• Bulletin of the Korean Chemical Society
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• 제25권4호
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• pp.533-538
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• 2004

Canonical sampling method has been presented to generate the initial conditions for reactive flux studies of organic reactions in water. Velocity Verlet version of Nose-Hoover chain dynamics algorithm has been employed to sample the initial conditions according to canonical distribution. The unstable normal mode of a transition state has been introduced to define a dividing plane separating reactant and product regions in reaction processes. This method has been implemented and tested for the case iels-Alder reaction of methyl vinyl ketone (MVK) and cyclopentadiene (CPD) in water, providing a reliable tool for further reactive flux molecular dynamics studies in condensed media.

• 에너지공학
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• 제18권2호
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• pp.125-131
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• 2009

경도, 내마모성과 내부식성 등과 같은 금속의 물리적 특성은 이온주입에 의해 인위적으로 제어되어 질 수 있다. 이온주입의 특성을 관찰하기 위하여 분자동역학법을 이용하여 이온과 표면원자사이의 상호작용에 대해 미시적인 원자.분자 스케일로 현상을 모델화하여 수치해석을 수행하였다. 본 연구는 이온주입의 특성을 개선하기 위한 수치해석 연구로써 미시적인 관점에서 이온주입의 프로세스를 관찰하고자 하였다. 이를 위해 주입이온속도에 따른 주입메카니즘과 초기표면온도, 이온분자량 등의 영향을 조사하였다. 그 결과 초기 표면원자층의 온도가 높은 경우에 주입에너지가 어느 값 이상이 되면 오히려 주입확률이 감소하며 또한 비결정질상태인 표면원자층에 대한 이온주입은 양호한 조건의 설정에 따라 더 효과적일 수 있음을 알 수 있었다.

• Bulletin of the Korean Chemical Society
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• 제35권7호
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• pp.2097-2108
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• 2014

Chemical feature based quantitative pharmacophore models were generated using the HypoGen module implemented in DS2.5. The best hypothesis, Hypo1, which was characterized by the highest correlation coefficient (0.96), the highest cost difference (61.60) and the lowest RMSD (0.74), consisted of one hydrogen bond acceptor, one hydrogen bond donor, one hydrophobic and one ring aromatic. The reliability of Hypo1 was validated on the basis of cost analysis, test set, Fischer's randomization method and GH test method. The validated Hypo1 was used as a 3D search query to identify novel inhibitors. The screened molecules were further refined by employing ADMET, docking studies and visual inspection. Three compounds with novel scaffolds were selected as the most promising candidates for the designing of Mcl-1 antagonists. Finally, a 10 ns molecular dynamics simulation was carried out on the complex of receptor and the retrieved ligand to demonstrate that the binding mode was stable during the MD simulation.

• 한국소음진동공학회:학술대회논문집
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• 한국소음진동공학회 2008년도 추계학술대회논문집
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• pp.668-669
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• 2008

In this paper, we introduce various coarse-grained elastic network modeling (ENM) techniques as a novel computational method for simulating atomic scale dynamics in macromolecules including DNA, RNA, protein, and polymer. In ENM, a system is modeled as a spring network among representative atoms in which each linear elastic spring is well designed to replace both bonded and nonbonded interactions among atoms in the sense of quantum mechanics. Based on this simplified system, a harmonic Hookean potential is defined and used for not only calculating intrinsic vibration modes of a given system, but also predicting its anharmonic conformational change, both of which are strongly related with its functional features. Various nano and bio applications of ENM such as fracture mechanics of nanocomposite and protein dynamics show that ENM is one of promising tools for simulating atomic scale dynamics in a more effective and efficient way comparing to the traditional molecular dynamics simulation.

• Korea-Australia Rheology Journal
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• 제14권4호
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• pp.161-174
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• 2002

A new technique for numerical calculation of viscoelastic flow based on the combination of Neural Net-works (NN) and Brownian Dynamics simulation or Stochastic Simulation Technique (SST) is presented in this paper. This method uses a "universal approximator" based on neural network methodology in combination with the kinetic theory of polymeric liquid in which the stress is computed from the molecular configuration rather than from closed form constitutive equations. Thus the new method obviates not only the need for a rheological constitutive equation to describe the fluid (as in the original Calculation Of Non-Newtonian Flows: Finite Elements St Stochastic Simulation Techniques (CONNFFESSIT) idea) but also any kind of finite element-type discretisation of the domain and its boundary for numerical solution of the governing PDE's. As an illustration of the method, the time development of the planar Couette flow is studied for two molecular kinetic models with finite extensibility, namely the Finitely Extensible Nonlinear Elastic (FENE) and FENE-Peterlin (FENE-P) models.P) models.

