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

• BMB Reports
• /
• v.29 no.4
• /
• pp.380-385
• /
• 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
• /
• v.5 no.1
• /
• pp.40-43
• /
• 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
• /
• v.34 no.8
• /
• pp.2466-2472
• /
• 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.

• Tunnel and Underground Space
• /
• v.10 no.1
• /
• pp.70-79
• /
• 2000

We carried out NPT-ensemble (constant-number of particles, pressure, and temperature) Molecular Dynamics (MD) simulations for measuring strength anisotropy under uniaxial compressive stress rotated to the crystallographic axes in $\alpha$-quartz. Uniaxial compressive strengths of a single quartz crystal were measured in directions of the a- and c-axis. Measured uniaxial strength of a single quartz crystal was higher in the direction parallel to the c-axis than that measured in the direction normal to the c-axis. However the reverse was found in calculated uniaxial strengths by MD simulation. The contradictive result of strengths was observed in both cases but was found to be different in origin. Strength anisotropy of defectless $\alpha$-quartz crystal in MD simulation is basically caused by structural difference of quartz. By contrast, anisotropy of measured strength in the uniaxial compression test is related to oriented micro-defects developed during crystal growth.

• Membrane Journal
• /
• v.24 no.5
• /
• pp.341-349
• /
• 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
• /
• v.2 no.4
• /
• pp.353-374
• /
• 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.

• Proceedings of the KSME Conference
• /
• 2008.11a
• /
• pp.678-683
• /
• 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
• /
• v.36 no.3
• /
• pp.229-236
• /
• 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
• /
• v.5 no.2
• /
• pp.115-129
• /
• 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.