Revealing metallic ink in Herculaneum papyri.

Writing on paper is essential to civilization, as Pliny the Elder remarks in his Natural History, when he describes the various types of papyri, the method of manufacturing them, and all that concerns writing materials in the mid-first century AD. For this reason, a rigorous scientific study of writing is of fundamental importance for the historical understanding of ancient societies. We show that metallic ink was used several centuries earlier than previously thought. In particular, we found strong evidence that lead was intentionally used in the ink of Herculaneum papyri and discuss the possible existence of ruled lines traced on the papyrus texture. In addition, the metallic concentrations found in these fragments deliver important information in view of optimizing future computed tomography (CT) experiments on still-unrolled Herculaneum scrolls to improve the readability of texts in the only surviving ancient Greco-Roman library.

Automatic Debye-Scherrer elliptical ring extraction via a computer vision approach.

The accurate calibration of powder diffraction data acquired from area detectors using calibration standards is a crucial step in the data reduction process to attain high-quality one-dimensional patterns. A novel algorithm has been developed for extracting Debye-Scherrer rings automatically using an approach based on computer vision and pattern recognition techniques. The presented technique requires no human intervention and, unlike previous approaches, makes no restrictive assumptions on the diffraction setup and/or rings. It can detect complete rings as well as portions of them, and works on several types of diffraction images with various degrees of ring graininess, textured diffraction patterns and detector tilt with respect to the incoming beam.

Structural and Thermodynamic Properties of Nanoparticle-Protein Complexes: A Combined SAXS and SANS Study.

We propose a novel method for determining the structural and thermodynamic properties of nanoparticle-protein complexes under physiological conditions. The method consists of collecting a full set of small-angle X-ray and neutron-scattering measurements in solutions with different concentrations of nanoparticles and protein. The nanoparticle-protein dissociation process is described in the framework of the Hill cooperative model, based on which the whole set of X-ray and neutron-scattering data is fitted simultaneously. This method is applied to water solutions of gold nanoparticles in the presence of human serum albumin without any previous manipulation and can be, in principle, extended to all systems. We demonstrate that the protein dissociation constant, the Hill coefficient, and the stoichiometry of the nanoparticle-protein complex are obtained with a high degree of confidence.

Nanoscale Structural Features in Major Ampullate Spider Silk.

Spider major ampullate silk is often schematically represented as a two-phase material composed of crystalline nanodomains in an amorphous matrix. Here we are interested in revealing its more complex nanoscale organization by probing Argiope bruennichi dragline-type fibers using scanning X-ray nanodiffraction. This allows resolving transversal structural features such as an about 1 µm skin layer composed of around 100 nm diameter nanofibrils serving presumably as an elastic sheath. The core consists of a composite of several nm size crystalline nanodomains with poly(l-alanine) microstructure, embedded in a polypeptide network with short-range order. Stacks of nanodomains separated by less ordered nanosegments form nanofibrils with a periodic axial density modulation which is particularly sensitive to radiation damage. The precipitation of larger ß-type nanocrystallites in the outer core-shell is attributed to MaSp1 protein molecules.

Molecular ordering in the high-temperature nematic phase of an all-aromatic liquid crystal.

We report the structural characterization of the nematic phase of 2,6-biphenyl naphthalene (PPNPP). This lath-like all-aromatic mesogen provides a valuable benchmark for classical theories of nematic order. PPNPP exhibits a very high temperature nematic phase (417-489 °C) above an enantiotropic smectic A phase. X-ray diffraction reveals a surprisingly strong tendency towards molecular layering in the nematic phase, indicative of "normal cybotaxis" (i.e. SmA-like stratification within clusters of mesogens). Although stronger at low temperatures, the layering is evident well above the smectic A-nematic transition. The nematic order parameter is evaluated as a function of temperature from the broadening of the wide-angle diffuse diffraction feature. Measured values of the orientational order parameter are slightly larger than those predicted by the Maier-Saupe theory over the entire nematic range except for a narrow region just below the clearing point where they significantly drop below the theoretical prediction.

