• 한국재료학회지
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• 제19권5호
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• pp.276-280
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• 2009

The effect of the initial packing structure on the plasticity of amorphous alloys was investigated by tracing the structural evolution of the amorphous solid inside a shear band. According to the molecular dynamics simulations, the structural evolution of the amorphous solids inside the shear band was more abrupt in the alloy with a higher initial packing density. Such a difference in the structural evolution within the shear band observed from the amorphous alloys with different initial packing density is believed to cause different degrees of shear localization, providing an answer to the fundamental question of why amorphous alloys show different plasticity. We clarify the structural origin of the plasticity of bulk amorphous alloys by exploring the microstructural aspects in view of the structural disordering, disorder-induced softening, and shear localization using molecular dynamics simulations based on the recently developed MEAM (modified embedded atom method) potential.

• Bulletin of the Korean Chemical Society
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• 제29권2호
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• pp.408-412
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• 2008

FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1) in Arabidopsis are homologous proteins that perform opposite functions: FT is an activator of flowering, and TFL1 is a repressor. It was shown before that change of a single amino acid (His88) of TFL1 to the corresponding amino acid (Tyr) of FT is enough to convert the floral repressor to an activator. However, structural basis of the functional conversion has not been understood. In our molecular dynamics simulations on modified TFL1 proteins, a hydrogen bond present in native TFL1 between the His88 residue and a residue (Asp144) in a neighboring external loop became broken by change of His88 to Tyr. This breakage induced conformational change of the external loop whose structure was previously reported to be another key functional determinant. These findings reveal that the two important factors determining the functional specificities of the floral regulators, the key amino acid (His88) and the external loop, are correlated, and the key amino acid determines the functional specificity indirectly by affecting the conformation of the external loop.

• Bulletin of the Korean Chemical Society
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• 제29권2호
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• pp.363-371
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• 2008

As a computational method for the discovery of the effective agonists for PPARd, we address the usefulness of molecular dynamics free energy (MDFE) simulation with explicit solvent in terms of the accuracy and the computing cost. For this purpose, we establish an efficient computational protocol of thermodynamic integration (TI) that is superior to free energy perturbation (FEP) method in parallel computing environment. Using this protocol, the relative binding affinities of GW501516 and its derivatives for PPARd are calculated. The accuracy of our protocol was evaluated in two steps. First, we devise a thermodynamic cycle to calculate the absolute and relative hydration free energies of test molecules. This allows a self-consistent check for the accuracy of the calculation protocol. Second, the calculated relative binding affinities of the selected ligands are compared with experimental IC50 values. The average deviation of the calculated binding free energies from the experimental results amounts at the most to 1 kcal/mol. The computational efficiency of current protocol is also assessed by comparing its execution times with those of the sequential version of the TI protocol. The results show that the calculation can be accelerated by 4 times when compared to the sequential run. Based on the calculations with the parallel computational protocol, a new potential agonist of GW501516 derivative is proposed.

• Bulletin of the Korean Chemical Society
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• 제34권10호
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• pp.2925-2930
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• 2013

We present results of molecular dynamics simulations for hydroxide ion in supercritical water of densities 0.22, 0.31, 0.40, 0.48, 0.61, and 0.74 g/cc using the SPC/E water potential with Ewald summation. The limiting molar conductance of $OH^-$ ion at 673 K monotonically increases with decreasing water density. It is also found that the hydration number of water molecules in the first hydration shells around the $OH^-$ ion decreases and the potential energy per hydrated water molecule also decreases in the whole water density region with decreasing water density. Unlike the case in our previous works on LiCl, NaCl, NaBr, and CsBr [Lee at al., Chem. Phys. Lett. 1998, 293, 289-294 and J. Chem. Phys. 2000, 112, 864-869], the number of hydrated water molecules around ions and the potential energy per hydrated water molecule give the same effect to cause a monotonically increasing of the diffusion coefficient with decreasing water density in the whole water density region. The decreasing residence times are consistent with the decreasing potential energy per hydrated water molecule.

• 한국전산구조공학회:학술대회논문집
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• 한국전산구조공학회 2007년도 정기 학술대회 논문집
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• pp.421-426
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• 2007

A parametric study to investigate the effects of composition variables on the glass transition and mechanical properties of CNT-based nanocomposites was performed using molecular dynamics simulations. In this study, matrix chain length and CNT length were chosen as the candidate characteristic parameters. In order to understand the effect of both parameters in detail, three sample sets having different chain lengths with the same CNT configuration and two sample sets having different CNT lengths with same chain length were prepared. Other parameters such as volume fraction and density were fixed to enable rigorous comparisons. Amorphous polyethylene is used as matrix polymer and (10,0) zigzag CNT is embedded into the matrix to reinforce polymer matrix. As a result, longer polymer chain length of matrix solely increased glass transition temperature but no reinforcing enhancement was observed. CNT length showed similar increase with little enhancement of elastic modulus. In addition to this, nanocomposites showed temperature-dependent elastic modulus jump passing thorough the glass transition region agrees well with experimental results.

