Universal tight binding model for chemical reactions in solution and at surfaces. II. Water

A revised water model intended for use in condensed phase simulations in the framework of the self consistent polarizable ion tight binding theory is constructed. The model is applied to water monomer, dimer, hexamers, ice, and liquid, where it demonstrates good agreement with theoretical results obtained by more accurate methods, such as DFT and CCSD(T), and with experiment. In particular, the temperature dependence of the self diffusion coefficient in liquid water predicted by the model, closely reproduces experimental curves in the temperature interval between 230 K and 350 K. In addition, and in contrast to standard DFT, the model properly orders the relative densities of liquid water and ice. A notable, but inevitable, shortcoming of the model is underestimation of the static dielectric constant by a factor of two. We demonstrate that the description of inter and intramolecular forces embodied in the tight binding approximation in quantum mechanics leads to a number of valuable insights which can be missing from ab initio quantum chemistry and classical force fields. These include a discussion of the origin of the enhanced molecular electric dipole moment in the condensed phases, and a detailed explanation for the increase of coordination number in liquid water as a function of temperature and compared with ice-leading to insights into the anomalous expansion on freezing. The theory holds out the prospect of an understanding of the currently unexplained density maximum of water near the freezing point. 

Universal tight binding model for chemical reactions in solution and at surfaces. III. Stoichiometric and reduced surfaces of titania and the adsorption of water

We demonstrate a model for stoichiometric and reduced titanium dioxide intended for use in molecular dynamics and other atomistic simulations and based in the polarizable ion tight binding theory. This extends the model introduced in two previous papers from molecular and liquid applications into the solid state, thus completing the task of providing a comprehensive and unified scheme for studying chemical reactions, particularly aimed at problems in catalysis and electrochemistry. As before, experimental results are given priority over theoretical ones in selecting targets for model fitting, for which we used crystal parameters and band gaps of titania bulk polymorphs, rutile and anatase. The model is applied to six low index titania surfaces, with and without oxygen vacancies and adsorbed water molecules, both in dissociated and non-dissociated states. Finally, we present the results of molecular dynamics simulation of an anatase cluster with a number of adsorbed water molecules and discuss the role of edge and corner atoms of the cluster. (C) 2014 AIP Publishing LLC.

Universal tight binding model for chemical reactions in solution and at surfaces. I. Organic molecules

As is now well established, a first order expansion of the Hohenberg-Kohn total energy density functional about a trial input density, namely, the Harris-Foulkes functional, can be used to rationalize a non self consistent tight binding model. If the expansion is taken to second order then the energy and electron density matrix need to be calculated self consistently and from this functional one can derive a charge self consistent tight binding theory. In this paper we have used this to describe a polarizable ion tight binding model which has the benefit of treating charge transfer in point multipoles. This admits a ready description of ionic polarizability and crystal field splitting. It is necessary in constructing such a model to find a number of parameters that mimic their more exact counterparts in the density functional theory. We describe in detail how this is done using a combination of intuition, exact analytical fitting, and a genetic optimization algorithm. Having obtained model parameters we show that this constitutes a transferable scheme that can be applied rather universally to small and medium sized organic molecules. We have shown that the model gives a good account of static structural and dynamic vibrational properties of a library of molecules, and finally we demonstrate the model's capability by showing a real time simulation of an enolization reaction in aqueous solution. In two subsequent papers, we show that the model is a great deal more general in that it will describe solvents and solid substrates and that therefore we have created a self consistent quantum mechanical scheme that may be applied to simulations in heterogeneous catalysis.

Photosensitisers - the progression from photodynamic therapy to anti-infective surfaces

Introduction: The application of light as a stimulus in pharmaceutical systems and the associated ability to provide precise spatiotemporal control over location, wavelength and intensity, allowing ease of external control independent of environmental conditionals, has led to its increased use. Of particular note is the use of light with photosensitisers.

Areas covered: Photosensitisers are widely used in photodynamic therapy to cause a cidal effect towards cells on irradiation due to the generation of reactive oxygen species. These cidal effects have also been used to treat infectious diseases. The effects and benefits of photosensitisers in the treatment of such conditions are still being developed and further realised, with the design of novel delivery strategies. This review provides an overview of the realisation of the pharmaceutically relevant uses of photosensitisers, both in the context of current research and in terms of current clinical application, and looks to the future direction of research.

Expert opinion: Substantial advances have been and are being made in the use of photosensitisers. Of particular note are their antimicrobial applications, due to absence of resistance that is so frequently associated with conventional treatments. Their potency of action and the ability to immobilise to polymeric supports is opening a wide range of possibilities with great potential for use in healthcare infection prevention strategies.

