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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

GENFIT: software for the analysis of small-angle X-ray and neutron scattering data of macro-molecules in solution.

Many research topics in the fields of condensed matter and the life sciences are based on small-angle X-ray and neutron scattering techniques. With the current rapid progress in source brilliance and detector technology, high data fluxes of ever-increasing quality are produced. In order to exploit such a huge quantity of data and richness of information, wider and more sophisticated approaches to data analysis are needed. Presented here is GENFIT, a new software tool able to fit small-angle scattering data of randomly oriented macromolecular or nanosized systems according to a wide list of models, including form and structure factors. Batches of curves can be analysed simultaneously in terms of common fitting parameters or by expressing the model parameters via physical or phenomenological link functions. The models can also be combined, enabling the user to describe complex heterogeneous systems.

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.

Evidence of Cybotactic Order in the Nematic Phase of a Main-Chain Liquid Crystal Polymer with Bent-Core Repeat Unit.

We report the synthesis and structural characterization of a main-chain liquid crystal polymer constituted by a 1,2,4-oxadiazole-based bent-core repeat unit. For the first time, a liquid crystal polymer made of bent mesogenic units is demonstrated to exhibit cybotactic order in the nematic phase. Coupled with the chain-bond constraints, cybotaxis results in maximized molecular correlations that make this material of great potential in the search for the elusive biaxial and ferroelectric nematic phases. Indeed, repolarization current measurements in the nematic phase hint at a ferroelectric-like switching response (upon application of an electric field of only 1.0 V µm-1) that, albeit to be definitely confirmed by complementary techniques, is strongly supported by the comparative repolarization current measurements in the nematic and isotropic phases. Finally, the weak tendency of this polymer to crystallize makes it possible to supercool the cybotactic nematic phase down to room temperature, thus, paving the way for a glassy phase in which the biaxial (and possibly polar) order is frozen at room temperature.

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.

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.

Quaternary structure heterogeneity of oligomeric proteins: a SAXS and SANS study of the dissociation products of Octopus vulgaris hemocyanin.

Octopus vulgaris hemocyanin shows a particular self-assembling pattern, characterized by a hierarchical organization of monomers. The highest molecular weight aggregate is a decamer, the stability of which in solution depends on several parameters. Different pH values, buffer compositions, H2O/D2O ratios and Hofmeister's salts result in modifications of the aggregation state of Octopus vulgaris hemocyanin. The new QUAFIT method, recently applied to derive the structure of the decameric and the monomeric assembly from small-angle scattering data, is used here to model the polydisperse system that results from changing the solution conditions. A dataset of small-angle X-rays and neutron scattering curves is analysed by QUAFIT to derive structure, composition and concentration of different assemblies present in solution. According to the hierarchy of the association/dissociation processes and the possible number of different aggregation products in solution, each sample has been considered as a heterogeneous mixture composed of the entire decamer, the dissociated "loose" monomer and all the intermediate dissociation products. Scattering curves corresponding to given experimental conditions are well fitted by using a linear combination of single particle form factors. QUAFIT has proved to be a method of general validity to describe solutions of proteins that, even after purification processes, result to be intrinsically heterogeneous.

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.

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.