• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.785-791
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• 2003

We have studied the folding mechanism of β-hairpins from proteins of 1GB1, 3AIT and 1A2P by unfolding simulations at high temperatures. The analysis of trajectories obtained from molecular dynamics simulations in explicit aqueous solution suggests that the three β-hairpin structures follow different mechanism of folding. The results of unfolding simulations showed that the positions of the hydrophobic core residues influence the folding dynamics. We discussed the characteristics of different mechanisms of β-hairpin folding based on the hydrogen-bond-centric and the hydrophobic-centric models.

• Transactions of the Korean Society of Automotive Engineers
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• v.10 no.6
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• pp.187-193
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• 2002

Since the bus is regarded as the one of the most public transportation systems, research on the safety and facilities of the bus has been increased actively in recent years. In this paper, we concern the design of the bus door mechanism that is composed of many linkages and actuators(or motors). In particular, the folding door mechanism is representative system installed in most of urban buses. To design the folding door mechanism, we construct the kinematic and dynamic analysis model fur computer simulation. Also, the dynamic analysis is accomplished by both direct dynamics and inverse dynamics. Since the folding door mechanism has many design variables, the analysis program is developed to perceive kinematic and dynamic characteristics according to the design variables and simulation conditions.

• Bulletin of the Korean Chemical Society
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• v.29 no.4
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• pp.741-748
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• 2008

We have studied the folding mechanism of $\beta$ -hairpins in the proteins 1GB1, 3AIT and 1A2P by conducting unfolding simulations at moderately high temperatures. The analysis of trajectories obtained from molecular dynamics simulations in explicit aqueous solution suggests that the positions of the hydrophobic core residues lead to subtle differences in the details of folding dynamics. However, the folding of three different hairpins can be explained by a unified mechanism that is a blend of the hydrogen-bond-centric and the hydrophobiccentric models. The initial stage of $\beta$-hairpin folding involves various partially folded intermediate structures which are stabilized by both the van der Waals interactions of hydrophobic core residues and the electrostatic interactions of non-native hydrogen bonds. The native structure is obtained by forming native contacts in the final tune-up process. Depending on the relative positions of the hydrophobic residues, the actual mechanism of hairpi n folding may or may not exhibit well-defined intermediates.

• Bulletin of the Korean Chemical Society
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• v.29 no.11
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• pp.2172-2182
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• 2008

• Journal of the Society of Naval Architects of Korea
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• v.61 no.2
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• pp.68-76
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• 2024

The rotor sail is one of the representative devices in eco-friendly wind-assisted propulsion systems that have been practically applied to commercial ships. The present study proposes an asymmetric vertical folding rotor sail (AFRS) designed for small ships, featuring asymmetric geometry along the vertical direction and the function of vertical folding. To evaluate the aerodynamic performance of rotor sail, the drag, lift and lift-to-drag ratio were derived using computational fluid dynamics. The aerodynamic performance of AFRS was compared with that of normal rotor sail with different aspect ratios and spin ratios. The effect of geometric parameters on the aerodynamic performance of AFRS was assessed by varying the asymmetric diameter ratio. The maximum improvement in lift-to-drag ratio for AFRS was approximately 12% in the considered case. Additionally, the resistance is decreased when AFRS is vertically folded without rotating. Throughout the present study, improved aerodynamic and resistance performances for AFRS were confirmed, which will successfully provide additional propulsion to small ships.

• Proceedings of the Korean Magnetic Resonance Society Conference
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• 2002.08a
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• pp.29-29
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• 2002

• 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.

• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.697-698
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• 2014

• International Journal of Automotive Technology
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• v.6 no.4
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• pp.403-411
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• 2005

The bus is regarded as one of the most frequently used public transportation systems, the research and development on driving stability, safety, and convenience for drivers and passengers has tremendously increased in recent days. This paper investigated the design of the bus door mechanism composed of an actuator (or motor) and linkages. The bus door mechanism is divided into many types according to the coupling of the linkages and the driving system. The mathematical models of all types of door mechanism have been constructed for computer simulation. To design the bus door mechanism, we developed a simulation program, which automates the kinematic and dynamic analysis according to the input parameters of each linkage and the driving system. Using this program, we investigated the design parameters that affect the kinematic and dynamic characteristics of the bus door mechanism under various simulation conditions. In addition, simple examples are examined to validate the developed program.

• Proceedings of the Korean Society of Potoscience Conference
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• 2005.06a
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• pp.97-97
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• 2005