• Korean Journal of Computational Design and Engineering
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• v.11 no.2
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• pp.97-106
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• 2006

Voronoi diagrams have been known for numerous important applications in science and engineering including CAD/CAM. Especially, the Voronoi diagram for 3D spheres has been known as very useful tool to analyze spatial structural properties of molecules or materials modeled by a set of spherical atoms. In this paper, we present two algorithms, the edge-tracing algorithm and the region-expansion algorithm, for constructing the Voronoi diagram of 3D spheres and applications to protein structure analysis. The basic scheme of the edge-tracing algorithm is to follow Voronoi edges until the construction is completed in O(mn) time in the worst-case, where m and n are the numbers of edges and spheres, respectively. On the other hand, the region-expansion algorithm constructs the desired Voronoi diagram by expanding Voronoi regions for one sphere after another via a series of topology operations, starting from the ordinary Voronoi diagram for the centers of spheres. It turns out that the region-expansion algorithm also has the worst-case time complexity of O(mn). The Voronoi diagram for 3D spheres can play key roles in various analyses of protein structures such as the pocket recognition, molecular surface construction, and protein-protein interaction interface construction.

• Journal of Advanced Navigation Technology
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• v.8 no.1
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• pp.57-65
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• 2004

In this paper, keeping pace with light weight, pocket-size, lower-price, we design VCO(Voltage Controlled Oscillator) X/Ku band for using at public RD(Radar Detector) to apply to controlled voltage on base in transistor which used as a oscillator, without using varactor diode in part of VCO tuner. As a result of simulation, we conclude VCO could be have 110 MHz by controlled voltage 4.25 V to 4.80 V and show its output 9.63 dBm at operating frequency, 11.46 GHz, and its phase noise -107.2 dBc at 1 MHz offset frequency. So it turned out suitable performance for commercial use.

• Journal of the Korean Society for Precision Engineering
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• v.17 no.6
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• pp.176-184
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• 2000

Reverse engineering (RE) is a process to create computer aided design (CAD) models from the scanned data of an existing part acquired using 3D position scanners. This paper proposes a novel methodology of extracting geometric features directly from a set of 3D scanned points, which utilizes the concepts of feature-based technology and artificial neural networks (ANNs). The use of ANN has enabled the development of a flexible feature-based RE application that can be trained to deal with various features. The following four main tasks were mainly investigated and implemented: (1) Data reduction; (2) edge detection; (3) ANN-based feature recognition; (4) feature extraction. This approach was validated with a variety of real industrial components. The test results show that the developed feature-based RE application proved to be suitable for reconstructing prismatic features such as block, pocket, step, slot, hole, and boss, which are very common and crucial in mechanical engineering products.

• BMB Reports
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• v.29 no.1
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• pp.58-62
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• 1996

The structural changes in the electron donor side of the PSII reaction center have been monitored since heat treatment ($45^{\circ}C$ for 5 min) of thylakoids is known to decrease the oxygen evolving activity. In heat-treated spinach chloroplast thylakoids, the inhibitory effect of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) on the electron transport activity of the PSII reaction center from diphenyl carbazide to dichlorophenolindophenol became reduced approximately 3.8 times and [$^{14}C$]-labeled DCMU binding on the D1 polypeptide decreased to 25~30% that of intact thylakoid membranes, implying that the conformational changes of the DCMU binding pocket, residing on the D1 polypeptide, occur by heat treatment. The accessibility of trypsin to the $NH_2$-terminus of the cytochrome b-559 ${\alpha}$-subunit, assayed with Western blot using an antibody generated against the synthetic peptide (Arg-68 to Arg-80) of the COOH-terminal domain, was also increased, indicating that heat-treatment caused changes in the structural environments near the stromal side of the cytochrome b-559 ${\alpha}$-subunit, allowing trypsin more easily to cleave the $NH_2$-terminal domain. Therefore, the structural changes in the electron donor side of the PSII reaction center complexes could be one of the reasons why the oxygen evolving activity of the heat-treated thylakoid membranes decreased.

• Bulletin of the Korean Chemical Society
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• v.27 no.12
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• pp.1969-1975
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• 2006

3D-QSAR model that correlates the biological activities with the chemical structures of quipazine derivatives acting on the serotonine transporter (SERT) was developed by comparative molecular field analysis (CoMFA). Total 8 models were constructed and a more accurate model, using close 1 $\AA$ grid spacing and StDev*Coefficients weight value gave better results. The contour maps with the best model, the resulting cross-validated correlation ($q^2$ : 0.744), and non-cross-validated correlation ($r^2$ : 0.966) indicate the steric and electrostatic environment of inhibitors in the SERT binding pocket. This study can be used as a putative picture of the pharmacophore in the design of novel and potent inhibitors.

