• BMB Reports
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• v.44 no.2
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• pp.118-122
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• 2011

Most widely used secondary structure assignment methods such as DSSP identify structural elements based on N-H and C=O hydrogen bonding patterns from X-ray or NMR-determined coordinates. Secondary structure assignment algorithms using limited $C{\alpha}$ information have been under development as well, but their accuracy is only ~80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with ~90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous $C{\alpha}s$. SABA is capable of identifying $\alpha$-helices, $3_{10}$-helices, and $\beta$-strands with high accuracy by using cut-off criteria on distances and dihedral angles between two or more pseudo centers. In addition to assigning secondary structures to $C{\alpha}$-only structures, algorithms using limited $C{\alpha}$ information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison.

• Journal of the Korean Institute of Rural Architecture
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• v.4 no.1
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• pp.71-86
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• 2002

This research aims to illustrate the structure of the ancient Korean wooden buildings by a comparative study of the historical resources such as stone remains, wall paintings historiographies and excavations. As stone pagodas are the most typical stone remains, I selected for analysis some stone pagodas which contain architectural elements and results of the study are as follows: 1) The number of stories and structural modes of the base stone part show the wooden architectural aspects: they have one or two stories and their base part is constructed in the mode of assembling rectangular stones. 2) The body of the pagoda contains such architectural elements as pillars, door and windows, crossbeams, balcony, bracket sets. 3) The roof of the stone pagoda contains such architectural elements as eaves, roofs and modes of stone assembling. The results inferred through this research could be of help for further comparative studies with the other secondary materials by providing basic knowledge for it.

• Proceedings of the KSME Conference
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• 2008.11a
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• pp.674-677
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• 2008

An advanced computational strategy for improvement of the accuracy of the structural analysis is developed in this paper. The finite elements connecting the primary nodes are constructed as a ground mesh in a domain, and the secondary nodes can be placed arbitrarily without reconstruction of a mesh. The support domains of the secondary nodes are defined on the basis of finite element mesh, and the shape functions are constructed by using MLS(moving least square) approximations. The present method is useful for controlling the errors without reconstruction of mesh when you add or remove nodes in a domain.

• Bulletin of the Korean Chemical Society
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• v.25 no.6
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• pp.838-842
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• 2004

Amyloid peptide (A${\beta}$) is the major component of senile plaques found in the brain of patient of Alzheimer's disease. ${\beta}$-amyloid peptide (25-35) (A${\beta}$25-35) is biologically active fragment of A${\beta}$. The three-dimensional structure of A${\beta}$25-35 in aqueous solution with 50% (vol/vol) TFE determined by NMR spectroscopy previously adopts an ${\alpha}$-helical conformation from $Ala^{30}$ to $Met^{35}$. It has been proposed that A${\beta}$(25-35) exhibits pH- and concentration-dependent ${\alpha}-helix{\leftrightarrow}{\beta}$sheet transition. This conformational transition with concomitant peptide aggregation is a possible mechanism of plaque formation. Here, in order to gain more insight into the mechanism of ${\alpha}$-helix formation of A${\beta}$25-35 peptide by TFE, which particularly stabilizes ${\alpha}$-helical conformation, we studied the secondary-structural elements of A${\beta}$25-35 peptide by molecular dynamics simulations. Secondary structural elements determined from NMR spectroscopy in aqueous TFE solution are preserved during the MD simulation. TFE/water mixed solvent has reduced capacity for forming hydrogen bond to the peptide compared to pure water solvent. TFE allows A${\beta}$25-35 to form bifurcated hydrogen bonds to TFE as well as to residues in peptide itself. MD simulation in this study supports the notion that TFE can act as an ${\alpha}$-helical structure forming solvent.

• Journal of Plant Biology
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• v.36 no.1
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• pp.35-42
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• 1993

This study deals with the effect of dwarf growth for the wood and the structural changes of cambium in Pinus koraiensis subjected to water stress. The length and wall thickness of tracheary elements in dwarf trees was shorter and thicker than that in normal trees. The redial width and cell number of the annual rings are narrower and smaller in dwarf trees than those in normal trees. In serial tangential sections, the frequency of anticlinal division is low and loss of cambial initials is small in dwarf trees. The length of cambial initials in water deficit, trees are slightly shorter than that in normal trees, and the instructive growth of cambial initials during differentiation of xylem mother cells is inactive in dwarf trees. Thus, it is interpreted that the shortening of tracheary elements in dwarf trees is due to the fact that the length of cambial initials are shortened and the intrusive growth of those during differentiation of xylem mother cells is inactive. The structural variations in the wood of naturally occurring dwarf trees are similar to those of trees subjected to artificial water stress. Therefore, it is suggested that the variation of xylem element in dwarf trees are related to water conditions.

