• 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.

• 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.

• 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.

• 한국전산유체공학회:학술대회논문집
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• 한국전산유체공학회 2008년도 학술대회
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• pp.204-207
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• 2008

Stochastic molecular dynamics simulation is a variation of standard molecular dynamics simulation that basically omits water molecules. The omission of water molecules, occupying a majority of space, enables flow simulation at microscale. This study reports our stochastic molecular dynamics simulation of particles diffusing in rectangular microchannels. We interestingly found that diffusion patterns in channels with a very small aspect ratio differ by dimensions. We will also discuss the future direction of our research toward a more realistic simulation of micromixing.

• 한국전산유체공학회:학술대회논문집
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• 한국전산유체공학회 2008년 추계학술대회논문집
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• pp.204-207
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• 2008

Stochastic molecular dynamics simulation is a variation of standard molecular dynamics simulation that basically omits water molecules. The omission of water molecules, occupying a majority of space, enables flow simulation at microscale. This study reports our stochastic molecular dynamics simulation of particles diffusing in rectangular microchannels. We interestingly found that diffusion patterns in channels with a very small aspect ratio differ by dimensions. We will also discuss the future direction of our research toward a more realistic simulation of micromixing.

• Carbon letters
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• 제11권4호
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• pp.316-324
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• 2010

The effects of geometrical parameters on mechanical properties of graphite-vinylester nanocomposites and their constituents (matrix, reinforcement and interface) are studied using molecular dynamics (MD) simulations. Young's modulii of 1.3 TPa and 1.16 TPa are obtained for graphene layer and for graphite layers respectively. Interfacial shear strength resulting from the molecular dynamic (MD) simulations for graphene-vinylester is found to be 256 MPa compared to 126 MPa for graphitevinylester. MD simulations prove that exfoliation improves mechanical properties of graphite nanoplatelet vinylester nanocomposites. Also, the effects of bromination on the mechanical properties of vinylester and interfacial strength of the graphene.brominated vinylester nanocomposites are investigated. MD simulation revealed that, although there is minimal effect of bromination on mechanical properties of pure vinylester, bromination tends to enhance interfacial shear strength between graphite-brominated vinylester/graphene-brominated vinylester in a considerable magnitude.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2001년도 추계학술대회논문집A
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• pp.252-257
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• 2001

With the help of newly arrived technology such as PC clustering, molecular dynamics (MD) seems to be promising for large-scale materials simulations. A cost-effective cluster is set up using commodity PCs connected over Ethernet with fast switching devices and free software Linux. Executing MD simulations in the parallel sessions makes it possible to carry out large-scale materials simulations at acceptable computation time and costs. In this study, the MD computer code for fracture simulation is modified to comply with MPI (Message Passing Interface) specification, and runs on the PC cluster in parallel mode flawlessly. It is noted that PC clusters can provide a rather inexpensive high-performance computing environment comparing to supercomputers, if properly arranged.

• Bulletin of the Korean Chemical Society
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• 제23권1호
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• pp.107-111
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• 2002

The OSS2 (Oj？me-Shavitt-Singer 2)[L. Oj？me et al., J. Chem. Phys. 109, 5547 (1998)] model for the solvated proton in water is examined for $H_2O,\;H_3O^+,\;H_5O_2^+,\;H_7O_3^+,\;and\;H_9O_4^-$ by molecular dynamics (MD) simulations. The equilibrium molecular geometries and energies obtained from MD simulations at 5.0 and 298.15 K agree very well with the optimized calculations.

• 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.