• Bulletin of the Korean Chemical Society
• /
• v.29 no.3
• /
• pp.641-646
• /
• 2008

Equilibrium molecular dynamics simulations in a canonical ensemble are performed to evaluate the transport coefficients of several Lennard-Jones (LJ) mixtures at a liquid argon states of 94.4 K and 1 atm via modified Green-Kubo formulas. Two component mixture of A and B is built by considering the interaction between A and A as the attractive (A) potential, that between A and B as the attractive potential (A), and that between B and B as the repulsive potential (R), labelled as AAR mixture. Three more mixtures - ARA, ARR, and RAR are created in the same way. The behavior of the LJ energy and the transport properties for all the mixtures is easily understood in terms of the portion of attractive potential (A %). The behavior of the thermal conductivities by the translational energy transport due to molecular motion exactly coincides with that of diffusion constant while that of the thermal conductivities by the potential energy transport due to molecular motion is easily understood from the fact that the LJ energy of AAR, ARR, and RAR mixtures increases negatively with the increase of A % from that of the pure repulsive system while that of ARA changes rarely.

• Journal of the Korean institute of surface engineering
• /
• v.39 no.2
• /
• pp.76-81
• /
• 2006

Molecular dynamics simulations were carried out to investigate physical sputtering of Fe(100) substrate due to energetic ion bombardments. Repulsive interatomic potentials at short internuclear distances were determined with ab initio calculations using the density functional theory. Bohr potentials were fitted to the ab initio results on diatomic pairs (Ar-Fe, Fe-Fe) and used as repulsive screened Coulombic potentials in sputtering simulations. The fitted-Bohr potentials improve the accuracy of the sputtering yields predicted by molecular dynamics for sputtering of Fe(100), whereas Moliere and ZBL potentials were found to be too repulsive and gave relatively high sputtering yields. In spite of assumptions and limitations in this simulation work, the sputtering yields predicted by the molecular dynamics method were in fairly good accordance with the obtainable experimental data in absolute values as well as in manner of the variation according to the Incident energy. Threshold energy for sputtering of Fe(100) substrate was found to be about 40 eV. Additionally, distributions of kinetic energies of sputtered atoms and their original depths could be obtained.

• Journal of Integrative Natural Science
• /
• v.13 no.4
• /
• pp.170-180
• /
• 2020

Abnormal regulation, hyperphosphorylation, and aggregation of the tau protein are the hallmark of several types of dementia, including Alzheimer's Disease. Increased activity of Glycogen Synthase Kinase-3β (GSK-3β) in the Central Nervous System (CNS), increased the tau hyperphosphorylation and caused the neurofibrillary tangles (NFTs) formation in the brain cells. Over the last two decades, numerous adenosine triphosphate (ATP) competitive inhibitors have been discovered that show inhibitory activity against GSK-3β. But these compounds exhibited off-target effects which motivated researchers to find new GSK-3β inhibitors. In the present study, we have collected the dataset of 31 C-Glycosylflavones derivatives that showed inhibitory activity against GSK-3β. Among the dataset, the most active compound was docked with the GSK-3β and molecular dynamics (MD) simulation was performed for 50 ns. Based on the 50 ns MD pose of the most active compound, the other dataset compounds were sketched, minimized, and aligned. The 3D-QSAR based Comparative Molecular Field Analysis (CoMFA) model was developed, which showed a reasonable value of q2=0.664 and r2=0.920. The contour maps generated based on the CoMFA model elaborated on the favorable substitutions at the R2 position. This study could assist in the future development of new GSK-3β inhibitors.

• Bulletin of the Korean Chemical Society
• /
• v.24 no.1
• /
• pp.95-98
• /
• 2003

Enantioselectivity of the propranolol on β-cyclodextrin was simulated by molecular modeling. Monte Carlo (MC) docking and molecular dynamics (MD) simulations were applied to investigate the molecular mechanism of enantioselective difference of both enantiomeric complexes. An energetic analysis of MC docking simulations coupled to the MD simulations successfully explains the experimental elution order of propranolol enantiomers. Molecular dynamics simulations indicate that average energy difference between the enantiomeric complexes, frequently used as a measure of chiral recognition, depends on the length of the simulation time. We found that, only in case of much longer MD simulations, noticeable chiral separation was observed.

• KIISE Transactions on Computing Practices
• /
• v.20 no.10
• /
• pp.534-542
• /
• 2014

Multiscale modeling is a new simulation approach which can manage different spatial and temporal scales of system. In this study, as part of multiscale modeling research, we propose the way of combining two different simulation methods, molecular dynamics(MD) and stochastic rotation dynamics(SRD). Our conceptual implementations are based on LAMMPS, one of the well-known molecular dynamics programs. Our prototype of multiscale modeling follows the form of the third party implementation of LAMMPS. It added MD to SRD in order to simulate the boundary area of the simulation box. Because it is important to guarantee the seamless simulation, we also designed the overlap zones and communication zones. The preliminary experimental results showed that our proposed scheme is properly worked out and the execution time is also reduced.

