• Wind and Structures
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• v.27 no.6
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• pp.381-397
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• 2018

Nonlinear behavior in fluid-structure interaction (FSI) of bridge decks becomes increasingly significant for modern bridges with increasing spans, larger flexibility and new aerodynamic deck configurations. Better understanding of the nonlinear aeroelasticity of bridge decks and further development of reduced-order nonlinear models for the aeroelastic forces become necessary. In this paper, the amplitude-dependent and neutral angle dependent nonlinearities of the motion-induced loads are further highlighted by series of computational fluid dynamics (CFD) simulations. An effort has been made to investigate a semi-analytical time-domain model of the nonlinear motion induced loads on the deck, which enables nonlinear time domain simulations of the aeroelastic responses of the bridge deck. First, the computational schemes used here are validated through theoretically well-known cases. Then, static aerodynamic coefficients of the Great Belt East Bridge (GBEB) cross section are evaluated at various angles of attack, leading to the so-called nonlinear backbone curves. Flutter derivatives of the bridge are identified by CFD simulations using forced harmonic motion of the cross-section with various frequencies. By varying the amplitude of the forced motion, it is observed that the identified flutter derivatives are amplitude-dependent, especially for $A^*_2$ and $H^*_2$ parameters. Another nonlinear feature is observed from the change of hysteresis loop (between angle of attack and lift/moment) when the neutral angles of the cross-section are changed. Based on the CFD results, a semi-analytical time-domain model for describing the nonlinear motion-induced loads is proposed and calibrated. This model is based on accounting for the delay effect with respect to the nonlinear backbone curve and is established in the state-space form. Reasonable agreement between the results from the semi-analytical model and CFD demonstrates the potential application of the proposed model for nonlinear aeroelastic analysis of bridge decks.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.2
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• pp.83-87
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• 2015

Syndesmos, which is co-localized with syndecan-4 cytoplasmic domain ($Syn4^{cyto}$) in focal contacts, interacts with various cell adhesion adaptor proteins including $Syn4^{cyto}$ to control cell signaling. Syndesmos consists of 211 amino acids and it exists as a dimer (44kDa) in solution. Recently, we have determined the structure of syndesmos by x-ray crystallography, however, dynamics related to syndecan binding still remain elusive. In this report, we performed NMR experiments to acquire biochemical and structural information of syndesmos. Based on a series of three-dimensional triple resonance experiments on a $^{13}C/^{15}N/^2H$ labeled protein, NMR spectra were obtained with well dispersed and homogeneous NMR data. We present the sequence specific backbone assignment of syndesmos and assigned NMR data with combination structural information can be directly used for the studies on interaction with $Syn4^{cyto}$ and other binding molecules.

• Journal of the Korean Magnetic Resonance Society
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• v.14 no.1
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• pp.45-54
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• 2010

HP1423 (Y1423_HELPY) is a conserved hypothetical protein from H. pylori strain 26695. However, Sequence Blast result indicates that HP1423 belongs to S4 (PF01479) superfamily. According to Pfam database, the S4 domain is a small domain consisting of 60-65 amino acid residues, that probably mediates binding to RNA. In this study, we report the sequence-specific backbone resonance assignment of HP1423, which has 84 amino acid residues. We could assign unambiguously about 88% of all $^{1}H_{N}$, $^{15}N$, $^{13}C_{\alpha}$, $^{13}C_{\beta}$ and $^{13}C=O$ resonances. We could not detect the resonances from residues 15-20, and disappearance of these peaks seems to be related with the intermediate-conformational exchange. These assigned NMR peaks of HP1423 can be used for studying the role of protein dynamics in millisecond timescale, and Protein-RNA binding.

• BMB Reports
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• v.34 no.1
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• pp.1-7
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• 2001

Structural and physical properties of type wild type and various selected mutants of the vnd/NK-2 homeodomain, the protein product of the homeobox, and the implication in genetic disease are reviewed. The structure, dynamics and thermodynamics have been Investigated by NMR and by calorimetry. The interactions responsible for the nucleotide sequence-specific binding of the homeodomain to its consensus DNA binding site have been identified. There is a strong correlation between significant structural alterations within the homeodomain or its DNA complex and the appearance of genetic disease. Mutations in positions known to be important in genetic disease have been examined carefully For example, mutation of position 52 of vnd/NK-2 results in a significant structural modification and mutation of position 54 alters the DNA binding specificity and amity The $^{15}N$ relaxation behavior and heteronuclear Overhauser effect data was used to characterize and describe the protein backbone dynamics. These studies were carried out on the wild type and the double mutant proteins both in the free and in the DNA bound states. Finally, the thermodynamic properties associated with DNA binding are described for the vnd/NK-2 homeodomain. These thermodynamic measurements reinforce the hypothesis that water structure around a protein and around DNA significantly contribute to the protein-DNA binding behavior. The results, taken together, demonstrate that structure and dynamic studies of proteins combined with thermodynamic measurements provide a significantly more complete picture of the solution behavior than the individual studies.

