• Bulletin of the Korean Chemical Society
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• v.34 no.1
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• pp.299-302
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• 2013

• YAKHAK HOEJI
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• v.60 no.2
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• pp.78-84
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• 2016

N-Phenylthiourea derivatives and catechol oxidase receptor complex was studied using molecular mechanics method. The starting structure was adopted from the protein databank and the calculation of energy minimization and molecular dynamics was performed with AMBER package. The molecular dynamics showed that the simulation time span of 20 ns was long enough to observe the interaction profile and stationary ligand-receptor configuration in the complex. The conformation of the ligand was related to the interaction to the receptor and the efficacy was also interpreted in this context.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.38 no.2
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• pp.121-127
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• 2014

An atomistic-based finite bond element model for predicting the tearing mode (mode III) fracture of a single-layer graphene sheet (SLGS) is developed. The model uses the modified Morse potential for predicting the maximum strain relationship of graphene sheets. The mode III fracture of graphene under out-of-plane shear loading is investigated with extensive molecular mechanics simulations. Molecular mechanics is used for describing the displacements of atoms in the area near a crack tip, and linear elastic fracture mechanics is used outside this area. This work shows that the molecular mechanics method can provide a reliable and yet simple method for determining not only the shear properties of SLGS but also its mode III fracture toughness in the armchair and the zigzag directions; the determined mode III fracture toughness values of SLGS are $0.86MPa{\sqrt{m}}$ and $0.93MPa{\sqrt{m}}$, respectively.

• Macromolecular Research
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• v.8 no.5
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• pp.224-230
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• 2000

Molecular mechanics technique has been used for finding energy-minimized conformation to understand the mechanism of yielding of glassy polymers in atomistic level. As a model polymer, amor- phous isotactic polypropylene (iPP) was generated by molecular mechanics and molecular dynamics methods. The stress-strain cone was successfully obtained by using molecular mechanics technique. The torsional angle distribution showed no significant change during extension, although the torsional angles of certain bonds in polymer backbone changed more largely than other bonds. No significant change in the van der Waals interaction is observed at yielding point, whereas the torsional angle energy starts to decrease at yield strain.

• Bulletin of the Korean Chemical Society
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• v.21 no.5
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• pp.465-470
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• 2000

The conformations and energies of p-tert-butylcalix[4] crown-6-ether (1) and its alkyl ammonium complexes have been simulated by AM1 semi-empirical quantum mechanics and molecular mechanics calculations using a variety of forcefields (MM2, MM+, CVFF). We performed molecular dynamics calculations to simulate the behavior of these coplexes primartily focusing on the three representative conformations (cone, partial cone, 1,3-alternate) of host molecule 1. When we performed AM1 semi-empirical and molecular mechanics calculations, the one conformation was generally found to be most stable for all the employed calculation methods. The primary binding site of host 1 for the recognition of alkyl ammonium guests was confirmed to be the central part of the crown moiety. The complexation enthalpy calculations revealed that the alkyl amonium cations having smaller and linear alkyl group showed the better complexation efficiencies when combined with p-tert-butylcalix[4]crown-6-ether, that is in satisfactory agreement with the experimental results.

• Smart Structures and Systems
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• v.13 no.4
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• pp.685-709
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• 2014

Carbon nanotubes are due to their outstanding mechanical properties destined for a wide range of possible applications. Since the knowledge of the material behavior is vital regarding the possible applications, experimental and theoretical studies have been conducted to investigate the properties of this promising material. The aim of the present research is the calculation of mechanical properties and of the mechanical behavior of single wall carbon nanotubes (SWCNTs). The numerical simulation was performed on basis of a molecular mechanics approach. Within this approach two different issues were taken into account: (i) the nanotube geometry and (ii) the modeling of the covalent bond. The nanotube geometry is captured by two different approaches, the roll-up and the exact polyhedral model. The covalent bond is modeled by a structural molecular mechanics approach according to Li and Chou. After a short introduction in the applied modeling techniques, the results for the Young's modulus for several SWCNTs are presented and are discussed extensively. The obtained numerical results are compared to results available in literature and show an excellent agreement. Furthermore, deviations in the geometry stemming from the different models are given and the resulting differences in the numerical findings are shown. Within the investigation of the deformation mechanisms occurring in SWCNTs, the basic contributions of each individual covalent bond are considered. The presented results of this decomposition provide a deeper understanding of the governing deformation mechanisms in SWCNTs.

