SOLEIL shining on the solution‐state structure of biomacromolecules by synchrotron X‐ray footprinting at the Metrology beamline

Synchrotron X‐ray footprinting complements the techniques commonly used to define the structure of molecules such as crystallography, small‐angle X‐ray scattering and nuclear magnetic resonance. It is remarkably useful in probing the structure and interactions of proteins with lipids, nucleic acids or with other proteins in solution, often better reflecting the in vivo state dynamics. To date, most X‐ray footprinting studies have been carried out at the National Synchrotron Light Source, USA, and at the European Synchrotron Radiation Facility in Grenoble, France. This work presents X‐ray footprinting of biomolecules performed for the first time at the X‐ray Metrology beamline at the SOLEIL synchrotron radiation source. The installation at this beamline of a stopped‐flow apparatus for sample delivery, an irradiation capillary and an automatic sample collector enabled the X‐ray footprinting study of the structure of the soluble protein factor H (FH) from the human complement system as well as of the lipid‐associated hydrophobic protein S3 oleosin from plant seed. Mass spectrometry analysis showed that the structural integrity of both proteins was not affected by the short exposition to the oxygen radicals produced during the irradiation. Irradiated molecules were subsequently analysed using high‐resolution mass spectrometry to identify and locate oxidized amino acids. Moreover, the analyses of FH in its free state and in complex with complement C3b protein have allowed us to create a map of reactive solvent‐exposed residues on the surface of FH and to observe the changes in oxidation of FH residues upon C3b binding. Studies of the solvent accessibility of the S3 oleosin show that X‐ray footprinting offers also a unique approach to studying the structure of proteins embedded within membranes or lipid bodies. All the biomolecular applications reported herein demonstrate that the Metrology beamline at SOLEIL can be successfully used for synchrotron X‐ray footprinting of biomolecules.     

Electric quadrupole interaction measurements in YBa2Cu3O x and related compounds

In this work we present Electric Quadrupole Interaction (EQI) measurements, made by Time Differential Perturbed Angular Correlation (TDPAC), on¹¹¹Cd in YBa₂Cu₃O _x and some related compounds. These studies were intended to determine the relationship between the EQI and the actual probe site. The probes were introduced into the materials as a diluted¹¹¹In-complex or via In(¹¹¹In)₂O₃. Our observations indicated that there is no need to suppose the presence of many probe sites in YBa₂Cu₃O _x to explain the experimental results.     

Structural changes in data communication in wireless sensor networks

Wireless sensor networks are an important technology for making distributed autonomous measures in hostile or inaccessible environments. Among the challenges they pose, the way data travel among them is a relevant issue since their structure is quite dynamic. The operational topology of such devices can often be described by complex networks. In this work, we assess the variation of measures commonly employed in the complex networks literature applied to wireless sensor networks. Four data communication strategies were considered: geometric, random, small-world, and scale-free models, along with the shortest path length measure. The sensitivity of this measure was analyzed with respect to the following perturbations: insertion and removal of nodes in the geometric strategy; and insertion, removal and rewiring of links in the other models. The assessment was performed using the normalized Kullback-Leibler divergence and Hellinger distance quantifiers, both deriving from the Information Theory framework. The results reveal that the shortest path length is sensitive to perturbations.     

Influence of laser repetition rate on ferroelectric properties of pulsed laser deposited BaTiO3 films on platinized silicon substrate

BaTiO₃ thin films were deposited by pulsed laser deposition on Pt–Si at different laser pulse repetition frequencies. X-ray diffraction spectra show that preferred oriented films can be grown by adjusting the pulse repetition frequency. Enhanced dielectric and ferroelectric properties obtained in films deposited at 1 Hz is attributed to preferred orientation, low strain and homogeneous grain distribution. The films deposited at 1 Hz show an impressive remanent polarization of 21.4 μC/cm² with a coercive field of 70.0 kV/cm. The shift in Curie temperature, which stems from changing the laser pulse repetition frequency, is associated with the strain state in the film.     

Pion mass dependence of the nucleon mass in the chiral quark soliton model

The dependence of the nucleon mass on the mass of the pion is studied in the framework of the chiral quark-soliton model. A remarkable agreement is observed with lattice data from recent full dynamical simulations. The possibility and limitations to use the results from the chiral quark soliton model as a guideline for the chiral extrapolation of lattice data are discussed.     

