• 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.4
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• pp.795-798
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• 2008

The formation of complex $XeHCl^+$ in the collision-induced reaction of $Xe^+$ with HCl has been studied by use of classical dynamics procedures using the London-Eyring-Polanyi-Sato empirical potential energy surfaces. A small fraction of trajectories on the $Xe^+$ + HCl and Xe + $HCl^+$ surfaces lead to the formation of complex $XeHCl^+$ with life-times of 1-2 ps which is long enough to survive many rotations before redissociating back to the reactant state. The formation of complex $XeHCl^+$ occurs mainly from collision angle of $\Theta$ = ${45^{\circ}}$.

• Nuclear Engineering and Technology
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• v.42 no.3
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• pp.259-270
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• 2010

New generation nuclear reactors are designed using advanced safety analysis methods. A thorough understanding of different interacting physical phenomena is necessary to avoid underestimation and overestimation of consequences of off-normal transients in the reactor safety analysis results. This feature requires a multiphysics reactor simulation model. In this context, a coupled dynamics model based on a multiphysics formulation is developed indigenously for the transient analysis of large pressurized VVER reactors. Major simplifications are employed in the model by making several assumptions based on the physics of individual phenomenon. Space and time grids are optimized to minimize the computational bulk. The capability of the model is demonstrated by solving a series of international (AER) benchmark problems for VVER reactors. The developed model was used to analyze a number of reactivity transients that are likely to occur in VVER reactors.

• Bulletin of the Korean Chemical Society
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• v.28 no.4
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• pp.607-612
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• 2007

Relationship between charge transfer mechanism and quantum coherence has been investigated using a realtime quantum dynamics approach. In the on-the-fly filtered propagator functional path integral simulation, by separating paths that belong to different mechanisms and by integrating contributions of correspondingly sorted paths, it was possible to accurately obtain quantitative contribution of different transport mechanisms. For a 5'-GAGGG-3' DNA sequence, we analyze charge transfer processes quantitatively such that the governing mechanism alters from coherent to incoherent charge transfer with respect to the friction strength arising from dissipative environments. Although the short DNA sequence requires substantially strong dissipation for completely incoherent hopping transfer mechanism, even a weak system-environment interaction markedly destroys the coherence within the quantum mechanical system and the charge transfer dynamics becomes incoherent to some degree. Based on the forward-backward path deviation analysis, the coherence variation depending on the environment is investigated numerically.

• Bulletin of the Korean Chemical Society
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• v.25 no.8
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• pp.1130-1132
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• 2004

Photodissociation dynamics of tert-butyl isocyanide at 193 nm has been investigated by measuring rotationally resolved laser induced fluorescence spectra of CN fragments that were exclusively produced in the ground electronic state. From the spectra, internal energies of CN and translational energy releases in the products were obtained. The dissociation takes place in the excited triplet states which are strongly repulsive along the dissociation coordinate via curve crossing from the initially prepared state.

• Bulletin of the Korean Chemical Society
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• v.30 no.8
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• pp.1845-1850
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• 2009

We have performed replica-exchange molecular dynamics (REMD) simulations on the dimer formation of fibrilforming segments of $\alpha$-Synuclein (residues 71 - 82) using implicit solvation models with two kinds of force fields- AMBER parm99SB and parm96. We observed spontaneous formation of dimers from the extensive simulations, demonstrating the self-aggregating and fibril forming properties of the peptides. Secondary structure profile and clustering analysis showed that dimers with antiparallel $\beta$-sheet conformations, stabilized by well-defined hydrogen boding, are major species corresponding to global free energy minimum. Parallel dimers with partial $\beta$-sheets are found to be off-pathway intermediates. The relative instability of the parallel arrangements is due to the repulsive interactions between bulky and polar side chains as well as weaker backbone hydrogen bonds.

• Journal of the Korea Institute of Military Science and Technology
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• v.13 no.6
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• pp.1013-1018
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• 2010

This paper presents a numerical evaluation of the launch dynamics and thermo-fluid phenomena for gas generator launch eject system. The existing gas dynamic model for launching eject body used ideal gas and adiabatic assumption with empirical energy loss model. In present study, a turbulent Navier-Stokes solver with CHIMERA mesh is employed to predict the detail unsteady thermo-fluid dynamics for the launched body. The calculation results show that proper grid number is necessary for good agreement with experimental data. The important effects for accurate prediction are a gap distance and thermal boundary condition on the wall. The computational results show good agreement with experiment data.

• BMB Reports
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• v.52 no.12
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• pp.679-688
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• 2019

The decrease of metabolism in the brain has been observed as the important lesions of Alzheimer's disease (AD) from the early stages of diagnosis. The cumulative evidence has reported that the failure of mitochondria, an organelle involved in diverse biological processes as well as energy production, maybe the cause or effect of the pathogenesis of AD. Both amyloid and tau pathologies have an impact upon mitochondria through physical interaction or indirect signaling pathways, resulting in the disruption of mitochondrial function and dynamics which can trigger AD. In addition, mitochondria are involved in different biological processes depending on the specific functions of each cell type in the brain. Thus, it is necessary to understand mitochondrial dysfunction as part of the pathological phenotypes of AD according to each cell type. In this review, we summarize that 1) the effects of AD pathology inducing mitochondrial dysfunction and 2) the contribution of mitochondrial dysfunction in each cell type to AD pathogenesis.

• Advances in nano research
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• v.8 no.2
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• pp.103-114
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• 2020

In this research, buckling and free vibration of rectangular polymeric laminate reinforced by graphene sheets are investigated. Various patterns are considered for augmentation of each laminate. Critical buckling load is evaluated for different parameters, including boundary conditions, reinforcement pattern, loading regime, and laminate geometric states. Furthermore, vibration analysis is investigated for square laminate. Elastic properties of the composite are calculated using a combination of both molecular dynamics (MD) and the rule of mixture (MR). Kinematics of the plate is approximated based on the first shear deformation theory (FSDT). The current analysis is performed based on the energy method. For the numerical investigation, Ritz method is applied, and for shape functions, Chebyshev polynomials are utilized. It is found that the number of layers is effective on the buckling load and natural frequency of laminates which made from non-uniform layers.

• Proceedings of the KSME Conference
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• 2004.04a
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• pp.547-550
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• 2004

We present a multiscale scheme which describes the dynamic pictures of atoms in the multiple length-scale systems. Large-scale atomic systems are reduced to coarse grained system by the quasicontinuum, of which the dynamic pathways are rendered by the action-derived molecular dynamics proved effective for multiple time-scale problems such as rare events. Adatom diffusions on the metal (001) surface are selected for our numerical examples. The energy barriers of the diffusions and the real dynamic trajectories of the adatoms are calculated.