Correlation of refractive index based and THz streaking arrival time tools for a hard X-ray free-electron laser.

To fully exploit ultra-short X-ray pulse durations routinely available at X-ray free-electron lasers to follow out-of-equilibrium dynamics, inherent arrival time fluctuations of the X-ray pulse with an external perturbing laser pulse need to be measured. In this work, two methods of arrival time measurement were compared to measure the arrival time jitter of hard X-ray pulses. The methods were photoelectron streaking by a THz field and a transient refractive index change of a semiconductor. The methods were validated by shot-to-shot correction of a pump-probe transient reflectivity measurement. An ultimate shot-to-shot full width at half-maximum error between the devices of 19.2 ± 0.1 fs was measured.

Advances in long-wavelength native phasing at X-ray free-electron lasers.

Long-wavelength pulses from the Swiss X-ray free-electron laser (XFEL) have been used for de novo protein structure determination by native single-wavelength anomalous diffraction (native-SAD) phasing of serial femtosecond crystallography (SFX) data. In this work, sensitive anomalous data-quality indicators and model proteins were used to quantify improvements in native-SAD at XFELs such as utilization of longer wavelengths, careful experimental geometry optimization, and better post-refinement and partiality correction. Compared with studies using shorter wavelengths at other XFELs and older software versions, up to one order of magnitude reduction in the required number of indexed images for native-SAD was achieved, hence lowering sample consumption and beam-time requirements significantly. Improved data quality and higher anomalous signal facilitate so-far underutilized de novo structure determination of challenging proteins at XFELs. Improvements presented in this work can be used in other types of SFX experiments that require accurate measurements of weak signals, for example time-resolved studies.

PtychoShelves, a versatile high-level framework for high-performance analysis of ptychographic data.

Over the past decade, ptychography has been proven to be a robust tool for non-destructive high-resolution quantitative electron, X-ray and optical microscopy. It allows for quantitative reconstruction of the specimen's transmissivity, as well as recovery of the illuminating wavefront. Additionally, various algorithms have been developed to account for systematic errors and improved convergence. With fast ptychographic microscopes and more advanced algorithms, both the complexity of the reconstruction task and the data volume increase significantly. PtychoShelves is a software package which combines high-level modularity for easy and fast changes to the data-processing pipeline, and high-performance computing on CPUs and GPUs.

Nanocellulose Fragmentation Mechanisms and Inversion of Chirality from the Single Particle to the Cholesteric Phase.

Understanding how nanostructure and nanomechanics influence physical material properties on the micro- and macroscale is an essential goal in soft condensed matter research. Mechanisms governing fragmentation and chirality inversion of filamentous colloids are of specific interest because of their critical role in load-bearing and self-organizing functionalities of soft nanomaterials. Here we provide a fundamental insight into the self-organization across several length scales of nanocellulose, an important biocolloid system with wide-ranging applications as structural, insulating, and functional material. Through a combined microscopic and statistical analysis of nanocellulose fibrils at the single particle level, we show how mechanically and chemically induced fragmentations proceed in this system. Moreover, by studying the bottom-up self-assembly of fragmented carboxylated cellulose nanofibrils into cholesteric liquid crystals, we show via direct microscopic observations that the chirality is inverted from right-handed at the nanofibril level to left-handed at the level of the liquid crystal phase. These results improve our fundamental understanding of nanocellulose and provide an important rationale for its application in colloidal systems, liquid crystals, and nanomaterials.

Dynamics of the photoinduced insulator-to-metal transition in a nickelate film.

Material properties can be controlled via strain, pressure, chemical composition, or dimensionality. Nickelates are particularly susceptible due to their strong variations of the electronic and magnetic properties on such external stimuli. Here, we analyze the photoinduced dynamics in a single crystalline NdNiO3 film upon excitation across the electronic gap. Using time-resolved reflectivity and resonant x-ray diffraction, we show that the pump pulse induces an insulator-to-metal transition, accompanied by the melting of the charge order. Finally, we compare our results with similar studies in manganites and show that the same model can be used to describe the dynamics in nickelates, hinting towards a unified description of these photoinduced electronic ordering phase transitions.