Structural and Thermodynamic Properties of Septin 3 Investigated by Small-Angle X-Ray Scattering.

Septins comprise a family of proteins involved in a variety of cellular processes and related to several human pathologies. They are constituted by three structural domains: the N- and C-terminal domains, highly variable in length and composition, and the central domain, involved in the guanine nucleotide (GTP) binding. Thirteen different human septins are known to form heterogeneous complexes or homofilaments, which are stabilized by specific interactions between the different interfaces present in the domains. In this work, we have investigated by in-solution small-angle x-ray scattering the structural and thermodynamic properties of a human septin 3 construct, SEPT3-GC, which contains both of both interfaces (G and NC) responsible for septin-septin interactions. In order to shed light on the role of these interactions, small-angle x-ray scattering measurements were performed in a wide range of temperatures, from 2 up to 56°C, both with and without a nonhydrolysable form of GTP (GTPγS). The acquired data show a temperature-dependent coexistence of monomers, dimers, and higher-order aggregates that were analyzed using a global fitting approach, taking into account the crystallographic structure of the recently reported SEPT3 dimer, PDB:3SOP. As a result, the enthalpy, entropy, and heat capacity variations that control the dimer-monomer dissociation equilibrium in solution were derived and GTPγS was detected to increase the enthalpic stability of the dimeric species. Moreover, a temperature increase was observed to induce dissociation of SEPT3-GC dimers into monomers just preceding their reassembling into amyloid aggregates, as revealed by the Thioflavin-T fluorescence assays.

Thermally induced self-assembly of cylindrical nanodomains in low molecular weight PS-b-PMMA thin films.

The phase behaviour in thin films of an asymmetric polystyrene-b-polymethylmethacrylate (PS-b-PMMA) block copolymer with a molecular weight of 39 kg mol(-1) was assessed at a wide range of temperatures and times. Cylindrical PMMA structures featuring a diameter close to 10 nm and perpendicularly oriented with respect to the substrate were obtained at 180 °C in relatively short annealing times (t ≤ 30 min) by means of a simple thermal treatment performed in a standard rapid thermal processing machine.

An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy.

Medical imaging and radiation therapy are widely used synchrotron-based techniques which have one thing in common: a significant dose delivery to typically biological samples. Among the ways to provide the experimenters with image guidance techniques indicating optimization strategies, Monte Carlo simulation has become the gold standard for accurately predicting radiation dose levels under specific irradiation conditions. A highly important hampering factor of this method is, however, its slow statistical convergence. A track length estimator (TLE) module has been coded and implemented for the first time in the open-source Monte Carlo code GATE/Geant4. Results obtained with the module and the procedures used to validate them are presented. A database of energy-absorption coefficients was also generated, which is used by the TLE calculations and is now also included in GATE/Geant4. The validation was carried out by comparing the TLE-simulated doses with experimental data in a synchrotron radiation computed tomography experiment. The TLE technique shows good agreement versus both experimental measurements and the results of a classical Monte Carlo simulation. Compared with the latter, it is possible to reach a pre-defined statistical uncertainty in about two to three orders of magnitude less time for complex geometries without loss of accuracy.

Optimized x-ray multilayer mirrors for single nanometer focusing.

We present numerical simulations optimizing the layer shapes of curved focusing x-ray multilayer mirrors deployed at synchrotron radiation facilities using a wave-optical model. The confocal elliptical shapes of the inner layers are corrected for refraction based on the modified Bragg law. Simulated wave amplitudes are further propagated to the focal region, promising nanometer focusing.

Wave-optical theory of nanofocusing x-ray multilayer mirrors.

We have derived a wave-optical model of curved nanofocusing x-ray multilayer mirrors used at synchrotron radiation sources, using a Takagi-Taupin-like approach. In a first approximation, the individual layers are assumed to be confocal elliptical. This assumption leads to a convenient spatial description in elliptical coordinates. As a first optimization, we study a rotation-like modification and compare numerical simulations to established results for planar multilayers.

