Molecular dynamics studies of the melting of copper with vacancies and dislocations at high pressures

Molecular dynamics simulations of the melting process of bulk copper were performed using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) with the interatomic potentials being described by the embedded atom method. The aim of the study was to understand the effects of high pressures and defects on the melting temperature. The simulations were visualised using Visual Molecular Dynamics (VMD). The melting temperature of a perfect copper crystal, was found to be slightly higher than the experimentally observed value. The melting temperature as a function of pressure was determined and compared with experiment. Point and line defects, in the form of dislocations, were then introduced into crystal and the new melting temperature of the crystal determined. We find that the melting temperature decreases as the defect density is increased. Additionally, the slope of the melting temperature curve was found to decrease as the pressure was increased while the vacancy formation energy increases with pressure

Coarse grained molecular dynamic simulations of the interaction a carbon nanotube with a bilayer membrane

In coarse grained molecular dynamics (CGMD) simulations, small groups of atoms are treated as single particles (beads) and the forces between these particles are derived from the interatomic forces. The effect of this is to severely reduce the number of particles in a simulation, thereby allowing for the consideration of a larger number of atoms. It has also proven to be a valuable tool in probing time and length scales of systems beyond that used in all-atom molecular dynamics (AAMD) simulations. The down side of this is that the inter-particle interactions are less accurate. However, if these coarse grained particles are chosen carefully, such simulations can provide much useful information. There are different levels of how the coarse grains are constructed. For example, CG systems have been developed using tens or hundreds of atoms per CG bead in some studies of amino acids in biological science. By contrast, for other systems, a single CG bead is used to replace just two or three atoms. In this paper, the interaction of a carbon nanotube (CNT) with a lipid bilayer membrane is studied using both coarse grained and atomistic MD in an effort to understand the usefulness of the CGMD method for such simulations. Our preliminary studies of the interaction of a CNT with a lipid bilayer points indicates that such nano-tubes inserted into a membrane could be stable. This means that it could be used as an agent in the delivery of drugs. It would be good if these simulations could be repeated using AAMD simulations to confirm the validity of these results

Simulation Studies of Polymer Translocation through a Channel

Monte Carlo simulation studies of the translocation of homopolymers of length N driven through a channel have been performed. We find that the translocation time τ depends on temperature in a nontrivial way. For temperatures below some critical temperature θc, τ∼T-1.4, whereas for T>θc, τ increases with temperature. The low temperature results are in good agreement with experimental findings as is the dependence of τ on the driving field strength. The velocity of translocation displays the same characteristics as found in experiment but the N dependence of τ shows the linear relationship observed in experiment only for large values of N. A possible reason for this is suggested

Molecular dynamics simulations of polymer translocations

Molecular dynamics simulation studies of the translocation of charged homopolymers of length, N, driven by an electric potential gradient through a channel have been performed. We find that the translocation time, τ, displays an inverse power dependence on the temperature of the simulation τ ∼ (T − T0)−7/4, which is in very good agreement with experimental results. In addition, the dependence of τ on the driving field strength and the velocity of translocation on the polymer length N have also been obtained. The results suggest that such minimalist models are useful in modelling biological processes and that the molecular dynamics method is a suitable approach for carrying out these simulations

Metal-semiconductor fluctuations on reconstructed Sn--Si(111) surfaces

We present soft X-ray photoelectron spectroscopy results from the T4single bondSn/Si(111)−(3×3)R30° (√3 for short) and the Sn/Si(111)−(2√3× 2√3)R30° (2√3 for short). Sn 4d spectra recorded using 110 eV photons reveal two components for the 2√3 phase with the smaller one shifted by 0.38 eV towards low kinetic energy relative to the larger one. The √3 phase on the other hand could only be fitted with three components. The intensity of the largest component decreases with increasing Sn coverage and almost disappears at 1.1 monolayers (i.e. corresponding to the 2√3). From our analysis, we find that in the √3 phase, 10% of the surface is covered by 2√3 reconstruction and 90% by √3 reconstruction. These results suggest metal-semiconductor fluctuations on the √3 reconstruction as well as for mixed √3 and 2√3 phase

Reflectance anisotropy of reconstructed GaAs(001) surfaces

We have performed ab initio pseudopotential calculations of three alternative structures of the GaAs(001) surface to examine the dependence of the reflectance anisotropyspectrum (RAS) upon the precise surface configuration. Spectra were calculated based upon a hypothetical (2×1) surface, a (2×4)‐β surface using experimentally measured atom positions, and a (2×4)‐β surface using atom positions given by total‐energy minimization. It was found that the RA spectra depended significantly upon the atom positions, and in particular, that proper surface relaxation, including the Ga layer below the surface, was necessary in order to account for the low‐energy (2.5 eV) feature in the experimentally observed spectru

Reflectance anisotropy of reconstructed GaAs(001) surfaces

We have performed ab initio pseudopotential calculations of three alternative structures of the GaAs(001) surface to examine the dependence of the reflectance anisotropyspectrum (RAS) upon the precise surface configuration. Spectra were calculated based upon a hypothetical (2×1) surface, a (2×4)‐β surface using experimentally measured atom positions, and a (2×4)‐β surface using atom positions given by total‐energy minimization. It was found that the RA spectra depended significantly upon the atom positions, and in particular, that proper surface relaxation, including the Ga layer below the surface, was necessary in order to account for the low‐energy (2.5 eV) feature in the experimentally observed spectru