Small-angle X-ray scattering tensor tomography: model of the three-dimensional reciprocal-space map, reconstruction algorithm and angular sampling requirements.

Small-angle X-ray scattering tensor tomography, which allows reconstruction of the local three-dimensional reciprocal-space map within a three-dimensional sample as introduced by Liebi et al. [Nature (2015), 527, 349-352], is described in more detail with regard to the mathematical framework and the optimization algorithm. For the case of trabecular bone samples from vertebrae it is shown that the model of the three-dimensional reciprocal-space map using spherical harmonics can adequately describe the measured data. The method enables the determination of nanostructure orientation and degree of orientation as demonstrated previously in a single momentum transfer q range. This article presents a reconstruction of the complete reciprocal-space map for the case of bone over extended ranges of q. In addition, it is shown that uniform angular sampling and advanced regularization strategies help to reduce the amount of data required.

X-ray ptychography with extended depth of field.

Ptychographic X-ray computed tomography is a coherent diffractive imaging method that offers nanometer-scale resolution with quantitative contrast. It offers the possibility to study relatively thick samples by using high energy X-ray photons and exploiting the phase contrast. However, the limited depth of field forces a compromise between resolution and sample thickness. Multi-slice techniques have been used to account for propagation effects within the sample, enabling imaging beyond the depth-of-field limit. Here we introduce and experimentally demonstrate our multi-slice algorithms that allow for the reconstruction of multiple object slices and the incident illumination, as well as the retrieval of unknown object thickness. Additionally, through numerical studies, we show that smaller scanning steps surprisingly increase the depth of field, which can be further extended by the use of multi-slice methods under conditions stated by theoretical expressions. The results presented here will be instrumental for the routine implementation of the technique for X-ray nanotomography.

Nematic field transfer in a two-dimensional protein fibril assembly.

We perform Atomic Force Microscopy and numerical simulations of a bimodal solution containing long, semiflexible ß-lactoglobulin fibrils and short, flexible ß-lactoglobulin linear aggregates at an air-water interface. Short aggregates orient perpendicular to fibrils at very short distances and preferentially parallel at intermediate distances. At even larger distances an isotropic distribution is observed. Parallel ordering coincides with aggregate stretching: by straightening, small aggregates are able to approach the fibrils within a distance smaller than their radius of gyration. These findings contribute to the understanding of how anisotropic interactions are transferred in two-dimensional bimodal nematic fields of biopolymers at liquid interfaces.

Understanding nanocellulose chirality and structure-properties relationship at the single fibril level.

Nanocellulose fibrils are ubiquitous in nature and nanotechnologies but their mesoscopic structural assembly is not yet fully understood. Here we study the structural features of rod-like cellulose nanoparticles on a single particle level, by applying statistical polymer physics concepts on electron and atomic force microscopy images, and we assess their physical properties via quantitative nanomechanical mapping. We show evidence of right-handed chirality, observed on both bundles and on single fibrils. Statistical analysis of contours from microscopy images shows a non-Gaussian kink angle distribution. This is inconsistent with a structure consisting of alternating amorphous and crystalline domains along the contour and supports process-induced kink formation. The intrinsic mechanical properties of nanocellulose are extracted from nanoindentation and persistence length method for transversal and longitudinal directions, respectively. The structural analysis is pushed to the level of single cellulose polymer chains, and their smallest associated unit with a proposed 2 × 2 chain-packing arrangement.

Anomalous stiffening and ion-induced coil-helix transition of carrageenans under monovalent salt conditions.