The architecture of starch blocklets follows phyllotaxic rules.

The starch granule is Nature's way to store energy in green plants over long periods. Irrespective of their origins, starches display distinct structural features that are the fingerprints of levels of organization over six orders of magnitude. We hypothesized that Nature retains hierarchical material structures at all levels and that some general rules control the morphogenesis of these structures. We considered the occurrence of a «phyllotaxis¼ like features that would develop at scales ranging from nano to micrometres, and developed a novel geometric model capable of building complex structures from simple components. We applied it, according to the Fibonacci Golden Angle, to form several Golden Spirals, and derived theoretical models to simulate scattering patterns. A GSE, constructed with elements made up of parallel stranded double-helices, displayed shapes, sizes and high compactness reminiscent of the most intriguing structural element: the 'blocklet'. From the convergence between the experimental findings and the theoretical construction, we suggest that the «phyllotactic¼ model represents an amylopectin macromolecule, with a high molecular weight. Our results offer a new vision to some previous models of starch. They complete a consistent description of the levels of organization over four orders of magnitude of the starch granule.

K vs. Na Effects on the Self-Assembly of Guanosine 5'-Monophosphate: A Solution SAXS Structural Study+.

The hierarchical process of guanosine (G) self-assembly, leading in aqueous solution and in the presence of metal cations to the formation of G-quadruplexes, represents an intriguing topic both for the biological correlation with telomerase activity and for the nano-technological applications, as demonstrated by the current measured in a quadruplex wire 100 nm long. Similar to G-rich DNA sequences and G-oligonucleotides, the guanosine 5'-monophosphate (GMP) self-aggregates in water to form quadruplexes. However, due to the absence of a covalent axial backbone, this system can be very useful to understand the chemical-physical conditions that govern the guanosine supramolecular aggregation. We have then investigated by in-solution Synchrotron Small Angle X-ray Scattering technique the role of different cations in promoting the quadruplex formation as a function of concentration and temperature. Results show how potassium, with its peculiar biological traits, favours the G-quadruplex elongation process in respect to other cations (Na + , but also NH 4 + and Li + ), determining the longest particles in solution. Moreover, the formation and the elongation of G-quadruplexes have been demonstrated to be controlled by both GMP concentration and excess cation content, even if they specifically contribute to these processes in different ways. The occurrence of condensed liquid crystalline phases was also detected, proving that excess cations play also unspecific effects on the effective charges on the G-quadruplex surface.

Local Structure and Magnetism of Fe2O3 Maghemite Nanocrystals: The Role of Crystal Dimension.

Here we report on the impact of reducing the crystalline size on the structural and magnetic properties of γ-Fe2O3 maghemite nanoparticles. A set of polycrystalline specimens with crystallite size ranging from ~2 to ~50 nm was obtained combining microwave plasma synthesis and commercial samples. Crystallite size was derived by electron microscopy and synchrotron powder diffraction, which was used also to investigate the crystallographic structure. The local atomic structure was inquired combining pair distribution function (PDF) and X-ray absorption spectroscopy (XAS). PDF revealed that reducing the crystal dimension induces the depletion of the amount of Fe tetrahedral sites. XAS confirmed significant bond distance expansion and a loose Fe-Fe connectivity between octahedral and tetrahedral sites. Molecular dynamics revealed important surface effects, whose implementation in PDF reproduces the first shells of experimental curves. The structural disorder affects the magnetic properties more and more with decreasing the nanoparticle size. In particular, the saturation magnetization reduces, revealing a spin canting effect. Moreover, a large effective magnetic anisotropy is measured at low temperature together with an exchange bias effect, a behavior that we related to the existence of a highly disordered glassy magnetic phase.

Extending the possibilities in phase space analysis of synchrotron radiation x-ray optics.

