• 지질공학
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• 제11권3호
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• pp.269-278
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• 2001

MD 시뮬레이션을 이용하여 $\alpha$-quartz, 백운모, 조장석의 열팽창계수를 산정하였다. MD 시뮬레이션에서 가장 중요한 포텐셜 함수로는 부분이온성 두입자간 포텐셜을 이용하였다. 열팽창계수는 격자구조의 온도에 따라 변화를 NPT-ensemble 시뮬레이션을 통하여 계산하여 산정하였으며 그 결과를 실험결과와 비교하였다. 시뮬레이션을 통하여 산정된 열팽창계수는 시험결과와 잘 일치하고 있으며, 유효한 수준의 결과를 보이고 있다.

• BMB Reports
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• 제29권4호
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• pp.380-385
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• 1996

Ovomucoid third domain is a serine proteinase inhibitor protein which consists of 56 amino acid residues. A fifty picosecond molecular dynamics (MD) simulation was carried out for ovomucoid third domain protein with 5 $\AA$ layer of water molecules. A comparison of main chain atoms in the MD averaged structure with the crystal structure showed that most of the backbone structures are maintained during the simulation. Investigation of the intramolecular hydrogen bondings indicated that most of the interactions between main chain atoms were conserved, whereas those between side chains were reorganized for the period of the simulation. Especially, the side chain interactions around the scissile bond of reactive site P1 (Met18) were found to be more extensive for the MD structures. During the simulation, hydrogen bonds were maintained between the side chains of Glu19 and Arg21 as well as those of Thr17 and Glu19. Extensive side chain interactions observed in the MD structures may shed light on the question of why protein proteinase inhibitors are strong inhibitors for proteinases rather than good substrates.

• The Korean Journal of Ceramics
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• 제5권1호
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• pp.40-43
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• 1999

In order to investigate Sn substitution sites and interstitial O atoms in tin-doped indium oxide, molecular dynamics (MD) simulations were carried out. There are two kinds of cation sites in $In_2O_3$, namely b-site and d-site. NTP-MD simulations under the condition of 300 K and 0 GPa were performed with two kinds of cells substituted by Sn atoms at each site. The excess oxygen atom accompanied with Sn doping was also taken into consideration. According to the calculations of Sn potential energies in each site, it was revealed that Sn atoms were substituted for b-sites rather than for d-sites. It was also revealed that the interstitial excess oxygen atoms tend to be connected with the Sn atoms substituted for the d-sites Sn rather than for the b-site. There MD simulation results well agreed with the experimental results.

• Bulletin of the Korean Chemical Society
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• 제34권8호
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• pp.2466-2472
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• 2013

Human immunodeficiency virus type-1 (HIV-1) is a causative agent of Acquired immunodeficiency syndrome (AIDS), which has affected a large population of the world. Viral envelope glycoprotein (gp120) is an intrinsic protein for HIV-1 to enter into human host cells. Molecular docking guided molecular dynamics (MD) simulation was performed to explore the interaction mechanism of heterobiaryl derivative with gp120. MD simulation result of inhibitor-gp120 complex demonstrated stability. Our MD simulation results are consistent with most of the previous mutational and modeling studies. Inhibitor has an interaction with the CD4 binding region. Van der Waals interaction between inhibitor and Val255, Thr257, Asn425, Met426 and Trp427 were important. This preliminary MD model could be useful in exploiting heterobiaryl-gp120 interaction in greater detail, and will likely to shed lights for further utilization in the development of more potent inhibitors.

• 터널과지하공간
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• 제10권1호
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• pp.70-79
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• 2000

입자수, 압력, 온도일정의 앙상블(NPT-ensemble) 분자동력학(MD) 시뮬레이션을 이용하여 300$^{\circ}$K에서 $\alpha$-quartz의 결정축에 따른 일축압축강도를 계산하고, 자연산 $\alpha$-quartz 단결정 코아를 제작하여 일축압축강도시험을 실시하였다. $\alpha$-quartz 단결정 코아에 대한 일축압축시험에서 측정된 결과에 의하면 재하 방향이 c축에 평행한 경우가 수직인 경우보다 높은 강도를 나타내지만, MD 시뮬레이션에서 계산된 완전무결함 $\alpha$-quartz의 경우 이와 반대의 결과를 보이고 있다. 두 경우 모두 재하방향에 따른 강도 이방성을 보이고 있으나, 그 이유는 서로 다르다. MD 시뮬레이션에 의해 계산된 무결함 $\alpha$-quartz의 강도 이방성은 결정구조의 차이에 기인하는 것으로 사료된다. 이에 반해 일축압축시험을 통해 측정된 $\alpha$-quartz의 강도 이방성은 결정성장과정에서 생기는 주상 미세결함에 의해 영향을 받는다.

