• 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.

• Interaction and multiscale mechanics
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• v.5 no.2
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• pp.115-129
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• 2012

Nanowires (NWs) have attracted intensive researches owing to the broad applications that arise from their remarkable properties. Over the last decade, immense numerical studies have been conducted for the numerical investigation of mechanical properties of NWs. Among these numerical simulations, the molecular dynamics (MD) plays a key role. Herein we present a brief review on the current state of the MD investigation of nanowires. Emphasis will be placed on the FCC metal NWs, especially the Cu NWs. MD investigations of perfect NWs' mechanical properties under different deformation conditions including tension, compression, torsion and bending are firstly revisited. Following in succession, the studies for defected NWs including the defects of twin boundaries (TBs) and pre-existing defects are discussed. The different deformation mechanism incurred by the presentation of defects is explored and discussed. This review reveals that the numerical simulation is an important tool to investigate the properties of NWs. However, the substantial gaps between the experimental measurements and MD results suggest the urgent need of multi-scale simulation technique.

• Journal of the Korean Chemical Society
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• v.56 no.6
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• pp.669-672
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• 2012

Classical molecular dynamics (MD) simulations using a scaled OSS2 potential originally derived from ab initio calculations are used to study the radial distribution functions of water. The original OSS2 water potential is shown to represent a glassy or an ice at ambient temperature, but the diffusion coefficient increases on increasing the temperature of the system or decreasing the density. This suggests scaling the OSS2 potential. The O-O, O-H, and H-H radial distribution functions and the corresponding coordination numbers for the scaled OSS2 potential, obtained by MD simulation, are in good agreement with the experiment results and calculations for the SPC/E water potential over a range of temperatures.

• Bulletin of the Korean Chemical Society
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• v.32 no.11
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• pp.3909-3913
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• 2011

In this paper we have carried out molecular dynamics simulations (MD) for model systems of liquid n-alkane oligomers ($C_{12}{\sim}C_{80}$) at high temperatures (~2300 K) in a canonical ensemble to calculate viscosity ${\eta}$, self-diffusion constants D, and monomeric friction constant ${\zeta}$. We found that the long chains of these n-alkanes at high temperatures show an abnormality in density and in monomeric friction constant. The behavior of both activation energies, $E_{\eta}$ and $E_D$, and the mass and temperature dependence of ${\eta}$, D, and ${\zeta}$ are discussed.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.506-511
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• 2007

Mechanical behavior of copper nanowire is investigated. An FCC nanowire model composed of 1,408 atoms is used for MD simulation. Simulations are performed within NVT ensemble setting without periodic boundary conditions. $Nos\acute{e}-Poincar\acute{e}$ MD algorithm is employed to guarantee preservation of Hamiltonian and temperature. Numerical tensile tests of Nanowire are carried out with constant strain rate. Additionally, temperature and strain rate effects are considered. Stress-strain curve is constructed from the calculated Cauchy stresses and specified strain values. In (22,4,4) Copper nanowire, non-linear behavior appears around ${\epsilon}\simeq0.09.$ At this instance, starting of structural reorientations are observed. At the onset of reorientation, the modulus characteristics are also investigated.

• Bulletin of the Korean Chemical Society
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• v.19 no.11
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• pp.1217-1221
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• 1998

We present results of molecular dynamic (MD) simulations for the segmental motion of liquid n-heptadecane in order to investigate conformational transitions from one rotational isomeric state to another. The behavior of the hazard plots for n-heptadecane obtained from our MD simulations are compared with that for polymer of Brownian dynamics (BD) study. The transition rate at the ending dihedrals of the n-heptadecane chain is much higher than that at the central dihedrals. In the study of correlation between transitions of neighboring dihedrals, the large value of c2 implies that some 30% of the transitions of the second neighbors can be regarded as following transitions two bonds away in a correlated fashion. Finally the analysis of multiple transitions and the number of times occurred in the initial 0.005 ns are discussed.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 2010.11a
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• pp.431-432
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• 2010

• Bulletin of the Korean Chemical Society
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• v.21 no.1
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• pp.93-96
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• 2000

A diffusion-influenced pseudo-first order reversible reaction A + B ⇔C + B is investigated by the molecular dynamics (MD) simulation method. Theoretical finding that the temporal evolution of reactants [conditional probabilities] in the reversible system can be expressed by the irreversible survival probability with an effective rate parameter is confirmed even in the presence of solvent particles. We carry out molecular dynamics simulations for both the irreversible and the reversible cases to evaluate the survival and the conditional probabilities for each cases. When the resultant irreversible survival probability is inserted into the proposed relation, the conditional probabilities given by the simulation are exactly reproduced.

• Membrane Journal
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• v.30 no.6
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• pp.433-442
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• 2020

In this study, in order to build a molecular dynamics simulation model of ionomer for water electrolysis, an ionomer model that reflects the characteristics of a water electrolysis system in which excess water molecules exist was compared to an ionomer built according to the conventional simulation method of the fuel cells membrane. The final ionomer MD models have a strong phase separation and water channel that is one of the important characteristics of the perfluorinated ionomer, and are stable and water-insoluble under excessive water and high temperature conditions. In the ionomer MD models built in this study, the excess water molecules decrease an ion conductivity due to the dilution of ions, but increase a hydrogen diffusivity. Therefore, it is necessary to design the molecular structure of ionomers for water electrolysis in experimental studies as well as molecular dynamics studies according to the characteristics of the water electrolysis system reported in this study.

• Journal of Photoscience
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• v.9 no.2
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• pp.134-137
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• 2002

PYP consists of a water-soluble apoprotein and 4-hydroxycinnamyl chromophore bound to Cys69 via thiolester linkage, Upon absorption of a photon, the photocycle is initiated, leading to formation of several photo-intermediates. Among them, M intermediate is important to understand the signal transduction mechanism of PYP, because it is a putative signaling state. As well known, the dynamics of a protein is closely correlated with the occurrence of its function. Here we report the results of IO ns molecular dynamics (MD) simulation for the M intermediate in aqueous solution and discuss the characteristic feature of this state from a viewpoint of structural fluctuation.