• Journal of the Korea Safety Management & Science
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• v.18 no.4
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• pp.139-149
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• 2016

Service industry can be divided largely into commercial industry, banking industry, insurance industry, advertising industry, and tourism industry. Of these, banking industry is playing an essential role as it constitutes the backbone of economy. Banking industry, which belongs to financial industry, is sensitive to external environment. In this kind of industry, internal dynamics of an organization is very important. The purpose of this research is to find out what kind of influence the relation of internal dynamics perceived by members of Nonghyup organization has on customer orientation via quality of internal service. For the purpose, we have reviewed preceding studies on variables that affect customer orientation and developed a measuring tool in a form that fits banking organizations. Internal service quality, job satisfaction, and organizational immersion which play a mediating role in the model of this research not only turned out to have a significant influence on customer orientation, they also turned out to have the strongest influence. This research has academic significance as it carried out a research with an emphasis on variables that affect customer orientation of members of Nonghyup organization. Regarding practical significance, it was intended to present useful data that can be utilized for an analysis of internal service quality management and capability of human resource management.

• Current Applied Physics
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• v.18 no.11
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• pp.1313-1319
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• 2018

The coil-to-globule behavior of poly{${\gamma}$-2-[2-(2methoxyethoxy)ethoxy]ethoxy-3-caprolactone} (PMEEECL) as a ${\gamma}$-substituted poly (${\varepsilon}$-caprolactone) was investigated via atomistic molecular dynamics (MD) simulation. For this purpose, radius of gyration, end-to-end distance and radial distribution function of the chain in the presence of water were calculated. Consequently, the lower critical solution temperature (LCST) of PMEEECL chain at which the coil-to-globule transition takes place, was determined in each calculated parameter curve. The simulation results indicated that the LCST of PMEEECL was occurred at close to 320 K, which is in a good agreement with previous experimental results. Additionally, the appearance of sudden change in both Flory-Huggins interaction parameter (${\chi}$) and interaction energy between the PMEEECL chain and water molecules at about 320 K confirmed the calculated LCST result. The radial distribution function (RDF) results showed that the affinity of the PMEEECL side chain to water molecules is lower than its backbone.

• Bulletin of the Korean Chemical Society
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• v.35 no.6
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• pp.1713-1719
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• 2014

1FSD is a 28-residue designed protein with a ${\beta}{\beta}{\alpha}$ motif. Since this protein displays most essential features of protein structures in such a small size, this model protein can be an outstanding system for evaluating the balance in the propensity of the secondary structures and the quality of all-atom protein force fields. Particularly, this protein would be difficult to fold to its correct native structure without establishing proper balances between the secondary structure elements in all-atom energy functions. In this work, a series of the recently optimized five amber protein force fields [$ff03^*$, $f99sb^*$-ildn, ff99sb-${\phi}^{\prime}$-ildn, ff99sb-nmr1-ildn, ff99sb-${\Phi}{\Psi}$(G24, CS)-ildn] were investigated for the simulations of 1FSD using a conventional molecular dynamics (MD) and a biased-exchange meta-dynamics (BEMD) methods. Among those tested force fields, we found that ff99sb-nmr1-ildn and ff99sb-${\Phi}{\Psi}$(G24, CS)-ildn are promising in that both force fields can locate the native state of 1FSD with a high accuracy (backbone rmsd ${\leq}1.7{\AA}$) in the global free energy minimum basin with a reasonable energetics conforming to a previous circular dichroism (CD) experiment. Furthermore, both force fields led to a common set of two distinct folding pathways with a heterogeneous nature of the transition state to the folding. We anticipate that these force fields are reasonably well balanced, thereby transferable to many other protein folds.

• 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.

• Korean System Dynamics Review
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• v.12 no.4
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• pp.125-156
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• 2011

The information service management models developed thus far have put their focuses mostly on technical dimensions of information systems (IS), finding their rationale from the goods-dominant logic (GDL) that IS as goods has value in itself. Information systems, however, is nothing more than a mechanism by which value is delivered to the users. According to the service-dominant logic (SDL), value is created and determined not at the time serve is made by the providers but at the time it is consumed by the users. The users therefore should be regarded as active value creators not as passive consumers of the value delivered by the providers. Based on the service-dominant logic, DISQM (Dynamic Information Service Quality Model) is developed. DISQM's backbone is designed in causal loop diagrams referring to and reinterpreting in systems thinking the 'Parasuraman, Zeithaml & Berry's GAP Model' and 'SERVQUAL' as an operational tool for the GAP Model, and the main IS success constructs are mapped onto the model exploiting the 'DeLone & MacLean's IS Success Model'. With VENSIM simulation software, this paper also shows how DISQM works in computer-simulation settings. After confirming DISQM's validity with the base simulation run, two scenarios are developed for the exemplary purpose and tested in terms of IS quality, service quality, and net benefits from the service for the public information service. Implications from the simulation runs are also discussed.

• Macromolecular Research
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• v.8 no.5
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• pp.224-230
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• 2000

Molecular mechanics technique has been used for finding energy-minimized conformation to understand the mechanism of yielding of glassy polymers in atomistic level. As a model polymer, amor- phous isotactic polypropylene (iPP) was generated by molecular mechanics and molecular dynamics methods. The stress-strain cone was successfully obtained by using molecular mechanics technique. The torsional angle distribution showed no significant change during extension, although the torsional angles of certain bonds in polymer backbone changed more largely than other bonds. No significant change in the van der Waals interaction is observed at yielding point, whereas the torsional angle energy starts to decrease at yield strain.