Development of a machine learning interatomic potential for exploring pressure-dependent kinetics of phase transitions in germanium.

We introduce a data-driven potential aimed at the investigation of pressure-dependent phase transitions in bulk germanium, including the estimate of kinetic barriers. This is achieved by suitably building a database including several configurations along minimum energy paths, as computed using the solid-state nudged elastic band method. After training the model based on density functional theory (DFT)-computed energies, forces, and stresses, we provide validation and rigorously test the potential on unexplored paths. The resulting agreement with the DFT calculations is remarkable in a wide range of pressures. The potential is exploited in large-scale isothermal-isobaric simulations, displaying local nucleation in the R8 to ß-Sn pressure-induced phase transformation, taken here as an illustrative example.

Anisotropic extended misfit dislocations in overcritical SiGe films by local substrate patterning.

In this work we will show how local substrate patterning leads to a long range controlled propagation of dislocations in SiGe films grown on Si(001) substrates. Dislocations preferentially nucleate in the inhomogeneous strain field associated with the patterned pits, and then partialize on the local (111) surfaces which form the pit sidewalls. The resulting V-shaped defects extend for several microns and effectively block the propagation of randomly nucleated dislocations which propagate in the perpendicular direction. The surface morphology and strain fields associated with the extended defects have been characterized by atomic force microscopy and µRaman spectroscopy, and the defects have been directly observed with high resolution transmission electron microscopy.

Anomalous smoothing preceding island formation during growth on patterned substrates.

We show that on suitably pit-patterned Si(001), deposition of just a few atomic layers of Ge can trigger a far larger flow of Si into the pits. This surprising effect results in anomalous smoothing of the substrate preceding island formation in the pits. We show that the effect naturally arises in continuum simulations of growth, and we identify its physical origin in the composition dependence of the surface diffusivity. Our interpretation suggests that anomalous smoothing is likely to also occur in other technologically relevant heteroepitaxial systems.

Monolithic growth of ultrathin Ge nanowires on Si(001).

Self-assembled Ge wires with a height of only 3 unit cells and a length of up to 2 micrometers were grown on Si(001) by means of a catalyst-free method based on molecular beam epitaxy. The wires grow horizontally along either the [100] or the [010] direction. On atomically flat surfaces, they exhibit a highly uniform, triangular cross section. A simple thermodynamic model accounts for the existence of a preferential base width for longitudinal expansion, in quantitative agreement with the experimental findings. Despite the absence of intentional doping, the first transistor-type devices made from single wires show low-resistive electrical contacts and single-hole transport at sub-Kelvin temperatures. In view of their exceptionally small and self-defined cross section, these Ge wires hold promise for the realization of hole systems with exotic properties and provide a new development route for silicon-based nanoelectronics.

Formation of Ge nanoripples on vicinal Si (1110): from Stranski-Krastanow seeds to a perfectly faceted wetting layer.

Ge growth on high-indexed Si (1110) is shown to result in the spontaneous formation of a perfectly {105} faceted one-dimensional nanoripple structure. This evolution differs from the usual Stranski-Krastanow growth mode because from initial ripple seeds a faceted Ge layer is formed that extends down to the heterointerface. Ab initio calculations reveal that ripple formation is mainly driven by lowering of surface energy rather than by elastic strain relief and the onset is governed by the edge energy of the ripple facets. Wavelike ripple replication is identified as an effective kinetic pathway for the transformation process.

Assessing the composition of hetero-epitaxial islands via morphological analysis: an analytical model matching GeSi/Si(001) data.

A simple, but still three-dimensional, model describing the morphological stability of realistic SiGe islands on Si(001) is presented. The experimental evolution toward steeper islands with volume can be predicted for any average composition. Despite the use of elastic theory for stress relaxation under the assumption of a uniform SiGe distribution, and of a common mean surface energy of the faceted islands, the model seems to capture the essence of the energetic balance determining the morphological evolution with volume, with no fitting parameters. This is suggested by close comparison with molecular beam epitaxy data at three different temperatures (i.e. compositions). The good agreement also allows for interpreting the minor scattering of experimental data with temperature and provides a reliable tool for extracting the average Ge content from standard atomic force microscopy analysis.

Density functional study of the decomposition pathways of SiH3 and GeH3 at the Si(100) and Ge(100) surfaces.

