Abstract: A current method for the protection of cretaceous limestone present in various monuments consists of performing a passivating treatment with ammonium oxalate (AmOx). A calcium oxalate protective layer is formed on the surface and enhances the acid resistance of the stone. The in-depth formation of the calcium oxalate layer was investigated on cross sections by using combined micro X-ray fluorescence and micro X-ray powder diffraction (mu XRF/mu XRPD). XRPD showed the presence of both whewellite and weddellite in the calcite stone matrix. A correction was made for sample misalignment, which was visible in both the fluorescence and the diffraction line measurements. A semi-quantitative analysis was performed on the basis of Klug's equation for a two-phase mixture (the presence of weddellite was neglected) without the need for a known reference sample. By assuming two extreme compositions for a reference weight fraction (1 and 99wt%), it was possible to obtain whewellite concentration profiles, which can be used for comparing the effectiveness of different methods for the application of AmOx to the stone surface and the effect of treatment time and AmOx concentration used. It is shown that for the relative amounts of whewellite formed, the differences due to the assumed weight fractions are smaller than the errors due to sample heterogeneity and preferred orientation. Copyright (c) 2013 John Wiley & Sons, Ltd.

Abstract: In this work, the simultaneous iterative reconstruction technique (SIRT), the total variation minimization (TVM) reconstruction technique and the discrete algebraic reconstruction technique (DART) for electron tomography are compared and the advantages and disadvantages are discussed. Furthermore, we describe how the result of a three dimensional (3D) reconstruction based on TVM can provide objective information that is needed as the input for a DART reconstruction. This approach results in a tomographic reconstruction of which the segmentation is carried out in an objective manner.

Abstract: In the present paper, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high resolution high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. In order to count the number of atoms, it is assumed that the total scattered intensity scales with the number of atoms per atom column. These intensities are quantitatively determined using model-based statistical parameter estimation theory. The distribution describing the probability that intensity values are generated by atomic columns containing a specific number of atoms is inferred on the basis of the experimental scattered intensities. Finally, the number of atoms per atom column is quantified using this estimated probability distribution. The number of atom columns available in the observed STEM image, the number of components in the estimated probability distribution, the width of the components of the probability distribution, and the typical shape of a criterion to assess the number of components in the probability distribution directly affect the accuracy and precision with which the number of atoms in a particular atom column can be estimated. It is shown that single atom sensitivity is feasible taking the latter aspects into consideration.

Abstract: Principal component analysis (PCA) noise filtering is a popular method to remove noise from experimental electron energy loss (EELS) spectrum images. Here, we investigate the statistical behaviour of this method by applying it on a simulated data set with realistic noise levels. This phantom data set provides access to the true values contained in the data set as well as to many different realizations of the noise. Using least squares fitting and parameter estimation theory, we demonstrate that even though the precision on the estimated parameters can be better as the CramérRao lower bound, a significant bias is introduced which can alter the conclusions drawn from experimental data sets. The origin of this bias is in the incorrect retrieval of the principal loadings for noisy data. Using an expression for the bias and precision of the singular values from literature, we present an evaluation criterion for these singular values based on the noise level and the amount of information present in the data set. This criterion can help to judge when to avoid PCA noise filtering in practical situations. Further we show that constructing elemental maps of PCA noise filtered data using the background subtraction method, does not guarantee an increase in the signal to noise ratio due to correlation of the spectral data as a result of the filtering process.

