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: The characteristics of spin waves in ferromagnetic waveguides with non-uniform magnetization have been investigated for situations where the shape anisotropy field of the waveguide is comparable to the external bias field. Spin-wave generation was realized by the magnetoelastic effect by applying normal and shear strain components, as well as by the Oersted field emitted by an inductive antenna. The magnetoelastic excitation field has a non-uniform profile over the width of the waveguide because of the non-uniform magnetization orientation, whereas the Oersted field remains uniform. Using micromagnetic simulations, we indicate that both types of excitation fields generate quantised width modes with both odd and even mode numbers as well as tilted phase fronts. We demonstrate that these effects originate from the average magnetization orientation with respect to the main axes of the magnetic waveguide. Furthermore, it is indicated that the excitation efficiency of the second-order mode generally surpasses that of the first-order mode due to their symmetry. The relative intensity of the excited modes can be controlled by the strain state as well as by tuning the dimensions of the excitation area. Finally, we demonstrate that the nonreciprocity of spin-wave radiation due to the chirality of an Oersted field generated by an inductive antenna is absent for magnetoelastic spin-wave excitation.

Abstract: Novel stable ultra-thin phases of europium oxide are investigated by means of state-of-the-art first principles calculations. Total energy calculations show that single layers of EuO2 and Eu(OH)(2) can be stabilized in an octahedrally coordinated (1T) atomic structure. However, phonon calculations reveal that although both structures are energetically feasible, only the 1T-EuO2 phase has dynamical stability. The phonon spectrum of 1T-EuO2 displays three Raman active modes; a non-degenerate out-of-plane A(1g) mode at 353.5 cm(-1) and two doubly-degenerate in-plane E-g modes at 304.3 cm(-1). Furthermore, magnetic ground state and electronic band dispersion calculations show that the single layer EuO2 is a metal with net magnetic moment of 5(mu B) per unitcell resulting in a half-metallic ferrimagnetic behavior. Moreover, robustness of the half-metallic ferrimagnetic characteristics of EuO2 is confirmed by the application of electric field and charging. Single layer 1T-EuO2, with its stable ultra-thin structure and half-metallic ferrimagnetic feature, is a promising novel material for nanoscale electronic and spintronic applications.

Abstract: We present the in situ synthesis of Au nanoparticles within the Zr based Metal Organic Framework, UiO-66. The resulting Au@UiO-66 materials were characterized by means of N-2 sorption, XRPD, UV-Vis, XRF, XPS and TEM analysis. The Au nanoparticles (NP) are homogeneously distributed along the UiO-66 host matrix when using NaBH4 or H-2 as reducing agents. The Au@UiO-66 materials were evaluated as catalysts in the oxidation of benzyl alcohol and benzyl amine employing O-2 as oxidant. The Au@MOF materials exhibit a very high selectivity towards the ketone (up to 100%). Regenerability and stability tests demonstrate that the Au@UiO-66 catalyst can be recycled with a negligible loss of Au species and no loss of crystallinity. In situ IR measurements of UiO-66 and Au@UiO-66-NaBH4, before and after treatment with alcohol, showed an increase in IR bands that can be assigned to a combination of physisorbed and chemisorbed alcohol species. This was confirmed by velocity power spectra obtained from the molecular dynamics simulations. Active peroxo and oxo species on Au could be visualized with Raman analysis.

Abstract: First-principles density functional theory (DFT) calculations were carried out to investigate the structural and electronic properties of beryllium (Be) doped and Be and boron (B) co-doped graphene systems. We observed that not only the concentration of impurity atoms is important to tune the band-gap to some desired level, but also the specific substitution sites play a key role. In our system, which consists of 32 atoms, a maximum of 4Be and, in the co-doped state, 2Be and 3B atom substitutions are investigated. Both dopants are electron deficient relative to C atoms and cause the Fermi level to shift downward (p-type doping). A maximum band gap of 1.44 eV can be achieved on incorporation of 4Be atoms. The introduction of Be is more sensitive in terms of geometry and stability than B. However, in opening the energy gap, Be is more effective than B and N (nitrogen). Our results offer the possibility to modify the band-gap of graphene sufficiently for utilization in diverse electronic device applications.

