Molecular dynamics studies on the local disordering of σ3 and σ11 grain boundaries in aluminium bicrystal

Molecular dynamics (MD) simulations using Morse interaction potential are performed in studies of [110] symmetrical tilt grain boundary (GB) structures with mis-orientation angles 50.5 degrees(Sigma 11), 129.5 degrees(Sigma 11), 70.5 degrees(Sigma 3) and 109.5 degrees(Sigma 3) at various tempratures. The GB structures are found to start local disordering at about 0.5T(m)(T-m is the melting point of aluminium) for 50.5 degrees(Sigma 11), 0.32T(m) for 129.5 degrees(Sigma 11) and 0.38T(m) for 70.5 degrees(Sigma 3), respectively. These results agree with conclusions deduced from the anelastic measurements. But, for twin-boundary structure 109.5 degrees(Sigma 3), this disordering has not been found even when temperature increases up to 0.9T(m).

The structure and the dynamics of poly(vinyl methyl ether) PVME and in PVME concentrated water solution : a study by neutron scattering and fully atomistic molecular dynamics simulations

175 p. : il.

Molecular Dynamics Simulation of the Bio-Adhesion in Molecular Motors

Molecular dynamics (MD) simulation is employed to study the bio-adhesion in F1 ATP molecular motor. Histidine-peptide is widely used as linkage in micro systems because of its strong binding strength to metals. This paper focuses on the adhesion between a synthetic peptide containing 6xHis-tag (Gly-Gly-Lys-Gly-Gly-Lys-Gly-Gly-His-His-His-His-His-His) and metal substrate, which is used to define the position of the F1 ATP molecular motor on the metal substrate. It is shown that the binding strength between histidine and nickel substrate is the strongest, while that of copper is smaller and that of gold substrate is the smallest. From the result of simulation, we find that the stability of adhesion between histidine and the metal substate result of the ringed structure in histidine.

Molecular dynamics studies of brittle fracture of SiO2

By applying for molecular dynamics (MD) simulation and Griffith fracture criterion, the brittle behavior of crack extension of mode I type is investigated. The critical stress intensity factor (SIF)K-Ic(MD) of crack extension is calculated, and the evolution of atoms near crack tip is observed. It is found that K-Ic(MD) is in good agreement with the Griffith ftacture criterion K-Ic(Griffith).

Molecular dynamics simulation of adhesion forces in a dipalmitoylphosphatidylcholine membrane

Adhesion forces of Dipalmitoylphosphatidylcholine ( DPPC) membrane in the gel phase are investigated by molecular dynamics ( MD) simulation. In the simulations, individual DPPC molecules are pulled out of DPPC membranes with different rates and we get the maximum adhesion forces of DPPC membrane. We find that the maximum adhesion forces increase with pull rate, from about 400 to 700 pN when pull rates are from 0.001 to 0.03 nm/ps. We analyze the relationship between pull rate and adhesion forces of different origins using Brownian dynamics and notice that viscosity of solvent plays an important role in adhesion forces. Then we simulate the motion of a single DPPC molecule in solvent and it elucidates that the maximum drag force is almost linear with respect to the pull rate. We use Stokes' relation to describe the motion of a single DPPC molecule and deduce the effective length of a DPPC molecule. Conformational analyses indicate that the free energy variation of a DPPC molecule inside and outside of the DPPC membrane is an essential part of adhesion energy.

Effect Of Water On Brittle Fracture Of Sio2 By Molecular Dynamics Study

The influence of water on the brittle behavior of beta-cristobalite is studied by means of molecular dynamics (MD) simulation With the TTAM potential. Crack extension of mode 1 type is observed as the crack opening is filled LIP With water. The critical stress intensity factor K-lc(MD) is used to characterize the crack extension of MD simulation. The surface energy of SiO2 covered with layers of water is calculated at temperature of 300 K. Based oil the Griffith fracture criterion, the critical stress intensity factor K-lc(Griffith) is calculated, and it is in good agreement with that of MD simulation. (C) 2008 Elsevier B.V. All rights reserved.

Shape effects on the yield stress and deformation of silicon nanowires: A molecular dynamics simulation

The tension and compression of single-crystalline silicon nanowires (SiNWs) with different cross-sectional shapes are studied systematically using molecular dynamics simulation. The shape effects on the yield stresses are characterized. For the same surface to volume ratio, the circular cross-sectional SiNWs are stronger than the square cross-sectional ones under tensile loading, but reverse happens in compressive loading. With the atoms colored by least-squares atomic local shear strain, the deformation processes reveal that the failure modes of incipient yielding are dependent on the loading directions. The SiNWs under tensile loading slip in {111} surfaces, while the compressive loading leads the SiNWs to slip in the {110} surfaces. The present results are expected to contribute to the design of the silicon devices in nanosystems.

Molecular dynamics research of G249 and S249 substitutions of p53 protein.

,The molecular dynamics research of the core domain of p53 protein crystal structure shows that besides the stability in biochemistry this domain also shows a high stability in molecular mechanics. Based on that work, the residue R249 was substituted with amino acids Gly and Ser respectively, and molecular dynamics researches were performed separately. The results show that these substitutions cause a relax tendency between loop2 and 3 domains, leading to an alteration of the whole conformation of p53 core domain and ruining its stability. The results visually explains the mechanism of p53 changes in immunological and biochemical reactions, which are caused by 249 residue substitutions from 3-D structure variations.