Structural analysis of human CCR2b and primate CCR2b by molecular modeling and molecular dynamics simulation

CCR2b, a chemokine receptor for MCP-1, -2, -3, -4, plays an important role in a variety of diseases involving infection, inflammation, and/or injury, as well as being a coreceptor for HIV-1 infection. Two models of human CCR2b (hCCR2b) were generated by h

Molecular dynamics simulation on the complex of the tobramycin and 16S rRNA a site

A 3. 6 ns molecular dynamics simulation was carried out on the complex system of tobramycin and 16S rRNA in order to understand the speciality recognition mechanism between tobramycin and 16S rRNA at the molecular level. The results demonstrate that two l

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Molecular Dynamics Simulation on Characteristics of Decomposition of Methane Hydrate in the Presence of Hydrogen Peroxide Solution

In this work, the characteristics of the decomposition of methane hydrate Structure I (SI) in the presence of hydrogen peroxide solution is investigated using the molecular dynamics simulation. The mechanism of the transformation process from the solid hydrate to the liquid is analyzed with the effect of hydrogen peroxide (HP) solution. In addition, the effect of ethylene glycol (EG) with the same molar concentration with HP on the methane hydrate dissociation is also studied. The results illustrate that both HP and EG promote well the hydrate dissociation. The work provides the important reference value for the experimental investigation into the promotion effect of HP on the hydrate dissociation.

Molecular Dynamics Simulation of Methane Hydrate Dissociation Process in the Presence of Thermodynamic Inhibitor

The dissociation of methane hydrate in the presence of ethylene glycol (11.45 mol.L-1) at 277.0 K was studied using canonical ensemble (NVT) molecular dynamics simulations. Results show that hydrate dissociation starts from the surface layer of the solid hydrate and then gradually expands to the internal layer. Thus, the solid structure gradually shrinks until it disappears. A distortion of the hydrate lattice structure occurs first and then the hydrate evolves from a fractured frame to a fractional fragment. Finally, water molecules in the hydrate construction exist in the liquid state. The inner dissociating layer is, additionally, coated by a liquid film formed from outer dissociated water molecules outside. This film inhibits the mass transfer performance of the inner molecules during the hydrate dissociation process.

Molecular dynamics simulation of entropy and surface tension for grain boundary of α-Fe

The grain boundary is an interface and the surface tension is one of its important thermodynamic properties. In this paper, the surface tension of the ∑9 grain boundary for α-Fe at various temperatures and pressures is calculated by means of Computer Molecular Dynamics (CMD). The results agree satisfactorily with the experimental data. It is shown that the contribution of entropy to surface tension of grain boundary can be ignored.

Molecular dynamics simulation of sub-transition for polyethersulfone

Molecular dynamics (MD) simulations of a polyethersulfone (PES) chain are carried out in the amorphous state by using the Dreiding 2.21 force field at four temperatures. Two types of molecular motion, i.e, rotations of phenylene rings and torsions of large segments containing two oxygen atoms, two sulfur atoms, and five phenylene rings on the backbone, are simulated. The modeling results show that the successive phenylene rings should be in-phase cooperative rotations, whereas the successive large segments should be out-of-phase cooperative torsions. By calculating the diffusion coefficient for the phenylene ring rotations, it is found that this rotation contributes to the beta -transition of PES.

Phase transition temperatures of side chain liquid crystal polymer from molecular dynamics simulation

In this paper, phase transition temperatures of side chain liquid crystal polymer were predicted by molecular dynamics simulation. We analyzed the change of energy and the degree of similarity(S) with the temperature varying. The simulated phase transition temperatures agree with the experimental values in a proper deviation.

Molecular dynamics simulation of polystyrene-block-poly(methyl methacrylate)

Molecular dynamics is applied to the system of polystyrene-block-poly(methyl methacrylate). The simulation shows that for the block copolymer system, a layered structure, which reflects microphase separation, is obtained and this structure is stable. In order to elucidate that the formation of the layered structure is reasonable, some static properties such as the radial distribution function and the dipole moment are analyzed in some detail.

Molecular dynamics simulation of observed c(4x4) and c(4x3) C60 alignments on the Si(100) reconstructed surface.

We have implemented a large-scale classical molecular dynamics simulation at constant temperature to provide a theoretical insight into the results of a recently performed experiment on the monolayer and multi-layer formations of molecular films on the Si(100) reconstructed dimerized surface. Our simulation has successfully reproduced all of the morphologies observed on the monolayer film by this experiment. We have obtained the formation of both c(4 4) and c(4 3) structures of the molecules and have also obtained phase transitions of the former into the latter.

Molecular dynamics simulation of adsorption of Ag particles on a graphite substrate

We have performed for the first time a molecular dynamics simulation of the adsorption of gas-phase Ag particles on a graphite substrate to provide an insight into the results of a comprehensive STM-based experiment on this system. Both pair-wise and many-body interatomic potentials have been employed, and a Morse-type Ag–C potential was specifically constructed to describe the interactions at the interface. Our simulation has successfully reproduced a significant portion of the experimental findings. We have also observed the intercalation of silver in graphite.

Molecular dynamics simulation of fractures using an N-body potential

Molecular dynamics has been employed to model the fracture of a twodimensional triangular atomic lattice. The N-body Sutton-Chen potential developed for fcc metals and its extended version (Rafii-Tabar and Sutton) for fcc random binary alloys were used for the interatomic interactions. It is shown that at low temperatures cleavage fractures can occur in both an elemental metal and an alloy. At elevated temperatures the nucleation of dislocations is shown to cause a brittle-to-ductile transition. For the brittle crack propagation in the elemental metal, crack propagation speeds have been computed for different stress rates, and a crack instability found to exist as the speed reaches a critical value of about 32% of the Rayleigh wave speed. For the random alloy, we find that the dislocation movement can be affected by the distorted lattice.

Molecular dynamics simulation of fractures using an N-body potential

Molecular dynamics has been employed to model the fracture of a two dimensional triangular atomic lattice. The N-body Sutton-Chen potential developed for fcc metals and its extended version (Rafii-Tabar and Sutton) for fcc random binary alloys were used for the interatomic interactions. It is shown that at low temperatures cleavage fractures can occur in both an elemental metal and an alloy. At elevated temperatures the nucleation of dislocations is shown to cause a brittle-to-ductile transition. For the brittle crack propagation in the elemental metal, crack propagation speeds have been computed for different stress rates, and a crack instability found to exist as the speed reaches a critical value of about 32% of the Rayleigh wave speed. For the random alloy, we find that the dislocation movement can be affected by the distorted lattice.