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

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

• Carbon letters
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• v.11 no.4
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• pp.316-324
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• 2010

The effects of geometrical parameters on mechanical properties of graphite-vinylester nanocomposites and their constituents (matrix, reinforcement and interface) are studied using molecular dynamics (MD) simulations. Young's modulii of 1.3 TPa and 1.16 TPa are obtained for graphene layer and for graphite layers respectively. Interfacial shear strength resulting from the molecular dynamic (MD) simulations for graphene-vinylester is found to be 256 MPa compared to 126 MPa for graphitevinylester. MD simulations prove that exfoliation improves mechanical properties of graphite nanoplatelet vinylester nanocomposites. Also, the effects of bromination on the mechanical properties of vinylester and interfacial strength of the graphene.brominated vinylester nanocomposites are investigated. MD simulation revealed that, although there is minimal effect of bromination on mechanical properties of pure vinylester, bromination tends to enhance interfacial shear strength between graphite-brominated vinylester/graphene-brominated vinylester in a considerable magnitude.

• Proceedings of the KSME Conference
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• 2001.11a
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• pp.252-257
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• 2001

With the help of newly arrived technology such as PC clustering, molecular dynamics (MD) seems to be promising for large-scale materials simulations. A cost-effective cluster is set up using commodity PCs connected over Ethernet with fast switching devices and free software Linux. Executing MD simulations in the parallel sessions makes it possible to carry out large-scale materials simulations at acceptable computation time and costs. In this study, the MD computer code for fracture simulation is modified to comply with MPI (Message Passing Interface) specification, and runs on the PC cluster in parallel mode flawlessly. It is noted that PC clusters can provide a rather inexpensive high-performance computing environment comparing to supercomputers, if properly arranged.

• Current Applied Physics
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• v.18 no.11
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• pp.1352-1358
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• 2018

In recent years, one-dimensional (1D) magnetic nanostructures, such as magnetic nanorods and chains of magnetic nanoparticles have received great attentions due to the breadth of applications. Especially, magnetic nanorods has been opened an area of active research and applications in medicine, sensors, optofluidics, magnetic swimming, and microrheology since they possess the unique magnetic and geometric features. This study focuses on the molecular dynamics (MD) simulations of an infinitely long crystal ${\beta}-Fe_2O_3$ nanorod. To elucidate the structural properties and dynamics behavior of ${\beta}-Fe_2O_3$ nanorods, MD simulation is a powerful technique. The structural properties such as equation of state and radial distribution function of bulk ${\beta}-Fe_2O_3$ are performed by lattice dynamics (LD) simulations. In this work, we consider three main mechanisms affecting on deformation characteristics of a ${\beta}-Fe_2O_3$ nanorod: 1) temperature, 2) the rate of mechanical compression, and 3) the rate of mechanical torsion.

• Membrane Journal
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• v.26 no.5
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• pp.329-336
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• 2016

Proton exchange membrane (PEM) is one of the key components of membrane-electrode assembly (MEA), which plays important role in fuel cell performance together with catalysts. It is widely accepted that water channel morphology inside PEMs as a proton pathway significantly affects the PEM performance. Molecular dynamics (MD) simulations are a very useful tool to understand molecular and atomic structures of materials, so that many related researches are currently being studied. In this paper, we summarize the current research trend in MD simulations, present which properties can be characterized, and finally introduce the usefulness of MD simulations to the researchers for proton exchange membranes.

• Bulletin of the Korean Chemical Society
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• v.29 no.8
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• pp.1505-1509
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• 2008

Comparative molecular simulations were performed to establish molecular interaction and inhibitory effect of flavonoid myricetin on formation of amyloid fibris. For computational comparison, the conformational stability of myricetin with amyloid $\beta$ -peptide (A$\beta$ ) and $\beta$ -amyloid fibrils (fA$\beta$) were traced with multiple molecular dynamics simulations (MD) using the CHARMM program from Monte Carlo docked structures. Simulations showed that the inhibition by myricetin involves binding of the flavonoid to fA$\beta$ rather than A$\beta$ . Even in MD simulations over 5 ns at 300 K, myricetin/fA$\beta$ complex remained stable in compact conformation for multiple trajectories. In contrast, myricetin/A$\beta$ complex mostly turned into the dissociated conformation during the MD simulations at 300 K. These multiple MD simulations provide a theoretical basis for the higher inhibitory effect of myricetin on fibrillogenesis of fA$\beta$ relative to A$\beta$ . Significant binding between myricetin and fA$\beta$ observed from the computational simulations clearly reflects the previous experimental results in which only fA$\beta$ had bound to the myricetin molecules.

• Nuclear Engineering and Technology
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• v.41 no.1
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• pp.11-20
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• 2009

Radiation effects on materials are inherently multiscale phenomena in view of the fact that various processes spanning a broad range of time and length scales are involved. A multiscale modeling approach to embrittlement of pressure vessel steels is presented here. The approach includes an investigation of the mechanisms of defect accumulation, microstructure evolution and the corresponding effects on mechanical properties. An understanding of these phenomena is required to predict the behavior of structural materials under irradiation. We used molecular dynamics (MD) simulations at an atomic scale to study the evolution of high-energy displacement cascade reactions. The MD simulations yield quantitative information on primary damage. Using a database of displacement cascades generated by the MD simulations, we can estimate the accumulation of defects over diffusional length and time scales by applying kinetic Monte Carlo simulations. The evolution of the local microstructure under irradiation is responsible for changes in the physical and mechanical properties of materials. Mechanical property changes in irradiated materials are modeled by dislocation dynamics simulations, which simulate a collective motion of dislocations that interact with the defects. In this paper, we present a multi scale modeling methodology that describes reactor pressure vessel embrittlement in a light water reactor environment.

• CELLMED
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• v.6 no.4
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• pp.24.1-24.4
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• 2016

The emergence of influenza virus and antigenic drift are potential cause of world-wide pandemic. There are some commercially available drugs in the market to treat influenza. During past decade, however, critical resistances have been raised for biological targets. Because of structural complexity and flexibility of target proteins, applying a computational modeling tool is very beneficial for developing alternative anti-influenza drugs. In this review, we introduced molecular dynamics (MD) simulations approach to reflect full conformational flexibility of proteins during molecular modeling works. Case studies of MD works were summarized for the drug discovery and drug resistance mechanism of anti-influenza pharmaceuticals.

• Bulletin of the Korean Chemical Society
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• v.23 no.3
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• pp.441-446
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• 2002

We have presented the results of thermodynamic, structural and dynamic properties of liquid benzene, toluene, and p-xylene in canonical (NVT) ensemble at 293.15 K by molecular dynamics (MD) simulations. The molecular model adopted for these molecules is a combination of the rigid body treatment for the benzene ring and an atomistically detailed model for the methyl hydrogen atoms. The calculated pressures are too low in the NVT ensemble MD simulations. The various thermodynamic properties reflect that the intermolecular interactions become stronger as the number of methyl group attached into the benzene ring increases. The pronounced nearest neighbor peak in the center of mass g(r) of liquid benzene at 293.15 K, provides the interpretation that nearest neighbors tend to be perpendicular. Two self-diffusion coefficients of liquid benzene at 293.15 K calculated from MSD and VAC function are in excellent agreement with the experimental measures. The self-diffusion coefficients of liquid toluene also agree well with the experimental ones for toluene in benzene and for toluene in cyclohexane.