• Interaction and multiscale mechanics
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• v.2 no.4
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• pp.353-374
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• 2009

A new seamless multiscale simulation was developed for coupling the continuum model with its molecular dynamics. Kriging-based Finite Element Method (K-FEM) is employed to model the continuum base of the entire domain, while the molecular dynamics (MD) is confined in a localized domain of interest. In the coupling zone, where the MD domain overlaps the continuum model, the overall Hamiltonian is postulated by contributions from the continuum and the molecular overlays, based on a quartic spline scaling parameter. The displacement compatibility in this coupling zone is then enforced by the Lagrange multiplier technique. A multiple-time-step velocity Verlet algorithm is adopted for its time integration. The validation of the present method is reported through numerical tests of one dimensional atomic lattice. The results reveal that at the continuum/MD interface, the commonly reported spurious waves in the literature are effectively eliminated in this study. In addition, the smoothness of the transition from MD to the continuum can be significantly improved by either increasing the size of the coupling zone or expanding the nodal domain of influence associated with K-FEM.

• Interaction and multiscale mechanics
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• v.2 no.3
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• pp.223-233
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• 2009

This paper presents a new nonlocal stress variational principle approach for the transverse free vibration of an Euler-Bernoulli cantilever nanobeam with an initial axial tension at its free end. The effects of a nanoscale at molecular level unavailable in classical mechanics are investigated and discussed. A sixth-order partial differential governing equation for transverse free vibration is derived via variational principle with nonlocal elastic stress field theory. Analytical solutions for natural frequencies and transverse vibration modes are determined by applying a numerical analysis. Examples conclude that nonlocal stress effect tends to significantly increase stiffness and natural frequencies of a nanobeam. The relationship between natural frequency and nanoscale is also presented and its significance on stiffness enhancement with respect to the classical elasticity theory is discussed in detail. The effect of an initial axial tension, which also tends to enhance the nanobeam stiffness, is also concluded. The model and approach show potential extension to studies in carbon nanotube and the new result is useful for future comparison.

• Journal of Microbiology and Biotechnology
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• v.17 no.7
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• pp.1098-1105
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• 2007

Quantum mechanical and molecular dynamics simulation analysis has been performed on the model system for CALB (Candida antarctica lipase B) with esters to study the reaction mechanism and conformational preference of catalytic hydrolysis and the esterification reaction. Using quantum mechanical analysis, the ping-pong bi-bi mechanism was applied and energies and 3-dimensional binding configurations of the whole reaction pathways were calculated. Further molecular dynamics simulation analysis was performed on the basis of the transition state obtained from quantum mechanical study to observe the effect of structures of the substrates. Calculation results using substrates of different chain length and chiral configurations were compared for conformational preference. The calculated results showed very small influence on chain length, whereas chiral conformation showed big differences. Calculated results from molecular modeling studies have been compared qualitatively with the experimental data using racemic mixtures of (${\pm}$)-cis-4-acetamido-cyclopent-2-ene-1-ethyl acetate as substrates.

• Multiscale and Multiphysics Mechanics
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• v.1 no.4
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• pp.327-340
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• 2016

Poly(${\epsilon}$-caprolactone) (PCL) diol, with good biodegradation and biocompatibility, is one of the widely used soft segments (SSs) in composing bio-polyester-urethanes (Bio-PUs), which show great potential in both biomedical and tissue engineering applications. Properties of Bio-PUs are tunable by combining SS monomers with different molecular weights, structures, modifications, and ratio of components. Although numbers of research have reported many Bio-PUs properties, few studies have been done at the molecular scale. In this study, we use molecular dynamic (MD) simulation to construct atomistic models for two commonly used PCL diol SSs with different molecular weights 1247.58 Da and 1932.42 Da. We compare the simulation results by using two widely used classical force fields for organic molecules: Consistent Valence Force Field (CVFF) and CHARMM General Force Field (CGenFF), and discuss the validity and accuracy. Melt density, volume, polymer conformations, transition temperature, and mechanical properties of PCL diols are calculated and compared with experiments. Our results show that both force fields provide accurate predictions on the properties of PCL diol system at the molecular scale and could help the design of future Bio-PUs.