• Bulletin of the Korean Chemical Society
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• 제33권11호
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• pp.3805-3809
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• 2012

Results for molecular dynamics simulation method of small liquid drops of argon (N = 1200-14400 molecules) at 94.4 K through a Lennard-Jones intermolecular potential are presented in this paper as a preliminary study of drop systems. We have calculated the density profiles ${\rho}(r)$, and from which the liquid and gas densities ${\rho}_l$ and ${\rho}_g$, the position of the Gibbs' dividing surface $R_o$, the thickness of the interface d, and the radius of equimolar surface $R_e$ can be obtained. Next we have calculated the normal and transverse pressure tensor ${\rho}_N(r)$ and ${\rho}_T(r)$ using Irving-Kirkwood method, and from which the liquid and gas pressures ${\rho}_l$ and ${\rho}_g$, the surface tension ${\gamma}_s$, the surface of tension $R_s$, and Tolman's length ${\delta}$ can be obtained. The variation of these properties with N is applied for the validity of Laplace's equation for the pressure change and Tolman's equation for the effect of curvature on surface tension through two routes, thermodynamic and mechanical.

• 한국군사과학기술학회지
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• 제13권1호
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• pp.156-163
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• 2010

A nonequilibrium molecular dynamics(NEMD) simulation method is developed and applied to study shock waves propagating through argon gas. In this simulation method, shock waves are generated by pushing a piston at a constant speed from one side of a simulation box filled with argon molecules. A linear relationship between piston speeds and shock speeds is observed. Thermodynamic properties including density, temperature, and pressure before and after the shock front are obtained from the simulations and compared with the well-known Rankine-Hugoniot equations based on ideal gases. The comparison shows an excellent agreement, indicating that this NEMD simulation method can be employed to investigate various physical properties of shock waves further.

• 한국정보디스플레이학회:학술대회논문집
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• 한국정보디스플레이학회 2009년도 9th International Meeting on Information Display
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• pp.169-172
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• 2009

We developed ultra-accelerated quantum chemical molecular dynamics and characterization simulators for study and design of plasma display panel (PDP) related materials. By use of these simulators, realistic structure of PDP materials is drawn on the computer. Furthermore, based on the structures, various properties such as secondary electron emission coefficient are successfully evaluated. In this report, we will discuss the theoretical secondary electron emission coefficient for several protecting layer materials and the effect of surface structure on the properties based on the result of atomistic simulations.

• 한국전기전자재료학회논문지
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• 제18권5호
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• pp.414-422
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• 2005

This paper shows the results of atomistic modeling for the Interaction between spherical nano abrasive and substrate In chemical mechanical polishing processes. Atomistic modeling was achieved from 2-dimensional molecular dynamics simulations using the Lennard-jones 12-6 potentials. We proposed and investigated three mechanical models: (1) Constant Force Model; (2) Constant Depth Model, (3) Variable Force Model, and three chemical models, such as (1) Chemically Reactive Surface Model, (2) Chemically Passivating Surface Model, and (3) Chemically Passivating-reactive Surface Model. From the results obtained from classical molecular dynamics simulations for these models, we concluded that atomistic chemical mechanical polishing model based on both Variable Force Model and Chemically Passivating-reactive Surface Model were the most suitable for realistic simulation of chemical mechanical polishing in the atomic scale. The proposed model can be extended to investigate the 3-dimensional chemical mechanical polishing processes in the atomic scale.

• Bulletin of the Korean Chemical Society
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• 제31권4호
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• pp.959-964
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• 2010

In this work, equilibrium molecular dynamics (MD) simulations in a microcanonical ensemble are performed to evaluate the friction coefficient of a Brownian particle (BP) in a Lennard-Jones (LJ) solvent. The friction coefficients are determined from the time dependent friction coefficients and the momentum autocorrelation functions of the BP with its infinite mass at various ratios of LJ size parameters of the BP and solvent, ${\sigma}_B/{\sigma}_s$. The determination of the friction coefficients from the decay rates of the momentum autocorrelation functions and from the slopes of the time dependent friction coefficients is difficult due to the fast decay rates of the correlation functions in the momentum-conserved MD simulation and due to the scaling of the slope as 1/N (N: the number of the solvent particle), respectively. On the other hand, the friction coefficient can be determined correctly from the time dependent friction coefficient by measuring the extrapolation of its long time decay to t=0 and also from the decay rate of the momentum autocorrelation function, which is obtained by time integration of the time dependent friction coefficient. It is found that while the friction coefficient increases quadratically with the ratio of ${\sigma}_B/{\sigma}_s$ for all ${\sigma}_B$, for a given ${\sigma}_s$ the friction coefficient increases linearly with ${\sigma}_B$.