• Fire Science and Engineering
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• v.24 no.4
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• pp.86-91
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• 2010

In event of a tunnel fire, all kinds of equipment can be destroyed in high temperature that can exceed $1300^{\circ}C$, fatal structural demage can be caused by spalling of concrete structural elements. To make matters worse, there is a high possibility of the secondary damage which can lead to the collapse of the shear resisting structure. Accordingly, it is time that we developed the technology to counter fires in connection with the fire-resistant design of a tunnel structure. To secure the reliability of the fire-resistance performance of a tunnel structure, it is necessary to assess the fire's behavior on every structural element exposed to the fire as well as to calculate the tunnel fire intensity and the quantity of heat released. In this study, we drew out the fire damage range of each structural element of a tunnel and the minimum thickness of concrete cover for each fire-resistant material through some actual experiments of fire behavior on the structural elements of a tunnel.

• Molecules and Cells
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• v.41 no.10
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• pp.889-899
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• 2018

Intrinsically disordered proteins (IDPs) are highly unorthodox proteins that do not form three-dimensional structures under physiological conditions. The discovery of IDPs has destroyed the classical structure-function paradigm in protein science, 3-D structure = function, because IDPs even without well-folded 3-D structures are still capable of performing important biological functions and furthermore are associated with fatal diseases such as cancers, neurodegenerative diseases and viral pandemics. Pre-structured motifs (PreSMos) refer to transient local secondary structural elements present in the target-unbound state of IDPs. During the last two decades PreSMos have been steadily acknowledged as the critical determinants for target binding in dozens of IDPs. To date, the PreSMo concept provides the most convincing structural rationale explaining the IDP-target binding behavior at an atomic resolution. Here we present a brief developmental history of PreSMos and describe their common characteristics. We also provide a list of newly discovered PreSMos along with their functional relevance.

• Economic and Environmental Geology
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• v.36 no.5
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• pp.365-374
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• 2003

Various deleterious chemicals can be introduced to existing concrete structures from various external sources. The deterioration of concrete by seawater attack is involved in complex processes due to various elements contained in seawater. In the present study, attention was paid to the formation of secondary minerals and characteristics of mineralogical and micro-structural changes involved in concrete deterioration caused by the influence of major seawater composition. The characteristics of deterioration occurred in existing concrete structures was carefully observed and samples were collected at many locations of coastal areas in Busan-Kyungnam. The petrographic, XRD, SEM/EDAX analyses were conducted to determine chemical, mineralogical and micro-structural changes in the aggregate and cement paste of samples. The experimental concrete deteriorations were performed using various chloride solutions (NaCl, CaCl, $MgCl_2$ and $Na_2SO_4$ solution. The experimental results were compared with the observation results in order to determine the effect of major elements in seawater on the deterioration. The alkalies in seawater appear to accelerate alkali-silica reaction (ASR). The gel formed by ASR is alkali-calcium-silica gel which known to cause severe expansion and cracking in concrete. Carbonation causes the formation of abundant less-cementitious calcite and weaken the cement paste. Progressive carbonation significantly affects on the composition and stability of some secondary minerals. Abundant gypsum generally occurs in concretes subjected to significant carbonation, but thaumasite ({$Ca_6/[Si(OH)_6]_2{\cdot}24H_2O$}${\cdot}[(SO_4)_2]{\cdot}[(CO_3))2]$) occurs as ettringite-thaumasite solid solution in concretes subjected to less significant carbonation. Experimentally, ettringite can be transformed to trichloroaluminate or decomposed by chloride ingress under controlled pH conditions. Mg ions in seawater cause cement paste deterioration by forming non-cementitious brucite and magnesium silicate hydrate (MSH).

• Journal of Korea Society of Digital Industry and Information Management
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• v.9 no.3
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• pp.155-171
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• 2013

This research paper is focused on a theoretical study of the influences the structural factors and social capital within an industrial cluster have on innovative performance, and expanding the understanding of the influence through positive analyses based on public surveys. The study adopts a concept of social capital that can formulate a social relationship, and maintains that the social capital either works as a mediator for structural factors or independently exerts strong influences on innovative performance. In the research, the social capital is divided into two categories, bonding social capital and bridging social capital, and their influences are analyzed separately. The result of the analyses shows that unlike the traditional perception based on Korea's unique culture, the influence of bridging social capital is stronger than that of bonding social capital. It is also found that the structural factors exert influence by themselves on the contrary the previous study, simultaneously they still have influence upon innovative performance through bridging social capital calculated via the elements such as secondary relationships, network activity support and organizational openness.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.18 no.1
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• pp.13-20
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• 2005

Since High Tensile Steel has been widely used to thin plate on the steel structure and marine structure, It has increased possibility of buckling. Especially, initial deflection of ship structure is mainly caused by heat processing of welding or cutting etc. This initial deflection has negative effect to thin plate, which would incur a complicated nonlinear behavior accompanied with secondary buckling. If idealized initial deflection is considered in early marine structure design of secondary buckling, accuracy and reliability will be improved considerably. The measurement data of initial deflection from experiment is applied to finite element series analysis. For FEA(ANSYS), Applied nonlinear buckling analysis is used by Newton-Raphson method & Arc-length method included in this program.