• Bulletin of the Korean Chemical Society
• /
• v.33 no.2
• /
• pp.728-730
• /
• 2012

• Bulletin of the Korean Chemical Society
• /
• v.23 no.1
• /
• pp.107-111
• /
• 2002

The OSS2 (Oj？me-Shavitt-Singer 2)[L. Oj？me et al., J. Chem. Phys. 109, 5547 (1998)] model for the solvated proton in water is examined for $H_2O,\;H_3O^+,\;H_5O_2^+,\;H_7O_3^+,\;and\;H_9O_4^-$ by molecular dynamics (MD) simulations. The equilibrium molecular geometries and energies obtained from MD simulations at 5.0 and 298.15 K agree very well with the optimized calculations.

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

• Proceedings of the Korean Society for Technology of Plasticity Conference
• /
• 2003.10a
• /
• pp.347-354
• /
• 2003

The dynamics of fluid flow through nanomachines is completely different from that of continuum. In this study, molecular dynamics simulations were performed for the flow of helium, neon, argon inside carbon(graphite) nanotubes of several sizes. The fluid was introduced into the nanotube at a given initial velocity according to given temperature. Diffusion coefficients were evaluated by Green-Kubo equation derived from Einstein relationship. The behaviour of the fluid was strongly dependent on the density of fluid and tube diameter, not on the tube length. It was found that the diffusion Coefficients increased With decreasing the density of molecules and increasing the diameter and temperature.

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

• Bulletin of the Korean Chemical Society
• /
• v.32 no.2
• /
• pp.515-518
• /
• 2011

We investigated how temperature influences the structural and energetic dynamics of carbon nanotubes (CNTs) undergoing a high-speed impact with a Si (110) surface. By performing molecular dynamics simulations in the temperature range of 100 - 300 K, we found that a low temperature CNT ends up with a higher vibrational energy after collision than a high temperature CNT. The vibrational temperature of CNT increases by increasing the surface temperature. Overall, the structural and energy relaxation of low temperature CNTs are faster than those of high temperature CNTs.

• Advances in Computational Design
• /
• v.3 no.2
• /
• pp.147-163
• /
• 2018

Cementitious composites are multiphase heterogeneous materials with distinct dissimilarity in strength under compression and tension (high under compression and very low under tension). At macro scale, the phenomenon can be well-explained as the material contains physical heterogeneity and pores. But, it is interesting to note that this dissimilarity initiates at molecular level where there is no heterogeneity. In this regard, molecular dynamics based computational investigations are carried out on cement clinkers and calcium silicate hydrate (C-S-H) under tension and compression to trace out the origin of dissimilarity. In the study, effect of strain rate, size of computational volume and presence of un-structured atoms on the obtained response is also investigated. It is identified that certain type of molecular interactions and the molecular structural parameters are responsible for causing the dissimilarity in behavior. Hence, the judiciously modified or tailored molecular structure would not only be able to reduce the extent of dissimilarity, it would also be capable of incorporating the desired properties in heterogeneous composites. The findings of this study would facilitate to take step to scientifically alter the structure of cementitious composites to attain the desired mechanical properties.

• Journal of Mechanical Science and Technology
• /
• v.16 no.11
• /
• pp.1440-1447
• /
• 2002

Adhesion of a hemispherical tip to the flat surface in nano-structures is simulated using the molecular dynamics technique. The tip and plates are modeled with the Lennard-Jones molecules. The simulation focuses on the deformation of the tip. Detailed descriptions on the evolution of interaction force, the energy dissipation due to adhesion hysteresis, the forma- tion-growth-breakage of adhesive junction as well as the evolution of molecular distribution during the process are presented. The effects of the tip size, the maximum tip approach, the tip temperature, and the affinity between the tip and the mating plate are also discussed.

• Proceedings of the KSME Conference
• /
• 2007.05b
• /
• pp.2678-2683
• /
• 2007

The interaction between metal molecules and liquid metal molecules was modeled in the molecular scale and simulated by the molecular dynamics method in order to understand behaviors of the cluster on metallic surface in collision process. Lennard-Jones potential had been used as intermolecular potential, and only attraction 때 d repulsion had been used for the behavior of the cluster on the metal surface. As results, the behavior of the cluster was so much influenced by the cluster of liquid metal temperature and function of molecules forces, such as attraction and repulsion, in the collision progress. These results of simulation will be the foundation for the micro fabrication manufacturing by using spray application technology.

• Bulletin of the Korean Chemical Society
• /
• v.30 no.9
• /
• pp.2087-2092
• /
• 2009

We performed molecular dynamics simulations on dimyristoylphosphatidylcholine lipid bilayer with 50 mol% halothane. The structural properties, electron density profile, segmental order parameter of acyl chains, headgroup orientation distribution, water dipole orientation distribution, have been examined. Overall the effects of the halothane molecules on structural properties of DMPC lipid bilayer were found to be small. The electron density profiles, the segmental order parameter, the headgroup orientation, the water dipole orientation were not affected significantly by the halothane molecules. Pressure tensor calculations shows that the lateral pressure increases at the hydrocarbon tail region and the headgroup region, and decreases at the water-headgroup interfacial region.