• Composites Research
• /
• v.30 no.6
• /
• pp.371-378
• /
• 2017

In this study, hygroelastic behavior of thermosetting epoxy is predicted by molecular dynamics simulations. Since consistent exposures to humid environments lead to macroscopic degradation of polymer composite, computational simulation study of the hygroscopically aged epoxy cell is essential for long-time durability. Therefore, we modeled amorphous epoxy molecular unit cell structures at a crosslinking ratio of 30, 90% and with the moisture weight fraction of 0, 4 wt% respectively. Diglycidyl ether of bisphenol F (EPON862) and triethylenetetramine (TETA) are chosen as resin and curing agent respectively. Incorporating equilibrium and non-equilibrium ensemble simulation with a classical interatomic potential, various hygroelastic properties including diffusion coefficient of water, coefficient of moisture expansion (CME), stress-strain curve and elastic modulus are predicted. To establish the structural property relationship of pure epoxy, free volume and internal non-bond potential energy of epoxy are examined.

• Journal of the Korean Society for Aeronautical & Space Sciences
• /
• v.30 no.5
• /
• pp.15-23
• /
• 2002

For molecular dynamics requires high-performance computers or supercomputers to handle huge amount of computation, it is not until recent days that the application of molecular dynamics to materials fracture simulations draw some attention from many researchers. With the recent advent of high-performance computers, computation intensive methods become more tractable than ever. However, carrying out materials simulation on high-performance computers costs too much in general. In this study, a PC cluster consisting of multiple commodity PCs is established and computer simulations of materials with cracks are carried out on it via molecular dynamics technique. The effect of the number of nodes, speedup factors, and communication time between nodes are measured to verify the performance of the PC cluster. Upon using the PC cluster, materials fracture simulations with more than 50,000 molecules are carried out successfully.

• Polymer(Korea)
• /
• v.35 no.4
• /
• pp.325-331
• /
• 2011

Molecular simulations via the molecular dynamics method have been carried out to an equation of state of penetrable-sphere model fluids over a wide range of packing fraction ${\phi}$ and finite repulsive energy ${\varepsilon}^*$. The resulting simulation data are compared to theoretical predictions from the two limiting cases of high- and low-penetrability approximations available in the literature. A good agreement between theoretical and simulation results is observed ill the case of ${\varepsilon}^*$ <3.0. However, for the highly repulsive energy systems of ${\varepsilon}^*{\geqq}3.0$, where the potential energy barrier is more than two times higher than the particle kinetic energy, a poor agreement is found due to the clustering formation and the non-continuum size effects in the dense systems of ${\phi}{\geqq}0.7$ and ${\varepsilon}^*$=6.0.

• Nuclear Engineering and Technology
• /
• v.52 no.2
• /
• pp.337-343
• /
• 2020

Oxide dispersed strengthened (ODS) steel is an important candidate for Gen-IV reactors. Oxide embedded in Fe can help to trap irradiation defects and enhances the strength of steel. It was observed in this study that the size of oxide has a profound impact on the depinning mechanism. For smaller sizes, the oxide acts as a void; thus, letting the dislocation bypass without any shear. On the other hand, oxides larger than 2 nm generate new dislocation segments around themselves. The depinning is similar to that of Orowan mechanism and the strengthening effect is likely to be greater for larger oxides. It was found that higher shear deformation rates produce more fine-tuned stress-strain curve. Both molecular dynamics (MD) simulations and BKS (Bacon-Knocks-Scattergood) model display similar characteristics whereby establishing an inverse relation between the depinning stress and the obstacle distance. It was found that (110)_oxide || (111)_Fe (oriented oxide) also had similar characteristics as that of (100)_oxide || (111)_Fe but resulted in an increased depinning stress thereby providing greater resistance to dislocation bypass. Our simulation results concluded that critical depinning stress depends significantly on the size and orientation of the oxide.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.9
• /
• pp.2581-2587
• /
• 2010

Nitration of tyrosine and tryptophan residues is common in cells under nitrative stress. However, physiological consequences of protein nitration are not well characterized on a molecular level due to limited availability of the 3D structures of nitrated proteins. Molecular dynamics (MD) simulation can be an alternative tool to probe the structural perturbations induced by nitration. In this study we developed molecular mechanics parameters for 3-nitrotyrosine (NIY) and 6-nitrotryptophan (NIW) that are compatible with the AMBER-99 force field. Partial atomic charges were derived by using a multi-conformational restrained electrostatic potential (RESP) methodology that included the geometry optimized structures of both $\alpha$- and $\beta$-conformers of a capped tripeptide ACE-NIY-NME or ACE-NIW-NME. Force constants for bonds and angles were adopted from the generalized AMBER force field. Torsional force constants for the proper dihedral C-C-N-O and improper dihedral C-O-N-O of the nitro group in NIY were determined by fitting the torsional energy profiles obtained from quantum mechanical (QM) geometry optimization with those from molecular mechanical (MM) energy minimization. Force field parameters obtained for NIY were transferable to NIW so that they reproduced the QM torsional energy profiles of ACE-NIW-NME accurately. Moreover, the QM optimized structures of the tripeptides containing NIY and NIW were almost identical to the corresponding structures obtained from MM energy minimization, attesting the validity of the current parameter set. Molecular dynamics simulations of thioredoxin nitrated at the single tyrosine and tryptophan yielded well-behaved trajectories suggesting that the parameters are suitable for molecular dynamics simulations of a nitrated protein.