Abstract: Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions.

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: A hybrid Monte Carlofluid model is applied to simulate the wafer-temperature-dependent etching of silicon with SF6 inductively coupled plasmas (ICP). The bulk plasma within the ICP reactor volume as well as the surface reactions occurring at the wafer are self-consistently described. The calculated etch rates are validated by experiments. The calculations and experiments are performed at two different wafer temperatures, i.e. 300 and 173 K, resembling conventional etching and cryoetching, respectively. In the case of cryoetching, a physisorbed SFx layer (x = 06) is formed on the wafer, which is negligible at room temperature, because of fast thermal desorption, However, even in the case of cryoetching, this layer can easily be disintegrated by low-energy ions, so it does not affect the etch rates. In the investigated pressure range of 19 Pa, the etch rate is always slightly higher at cryogenic conditions, both in the experiments and in the model, and this could be explained in the model due to a local cooling of the gas above the wafer, making the gas denser and increasing the flux of reactive neutrals, like F and F2, towards the wafer.

Abstract: A one-dimensional, implicit particle-in-cell Monte Carlo collision model is used to simulate the plasma kinetic properties at a steady state in a parallel-plate direct current argon glow microdischarge under various operating conditions, such as driving voltage (301000 V) and gap size (101000 µm) at atmospheric pressure. First, a comparison between rf and dc modes is shown for the same pressure, driving voltage and gap spacing. Furthermore, the effect of gap size scaling (in the range of 101000 µm) on the breakdown voltage, peak electron density and peak electron current density at the breakdown voltage is examined. The breakdown voltage is lower than 150 V in all gaps considered. The microdischarge is found to have a neutral bulk plasma region and a cathode sheath region with size varying with the applied voltage and the discharge gap. In our calculations, the electron and ion densities are of the order of 10181023 m−3, which is in the glow discharge limit, as the ionization degree is lower than 1% . The electron energy distribution function shows a two-energy group distribution at a gap of 10 µm and a three-energy group distribution at larger gaps such as 200 µm and 1000 µm, emphasizing the importance of the gap spacing in dc microdischarges.

Abstract: Plasma medicine is a rapidly evolving multidisciplinary field at the intersection of chemistry, biochemistry, physics, biology, medicine and bioengineering. It holds great potential in medical, health care, dentistry, surgical, food treatment and other applications. This multidisciplinary nature and variety of possible applications come along with an inherent and intrinsic complexity. Advancing plasma medicine to the stage that it becomes an everyday tool in its respective fields requires a fundamental understanding of the basic processes, which is lacking so far. However, some major advances have already been made through detailed experiments over the last 15 years. Complementary, computer simulations may provide insight that is difficultif not impossibleto obtain through experiments. In this review, we aim to provide an overview of the various simulations that have been carried out in the context of plasma medicine so far, or that are relevant for plasma medicine. We focus our attention mostly on atomistic simulations dealing with plasmabiomolecule interactions. We also provide a perspective and tentative list of opportunities for future modelling studies that are likely to further advance the field.

Abstract: High density polyethylene surfaces were exposed to the atmospheric post-discharge of a radiofrequency plasma torch supplied in helium and oxygen. Dynamic water contact angle measurements were performed to evaluate changes in surface hydrophilicity and angle resolved x-ray photoelectron spectroscopy was carried out to identify the functional groups responsible for wettability changes and to study their subsurface depth profiles, up to 9 nm in depth. The reactions leading to the formation of CO, C = O and OC = O groups were simulated by molecular dynamics. These simulations demonstrate that impinging oxygen atoms do not react immediately upon impact but rather remain at or close to the surface before eventually reacting. The simulations also explain the release of gaseous species in the ambient environment as well as the ejection of low molecular weight oxidized materials from the surface.

Abstract: Current-voltage analysis using different optical band pass filters has been performed on Cu2ZnSnSe4 and Cu2ZnSn(S, Se)(4) thin-film solar cells. When using red or orange light (i.e. wavelengths above 600 nm), a distortion appears in the I-V curve of the Cu2ZnSnSe4 solar cell, indicating an additional potential barrier to the current flow in the device for these conditions of illumination. This barrier is reduced when using a Cu2ZnSn(S, Se)(4) absorber. Numerical simulations demonstrate that the barrier visible under red light could be explained by a positive conduction band offset at the front interface coupled with compensating defects in the buffer layer.