By means of first-principles calculations we studied the decomposition pathways of SiH3 on Ge(100) and of GeH3 on Si(100), of interest for the growth of crystalline SiGe alloys and Si/Ge heterostructures by plasma-enhanced chemical vapor deposition. We also investigated H desorption via reaction of two adsorbed SiH2/GeH2 species (ß2 reaction) or via Eley-Rideal abstraction of surface H atoms from the impinging SiH3 and GeH3 species. The calculated activation energies for the different processes suggest that the rate-limiting step for the growth of Si/Ge systems is still the ß2 reaction of two SiH2 as in the growth of crystalline Si.

Temperature-dependent evolution of the wetting layer thickness during Ge deposition on Si(001).

The evolution of the wetting layer (WL) thickness during Ge deposition on Si(001) is analyzed with the help of a rate-equation approach. The combined role of thickness, island volume and shape-dependent chemical potentials is considered. Several experimental observations, such as WL thinning following the pyramid-to-dome transformation, are captured by the model, as directly demonstrated by a close comparison with photoluminescence measurements (PL) on samples grown at three different temperatures. The limitations of the model in describing late stages of growth are critically addressed.

Optimal Growth Conditions for Selective Ge Islands Positioning on Pit-Patterned Si(001).

We investigate ordered nucleation of Ge islands on pit-patterned Si(001) using an original hybrid Kinetic Monte Carlo model. The method allows us to explore long time-scale evolution while using large simulation cells. We analyze the possibility to achieve selective nucleation and island homogeneity as a function of the various parameters (flux, temperature, pit period) able to influence the growth process. The presence of an optimal condition where the atomic diffusivity is sufficient to guarantee nucleation only within pits, but not so large to induce significant Ostwald ripening, is clearly demonstrated.

Collective shape oscillations of SiGe islands on pit-patterned Si(001) substrates: a coherent-growth strategy enabled by self-regulated intermixing.

The shape of coherent SiGe islands epitaxially grown on pit-patterned Si(001) substrates displays very uniform collective oscillations with increasing Ge deposition, transforming cyclically between shallower "dome" and steeper "barn" morphologies. Correspondingly, the average Ge content in the alloyed islands also displays an oscillatory behavior, superimposed on a progressive Si enrichment with increasing size. We show that such a growth mode, remarkably different from the flat-substrate case, allows the islands to keep growing in size while avoiding plastic relaxation.

Enhanced relaxation and intermixing in Ge islands grown on pit-patterned Si(001) substrates.

We compare elastic relaxation and Si-Ge distribution in epitaxial islands grown on both pit-patterned and flat Si(001) substrates. Anomalous x-ray diffraction yields that nucleation in the pits provides a higher relaxation. Using an innovative, model-free fitting procedure based on self-consistent solutions of the elastic problem, we provide compositional and elastic-energy maps. Islands grown on flat substrates exhibit stronger composition gradients and do not show a monotonic decrease of elastic energy with height. Both phenomena are explained using both thermodynamic and kinetic arguments.

A fast computational method for determining equilibrium concentration profiles in intermixed nanoislands.

An efficient computational method for finding the equilibrium concentration profiles which minimize the free energy of intermixed heteroepitaxial islands of assigned shape and average composition is described. A combination of a Monte Carlo method and continuum elasticity theory solved by a finite element method is shown to provide the desired profiles allowing for a significant computational gain with respect to atomistic approaches. The role played by dimensionality (ridges versus islands) and by entropy is discussed.

Thermal-hydrogen promoted selective desorption and enhanced mobility of adsorbed radicals in silicon film growth.

Car-Parrinello simulations and static density-functional theory calculations reveal how hydrogen promotes growth of epitaxial, ordered Si films in plasma-enhanced chemical vapor deposition at low-temperature conditions where the exposed Si(001)-(2x1) surface is fully hydrogenated. Thermal H atoms, indeed, are shown to selectively etch adsorbed silyl back to the gas phase or to form adsorbed species which can be easily incorporated into the crystal down to T approximately 200 degrees C and start diffusing around T approximately 300 degrees C. Our results are well consistent with earlier experiments.

Critical shape and size for dislocation nucleation in Si1-xGex islands on Si(001).

The critical volume for the onset of plastic strain relaxation in SiGe islands on Si(001) is computed for different Ge contents and realistic shapes by using a three-dimensional model, with position-dependent dislocation energy. It turns out that the critical bases for dome- and barnlike islands are different for any composition. By comparison to extensive atomic force microscopy measurements of the footprints left on the Si substrates by islands grown at different temperatures (and compositions), we conclude that, in contrast with planar films, dislocation nucleation in 3D islands is fully thermodynamic.

