• YAKHAK HOEJI
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• v.54 no.1
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• pp.67-74
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• 2010

Some of the benzopyrene (BP)-DNA adduct are known to build intercalated motif between flanking base pairs in damaged DNA depending on the structural condition. The size of benzopyrene itself is definitely not comparable with 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 dynamics simulation based on the theory of molecular mechanics. The specific consequences about the structural properties of the intercalated structures and benzopyrene motif in minor groove of the double helix are deduced after 5 ns simulation time.

• Journal of the Optical Society of Korea
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• v.14 no.3
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• pp.199-203
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• 2010

A mobile direct detection Doppler LIDAR based on molecular backscattering for measurement of wind in the stratosphere has been developed in Hefei, China. First, the principle of wind measurement with direct detection Doppler LIDAR is presented. Then the configuration of the LIDAR system is described. Finally, the primary experimental results are provided and analyzed. The results indicate that the detection range of the designed Doppler LIDAR reached 50 km altitude, and there is good consistency between the molecular Doppler wind LIDAR(DWL) and the wind profile radar(WPR) in the low troposphere.

• Structural Engineering and Mechanics
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• v.73 no.1
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• pp.37-52
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• 2020

This paper investigates the free and forced longitudinal vibration of a double nanorod system using doublet mechanics theory. The doublet mechanics theory is a multiscale theory spanning between lattice dynamics and continuum mechanics. Equations of motion and boundary conditions for the double nanorod system are obtained using Hamilton's principle. Clamped-clamped and clamped-free boundary conditions are considered. Frequencies and dynamic displacements are determined to demonstrate the effects of length scale parameter of considered material and geometry of the nanorods. It is shown that frequencies obtained by the doublet mechanics theory are bounded from above (van Hove singularity) and unlike classical elasticity theory doublet mechanics theory predicts finite number of modes depending on the length of the nanotube. The present doublet mechanics results have been compared to molecular dynamics, experimental and nonlocal theory results and good agreement is observed between the present and other mentioned results. The difference between wave frequencies of graphite is less than 10% between doublet mechanics and experimental results near to the end of the first Brillouin zone.

• Bulletin of the Korean Chemical Society
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• v.18 no.5
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• pp.488-495
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• 1997

The stability of bridgehead olefins containing 8 and 10 membered rings has been investigated by the MMX molecular mechanics calculation together with the GMMX conformational searching program. A number of 'hyperstable' bridgehead olefins, which have negative olefin strain values, have been found from the calculated values of strain energy and olefin strain for the series of in- and out-bicyclo[n.3.3]alk-1-ene and in- and out-bicyclo[n.4.4]alk-1-ene (n=1 to 8). For the bridgehead olefins with 'out' topology, hyperstable olefins were found in the systems having cyclononene or larger rings. For the bridgehead olefins with 'in' topology, hyperstable olefins were found in the systems having cyclodecene or larger rings.

• Bulletin of the Korean Chemical Society
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• v.10 no.2
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• pp.185-190
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• 1989

Geometries for a number of representative ${\beta}$ -lactam antibiotics (penams, cephems and monobactams) have been calculated by computer graphics/molecular mechanics energy minimization procedures using both MM2 and AMBER force fields. The calculated geometries have been found in reasonable agreement with the geometries reported in the X-ray crystal structures, especially in terms of the pyramidal character of the amide nitrogen in the ${\beta}$-lactam ring and the Cohen distance. Based on these calculations, it is suggested that the nitrogen atom in the monobactams may also have pyramidal geometries in the biologically active conformations.

• Bulletin of the Korean Chemical Society
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• v.11 no.4
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• pp.313-317
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• 1990

Geometries for several representative quinolone carboxylate type antibacterials have been calculated by computer graphics/molecular mechanics energy minimization procedures using both MM2 and AMBER force fields. The calculated geometries were found to be in reasonable agreements with the corresponding X-ray crystal structures. It has been pointed out that notwithstanding the weaknesses associated with calculating the resonance and hydrogen bonding contributions, the employed methods are capable of generating credible ring geometries and torsional angle dispositions of N(1)-ethyl and 3-carboxylate substituents of the quinolones.

• Interaction and multiscale mechanics
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• v.6 no.2
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• pp.127-136
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• 2013

In this study, atomistic simulations are performed to study the effect of Al solute on the behaviour of edge dislocation in Mg alloys. After the dissociation of an Mg basal edge dislocation into two Shockley partials using molecular mechanics, the interaction between the dislocation and Al solute at different temperatures is studied using molecular dynamics. It appears from the simulations that the critical shear stress increases with the Al solute concentration. Comparing with the solute effect at T = 0 K, however, the critical shear stress at a finite temperature is lower since the kinetic energy of the atoms can help the dislocation conquer the energy barriers created by the Al atoms. The velocity of the edge dislocation decreases as the Al concentration increases when the external shear stress is relatively small regardless of temperature. The Al concentration effect on the dislocation velocity is not significant at very high shear stress level when the solute concentration is below 4.0 at%. Drag coefficient B increases with the Al concentration when the stress to temperature ratio is below 0.3 MPa/K, although the effect is more significant at low temperatures.

• Proceedings of the Korean Society for Noise and Vibration Engineering Conference
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• 2008.11a
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• pp.668-669
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• 2008

In this paper, we introduce various coarse-grained elastic network modeling (ENM) techniques as a novel computational method for simulating atomic scale dynamics in macromolecules including DNA, RNA, protein, and polymer. In ENM, a system is modeled as a spring network among representative atoms in which each linear elastic spring is well designed to replace both bonded and nonbonded interactions among atoms in the sense of quantum mechanics. Based on this simplified system, a harmonic Hookean potential is defined and used for not only calculating intrinsic vibration modes of a given system, but also predicting its anharmonic conformational change, both of which are strongly related with its functional features. Various nano and bio applications of ENM such as fracture mechanics of nanocomposite and protein dynamics show that ENM is one of promising tools for simulating atomic scale dynamics in a more effective and efficient way comparing to the traditional molecular dynamics simulation.

• Tribology and Lubricants
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• v.25 no.4
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• pp.236-242
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• 2009

Oil viscosity is one of the important parameters for machinery condition monitoring. Basically, it is expressed as kinematic viscosity measured by capillary flow and dynamic or absolute viscosity measured by rotary shear viscometry. Recently, acoustic wave techniques appear in the market, measuring viscosity as the product of dynamic viscosity and density. For Newtonian fluids, knowledge of density allows conversion from one viscosity parameter to the other at a specific shear rate and temperature. In this work, oil samples with different chain lengths of viscosity index (VI) improvers and concentrations were examined by different viscometric techniques. Results showed that acoustic viscosity measurements give misleading results for oil samples with high molecular weight VI improvers and at low temperatures ${\leq}40^{\circ}C$.

• Journal of the Korean Society of Manufacturing Technology Engineers
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• v.24 no.4
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• pp.421-427
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• 2015

In this paper, a description is given of finite element method (FEM) simulations of the elastic bending modulus of multi-layered graphene sheets that were carried out to investigate the mechanical behavior of graphene sheets with different gap thicknesses through molecular mechanics theory. The interaction forces between layers with various gap thicknesses were considered based on the van der Waals interaction. A finite element (FE) model of a multi-layered rectangular graphene sheet was proposed with beam elements representing bonded interactions and spring elements representing non-bonded interactions between layers and between diagonally adjacent atoms. As a result, the average elastic bending modulus was predicted to be 1.13 TPa in the armchair direction and 1.18 TPa in the zigzag direction. The simulation results from this work are comparable to both experimental tests and numerical studies from the literature.