Determinants of root-associated fungal communities within Asteraceae in a semi-arid grassland

Summary

1.While plant–fungal interactions are important determinants of plant community assembly and ecosystem functioning, the processes underlying fungal community composition are poorly understood.
2.Here, we studied for the first time the root-associated eumycotan communities in a set of co-occurring plant species of varying relatedness in a species-rich, semi-arid grassland in Germany. The study system provides an opportunity to evaluate the importance of host plants and gradients in soil type and landscape structure as drivers of fungal community structure on a relevant spatial scale. We used 454 pyrosequencing of the fungal internal transcribed spacer region to analyse root-associated eumycotan communities of 25 species within the Asteraceae, which were sampled at different locations within a soil type gradient. We partitioned the variance accounted for by three predictors (host plant phylogeny, spatial distribution and soil type) to quantify their relative roles in determining fungal community composition and used null model analyses to determine whether community composition was influenced by biotic interactions among the fungi.
3.We found a high fungal diversity (156 816 sequences clustered in 1100 operational taxonomic units (OTUs)). Most OTUs belonged to the phylum Ascomycota (35.8%); the most abundant phylotype best-matched Phialophora mustea. Basidiomycota were represented by 18.3%, with Sebacina as most abundant genus. The three predictors explained 30% of variation in the community structure of root-associated fungi, with host plant phylogeny being the most important variance component. Null model analysis suggested that many fungal taxa co-occurred less often than expected by chance, which demonstrates spatial segregation and indicates that negative interactions may prevail in the assembly of fungal communities.
4.Synthesis. The results show that the phylogenetic relationship of host plants is the most important predictor of root-associated fungal community assembly, indicating that fungal colonization of host plants might be facilitated by certain plant traits that may be shared among closely related plant species.

Reconfigurable frequency selective surfaces with interleaved spiral slots

A new type of active frequency selective surface (AFSS) is proposed to realise a voltage controlled bi-state (transparent and reflecting) response at the specified frequencies. The bi-state switching is achieved by combining a passive array of interleaved spiral slots in conducting screens and active dipole arrays with integrated pin diodes at the opposite sides of a thin dielectric substrate. Simulation results show that such active surfaces have high isolation between the transparency and reflection states, while retaining the merits of substantially sub-wavelength response of the unit cell and large fractional bandwidths (FBWs) inherent to the original passive interwoven spiral arrays. Potential applications include reconfigurable and controllable electromagnetic architecture of buildings.

Active singly and dual polarised interwoven spiral frequency selective surfaces

Reconfigurable bi-state interwoven spiral FSSs are explored in this work. Their switching capability is realized by pin diodes that enable the change of the electromagnetic response between transparent and reflecting modes at the specified frequencies in both singly and dual polarised unit cell configurations. The proposed topologies are single layer FSS with their elements acting also as dc current carrying conductors supplying the bias signal for switching pin diodes between the on and off states, thus avoiding the need of external bias lines that can cause parasitic resonances and affect the response at oblique incidence. The presented simulation results show that such active FSSs have potentially good isolation between the transmission and reflection states, while retaining the substantially subwavelength response of the unit cell with large fractional bandwidths (FBWs) inherent to the original passive FSSs.

Root Cause Analysis by a Combined Sparse Classification and Monte Carlo Approach

Classification methods with embedded feature selection capability are very appealing for the analysis of complex processes since they allow the analysis of root causes even when the number of input variables is high. In this work, we investigate the performance of three techniques for classification within a Monte Carlo strategy with the aim of root cause analysis. We consider the naive bayes classifier and the logistic regression model with two different implementations for controlling model complexity, namely, a LASSO-like implementation with a L1 norm regularization and a fully Bayesian implementation of the logistic model, the so called relevance vector machine. Several challenges can arise when estimating such models mainly linked to the characteristics of the data: a large number of input variables, high correlation among subsets of variables, the situation where the number of variables is higher than the number of available data points and the case of unbalanced datasets. Using an ecological and a semiconductor manufacturing dataset, we show advantages and drawbacks of each method, highlighting the superior performance in term of classification accuracy for the relevance vector machine with respect to the other classifiers. Moreover, we show how the combination of the proposed techniques and the Monte Carlo approach can be used to get more robust insights into the problem under analysis when faced with challenging modelling conditions.