The macromolecular conformations of anionic polysaccharides with decreasing linear charge densities­lambda, iota, and kappa carrageenan­, at varying NaCl concentrations, are studied by single-chain statistical analysis of high-resolution atomic force microscopy (AFM) images. Lambda remains in the random coil conformation, whereas iota and kappa undergo ion-induced coil-helix transitions, with a 2-3-fold increase in chain rigidity. At low ionic strengths, I, the polymer chains sequester Na⁺, leading to a greater flexibility, and beyond a critical I to the formation of an intramolecular single helix. The persistence length exhibits a sublinear dependence on the Debye screening length, κ⁻¹, L(p)(e) ∼ κ(-y) (with 0 < y < 1), deviating from the classical polyelectrolyte behavior expressed by Odijk-Skolnick-Fixman or Barrat-Joanny models. Above a certain I, the L(p) shows an upturn, resulting in polymer stiffening and nonmonotonic behavior. This phenomenon is inferred from specific ion-polymer interactions and/or nonlinear electrostatic physics involving ion-ion correlations.

Adsorption at liquid interfaces induces amyloid fibril bending and ring formation.

Protein fibril accumulation at interfaces is an important step in many physiological processes and neurodegenerative diseases as well as in designing materials. Here we show, using ß-lactoglobulin fibrils as a model, that semiflexible fibrils exposed to a surface do not possess the Gaussian distribution of curvatures characteristic for wormlike chains, but instead exhibit a spontaneous curvature, which can even lead to ring-like conformations. The long-lived presence of such rings is confirmed by atomic force microscopy, cryogenic scanning electron microscopy, and passive probe particle tracking at air- and oil-water interfaces. We reason that this spontaneous curvature is governed by structural characteristics on the molecular level and is to be expected when a chiral and polar fibril is placed in an inhomogeneous environment such as an interface. By testing ß-lactoglobulin fibrils with varying average thicknesses, we conclude that fibril thickness plays a determining role in the propensity to form rings.

Correlation between nanomechanics and polymorphic conformations in amyloid fibrils.

Amyloid fibrils occur in diverse morphologies, but how polymorphism affects the resulting mechanical properties is still not fully appreciated. Using formalisms from the theory of elasticity, we propose an original way of averaging the second area moment of inertia for non-axisymmetric fibrils, which constitutes the great majority of amyloid fibrils. By following this approach, we derive theoretical expressions for the bending properties of the most common polymorphic forms of amyloid fibrils (twisted ribbons, helical ribbons, and nanotubes), and we benchmark the predictions to experimental cases. These results not only allow an accurate estimation of the amyloid fibrils' elastic moduli but also bring insight into the structure-property relationships in the nanomechanics of amyloid systems, such as in the closure of helical ribbons into nanotubes.

Polymorphism complexity and handedness inversion in serum albumin amyloid fibrils.

Protein-based amyloid fibrils can show a great variety of polymorphic structures within the same protein precursor, although the origins of these structural homologues remain poorly understood. In this work we investigate the fibrillation of bovine serum albumin--a model globular protein--and we follow the polymorphic evolution by a statistical analysis of high-resolution atomic force microscopy images, complemented, at larger length scales, by concepts based on polymer physics formalism. We identify six distinct classes of coexisting amyloid fibrils, including flexible left-handed twisted ribbons, rigid right-handed helical ribbons and nanotubes. We show that the rigid fibrils originate from flexible fibrils through two diverse polymorphic transitions, first, via a single-fibril transformation when the flexible left-handed twisted ribbons turn into the helical left-handed ribbons, to finally evolve into nanotube-like structures, and second, via a double-fibril transformation when two flexible left-handed twisted ribbons wind together resulting in a right-handed twisted ribbon, followed by a rigid right-handed helical ribbon polymorphic conformation. Hence, the change in handedness occurs with an increase in the level of the fibril's structural organization.

Non-equilibrium nature of two-dimensional isotropic and nematic coexistence in amyloid fibrils at liquid interfaces.

Two-dimensional alignment of shape-anisotropic colloids is ubiquitous in nature, ranging from interfacial virus assembly to amyloid plaque formation. The principles governing two-dimensional self-assembly have therefore long been studied, both theoretically and experimentally, leading, however, to diverging fundamental interpretations on the nature of the two-dimensional isotropic-nematic phase transition. Here we employ single-molecule atomic force microscopy, cryogenic scanning electron microscopy and passive probe particle tracking to study the adsorption and liquid crystalline ordering of semiflexible ß-lactoglobulin fibrils at liquid interfaces. Fibrillar rigidity changes on increasing interfacial density, with a maximum caused by alignment and a subsequent decrease stemming from crowding and domain bending. Coexistence of nematic and isotropic regions is resolved and quantified by a length scale-dependent order parameter S(2D)(d). The nematic surface fraction increases with interfacial fibril density, but depends, for a fixed interfacial density, on the initial bulk concentration, ascribing the observed two-dimensional isotropic-nematic coexistence to non-equilibrium phenomena.

