In recent years there has been growing interest in the use of low-temperature atmospheric pressure plasmas for biomedical applications. Currently, however, there is very little fundamental knowledge regarding the relevant interaction mechanisms of plasma species with living cells. In this paper, we investigate the interaction of important plasma species, such as O 3 , O 2 and O atoms, with bacterial peptidoglycan (or murein) by means of reactive molecular dynamics simulations. Specifically, we use the peptidoglycan structure to model the gram-positive bacterium Staphylococcus aureus murein. Peptidoglycan is the outer protective barrier in bacteria and can therefore interact directly with plasma species. Our results demonstrate that among the species mentioned above, O 3 molecules and especially O atoms can break important bonds of the peptidoglycan structure (i.e. C-O, C-N and C-C bonds), which subsequently leads to the destruction of the bacterial cell wall. This study is important for gaining a fundamental insight into the chemical damaging mechanisms of the bacterial peptidoglycan structure on the atomic scale.

Using reactive molecular dynamics simulations by means of the ReaxFF potential, we studied the growth mechanism of ultrathin silica (SiO 2 ) layers during hyperthermal oxidation at room temperature. Oxidation of Si(100){2 Â 1} surfaces by both atomic and molecular oxygen was investigated in the energy range 1À5 eV. The oxidation mechanism, which differs from thermal oxidation, is discussed. In the case of oxidation by molecular O 2 , silica is quickly formed and the thickness of the formed layers remains limited compared to oxidation by atomic oxygen. The Si/SiO 2 interfaces are analyzed in terms of partial charges and angle distributions. The obtained structures of the ultrathin SiO 2 films are amorphous, including some intrinsic defects. This study is important for the fabrication of silica-based devices in the micro-and nanoelectronics industry, and more specifically for the fabrication of metal oxide semiconductor devices.

Atomic scale simulations of the nucleation and growth of carbon nanotubes is essential for understanding their growth mechanism. In spite of over twenty years of simulation efforts in this area, limited progress has so far been made on addressing the role of the hydrocarbon growth precursor. Here we report on atomic scale simulations of cap nucleation of single-walled carbon nanotubes from hydrocarbon precursors. The presented mechanism emphasizes the important role of hydrogen in the nucleation process, and is discussed in relation to previously presented mechanisms. In particular, the role of hydrogen in the appearance of unstable carbon structures during in situ experimental observations as well as the initial stage of multi-walled carbon nanotube growth is discussed. The results are in good agreement with available experimental and quantum-mechanical results, and provide a basic understanding of the incubation and nucleation stages of hydrocarbon-based CNT growth at the atomic level.

Using reactive molecular dynamics simulations based on the ReaxFF potential, we studied the growth mechanism of ultrathin silica (SiO2) layers during hyperthermal oxidation as a function of temperature in the range 100–1300 K. Oxidation of Si(100){2 × 1} surfaces by both atomic and molecular oxygen was investigated for hyperthermal impact energies in the range of 1 to 5 eV. Two different growth mechanisms are found, corresponding to a low temperature oxidation and a high temperature one. The transition temperature between these mechanisms is estimated to be about 700 K. Also, the initial step of the Si oxidation process is analyzed in detail. Where possible, we validated our results with experimental and ab initio data, and good agreement was obtained. This study is important for the fabrication of silica-based devices in the micro- and nanoelectronics industry and, more specifically, for the fabrication of metal–oxide semiconductor devices.

Recently, core shell silicon nanowires (Si-NWs) have been envisaged to be used for field-effect transistors and photovoltaic applications. In spite of the constant downsizing of such devices, the formation of ultrasmall diameter core−shell Si-NWs currently remains entirely unexplored. We report here on the modeling of the formation of such core shell Si-NWs using a dry thermal oxidation of 2 nm diameter (100) Si nanowires at 300 and 1273 K, by means of reactive molecular dynamics simulations using the ReaxFF potential. Two different oxidation mechanisms are discussed, namely a self-limiting process that occurs at low temperature (300 K), resulting in a Si core | ultrathin SiO 2 silica shell nanowire, and a complete oxidation process that takes place at a higher temperature (1273 K), resulting in the formation of an ultrathin SiO 2 silica nanowire. The oxidation kinetics of both cases and the resulting structures are analyzed in detail. Our results demonstrate that precise control over the Si-core radius of such NWs and the SiO x (x ≤ 2.0) oxide shell is possible by controlling the growth temperature used during the oxidation process.