• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.305-310
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• 2005

Internal motion of the protein has been described in many papers with C$_{\alpha}$ correlation coefficients to find motional correlation and functional characteristics. To describe the secondary structural motion and stability in protein, we have studied molecular dynamics (MD) simulations on FADD Death Domain and FADD Death Effector Domain which have a similar structure but have different functional characteristics. After 10ns MD simulations, the inter-helical motional correlations and the hydrogen bond ratios were compared between the two domains. From these data we could distinctly compare the internal motions of them and could explain the differences in experimental thermodynamic melting behaviors at molecular level.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2007년도 춘계학술대회A
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• pp.326-331
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• 2007

Large-scale molecular dynamics simulations are performed to verify the deformation characteristics of grain boundaries in nanolithography process. The copper substrate made of 200,000 atoms is constructed by two grains in different crystal orientations using dynamic relaxation method. The grain boundary is located in the middle of the substrate with $45\sim135$ degree angles. The plowing tip is made of diamond-like-carbon atoms in a variety of shapes. In the simulations, the generation, propagation, and accumulation of dislocations are observed inside the substrate. From the numerical results, we address the dynamic behavior of the grain boundaries as well as the frictional characteristics in terms of the morphology of initial grain boundaries.

• 한국소성가공학회:학술대회논문집
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• 한국소성가공학회 2006년도 춘계학술대회 논문집
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• pp.77-80
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• 2006

Structural phase transformations of silicon during nanoindentation were investigated in detail at the atomic level. The molecular dynamics simulations of nanoindentation on the (100), (110) and (111) surface of single crystalline silicon were simulated, and this supported the theoretical prediction of the anisotropic behavior of structural phase transformations. Simulations showed that microscopic aspects of phase transformation varied according to the crystallographic orientation of the contact surface and were directly linked to the slip system.

• 천문학회지
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• 제40권4호
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• pp.119-122
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• 2007

From the HCN observations of dense molecular cloud L694-2, Lee et al.(2007) determined internal distributions of density and velocity for the cloud. The density profile collaborates roughly with the Bonnor- Ebert gas sphere, but the velocity field departs significantly from the result of numerical simulations that are started from the BE sphere. Taking L694-2 as an example of collapsing clouds, we have performed a series of collapse simulations and determined initial configurations for the cloud in such a way that the resulting density and velocity profiles both match with the empirically deduced ones. Among many trial configurations the cloud which is initially uniform in density and bound by an expanding envelop depicts most closely the empirically obtained profiles of both density and velocity.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2010년도 제39회 하계학술대회 초록집
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• pp.93-93
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• 2010

In this talk, I will introduce a reactive force field (ReaxFF) molecular dynamics (MD) simulation. In contrast to common MD simulations with empirical FFs, we can predict chemical reactions (bond breaking and formation) in large scale systems with the ReaxFF simulation where all of the ReaxFF parameters are from quantum mechanical calculations such as density functional theory to provide high accuracy. Accordingly, the ReaxFF simulation provides both accuracy of quantum mechanical calculations and description of large scale systems of atomistic simulations at the same time. Here, I will first discuss a theory in the ReaxFF including the differences from other empirical FFs, and then show several applications for studying chemical reactions of SiHx radicals on Si surfaces, which is an important issue in Si process.

• Bulletin of the Korean Chemical Society
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• 제30권8호
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• pp.1845-1850
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• 2009

We have performed replica-exchange molecular dynamics (REMD) simulations on the dimer formation of fibrilforming segments of $\alpha$-Synuclein (residues 71 - 82) using implicit solvation models with two kinds of force fields- AMBER parm99SB and parm96. We observed spontaneous formation of dimers from the extensive simulations, demonstrating the self-aggregating and fibril forming properties of the peptides. Secondary structure profile and clustering analysis showed that dimers with antiparallel $\beta$-sheet conformations, stabilized by well-defined hydrogen boding, are major species corresponding to global free energy minimum. Parallel dimers with partial $\beta$-sheets are found to be off-pathway intermediates. The relative instability of the parallel arrangements is due to the repulsive interactions between bulky and polar side chains as well as weaker backbone hydrogen bonds.

