• Advances in nano research
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• v.9 no.2
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• pp.83-90
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• 2020

This research investigates the effect of single walled carbon nanotubes (SWCNTs) dimensions in terms of diameter on the mechanical properties (longitudinal and transverse Young's modulus) of the simulated nanocomposites by molecular dynamics (MDs) method. MDs utilized to create nanocomposite models consisting of five case studies of SWCNTs with different chiralities (5, 0), (10, 0), (15, 0), (20, 0) and (25, 0) as the reinforcement and using polymethyl methacrylate (PMMA) as the common matrix. The results show that with increasing of SWCNTs diameter, the mechanical and physical properties increase. It is important that with the increasing of SWCNTs diameter, density, longitudinal and transverse Young's modulus, shear modulus, poisson's ratio, and bulk modulus of simulated nanocomposite from (5, 0) to (25, 0) approximately becomes 1.54, 3, 2, 1.43, 1.11 and 1.75 times more than (5, 0), respectively. Then to validate the results, the stiffness matrix is obtained by Materials studio software.

• Bulletin of the Korean Chemical Society
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• v.35 no.6
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• pp.1769-1776
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• 2014

Binding modes of a series of catechol derivatives such as protein tyrosine phosphatase 1B (PTP1B) inhibitors were identified by molecular modeling techniques. Docking, molecular dynamics simulations and free energy calculations were employed to determine the modes of these new inhibitors. Binding free energies were calculated by involving different energy components using the Molecular Mechanics-Poisson-Boltzmann Surface Area and Generalized Born Surface Area methods. Relatively larger binding energies were obtained for the catechol derivatives compared to one of the PTP1B inhibitors already in use. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy decomposition analysis indicated that the hydroxyl functional groups and biphenyl ring system had favorable interactions with Met258, Tyr46, Gln262 and Phe182 residues of PTP1B. The results of hydrogen bound analysis indicated that catechol derivatives, in addition to hydrogen bonding interactions, Val49, Ile219, Gln266, Asp181 and amino acid residues of PTP1B are responsible for governing the inhibitor potency of the compounds. The information generated from the present study should be useful for the design of more potent PTP1B inhibitors as anti-diabetic agents.

• Journal of the Mineralogical Society of Korea
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• v.27 no.4
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• pp.271-281
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• 2014

The physicochemical properties of clay minerals have been investigated at the atomistic to nano scale. The microscopic studies are often challenging to perform by using experimental approaches alone. In particular, hydroxyl groups of octahedral sheets in 2:1 clay minerals have been hypothesized to impact the sorption process of metal cations; however, X-ray based techniques alone, a common tool for mineral structure examination, cannot properly test the hypothesis. The current study has examined whether computational mineralogy techniques can be applied to examine the hydroxyl structures of clay minerals. Based on quantum-mechanics and molecular-mechanics computational methods, geometry optimizations were carried out for representative dioctahedral and trioctahedral phyllosilicate minerals. Both methods well reproduced the experimental lattice parameters; however, for structural distortion occurring in the tetrahedral or octahedral sheets, molecular mechanics showed significant deviations from experimental data. The orientation angle of the hydroxyl with respect to (001) basal plane is determined by the balance of repulsion between the hydroxyl proton and Si cations of tetrahedral sites; the quantum-mechanics method predicted $25-26^{\circ}$ for the angle, whereas the angle predicted by the molecular-mechanics method was much higher by $10^{\circ}$ (i.e., $35^{\circ}$). These results demonstrate that computational mineralogy techniques are a reliable tool for clay mineral studies and can be used to further elucidate the roles of hydroxyls in metal sorption process.

• Computational Structural Engineering
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• v.18 no.2 s.68
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• pp.25-33
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• 2005

• Bulletin of the Korean Chemical Society
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• v.10 no.2
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• pp.216-218
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• 1989

• Macromolecular Research
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• v.14 no.4
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• pp.430-437
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• 2006

The ultra-drawing process of an ultra high molecular weight polyethylene (UHMWPE) gel film was examined by incorporating linear low-density polyethylene (LLDPE) and $BaTiO_3$ nanoparticles. The effects of LLDPE and the draw ratios on the morphological development and mechanical properties of the nanocomposite membrane systems were investigated. By incorporating $BaTiO_3$ nanoparticles in the UHMWPE/LLDPE blend systems, the ultra-drawing process provided a highly extended, fibril structure of UHMWPE chains to form highly porous, composite membranes with well-dispersed nanoparticles. The ultra-drawing process of UHMWPE/LLDPE dry-gel films desirably dispersed the highly loaded $BaTiO_3$ nanoparticles in the porous membrane, which could be used to form multi-layered structures for electronic applications in various embedded, printed circuit board (PCB) systems.

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

• Transactions of Materials Processing
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• v.10 no.6
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• pp.449-456
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• 2001

The concept of stress wave was introduced through the quantized kinetic energy which is related to the potentional energy change of atom, molecular bond energy. Differentiated molecular bond energy $\varphi$() by the lst order displacement u becomes force F(F = d$\varphi$($u_i$)/du), if resversely stated, causing physically atomic displacement $u_i$. Such physical phenomena lead stress(force/area of applied force) can be expressed by wave equation of linearly quantized physical property. Through the stress wave concept, formation of dislocation, which could not explained easily from a theory of continuum mechanics, can be explained. Moreover, this linearly quantized stress wave equation with a stress concept for grains in a crystalline solid was applied to three typical metallic microstructures and a simple shape. The result appears to be a product from well treated equations of a quantized stress wave. From this result, it can be expected to answer the reason why the defect free and very fine diameters of long crystalline shapes exhibit ideal tensile strength of materials.

• Bulletin of the Korean Chemical Society
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• v.23 no.1
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• pp.48-52
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• 2002

Using several molecular modeling programs we have performed computer simulations to investigate the complexation behaviors of an ester derivative of p-tert-butylcalix[5]arene (1e) toward a variety of butylammonium ions. Semi-empirical AM1 method was used for calculating the binding energies and the formation enthalpies. MM and CVFF forcefields for molecular mechanics calculations were adapted to express the complexation energies of the host. Molecular dynamics were performed to the calculated complex systems to simulate the ionophoric behavior of the host-guest complexes. The absolute Gibbs free energies of the host (1e) complexed with four kinds of butylammonium ions have been calculated using the Finite Difference Thermodynamic Integration (FDTI) method in Discover. Calculation results show that the trend in complex formation is n-$BuNH_3^+$ > iso-$BuNH_3^+$ >> sec-$BuNH_3^+$ > tert-$BuNH_3^+$, which is in good agreement with the experimental results.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.862-868
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• 2012

Based on the recently derived general expression for the rates of diffusion-controlled reactions, we calculate the rates of dismutation of the superoxide anion radical catalyzed by Cu/Zn superoxide dismutases (SOD). This is the first attempt to calculate the absolute rates of diffusion-controlled enzyme reactions based on the atomiclevel molecular dynamics simulations. All solvent molecules are included explicitly and the effects of the structural flexibility of enzyme, especially those of side chain motions near the active site, are included in the present calculation. In addition, the actual mobility of the substrate molecule is taken into account, which may change as the molecule approaches the active site of enzyme from the bulk solution. The absolute value of the rate constant for the wild type SOD reaction obtained from MD simulation is shown to be in good agreement with the experimental value. The calculated reactivity of a mutant SOD is also in agreement with the experimental result.