• 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.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.

• 한국추진공학회지
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• 제19권6호
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• pp.54-63
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• 2015

본 연구에서는 고온/고압의 연소가스에 의해 야기되는 노즐목 삭마현상의 분자수준 메커니즘을 분자동역학 시뮬레이션을 이용하여 관찰한다. 노즐목은 두 개의 그래핀으로 구성된 그래파이트로 모델링하고 분자동역학 시뮬레이션은 충분한 속도를 가지고 그래파이트에 충돌하는 $H_2O$ 분자와 $CO_2$ 분자가 지속적으로 생성되는 과정과 평형상태의 시뮬레이션으로 구성된다. 반응을 모사할 수 있는 ReaxFF 포텐셜을 사용하며, 충돌에 의해 야기되는 $H_2O$ 및 $CO_2$ 분자의 해리와 화학적 삭마와의 관계에 중점을 두고 관찰하고자 하며, 거시적인 관찰결과들과 비교하고자 한다.

• 한국윤활학회:학술대회논문집
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• 한국윤활학회 2002년도 proceedings of the second asia international conference on tribology
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• pp.61-62
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• 2002

In order to clarify the contact mechanism between specimen surface and probe tip in the surface observation by the AFM (atomic force microscope) or the FFM (friction force microscope), several molecular dynamics simulations have been performed. In the simulation, a 3-dimensional simulation model is proposed where the specimen and the probe are assumed to consist of mono-crystal line copper and a carbon atom respectively and the effect of cantilever stiffness is also taken into considered. The surface observation process on a well-defined Cu{100} is simulated. The influences of cantilever stiffness on the reactive force images and the behavior of probe tip were evaluated. As a resuIt, several phenomena similar to those observed by the actual surface observation experiment, such as double-slip behavior and dispersion in the stick-slip wave period were observed.

• Interaction and multiscale mechanics
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• 제4권4호
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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.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2007년도 춘계학술대회A
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• pp.343-348
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• 2007

Molecular dynamics study of thermal NIL (Nano Imprint Lithography) process is performed to examine stamp-resist interactions. A layered structure consists of Ni stamp, poly-(methylmethacrylate) thin film resist and Si substrate was constructed for isothermal ensemble simulations. Imposing confined periodicity to the layered unit-cell, sequential movement of stamp followed by NVT simulation was implemented in accordance with the real NIL process. Both vdW and electrostatic potentials were considered in all non-bond interactions and resultant interaction energy between stamp and PMMA resist was monitored during stamping and releasing procedures. As a result, the stamp-resist interaction energy shows repulsive and adhesive characteristics in indentation and release respectively and irregular atomic concentration near the patterned layer were observed. Also, the spring back and rearrangement of PMMA molecules were analyzed in releasing process.

• 한국윤활학회:학술대회논문집
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• 한국윤활학회 2004년도 학술대회지
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• pp.83-89
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• 2004

In this paper, molecular dynamics simulations are performed to analyze the adhesion between a diamond mould and a copper substrate in diamond nanoimprint lithography. The diamond nanoimprint lithography process is simplified as punch-type nanoindentation. The copper substrates are assumed to monocrystalline and defect free and consist of $22500\~80000$ atoms depending on their dimension. The diamond moulds consist of 916 or 2414 atoms, which is assumed to be rigid. The consistent results lot the maximum normal force and the adhesion force are obtained regardless of the size of substrates and the adhesion hysteresis is shown in all cases. It is found that the friction acting on the sidewalls of the mould affects the adhesion significantly when the mould is released from the substrate.

• Tribology and Lubricants
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• 제20권2호
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• pp.102-108
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• 2004

In this paper, friction and wear behaviors between monocrystalline, defect-free copper and carbon on the atomic scale are investigated by using 2-dimensional molecular dynamics simulation. It is assumed that all interatomic forces are given by Morse potential. The deformation of carbon is assumed to be neglected and vacuum condition is also assumed. Average friction and normal forces for various surface conditions, various scratch speeds and scratch depths are obtained from simulations. Changes of wear behaviors for various scratch speeds and surface conditions are investigated by observing snapshots in scratch process. The effects of surface conditions, scratch speeds, and scratch depths on the friction force, normal force, and friction coefficient are also investigated.