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: The wide range of liquid-phase reactions required for the catalytic conversion of biomass compounds into new bioplatform molecules defines a new set of challenges for the development of active, selective, and stable catalysts. The potential of bifunctional Ru/H-USY catalysts for conversions in hot liquid water (HLW) is assessed in terms of physicochemical stability and long-term catalytic performance of acid sites and noble metal functionality, as probed by hydrolytic hydrogenation of cellulose. It is shown that zeolite desilication is the main zeolite degradation mechanism in HLW. USY zeolite stability depends on two main parameters, viz., framework and extra-framework aluminum content. The former protects the zeolite lattice by counteracting hydrolysis of framework bonds, and the latter, when located at the external crystal surface, prevents solubilization of the zeolite framework which is the result of its low water-solubility. Hence, the hot liquid water stability of commercial H-USY zeolites, in contrast to their steam stability, increased with decreasing Si/AI ratio. As a result, mildly steamed USY zeolites containing a high amount of both Al species exhibit the highest resistance to HLW. During an initial period of transformations, Al-rich zeolites form additional protective extra-framework Al species at the outer surface, self-stabilizing the framework. A critical bulk Si/AI ratio of 3 was determined whereby USY zeolites with a lower Si/AI ratio will self-stabilize over time. Besides, due to the initial transformation period, the accessibility of the catalytic active sites is extensively enhanced resulting in a material that is more stable and drastically more accessible to large substrates than the original zeolite. When these findings are applied in the hydrolytic hydrogenation of cellulose, unprecedented nearly quantitative hexitol yields were obtained with a stable catalytic system.

Abstract: A marker function designed to indicate in which regions of a generic flow field the results from linear eddy-viscosity turbulence models are plausibly inaccurate is introduced. The marker is defined to identify regions that deviate from parallel shear flow. For two different flow fields it is shown that these regions largely coincide with regions where the prediction of the Reynolds stress divergence is inaccurate. The marker therefore offers a guideline for interpreting results obtained from Reynolds-averaged Navier-Stokes simulations and provides a basis for the further development of turbulence model-form uncertainty quantification methods. (C) 2014 AIP Publishing LLC.

Abstract: Using Brownian dynamics simulations, we investigate the dynamics of colloids confined in two-dimensional narrow channels driven by a nonuniform force Fdr(y). We considered linear-gradient, parabolic, and deltalike driving-force profiles. This driving force induces melting of the colloidal solid (i.e., shear-induced melting), and the colloidal motion experiences a transition from elastic to plastic regime with increasing Fdr. For intermediate Fdr (i.e., in the transition region) the response of the system, i.e., the distribution of the velocities of the colloidal chains õi(y), in general does not coincide with the profile of the driving force Fdr(y), and depends on the magnitude of Fdr, the width of the channel, and the density of colloids. For example, we show that the onset of plasticity is first observed near the boundaries while the motion in the central region is elastic. This is explained by: (i) (in)commensurability between the chains due to the larger density of colloids near the boundaries, and (ii) the gradient in Fdr. Our study provides a deeper understanding of the dynamics of colloids in channels and could be accessed in experiments on colloids (or in dusty plasma) with, e.g., asymmetric channels or in the presence of a gradient potential field.

Abstract: Single-file diffusion (SFD) of an infinite one-dimensional chain of interacting particles has a long-time mean-square displacement ∝t1/2, independent of the type of interparticle repulsive interaction. This behavior is also observed in finite-size chains, although only for certain intervals of time t depending on the chain length L, followed by the ∝t for t→∞, as we demonstrate for a closed circular chain of diffusing interacting particles. Here, we show that spatial correlation of noise slows down SFD and can result, depending on the amount of correlated noise, in either subdiffusive behavior ∝tα, where 0<α<1/2, or even in a total suppression of diffusion (in the limit N→∞). Spatial correlation can explain the subdiffusive behavior in recent SFD experiments in circular channels.

Abstract: Because of strong flux confinement in mesoscopic superconductors, a giant vortex may appear in the ground state of the system in an applied magnetic field. This multiquanta vortex can then split into individual vortices (and vice versa) as a function of, e.g., applied current, magnetic field, or temperature. Here we show that such transitions can be identified by calorimetry, as the formation or splitting of a giant vortex results in a clear jump in measured heat capacity versus external drive. We attribute this phenomenon to an abrupt change in the density of states of the quasiparticle excitations in the vortex core(s), and further link it to a sharp change of the magnetic susceptibility at the transitionproving that the formation of a giant vortex can also be detected by magnetometry.

Abstract: Thermal fluctuations of the order parameter in an ultrathin triangular-shaped superconducting structure are studied near Tc, in zero applied field. We find that the order parameter is prone to much larger fluctuations in the corners of the structure as compared to its interior. This geometry-induced localization of thermal fluctuations is attributed to the fact that condensate confinement in the corners is characterized by a lower effective dimensionality, which favors stronger fluctuations.