• Bulletin of the Korean Chemical Society
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• v.23 no.3
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• pp.447-453
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• 2002

In this paper we have presented the results of thermodynamic, structural, and dynamic properties of model systems for liquid benzene, toluene and p-xylene in an isobaric-isothermal (NpT) ensemble at 283.15, 303.15, 323.15, and 343.15 K using molecular dynamics (MD) simulation. This work is initiated to compensate for our previous canonical (NVT) ensemble MD simulations [Bull. Kor. Chem. Soc. 2001, 23, 441] for the same systems in which the calculated pressures were too low. The calculated pressures in the NpT ensemble MD simulations are close to 1 atm and the volume of each system increases with increasing temperature. The first and second peaks in the center of mass g(r) diminish gradually and the minima increase as usual for the three liquids as the temperature increases. The three peaks of the site-site gC-C(r) at 283.15 K support the perpendicular structure of nearest neighbors in liquid benzene. Two self-diffusion coefficients of liquid benzene via the Einstein equation and via the Green-Kubo relation are in excellent agreement with the experimental measures. The self-diffusion coefficients of liquid toluene and p-xylene are in accord with the trend that the self-diffusion coefficient decreases with increasing number of methyl group. The friction constants calculated from the force auto-correlation (FAC) function with the assumption that the fast random force correlation ends at time which the FAC has the first negative value give a correct qualitative trends: decrease with increase of temperature and increase with the number of methyl group. The friction constants calculated from the FAC's are always less than those obtained from the friction-diffusion relation which reflects that the random FAC decays slower than the total FAC as described by Kubo [Rep. Prog. Phys. 1966, 29, 255].

• Genomics & Informatics
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• v.20 no.3
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• pp.33.1-33.17
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• 2022

Nervous necrosis virus (NNV) is a deadly infectious disease that affects several fish species. It has been found that the NNV utilizes grouper heat shock cognate protein 70 (GHSC70) to enter the host cell. Thus, blocking the virus entry by targeting the responsible protein can protect the fishes from disease. The main objective of the study was to evaluate the inhibitory potentiality of 70 compounds of Azadirachta indica (Neem plant) which has been reported to show potential antiviral activity against various pathogens, but activity against the NNV has not yet been reported. The binding affinity of 70 compounds was calculated against the GHSC70 with the docking and molecular dynamics (MD) simulation approaches. Both the docking and MD methods predict 4 (PubChem CID: 14492795, 10134, 5280863, and 11119228) inhibitory compounds that bind strongly with the GHSC70 protein with a binding affinity of -9.7, -9.5, -9.1, and -9.0 kcal/mol, respectively. Also, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the compounds confirmed the drug-likeness properties. As a result of the investigation, it may be inferred that Neem plant compounds may act as significant inhibitors of viral entry into the host cell. More in-vitro testing is needed to establish their effectiveness.

• Transactions of Materials Processing
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• v.15 no.5 s.86
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• pp.395-401
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• 2006

It is reported that semi-solid forming process takes many advantages over the conventional forming process, such as a long die life, good mechanical properties and energy saves. It is important to predict the deformation behavior for optimization of the forging process with semi-solid materials and to control liquid segregation for mechanical properties of materials. But rheology material has thixotropic, pseudo-plastic and shear-thinning characteristics. So, it is difficult for a numerical simulation of the rheology process to be performed because complicated processes such as the filling to include the state of the free surface and solidification in the phase transformation must be considered. General plastic or fluid dynamic analysis is not suitable for the analysis of the rheology material behavior. Recently, molecular dynamics is used for the behavior analysis of the rheology material and turned out to be suitable among several methods. In this study, molecular dynamics simulation was performed for the control of liquid segregation, forming velocity, and viscosity in compression experiment as a part of study on the analysis of rheology forming process.

• Proceedings of the KSME Conference
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• 2003.04a
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• pp.1366-1371
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• 2003

Molecular dynamics (MD) simulations are conducted to investigate the thermophysical characteristics and the stability of liquid threads for various conditions. A cylindrical thread in the simulation domain is made of Lennard-Jones molecules. The surface tension of liquid threads can be determined from local densities, local normal and transverse components of the pressure force. In order to understand the effects of thread radii on surface tensions, the Tolman equation is modified on the basis of the cylindrical coordinates for prediction of surface tensions. Surface tensions calculated from the MD simulation agree with the prediction from the modified Tolman equation. In addition, surface tensions decrease linearly with increasing system temperature. For a binary system, the surface tension decreased linearly compared to that for a pure system with increasing binary ratio of solute molecules which have relatively large value of the affinity coefficient. For a fixed binary ratio, the surface tension increased slightly with the affinity coefficient and the maximum value appear around where the affinity coefficient is 1.5 and decreased rapidly for upper value of 1.5. In addition, the critical wavelengths of perturbations are proven to be directly proportional to the equimolar dividing radii of the liquid threads.