Converged properties of clean metal surfaces by all-electron first-principles calculations

All-electron full-potential linearized augmented plane-wave calculations of the surface energy, work function, and interlayer spacings of close-packed metal surfaces are presented, in particular, for the free-electron-like metal surfaces, Mg(0 0 0 1) and Al(1 1 1), and for the transition metal surfaces, Ti(0 0 0 1), Cu(1 1 1), Pd(1 1 1), and Pt(1 1 1). We investigate the convergence of the surface energy as a function of the number of layers in the slab, using the Cu(1 1 1) surface as an example. The results show that the surface energy, as obtained using total energies of the slab and bulk from separate calculations, converges well with respect to the number of layers in the slab. Obviously, it is necessary that bulk and surface calculations are performed with the same high accuracy. Furthermore, we discuss the performance of the local-density and generalized gradient approximations for the exchange-correlation functional in describing the various surface properties.     

UV laser induced desorption of CsI and RbI ion clusters

Experimental results of laser sputtering of cesium and rubidium iodide secondary ions are presented. A TOF mass spectrometer, operating in linear mode, continuous extraction for positive or negative ions, was used for the analysis of (CsI)_nCs⁺, (CsI)_nI⁻, (RbI)_nRb⁺ and (RbI)_nI⁻ ion emission as a function of the laser irradiance. Experimental data show that the cluster ion emission yields decrease exponentially with n, for all the laser irradiances applied. Theoretical analysis of the clusters structure was performed using density functional theory at the B3LYP/LACV3P level, for the positive and negative cluster series. A quasi-equilibrium evolution of the clusters is proposed to extract a parameter characteristic of the cluster recombination process: the effective temperature. The hypothesis of the atomic species’ recombination (during the expansion of a high density highly ionized cloud) leading to cluster formation is confirmed to some extent in a second set of experiments: the UV laser ablation of a mixed and non-mixed cesium iodide and potassium bromide targets. These experiments show that the emission yields contain contributions from both the recombination process and from the sample stoichiometry, even for high laser irradiances.     

Interspecific allometry of bone dimensions: A review of the theoretical models

A fascinating problem in biological scaling is the variation of long-bone length (or diameter) Y with body mass M in mammals, birds, and other vertebrates. It turns out that Y and M are related by a power law, namely Y=Y₀M^b, where Y₀ is a constant and b is the so-called allometric exponent. The origin of these power laws is still unclear because, in general, biological laws do not follow from physical ones in a simple manner.Here we make a historical review of this subject, summarizing the main experimental papers as well as discussing the main theoretical proposals. Long-bone allometry seems to be determined by the need to resist the particular loads applied to each bone in each taxon. Experimental measurements of in vivo stresses have found that mammalian long bones are subjected mainly to compression and bending, while avian wing-bones and reptilian limb-bones suffer a high degree of torsion. A recent model, based on the hypothesis that mammalian long-bone allometry is determined by compressive and bending loads, was able elucidate several aspects of mammalian limb-bone scaling. However, an explanation for avian and reptilian long-bone allometry is still missing.     

Synthesis of modified vermiculite by interaction with aromatic heterocyclic amines

Vermiculite of general formula [Si_6.85Al_1.15][Mg_4.68Al_0.51Fe_0.63]O₂₀(OH)₄Ca_0.128Na_0.032K_0.094 reacted with heteroaromatic amines α-, β-, and γ-picolines from aqueous solution. The products were characterized by elemental analysis, infrared spectroscopy, and X-ray diffraction. The intercalated nanocompounds maintained the crystallinity and changed the original interlayer distance of 1422 pm to 1474, 1456, and 1474 pm, for the sequence of the guest picoline molecules. Natural and intercalated vermiculite can remove copper at the solid/liquid interface; removal 0.40 mmol g⁻¹ was obtained for the original matrix, and 1.10, 0.92, and 1.33 mmol g⁻¹ for the intercalated forms. These values are near the capacity of cation exchange (CEC) of this clay mineral, which can be possibly used as source of copper removal from aqueous solution.     

Optical properties of in situ doped and undoped titania nanocatalysts and doped titania sol-gel nanofilms

In this paper we present spectroscopic properties of doped and undoped titanium dioxide (TiO₂) as nanofilms prepared by the sol-gel process with rhodamine 6G doping and studied by photoacoustic absorption, excitation and emission spectroscopy. The absorption spectra of TiO₂ thin films doped with rhodamine 6G at very low concentration during their preparation show two absorption bands, one at 2.3 eV attributed to molecular dimmer formation, which is responsible for the fluorescence quenching of the sample and the other at 3.0 eV attributed to TiO₂ absorption, which subsequently yields a strong emission band at 600 nm. The electronic band structure and optical properties of the rutile phase of TiO₂ are calculated employing a fully relativistic, full-potential, linearized, augmented plane-wave (FPLAPW) method within the local density approximation (LDA). Comparison of this calculation with experimental data for TiO₂ films prepared for undoped sol-gels and by sputtering is performed.