• Interaction and multiscale mechanics
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• v.1 no.2
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• pp.303-315
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• 2008

In this paper, thermodynamical properties of crystalline silicon under strain are calculated using classical molecular dynamics (MD) simulations based on the Tersoff interatomic potential. The Helmholtz free energy of the silicon crystal under strain is calculated by using the ensemble method developed by Frenkel and Ladd (1984). To account for quantum corrections under strain in the classical MD simulations, we propose an approach where the quantum corrections to the internal energy and the Helmholtz free energy are obtained by using the corresponding energy deviation between the classical and quantum harmonic oscillators. We calculate the variation of thermodynamic properties with temperature and strain and compare them with results obtained by using the quasi-harmonic model in the reciprocal space.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 2003.06a
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• pp.1182-1185
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• 2003

Recently, the research of the nano technology has been done on a lot of area over the world. Especially, the interest of them is much higher for semiconductor companies and other super accuracy processing area. In this thesis, we have approached the characteristic of the tensile and bonding of copper, frequently used to nano wires, by molecular dynamics simulation. And the simulation was done by EAM, Embedded Atom Method which has the most highest accuracy for metal. Then the feature of copper at atom space is understood through the simulation of nano wire.

• Macromolecular Research
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• v.8 no.3
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• pp.125-130
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• 2000

Resorcinol formaldehyde resins are synthesized by polycondensation of resorcinol with formal-dehyde and have various structures by the condensation type. The influence of polycondensation type on the stability and structure of the resorcinol formaldehyde resin was studied by molecular mechanics and molecular dynamics. The resins formed by 2,6-polycondensation and 4,6-polycondensationwith head-to-tail orientations have structures of intramolecular hydrogen bonds between 1-hydroxyl groups and between outer hydroxyl groups of the adjacent resorcinols, respectively. The resin formed by 2,6-polycon-densation with head-to-head orientation has a structure that inner hydroxyl groups cluster in the center of the molecule. Energetical stability of the resin is affected by both the intramolecular hydrogen bonds and the steric' hindrance by phenyl group.

• Bulletin of the Korean Chemical Society
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• v.17 no.12
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• pp.1112-1117
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• 1996

The electronic structures of twenty-seven isomers of a macrocyclic fulleropyrrolidine are investigated with semi-empirical extended Huckel (EH) molecular orbital method. The geometry of each isomer is determined by the molecular mechanics and dynamics methods based on UFF (universal force field) empirical force field. The calculated geometries, such as the carbon-carbon distances of the fullerene moiety, are in good agreement with those of related fullerene derivatives. The EH calculation shows that the formation of macrocyclic pyrrolidine ring on fullerene moiety results in the reduction of the HOMO-LUMO energy gap. From the graphical analysis of the DOS (density of states), PDOS (projected DOS), and MOOP (molecular orbital overlap population) curves, we can find that this reduction is due to splitting of the HOMO of fullerene moiety, which results from the symmetry-breaking and the distortion of the buckminsterfullerene framework from its ideal icosahedral structure.

• Bulletin of the Korean Chemical Society
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• v.20 no.2
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• pp.203-210
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• 1999

Structural characteristics of isotactic p-alkylphenol acetaldehyde novolak resins with methyl, t-butyl, and t-octyl as the p-substituent and p-t-butylphenol aldehyde novolak resins with methylene, ethylidene, and propylidene as the linkage were calculated using molecular mechanics and molecular dynamics. The five p-alkylphenol aldehyde resins were found to have common structural characteristics that hydroxyl groups of the p-alkylphenols cluster in the center of the molecule by intramolecular hydrogen bonds of hydroxyl groups of the adjacent p-alkylphenols and the alkyl groups are extended out. Distances between oxygen atoms and between p-carbon atoms of the adjacent p-alkylphenols become longer as the size of the p-substituent increases from methyl to toctyl. Bond angles of the linkage built between the adjacent p-alkylphenols become wider by increasing the p-substituent size and by decreasing the linkage size.

• Bulletin of the Korean Chemical Society
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• v.10 no.3
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• pp.247-250
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• 1989

The molecular structure of cyclobutylmethyl ketone (c-$C_4H_7COCH_3$) has been investigated by molecular mechanics II (MM2). For the monosubstituted cyclobutane there are two possible ring conformations, the equatorial and axial form, but for the cyclobutylmethyl ketone the equatorial form is predominant conformation. For the $COCH_3$ moiety there are two stable orientations which are the equatorial-gauche and the equatorial-trans form. The equatorial-gauche form where the C = O bond is nearly eclipsing (torsional angle ${\angle}C4-C3-C2-O10=14.5^{\circ}$) one of the ${\alpha}$C-C bonds of the four-membered ring was preferred conformer with steric energy of 13.37 kcal/mol. The equatorial-trans form where the C = O bond is nearly eclipsing (${\angle}C4-C3-C2-O10=145.0^{\circ}$) the ${\alpha}$ C-H bond of the four-membered ring was less stable conformer with steric energy of 15.40 kcal/mol.

