Abstract: We propose that low-strain Si/O superlattices can be constructed by connecting reconstructed Si{001} surfaces by Si-O-Si bridges. Ab initio calculations show that our models are energetically more favorable than all the models proposed so far. The part of our Si/O superlattice model is experimentally accessible just by oxidizing a Si( 001) substrate. To complete our Si/O superlattice model, we propose a three-step method. We also explore the potential of our Si/O superlattice models for new materials used in future Si electronics. We find that the location of the channel where the carriers travel can be controlled between the interfaces and the Si layers by the insertion of O atoms into the Si-Si dimers. By revealing the origins of the interface electron and hole states, we find that similar interface states should be easily achieved for Si slabs and Si substrates. Interestingly, the interface electrons and holes have small effective masses in the direction parallel to the channel and large effective masses in the direction normal to the channel, which makes the Si/O superlattices attractive to be used for channel materials. We also find that the valley splitting of Si is enhanced by the formation of the Si/O/Si interfaces, which is ideal for developing Si-based qubits. Our findings open new perspectives to design and control the electronic properties of Si.

Abstract: A chemical kinetics model is developed for a CO2/N2 microwave plasma, focusing especially on the vibrational levels of both CO2 and N2. The model is used to calculate the CO2 and N2 conversion as well as the energy efficiency of CO2 conversion for different power densities and for N2 fractions in the CO2/N2 gas mixture ranging from 0 to 90%. The calculation results are compared with measurements, and agreements within 23% and 33% are generally found for the CO2 conversion and N2 conversion, respectively. To explain the observed trends, the destruction and formation processes of both CO2 and N2 are analyzed, as well as the vibrational distribution functions of both CO2 and N2. The results indicate that N2 contributes in populating the lower asymmetric levels of CO2, leading to a higher absolute CO2 conversion upon increasing N2 fraction. However, the effective CO2 conversion drops because there is less CO2 initially present in the gas mixture; thus, the energy efficiency also drops with rising N2 fraction.

Abstract: In this paper, the negative ion behavior in a C4F8 inductively coupled plasma (ICP) is investigated using a hybrid model. The model predicts a non-monotonic variation of the total negative ion density with power at low pressure (1030 mTorr), and this trend agrees well with experiments that were carried out in many fluorocarbon (fc) ICP sources, like C2F6, CHF3, and C4F8. This behavior is explained by the availability of feedstock C4F8 gas as a source of the negative ions, as well as by the presence of low energy electrons due to vibrational excitation at low power. The maximum of the negative ion density shifts to low power values upon decreasing pressure, because of the more pronounced depletion of C4F8 molecules, and at high pressure (∼50 mTorr), the anion density continuously increases with power, which is similar to fc CCP sources. Furthermore, the negative ion composition is identified in this paper. Our work demonstrates that for a clear understanding of the negative ion behavior in radio frequency C4F8 plasma sources, one needs to take into account many factors, like the attachment characteristics, the anion composition, the spatial profiles, and the reactor configuration. Finally, a detailed comparison of our simulation results with experiments is conducted.

Abstract: The tumor suppressor protein p53 can lose its function upon DNA-contact mutations (R273C and R273H) in the core DNA-binding domain. The activity can be restored by second-site suppressor or rescue mutations (R273CT284R, R273HT284R, and R273HS240R). In this paper, we elucidate the structural and functional consequence of p53 proteins upon DNA-contact mutations and rescue mutations and the underlying mechanisms at the atomic level by means of molecular dynamics simulations. Furthermore, we also apply the docking approach to investigate the binding phenomena between the p53 protein and DNA upon DNA-contact mutations and rescue mutations. This study clearly illustrates that, due to DNA-contact mutants, the p53 structure loses its stability and becomes more rigid than the native protein. This structural loss might affect the p53-DNA interaction and leads to inhibition of the cancer suppression. Rescue mutants (R273CT284R, R273HT284R and R273HS240R) can restore the functional activity of the p53 protein upon DNA-contact mutations and show a good interaction between the p53 protein and a DNA molecule, which may lead to reactivate the cancer suppression function. Understanding the effects of p53 cancer and rescue mutations at the molecular level will be helpful for designing drugs for p53 associated cancer diseases. These drugs should be designed so that they can help to inhibit the abnormal function of the p53 protein and to reactivate the p53 function (cell apoptosis) to treat human cancer.