• 멤브레인
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• 제24권5호
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• pp.341-349
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• 2014

분자 동력학(Molecular dynamics; MD) 전산모사 기술은 대상이 되는 입자(일반적으로, 원자)의 위치와 속도를 계산하여, 원자 및 분자들의 다양한 구조 및 동적 특성을 분석하는 데에 있어서 매우 유용한 기술이다. 기체 분리막 연구에 있어서도 MD는 그동안 free volume 분석, conformation search 등과 같은 고분자 구조 분석 및 permeability, diffusivity와 같은 기체 투과 거동을 연구하는 데 널리 사용되어 왔다. 본 총설에서는 기체 분리막 분야에 MD를 적용하는 일반적인 방법론에 대하여 서술하고, 다양한 관련 연구들을 소개하고자 한다.

• Interaction and multiscale mechanics
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• 제2권4호
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• pp.353-374
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• 2009

A new seamless multiscale simulation was developed for coupling the continuum model with its molecular dynamics. Kriging-based Finite Element Method (K-FEM) is employed to model the continuum base of the entire domain, while the molecular dynamics (MD) is confined in a localized domain of interest. In the coupling zone, where the MD domain overlaps the continuum model, the overall Hamiltonian is postulated by contributions from the continuum and the molecular overlays, based on a quartic spline scaling parameter. The displacement compatibility in this coupling zone is then enforced by the Lagrange multiplier technique. A multiple-time-step velocity Verlet algorithm is adopted for its time integration. The validation of the present method is reported through numerical tests of one dimensional atomic lattice. The results reveal that at the continuum/MD interface, the commonly reported spurious waves in the literature are effectively eliminated in this study. In addition, the smoothness of the transition from MD to the continuum can be significantly improved by either increasing the size of the coupling zone or expanding the nodal domain of influence associated with K-FEM.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2008년도 추계학술대회A
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• pp.678-683
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• 2008

Moment-based reliability analysis is the method to calculate reliability using Pearson System with first-four raw moments obtained from simulation model. But it is too expensive to calculate first four moments from complicate simulation model. To overcome this drawback the MD(multiplicative decomposition) method which approximates simulation model to kriging metamodel and calculates first four raw moments explicitly with multiplicative decomposition techniques. In general, kriging metamodel is an interpolation model that is decomposed of global model and local model. The global model, in general, can be used as the constant global model, the 1st order global model, or the 2nd order global model. In this paper, the influences of global models on the accuracy and robustness of raw moments are examined and compared. Finally, we suggest the best global model which can provide exact and robust raw moments using MD method.

• Nuclear Engineering and Technology
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• 제36권3호
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• pp.229-236
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• 2004

Radiation hardening is a multiscale phenomenon involving various processes over a wide range of time and length. We present a multiscale model for estimating the amount of radiation hardening in pressure vessel steel in the environment of a light water reactor. The model comprises two main parts: molecular dynamics (MD) simulation and a point defect cluster (PDC) model. The MD simulation was used to investigate the primary damage caused by displacement cascades. The PDC model mathematically formulates interactions between point defects and their clusters, which explains the evolution of microstructures. We then used a dislocation barrier model to calculate the hardening due to the PDCs. The key input for this multiscale model is a neutron spectrum at the inner surface of reactor pressure vessel steel of the Younggwang Nuclear Power Plant No.5. A combined calculation from the MD simulation and the PDC model provides a convenient tool for estimating the amount of radiation hardening.

• Interaction and multiscale mechanics
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• 제5권2호
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• pp.115-129
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• 2012

Nanowires (NWs) have attracted intensive researches owing to the broad applications that arise from their remarkable properties. Over the last decade, immense numerical studies have been conducted for the numerical investigation of mechanical properties of NWs. Among these numerical simulations, the molecular dynamics (MD) plays a key role. Herein we present a brief review on the current state of the MD investigation of nanowires. Emphasis will be placed on the FCC metal NWs, especially the Cu NWs. MD investigations of perfect NWs' mechanical properties under different deformation conditions including tension, compression, torsion and bending are firstly revisited. Following in succession, the studies for defected NWs including the defects of twin boundaries (TBs) and pre-existing defects are discussed. The different deformation mechanism incurred by the presentation of defects is explored and discussed. This review reveals that the numerical simulation is an important tool to investigate the properties of NWs. However, the substantial gaps between the experimental measurements and MD results suggest the urgent need of multi-scale simulation technique.