In situ study of nanostructure and morphological development during the crystal-mesophase transition of poly(di-n-hexylsilane) and poly(di-n-butylsilane) by X-ray and hot-stage AFM

Nanostructure and morphology and their development of poly(di-n-hexylsilane) (PDHS) and poly(di-n-butylsilane) (PDBS) during the crystal-mesophase transition are investigated using small angle X-ray scattering (SAXS), wide angle X-ray diffraction and hot-stage atomic force microscopy. At room temperature, PDHS consists of stacks of lamellae separated by mesophase layers, which can be well accounted using an ideal two-phase model. During the crystal-mesophase transition, obvious morphological changes are observed due to the marked changes in main chain conformation and intermolecular distances between crystalline phase and mesophase. In contrast to PDHS, the lamellae in PDBS barely show anisotropy in dimensions at room temperature. The nonperiodic structure and rather small electronic density fluctuation in PDBS lead to the much weak SAXS. The nonperiodic structure is preserved during the crystal-mesophase transition because of the similarity of main chain conformation and intermolecular distances between crystalline phase and mesophase.

Self-assembled monolayer of polyoxometalate on gold surfaces: Quartz crystal microbalance, electrochemistry, and in-situ scanning tunneling microscopy study

A new kind of inorganic self-assembled monolayer (SAM) was prepared by spontaneous adsorption of polyoxometalate anion, AsMo11VO404-, onto a gold surface from acidic aqueous solution. The adsorption process, structure, and electrochemical properties of the AsMo11VO404- SAM were investigated by quartz crystal microbalance (QCM), electrochemistry, and scanning tunneling microscopy (STM). The QCM data suggested that the self-assembling process could be described in terms of the Langmuir adsorption model, providing the value of the free energy of adsorption at -20 KJ mol(-1). The maximum surface coverage of the AsMo11VO404- SAM on gold surface was determined from the QCM data to be 1.7 x 10(-10) mol cm(-2), corresponding to a close-packed monolayer of AsMo11VO404- anion. The analysis of the voltammograms of the AsMo11VO404- SAM on gold electrode showed three pairs of reversible peaks with an equal surface coverage of 1.78 x 10(-10) mol cm(-2) for each of the peaks, and the value was agreed well with the QCM data. In-situ STM image demonstrated that the AsMo11VO404- SAM was very uniform and no aggregates or multilayer could be observed. Furthermore, the high-resolution STM images revealed that the AsMo11VO404- SAM on Au(lll) surface was composed of square unit cells with a lattice space of 10-11 Angstrom at +0.7 V (vs Ag\AgCl). The value was quite close to the diameter of AsMo11VO404- anion obtained from X-ray crystallographic study. The surface coverage of the AsMo11VO404- SAM on gold electrode estimated from the STM image was around 1.8 x 10(-10) mol cm(-2), which was consistent with the QCM and electrochemical results.

In-situ microscopic FT-IR spectroelectrochemical investigation of polythiophene film modified electrode

A polythiophene film was electrochemically deposited on a Pt micro-plate electrode and investigated by cyclic voltammetry and in-situ reflection microscopic FTIR spectroscopy. The FTIR analysis showed that the electropolymerization of thiophene on the Pt surface was affected Lv the surface adsorption processes of thiophene molecules. Two adsorption modes were identified. Two structure models of the polythiophene chain were observed simultaneously. It was proposed that the good conductibility of the polythiophene film was originated from a co-vibratory equilibrium of the link part of model I and model II.

In situ electrochemical scanning tunneling microscopy investigation of renewing graphite surface accompanied by electrochemical reaction

In situ electrochemical scanning tunneling microscopy (ECSTM) has been employed to follow the renewal process of a graphite electrode accompanied by flavin adenine dinucleotide (FAD) electrochemical reaction which involves adsorption of the reduced form (FADH(2)) and desorption of the oxidized form (FAD). The renewal process initiates from steps or kinks on the electrode surface, which provide high active sites for adsorption. This renewal depends on the working electrode potential, especially in the range near the FAD redox potential. Our experiment suggests that delamination of the graphite surface is caused by interaction between the substrate and adsorbed molecules. A simple model is proposed to explain this phenomenon.