A simple analytical approach to phase space analysis of the performance of x-ray optical setups (beamlines) combining several elements in position-angle-wavelength space is presented. The mathematical description of a large class of optical elements commonly used on synchrotron beamlines has been reviewed and extended with respect to the existing literature and is reported in a revised form. Novel features are introduced, in particular, the possibility to account for imperfections on mirror surfaces and to incorporate nanofocusing devices like refractive lenses in advanced beamline setups using the same analytical framework. Phase space analysis results of the simulation of an undulator beamline with focusing optics at the European Synchrotron Radiation Facility compare favorably with results obtained by geometric ray-tracing methods and, more importantly, with experimental measurements. This approach has been implemented into a simple and easy-to-use program toolkit for optical calculations based on the Mathematica software package.

Pressure effects on lipidic direct phases: the dodecyl trimethyl ammonium chloride-water system.

The direct lyotropic polymorphism of dodecyltrimethylammonium chloride (DTAC) was investigated by synchrotron X-ray diffraction at different water concentrations under compression up to 2 kbar, i.e., in the pressure intermediate range where interesting biophysical transformations occur and the functional characteristics of cell membranes are altered. The results show that pressure induces the transition from the hexagonal phase to the micellar Pm3n cubic phase in hydrated samples (c between 0.5 and 0.6, c being the weight concentration of lipid in the mixture) and the transition from the bicontinuous Ia3d cubic phase to the hexagonal phase in drier samples (c = 0.8). By increasing the pressure on very dry samples, a lamellar L(alpha) phase was observed to form transitorily at the Ia3d cubic-hexagonal phase transition. Phase compressibility and then the lipid and water partial molecular compressibilities were derived as a function of pressure and concentration. As a result, we assessed the very low compressibility of the hydration water within the lipid phases, and we demonstrated that the compressibility of DTAC is very dependent on pressure. Moreover, the molecular parameters of DTAC calculated in the different phases during compression confirmed that pressure induces small but continuous conformational changes, definitely different from the large changes observed in lipid molecules forming type II structures.

Tracking ink composition on Herculaneum papyrus scrolls: quantification and speciation of lead by X-ray based techniques and Monte Carlo simulations.

The writing in carbonized Herculaneum scrolls, covered and preserved by the pyroclastic events of the Vesuvius in 79 AD, was recently revealed using X-ray phase-contrast tomography, without the need of unrolling the sensitive scrolls. Unfortunately, some of the text is difficult to read due to the interference of the papyrus fibers crossing the written text vertically and horizontally. Recently, lead was found as an elemental constituent in the writing, rendering the text more clearly readable when monitoring the lead X-ray fluorescence signal. Here, several hypotheses are postulated for the origin and state of lead in the papyrus writing. Multi-scale X-ray fluorescence micro-imaging, Monte Carlo quantification and X-ray absorption microspectroscopy experiments are used to provide additional information on the ink composition, in an attempt to determine the origin of the lead in the Herculaneum scrolls and validate the postulated hypotheses.

Locating counterions in guanosine quadruplexes: a contrast-variation neutron diffraction experiment in condensed hexagonal phase.

Guanosine, one of the primary components of nucleic acids, self-associates in water to form G-quadruplexes, four-stranded helicoidal aggregates, made by stacked planar tetramers, consisting of four planar guanine molecules. Essential for the stability of these supramolecular aggregates is the presence of monovalent cations. As G-quadruplexes show a lyotropic polymorphism, neutron diffraction, in combination with the H2O/D2O contrast variation technique, has been applied to study the cation structural features of quadruplexes in hexagonal phase at different hydrations and counterion concentrations. The guanosine 5'-monophosphate, dipotassium salt, was considered and G-quadruplexes in hexagonal phase were prepared in the different experimental conditions (contrast, hydration and KCl solution concentration) by using the osmotic stress technique. The calculated scattering length density distribution maps show that counterions fill the helix inner cavity and that atmospheric cations are bound to a second site, close to the external phosphate groups. The site occupancy turned out to be very high: we found on the inner site 0.87 K ions per tetramer in G-quadruplexes prepared in pure water and 0.97 K ions per tetramer in G-quadruplexes prepared in KCl 0.5 M, while in all cases 6 ions per unit cell were detected to occupy the outer sites, partially neutralizing the two formal negative charges per phosphate group. The very large K ions concentration difference between the binding sites and the bulk solution demonstrates that counterions are structurally involved in the formation and in the stabilization of the helices.

