• BMB Reports
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• v.29 no.4
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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.

• Membrane Journal
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• v.24 no.5
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• pp.341-349
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• 2014

Molecular dynamics (MD) computer simulation is a very useful tool to calculate the trajectory and velocity of particles (generally, atoms), and thus to analyze the various structures and kinetic properties of atoms and molecules. For gas separation membranes, MD has been widely used for structure analysis of polymers such as free volume analysis and conformation search, and for the study of gas transport behavior such as permeability and diffusivity. In this paper, general methodology how to apply MD on gas separation membranes will be described and various related researches will be introduced.

• Interaction and multiscale mechanics
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• v.2 no.4
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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.

• The Journal of Engineering Geology
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• v.11 no.3
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• pp.269-278
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• 2001

We describe the calculation of thermal expansion coefficients of $\alpha$-quartz, muscovite and albite using a MD simulation method. The selection of interatomic potentials is important for the MD calculation, and we used the 2-body interatomic potential function. The coefficients are calculated using a differential operation of the temperature dependence of the lattice constant obtained from the NPT-ensemble molecular dynamics simulation. Reasonable agreement is found between the analytical results and measured data.

• 한국전산유체공학회:학술대회논문집
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• 2008.03a
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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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• 2008.10a
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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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• v.11 no.4
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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.

• Proceedings of the KSME Conference
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• 2001.11a
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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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• v.23 no.1
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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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• v.34 no.8
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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.