SwissDock, a protein-small molecule docking web service based on EADock DSS.

Most life science processes involve, at the atomic scale, recognition between two molecules. The prediction of such interactions at the molecular level, by so-called docking software, is a non-trivial task. Docking programs have a wide range of applications ranging from protein engineering to drug design. This article presents SwissDock, a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine, combined with setup scripts for curating common problems and for preparing both the target protein and the ligand input files. An efficient Ajax/HTML interface was designed and implemented so that scientists can easily submit dockings and retrieve the predicted complexes. For automated docking tasks, a programmatic SOAP interface has been set up and template programs can be downloaded in Perl, Python and PHP. The web site also provides an access to a database of manually curated complexes, based on the Ligand Protein Database. A wiki and a forum are available to the community to promote interactions between users. The SwissDock web site is available online at http://www.swissdock.ch. We believe it constitutes a step toward generalizing the use of docking tools beyond the traditional molecular modeling community.

Research and development of III-V semiconductor surfaces for improved device interfaces

This thesis is devoted to understanding and improving technologically important III-V compound semiconductor (e.g. GaAs, InAs, and InSb) surfaces and interfaces for devices. The surfaces and interfaces of crystalline III-V materials have a crucial role in the operation of field-effect-transistors (FET) and highefficiency solar-cells, for instance. However, the surfaces are also the most defective part of the semiconductor material and it is essential to decrease the amount of harmful surface or interface defects for the next-generation III-V semiconductor device applications. Any improvement in the crystal ordering at the semiconductor surface reduces the amount of defects and increases the material homogeneity. This is becoming more and more important when the semiconductor device structures decrease to atomic-scale dimensions. Toward that target, the effects of different adsorbates (i.e., Sn, In, and O) on the III-V surface structures and properties have been investigated in this work. Furthermore, novel thin-films have been synthesized, which show beneficial properties regarding the passivation of the reactive III-V surfaces. The work comprises ultra-high-vacuum (UHV) environment for the controlled fabrication of atomically ordered III-V(100) surfaces. The surface sensitive experimental methods [low energy electron diffraction (LEED), scanning tunneling microscopy/spectroscopy (STM/STS), and synchrotron radiation photoelectron spectroscopy (SRPES)] and computational density-functionaltheory (DFT) calculations are utilized for elucidating the atomic and electronic properties of the crucial III-V surfaces. The basic research results are also transferred to actual device tests by fabricating metal-oxide-semiconductor capacitors and utilizing the interface sensitive measurement techniques [capacitance voltage (CV) profiling, and photoluminescence (PL) spectroscopy] for the characterization. This part of the thesis includes the instrumentation of home-made UHV-compatible atomic-layer-deposition (ALD) reactor for growing good quality insulator layers. The results of this thesis elucidate the atomic structures of technologically promising Sn- and In-stabilized III-V compound semiconductor surfaces. It is shown that the Sn adsorbate induces an atomic structure with (1×2)/(1×4) surface symmetry which is characterized by Sn-group III dimers. Furthermore, the stability of peculiar ζa structure is demonstrated for the GaAs(100)-In surface. The beneficial effects of these surface structures regarding the crucial III-V oxide interface are demonstrated. Namely, it is found that it is possible to passivate the III-V surface by a careful atomic-scale engineering of the III-V surface prior to the gate-dielectric deposition. The thin (1×2)/(1×4)-Sn layer is found to catalyze the removal of harmful amorphous III-V oxides. Also, novel crystalline III-V-oxide structures are synthesized and it is shown that these structures improve the device characteristics. The finding of crystalline oxide structures is exploited by solving the atomic structure of InSb(100)(1×2) and elucidating the electronic structure of oxidized InSb(100) for the first time.