IN-SITU SCANNING-TUNNELING-MICROSCOPY IMAGE OF A HIGHLY ORIENTED PYROLYTIC-GRAPHITE ELECTRODE MODIFIED WITH POTASSIUM BIS(11-MOLYBDOSILICATO) DYSPROSATE(III) IN SODIUM-SULFATE SOLUTION

The variation in molecule adsorption mode on pretreated highly oriented pyrolytic graphite electrodes, modified with the title complex K10H3[Dy(SiMo11O39)(2)] by cyclic voltammetry in the title complex solution, was observed in situ by electrochemical scanning tunnelling microscopy (ECSTM) with molecular resolution in sodium sulphate solution. According to the ECSTM images and the known molecular structure we conclude that the adsorption mode of the title complex modified electrode changed during potential cycling from ''vertical'' to ''inclined'' and then ''horizontal'' or ''flat'' mode, i.e. the title complex adsorbed on the surface of electrode by one ligand of the complex at first, then began to incline and was finally adsorbed by two ligands of the complex. This result indicates that the adsorption mode on the modified electrode surface changed during potential cycling in the sulphate solution and a much more stable molecular layer was formed. The change in adlattice of adsorbates on the modified electrode surface from hexagonal to rectangular was also observed by ECSTM. A plausible model was given to explain this process.

Alignment of the genomes of brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization

Robert Hasterok, Agnieszka Marasek, Iain S. Donnison, Ian Armstead, Ann Thomas, Ian P. King, Elzbieta Wolny, Dominika Idziak, John Draper and Glyn Jenkins (2006). Alignment of the genomes of brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization.Genetics, 73 (1), 349-362. Sponsorship: Royal Society / BBSRC;BBSRC RAE2008

Foraging success of biological Levy flights recorded in situ

It is an open question how animals find food in dynamic natural environments where they possess little or no knowledge of where resources are located. Foraging theory predicts that in environments with sparsely distributed target resources, where forager knowledge about resources’ locations is incomplete, Lévy flight movements optimize the success of random searches. However, the putative success of Lévy foraging has been demonstrated only in model simulations. Here, we use high-temporal-resolution Global Positioning System (GPS) tracking of wandering (Diomedea exulans) and black-browed albatrosses (Thalassarche melanophrys) with simultaneous recording of prey captures, to show that both species exhibit Lévy and Brownian movement patterns. We find that total prey masses captured by wandering albatrosses during Lévy movements exceed daily energy requirements by nearly fourfold, and approached yields by Brownian movements in other habitats. These results, together with our reanalysis of previously published albatross data, overturn the notion that albatrosses do not exhibit Lévy patterns during foraging, and demonstrate that Lévy flights of predators in dynamic natural environments present a beneficial alternative strategy to simple, spatially intensive behaviors. Our findings add support to the possibility that biological Lévy flight may have naturally evolved as a search strategy in response to sparse resources and scant information.

An assessment of phytoplankton primary productivity in the Arctic Ocean from satellite ocean color/in situ chlorophyll-abased models

We investigated 32 net primary productivity (NPP) models by assessing skills to reproduce integrated NPP in the Arctic Ocean. The models were provided with two sources each of surface chlorophyll-a concentration (chlorophyll), photosynthetically available radiation (PAR), sea surface temperature (SST), and mixed-layer depth (MLD). The models were most sensitive to uncertainties in surface chlorophyll, generally performing better with in situ chlorophyll than with satellite-derived values. They were much less sensitive to uncertainties in PAR, SST, and MLD, possibly due to relatively narrow ranges of input data and/or relatively little difference between input data sources. Regardless of type or complexity, most of the models were not able to fully reproduce the variability of in situ NPP, whereas some of them exhibited almost no bias (i.e., reproduced the mean of in situ NPP). The models performed relatively well in low-productivity seasons as well as in sea ice-covered/deep-water regions. Depth-resolved models correlated more with in situ NPP than other model types, but had a greater tendency to overestimate mean NPP whereas absorption-based models exhibited the lowest bias associated with weaker correlation. The models performed better when a subsurface chlorophyll-a maximum (SCM) was absent. As a group, the models overestimated mean NPP, however this was partly offset by some models underestimating NPP when a SCM was present. Our study suggests that NPP models need to be carefully tuned for the Arctic Ocean because most of the models performing relatively well were those that used Arctic-relevant parameters.