• Journal of the Korean Society of Industry Convergence
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• v.1 no.1
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• pp.43-49
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• 1998

The SS-phpm 4HCl(N,N'-bis-[2(S)-pyrrolidinylmethyl]phenylene-l,2-diamine-4-Hydrochloride) ligand having stereospecificity has been prepared and reacted with trans-[$Co(pyridine)_4Cl_2]$Cl. The resultants are purple crystals, which are identified to be ${\Delta}$-cis-${\beta}$-[$Co(SS-phpm)Cl_2$]Cl by elemental analysis and UV/Vis- and CD-absorption spectra, The conformation of SS-phpm in ${\Delta}$-cis-${\beta}$ complex is ${\delta}$ ${\varepsilon}$ ${\lambda}$ (SSSS) for each of the five-membered chelated ring. Futhermore, according to orientation of secondary amine, total strain energy on each isomers was calculated by molecular mechanics(MM) to verify structural characterization and spectral data. As the result, the most stabilized isomer was ${\Delta}$-cis-${\beta}$(SSSS). The value of total strain energy(U) of ${\Delta}$-cis-${\beta}$(SSSS) isomer was 63.21 kcal/mol, respectively.

• Bulletin of the Korean Chemical Society
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• v.31 no.2
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• pp.365-371
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• 2010

The multiconfiguration molecular mechanics (MCMM) algorithm was used to generate potential and vibrationally adiabatic energy surfaces for excited-state tautomerization in the 1:1 7-azaindole:$H_2O$ complex. Electronic structures and energies for reactant, product, transition state were computed at the CIS/6-31G(d,p) level of theory. The potential and vibrationally adiabatic energies along the reaction coordinate were generated step by step by using 16 high-level Shepard points, which were computed at the CIS/6-31G(d,p) level. This study shows that the MCMM method was applied successfully to make quite reasonable potential and adiabatic energy curves for the excited-state double proton transfer reaction. No stable intermediates are present in the potential energy curve along the reaction coordinate of the excited-state double proton transfer in the 1:1 7-azaindole:$H_2O$ complex, indicating that these two protons are transferred concertedly. The change in the bond distances along the reaction coordinate shows that two protons move very asynchronously to make an $H_3O^+$-like moiety at the transition state.

• Interaction and multiscale mechanics
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• v.1 no.4
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• pp.397-409
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• 2008

The interfacial thermal resistance of pristine and defective carbon nanotubes (CNTs) embedded in low-density polyethylene matrix is studied in this paper. Interface thermal resistance in nanosystems is one of the most important factors that lead to the large variation in thermal conductivities in literature and the novelty of this paper lies in the estimation of the interfacial thermal resistance for defective nanotubes-systems. Thermal properties of CNT nanostructures are estimated using molecular dynamics (MD) simulations and the simulations were carried out for various temperatures by rescaling the velocities of carbon atoms in the nanotube. This paper also deals with the mesoscale thermal conductivities of composite systems, using effective medium theories by considering the size effect in the form of interfacial thermal resistance and also using the conventional micromechanical methods like Hashin-Shtrikman bounds and Wakashima-Tsukamoto estimates.

• Interaction and multiscale mechanics
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• v.4 no.4
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• pp.247-255
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• 2011

Understanding the structural stability of carbon nanostructure under heat treatment is critical for tailoring the thermal properties of carbon-based material at small length scales. We investigate the heat resistance of the single carbon nanoball ($C_{60}$) and carbon nanoonions ($C_{20}@C_{80}$, $C_{20}@C_{80}@C_{180}$, $C_{20}@C_{80}@C_{180}C_{320}$) by performing molecular dynamics simulations. An empirical many-body potential function, Tersoff potential, for carbon is employed to calculate the interaction force among carbon atoms. Simulation results shows that carbon nanoonions are less resistive against heat treatment than single carbon nanoballs. Single carbon nanoballs such $C_{60}$ can resist heat treatment up to 5600 K, however, carbon nanoonions break down after 5100 K. This intriguing result offers insights into understanding the thermal-mechanical coupling phenomena of nanodevices and the complex process of fullerenes' formation.

• Journal of the Korean Chemical Society
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• v.56 no.2
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• pp.195-200
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• 2012

In this study we present a new approach for computing the partial atomic charge derived from the wavefunctions of molecules. This charge, which we call the "y_charge", was calculated by taking into account the energy level and orbital populations in each molecular orbital (MO). The charge calculations were performed in the software, which was developed by us, developed using the C# programming language. Partial atomic charges cannot be calculated directly from quantum mechanics. According to a partitioning function, the electron density of constituent molecular atoms depends on the electrostatic attraction field of the nucleus. Taking into account the Boltzmann population of each MO as a function of its energy and temperature we obtain a formula of partial charges.

• 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.