Spectroscopic Studies of III-V Semiconductor Materials for Improved Devices

Defects in semiconductor crystals and at their interfaces usually impair the properties and the performance of devices. These defects include, for example, vacancies (i.e., missing crystal atoms), interstitials (i.e., extra atoms between the host crystal sites), and impurities such as oxygen atoms. The defects can decrease (i) the rate of the radiative electron transition from the conduction band to the valence band, (ii) the amount of charge carriers, and (iii) the mobility of the electrons in the conduction band. It is a common situation that the presence of crystal defects can be readily concluded as a decrease in the luminescence intensity or in the current flow for example. However, the identification of the harmful defects is not straightforward at all because it is challenging to characterize local defects with atomic resolution and identification. Such atomic-scale knowledge is however essential to find methods for reducing the amount of defects in energy-efficient semiconductor devices. The defects formed in thin interface layers of semiconductors are particularly difficult to characterize due to their buried and amorphous structures. Characterization methods which are sensitive to defects often require well-defined samples with long range order. Photoelectron spectroscopy (PES) combined with photoluminescence (PL) or electrical measurements is a potential approach to elucidate the structure and defects of the interface. It is essential to combine the PES with complementary measurements of similar samples to relate the PES changes to changes in the interface defect density. Understanding of the nature of defects related to III-V materials is relevant to developing for example field-effect transistors which include a III-V channel, but research is still far from complete. In this thesis, PES measurements are utilized in studies of various III-V compound semiconductor materials. PES is combined with photoluminescence measurements to study the SiO2/GaAs, SiNx/GaAs and BaO/GaAs interfaces. Also the formation of novel materials InN and photoluminescent GaAs nanoparticles are studied. Finally, the formation of Ga interstitial defects in GaAsN is elucidated by combining calculational results with PES measurements.

An investigation of the emotion assumptions of just-world theory /

The purpose ofthis study was to investigate the emotion assumptions underlying just-world theory. This theory proposes that people have a need to believe in a just world - a world where people get what they deserve. The first emotion assumption is that people, therefore, find injustices (Le., undeserved outcomes) threatening and thus emotionally arousing. Second, it is this arousal that is assumed to drive subsequent strategies for maintaining the belief in a just world. One strategy an individual may use to maintain this belief is derogating victims of injustice, or seeing their character in a more negative light. To test these two assumptions, 102 participants viewed a video depicting either a victim who presumably presented a high threat to people's belief in ajust world (she was innocent and, therefore, undeserving of her fate) or low threat (she was not innocent and, therefore, more deserving of her fate) while their heart rate and EDA was measured. Half of the participants were then given the opportunity to help the victim whereas the other half were not given this opportunity. The manipulations were followed by both explicit and indirect measures of evaluations ofthe victim as well as self-report measures of affect experienced while watching the victim video, and an individual difference scale assessing the strength of participants' just-world beliefs (as well as other measures that were part ofa larger study). Results indicated that participants did report feeling more threatened by the innocent victim. Although there was some evidence of victim derogation on the implicit measure of victim evaluation, there was no evidence that emotional arousal drove the negative evaluations of the victim who could not be helped. Some interaction effects with individual differences in just-world beliefs did occur, but these were not entirely consistent with the rationale behind the individual difference scales. These results provide only weak support for the first emotion assumption ofjust-world theory. Implications of these findings as well as limitations of the study and future directions concerning just-world theory are discussed.

Preferential exposure of certain crystallographic planes on the surface of spinel ferrites: a study by LEIS on polycrystalline spinel ferrite surfaces

Spinel ferrites are commercially important because of their excellent magnetic and catalytic properties. The study by Low Energy Ion Scattering (LEIS) can reveal atomic scale information on the surface. The surface of selected spinel ferrites was investigated by LEIS. It has been found that it is the octahedral sites which are preferentially exposed on the surface of the spinel ferrites. So the probable planes which are exposed on spinel ferrite surfaces are D(110) or B(111). This prediction using LEIS gives scope for tailor-making compounds with catalytically active ions on the surface for various catalytic reactions.

