Dislocations in the crystallites of nanocrystalline alpha-Fe - A molecular dynamics study

Molecular dynamics simulations are carried out in order to study the atomic structure of crystalline component, of nanocrystalline alpha-Fe when it is consolidated from small grains. A two-dimensional computational block is used to simulate the consolidation process. All the preset dislocations in the original grains glide out of them in the consolidation process, but new dislocations can generate when the grain size is large enough. It shows that dislocations exist in the consolidated material rather than in the original grains. Whether dislocations exist in the crystalline component of the resultant model nana-material depends upon grain size. The critical value of grain size for dislocation generation appears to be about 9 nm. This result agrees with experiments qualitatively.

A BIEM optimization method for fracture dynamics inverse problem

In the present paper, based on the theory of dynamic boundary integral equation, an optimization method for crack identification is set up in the Laplace frequency space, where the direct problem is solved by the author's new type boundary integral equations and a method for choosing the high sensitive frequency region is proposed. The results show that the method proposed is successful in using the information of boundary elastic wave and overcoming the ill-posed difficulties on solution, and helpful to improve the identification precision.

Molecular dynamics simulation of interaction of a dislocation array from a crack tip with grain boundaries

The interaction of a dislocation array emitted from a crack tip under mode II loading with asymmetric tilt grain boundaries (GBs) is analysed by the molecular dynamics method. The GBs can generally be described by planar and linear matching zones and unmatching zones. All GBs are observed to emit dislocations. The GBs migrated easily due to their planar and linear matching structure and asymmetrical type. The diffusion induced by stress concentration is found to promote the GB migration. The transmissions of dislocations are either along the matched plane or along another plane depending on tilt angle theta. Alternate processes of stress concentration and stress relaxation take place ahead of the pileup. The stress concentration can be released either by transmission of dislocations, by atom diffusion along GBs, or by migration of GBs by formation of twinning bands. The simulated results also unequivocally demonstrate two processes, i.e. asymmetrical GBs evolving into symmetrical ones and unmatching zones evolving into matching ones during the loading process.

A stochastic jump and deterministic dynamics model of impact failure evolution with rate effect

Motivated by the observation of the rate effect on material failure, a model of nonlinear and nonlocal evolution is developed, that includes both stochastic and dynamic effects. In phase space a transitional region prevails, which distinguishes the failure behavior from a globally stable one to that of catastrophic. Several probability functions are found to characterize the distinctive features of evolution due to different degrees of nucleation, growth and coalescence rates. The results may provide a better understanding of material failure.

Molecular dynamics studies on the dislocation gliding near a tilt boundary

The gliding behavior of edge dislocation near a grain boundary(QB) in copper under pure shear stresses is simulated by using molecular dynamics(MD) method. Many-body potential incorporating the embedded atom method (EAM) is used. The critical shear stresses for a single disocation to pass across GB surface are obtained at values of sigma(c)=23MPa similar to 68 MPa and 137 MPa similar to 274 MPa for Sigma=165 small angle tilt GB at 300 K and 20 K, respectively. The first result agrees with the experimental yield stress sigma(y)(=42 MPa) quite well. It suggests that there might be one of the reasons of initial plastic yielding caused by single dislocation gliding across GB. In addition, there might be possibility to obtain yield strength from microscopic analysis. Moreover, the experimental value of sigma(y) at low temperature is generally higher than that at room temperature. So, these results are in conformity qualitatively with experimental fact. On the other hand, the Sigma=25 GB is too strong an obstacle to the dislocation. In this case, a dislocation is able to pass across GB under relatively low stress only when it is driven by other dislocations. This is taken to mean that dislocation pile-up must be built up in front of this kind of GB, if this GB may take effect on the process of plastic deformation.

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).

Molecular dynamics simulation of crack-tip processes in copper

The crack tip processes in copper under mode II loading have been simulated by a molecular dynamics method. The nucleation, emission, dislocation free zone (DFZ) and pile-up of the dislocations are analyzed by using a suitable atom lattice configuration and Finnis & Sinclair potential. The simulated results show that the dislocation emitted always exhibits a dissociated fashion. The stress intensity factor for dislocation nucleation, DFZ and dissociated width of partial dislocations are strongly dependent on the loading rate. The stress distributions are in agreement with the elasticity solution before the dislocation emission, but are not in agreement after the emission. The dislocation can move at subsonic wave speed (less than the shear wave speed) or at transonic speed (greater than the shear wave speed but less than the longitudinal wave speed), but at the longitudinal wave speed the atom lattice breaks down.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by "GAMESS", and the rest atoms are treated as MM part calculated by "TINKER". The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(100) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the in-tidazole rings are attached to the substrate more tightly than other bases in this peptide.

Molecular Dynamics Simulation of Barnacle Cement

Barnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated. We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard-Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate.

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).

An algorithm for coarse particle sedimentation simulation by Stokesian dynamics

Coarse Particle sedimentation is studied by using an algorithm with no adjustable parameters based on stokesian dynamics. Only inter-particle interactions of hydrodynamic force and gravity are considered. The sedimentation of a simple cubic array of spheres is used to verify the computational results. The scaling and parallelism with OpenMP of the method are presented. Random suspension sedimentation is investigated with Mont Carlo simulation. The computational results are shown in good agreement with experimental fitting at the lower computational cost of O(N In N).

Size-dependent elastic properties of Ni nanofilms by molecular dynamics simulation

Size-dependent elastic properties of Ni nanofilms are investigated by molecular dynamics ( MD) simulations with embedded atom method (EAM). The surface effects are considered by calculating the surface relaxation, surface energy, and surface stress. The Young's modulus and yield stress are obtained as functions of thickness and crystallographic orientation. It is shown that the surface relaxation has important effects on the the elastic properties at nanoscale. When the surface relaxation is outward, the Young's modulus decreases with the film thickness decreasing, and vice versa. The results also show that the yield stresses of the films increase with the films becoming thinner. With the thickness of the nanofilms decreasing, the surface effects on the elastic properties become dominant.