Abstract: A multi-species Monte Carlo (MC) model, combined with an analytical surface model, has been developed in order to investigate the general plasma processes occurring during the sputter deposition of complex oxide films in a dual-magnetron sputter deposition system. The important plasma species, such as electrons, Ar+ ions, fast Ar atoms and sputtered metal atoms (i.e. Mg and Al atoms) are described with the so-called multi-species MC model, whereas the deposition of MgxAlyOz films is treated by an analytical surface model. Targetsubstrate distances for both magnetrons in the dual-magnetron setup are varied for the purpose of growing stoichiometric complex oxide thin films. The metal atoms are sputtered from pure metallic targets, whereas the oxygen flux is only directed toward the substrate and is high enough to obtain fully oxidized thin films but low enough to avoid target poisoning. The calculations correspond to typical experimental conditions applied to grow these complex oxide films. In this paper, some calculation results are shown, such as the densities of various plasma species, their fluxes toward the targets and substrate, the deposition rates, as well as the film stoichiometry. Moreover, some results of the combined model are compared with experimental observations. Note that this is the first complete model, which can be applied for large and complicated magnetron reactor geometries, such as dual-magnetron configurations. With this model, we are able to describe all important plasma species as well as the deposition process. It can also be used to predict film stoichiometries of complex oxide films on the substrate.

Abstract: Topological insulators (TIs) have attracted a lot of interest in recent years due to their topologically protected surface states, as well as exotic proximity-induced phenomena and device applications for TI heterostructures. Since the first experimental studies of TIs, angle-resolved photoemission spectra (ARPES) showed that the electronic structure of the topological surface states significantly changes as a function of time after cleavage. The origin and underlying mechanism of this ageing effect are still under debate, despite its importance. Here we investigate the evolution of the surface Dirac cone for Bi2Se3 films upon asymmetric potassium (K) adsorption, using density-functional theory and a tight-binding model. We find that the K adatoms induce short-ranged downward band bending within 2-3 nm from the surface, due to charge transfer from the adatoms to the TI. These findings are in contrast to earlier proposals in the literature, that propose a long-ranged downward band bending up to 15 nm from the surface. Furthermore, as the charge transfer increases, we find that a new Dirac cone, localized slightly deeper into the TI than the original one, appears at the K-adsorbed surface, originating from strong Rashba-split conduction-band states. Our results suggest possible reinterpretations of experiments because the new Dirac cone might have been observed in ARPES measurements instead of the original one that appears immediately after cleavage. Our findings are consistent with ARPES data and provide insight into building TI-heterostructure devices by varying the band-bending potential or film thickness.

Abstract: In metallized film capacitors, there exists an air gap of about 0.2 μm between the films, with a pressure ranging generally from 130 atm. Because of the created potential difference between the two films, a microdischarge is formed in this gap. In this paper, we use an implicit particle-in-cell Monte Carlo collision simulation method to study the discharge properties in this direct-current microdischarge with 0.2 μm gap in a range of different voltages and pressures. The discharge process is significantly different from a conventional high pressure discharge. Indeed, the high electric field due to the small gap sustains the discharge by field emission. At low applied voltage (~15 V), only the electrons are generated by field emission, while both electrons and ions are generated as a stable glow discharge at medium applied voltage (~50 V). At still higher applied voltage (~100 V), the number of electrons and ions rapidly multiplies, the electric field reverses, and the discharge changes from a glow to an arc regime.

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: The plasma behavior in a parallel-plate dielectric barrier discharge (DBD) is simulated by a two-dimensional particle-in-cell/Monte Carlo collision model, comparing for the first time an unpacked (empty) DBD with a packed bed DBD, i.e., a DBD filled with dielectric spheres in the gas gap. The calculations are performed in air, at atmospheric pressure. The discharge is powered by a pulse with a voltage amplitude of −20 kV. When comparing the packed and unpacked DBD reactors with the same dielectric barriers, it is clear that the presence of the dielectric packing leads to a transition in discharge behavior from a combination of negative streamers and unlimited surface streamers on the bottom dielectric surface to a combination of predominant positive streamers and limited surface discharges on the dielectric surfaces of the beads and plates. Furthermore, in the packed bed DBD, the electric field is locally enhanced inside the dielectric material, near the contact points between the beads and the plates, and therefore also in the plasma between the packing beads and between a bead and the dielectric wall, leading to values of $4\times {10}

Abstract: We report the equilibrium vortex phase diagram of a rotating two-band Fermi gas confined to a cylindrically symmetric parabolic trapping potential, using the recently developed finite-temperature effective field theory (Klimin et al 2016 Phys. Rev. A 94 023620). A non-monotonic resonant dependence of the free energy as a function of the temperature and the rotation frequency is revealed for a two-band superfluid. We particularly focus on novel features that appear as a result of interband interactions and can be experimentally resolved. The resonant dependence of the free energy is directly manifested in vortex phase diagrams, where areas of stability for both integer and fractional vortex states are found. The study embraces the BCS-BEC crossover regime and the entire temperature range below the critical temperature T-c. Significantly different behavior of vortex matter as a function of the interband coupling is revealed in the BCS and BEC regimes.