An inventory of heavy metals inputs to agricultural soils in England and Wales

An inventory of heavy metal inputs (Zn, Cu, Ni, Pb, Cd, Cr, As and Hg) to agricultural soils in England and Wales in 2000 is presented, accounting for major sources including atmospheric deposition, sewage sludge, livestock manures, inorganic fertilisers and lime, agrochemicals, irrigation water, industrial by-product 'wastes' and composts. Across the whole agricultural land area, atmospheric deposition was the main source of most metals, ranging from 25 to 85% of total inputs. Livestock manures and sewage sludge were also important sources, responsible for an estimated 37-40 and 8-17% of total Zn and Cu inputs, respectively. However, at the individual field scale sewage sludge, livestock manures and industrial wastes could be the major source of many metals where these materials are applied. This work will assist in developing strategies for reducing heavy metal inputs to agricultural land and effectively targeting policies to protect soils from long-term heavy metal accumulation. (C) 2003 Elsevier Science B.V. All rights reserved.

Trophic interactions in a changing world: modelling aboveground-belowground interactions

The rate and scale of human-driven changes can exert profound impacts on ecosystems, the species that make them up and the services they provide that sustain humanity. Given the speed at which these changes are occurring, one of society's major challenges is to coexist within ecosystems and to manage ecosystem services in a sustainable way. The effect of possible scenarios of global change on ecosystem services can be explored using ecosystem models. Such models should adequately represent ecosystem processes above and below the soil surface (aboveground and belowground) and the interactions between them. We explore possibilities to include such interactions into ecosystem models at scales that range from global to local. At the regional to global scale we suggest to expand the plant functional type concept (aggregating plants into groups according to their physiological attributes) to include functional types of aboveground-belowground interactions. At the scale of discrete plant communities, process-based and organism-oriented models could be combined into "hybrid approaches" that include organism-oriented mechanistic representation of a limited number of trophic interactions in an otherwise process - oriented approach. Under global change the density and activity of organisms determining the processes may change non-linearly and therefore explicit knowledge of the organisms and their responses should ideally be included. At the individual plant scale a common organism-based conceptual model of aboveground-belowground interactions has emerged. This conceptual model facilitates the formulation of research questions to guide experiments aiming to identify patterns that are common within, but differ between, ecosystem types and biomes. Such experiments inform modelling approaches at larger scales. Future ecosystem models should better include this evolving knowledge of common patterns of aboveground-belowground interactions. Improved ecosystem models are necessary toots to reduce the uncertainty in the information that assists us in the sustainable management of our environment in a changing world. (C) 2004 Elsevier GmbH. All rights reserved.

Overview of mathematical approaches used to model bacterial chemotaxis I: the single cell

Mathematical modeling of bacterial chemotaxis systems has been influential and insightful in helping to understand experimental observations. We provide here a comprehensive overview of the range of mathematical approaches used for modeling, within a single bacterium, chemotactic processes caused by changes to external gradients in its environment. Specific areas of the bacterial system which have been studied and modeled are discussed in detail, including the modeling of adaptation in response to attractant gradients, the intracellular phosphorylation cascade, membrane receptor clustering, and spatial modeling of intracellular protein signal transduction. The importance of producing robust models that address adaptation, gain, and sensitivity are also discussed. This review highlights that while mathematical modeling has aided in understanding bacterial chemotaxis on the individual cell scale and guiding experimental design, no single model succeeds in robustly describing all of the basic elements of the cell. We conclude by discussing the importance of this and the future of modeling in this area.

CO migration in native and mutant myoglobin: atomistic simulations for the understanding of protein function

Molecular dynamics simulations of the events after the photodissociation of CO in the myoglobin mutant L29F in which leucine is replaced by phenylalanine are reported. Using both classical and mixed quantum-classical molecular dynamics calculations, we observed the rapid motion of CO away from the distal heme pocket to other regions of the protein, in agreement with recent experimental results. The experimentally observed and calculated infrared spectra of CO after dissociation are also in good agreement. We compared the results with data from simulations of WT myoglobin. As the time resolution of experimental techniques is increased, theoretical methods and models can be validated at the atomic scale by direct comparison with experiment.