DFT and in situ EXAFS investigation of gold/ceria-zirconia low-temperature water gas shift catalysts: Identification of the nature of the active form of gold

A combined experimental and theoretical investigation of the nature of the active form of gold in oxide-supported gold catalysts for the water gas shift reaction has been performed. In situ extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) experiments have shown that in the fresh catalysts the gold is in the form of highly dispersed gold ions. However, under water gas shift reaction conditions, even at temperatures as low as 100 degrees C, the evidence from EXAFS and XANES is only 14 consistent with rapid, and essentially complete, reduction of the gold to form metallic clusters containing about 50 atoms. The presence of Au-Ce distances in the EXAFS spectra, and the fact that about 15% of the gold atoms can be reoxidized after exposure to air at 150 degrees C, is indicative of a close interaction between a fraction (ca. 15%) of the gold atoms and the oxide support. Density functional theory (DFT) calculations are entirely consistent with this model and suggest that an important aspect of the active and stable form of gold under water gas shift reaction conditions is the location of a partially oxidized gold (Audelta+) species at a cerium cation vacancy in the surface of the oxide support. It is found that even with a low loading gold catalysts (0.2%) the fraction of ionic gold under water gas shift conditions is below the limit of detection by XANES (<5%). It is concluded that under water gas shift reaction conditions the active form of gold comprises small metallic gold clusters in intimate contact with the oxide support.

The effects of the specific adsorption of anion on the reactivity of the Ru(0001) surface towards CO adsorption and oxidation: in situ FTIRS studies

The dynamics of adsorption and oxidation of CO on Ru(0001) electrode in sulfuric acid solution have been studied using in situ FTIR spectroscopy under potential control and at open circuit, the latter at 20 and 55 degrees C. The in situ IR data show clearly that the bisulfate anion adsorbs on the Ru(0001) surface over the potential range from -200 mV to 350 mV (vs. Ag/AgCl) at 20 degrees C in the absence and presence of adsorbed CO; however, increasing the temperature to 55 degrees C and/ or increasing the concentration of dissolved O-2 reduces the bisulfate adsorption. The formation of surface (hydro-) oxide at higher potentials replaces the bisulfate adsorbates. Both linear (COL) and three-fold hollow bonded CO (COH) adsorbates were produced following CO adsorption at Ru(0001) in H2SO4, as was observed in our previous studies in HClO4. However, the amount of adsorbed CO observed in H2SO4 was ca. 10% less than that in HClO4; in addition, the COL and COH frequencies were higher in H2SO4, and the onset potential for COads oxidation 25 mV lower. These new results are interpreted in terms of a model in which the adsorbed bisulfate weakens the CO adlayer, allowing the active Ru oxide layer to form at lower potentials. Significantly different results were observed at open circuit in H2SO4 compared both to the data under potential control and to our earlier data in HClO4, and these observations were rationalized in terms of the adsorbed HSO4- anions (pre-adsorbed at -200 mV) inhibiting the oxidation of the surface at open circuit (after stepping from the initial potential of -200 mV), as the latter was no longer driven by the imposed electrochemical potential but via chemical oxidation by trace dissolved O-2. Results from experiments at open circuit at 55 degrees C and using oxygen-saturated H2SO4 supported this model. The difference in Ru surface chemistry between imposed electrochemical control and chemical control has potential implications with respect to fuel cell electrocatalysis.

Estimation of in situ stresses using anisotropic elasticity and suction measurements

Sampling and specimen preparation produce changes in mean effective stresses and pore water pressures, even with ‘perfect sampling’. The paper takes an existing simplified three-parameter cross-anisotropic elastic model and uses it to model these changes. The required ratio of cross-anisotropic parameters J/3G* can be obtained from standard CIU triaxial tests. If measurements are also made of suctions in unloaded specimens in the laboratory, then a combination of J/3G*, the measured suction, and the effective overburden pressure permits an estimation of the horizontal effective pressure and the K 0 ‘at rest’ coefficient. This can be helpful in numerical modelling that needs to start from in situ conditions, and in planning pressure levels for reconsolidation of clay specimens in the laboratory. Tests were done on Belfast Upper Boulder Clay from a depth of 28 m. Values of horizontal in situ effective stress estimated from these measurements compare favorably with conventional estimates of the ‘at rest’ coefficient K 0 and the overconsolidation ratio. Estimates of horizontal stress in London Clay were made using published data and the results compared with actual measurements. Again reasonable agreement was obtained.

