• Journal of the Mineralogical Society of Korea
• /
• v.32 no.3
• /
• pp.151-162
• /
• 2019

Todorokite, a tunnel-structured manganese oxide, can contain cations within the relatively large nanopores created by the $3{\times}3$ Mn octahedra. Because todorokite is poorly crystalline and found as aggregates mixed with other phases of Mn oxides in nature, the coordination structure of cations in the nanopores is challenging to fully characterize in experiment. In the current article, we report the atomistic coordination structures of $Mg^{2+}$ ions in todorokite tunnel nanopores using the classical molecular dynamics (MD) simulations. In experiment, $Mg^{2+}$ is known to occupy the center of the nanopores. In our MD simulations, 60 % of $Mg^{2+}$ ions were located at the center of the nanopores; 40 % of the ions were found at the corners. All $Mg^{2+}$ located at the center formed the six-fold coordination with water molecules, just as the ion in bulk aqueous solution. $Mg^{2+}$ ions at the corners also formed the six-fold coordination with not only water molecules but also Mn octahedral surface oxygens. The mean squared displacements were calculated to examine the dynamic features of $Mg^{2+}$ ions in the one-dimensional (1D) nanopores. Our MD simulations indicate that the dynamic features of water molecules and the cations observed in bulk aqueous solution are lost in the 1D nanopores of todorokite.

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

• Journal of Advanced Marine Engineering and Technology
• /
• v.28 no.3
• /
• pp.441-450
• /
• 2004

The velocity distribution of gas molecules from the experimental results was confirmed as the same with the Maxwell-Boltzmann's theoretical results within the experimental error. This study is on the realization of the Maxwell-Boltzmann's velocity distribution of gas molecules by the molecular dynamics(MD) method. The Maxwell-Boltzmann's velocity distribution of gas molecules is extremely important to confirm the equilibrium state because the properties of a thermodynamic system shall be obtained from the system's equilibrium configuration in the MD method. This study is the first trial in the successive researches to calculate the properties of a thermodynamic system by the computer simulations. We confirmed that the maxwell-boltzmann's velocity distribution is developed in some transient time after starting a simulation and dependent on the size of a system. Also it is found that the velocity distribution has no relation with an initial configuration of gas molecules.

• Transactions of the Korean Society of Mechanical Engineers A
• /
• v.32 no.12
• /
• pp.1047-1054
• /
• 2008

In this paper, the molecular dynamics (MD) simulations are performed with single-crystal copper blocks under simple shear and simple tension to investigate the effect of size and crystal orientation. There are many variances to give influences such as deformation path, temperature, specimen size and crystal orientation. Among them, the crystal orientation has a primary influence on the volume averaged stress. The numerical results show that the volume averaged shear stress decreases as the specimen size increases and as the crystal orientation changes from single to octal. Furthermore, the Schmid factor and yield stress for crystal orientation are evaluated by using the MD simulation on the standard triangle of stereographic projection.

• Journal of Powder Materials
• /
• v.22 no.4
• /
• pp.247-253
• /
• 2015

The sintering mechanisms of nanoscale copper powders have been investigated. A molecular dynamics (MD) simulation with the embedded-atom method (EAM) was employed for these simulations. The dimensional changes for initial-stage sintering such as characteristic lengths, neck growth, and neck angle were calculated to understand the densification behavior of copper nano-powders. Factors affecting sintering such as the temperature, powder size, and crystalline misalignment between adjacent powders have also been studied. These results could provide information of setting the processing cycles and material designs applicable to nano-powders. In addition, it is expected that MD simulation will be a foundation for the multi-scale modeling in sintering process.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2011.02a
• /
• pp.21-21
• /
• 2011

