroethylene, methyl alcohol, acetone, and dichloromethane carried out, and ozone is generated effectively at the same time. By passing through catalysts, ozone easily decomposed and further decomposed organic substances. And, 2-dimensional distribution of ozone using the optical measurement method is performed to identify the catalytic surface chemical reaction. In addition, CO is easily oxidized into $CO_2$ by this chemical reaction, which might be induced oxygen atom radicals formed at the surface of catalyst from ozone decomposition.

• Bulletin of the Korean Chemical Society
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• v.12 no.4
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• pp.434-437
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• 1991

Irradiation of 5-styryl-1,3-dimethyluracil (5-SDU) with 2,3-dimethyl-2-butene (DMB) gives a [4+2] cycloadduct which is converted into a [2+2] cycloadduct on the prolonged irradiation. Triplet sensitization, quenching, and external heavy atom effect on the [4+2] photocycloaddition reaction demonstrate the singlet pathway and salt effect excludes a radical ion pair precursor possibility. Polar solvents increase the reaction efficiency implying a polar exciplex involvement in the [4+2] photocycloaddition reaction. Inverse temperature dependence both on the reaction and DMB fluorescence quenching of 5-SDU indicates the presence of a singlet exciplex intermediate.

• Reproductive and Developmental Biology
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• v.29 no.1
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• pp.43-48
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• 2005

To search of a new porcine pheromonal odorants for biostimulation control system technologies to offer a potentially useful and practical way to improve reproductive efficiency in livestock species, the holographic quantitative structure activity relationship (HQSAR) model between odorants, 2-phenoxytetrahydrofurane (A), 2-cyclohexyl-oxytetrahydrofurane (B), derivatives and binding affinity constants (p[Od.]/sub 50/) for porcine odorant-binding protein (pOBP) as receptor of pig pheromones were derivated and disscused. The binding affinity constants of cyclohexyl substituents (A) for pOBP were higher (A>B) than that of phenyl substituents (B). It was revealed that the optimum HQSAR model XI using PLS analyses had a fragment length (5∼8) with chirality at 5 components and hologram length 97 bin, which had a cross-validated q²(predictablities) of 0.916, and a conventional correlation coefficient r² (fitness) of 0.988, respectively. From the atomic contribution, the C3 and C5 atom in 2-oxyfuryl group contributed to binding affinity constants, whereas the central carbon atom in tert-butyl group on the cyclohexyl ring and the C4 atom of furyl group parts showed no contribution.

• Korean Journal of Optics and Photonics
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• v.4 no.1
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• pp.47-56
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• 1993

Practical efficiencies of pulsed gas discharge lasers utilizing vaporized Au, Ba, Cu, Fe, Mn, Pb, TI atoms are numerically optimized for a discharge pulse of 30 ns rise time at 5 kHz pulse repetition rate. Calculated optimum operating temperatures are close to the values at which the vapor pressure of each atom is about 1 Torr and are in good agreement with experimental values reported elasewhere. The optimum charging voltage was about 4 kV for all atomic vapor lasers except the TI laser. The calculated maximum efficiencies that have been discussed for possible limiting efficiencies for each laser were considerably higher than the reported experimental values. Especially, they were as high as 6.8% for Mn laser and 15% for Ba laser that were comparable to the 8.5% of copper vapor laser, from which considerably higher efficiencies can be expected for these two lasers experimentally. But, the present calculation shows a very low efficiency of 0.058% and requires an exceptional operating condition for the TI laser.

• Korean Journal of Soil Science and Fertilizer
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• v.36 no.6
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• pp.376-383
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• 2003

To utilize composts more efficiently, combining composts with fertilizer to meet crop requirements is an appealing alternative. A pot experiment was conducted to study the effect of application rate of composted pig manure blended with fertilizer on the availability and loss of fertilizer-N. Chinese cabbage (Brassica campestris L. cv. Samjin) plants were cultivated for 30 and 60 days. 15N-Labeled urea ($5.24\;^{15}N\;atom\;%$) was added to soil at $450mg\;N\;kg^{-1}$, and unlabeled compost ($0.37\;^{15}N\;atom\;%$) was added at 0, 200, 400, and $600mg\;N\;kg^{-1}$. The amount of plant-N derived from urea was not affected by compost application at rate of $200mg\;N\;kg^{-1}$. However, compost application at 400 and $600mg\;N\;kg^{-1}$ significantly (P<0.05) increased plant assimilation of N from urea irrespective of sampling time, probably because of physicochemical changes in the soil properties allowing urea-N to be assimilated more efficiently. The amount of immobilized urea-N increased with increasing rate of compost application at both growth periods, as the results of increased microbial activities using organic C in the compost. Total recovery of urea-N (as percentage of added N) by Chinese cabbage and soil also increased with increasing rate of compost from 71.5 to 95.6% and from 67.0 to 88.2% at the 30- and 60-days of growth, respectively. These results suggest that increasing rate of compost blending increases plant uptake of fertilizer-N and enhances immobilization of fertilizer-N, which leads to decrease in loss of fertilizer-N. However, information about the fate of immobilized N during future crop cultivation is necessary to verify long-term effect of compost blending.