Abstract: Annular dark-field (ADF) scanning transmission electron microscopy (STEM) has become widely used in quantitative studies based on the opportunity to directly compare experimental and simulated images. This comparison merely requires the experimental data to be normalised and expressed in units of fractional beam-current. However, inhomogeneities in the response of electron detectors can complicate this normalisation. The quantification procedure becomes both experiment and instrument specific, requiring new simulations for the particular response of each instrument's detector, and for every camera-length used. This not only impedes the comparison between different instruments and research groups, but can also be computationally very time consuming. Furthermore, not all image simulation methods allow for the inclusion of an inhomogeneous detector response. In this work, we propose an alternative method for normalising experimental data in order to compare these with simulations that consider a homogeneous detector response. To achieve this, we determine the electron flux distribution reaching the detector by means of a camera-length series or a so-called atomic column cross-section averaged convergent beam electron diffraction (XSACBED) pattern. The result is then used to determine the relative weighting of the detector response. Here we show that the results obtained by this new electron flux weighted (EFW) method are comparable to the currently used method, while considerably simplifying the needed simulation libraries. The proposed method also allows one to obtain a metric that describes the quality of the detector response in comparison with the ideal detector response.

Abstract: The main features and the GPU implementation of the MULTEM program are presented and described. This new program performs accurate and fast multislice simulations by including higher order expansion of the multislice solution of the high energy Schrodinger equation, the correct subslicing of the three-dimensional potential and top-bottom surfaces. The program implements different kinds of simulation for CTEM, STEM, ED, PED, CBED, ADF-TEM and ABF-HC with proper treatment of the spatial and temporal incoherences. The multislice approach described here treats the specimen as amorphous material which allows a straightforward implementation of the frozen phonon approximation. The generalized transmission function for each slice is calculated when is needed and then discarded. This allows us to perform large simulations that can include millions of atoms and keep the computer memory requirements to a reasonable level. (C) 2015 Elsevier B.V. All rights reserved.

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: 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: Synchrotron X-ray diffraction and transmission electron microscopy (TEM) were applied to quantitatively characterize the average particle size and size distribution of free-standing TiB2 particles and TiB2 particles in an insitu grown Al–TiB2 composite. The detailed evaluations were carried out by X-ray line profile analysis using the restrictedmoment method and multiplewhole profile fitting procedure (MWP). Both numericalmethods indicate that the formed TiB2 particles are well crystallized and free of crystal defects. The average particle size determined from different Bragg reflections by the restricted moment method ranges between 25 and 55 nm, where the smallest particle size is determined using the 110 reflection suggesting the highest lateral-growth velocity of (110) facets. TheMWP method has shown that the in-situ grown TiB2 particles have a very low dislocation density (~1011 m−2) and their size distribution can be described by a log-normal distribution. Good agreement was found between the results obtained from the restricted moment and MWP methods, which was further confirmed by TEM.

Abstract: Because of the biocompatible properties of gelatine and the good affinity of aptamers for their targets, the combination of aptamer and gelatine type B is reported as promising for the development of biosensing devices. Here, an aptamer for chloramphenicol (CAP) is mixed with different types of gelatine and dropped on the surface of disposable gold screen printed electrodes. The signal of the CAP reduction is investigated using differential pulse voltammetry. The diagnostic performance of the sensor is described and a detection limit of 1.83 x 10(-10) M is found. The selectivity and the stability of the aptasensor are studied and compared to those of other CAP sensors described in literature.

Abstract: Since the 1960's it has been well known that the basic superconductive quantities can exhibit oscillations as functions of the thickness (diameter) in superconducting nanofilms (nanowires) due to the size quantization of the electronic spectrum. However, very little is known about the effects of quantum confinement on the microscopic properties of vortices. Based on a numerical solution to the Bogoliubov-de Gennes equations, we study the quantum-size oscillations of the vortex core resulting from the sequential interchange of the Kramer-Pesch and anti-Kramer-Pesch regimes with changing nanocylinder radius. The physics behind the anti-Kramer-Pesch anomaly is displayed by utilizing a semi-analytical Anderson approximate solution. We also demonstrate that the anti-Kramer-Pesch vortex core is robust against thermal smearing and results in a distinctive two-maxima structure in the local density of states, which can be used to identify the existence of the anti-Kramer-Pesch vortex.