Abstract: The effect of the magnetic impurities on the charge transport in a magnetic topological ultra-thin film (MTF) is analytically investigated by applying the semi-classical Boltzmann framework through a modified relaxation-time approximation. Our results for the relaxation time of electrons as well as the charge conductivity of the system exhibit two distinct regimes of transport. We show that the generated charge current in a MTF is always dissipative and anisotropic when both conduction bands are involved in the charge transport. The magnetic impurities induce a chirality selection rule for the transitions of electrons which can be altered by changing the orientation of the magnetic impurities. On the other hand, when a single conduction band participates in the charge transport, the resistivity is isotropic and can be entirely suppressed due to the corresponding chirality selection rule. Our findings propose a method to determine an onset thickness at which a crossover from a three-dimensional magnetic topological insulator to a (two-dimensional) MTF occurs.

Abstract: Topological properties of a double-stranded DNA (dsDNA) proximity-coupled by an s-wave superconductor are investigated, in which the energy spectra and the differential conductance are calculated within the framework of tight-binding approximation. Our results indicate that this dsDNA-superconductor system hosts Majorana zero modes (MZMs) when the Zeeman field is perpendicular to the helix axis, whereas no MZM could be observed when the Zeeman field is parallel to the helix axis, in sharp contrast to previous studies on nanowires including single-stranded DNA. In particular, two topological phase transitions could take place in the dsDNA-superconductor system by changing the Zeeman field, one from a topological trivial phase to a topological nontrivial phase with one pair of MZMs in small Zeeman field regime, and the other from a phase with one pair of MZMs to a phase with two pairs of MZMs by further increasing the Zeeman field. In the presence of a gate field normal to the helix axis, the topological nontrivial phase with two pairs of MZMs can transform into the phase with one pair of MZMs. The topological phase with one pair of MZMs is more stable and robust against Anderson disorder.

Abstract: We use atomistic-based simulations to investigate the behavior of ferromagnetic skyrmions being continuously compressed against a rigid wall under dc and ac drives. The compressed skyrmions can be annihilated close to the wall and form a conformal crystal with both a size and a density gradient, making it distinct from conformal crystals observed previously for superconducting vortices and colloidal particles. For both dc and ac driving, the skyrmions can move transverse to the compression direction due to a combination of density and size gradients. Forces in the compression direction are converted by the Magnus force into transverse motion. Under ac driving, the amount of skyrmion annihilation is reduced and we find a skyrmion Magnus ratchet pump. We also observe shear banding in which skyrmions near the wall move up to twice as fast as skyrmions further from the wall. When we vary the magnitude of the applied drive, we find a critical current above which the skyrmions are completely annihilated during a time scale that depends on the magnitude of the drive. By varying the magnetic parameters, we find that the transverse motion is strongly dependent on the skyrmion size. Smaller skyrmions are more rigid, which interferes with the size gradient and destroys the transverse motion. We also confirm the role of the size gradient by comparing our atomistic simulations with a particle-based model, where we find that the transverse motion is only transient. Our results are relevant for applications where skyrmions encounter repulsive magnetic walls, domain walls, or interfaces.

Abstract: By means of replica exchange molecular dynamics simulations we investigate how the length of a silk-like, alternating diblock oligopeptide influences its secondary and quaternary structure. We carry out simulations for two protein sizes consisting of three and five blocks, and study the stability of a single protein, a dimer, a trimer and a tetramer. Initial configurations of our simulations are β-roll and β-sheet structures. We find that for the triblock the secondary and quaternary structures upto and including the tetramer are unstable: the proteins melt into random coil structures and the aggregates disassemble either completely or partially. We attribute this to the competition between conformational entropy of the proteins and the formation of hydrogen bonds and hydrophobic interactions between proteins. This is confirmed by our simulations on the pentablock proteins, where we find that, as the number of monomers in the aggregate increases, individual monomers form more hydrogen bonds whereas their solvent accessible surface area decreases. For the pentablock β-sheet protein, the monomer and the dimer melt as well, although for the β-roll protein only the monomer melts. For both trimers and tetramers remain stable. Apparently, for these the entropy loss of forming β-rolls and β-sheets is compensated for in the free-energy gain due to the hydrogen-bonding and hydrophobic interactions. We also find that the middle monomers in the trimers and tetramers are conformationally much more stable than the ones on the top and the bottom. Interestingly, the latter are more stable on the tetramer than on the trimer, suggesting that as the number of monomers increases protein-protein interactions cooperatively stabilize the assembly.
According to our simulations, the β-roll and β-sheet aggregates must be approximately equally
stable.