Revealing letters in rolled Herculaneum papyri by X-ray phase-contrast imaging.

Hundreds of papyrus rolls, buried by the eruption of Mount Vesuvius in 79 AD and belonging to the only library passed on from Antiquity, were discovered 260 years ago at Herculaneum. These carbonized papyri are extremely fragile and are inevitably damaged or destroyed in the process of trying to open them to read their contents. In recent years, new imaging techniques have been developed to read the texts without unwrapping the rolls. Until now, specialists have been unable to view the carbon-based ink of these papyri, even when they could penetrate the different layers of their spiral structure. Here for the first time, we show that X-ray phase-contrast tomography can reveal various letters hidden inside the precious papyri without unrolling them. This attempt opens up new opportunities to read many Herculaneum papyri, which are still rolled up, thus enhancing our knowledge of ancient Greek literature and philosophy.

Percolating hierarchical defect structures drive phase transformation in Ce1-x Gd x O2-x/2: a total scattering study.

A new hierarchical approach is presented for elucidating the structural disorder in Ce1-x Gd x O2-x/2 solid solutions on different scale lengths. The primary goal of this investigation is to shed light on the relations between the short-range and the average structure of these materials via an analysis of disorder on the mesocopic scale. Real-space (pair distribution function) and reciprocal-space (Rietveld refinement and microstructure probing) analysis of X-ray powder diffraction data and electron spin resonance (ESR) investigations were carried out following this approach. On the local scale, Gd- and Ce-rich droplets (i.e. small regions a few ångströms wide) form, exhibiting either a distorted fluorite (CeO2) or a C-type (Gd2O3) structure in the whole compositional range. These droplets can then form C-type nanodomains which, for Gd concentrations x Gd ≤ 0.25, are embedded in the fluorite matrix. At the site percolation threshold p C for a cubic lattice (x Gd = p C ≃ 0.311), C-type nanodomains percolate inside each crystallite and a structural phase transformation is observed. When this occurs, the peak-to-peak ESR line width ΔH pp shows a step-like behaviour, which can be associated with the increase in Gd-Gd dipolar interactions. A general crystallographic rationale is presented to explain the fluorite-to-C-type phase transformation. The approach shown here could be adopted more generally in the analysis of disorder in other highly doped materials.

Synchrotron stereotactic radiotherapy: dosimetry by Fricke gel and Monte Carlo simulations.

Synchrotron stereotactic radiotherapy (SSR) consists in loading the tumour with a high atomic number element (Z), and exposing it to monochromatic x-rays from a synchrotron source (50-100 keV), in stereotactic conditions. The dose distribution results from both the stereotactic monochromatic x-ray irradiation and the presence of the high Z element. The purpose of this preliminary study was to evaluate the two-dimensional dose distribution resulting solely from the irradiation geometry, using Monte Carlo simulations and a Fricke gel dosimeter. The verification of a Monte Carlo-based dosimetry was first assessed by depth dose measurements in a water tank. We thereafter used a Fricke dosimeter to compare Monte Carlo simulations with dose measurements. The Fricke dosimeter is a solution containing ferrous ions which are oxidized to ferric ions under ionizing radiation, proportionally to the absorbed dose. A cylindrical phantom filled with Fricke gel was irradiated in stereotactic conditions over several slices with a continuous beam (beam section = 0.1 x 1 cm2). The phantom and calibration vessels were then imaged by nuclear magnetic resonance. The measured doses were fairly consistent with those predicted by Monte Carlo simulations. However, the measured maximum absolute dose was 10% underestimated regarding calculation. The loss of information in the higher region of dose is explained by the diffusion of ferric ions. Monte Carlo simulation is the most accurate tool for dosimetry including complex geometries made of heterogeneous materials. Although the technique requires improvements, gel dosimetry remains an essential tool for the experimental verification of dose distribution in SSR with millimetre precision.