The crossover from collective motion to periphery diffusion for 2D adatom-islands on Cu(111)

The diffusion of two dimensional adatom islands (up to 100 atoms) on Cu(111) has been studied, using the self-learning Kinetic Monte Carlo (SLKMC) method [1]. A variety of multiple- and single-atom processes are revealed in the simulations, and the size dependence of the diffusion coefficients and effective diffusion barriers are calculated for each. From the tabulated frequencies of events found in the simulation, we show a crossover from diffusion due to the collective motion of the island to a regime in which the island diffuses through periphery-dominated mass transport. This crossover occurs for island sizes between 13 and 19 atoms. For islands containing 19 to 100 atoms the scaling exponent is 1.5, which is in good agreement with previous work. The diffusion of islands containing 2 to 13 atoms can be explained primarily on the basis of a linear increase of the barrier for the collective motion with the size of the island

Atomistic studies of thin film growth

We present here a summary of some recent techniques used for atomistic studies of thin film growth and morphological evolution. Specific attention is given to a new kinetic Monte Carlo technique in which the usage of unique labeling schemes of the environment of the diffusing entity allows the development of a closed data base of 49 single atom diffusion processes for periphery motion. The activation energy barriers and diffusion paths are calculated using reliable manybody interatomic potentials. The application of the technique to the diffusion of 2-dimensional Cu clusters on Cu(111) shows interesting trends in the diffusion rate and in the frequencies of the microscopic mechanisms which are responsible for the motion of the clusters, as a function of cluster size and temperature. The results are compared with those obtained from yet another novel kinetic Monte Carlo technique in which an open data base of the energetics and diffusion paths of microscopic processes is continuously updated as needed. Comparisons are made with experimental data where available

Effect of misfit dislocation on surface diffusion

We apply molecular dynamics and molecular static methods to study the effect of misfit dislocations on adatom diffusion in close proximity to the dislocation core in heteroepitaxial systems, using many-body interaction potentials. Our system consists of several layers (three-seven) of Cu on top of a Ni(111) substrate. The misfit dislocations are created with the core located at the interface between the Cu film and the Ni substrate, using the repulsive biased potential method described earlier. We find that presence of the defect under the surface strongly affects the adatom trajectory, creating anisotropy in atomic diffusion, independent of the thickness of the Cu film. We also calculate the potential energy surface available to the adatom and compare the energy barriers for adatom diffusion in the proximity of the core region and on the defect-free surface

Off-Lattice Self-Learning Kinetic Monte Carlo: Application to 2D Cluster Diffusion on the fcc(111) Surface

We report developments of the kinetic Monte Carlo (KMC) method with improved accuracy and increased versatility for the description of atomic diffusivity on metal surfaces. The on-lattice constraint built into our recently proposed Self-Learning KMC (SLKMC) [1] is released, leaving atoms free to occupy Off-Lattice positions to accommodate several processes responsible for small-cluster diffusion, periphery atom motion and hetero-epitaxial growth. The technique combines the ideas embedded in the SLKMC method with a new pattern recognition scheme fitted to an Off-Lattice model in which relative atomic positions is used to characterize and store configurations. Application of a combination of the drag and the Repulsive Bias Potential (RBP) methods for saddle points searches, allows the treatment of concerted cluster, and multiple and single atom motions on equal footing. This tandem approach has helped reveal several new atomic mechanisms which contribute to cluster migration. We present applications of this Off-Lattice SLKMC to the diffusion of 2D islands of Cu (containing 2 to 30 atoms) on Cu and Ag(111), using interatomic potential from the Embedded Atom Method. For the hetero system Cu/Ag(111), this technique has uncovered mechanisms involving concerted motions such as shear, breathing and commensurate-incommensurate occupancies. Although the technique introduces complexities in storage and retrieval, it does not introduce noticeable extra computational cost

Minimum energy path for the nucleation of misfit dislocations in Ge/Si(001) heteroepitaxy