Abstract: Respiratory syncytial virus (RSV) is the most frequent agent of acute lower respiratory diseases and creates a significant burden of disease in children under 5 years all over the world. RSV causes severe lower respiratory tract infections (LRTI) that require hospitalization, especially in children <= 2 years. The aim of this study was to determine the incidence of RSV in children <= 2 years of age hospitalized for LRTI. Children <= 2 years of age hospitalized for one year for LRTI in the three largest hospitals of Bursa City Center, Turkey were evaluated. These three hospitals comprise 67.5% of all child beds in central Bursa, so this study allows us to evaluate the total disease burden and hospitalization incidence in central Bursa. Nasal swabs of the children were evaluated with RSV RespiStrip (Coris Bioconcept Organization). A total of 671 children were hospitalized for LRTI, and 254 (37.9%) had at least one hospitalization that was positive for RSV. Of all patients with LRTI, 54.8% (368/671) were hospitalized for acute bronchiolitis, while 45.2% (303/671) were hospitalized for pneumonia. Of patients with acute bronchiolitis or pneumonia, 41% (151/368) and 34% (103/303) were RSV+, respectively. Of RSV+ hospitalized children, 59.5% (151/254) were diagnosed as acute bronchiolitis and 40.5% (103/254) as pneumonia. The annual incidences of hospitalization due to LRTI, acute bronchiolitis and pneumonia were 20.5/1000, 11.2/1000 and 9.3/1000, respectively, in children <= 2 years of age. The annual incidences of hospitalization due to RSV+ LRTI, acute bronchiolitis and pneumonia were found as 7.8/1000, 4.6/1000 and 3.2/1000, respectively, in children <= 2 years of age. More than one-third of all children hospitalized with LRTI (38.3%, n=257) were in the 0-3 months age group. Compared to other age groups, RSV positivity was highest in that age group for acute bronchiolitis (57%), pneumonia (39.5%) and also total children with LRTI (47.9%). RSV is a very important cause of lower respiratory infections in children <= 2 years of age and occurred most frequently in those 0-3 months of age in our study. Since there is no other study assessing the annual hospitalization incidence of RSV+ LRTIs in one city in Turkey, our study has unique importance for providing valuable statistical data about RSV+ LRTIs.

Abstract: In this contribution, we present an overview of the various techniques for combining atomistic molecular dynamics with Monte Carlo simulations, mainly in the context of condensed matter systems, as well as a brief summary of the main accelerated dynamics techniques. Special attention is given to the force bias Monte Carlo technique and its combination with molecular dynamics, in view of promising recent developments, including a definable timescale. Various examples of the application of combined molecular dynamics / Monte Carlo simulations are given, in order to demonstrate the enhanced simulation efficiency with respect to either pure molecular dynamics or Monte Carlo.

Abstract: The presence of persistent organic pollutants in Tanzanian environment is not well monitored despite the existing pollution potential from a number of sources. In this study, we investigated for the first time, the concentration profiles of different organohalogen compounds such as organochlorine pesticide residues (OCPs), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) in environmental samples (water and sediments) from the Pangani river basin (PRB). The PRB is one of the largest drainage basins in Tanzania, with its watershed exposed to multiple input sources of trace organic contaminants. Surface water and sediments were sampled from 12 representative stations of diverse characteristics and land-use practices, in three distinct seasons, and extracted by liquidliquid and Soxhlet extraction methods, respectively. Water samples were analyzed by GC-ECD for OCPs only, while sediment samples were analyzed for OCPs, PCBs and PBDEs by GC/MS. Seven compounds, dominated by HCH isomers (5104460 pg/L) and DDT analogs (1601460 pg/L),were detected in the water samples. These concentrations are far below the WHO guidelines for drinking water quality. A total of 42 compounds (8 OCPs, 28 PCB congeners and 6 PBDE congeners) were detected in the sediment samples. Their respective total concentration ranges were 24510,230; 35711,000 and 382175 pg/g dry weight. The spatial distribution patterns and Hierarchical Cluster Analysis reflected the impact of historical agricultural usage in sugarcane plantations (OCPs), and urbanization (PCBs and PBDEs). Risk assessment using sediment quality guidelines indicated no ecotoxicological risks. The results we have found provide preliminary data on levels of the organic contaminants in Pangani river basin as a new insight on the environmental quality of the area.

Abstract: The calculation of defect levels in semiconductors within a density functional theory approach suffers greatly from the band gap problem. We propose a band gap correction scheme that is based on the separation of energy differences in electron addition and relaxation energies. We show that it can predict defect levels with a reasonable accuracy, particularly in the case of defects with conduction band character, and yet is simple and computationally economical. We apply this method to ZnO doped with group III elements (Al, Ga, In). As expected from experiment, the results indicate that Zn substitutional doping is preferred over interstitial doping in Al, Ga, and In-doped ZnO, under both zinc-rich and oxygen-rich conditions. Further, all three dopants act as shallow donors, with the +1 charge state having the most advantageous formation energy. Also, doping effects on the electronic structure of ZnO are sufficiently mild so as to affect little the fundamental band gap and lowest conduction bands dispersion, which secures their n-type transparent conducting behavior. A comparison with the extrapolation method based on LDA+U calculations and with the HeydScuseriaErnzerhof hybrid functional (HSE) shows the reliability of the proposed scheme in predicting the thermodynamic transition levels in shallow donor systems.

