• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2006.06a
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• pp.11-11
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• 2006

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.91-98
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• 2015

Formamide의 중성가수분해 mechanism은 QM/MM (quantum mecahnics/molecular mechanics) molecular dynamics simulations 및 CPMD과 같은 방법으로 연구되어왔다. 본 연구에서는. Umbrella sampling을 이용한 QM/MM-MD simulation을 사용하여 4가지 반응의 free energy surface를 도출해냈다. 전체적으로, 가장 선호되는 메커니즘은 two step으로 구성된 water assisted stepwise mechanism이었으며 모든 mechanism은 ab-initio calculation과 QM/MM-MD simulation이 수행되었다. water assisted stepwise mechanism을 살펴보면, 첫 번째 step에서 formamide의 carbonyl group이 hydrate되면서 gem-diol intermediate를 형성한다. 다음 step에서, intermediate의 hydroxyl group으로부터 amino group으로 water-assisted proton transfer이 일어난다. 두 반응 모두에서 물이 proton transfer를 직접적으로 도와주는 것을 관찰할 수 있었다. 특히, ab-initio calculation과는 다르게 QM/MM-MD에서는 gem-diol intermediate가 안정화되는 것으로 solvent effect를 잘 보여준다.

• Proceedings of the Botanical Society of Korea Conference
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• 2001.04a
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• pp.8-8
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• 2001

• The Plant Pathology Journal
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• v.15 no.2
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• pp.93-98
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• 1999

• Proceedings of the KSME Conference
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• 2004.11a
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• pp.410-415
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• 2004

Molecular dynamics simulations of nanoimprint lithography in which a stamp with patterns is pressed onto amorphous poly-(methylmethacrylate) (PMMA) surface are performed to study the deformation of polymer. Force fields including bond, angle, torsion, inversion, van der Waals and electrostatic potential are used to describe the intermolecular and intramolecular force of PMMA molecules and stamp. Periodic boundary condition is used in horizontal direction and $Nos\acute{e}$-Hoover thermostat is used to control the system temperature. As the simulation results, the adhesion forces between stamp and polymer are calculated and the mechanism of deformation are investigated. The effects of the adhesion force and friction force on the polymer deformation are also studied to analyze the pattern transfer in nanoimprint lithography. The mechanism of polymer deformation is investigated by means of inspecting the indentation process, molecular configurational properties, and molecular configurational energies.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.29 no.6 s.237
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• pp.852-859
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• 2005

Molecular dynamics simulations of nanoimprint lithography in which a stamp with patterns is pressed onto amorphous poly-(methylmethacrylate) (PMMA) surface are performed to study the deformation of polymer. Force fields including bond, angle, torsion, inversion, van der Waals and electrostatic potential are used to describe the intermolecular and intramolecular force of PMMA molecules and stamp. Periodic boundary condition is used in horizontal direction and Nose-Hoover thermostat is used to control the system temperature. As the simulation results, the adhesion forces between stamp and polymer are calculated and the mechanism of deformation are investigated. The effects of the adhesion and friction forces on the polymer deformation are also studied to analyze the pattern transfer in nanoimprint lithography. The mechanism of polymer deformation is investigated by means of inspecting the indentation process, molecular configurational properties, and molecular configurational energies.

• 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.

• Proceedings of the KSME Conference
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• 2001.11b
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• pp.487-492
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• 2001

The Multi-bubble sonoluminescence(MBSL) provides a unique environment, that is, very high temperature$(5,000\sim20,000K)$ and high pressure$(500\sim10,000\;atm)$. However, the mechanism for the MBSL has been elusive. Recently, it has been suggested that the mechanism be continuous and also of discrete peaks that are caused by molecular transitions. In this article, this mechanism has been examined for the Ar/water system by the combined hydrodynamics and molecular transition.

• Bulletin of the Korean Chemical Society
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• v.27 no.8
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• pp.1154-1158
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• 2006

Anomalously high ionic mobilities of H+ and $OH^-$ are owing to the transfer of $H^+$ by the Grotthus chain mechanism. Molecular dynamics simulations for the system of 215 water including $OH^-$ ion at 298.15 K using the OSS2 model [J. Chem. Phys. 109, 5547 (1998)] as a dissociable water model with the use of Ewald summation were carried out in order to study the dynamics of $OH^-$ in water. The calculated ionic mobility of $OH^-$ is in good agreement with the experimental result and the Grotthus chain mechanism is fully understood.

• Molecules and Cells
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• v.39 no.6
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• pp.447-459
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• 2016

Many studies have been conducted to understand plant stress responses to salinity because irrigation-dependent salt accumulation compromises crop productivity and also to understand the mechanism through which some plants thrive under saline conditions. As mechanistic understanding has increased during the last decades, discovery-oriented approaches have begun to identify genetic determinants of salt tolerance. In addition to osmolytes, osmoprotectants, radical detoxification, ion transport systems, and changes in hormone levels and hormone-guided communications, the Salt Overly Sensitive (SOS) pathway has emerged to be a major defense mechanism. However, the mechanism by which the components of the SOS pathway are integrated to ultimately orchestrate plant-wide tolerance to salinity stress remains unclear. A higher-level control mechanism has recently emerged as a result of recognizing the involvement of GIGANTEA (GI), a protein involved in maintaining the plant circadian clock and control switch in flowering. The loss of GI function confers high tolerance to salt stress via its interaction with the components of the SOS pathway. The mechanism underlying this observation indicates the association between GI and the SOS pathway and thus, given the key influence of the circadian clock and the pathway on photoperiodic flowering, the association between GI and SOS can regulate growth and stress tolerance. In this review, we will analyze the components of the SOS pathways, with emphasis on the integration of components recognized as hallmarks of a halophytic lifestyle.