SURFACE ENHANCED RAMAN-SCATTERING FROM MILDLY ROUGHENED SURFACES - VARIATION OF SIGNAL WITH METAL GRAIN-SIZE

The intensity of surface enhanced Raman scattering from benzoic acid derivatives on mildly roughened, thermally evaporated Ag films shows a remarkably strong dependence on metal grain size. Large grained (slowly deposited) films give a superior response, by up to a factor of 10, to small grained (quickly deposited) films, with films of intermediate grain size yielding intermediate results. The optical field amplification underlying the enhancement mechanism is due to the excitation of surface plasmon polaritons (SPPs). Since surface roughness characteristics, as determined by STM, remain relatively constant as a function of deposition rate, it is argued that the contrast in Raman scattering is due to differences in elastic grain boundary scattering of SPPs (leading to different degrees of internal SPP damping), rather than differences in the interaction of SPPs with surface inhomogeneities.

Near-monochromatic high-harmonic radiation from relativistic laser-plasma interactions with blazed grating surfaces

Intense, femtosecond laser interactions with blazed grating targets are studied through experiment and particle-in-cell (PIC) simulations. The high harmonic spectrum produced by the laser is angularly dispersed by the grating leading to near-monochromatic spectra emitted at different angles, each dominated by a single harmonic and its integer-multiples. The spectrum emitted in the direction of the third-harmonic diffraction order is measured to contain distinct peaks at the 9th and 12th harmonics which agree well with two-dimensional PIC simulations using the same grating geometry. This confirms that surface smoothing effects do not dominate the far-field distributions for surface features with sizes on the order of the grating grooves whilst also showing this to be a viable method of producing near-monochromatic, short-pulsed extreme-ultraviolet radiation.

Harmonic Generation from Relativistic Plasma Surfaces in Ultrasteep Plasma Density Gradients

Harmonic generation in the limit of ultrasteep density gradients is studied experimentally. Observations reveal that, while the efficient generation of high order harmonics from relativistic surfaces requires steep plasma density scale lengths (L-p/lambda <1), the absolute efficiency of the harmonics declines for the steepest plasma density scale length L-p -> 0, thus demonstrating that near-steplike density gradients can be achieved for interactions using high-contrast high-intensity laser pulses. Absolute photon yields are obtained using a calibrated detection system. The efficiency of harmonics reflected from the laser driven plasma surface via the relativistic oscillating mirror was estimated to be in the range of 10(-4)-10(-6) of the laser pulse energy for photon energies ranging from 20-40 eV, with the best results being obtained for an intermediate density scale length.

Broadband XUV polarimetry of high harmonics from plasma surfaces using multiple Fresnel reflections

High-harmonic generation (HHG) by nonlinear interaction of intense laser pulses with gases or plasma surfaces is the most prominent way of creating highly coherent extreme ultraviolet (EUV/XUV) pulses. In the last years, several scientific applications have been found which require the measurement of the polarization of the harmonic radiation. We present a broadband XUV polarimeter based on multiple Fresnel reflections providing an extinction rate of 5-25 for 17-45 nm which is particularly suited for surface harmonics. The device has first been tested at a gas harmonic source providing linearly polarized XUV radiation. In a further experiment using HHG from plasma surfaces, the XUV polarimeter allowed a polarization measurement of high harmonic radiation from plasma surfaces for the first time which reveals a linear polarization state as predicted for our generation parameters. The generation and control of intense polarized XUV pulses-together with the availability of broadband polarizers in the XUV-open the way for a series of new experiments. For instance, dichroism in the XUV, elliptically polarized harmonics from aligned molecules, or the selection rules of relativistic surface harmonics can be studied with the broadband XUV polarimeter.

Differential affinity of FLIP and procaspase 8 for FADD's DED binding surfaces regulates DISC assembly

Death receptor activation triggers recruitment of FADD, which via its death effector domain (DED) engages the DEDs of procaspase 8 and its inhibitor FLIP to form death-inducing signalling complexes (DISCs). The DEDs of FADD, FLIP and procaspase 8 interact with one another using two binding surfaces defined by α1/α4 and α2/α5 helices, respectively. Here we report that FLIP has preferential affinity for the α1/α4 surface of FADD, whereas procaspase 8 has preferential affinity for FADD's α2/α5 surface. These relative affinities contribute to FLIP being recruited to the DISC at comparable levels to procaspase 8 despite lower cellular expression. Additional studies, including assessment of DISC stoichiometry and functional assays, suggest that following death receptor recruitment, the FADD DED preferentially engages FLIP using its α1/α4 surface and procaspase 8 using its α2/α5 surface; these tripartite intermediates then interact via the α1/α4 surface of FLIP DED1 and the α2/α5 surface of procaspase 8 DED2.