Polymorphism in bovine serum albumin fibrils: morphology and statistical analysis.

We investigate the self-assembly process of the globular protein bovine serum albumin (BSA) into fibrillar structures upon incubating the protein solution at high temperature (90 degreeC) and in an acidic environment (pH 2) for several days. The investigation is performed by atomic force microscopy (AFM) on the self-assembled fibrillar structures, adsorbed on mica substrates from a solution at different fibrillation time snapshots. A rigorous study of structural morphology reveals a sophisticated hierarchy of the BSA fibrils, where two major classes can be identified: flexible and rigid fibrils, with an order of magnitude of difference in their stiffness. Furthermore, each main class can be divided into two subclasses of thin and thick fibrils according to their average height. It is also shown that all types of flexible ribbon-like fibrils at some stage can wrap and close into nanotubes, that is into a rigid class of fibril. A precise statistical analysis of all the subclasses identified is developed throughout the manuscript. The determination of height and contour length distributions, persistence lengths, and other topological characteristics is carried out by processing the coordinates of BSA fibrils acquired from AFM imaging using in-house developed software. The resulting statistical analysis allows better understanding the fibrillation process and the structural properties of the BSA fibrils.

Formation of self-assembled organosilicon-functionalized quinquethiophene monolayers by fast processing techniques.

Different techniques for a relatively fast self-assembled monolayer film formation such as Langmuir-Blodgett (LB), spin-coating, and dip-coating methods have been compared using chloro[11-(5''''-ethyl-2,2':5',2″:5''',2''':5''',2''''-quinquethiophene-5-yl)undecyl]dimethylsilane as a reactive precursor. It was shown that both spin-coating and LB techniques are very promising methods for preparation of highly ordered monolayer films of organosilicon-functionalized quinquethiophene with vertical orientation of oligothiophene fragments, while dip-coating gives only partial coverage. Optimal conditions for complete filling out the substrate surface by the quinquethiophene-containing monolayer by spin-coating and LB methods have been found. Grazing incidence X-ray diffraction measurements confirmed formation of in-plane crystalline order within the monolayer film. Changes in the layer structure were established by X-ray reflectivity and grazing incidence X-ray diffraction methods.

Measurement of intrinsic properties of amyloid fibrils by the peak force QNM method.

We report the investigation of the mechanical properties of different types of amyloid fibrils by the peak force quantitative nanomechanical (PF-QNM) technique. We demonstrate that this technique correctly measures the Young's modulus independent of the polymorphic state and the cross-sectional structural details of the fibrils, and we show that values for amyloid fibrils assembled from heptapeptides, α-synuclein, Aß(1-42), insulin, ß-lactoglobulin, lysozyme, ovalbumin, Tau protein and bovine serum albumin all fall in the range of 2-4 GPa.

Sub-persistence-length complex scaling behavior in lysozyme amyloid fibrils.

We combine atomic force microscopy single-molecule analysis with polymer physics concepts to study molecular conformations of lysozyme amyloid fibrils. We resolve a wavy structure of the fibrils in which the scaling behavior varies at multiple length scales. Bond and pair correlation functions, end-to-end distribution, and wormlike chain model identify three characteristic length scales. At short length scales (≈150 nm), there is a first bending transition of the fibrils corresponding to a bending length L(b). At larger length scales (>2L(b)), fibrils become pseudoperiodic and start to undulate. Finally, at length scales larger than the persistence length (~ µm), the fibrils become flexible and follow a 2D self-avoiding random walk. We interpret these results in terms of the twisting of the fibrils and the impact this has on the area moment of inertia and the propensity of the fibril to bend.