Abstract: Computer simulations are performed for an argon inductively coupled plasma (ICP) with a capacitive radio-frequency bias power, to investigate the bias effect on the discharge mode transition and on the plasma characteristics at various ICP currents, bias voltages, and bias frequencies. When the bias frequency is fixed at 13.56 MHz and the ICP current is low, e.g., 6A, the spatiotemporal averaged plasma density increases monotonically with bias voltage, and the bias effect is already prominent at a bias voltage of 90 V. The maximum of the ionization rate moves toward the bottom electrode, which indicates clearly the discharge mode transition in inductive/capacitive discharges. At higher ICP currents, i.e., 11 and 13 A, the plasma density decreases first and then increases with bias voltage, due to the competing mechanisms between the ion acceleration power dissipation and the capacitive power deposition. At 11 A, the bias effect is still important, but it is noticeable only at higher bias voltages. At 13 A, the ionization rate is characterized by a maximum at the reactor center near the dielectric window at all selected bias voltages, which indicates that the ICP power, instead of the bias power, plays a dominant role under this condition, and no mode transition is observed. Indeed, the ratio of the bias power to the total power is lower than 0.4 over a wide range of bias voltages, i.e., 0300V. Besides the effect of ICP current, also the effect of various bias frequencies is investigated. It is found that the modulation of the bias power to the spatiotemporal distributions of the ionization rate at 2MHz is strikingly different from the behavior observed at higher bias frequencies. Furthermore, the minimum of the plasma density appears at different bias voltages, i.e., 120V at 2MHz and 90V at 27.12 MHz.

Abstract: Magnetron sputtering is a widely used physical vapor deposition technique for deposition and formation of nanocatalyst thin films and clusters. Nevertheless, so far only few studies investigated this formation process at the fundamental level. We here review atomic scale molecular dynamics simulations aimed at elucidating the nanocatalyst growth process through magnetron sputtering. We first introduce the basic magnetron sputtering background and machinery of molecular dynamics simulations, and then describe the studies conducted in this field so far. We also present a perspective view on how the field may be developed further.

Abstract: Bacteria can be inactivated through various physical and chemical means, and these have always been the focus of extensive research. To further improve the methodology for these ends, two types of plasma systems were investigated: nano-second pulsed plasma (NPP) as liquid discharge plasma and an Argon gas-feeding dielectric barrier discharge (Ar-DBD) as a form of surface plasma. To understand the sterilizing action of these two different plasma sources, we performed experiments with Staphylococcus aureus (S. aureus) bacteria (wild type) and multidrug resistant bacteria (Penicillum-resistant, Methicillin-resistant and Gentamicin-resistant). We observed that both plasma sources can inactivate both the wild type and multidrug-resistant bacteria to a good extent. Moreover, we observed a change in the surface morphology, gene expression and β-lactamase activity. Furthermore, we used X-ray photoelectron spectroscopy to investigate the variation in functional groups (C-H/C-C, C-OH and C=O) of the peptidoglycan (PG) resulting from exposure to plasma species. To obtain atomic scale insight in the plasma-cell interactions and support our experimental observations, we have performed molecular dynamics simulations to study the effects of plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, on the dissociation/formation of above mentioned functional groups in PG.

Abstract: While it is well-known that the plasma-enhanced catalytic chemical vapor deposition (PECVD) of carbon nanotubes (CNTs) offers a number of advantages over thermal CVD, the influence of the various individual contributing factors is not well understood. Especially the role of ions is unclear, since ions in plasmas are generally associated with sputtering rather than with growing a material. Even so, various studies have demonstrated the beneficial effects of ion bombardment during the growth of CNTs. This review looks at the role of the ions in plasma-enhanced CNT growth as deduced from both experimental and simulation studies. Specific attention is paid to the beneficial effects of ion bombardment. Based on the available literature, it can be concluded that ions can be either beneficial or detrimental for carbon nanotube growth, depending on the exact conditions and the control over the growth process.

Abstract: The use of plasma technology for CO2 splitting is gaining increasing interest, but one of the major obstacles to date for industrial implementation is the considerable energy cost. We demonstrate that the introduction of a packing of dielectric zirconia (ZrO2) beads into a dielectric barrier discharge (DBD) plasma reactor can enhance the CO2 conversion and energy efficiency up to a factor 1.9 and 2.2, respectively, compared to that in a normal (unpacked) DBD reactor. We obtained a maximum conversion of 42 % and a maximum energy efficiency of 9.6 %. However, it is the ability of the packing to almost double both the conversion and the energy efficiency simultaneously at certain input parameters that makes it very promising. The improved conversion and energy efficiency can be explained by the higher values of the local electric field and electron energy near the contact points of the beads and the lower breakdown voltage, demonstrated by 2 D fluid modeling.