Postglacial dispersal, rather than in situ glacial survival, best explains the disjunct distribution of the Lusitanian plant species Daboecia cantabrica (Ericaceae)

Aim:

The distribution of the Lusitanian flora and fauna, species which are found only in southern and western Ireland and in northern Spain and Portugal but which are absent from intervening countries, represents one of the classic conundrums of biogeography. The aim of the present study was to determine whether the distribution of the Lusitanian plant species Daboecia cantabrica was due to persistence in separate Irish and Iberian refugia, or has resulted from post-glacial recolonization followed by subsequent extinction of intervening populations.

Location:

Northern Spain and Co. Galway, western Ireland.

Methods:

Palaeodistribution modelling using Maxent was employed to identify putative refugial areas for D. cantabrica at the Last Glacial Maximum (LGM). Phylogeographical analysis of samples from 64 locations in Ireland and Spain were carried out using a chloroplast marker (atpB–rbcL), the nuclear ITS region, and an anonymous nuclear single-copy locus.

Results:

The palaeodistribution model indicated areas with a high probability of survival for D. cantabrica at the LGM off the western coast of Galicia in Spain, and in the Bay of Biscay. Spanish populations exhibited substantially higher genetic diversity than Irish populations at all three loci, as well as geographical structuring of haplotypes within Spain consistent with divergence in separate refugia. Spanish populations also exhibited far more endemic haplotypes. Divergence time between Irish and Spanish populations associated with the putative Biscay refugium was estimated as 3.333–32 ka.

Main conclusions:

Our data indicate persistence by D. cantabrica throughout the LGM in two separate southern refugia: one in western Galicia and one in the area off the coast of western France which now lies in the Bay of Biscay. Spain was recolonized from both refugia, whilst Ireland was most likely recolonized from the Biscay refugium. On the balance of evidence across the three marker types and the palaeodistribution modelling, our findings do not support the idea of in situ survival of D. cantabrica in Ireland, contrary to earlier suggestions. The fact that we cannot conclusively rule out the existence of a small, more northerly refugium, however, highlights the need for further analysis of Lusitanian plant species.

A pre-embedding immunogold approach for detection of synaptic endocytic proteins in situ

During the past decade, many molecular components of clathrin-mediated endocytosis have been identified and proposed to play various hypothetical roles in the process [Nat. Rev. Neurosci. 1 (2000) 161; Nature 422 (2003) 37]. One limitation to the evaluation of these hypotheses is the efficiency and resolution of immunolocalization protocols currently in use. In order to facilitate the evaluation of these hypotheses and to understand more fully the molecular mechanisms of clathrin-mediated endocytosis, we have developed a protocol allowing enhanced and reliable subcellular immunolocalization of proteins in synaptic endocytic zones in situ. Synapses established by giant reticulospinal axons in lamprey are used as a model system for these experiments. These axons are unbranched and reach up to 80-100 microm in diameter. Synaptic active zones and surrounding endocytic zones are established on the surface of the axonal cylinder. To provide access for antibodies to the sites of synaptic vesicle recycling, axons are lightly fixed and cut along their longitudinal axis. To preserve the ultrastructure of the synaptic endocytic zone, antibodies are applied without the addition of detergents. Opened axons are incubated with primary antibodies, which are detected with secondary antibodies conjugated to gold particles. Specimens are then post-fixed and processed for electron microscopy. This approach allows preservation of the ultrastructure of the endocytic sites during immunolabeling procedures, while simultaneously achieving reliable immunogold detection of proteins on endocytic intermediates. To explore the utility of this approach, we have investigated the localization of a GTPase, dynamin, on clathrin-coated intermediates in the endocytic zone of the lamprey giant synapse. Using the present immunogold protocol, we confirm the presence of dynamin on late stage coated pits [Nature 422 (2003) 37] and also demonstrate that dynamin is recruited to the coat of endocytic intermediates from the very early stages of the clathrin coat formation. Thus, our experiments show that the current pre-embedding immunogold method is a useful experimental tool to study the molecular mechanisms of synaptic vesicle recycling.