• Corrosion Science and Technology
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• v.21 no.1
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• pp.21-31
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• 2022

Potentiodynamic polarization, EIS measurements, quantum chemical calculations, and molecular dynamic simulations were used to investigate the corrosion behavior of mild steel in 0.5 M aqueous hydrochloric acid medium in the presence or absence of nystatin drug. Potentiodynamic tests suggested that this molecule could act as a mixed inhibitor due to its adsorption on the mild steel surface. The objective of this study was to exploit theoretical calculations to gain a better understanding mechanism of inhibition. Calculating the adsorption behavior of the investigated molecule on Fe (1 1 0) surface was accomplished using Monte Carlo simulation. Molecules were also investigated using Density Functional Theory (DFT), specifically PBE functional, in order to identify the link between molecular structure and corrosion inhibition behavior of the compound under investigation. Adsorption energies between nystatin and iron were estimated more accurately by utilizing Molecular Mechanics calculation with Periodic Boundary Conditions (PBC). Estimated theoretical parameters significantly assisted our understanding of the corrosion inhibition mechanism exhibited by this molecule. They were found to be in accord with experimental results.

• Tribology and Lubricants
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• v.30 no.5
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• pp.278-283
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• 2014

Carbon nanotubes (CNTs) are used in various composite materials to enhance electrical, thermal and mechanical properties of composite materials. In this study, we investigate the wear characteristics of polycarbonate/acrylonitrile-butadiene-styrene (PC/ABS) blends containing multi-walled carbon nanotubes (MWCNTs). PC/ABS blends are commonly used in many industrial applications such as cellular phones and display cases and MWCNTs have been added to the PC/ABS blends to improve their electromagnetic interference shielding (EMS). We performed wear tests on PC/ABS blends containing MWCNTs under reciprocating linear sliding conditions with chrome steel balls as a counterpart material. The normal loads were 10, 30, 50, 70, 100 N, the sliding speed was 10 mm/s, the stroke length was 15 mm, and the tests lasted 900 s. The MWCNTs included in the PC/ABS blends lower the wear volume and friction coefficient of the composites. We analyzed the wear debris collected from the composites during the tests in terms of the MWCNT concentration using inductively coupled plasma optical emission spectroscopy. The results show that the quantity of MWCNTs in the debris is proportional to the concentration of MWCNTs in the composite, indicating that the exposure of the MWCNTs to environments by wear could be increased with their concentration in the composite.

• Computers and Concrete
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• v.27 no.2
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• pp.111-130
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• 2021

In the present work, an extensive study for predicting efficiency parameters (��i) of various simulated nanocomposites including Polymethyl methacrylate (PMMA) as matrix and different structures including various sizes of graphene platelets (GPLs), single, double, and multi-walled carbon nanotubes (SWCNTs-DWCNTs-MWCNTs), and single and double-walled boron nitride nanotubes (SWBNNTs-DWBNNTs) are investigated. It should be stated that GPLs, carbon and boron nitride nanotubes (CNTs, BNNT) with different chiralities (5, 0), (5, 5), (10, 0), and (10, 10) as reinforcements are considered. In this research, molecular dynamics (MDs) method with Materials studio software is applied to examine the mechanical properties (Young's modulus) of simulated nanocomposite boxes and calculate η1 of each nanocomposite boxes. Then, it is noteworthy that by changing length (6.252, 10.584, and 21.173 nm) and width (7.137, 10.515, and 19.936) of GPLs, ��1, ��2, and ��3 approximately becomes (0.101, 0.114, and 0.124), (1.15, 1.22, and 1.26), (1.04, 1.05, and 1.07) respectively. After that efficiency parameters of SWCNTs, DWCNTs, and MWCNTs are calculated and discussed separately. Finally efficiency parameters of SWBNNTs and DWBNNTs with different chiralities by PMMA as matrix are determined by MD and discussed separately. It is known that the accurate efficiency parameters helps a lot to calculate the properties of nanocomposite analytically. In particular, the obtained results from this research can be used for analytical work based on the extended rule of mixture (ERM) in bending, buckling and vibration analysis of structure in future study.

• Molecules and Cells
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• v.46 no.8
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• pp.513-525
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• 2023

Orange carotenoid protein (OCP) of photosynthetic cyanobacteria binds to ketocarotenoids noncovalently and absorbs excess light to protect the host organism from light-induced oxidative damage. Herein, we found that mutating valine 40 in the α3 helix of Gloeocapsa sp. PCC 7513 (GlOCP1) resulted in blue- or red-shifts of 6-20 nm in the absorption maxima of the lit forms. We analyzed the origins of absorption maxima shifts by integrating X-ray crystallography, homology modeling, molecular dynamics simulations, and hybrid quantum mechanics/molecular mechanics calculations. Our analysis suggested that the single residue mutations alter the polar environment surrounding the bound canthaxanthin, thereby modulating the degree of charge transfer in the photoexcited state of the chromophore. Our integrated investigations reveal the mechanism of color adaptation specific to OCPs and suggest a design principle for color-specific photoswitches.