Abstract: A one-dimensional fluid model for a dielectric barrier discharge in CH4/O2 and CH4/CO2 gas mixtures is developed. The model describes the gas-phase chemistry for partial oxidation and for dry reforming of methane. The spatially averaged densities of the various plasma species are presented as a function of time and initial gas mixing ratio. Besides, the conversion of the inlet gases and the selectivities of the reaction products are calculated. Syngas, higher hydrocarbons, and higher oxygenates are typically found to be important reaction products. Furthermore, the main underlying reaction pathways for the formation of syngas, methanol, formaldehyde, and other higher oxygenates are determined.

Abstract: Cold atmospheric pressure plasmas have proven to provide an alternative treatment of cancer by targeting tumorous cells while leaving their healthy counterparts unharmed. However, the underlying mechanisms of the plasma–cell interactions are not yet fully understood. Reactive oxygen species, and in particular hydroxyl radicals (OH), are known to play a crucial role in plasma driven apoptosis of
malignant cells. In this paper we investigate the interaction of OH radicals, as well as H2O2 molecules and HO2 radicals, with DNA by means of reactive molecular dynamics simulations using the ReaxFF force field. Our results provide atomic-scale insight into the dynamics of oxidative stress on DNA caused by the OH radicals, while H2O2 molecules appear not reactive within the considered timescale. Among the observed processes are the formation of 8-OH-adduct radicals, forming the first stages towards the formation of 8-oxoGua and 8-oxoAde, H-abstraction reactions of the amines, and the partial opening of loose DNA ends in aqueous solution.

Abstract: A packed bed dielectric barrier discharge plasma reactor is computationally studied with a fluid model. Two different complementary axisymmetric 2D geometries are used to mimic the intrinsic 3D problem. It is found that a packing enhances the electric field strength and electron temperature at the contact points of the dielectric material due to polarization of the beads by the applied potential. As a result, these contact points prove to be of direct importance to initiate the plasma. At low applied potential, the discharge stays at the contact points, and shows the properties of a Townsend discharge. When a high enough potential is applied, the plasma will be able to travel through the gaps in between the beads from wall to wall, forming a kind of glow discharge. Therefore, the inclusion of a so-called ‘channel of voids’ is indispensable in any type of packed bed modelling.

Abstract: 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.

Abstract: We study the evolution of the structural and electronic properties of crystalline indium gallium zinc oxide (IGZO) upon amorphization by first-principles calculation. The bottom of the conduction band (BCB) is found to be constituted of a pseudo-band of molecular orbitals that resonate at the same energy on different atomic sites. They display a bonding character between the s orbitals of the metal sites and an anti-bonding character arising from the interaction between the oxygen and metal s orbitals. The energy level of the BCB shifts upon breaking of the crystal symmetry during the amorphization process, which may be attributed to the reduction of the coordination of the cationic centers. The top of the valence band (TVB) is constructed from anti-bonding oxygen p orbitals. In the amorphous state, they have random orientation, in contrast to the crystalline state. This results in the appearance of localized tail states in the forbidden gap above the TVB. Zinc is found to play a predominant role in the generation of these tail states, while gallium hinders their formation. Last, we study the dependence of the fundamental gap and effective mass of IGZO on mechanical strain. The variation of the gap under strain arises from the enhancement of the anti-bonding interaction in the BCB due to the modification of the length of the oxygen-metal bonds and/or to a variation of the cation coordination. This effect is less pronounced for the amorphous material compared to the crystalline material, making amorphous IGZO a semiconductor of choice for flexible electronics. Finally, the effective mass is found to increase upon strain, in contrast to regular materials. This counterintuitive variation is due to the reduction of the electrostatic shielding of the cationic centers by oxygen, leading to an increase of the overlaps between the metal orbitals at the origin of the delocalization of the BCB. For the range of strain typically met in flexible electronics, the induced variation in the effective mass is found to be negligible (less than 1%).

Abstract: Device performance of Si|SiOx core-shell based nanowires critically depends on the exact control over the oxide thickness. Low-temperature plasma oxidation is a highly promising alternative to thermal oxidation allowing for improved control over the oxidation process, in particular for ultrasmall Si nanowires. We here elucidate the room temperature plasma oxidation mechanisms of ultrasmall Si nanowires using hybrid molecular dynamics / force-bias Monte Carlo simulations. We demonstrate how the oxidation and concurrent water formation mechanisms are a function of the oxidizing plasma species and we demonstrate how the resulting core-shell oxide thickness can be controlled through these species. A new mechanism of water formation is discussed in detail. The results provide a detailed atomic level explanation of the oxidation process of highly curved Si surfaces. These results point out a route toward plasma-based formation of ultrathin core-shell Si|SiOx nanowires at room temperature.