• Bulletin of the Korean Chemical Society
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• 제18권5호
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• pp.478-484
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• 1997

In a recent paper[Bull. Kor. Chem. Soc. 17, 735 (1996)] we reported results of molecular dynamic (MD) simulations for the thermodynamic and structural properties of liquid n-alkanes, from n-butane to n-heptadecane, using three different models. Two of the three classes of models are collapsed atomic models while the third class is an atomistically detailed model. In the present paper we present results of MD simulations for the dynamic properties of liquid n-alkanes using the same models. The agreement of two self-diffusion coefficients of liquid n-alkanes calculated from the mean square displacements (MSD) via the Einstein equation and the velocity auto-correlation (VAC) functions via the Green-Kubo relation is excellent. The viscosities of n-butane to n-nonane calculated from the stress auto-correlation (SAC) functions and the thermal conductivities of n-pentane to n-decane calculated from the heat-flux auto-correlation (HFAC) functions via the Green-Kubo relations are smaller than the experimental values by approximately a factor of 2 and 4, respectively.

• Bulletin of the Korean Chemical Society
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• 제18권5호
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• pp.501-509
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• 1997

In recent papers[Bull. Kor. Chem. Soc. 1996, 17, 735; ibid 1997, 18, 478] we reported results of molecular dynamics (MD) simulations for the thermodynamic, structural, and dynamic properties of liquid normal alkanes, from n-butane to n-heptadecane, using three different models. Two of the three classes of models are collapsed atomic models while the third class is an atomistically detailed model. In the present paper we present results of MD simulations for the corresponding properties of liquid branched-chain alkanes using the same models. The thermodynamic property reflects that the intermolecular interactions become weaker as the shape of the molecule tends to approach that of a sphere and the surface area decreases with branching. Not like observed in the straight-chain alkanes, the structural properties of model Ⅲ from the site-site radial distribution function, the distribution functions of the average end-to-end distance and the root-mean-squared radii of gyration are not much different from those of models Ⅰ and Ⅱ. The branching effect on the self diffusion of liquid alkanes is well predicted from our MD simulation results but not on the viscosity and thermal conductivity.

• Bulletin of the Korean Chemical Society
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• 제19권10호
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• pp.1068-1072
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• 1998

We present results of molecular dynamic (MD) simulations for the segmental motion of liquid n-butane as the base case for a consistent study for conformational transition from one rotational isomeric state to another in long chains of liquid n-alkanes. The behavior of the hazard plots for n-butane obtained from our MD simulations are compared with that for n-butane of Brownian dynamics study. The MD results for the conformational transition of n-butane by a Poisson process form the total first passage times are different from those from the separate t-g and g-t first passage times. This poor agreement is probably due to the failure of the detailed balance between the fractions of trans and gauche. The enhancement of the transitions t-g and g-t at short time regions are also discussed.

• Bulletin of the Korean Chemical Society
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• 제19권11호
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• pp.1217-1221
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• 1998

We present results of molecular dynamic (MD) simulations for the segmental motion of liquid n-heptadecane in order to investigate conformational transitions from one rotational isomeric state to another. The behavior of the hazard plots for n-heptadecane obtained from our MD simulations are compared with that for polymer of Brownian dynamics (BD) study. The transition rate at the ending dihedrals of the n-heptadecane chain is much higher than that at the central dihedrals. In the study of correlation between transitions of neighboring dihedrals, the large value of c2 implies that some 30% of the transitions of the second neighbors can be regarded as following transitions two bonds away in a correlated fashion. Finally the analysis of multiple transitions and the number of times occurred in the initial 0.005 ns are discussed.