• 한국정밀공학회:학술대회논문집
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• 한국정밀공학회 2003년도 춘계학술대회 논문집
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• pp.1182-1185
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• 2003

Recently, the research of the nano technology has been done on a lot of area over the world. Especially, the interest of them is much higher for semiconductor companies and other super accuracy processing area. In this thesis, we have approached the characteristic of the tensile and bonding of copper, frequently used to nano wires, by molecular dynamics simulation. And the simulation was done by EAM, Embedded Atom Method which has the most highest accuracy for metal. Then the feature of copper at atom space is understood through the simulation of nano wire.

• Bulletin of the Korean Chemical Society
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• 제35권5호
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• pp.1469-1478
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• 2014

Use of acetonitrile in electrolytes promotes better operation of supercapacitors. Recent efforts show that electrolytes containing acetonitrile can also function in a wide range of operating temperatures. Therefore, this paper addresses the dielectric relaxation processes, structure and dynamic properties of the bulk acetonitrile at various temperatures. Systems of acetonitrile were modeled using canonical ensemble and simulated by employing Molecular Dynamics method. Results show that interactions among the molecules were correlated within a cut-off radius while parallel and anti-parallel arrangements are observed beyond this radius at relatively high and low temperatures respectively. Furthermore, effects of C-C-N and C-H bending modes were greatly appreciated on the power spectral density of time rate change of dipole-dipole correlations whereas frequency shifts were observed on all modes at the lowest temperature under consideration. Linear variations with temperature were depicted for reorientation times and self-diffusion coefficients. Shear viscosity was also computed with a good accuracy within a certain range of the temperature as well.

• Interaction and multiscale mechanics
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• 제1권2호
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• pp.303-315
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• 2008

In this paper, thermodynamical properties of crystalline silicon under strain are calculated using classical molecular dynamics (MD) simulations based on the Tersoff interatomic potential. The Helmholtz free energy of the silicon crystal under strain is calculated by using the ensemble method developed by Frenkel and Ladd (1984). To account for quantum corrections under strain in the classical MD simulations, we propose an approach where the quantum corrections to the internal energy and the Helmholtz free energy are obtained by using the corresponding energy deviation between the classical and quantum harmonic oscillators. We calculate the variation of thermodynamic properties with temperature and strain and compare them with results obtained by using the quasi-harmonic model in the reciprocal space.

• Journal of Information Display
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• 제12권3호
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• pp.135-139
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• 2011

This paper presents the directly obtained rotational viscosity values of E7, which includes pentylcyanobiphenol, heptylcyanobiphenol, 4-cyano-4'-n-octyloxy-1,1'-biphenyl, and 4-cyano-4"-n-pentyl-1,1',1"-terphenyl, at various tempe using molecular dynamics computer simulation. The director mean squared displacement was achieved from the squared displacement of the mean director using the concept of the mean director of various nematic liquid crystals. The calculated values were compared with the experiment results that predicted a good agreement. Additional points that must be considered for further study are also discussed.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2007년도 춘계학술대회A
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• pp.502-505
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• 2007

PMMA has been extensively adopted in Nano Imprint Lithography(NIL). PMMA nano-structures experience severe mechanical load and deformation during NIL process, and understanding its mechanical behavior is very important in designing and optimizing NIL process. One of the most promising techniques for characterizing the mechanical behavior of nano structures is nano pillar compression test. In this study, the mechanical behaviors of PMMA pillars during compression test are analyzed using Molecular Dynamics. Two methods for simulation of PMMA nano pillars are proposed. The stress-strain relationship of nano-scale PMMA structure is obtained based on CVFF(Covalent Valence Force Fields) potential and the dependency of the applied strain rate on the stress-strain relationship is analyzed. The obtained stress-strain relationships can be useful in simulating nano-scale PMMA structures using Finite Element Method(FEM) and understanding the experimental results obtained by compression test of PMMA nano pillars.