SAXS in inorganic and bioinspired research

INSIGHT: in situ heuristic tool for the efficient reduction of grazing-incidence X-ray scattering data

INSIGHT is a Python-based software tool for processing and reducing 2D grazing-incidence wide- and small-angle X-ray scattering (GIWAXS/GISAXS) data. It offers the geometric transformation of the 2D GIWAXS/GISAXS detector image to reciprocal space, including vectorized and parallelized pixel-wise intensity correction calculations. An explicit focus on efficient data management and batch processing enables full control of large time-resolved synchrotron and laboratory data sets for a detailed analysis of kinetic GIWAXS/GISAXS studies of thin films. It processes data acquired with arbitrarily rotated detectors and performs vertical, horizontal, azimuthal and radial cuts in reciprocal space. It further allows crystallographic indexing and GIWAXS pattern simulation, and provides various plotting and export functionalities. Customized scripting offers a one-step solution to reduce, process, analyze and export findings of large in situ and operando data sets.

Magnetic Alignment of Collagen: Principles, Methods, Applications, and Fiber Alignment Analyses

Anisotropically aligned collagen scaffolds mimic the microarchitectural properties of native tissue, possess superior mechanical properties, and provide the essential physicochemical cues to guide cell response. Biofabrication methodologies to align collagen fibers include mechanical, electrical, magnetic, and microfluidic approaches. Magnetic alignment of collagen was first published in 1983 but widespread use of this technique was hindered mainly due to the low diamagnetism of collagen molecules and the need for very strong tesla-order magnetic fields. Over the last decade, there is a renewed interest in the use of magnetic approaches that employ magnetic particles and low-level magnetic fields to align collagen fibers. In this review, the working principle, advantages, and limitations of different collagen alignment techniques with special emphasis on the magnetic alignment approach are detailed. Key findings from studies that employ high-strength magnetic fields and the magnetic particle-based approach to align collagen fibers are highlighted. In addition, the most common qualitative and quantitative image analyses methods to assess collagen alignment are discussed. Finally, current challenges and future directions are presented for further development and clinical translation of magnetically aligned collagen scaffolds.

Evolution of the Astonishing Naica Giant Crystals in Chihuahua, Mexico

Calcium sulfate (CaSO4) is one of the most common evaporites found in the earth’s crust. It can be found as four main variations: gypsum (CaSO4∙2H2O), bassanite (CaSO4∙0.5H2O), soluble anhydrite, and insoluble anhydrite (CaSO4), being the key difference the hydration state of the sulfate mineral. Naica giant crystals’ growth starts from a supersaturated solution in a delicate thermodynamic balance close to equilibrium, where gypsum can form nanocrystals able to grow up to 11–12 m long. The growth rates are reported to be as slow as (1.4 ± 0.2) × 10−5 nm/s, taking thousands of years to form crystals with a unique smoothness and diaphaneity, which may or may not include solid or liquid inclusions. Conservation efforts can be traced back to other gypsum structures found prior to Naica’s. Furthermore, in the last two decades, several authors have explored the unique requirements in which these crystals grow, the characterization of their environment and microclimatic conditions, and the prediction of deterioration scenarios. We present a state-of-the-art review on the mentioned topics. Beyond the findings on the origin, in this work we present the current state and the foreseeable future of these astounding crystals.

Sol-Gel Processes in Micro-Environments of Black Shale: Learning from the Industrial Production of Nanometer-Sized TiO2 Polymorphs

Micro-environments in black shale are reactors for geochemical reactions that differ from the bulk scale. They occur in small isolated pores of several 10 s to 100 s of nanometers without or with limited ionic exchange by diffusion to the surrounding matrix. The example of the formation of titania polymorphs brookite (and anatase) in black shale demonstrates that pH < 4 of the pore waters or lower must prevail to enable dissolution of Ti-bearing precursors followed by the precipitation of these metastable solids. Comparably low pH is applied during the industrial production of nanometer-sized brookite or anatase by sol-gel methods. The process parameters during industrial production such as low pH, negative Eh, or low ionic strength (to promote agglomeration) allow a comparison with parameters during geochemical processes leading to titania formation in black shale. Sol-gel processes are suggested herein as key geochemical processes in micro-environments of black shale in order to understand the formation of single brookite crystals or agglomerates on a nanometer scale.

Mechanism of silica-lysozyme composite formation unravelled by in situ fast SAXS

A quantitative understanding of aggregation mechanisms leading to the formation of composites of inorganic nanoparticles (NPs) and proteins in aqueous media is of paramount interest for colloid chemistry. In particular, the interactions between silica (SiO₂) NPs and lysozyme (LZM) have attracted attention, because LZM is well-known to adsorb strongly to silica NPs, while at the same time preserving its enzymatic activity. The inherent nature of the aggregation processes leading to NP-LZM composites involves structural changes at length scales from few to at least hundreds of nanometres but also time scales much smaller than one second. To unravel these we used in situ synchrotron-based small-angle X-ray scattering (SAXS) and followed the subtle interparticle interactions in solution at a time resolution of 50 ms/frame (20 fps). We show that if the size of silica NPs (ca. 5 nm diameter) is matched by the dimensions of LZM, the evolving scattering patterns contain a unique structure-factor contribution originating from the presence of LZM. We developed a scattering model and applied it to analyse this structure function, which allowed us to extract structural information on the deformation of lysozyme molecules during aggregation, as well as to derive the mechanisms of composite formation.

Counting crystal clusters – a neutron reflectometry study of calcium phosphate nano-cluster adsorption at the air–liquid Interface

An 11 Å mineral film above a dense prenucleation cluster subphase is shown to be the structure of the early stage of calcium phosphate nucleation from a simulated body fluid.

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.