Abstract: The application of nonthermal atmospheric pressure plasma is emerging as an alternative and efficient technique for the inactivation of bacterial biofilms. In this study, reactive molecular dynamics simulations were used to examine the reaction mechanisms of hydroxyl radicals, as key reactive oxygen plasma species in biological systems, with several organic molecules (i.e., alkane, alcohol, carboxylic acid, and amine), as prototypical components of biomolecules in the biofilm. Our results demonstrate that organic molecules containing hydroxyl and carboxyl groups may act as trapping agents for the OH radicals. Moreover, the impact of OH radicals on N-acetyl-glucosamine, as constituent component of staphylococcus epidermidis biofilms, was investigated. The results show how impacts of OH radicals lead to hydrogen abstraction and subsequent molecular damage. This study thus provides new data on the reaction mechanisms of plasma species, and particularly the OH radicals, with fundamental components of bacterial biofilms.

Abstract: The combined use of clean technologies can lead amongst other benefits to reduced environmental impacts, improved system efficiencies, better management of land scarcity, and diminishment of the effect of power variability of intermittent clean energy sources. Nonetheless, private investors facing budgetary constraints will only opt to invest in the combination of technologies if the latter is more profitable than the investment in a single technology. The aim of the paper is to provide a systematic model for decision makers that allows them to evaluate the profitability of any random combination of technologies under budgetary constraints, and to compare this profitability with that of the individual projects in isolation. This research goes beyond the state of art in the field of financial management and more specifically in the field of the rationing of capital amongst interdependent projects, by developing a method to calculate the payoff of interdependent projects undertaken together. Moreover, this paper develops a computational model from the investor's point of view, of which the purpose is threefold: First, the model allows to directly compare the economic payoff of individual complementary technologies with the economic payoff of their integrated combination, under budgetary constraints. Second, the model calculates economic synergies labeled benefits of combined technologies' (BOCT) when combining complementary technologies. Third, the model explains the rationalization behind the presence of BOCT. The model exemplifies an ex ante cost benefit analysis developed for business and non-governmental use. A four step methodology is proposed and illustrated by means of a case study of PV solar power and battery electric vehicles (BEVs) for a small Belgian enterprise. Results show that at low electricity prices (<Euro0.112/kWh) it is most profitable to invest in BEVs. When the price of electricity rises (>Euro0.134/kWh), investment in exclusively PV becomes most attractive. In all other cases, it is more profitable to invest in the combination of both technologies. Copyright (c) 2015 John Wiley & Sons, Ltd.

Abstract: A two-dimensional hybrid Monte Carlofluid model is applied to study HBr/He inductively coupled plasmas used for etching of Si. Complete sets of gas-phase and surface reactions are presented and the effects of the gas mixing ratio on the plasma characteristics and on the etch rates are discussed. A comparison with experimentally measured etch rates is made to validate the modelling results. The etch rate in the HBr plasma is found to be quite low under the investigated conditions compared to typical etch rates of Si with F- or Cl-containing gases. This allows for a higher control and fine-tuning of the etch rate when creating ultra-small features. Our calculations predict a higher electron temperature at higher He fraction, because the electrons do not lose their energy so efficiently in vibrational and rotational excitations. As a consequence, electron impact ionization and dissociation become more important, yielding higher densities of ions, electrons and H atoms. This results in more pronounced sputtering of the surface. Nevertheless, the overall etch rate decreases upon increasing He fraction, suggesting that chemical etching is still the determining factor for the overall etch rate.

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 lot of attention in the debate on the 2014-2020 programming period of the EU CAP and rural development policy revolves around the policy's contribution to enhancing resource use efficiency, decreasing environmental impact, restoring ecosystems and how to ensure more efficient and effective agrienvironmental measures (AEMs). Nevertheless, studies that simultaneously address multiple measures with multiple environmental objectives and targets are underrepresented in the scientific literature. The objectives of the present article are (i) to present an integrated tool-kit for AEM design resulting from the combination of farm modelling with the Sustainable Value Approach (SVA), and (ii) to evaluate the potential of the tool-kit to support AEM design through an application to estimate cost-effective organic agriculture payments for the dairy sector in Mugello, northern Tuscany. Sustainability assessment of organic and conventional farming systems (OFS and CFS, respectively.) under the 2007-2013 EU CAP support schemes and a no EU support scenario show better OFS performances regarding nitrogen leaching (-52% and -47% under the current CAP and the no EU support scenarios, respectively), soil erosion (-24% and -34%), potential pesticide risks (-100%), biodiversity (+13% and +30%). Income foregone for the production of environmental benefits from organic agriculture under a no EU support scenario is equal to 210 Euro/ha. Sustainable value calculations combined with modelling results indicate soil erosion and nitrogen leaching as the environmental processes to be addressed with specific policy measures to further increase the efficiency of organic farming. A new organic agriculture support scheme designed based on such indications further increases the OFS SV and almost closes the GAP with a benchmark farm of the area, featured with ideal performances in terms of environmental and economic indicators. The payment scheme we designed with the support of the integrated tool-kit shows to be more cost-effective and efficient of current AEMs. (C) 2015 Elsevier Ltd. All rights reserved.

