• Proceeding of EDISON Challenge
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• 2013.04a
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• pp.179-191
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• 2013

NPT ensemble을 이용하여 Joule-Thomson 반전 곡선 (Joule-Thomson inversion curve, JTIC)를 구하는 기존의 모의실험 방법들과는 달리, 본 연구에서는 NVT 분자동역학 모의실험을 이용하여 JTIC를 구하는 방법을 개발하고, 이 방법을 이용하여 아르곤 기체의 JTIC를 구할 수 있음을 보인다. 본 연구 결과를 실험 및 다른 이론들과 비교, 분석한 결과, 낮은 온도에서의 JTIC는 실험 및 이론 결과와 유사한 반면, 높은 온도에서는 일정 정도의 차이를 나타냄을 알 수 있다. 이 차이는 분자동역학 모의실험에 사용하는 적은 입자 수와 모의실험 시간, 그리고 curve fitting 방법 등에 기인하는 것으로 여겨진다. 또한 본 연구를 통하여 NVT 분자동역학 모의실험 방법만 가능한, EDISON 계산화학 프로그램 중 하나인 "Mixed LJ(12-6) particles MD"가 JTIC를 구하는데 유용하게 사용될 수 있고, 이를 통해 학부생들이 열역학의 기본 개념을 이해하는데 도움을 줄 것으로 기대한다.

• Bulletin of the Korean Chemical Society
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• v.23 no.3
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• pp.441-446
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• 2002

We have presented the results of thermodynamic, structural and dynamic properties of liquid benzene, toluene, and p-xylene in canonical (NVT) ensemble at 293.15 K by molecular dynamics (MD) simulations. The molecular model adopted for these molecules is a combination of the rigid body treatment for the benzene ring and an atomistically detailed model for the methyl hydrogen atoms. The calculated pressures are too low in the NVT ensemble MD simulations. The various thermodynamic properties reflect that the intermolecular interactions become stronger as the number of methyl group attached into the benzene ring increases. The pronounced nearest neighbor peak in the center of mass g(r) of liquid benzene at 293.15 K, provides the interpretation that nearest neighbors tend to be perpendicular. Two self-diffusion coefficients of liquid benzene at 293.15 K calculated from MSD and VAC function are in excellent agreement with the experimental measures. The self-diffusion coefficients of liquid toluene also agree well with the experimental ones for toluene in benzene and for toluene in cyclohexane.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.225-235
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• 2014

6종의 Intermediate filament 중 type IV인 Neurofilaments (NFs)는 신경세포에 존재하는 세포골격세사로 heavy NF(NF-H), medium NF(NF-M), light NF(NF-L) 세가지의 분자 질량 단백질로 구성되어 있다. NF의 side arm은 interfilament spacing과 axonal caliber를 조절하는 중요한 역할을 한다고 생각되어왔다. 또한 이에 대해서 각각의 protein의 역할은 알아내기 위해 isolated NF의 형태와 구조에 대해 많은 연구가 이루어졌는데, NF의 구조적 특성은 NF sidearm의 tail 부분에서 phosphorylation의 정도에 따른 Lys-Ser-Pro(KSP) repeats의 charge distribution을 통해 알 수 있다. 지금까지 NF에 대한 많은 연구가 이루어졌지만 인간에 한해서만 진행되었다. 그렇기 때문에 본 연구에서는 주어진 amino acid sequence와 각 species의 NF-H:NF-M:NF-L의 비율의 정보를 이용하여 The constant-NVT ensemble MC simulation을 통해 인간뿐만이 아닌 다른 species에 대한 NF의 구조적 특성을 알아보고자 한다.

• Bulletin of the Korean Chemical Society
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• v.23 no.3
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• pp.447-453
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• 2002

