Molecular dynamics simulation of the role of dislocations in microcrack healing

The molecular dynamics method is used to simulate microcrack healing during heating or/and under compressive stress. A centre microcrack in Cu crystal would be sealed under compressive stress or by heating. The role of compressive stress and heating in crack healing was additive. During microcrack healing, dislocation generation and motion occurred. When there were pre-existing dislocations around the microcrack, the critical temperature or compressive stress necessary for microcrack healing would decrease, and, the higher the number of dislocations, the lower the critical temperature or compressive stress. The critical temperature necessary for microcrack healing depended upon the orientation of the crack plane. For example, the critical temperature for the crack along the (001) plane was the lowest, i.e. 770K.

Molecular dynamics simulations of DFZ

Dislocation emission from the crack tip in copper under mode II loading is simulated with molecular dynamics method. After 26 partial dislocations are emitted and then relaxed to reach the equilibrium under the constant displacement, the double pile-ups (including an inverse pile-up and a pile-up) are formed. i.e., the first dislocation is piled up before the obstruction, and the last dislocation is piled up ahead of the crack tip. These results conform to the TEM observations.

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.

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 theQMpart 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(1 0 0) 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 imidazole 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.

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.

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.

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.

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.

Splitting the fast and slow motions in molecular dynamics simulations based on the change of cold potential well bottom

Abstract. 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.

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.

Calculating the equation of state parameters and predicting the spinodal curve of isotactic polypropylene/poly(ethylene-co-octene) blend by molecular dynamics simulations combined with Sanchez-Lacombe lattice fluid theory

Molecular dynamics simulations are adopted to calculate the equation of state characteristic parameters P*, rho*, and T* of isotactic polypropylene (iPP) and poly(ethylene-co-octene) (PEOC), which can be further used in the Sanchez-Lacombe lattice fluid theory (SLLFT) to describe the respective physical properties. The calculated T* is a function of the temperature, which was also found in the literature. To solve this problem, we propose a Boltzmann fitting of the data and obtain T* at the high-temperature limit. With these characteristic parameters, the pressure-volume-temperature (PVT) data of iPP and PEOC are predicted by the SLLFT equation of state. To justify the correctness of our results, we also obtain the PVT data for iPP and PEOC by experiments. Good agreement is found between the two sets of data. By integrating the Euler-Lagrange equation and the Cahn-Hilliard relation, we predict the density profiles and the surface tensions for iPP and PEOC, respectively. Furthermore, a recursive method is proposed to obtain the characteristic interaction energy parameter between iPP and PEOC. This method, which does not require fitting to the experimental phase equilibrium data, suggests an alternative way to predict the phase diagrams that are not easily obtained in experiments.