Abstract: This paper reviews the conditions of in vivo mastication and describes a novel method of measuring in vitro wear. Methods: parameters of intraoral wear are reviewed in this analysis, including chewing force, tooth sliding distance, food abrasivity, saliva lubrication, and antagonist properties. Results: clinical measurement of mastication forces indicates a range of normal forces between 20 and 140 N for a single molar. During the sliding phase of mastication, horizontal movement has been measured between 0.9 and 2.86 mm. In vivo wear occurs by three-body abrasion when food particles are interposed between teeth and by two-body abrasion after food clearance. Analysis of food particles used in wear testing reveals that food particles are softer than enamel and large enough to separate enamel and restoration surfaces and act as a solid lubricant. In two-body wear, saliva acts as a boundary lubricant with a viscosity of 3 cP. Enamel is the most relevant antagonist material for wear testing. The shape of a palatal cusp has been estimated as a 0.6 mm diameter ball and the hardest region of a tooth is its enamel surface. pH values and temperatures have been shown to range between 2-7 and 5-55 degrees C in intraoral fluids, respectively. These intraoral parameters have been used to modify the Alabama wear testing method.

Abstract: A zero-dimensional, semi-empirical model is used to describe the plasma chemistry in an argon plasma jet flowing into humid air, mimicking the experimental conditions of a setup from the Eindhoven University of Technology. The model provides species density profiles as a function of the position in the plasma jet device and effluent. A reaction chemistry set for an argon/humid air mixture is developed, which considers 84 different species and 1880 reactions. Additionally, we present a reduced chemistry set, useful for higher level computational models. Calculated species density profiles along the plasma jet are shown and the chemical pathways are explained in detail. It is demonstrated that chemically reactive H, N, O and OH radicals are formed in large quantities after the nozzle exit and H2, O2(1Δg), O3, H2O2, NO2, N2O, HNO2 and HNO3 are predominantly formed as 'long living' species. The simulations show that water clustering of positive ions is very important under these conditions. The influence of vibrational excitation on the calculated electron temperature is studied. Finally, the effect of varying gas temperature, flow speed, power density and air humidity on the chemistry is investigated.

Abstract: A two-dimensional self-consistent fluid model combined with the full set of Maxwell equations is employed to investigate an Ar/CF4 capacitively coupled plasma, focusing on the phase-shift effect on the plasma characteristics at various frequencies and gas mixture ratios. When the discharge is sustained by a single frequency at 13.56 MHz in an Ar/CF4 mixture with a ratio of 0.9/0.1, no obvious difference is detected between the electron densities obtained in the so-called electrostatic model (with only the static electric fields taken into account) and the electromagnetic model (which includes the electromagnetic effects). However, as the frequency increases to 60 and 100 MHz, the difference becomes distinct, due to the significant influence of the electromagnetic effects. The phase-shift effect on the plasma radial uniformity has also been investigated in a dual frequency discharge, i.e. when the top driven source is switched on with a phase difference phiv ranging from 0 to π, in the frequency range 13.56100 MHz. At low concentration of CF4 (10%), Ar+ ions are the major positive ions in the entire range of frequencies. When the frequency is low, i.e. 13.56 MHz, the Ar+ density exhibits an off-axis peak at phiv = 0 due to the edge effect, and a better uniformity caused by the phase-shift modulation is obtained at phiv = π. At 60 MHz, the Ar+ density varies from edge-peaked at phiv = 0 to uniform (i.e. at phiv = 0.53π), and finally at phiv = π, a broad maximum is observed at the centre due to the standing-wave effect. As the frequency increases to 100 MHz, the best radial uniformity is reached at 0.25π, and the maximum moves again towards the radial wall in the reverse-phase case (phiv = π) due to the dominant skin effect. When the frequency is fixed at 100 MHz, the phase-shift control shows a different behaviour at a high concentration of CF4. For instance, the ${\rm CF}_3

Abstract: The size and lattice constant evolution of Pb nanoparticles (NPs) synthesized by high fluence implantation in crystalline Si have been studied with a variety of experimental techniques. Results obtained from small-angle x-ray scattering showed that the Pb NPs grow with increasing implantation fluence and annealing duration. The theory of NP growth kinetics can be applied to qualitatively explain the size evolution of the Pb NPs during the implantation and annealing processes. Moreover, the lattice constant of the Pb NPs was evaluated by conventional x-ray diffraction. The lattice dilatation was observed to decrease with increasing size of the Pb NPs. Such lattice constant tuning can be attributed to the pseudomorphism caused by the lattice mismatch between the Pb NPs and the Si matrix.