In this paper we have presented the results of thermodynamic, structural, and dynamic properties of model systems for liquid benzene, toluene and p-xylene in an isobaric-isothermal (NpT) ensemble at 283.15, 303.15, 323.15, and 343.15 K using molecular dynamics (MD) simulation. This work is initiated to compensate for our previous canonical (NVT) ensemble MD simulations [Bull. Kor. Chem. Soc. 2001, 23, 441] for the same systems in which the calculated pressures were too low. The calculated pressures in the NpT ensemble MD simulations are close to 1 atm and the volume of each system increases with increasing temperature. The first and second peaks in the center of mass g(r) diminish gradually and the minima increase as usual for the three liquids as the temperature increases. The three peaks of the site-site gC-C(r) at 283.15 K support the perpendicular structure of nearest neighbors in liquid benzene. Two self-diffusion coefficients of liquid benzene via the Einstein equation and via the Green-Kubo relation are in excellent agreement with the experimental measures. The self-diffusion coefficients of liquid toluene and p-xylene are in accord with the trend that the self-diffusion coefficient decreases with increasing number of methyl group. The friction constants calculated from the force auto-correlation (FAC) function with the assumption that the fast random force correlation ends at time which the FAC has the first negative value give a correct qualitative trends: decrease with increase of temperature and increase with the number of methyl group. The friction constants calculated from the FAC's are always less than those obtained from the friction-diffusion relation which reflects that the random FAC decays slower than the total FAC as described by Kubo [Rep. Prog. Phys. 1966, 29, 255].

• Proceedings of the KSME Conference
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• 2007.05a
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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.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.337-342
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• 2007

In this study, molecular dynamics simulation of nano imprint lithography in which patterned stamp is pressed onto amorphous polyethylene(PE) surface are performed to study the behaviour of polymer. Force fields including bond, angle, torsion, and Lennard Jones potential are used to describe the inter-molecular and intra-molecular force of PE molecules and stamp, substrate. Periodic boundary condition is used in horizontal direction and canonical NVT ensemble is used to control the system temperature. As the simulation results, the behaviour of polymer is investigated during the imprinting process. The mechanism of polymer deformation is studied by means of inspecting the surface shape, volume, density, atom distribution. Deformation of the polymer resist was found for various of the stamp geometry and the alignment state of the polymer molecules.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.506-511
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• 2007

Mechanical behavior of copper nanowire is investigated. An FCC nanowire model composed of 1,408 atoms is used for MD simulation. Simulations are performed within NVT ensemble setting without periodic boundary conditions. $Nos\acute{e}-Poincar\acute{e}$ MD algorithm is employed to guarantee preservation of Hamiltonian and temperature. Numerical tensile tests of Nanowire are carried out with constant strain rate. Additionally, temperature and strain rate effects are considered. Stress-strain curve is constructed from the calculated Cauchy stresses and specified strain values. In (22,4,4) Copper nanowire, non-linear behavior appears around ${\epsilon}\simeq0.09.$ At this instance, starting of structural reorientations are observed. At the onset of reorientation, the modulus characteristics are also investigated.

• Bulletin of the Korean Chemical Society
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• v.34 no.12
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• pp.3800-3804
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• 2013

In this study, molecular dynamics simulations of SPC/E (extended simple point charge) model have been carried out in the canonical NVT ensemble over the range of temperatures 300 to 550 K with and without Ewald summation. The quaternion method was used for the rotational motion of the rigid water molecule. Radial distribution functions $g_{OO}(r)$, $g_{OH}(r)$, and $g_{HH}(r)$ and self-diffusion coefficients D for SPC/E water were determined at 300-550 K and compared to experimental data. The temperature dependence on the structural and diffusion properties of SPC/E water was discussed.

• Proceedings of the KSME Conference
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• 2003.04a
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• pp.1083-1088
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• 2003

Molecular dynamics simulations on the deformation behavior of single-walled carbon nanotube are performed. Formation energies of CNT's by interatomic potentials are computed and compared with ab initio results. Bending and axial compression are applied under lattice statics and NVT ensemble conditions. Specifically, we focus on the mechanism of kink formation in bending. The simulation results are comprehensively explained in the framework of atomistic energetics. The effects of temperature and chirality on the deformation of carbon nanotube are also studied.

• Proceedings of the Computational Structural Engineering Institute Conference
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• 2007.04a
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• pp.433-438
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• 2007

Mechanical behavior of copper Nanowire is investigated, An FCC Nanowire model composed of 1,408 atoms is used for NID simulation, Simulations are performed within NVT ensemble setting without periodic boundary conditions, Nose-Poincare MD algorithm is employed to guarantee preservation of Hamiltonian. Numerical tensile tests are carried out with constant strain rate, Stress-strain curve is constructed from the calculated Cauchy stresses and specified strain values, Non-linear behavior appears around $\varepsilon$=0.064, At this instance, starting of structural reorientations are observed.