• Bulletin of the Korean Chemical Society
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• v.18 no.2
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• pp.143-149
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• 1997

We have investigated a relationship between conformational preferences of various substituents in monosubstituted cyclohexanes and pertinent torsional parameter values in molecular mechanics calculations. We have manipulated torsional parameters to supply a certain energy difference between gauche and anti conformers, and applied those parameters to monosubstituted cyclohexanes. After investigating 6 different substituents, namely Me, SiH3, F, Cl, Br, and I, MM3 calculations show that (1) the MM3 calculated A values with the current torsional parameters reproduce the available experimental values well, (2) the conformational energy difference between axial and equatorial conformations (the A value) correlates perfectly with the gauche/anti energy differences of the corresponding butane-like fragment (correlation coefficient=l.000), and (3) the A values are essentially twice as the gauche/anti energy differences (slopes=1.86-2.00). On the basis of our analysis, the A values as well as the gauche/anti energy differences are easily calibrated by an adjustment of the relevant torsional parameter. Thus, our technique for tuning the torsional parameters may be of great use in updating molecular mechanics results about conformational preferences whenever a further refinement is necessary.

• Nuclear Engineering and Technology
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• v.56 no.4
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• pp.1480-1489
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• 2024

Displacement cascade behaviors of Ti-6Al-4V alloys are investigated using molecular dynamics (MD) simulation. The embedded atom method (EAM) potential including Ti, Al and V elements is modified by adding Ziegler-Biersack-Littmark (ZBL) potential to describe the short-range interaction among different atoms. The time evolution of displacement cascades at the atomic scale is quantitatively evaluated with the energy of primary knock-on atom (PKA) ranging from 0.5 keV to 15 keV, and that for pure Ti is also computed as a comparison. The effects of temperature and incident direction of PKA are studied in detail. The results show that the temperature reduces the number of surviving Frenkel pairs (FPs), and the incident direction of PKA shows little correlation with them. Furthermore, the increasing temperature promotes the point defects to form clusters but reduces the number of defects due to the accelerated recombination of vacancies and interstitial atoms at relatively high temperature. The cluster fractions of interstitials and vacancies both increase with the PKA energy, whereas the increase of interstitial cluster is slightly larger due to their higher mobility. Compared to pure Ti, the presence of Al and V is beneficial to the formation of interstitial clusters and indirectly hinders the production of vacancy clusters.

• Coupled systems mechanics
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• v.4 no.2
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• pp.137-155
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• 2015

This paper presents a simple procedure to obtain a substitute, homogenized mechanical response of single layer graphene sheet. The procedure is based on the judicious combination of molecular mechanics simulation results and homogenization method. Moreover, a series of virtual experiments are performed on the representative graphene lattice. Following these results, the constitutive model development is based on the well-established continuum mechanics framework, that is, the non-linear membrane theory which includes the hyperelastic model in terms of principal stretches. A proof-of-concept and performance is shown on a simple model problem where the hyperelastic strain energy density function is chosen in polynomial form.

• YAKHAK HOEJI
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• v.54 no.1
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• pp.62-66
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• 2010

Benzopyrene is known to be one of the most powerful carcinogens which can build intercalated motif between base pairs in damaged DNA. The dimension of benzopyrene itself is much bigger than any of the DNA bases and thus the question whether the lesion of some base pair by insertion of benzopyrene can happen with or without a dramatic distortion of the helical structure is a highly interesting theme. In this work we used a molecular mechanics simulation using AMBER program package to go into the conformational characteristics. The condition of the insertion process of the benzopyrene motif from minor groove of the starting structure between the base pairs in the internal area of double helix was investigated using the molecular dynamics simulation at elevated temperature.