Abstract: CO2 dissociation and its subsequent conversion into added-value chemicals is a promising strategy for recycling CO2 gas into reusable products. One of the possible methods is direct plasma-induced dissociation. In this work we study the efficiency of CO2 dissociation in pulsed atmospheric-pressure gas discharge between two conducting electrodes by a 0-D numerical plasma model. The purpose of the study is to provide results on the optimal conditions of CO2 conversion with respect to the energy efficiency and dissociation by varying the maximum power density value and the pulse length. The power density is directly related to the discharge current and the reduced electric field in the discharge. We consider pulse lengths in the range from hundreds of nanosecond up to milliseconds. The results obtained show that the dissociation degree and energy efficiency are sensitive to the pulse length (duration) and the power density, so that a considerable improvement of the discharge performance can be achieved by fine-tuning these parameters. The study is intended to provide guidance in designing an experimental set-up and a power supply with the characteristics necessary to achieve optimal conversion.

Abstract: The magnetic properties of a superconducting disk change dramatically when its dimensions become mesoscopic. Unlike large disks, where the screening currents induced by an applied magnetic field are strong enough to force vortices to accumulate in a 'puddle' at the centre, in a mesoscopic disk the interaction between one of these vortices and the edge currents can be comparable to the intervortex repulsion, resulting in a destruction of the ordered triangular vortex lattice structure at the centre. Vortices instead form clusters which adopt polygonal and shell-like structures which exhibit magic number states similar to those of charged particles in a confining potential, and electrons in artificial atoms. We have fabricated mesoscopic high temperature superconducting Bi2Sr2CaCu2O8+δ disks and investigated their magnetic properties using magneto-optical imaging (MOI) and high resolution scanning Hall probe microscopy (SHPM). The temperature dependence of the vortex penetration field measured using MOI is in excellent agreement with models of the thermal excitation of pancake vortices over edge barriers. The growth of the central vortex puddle has been directly imaged using SHPM and magic vortex numbers showing higher stability have been correlated with abrupt jumps in the measured local magnetisation curves.

Abstract: Iron mineral containing sensory dendrites in the inner lining of the upper beak of homing pigeons [1] and various bird species [2] are the first candidate structures for an avian magnetic field receptor. A new concept of magnetoreception [3, 4] is based on detailed ultra-structural optical and electron microscopy analyses in combination with synchrotron radiation microscopic X-ray fluorescence analysis (micro-XRF) and microscopic X-ray absorption near edge structures (micro-XANES). Several behavioral experiments [5, 6] and first mathematical simulations [6] affirm our avian magnetoreceptor model. The iron minerals inside the dendrites are housed in three different subcellular compartments (bullets, platelets, vesicles), which could be clearly resolved and identified by electron microscopy on ultrathin sections [1, 3]. Micro-XRF and micro-XANES data obtained at HASYLAB beamline L added information about the elemental distribution and Fe speciation [3], but are averaged over the complete dendrite due to limited spatial resolution. Here we present recently performed micro-XRF maps with sub-micrometer resolution (ESRF ID21), which reveal for the first time subcellular structural information from almost bulk-like dendrite sample material. Due to the thickness of 30 μm the microarchitecture of the dendrites can be considered as undisturbed and artefacts introduced by sectioning might be widely reduced.

Abstract: We introduce a new method to measure structure factors from parallel beam electron diffraction (PBED) patterns. Bloch wave refinement routines were developed which can minimise the difference between simulated and experimental Bragg intensities via variation of structure factors, Debye parameters, specimen thickness and -orientation. Due to plane wave illumination, the PBED refinement is highly efficient not only in computational respect, but also concerning the experimental effort since energy filtering is shown to have no significant effect on the refinement results. The PBED method was applied to simulated GaAs diffraction patterns to derive systematic errors and rules for the identification of plausible refinement results. The evaluation of experimental GaAs PBED patterns yields a 200 X-ray structure factor of -6.33±0.14. Additionally, we obtained -6.35±0.13 from two-dimensional convergent beam electron diffraction refinements. Both results confirm density functional theory calculations published by Rosenauer et al. and indicate the inaccuracy of isolated atom scattering data, which is crucial e.g. for the composition evaluation by lattice fringe analysis.