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.

Controlling electronic structures by irradiation in single-walled SiC nanotubes: a first-principles molecular dynamics study

Using first-principles molecular dynamics simulations, the displacement threshold energy and defect configurations are determined in SiC nanotubes. The simulation results reveal that a rich variety of defect structures (vacancies, Stone-Wales defects and antisite defects) are formed with threshold energies from 11 to 64 eV. The threshold energy shows an anisotropic behavior and exhibits a dramatic decrease with decreasing tube diameter. The electronic structure can be altered by the defects formed by irradiation, which suggests that the electron irradiation may be a way to use defect engineering to tailor electronic properties of SiC nanotubes.

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 investigation on polarization retention of barium titanate nanofilm arising from ordered oxygen vacancy

Molecular-dynamics simulations have been carried out to investigate the electric hysteresis of barium titanate nanofilm containing oxygen vacancy ordering array parallel to the {101} crystal plane. The results obtained show a significant weakening of polarization retention from non-zero value to zero as the size of the array was reduced to a critical level, which was attributed to the formation and motion of head-to-head domain wall structure under external field loading process. By comparing with materials containing isolated oxygen vacancies, it was found that the zero retention was due to the oxygen vacancy ordering array rather than to the concentration of oxygen vacancy. Copyright (C) EPLA, 2010

Splitting the Fast and Slow Motions in Molecular Dynamics Simulations Based on the Change of Cold Potential Well Bottom

The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.