Abstract: The study of shock metamorphism of olivine might help to constrain impact events in the history of meteorites. Although shock features in olivine are well known, so far, there are processes that are not yet completely understood. In shock veins, olivine clasts with a complex structure, with a ringwoodite rim and a dense network of lamellae of unidentified nature in the core, have been reported in the literature. A highly shocked (S5-6), L6 meteorite, Asuka 09584, which was recently collected in Antarctica by a Belgian-Japanese joint expedition, contains this type of shocked olivine clasts and has been, therefore, selected for detailed investigations of these features by transmission electron microscopy (TEM). Petrographic, geochemical, and crystallographic studies showed that the rim of these shocked clasts consists of an aggregate of nanocrystals of ringwoodite, with lower Mg/Fe ratio than the unshocked olivine. The clast's core consists of an aggregate of iso-oriented grains of olivine and wadsleyite, with higher Mg/Fe ratio than the unshocked olivine. This aggregate is crosscut by veinlets of nanocrystals of olivine, with extremely low Mg/Fe ratio. The formation of the ringwoodite rim is likely due to solid-state, diffusion-controlled, transformation from olivine under high-temperature conditions. The aggregate of iso-oriented olivine and wadsleyite crystals is interpreted to have formed also by a solid-state process, likely by coherent intracrystalline nucleation. Following the compression, shock release is believed to have caused opening of cracks and fractures in olivine and formation of olivine melt, which has lately crystallized under postshock equilibrium pressure conditions as olivine.

Abstract: In this work, we study the abatement of dilute trichloroethylene (TCE) in air with a negative direct current corona discharge. A numerical model is used to theoretically investigate the underlying plasma chemistry for the removal of TCE, and a reaction pathway for the abatement of TCE is proposed. The Cl atom, mainly produced by dissociation of COCl, is one of the controlling species in the TCE destruction chemistry and contributes to the production of chlorine containing by-products. The effect of humidity on the removal efficiency is studied and a good agreement is found between experiments and the model for both dry (5 % relative humidity (RH)) and humid air (50 % RH). An increase of the relative humidity from 5 % to 50 % has a negative effect on the removal efficiency, decreasing by ±15 % in humid air. The main loss reactions for TCE are with ClO·, O· and CHCl2. Finally, the by-products and energy cost of TCE abatement are discussed.

Abstract: Large-eddy simulations (LESS) are frequently used to model the planetary boundary layer, and the choice of the grid cell size, numerical schemes and sub grid model can significantly influence the simulation results. In the present paper the impact of grid spacing on LES of an idealized atmospheric convective boundary layer (CBL), for which the statistics and flow structures are well understood, is assessed for two mesoscale models: the Regional Atmospheric Modeling System (RAMS) and the Weather Research and Forecasting model (WRF). Nine simulations are performed on a fixed computational domain (6 x 6 x 2 km), combining three different horizontal (120, 60, 30 m) and vertical (20, 10, 5 m) spacings. The impact of the cell size on the CBL is investigated by comparing turbulence statistics and velocity spectra. The results demonstrate that both WRF and RAMS can perform LES of the CBL under consideration without requiring extremely high computational loads, but they also indicate the importance of adopting a computational grid that is adequate for the numerical schemes and subgrid models used. In both RAMS and WRF a horizontal cell size of 30 m is required to obtain a suitable turbulence reproduction throughout the CBL height. Considering the vertical grid spacing, WRF produced similar results for all the three tested values, while in RAMS it should be ensured that the aspect ratio of the cells does not exceed a value of 3. The two models were found to behave differently in function of the grid resolution, and they have different shortcomings in their prediction of CBL turbulence. WRF exhibits enhanced damping at the smallest scales, while RAMS is prone to the appearance of spurious fluctuations in the flow when the grid aspect ratio is too high. (C) 2015 Elsevier Ltd. All rights reserved.