Copper deposition on TiO2 from copper(II)hexafluoroacetylacetonate

The authors have studied the adsorption of CuII(hfac)2 on the surface of a model oxide system, TiO2(110), and probed the molecular stability with respect to thermal cycling, using atomic scale imaging by scanning tunneling microscopy supported by x-ray photoemission spectroscopy. They find that at 473 K, the adsorbed metal-organic molecules begin to dissociate and release Cu atoms which aggregate and form Cu nanoparticles. These Cu nanoparticles ripen over time and the size (height) distribution develops into a bimodal distribution. Unlike other organometallic systems, which show a bimodal distribution due to enhanced nucleation or growth at surface step edges, the nanoparticles do not preferentially form at steps. The reduced mobility of the Cu islands may be related to the co-adsorbed ligands that remain in very small clusters on the surface.

Phase separation and surface segregation in ceria-zirconia solid solutions

Using a combination of density functional theory calculations and statistical mechanics, we show that a wide range of intermediate compositions of ceria – zirconia solid solutions are thermodynamically metastable with respect to phase separation into Ce-rich and Zr-rich oxides. We estimate that the maximum equilibrium concentration of Zr in CeO2 at 1373 K is ~2%, and therefore equilibrated samples with higher Zr content are expected to exhibit heterogeneity at the atomic scale. We also demonstrate that in the vicinity of the (111) surface, cation redistribution at high temperatures will occur with significant Ce enrichment of the surface, which we attribute to the more covalent character of Zr-O bonds compared to Ce-O bonds. Although the kinetic barriers for cation diffusion normally prevent the decomposition/segregation of ceria-zirconia solid solutions in typical catalytic applications, the separation behaviour described here can be expected to occur in modern three-way catalytic converters, where very high temperatures are reached.

Susceptibility of faba bean (Vicia faba L.) to heat stress during floral development and anthesis

Experiments were conducted over two years to quantify the response of faba bean (Vicia faba L.) to heat stress. Potted winter faba bean plants (cv. Wizard) were exposed to temperature treatments (18/10; 22/14; 26/18; 30/22; 34/26°C day/night) for five days during floral development and anthesis. Developmental stages of all flowers were scored prior to stress, plants were grown in exclusion from insect pollinators to prevent pollen movement between flowers, and yield was harvested at an individual pod scale, enabling effects of heat stress to be investigated at a high resolution. Susceptibility to stress differed between floral stages, flowers were most affected during initial green-bud stages. Yield and pollen germination of flowers present before stress showed threshold relationships to stress, with lethal temperatures (t50) ~28°C and ~32°C, while whole plant yield showed a linear negative relationship to stress with high plasticity in yield allocation, such that yield lost at lower nodes was partially compensated at higher nodal positions. Faba bean has many beneficial attributes for sustainable modern cropping systems but these results suggest that yield will be limited by projected climate change, necessitating the development of heat tolerant cultivars, or improved resilience by other mechanisms such as earlier flowering times.

Local order around of germanium atoms in Ga10Ge25S65 glass by EXAFS

Irreversible photoexpansion effect has been observed in amorphous Ga10Ge2S65 glasses when its surface was exposed to light with energy greater than the band gap, 3.52 eV. A volume change of about 5% was reached in bulk samples by controlling illumination time and the laser power density. To understand the atomic scale processes of the photoexpansion effect, extended X-ray absorption fine structure (EXAFS) spectroscopy has been used as a local probe of the germanium environment in the glass samples before and after illumination. Modifications are observed in the average coordination shell around Ge atoms in the illuminated sample compared to the non-illuminated one. For the non-illuminated sample, the Ge coordination shell is described by a distorted tetrahedron of sulfur atoms at around 2.20 Angstrom. After illumination, the EXAFS signal can be explained by introducing an additional contribution to this average environment. Based on an analysis of the EXAFS data we proposed a two-shell model of 0.5 oxygen atoms at 2.01 Angstrom and 3.6 sulfur atoms at a 2.20 Angstrom. The existence of Ge-O bonds in the glass after illumination was confirmed by infrared measurements. (C) 2002 Elsevier B.V. B.V. All rights reserved.

Elucidating the real-time Ag nanoparticle growth on alpha-Ag2WO4 during electron beam irradiation: experimental evidence and theoretical insights

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Elaboração de um material didático aplicado ao ensino de física para utilização do experimento virtual da dupla fenda

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)