Abstract: The influence of triaxial in-plane strain on the electronic properties of a hexagonal boron-nitride sheet is investigated using density functional theory. Different from graphene, the triaxial strain localizes the molecular orbitals of the boron-nitride flake in its center depending on the direction of the applied strain. The proposed technique for localizing the molecular orbitals that are close to the Fermi level in the center of boron nitride flakes can be used to actualize engineered nanosensors, for instance, to selectively detect gas molecules. We show that the central part of the strained flake adsorbs polar molecules more strongly as compared with an unstrained sheet.

Abstract: Continued miniaturization of metal-oxide-semiconductor field-effect transistors (MOSFETs) requires an ever-decreasing thickness of the gate oxide. The structure of ultrathin silicon oxide films, however, critically depends on the oxidation mechanism. Using reactive atomistic simulations, we here demonstrate how the oxidation mechanism in hyperthermal oxidation of such structures may be controlled by the oxidation temperature and the oxidant energy. Specifically, we study the interaction of hyperthermal oxygen with energies of 15 eV with thin SiOx (x ≤ 2) films with a native oxide thickness of about 10 Å. We analyze the oxygen penetration depth probability and compare with results of the hyperthermal oxidation of a bare Si(100){2 × 1} (c-Si) surface. The temperature-dependent oxidation mechanisms are discussed in detail. Our results demonstrate that, at low (i.e., room) temperature, the penetrated oxygen mostly resides in the oxide region rather than at the SiOx|c-Si interface. However, at higher temperatures, starting at around 700 K, oxygen atoms are found to penetrate and to diffuse through the oxide layer followed by reaction at the c-Si boundary. We demonstrate that hyperthermal oxidation resembles thermal oxidation, which can be described by the DealGrove model at high temperatures. Furthermore, defect creation mechanisms that occur during the oxidation process are also analyzed. This study is useful for the fabrication of ultrathin silicon oxide gate oxides for metal-oxide-semiconductor devices as it links parameters that can be straightforwardly controlled in experiment (oxygen temperature, velocity) with the silicon oxide structure.

Abstract: Nonthermal atmospheric pressure plasmas are gaining increasing attention for biomedical applications. However, very little fundamental information on the interaction mechanisms between the plasma species and biological cells is currently available. We investigate the interaction of important plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, with bacterial peptidoglycan by means of reactive molecular dynamics simulations, aiming for a better understanding of plasma disinfection. Our results show that OH, O, O3, and H2O2 can break structurally important bonds of peptidoglycan (i.e., CO, CN, or CC bonds), which consequently leads to the destruction of the bacterial cell wall. The mechanisms behind these breakups are, however, dependent on the impinging plasma species, and this also determines the effectiveness of the cell wall destruction.

Abstract: The effect of ultrasonication parameters, such as time and power applied, to exfoliate graphite in o-dichlorobenzene (o-DCB) and N-methyl-1,2-pyrrolidone (NMP) was examined. It was found that the concentration of graphene was higher in o-DCB, while its dispersibility was increased when sonication was applied for a longer period and/or at higher power. However, spectroscopic examination by X-ray photoelectron spectroscopy (XPS) revealed that ultrasonication causes defects and induces oxygen functional groups in the form of carboxylic acids and ethers/epoxides onto the graphene lattice. Additional proof for the latter arose from Raman, IR, and thermogravimetry studies. The carboxylic acids and ethers/epoxides onto exfoliated graphene were derived from air during ultrasonication and found independent of the solvent used for the exfoliation and the power and/or time ultrasonication applied. Quantitative evaluation of the amount of oxygenated species present on exfoliated graphene as performed by high-resolution XPS revealed that the relative oxygen percentage was higher when exfoliation was performed in NMP. Finally, the sonication time and/or power affected the oxygen content on exfoliated graphene, since extended ultrasonication resulted in a decrease in the oxygen content on exfoliated graphene, with a simultaneous increase of defected sp(3) carbon atoms.

Abstract: Seed-mediated growth is the most efficient methodology to control the size and shape of colloidal metal nanoparticles. In this process, the final nanocrystal shape is defined by the crystalline structure of the initial seed as well as by the presence of ligands and other additives that help to stabilize certain crystallographic facets. We analyze here the growth mechanism in aqueous solution of silver shells on presynthesized gold nanoparticles displaying various well-defined crystalline structures and morphologies. A thorough three-dimensional electron microscopy characterization of the morphology and internal structure of the resulting core-shell nanocrystals indicates that {100} facets are preferred for the outer silver shell, regardless of the morphology and crystallinity of the gold cores. These results are in agreement with theoretical analysis based on the relative surface energies of the exposed facets in the presence of halide ions.