A possible mechanism for the formation of a 90{\deg} misfit dislocation at the Ge/Si(001) interface through homogeneous nucleation is identified from atomic scale calculations where a minimum energy path connecting the coherent epitaxial state and a final state with a 90{\deg} misfit dislocation is found using the nudged elastic band method. The initial path is generated using a repulsive bias activation procedure in a model system including 75000 atoms. The energy along the path exhibits two maxima in the energy. The first maximum occurs as a 60{\deg} dislocation nucleates. The intermediate minimum corresponds to an extended 60{\deg} dislocation. The subsequent energy maximum occurs as a second 60{\deg} dislocation nucleates in a complementary, mirror glide plane, simultaneously starting from the surface and from the first 60{\deg} dislocation. The activation energy of the nucleation of the second dislocation is 30% lower than that of the first one showing that the formation of the second 60{\deg} dislocation is aided by the presence of the first one. The simulations represent a step towards unraveling the formation mechanism of 90{\deg} dislocations, an important issue in the design of growth procedures for strain released Ge overlayers on Si(100) surfaces, and more generally illustrate an approach that can be used to gain insight into the mechanism of complex nucleation paths of extended defects in solids

Self-learning Kinetic Monte-Carlo method: application to Cu(111)

We present a novel way of performing kinetic Monte Carlo simulations which does not require an {\it a priori} list of diffusion processes and their associated energetics and reaction rates. Rather, at any time during the simulation, energetics for all possible (single or multi-atom) processes, within a specific interaction range, are either computed accurately using a saddle point search procedure, or retrieved from a database in which previously encountered processes are stored. This self-learning procedure enhances the speed of the simulations along with a substantial gain in reliability because of the inclusion of many-particle processes. Accompanying results from the application of the method to the case of two-dimensional Cu adatom-cluster diffusion and coalescence on Cu(111) with detailed statistics of involved atomistic processes and contributing diffusion coefficients attest to the suitability of the method for the purpose.Comment: 18 pages, 9 figure

Diffusion of small two-dimensional Cu islands on Cu(111) studied with a kinetic Monte Carlo method

Diffusion of small two-dimensional Cu islands (containing up to 10 atoms) on Cu(111) has been studied using the newly developed self-learning Kinetic Monte Carlo (SLKMC) method which is based on a database of diffusion processes and their energetics accumulated automatically during the implementation of the SLKMC code. Results obtained from simulations in which atoms hop from one fcc hollow site to another are compared with those obtained from a parallel set of simulations in which the database is supplemented by processes revealed in complementary molecular dynamics simulations at 500K. They include processes involving the hcp (stacking-fault) sites, which facilitate concerted motion of the islands (simultaneous motion of all atoms in the island). A significant difference in the scaling of the effective diffusion barriers with island size is observed in the two cases. In particular, the presence of concerted island motion leads to an almost linear increase in the effective diffusion barrier with size, while its absence accounts for strong size-dependent oscillations and anomalous behavior for trimers and heptamers. We also identify and discuss in detail the key microscopic processes responsible for the diffusion and examine the frequencies of their occurrence, as a function of island size and substrate temperature.Peer reviewe

Atomic Force Microscopy Analysis of DNA Extracted from the Vegetative Cells and the Viable, but Nonculturable, Cells of Two Mycoplasmas ( Acholeplasma laidlawii

This article reports on a study of some characteristics of DNA extracted from the vegetative and viable, but nonculturable (VBNC), cells of two mycoplasma species (Acholeplasma laidlawii PG8 and Mycoplasma hominis PG37) using atomic force microscopy (AFM). DNA images were obtained by operating the AFM microscope in the tapping mode. It was found that DNA from the VBNC forms of M. hominis PG37 has decreased sizes (height: 0.177 ± 0.026 nm vs. 0.391 ± 0.041 nm for the vegetative forms, and width: 1.92 ± 0.099 vs. 2.17 ± 0.156 nm for the vegetative forms) in comparison to DNA from the vegetative forms of the mycoplasma. In the case of DNA from the A. laidlawii PG8 VBNC forms, we detected a decrease in width (1.506 ± 0.076 nm vs. 1.898 ± 0.117 nm for the vegetative forms), but an increase in height (0.641 ± 0.068 nm vs. 0.255 ± 0.010 nm for the vegetative forms) of the molecule. Analyzing the obtained results, one can speculate on some similarities in the physical-chemical properties of DNA from M. hominis PG37 and M. gallisepticum S6. In turn, this implies some general mechanisms of adaptation to a severe environment