• 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.

• Bulletin of the Korean Chemical Society
• /
• v.23 no.1
• /
• pp.107-111
• /
• 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
• /
• v.24 no.1
• /
• pp.95-98
• /
• 2003

Enantioselectivity of the propranolol on β-cyclodextrin was simulated by molecular modeling. Monte Carlo (MC) docking and molecular dynamics (MD) simulations were applied to investigate the molecular mechanism of enantioselective difference of both enantiomeric complexes. An energetic analysis of MC docking simulations coupled to the MD simulations successfully explains the experimental elution order of propranolol enantiomers. Molecular dynamics simulations indicate that average energy difference between the enantiomeric complexes, frequently used as a measure of chiral recognition, depends on the length of the simulation time. We found that, only in case of much longer MD simulations, noticeable chiral separation was observed.

• 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.

• 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.

• Carbon letters
• /
• v.11 no.4
• /
• pp.316-324
• /
• 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 Korean Society for Technology of Plasticity Conference
• /
• 2004.05a
• /
• pp.62-65
• /
• 2004

Recently, an approach for nanoscale deformation has been developed that couples the atomistic and continuum approaches using Finite Element Method (FEM) and Molecular Dynamics (MD). However, this approach still has problems to connect two approaches because of the difference of basic assumptions, continuum and atomistic. To solve this problem, an alternative way is developed that connects the quasimolecular dynamics (QMD) and molecular dynamics (MD). In this paper, we suggest the way to make and validate the MD-QMD coupled model.

• Membrane Journal
• /
• v.26 no.5
• /
• pp.329-336
• /
• 2016

Proton exchange membrane (PEM) is one of the key components of membrane-electrode assembly (MEA), which plays important role in fuel cell performance together with catalysts. It is widely accepted that water channel morphology inside PEMs as a proton pathway significantly affects the PEM performance. Molecular dynamics (MD) simulations are a very useful tool to understand molecular and atomic structures of materials, so that many related researches are currently being studied. In this paper, we summarize the current research trend in MD simulations, present which properties can be characterized, and finally introduce the usefulness of MD simulations to the researchers for proton exchange membranes.

• 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.

• Journal of the Korean Society of Manufacturing Process Engineers
• /
• v.8 no.1
• /
• pp.43-47
• /
• 2009

Recently, an approach for nano-scale material deformation has been developed that couples the atomistic and continuum approaches using Finite Element Method (FEM) and Molecular Dynamics (MD). However, this approach still has problems to connect two approaches because of the difference of basic assumptions, continuum and atomistic modeling. To solve this problem, an alternative way is developed that connects the QuasiMolecular Dynamics (QMD) and molecular dynamics. In this paper, we suggest the way to make and validate the MD-QMD coupled model.