• 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.

• 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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• 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.

• 한국분말재료학회지
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• 제5권4호
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• pp.324-328
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• 1998

This paper is aimed to study the computer simulation of sintering process for ceramics by Monte Carlo and molecular dynamics methods. Plural mechanisms of mass transfer were designed in the MC simulation of sintering process for micron size particles; the transfer of pore lattices for shrinkage and the transfer of solid lattices for grain growth ran in the calculation arrays. The MD simulation was performed in the case of nano size particles of ionic ceramics and showed the characteristic features in sintering process at atomic levels. The MC and MD simulations for sintering process are useful for microstructural design for ceramics.

• 한국진공학회지
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• 제14권1호
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• pp.40-48
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• 2005

분자 위치제어 메모리 시스템에 대하여 고전적인 분자동역학을 이용하여 결합에너지 및 다양한 외부전기장의 형태에 따른 셔틀 풀러렌 동작에 관하여 연구하였다. 단일 나노피포드 형(single-nanopeapod type)은 질화붕소 나노튜브(boron-nitride nanotube)속에 세 개의 엔도풀러렌(endo-fullerene)과 양쪽 끝에 구리 전극이 채워져 있는 구조를 갖고 있는 구조를 갖고 있다. 결론적으로, 분자동역학 시뮬레이션 결과로부터 이 나노메모리 시스템은 비휘발성임을 알 수 있었다. 안정적인 bit 변화를 위해서는 단일 나노피포드 형은 0.1 eV/Å 외부전기장이 필요로 함을 알 수 있었다.

• 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 ${\sigma}_B$.

• 한국전산유체공학회:학술대회논문집
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• 한국전산유체공학회 2009년 춘계학술대회논문집
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• pp.368-376
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• 2009

Studies on the effect of the wall-ion, wall-water, water-ion and ion-ion interaction on properties of water and ions in nano-channels have been performed through the use of different kinds of ions or different models of potential energy between wall-ion or wall-water. On this paper, we address the effect of water-wall interaction potential on the properties of confined aqueous solution by using the molecular dynamics (MD) simulations. As the interaction potential energies between water and wall we employed the models of the Weeks-Chandler-Andersen (WCA) and Lennard-Jones (LJ). On the MD simulations, 680 water molecules and 20 ions are included between uniformly charged plates that are separated by 2.6 nm. The water molecules are modeled by using the rigid SPC/E model (simple point charge/Extended) and the ions by the charged Lennard-Jones particle model. We compared the results obtained by using WCA potential with those by LJ potential. We also compared the results (e.g. ion density and electro-static potential distributions) in each of the above cases with those provided by solving the Poisson-Boltzmann equation.

• Interaction and multiscale mechanics
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• 제4권3호
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• pp.173-185
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• 2011

A multiscale modeling scheme that addresses the influence of the nanoparticle size in nanocomposites consisting of nano-sized spherical particles embedded in a polymer matrix is presented. A micromechanics-based constitutive model for nanoparticle-reinforced polymer composites is derived by incorporating the Eshelby tensor considering the interface effects (Duan et al. 2005a) into the ensemble-volume average method (Ju and Chen 1994). A numerical investigation is carried out to validate the proposed micromechanics-based constitutive model, and a parametric study on the interface moduli is conducted to investigate the effect of interface moduli on the overall behavior of the composites. In addition, molecular dynamics (MD) simulations are performed to determine the mechanical properties of the nanoparticles and polymer. Finally, the overall elastic moduli of the nanoparticle-reinforced polymer composites are estimated using the proposed multiscale approach combining the ensemble-volume average method and the MD simulation. The predictive capability of the proposed multiscale approach has been demonstrated through the multiscale numerical simulations.

• Nuclear Engineering and Technology
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• 제52권7호
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• pp.1537-1544
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• 2020

Molecular dynamics (MD) simulations were conducted to investigate the temperature effects on the primary damage in gallium nitride (GaN) material. Five temperatures ranging from 300 K to 900 K were studied for 10 keV Ga primary knock-on atom (PKA) with inject direction of [0001]. The results of MD simulations showed that threshold displacement energy (E_d) was affected by temperatures and at higher temperature, it was larger. The evolutions of defects under various temperatures were similar. However, the higher temperature was found to increase the peak number, peak time, final time and recombination efficiency while decreasing the final number. With regard to clusters, isolated point defects and little clusters were common clusters and the fraction of point defects increased with temperature for vacancy clusters, whereas it did not appear in the interstitial clusters. Finally, at each temperature, the number of Ga interstitial atoms was larger than that of N and besides that, there were other different results of specific types of split interstitial atoms.

• Journal of Electrochemical Science and Technology
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• 제10권3호
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• pp.257-270
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• 2019

The inhibition performance of sodium gluconate (SG), cetyltrimethylammonium bromide (CTAB) and their mixture (SG/CTAB) on the corrosion behavior of ${\alpha}$-brass in 0.5 M $H_2SO_4$ solution has been investigated by potentiodynamic polarization, electrochemical impedance spectroscopy (EIS), Scanning Electron Microscope with Energy-Dispersive Spectrometer (SEM-EDS), Inductively Coupled Plasma Spectrometry (ICPS) and molecular dynamics (MD) simulation techniques. The results reveal that SG with 5ppm CTAB, noted SG/CTAB, acts as a good corrosion inhibitor and its inhibition efficiency reached 89% after 24 h immersion in sulfuric acid solution, but slightly decreased at higher temperatures. The polarization curves displayed that SG/CTAB acts as a cathodic-kind inhibitor. Electrochemical impedance spectroscopy (EIS) studies revealed that the addition of 5ppm CTAB to different concentrations of SG considerably increases the corrosion resistance of ${\alpha}$-brass. The SEM-EDS and ICPS analyses support the experimental results. Further, molecular dynamics (MD) simulations were used to understand the adsorption profiles of SG/CTAB on Cu(111) and Zn(111) surfaces.