A series of Quasi-Elastic Neutron Scattering (QENS) experiments helps us to understand the single-particle (hydrogen atom) dynamics of a globular protein and its hydration water and strong coupling between them. We also performed Molecular Dynamics (MD) simulations on a realistic model of the hydrated hen-egg Lysozyme powder having two proteins in the periodic box. We found the existence of a Fragile-to-Strong dynamic Crossover (FSC) phenomenon in hydration water around a protein occurring at TL=$225{\pm}5K$ by analyzing Intermediate Scattering Function (ISF). On lowering of the temperature toward FSC, the structure of hydration water makes a transition from predominantly the High Density Liquid (HDL) form, a more fluid state, to predominantly the Low Density Liquid (LDL) form, a less fluid state, derived from the existence of a liquid?liquid critical point at an elevated pressure. We showed experimentally and confirmed theoretically that this sudden switch in the mobility of the hydration water around a protein triggers the dynamic transition (so-called glass transition) of the protein, at a temperature TD=220 K. Mean Square Displacement (MSD) is the important factor to show that the FSC is the key to the strong coupling between a protein and its hydration water by suggesting TL${\fallingdotseq}$TD. MD simulations with TIP4P force field for water were performed to understand hydration level dependency of the FSC temperature. We added water molecules to increase hydration level of the protein hydration water, from 0.30, 0.45, 0.60 and 1.00 (1.00 is the bulk water). These confirm the existence of the FSC and the hydration level dependence of the FSC temperature: FSC temperature is decreased upon increasing hydration level. We compared the hydration water around Lysozyme, B-DNA and RNA. Similarity among those suggests that the FSC and this coupling be universal for globular proteins, biopolymers.

• Bulletin of the Korean Chemical Society
• /
• v.26 no.8
• /
• pp.1203-1208
• /
• 2005

A computational study based on molecular dynamics (MD) simulations was performed in order to explain the difference in aqueous solubilities of two flavonoid/$\beta$-cyclodextrin ($\beta$-CD) complexes, hesperetin/$\beta$-CD and naringenin/$\beta$-CD. The aqueous solubility of each flavonoid/$\beta$-CD complex could be characterized by complexwater interaction not by flavonoid-CD interaction. The radial distribution of water around each inclusion complex elucidated the difference of an experimentally observed solubility of each flavonoid/$\beta$-CD complex. The analyzed results suggested that a bulky hydrophobic moiety (-$OCH_3$) of B-ring of hesperetin nearby primary rim of $\beta$-CD was responsible for lower aqueous solubility of the hesperetin/$\beta$-CD complex.

• The Korean Journal of Ceramics
• /
• v.5 no.1
• /
• pp.40-43
• /
• 1999

In order to investigate Sn substitution sites and interstitial O atoms in tin-doped indium oxide, molecular dynamics (MD) simulations were carried out. There are two kinds of cation sites in $In_2O_3$, namely b-site and d-site. NTP-MD simulations under the condition of 300 K and 0 GPa were performed with two kinds of cells substituted by Sn atoms at each site. The excess oxygen atom accompanied with Sn doping was also taken into consideration. According to the calculations of Sn potential energies in each site, it was revealed that Sn atoms were substituted for b-sites rather than for d-sites. It was also revealed that the interstitial excess oxygen atoms tend to be connected with the Sn atoms substituted for the d-sites Sn rather than for the b-site. There MD simulation results well agreed with the experimental results.

• Bulletin of the Korean Chemical Society
• /
• v.12 no.5
• /
• pp.490-494
• /
• 1991

The ${\beta} to {\alpha}$ phase transition in silver iodide is studied with the (N, V, E) and (N, P, T) molecular dynamics (MD) method. In experiments, the phase transition temperature is 420 K. Upon heating of ${\beta}$ form, the iodine ions undergo hcp to bcc transformation and silver ions become mobile. MD simulations for the ${\beta}$ and ${\alpha}$ phases are carried out at several temperatures and the radial distribution functions (rdf) are obtained at those temperatures in the (N, V, E) ensemble. But the phase transition is not found in our calculation. Next the phase transition is studied with the (N, P, T) MD and we find some evidences of phase transition. At 3 Kbars and 2 Kbars the phase transition temperatu re is about 300 K. For 3.55 Kbars, the phase transition is higher (420 K) than the low pressure case. The phase transition temperature is somewhat dependent on the pressure in our calculations.

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