• Mycobiology
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• v.30 no.2
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• pp.82-87
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• 2002

Species of Phellinus were known to harmful fungi causing white pocket rot and severe plant disease such as canker or heartrot in living trees in the West, but some species have been used to traditional medicines in the Orient for a long time. In this study the partial D1-D2 nucleotide sequences of 28S ribosomal DNA from 13 Phellinus strains were determined and compared with the sequences of 21 strains obtained from GenBank database. According to the neighbor-joining(NJ) method comparing the sequence data the phylogenetic tree was constructed. The phylogenetic tree displayed the presence of four groups. Group I includes P. ferreus, P. gilvus and P. johnsonianus, Group II contains P. laevigatus, P. conchatus and P. tremulae, Group III possesses P. linteus, P. weirianus, P. baumii, P. rhabarbarinus and P. igniarius, and Group IV comprises P. pini, P. chrysoloma. P. linteus and P. baumii, which were used mainly in traditional medicine, belong to the same group, but exactly speaking both were split into two different subgroups. To detect P. linteus only, we developed the PCR primer, D12HR. The primer showed the specific amplification of P linteus, which is permitted to medicinal mushroom in the East. The results make a potential to be incorporated in a PCR identification system that could be used for the rapid identification of this species from its related species, P. linteus especially.

• Journal of the Korean Society for Geothermal and Hydrothermal Energy
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• v.17 no.4
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• pp.79-90
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• 2021

This paper presents a study to reduce the effect of blast pressure on the blast valves installed in protection tunnels, where the shape of the tunnel entrance and the blast pocket is optimized based on the predetermined basic shape of the protective tunnels. The reliability of the numerical tunnel models was examined by performing analyses of mesh convergence and overpressure stability and with comparison to the data in blast-load design charts in UFC 3-340-02 (DoD, 2008). An optimal mesh size and a stabilized distance of overpressure were proposed, and the numerical results were validated based on the UFC data. A parametric study to reduce the blast overpressures in tunnel was conducted using the validated numerical model. Analysis was performed applying 1) the entrance slope of 90, 75, 60, and 45 degrees, 2) two blast pockets with the depth 0.5, 1.0, and 1.5 times the tunnel width, 3) the three types of curved back walls of the blast pockets, and 4) two types of the upper and lower surfaces of the blast pockets to the reference tunnel model. An optimal solution by combining the analysis results of the tunnel entrance shape, the depth of the blast pockets, and the upper and lower parts of the blast pockets was provided in comparison to the reference tunnel model. The blast overpressures using the proposed tunnel shape have been reduced effectively.

• Proceedings of the KSRS Conference
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• v.2
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• pp.695-697
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• 2006

Elshayal $Smart{\copyright}$ software is an almost First Arabian GIS $software{\copyright}$ which completely developed by Arabian developers team and independent of any commercial software package. The software current Features are View and Edit shape files, build new layers, add existing layers, remove layers, swap layers, save layers, set layer data sources, layer properties, zoom in & zoom out, pan, identify, selecting features, invert selection, show data table, data query builder, location query builder, build network, find shortest path, print map, save map image, copy map image to clipboard, save project map, edit move vertex, edit move features, snap vertexes, set vertex XY, move settings, converting coordinate system, applying VB script, copy selected features to another layer, move selected features to another layer, delete selected features, edit data table, modify table structure, edit map features, drawing new features, GPS tracking, 3D view, etc... The software expected Features are: Viewing raster image and image geo-referencing, read other map formats such as DXF Format and Tiger Line Format.

• Journal of the Semiconductor & Display Technology
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• v.19 no.2
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• pp.77-81
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• 2020

Silicon wafer etching in micro electro mechanical systems (MEMS) fabrication is challenging to form 3-D structures. Well known Si-wet etch of silicon employs potassium hydroxide (KOH), tetramethylammonium hydroxide (TMAH) and sodium hydroxide (NaOH). However, the existing silicon wet etching process has a fatal disadvantage that etching of the back side of the wafer is hard to avoid. In this study, a wet etching bath for 150 mm wafers was designed to prevent back-side etching of silicon wafer, and we demonstrated the optimized process recipe to have anisotropic wet etching of silicon wafer without any damage on the backside. We also presented the design of wet bath for 300 mm wafer processing as a promising process development.

• Biomolecules & Therapeutics
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• v.31 no.1
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• pp.108-115
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• 2023

Numerous psychotropic and addictive substances possess structural features similar to those of β-phenethylamine (β-PEA). In this study, we selected 29 β-PEA derivatives and determined their structure-activity relationship (SAR) to their ability to inhibit dopamine (DA) reuptake; conducted docking simulation for two selected compounds; and identified their potential functionals. The compounds were subdivided into arylethylamines, 2-(alkyl amino)-1-arylalkan-1-one derivatives and alkyl 2-phenyl-2-(piperidin-2-yl)acetate derivatives. An aromatic group, alkyl group, and alkylamine derivative were attached to the arylethylamine and 2-(alkyl amino)-1-arylalkan-1-one derivatives. The inhibitory effect of the compounds on dopamine reuptake increased in the order of the compounds substituted with phenyl, thiophenyl, and substituted phenyl groups in the aromatic position; compounds with longer alkyl groups and smaller ring-sized compounds at the alkylamine position showed stronger inhibitory activities. Docking simulation conducted for two compounds, 9 and 28, showed that the (S)-form of compound 9 was more stable than the (R)-form, with a good fit into the binding site covered by helices 1, 3, and 6 of human dopamine transporter (hDAT). In contrast, the (R, S)-configuration of compound 28 was more stable than that of other isomers and was firmly placed in the binding pocket of DAT bound to DA. DA-induced endocytosis of dopamine D₂ receptors was inhibited when they were co-expressed with DAT, which lowered extracellular DA levels, and uninhibited when they were pretreated with compound 9 or 28. In summary, this study revealed critical structural features responsible for the inhibition of DA reuptake and the functional role of DA reuptake inhibitors in regulating D₂ receptor function.