Self-ordering of a Ge island single layer induced by Si overgrowth.

We provide a direct experimental proof and the related modeling of the role played by Si overgrowth in promoting the lateral ordering of Ge islands grown by chemical vapor deposition on Si(001). The deposition of silicon induces a shape transformation, from domes to truncated pyramids with a larger base, generating an array of closely spaced interacting islands. By modeling, we show that the resulting gradient in the chemical potential across the island should be the driving force for a selective flow of both Ge and Si atoms at the surface and, in turn, to a real motion of the dots, favoring the lateral order.

Impact-driven effects in thin-film growth: steering and transient mobility at the Ag(110) surface.

Low-energy atomic impacts on the Ag(110) surface are investigated by molecular dynamics simulations based on reliable many-body semiempirical potentials. Trajectory deflections (steering) caused by the atom-surface interaction are observed, together with impact-following, transient-mobility effects. Such processes are quantitatively analysed and their dependence on the initial kinetic energy and on the impinging direction is discussed. A clear influence of the surface anisotropy on both steering and transient mobility effects is revealed by our simulations for the simple isolated-atom case and in the submonolayer-growth regime. For the latter case, we illustrate how steering and transient mobility affect the film morphology at the nanoscale.

Atomic-scale pathway of the pyramid-to-dome transition during ge growth on Si(001).

By high resolution scanning tunneling microscopy, we investigate the morphological transition from pyramid to dome islands during the growth of Ge on Si(001). We show that pyramids grow from top to bottom and that, from a critical size on, incomplete facets are formed. We demonstrate that the bunching of the steps delimiting these facets evolves into the steeper dome facets. Based on first principles and Tersoff-potential calculations, we develop a microscopic model for the onset of the morphological transition, able to reproduce closely the experimentally observed behavior.

Structure and mobility of defects formed from collision cascades in MgO.

We study radiation-damage events in MgO on experimental time scales by augmenting molecular dynamics cascade simulations with temperature accelerated dynamics, molecular statics, and density functional theory. At 400 eV, vacancies and mono- and di-interstitials form, but often annihilate within milliseconds. At 2 and 5 keV, larger clusters can form and persist. While vacancies are immobile, interstitials aggregate into clusters (In) with surprising properties; e.g., an I4 is immobile, but an impinging I2 can create a metastable I6 that diffuses on the nanosecond time scale but is stable for years.

Closing the gap between experiment and theory: crystal growth by temperature accelerated dynamics.

We present atomistic simulations of crystal growth where realistic experimental deposition rates are reproduced, without needing any a priori information on the relevant diffusion processes. Using the temperature accelerated dynamics method, we simulate the deposition of 4 monolayers (ML) of Ag/Ag(100) at the rate of 0.075 ML/s, thus obtaining a boost of several orders of magnitude with respect to ordinary molecular dynamics. In the temperature range analyzed (0-70 K), steering and activated mechanisms compete in determining the surface roughness.

Cell cycle effects of gemcitabine.

Gemcitabine (2',2'-difluoro-2'-deoxycytidine, or dFdC) is a promising anticancer agent with demonstrated clinical activity in solid tumours currently undergoing clinical trials. Despite extensive studies on the biochemical mechanism of action, cell cycle perturbations induced by dFdC have not yet been thoroughly investigated, apart from the expected inhibition of DNA synthesis. The aim of our study was to clarify whether cell population kinetics is a vital factor in the cytotoxicity of dFdC in single or repeated treatments and in the dFdC-cisplatin combination. Ovarian cancer cells growing in vitro were treated with dFdC for 1 hr in a range of concentrations from 10 nM to 10 microM. Cell kinetics was investigated by DNA-bromodeoxyuridine flow cytometry, using different experimental protocols to measure either the time course of DNA-synthesis inhibition or the fate of cells in G(1), S or G(2)M at the time of dFdC treatment or 24 hr later. A modified sulforhodamine B test was used to assess the growth inhibition caused by dFdC given alone or with cisplatin. Although dFdC promptly inhibited DNA synthesis, cytotoxicity on proliferating cells was not specific for cells initially in the S phase. DNA synthesis was restored after a G(1) block of variable, dose-dependent length, but recycling cells were intercepted at the subsequent checkpoints, resulting in delays in the G(2)M and G(1) phases. The activity of repeated treatment with dFdC + dFdC or dFdC + cisplatin was highly dependent on the interval length between them. These results suggest that the kinetics of cell recycling from a first dFdC treatment strongly affects the outcome of a second treatment with either dFdC itself or cisplatin.