• Korean Journal of Materials Research
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• v.20 no.9
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• pp.478-482
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• 2010

A series of molecular dynamic (MD), finite element (FE) and ab initio simulations are carried out to establish suitable modeling schemes for the continuum-based analysis of aluminum matrix nanocomposites reinforced with carbon nanotubes (CNTs). From a comparison of the MD with FE models and inferences based on bond structures and electron distributions, we propose that the effective thickness of a CNT wall for its continuum representation should be related to the graphitic inter-planar spacing of 3.4${\AA}$. We also show that shell element representation of a CNT structure in the FE models properly simulated the carbon-carbon covalent bonding and long-range interactions in terms of the load-displacement behaviors. Estimation of the effective interfacial elastic properties by ab initio simulations showed that the in-plane interfacial bond strength is negligibly weaker than the normal counterpart due to the nature of the weak secondary bonding at the CNT-Al interface. Therefore, we suggest that a third-phase solid element representation of the CNT-Al interface in nanocomposites is not physically meaningful and that spring or bar element representation of the weak interfacial bonding would be more appropriate as in the cases of polymer matrix counterparts. The possibility of treating the interface as a simply contacted phase boundary is also discussed.

• Journal of the Korean Society for Precision Engineering
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• v.29 no.4
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• pp.479-486
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• 2012

Two of fundamental approaches that can be used to understand ion-solid interaction are Monte Carlo (MC) and Molecular Dynamic (MD) simulations. For the simplicity of simulation Monte Carlo simulation method is widely preferred. In this paper, basic consideration and algorithm of Monte Carlo simulation will be presented as well as simulation results. Sputtering caused by incident ion beam will be discussed with distribution of sputtered particles and their energy distributions. Redeposition of sputtered particles that are experienced refraction at the substrate-vacuum interface additionally presented. In addition, reflection of incident ions with reflection coefficient will be presented together with spatial and energy distributions. This Monte Carlo simulation will be useful in simulating and describing ion beam related processes such as Ion beam induced deposition/etching process, local nano-scale distribution of focused ion beam implanted ions, and ion microscope imaging process etc.

• Bulletin of the Korean Chemical Society
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• v.18 no.4
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• pp.415-424
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• 1997

Conformational flexibilities of the GlcNAc(β1,3)Gal(β)OMe are investigated through NMR spectroscopy and molecular modeling. Adiabatic energy map generated with a dielectric constant of 50 contains three local minima. All of the molecular dynamics simulations on three local minimum energy structures show fluctuations between two low energy structures, N2 at φ=80° and ψ=60° and N3 at φ=60° and ψ=-40°. We have presented adequate evidences to state that GlcNAc(β1,3)Gal(β)OMe exists in two conformationally discrete forms. Two state model of N2 and N3 conformers with a population ratio of 40:60 is used to calculate the effective cross relaxation rate and reproduces the experimental NOEs very well. Molecular dynamics simulation in conjunction with two state model proves successfully the dynamic equilibrium existed in GlcNAc(β1,3)Gal(β)OMe and can be considered as a powerful method to analyze the motional properties in the structure of carbohydrate. This observation also cautions against the indiscriminate use of a rigid model to analyze NMR data.

• Proceedings of the KSME Conference
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• 2008.11a
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• pp.1891-1895
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• 2008

Water covers 70% of the earth's surface and the human body consist of 75% of it. It is clear that water is one of the prime elements responsible for life on earth. Over the last 30 years or so, numerous studies have attempted to find out more about the water microscopically. In this paper, we investigated how the receding and advancing contact angle of the moving water droplet changes on a solid surface having various LJ epsilon parameters. To observe the dynamic contact angle history, a body force applied to all water molecules after obtained the water droplet in equilibrium with the solid surface. We obtained the density profile and receding and advancing contact angle of the moving water droplet

• Journal of the Semiconductor & Display Technology
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• v.4 no.3 s.12
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• pp.11-15
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• 2005

This paper shows that carbon nanotubes can be applied to a nanopipette. Nano space in atomic force microscope multi wall carbon nanotube tips is filled with molecules and atoms with charges and then, the tips can be applied to nanopipette when the encapsulated media flow off under applying electrostatic farces. Since the nano space inside the tips can be refilled, the tips can be permanently used in ideal conditions of no chemical reaction and no mechanical deformation. Molecular dynamics simulations for nanopipette applications demonstrated the possibility of nano-lithography or single-metallofullerene-transistor array fabrication.

• Journal of Integrative Natural Science
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• v.6 no.1
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• pp.8-11
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• 2013

In this manuscript, we report a protocol to determine most of the lowest energy conformations from the ensemble of conformations. 12-crown-4 was taken as study compound to get the most of energy minima conformations. Molecular dynamic (MD) simulation for 1 nanosecond (ns) was performed at 300, 500, 700, 900 and 1100 K temperature. At particular interval conformations were sampled. Then Gaussian program was used to minimize compounds using PM6 energy levels. Duplicates were removed by checking energy as well as mirror image conformations, and only unique conformations were retained for the next $6-31+G^*$ level minimization. It was observed that upto certain increment in temperature the number of unique conformations were increased, but afterword it decreased.