Measurement of Donnan potentials in gels by in situ microelectrode voltammetry

This work describes the electrochemical methodology for the determination of the Donnan potential from diffusion-limited steady-state voltammograms of acrylamide gels. The technique is based upon the measurement of gel–sol systems that have reached Donnan equilibrium and contain Cd2+ as a probe ion. Au-amalgam microelectrodes are used to measure the Cd concentration in the gel phase relative to the solution phase, thus permitting comparison of the Cd voltammograms obtained in both phases. This approach yields two independent measures of the Donnan potential resulting from (i) the potential shift relative to the reference electrode, and (ii) the enhancement of the Cd2+ wave. Two suites of acrylamide gels containing 0.2% and 0.5% Na-acrylate were studied as a function of ionic strength by varying [NaNO3] and maintaining a constant concentration of the electroactive probe ion, [Cd2+] = 1 · 10 5 mol/L in the equilibrating solutions. Independent model predictions of the Donnan potential as a function of ionic strength that consider the effects of differential swelling on the charge density, the influence of a mixed electrolyte on the potential developed in the gel at the limit of low ionic strength and the effects of incomplete dissociation of the carboxylic functional groups were in agreement with the Donnan potentials independently measured by the twofold steady-state voltammetric approach.

Modeling of in-situ crystallization processes in the Permian mafic layered intrusion of Mont Collon (Dent Blanche nappe, western Alps)

The Mont Collon mafic complex is one of the best preserved examples of the Early Permian magmatism in the Central Alps, related to the intra-continental collapse of the Variscan belt. It mostly consists (> 95 vol.%) of ol+hy-nonnative plagioclase-wehrlites, olivine- and cpx-gabbros with cumulitic structures, crosscut by acid dikes. Pegmatitic gabbros, troctolites and anorthosites outcrop locally. A well-preserved cumulative, sequence is exposed in the Dents de Bertol area (center of intrusion). PT-calculations indicate that this layered magma chamber emplaced at mid-crustal levels at about 0.5 GPa and 1100 degrees C. The Mont Collon cumulitic rocks record little magmatic differentiation, as illustrated by the restricted range of clinopyroxene mg-number (Mg#(cpx)=83-89). Whole-rock incompatible trace-element contents (e.g. Nb, Zr, Ba) vary largely and without correlation with major-element composition. These features are characteristic of an in-situ crystallization process with variable amounts of interstitial liquid L trapped between the cumulus mineral phases. LA-ICPMS measurements show that trace-element distribution in the latter is homogeneous, pointing to subsolidus re-equilibration between crystals and interstitial melts. A quantitative modeling based on Langmuir's in-situ crystallization equation successfully duplicated the REE concentrations in cumulitic minerals of all rock facies of the intrusion. The calculated amounts of interstitial liquid L vary between 0 and 35% for degrees of differentiation F of 0 to 20%, relative to the least evolved facies of the intrusion. L values are well correlated with the modal proportions of interstitial amphibole and whole-rock incompatible trace-element concentrations (e.g. Zr, Nb) of the tested samples. However, the in-situ crystallization model reaches its limitations with rock containing high modal content of REE-bearing minerals (i.e. zircon), such as pegmatitic gabbros. Dikes of anorthositic composition, locally crosscutting the layered lithologies, evidence that the Mont Collon rocks evolved in open system with mixing of intercumulus liquids of different origins and possibly contrasting compositions. The proposed model is not able to resolve these complex open systems, but migrating liquids could be partly responsible for the observed dispersion of points in some correlation diagrams. Absence of significant differentiation with recurrent lithologies in the cumulitic pile of Dents de Bertol points to an efficiently convective magma chamber, with possible periodic replenishment, (c) 2005 Elsevier B.V. All rights reserved.