Fast extraction of three-dimensional nanofiber orientation from WAXD patterns using machine learning.

Structural disclosure of biological materials can help our understanding of design disciplines in nature and inspire research for artificial materials. Synchrotron microfocus X-ray diffraction is one of the main techniques for characterizing hierarchically structured biological materials, especially the 3D orientation distribution of their interpenetrating nanofiber networks. However, extraction of 3D fiber orientation from X-ray patterns is still carried out by iterative parametric fitting, with disadvantages of time consumption and demand for expertise and initial parameter estimates. When faced with high-throughput experiments, existing analysis methods cannot meet the real time analysis challenges. In this work, using the assumption that the X-ray illuminated volume is dominated by two groups of nanofibers in a gradient biological composite, a machine-learning based method is proposed for fast and automatic fiber orientation metrics prediction from synchrotron X-ray micro-focused diffraction data. The simulated data were corrupted in the training procedure to guarantee the prediction ability of the trained machine-learning algorithm in real-world experimental data predictions. Label transformation was used to resolve the jump discontinuity problem when predicting angle parameters. The proposed method shows promise for application in the automatic data-processing pipeline for fast analysis of the vast data generated from multiscale diffraction-based tomography characterization of textured biomaterials.

Scanning electron microscopy as a method for sample visualization in protein X-ray crystallography.

Developing methods to determine high-resolution structures from micrometre- or even submicrometre-sized protein crystals has become increasingly important in recent years. This applies to both large protein complexes and membrane proteins, where protein production and the subsequent growth of large homogeneous crystals is often challenging, and to samples which yield only micro- or nanocrystals such as amyloid or viral polyhedrin proteins. The versatile macromolecular crystallography microfocus (VMXm) beamline at Diamond Light Source specializes in X-ray diffraction measurements from micro- and nanocrystals. Because of the possibility of measuring data from crystalline samples that approach the resolution limit of visible-light microscopy, the beamline design includes a scanning electron microscope (SEM) to visualize, locate and accurately centre crystals for X-ray diffraction experiments. To ensure that scanning electron microscopy is an appropriate method for sample visualization, tests were carried out to assess the effect of SEM radiation on diffraction quality. Cytoplasmic polyhedrosis virus polyhedrin protein crystals cryocooled on electron-microscopy grids were exposed to SEM radiation before X-ray diffraction data were collected. After processing the data with DIALS, no statistically significant difference in data quality was found between datasets collected from crystals exposed and not exposed to SEM radiation. This study supports the use of an SEM as a tool for the visualization of protein crystals and as an integrated visualization tool on the VMXm beamline.

Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism.

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with large R values (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.

Area Selective Growth of Titanium Diselenide Thin Films into Micropatterned Substrates by Low-Pressure Chemical Vapor Deposition.

The neutral, distorted octahedral complex [TiCl4(Se n Bu2)2] (1), prepared from the reaction of TiCl4 with the neutral Se n Bu2 in a 1:2 ratio and characterized by IR and multinuclear (1H, 13C{1H}, 77Se{1H}) NMR spectroscopy and microanalysis, serves as an efficient single-source precursor for low-pressure chemical vapor deposition (LPCVD) of titanium diselenide, TiSe2, films onto SiO2 and TiN substrates. X-ray diffraction patterns on the deposited films are consistent with single-phase, hexagonal 1T-TiSe2 (P3̅m1), with evidence of some preferred orientation of the crystallites in thicker films. The composition and structural morphology was confirmed by scanning electron microscopy (SEM), energy dispersive X-ray, and Raman spectroscopy. SEM imaging shows hexagonal plate crystallites growing perpendicular to the substrate, but these tend to align parallel to the surface when the quantity of reagent is reduced. The resistivity of the crystalline TiSe2 films is 3.36 ± 0.05 × 10-3 Ω·cm with a carrier density of 1 × 1022 cm-3. Very highly selective film growth from the reagent was observed onto photolithographically patterned substrates, with film growth strongly preferred onto the conducting TiN surfaces of SiO2/TiN patterned substrates. TiSe2 is selectively deposited within the smallest 2 µm diameter TiN holes of the patterned TiN/SiO2 substrates. The variation in crystallite size with different diameter holes is determined by microfocus X-ray diffraction and SEM, revealing that the dimensions increase with the hole size, but that the thickness of the crystals stops increasing above ∼20 µm hole size, whereas their lengths/widths continue to increase.