Abstract: A two-dimensional fluid model, including the full set of Maxwell equations, has been developed and applied to investigate the effect of a phase shift between two power sources on the radial uniformity of several plasma characteristics in a hydrogen capacitively coupled plasma. This study was carried out at various frequencies in the range 13.56200 MHz. When the frequency is low, at 13.56 MHz, the plasma density is characterized by an off-axis peak when both power sources are in-phase (phgr = 0), and the best radial uniformity is obtained at phgr = π. This trend can be explained because the radial nonuniformity caused by the electrostatic edge effect can be effectively suppressed by the phase-shift effect at a phase difference equal to π. When the frequency rises to 60 MHz, the plasma density profiles shift smoothly from edge-peaked over uniform to centre-peaked as the phase difference increases, due to the pronounced standing-wave effect, and the best radial uniformity is reached at phgr = 0.3π. At a frequency of 100 MHz, a similar behaviour is observed, except that the maximum of the plasma density moves again towards the radial edge at the reverse-phase case (phgr = π), because of the dominant skin effect. When the frequency is 200 MHz, the bulk plasma density increases significantly with increasing phase-shift values, and a better uniformity is obtained at phgr = 0.4π. This is because the density in the centre increases faster than at the radial edge as the phase difference rises, due to the increasing power deposition Pz in the centre and the decreasing power density Pr at the radial edge. As the phase difference increases to π, the maximum near the radial edge becomes obvious again. This is because the skin effect has a predominant influence on the plasma density under this condition, resulting in a high density at the radial edge. Moreover, the axial ion flux increases monotonically with phase difference, and exhibits similar profiles to the plasma density. The calculation results illustrate that the radial uniformity of the various plasma characteristics is strongly dependent on the applied frequency and the phase shift between both power sources, which is important to realize, for controlling the uniformity of the plasma etch and deposition processes.

Abstract: In this paper, an overview of the fabrication and properties of high-quality La0.67Sr0.33MnO3 (LSMO) thin films is given. A high-quality LSMO film combines a smooth surface morphology with a large magnetization and a small residual resistivity, while avoiding precipitates and surface segregation. In the literature, typically only a few of these issues are adressed. We therefore present a thorough characterization of our films, which were grown by pulsed laser deposition. The films were characterized with reflection high energy electron diffraction, atomic force microscopy, x-ray diffraction, magnetization and transport measurements, x-ray photoelectron spectroscopy and scanning transmission electron microscopy. The films have a saturation magnetization of 4.0 µB/Mn, a Curie temperature of 350 K and a residual resistivity of 60 µΩ cm. These results indicate that high-quality films, combining both large magnetization and small residual resistivity, were realized. A comparison between different samples presented in the literature shows that focussing on a single property is insufficient for the optimization of the deposition process. For high-quality films, all properties have to be adressed. For LSMO devices, the thin-film quality is crucial for the device performance. Therefore, this research is important for the application of LSMO in devices.

Abstract: As electron energy-loss spectroscopy (EELS) and x-ray absorption spectroscopy (XAS) probe the same transitions from coreshell states to unoccupied states above the Fermi energy, it should always be possible to apply the two techniques to the same physical phenomena, such as magnetic dichroism, and obtain the same information. Indeed, the similarity in the expression of the electron and x-ray cross-sections had been already exploited to prove the equivalence of x-ray magnetic linear dichroism and anisotropy in EELS, by noting that the polarization vector of a photon plays the same role as the momentum transfer in electron scattering. Recently, the same was proven true for x-ray magnetic circular dichroism (XMCD) by establishing a new TEM technique called EMCD (electron energy-loss magnetic chiral dichroism) (Schattschneider P et al 2006 Nature 441 4868), which makes use of special electron scattering conditions to force the absorption of a circularly polarized virtual photon. The intrinsic advantage of EMCD over XMCD is the high spatial resolution of electron microscopes, which are readily available. Among the particular obstacles in EMCD that do not exist for synchrotron radiation, is the notoriously low signal and the very particular scattering conditions necessary to observe a chiral dichroic signal. In spite of that, impressive progress has been made in recent years. The signal strength could be considerably increased, and some innovations such as using a convergent beam have been introduced. EMCD has evolved into several techniques, which make full use of the versatility of the TEM and energy filtering, spectroscopy or STEM conditions (Rubino S 2007 Magnetic circular dichroism in the transmission electron microscope PhD Thesis Vienna University of Technology, Vienna, Austria).

Abstract: 'Bohm diffusion' causes the electrons to diffuse perpendicularly to the magnetic field lines. However, its origin is not yet completely understood: low and high frequency electric field fluctuations are both named to cause Bohm diffusion. The importance of including this process in a Monte Carlo (MC) model is demonstrated by comparing calculated ionization rates with particle-in-cell/Monte Carlo collisions (PIC/MCC) simulations. A good agreement is found with a Bohm diffusion parameter of 0.05, which corresponds well to experiments. Since the PIC/MCC method accounts for fast electric field fluctuations, we conclude that Bohm diffusion is caused by fast electric field phenomena.