Simultaneous fitting of X-ray and neutron diffuse scattering data

Conventional crystallographic refinement uses the Bragg-peak intensities and gives the single-site average crystal structure. Information about short-range order and local order is contained in the diffuse scattering that is distributed throughout reciprocal space. Models of the short-range order in materials can now be automatically refined. The complementarity of X-ray and neutron diffraction data, and the value of simultaneously refining a structural model against both types of data, has long been known. This paper presents the first refinement of a short-range-order model against comprehensive X-ray and neutron diffuse scattering data simultaneously. The sample is the organic molecular crystal benzil, C14H10O2 (for neutron work H is replaced by D). The technique gives new insights into local order in crystalline materials, including the dynamic correlation structure indicative of the dynamics of molecules in the crystalline state, and successfully overcomes limitations of using only the X-ray data set

The geometry, topology and structure of amorphous solids

Clusters of atoms can be divided into three categories depending on their topology. One of the categories provides the basis for development of a model of a perfectly random structure (ideal amorphous solid) using the non-equilateral triangle topology i

Constitutive modeling of the anisotropic behavior of Mullins softened filled rubbers

Original constitutive modeling is proposed for filled rubber materials in order to capture the anisotropic softened behavior induced by general non-proportional pre-loading histo-ries. The hyperelastic framework is grounded on a thorough analysis of cyclic experimental data. The strain energy density is based on a directional approach. The model leans on the strain amplification factor concept applied over material directions according to the Mul-lins softening evolution. In order to provide a model versatile that applies for a wide range of materials, the proposed framework does not require to postulate the mathematical forms of the elementary directional strain energy density and of the Mullins softening evo-lution rule. A computational procedure is defined to build both functions incrementally from experimental data obtained during cyclic uniaxial tensile tests. Successful compari-sons between the model and the experiments demonstrate the model abilities. Moreover, the model is shown to accurately predict the non-proportional uniaxial stress-stretch responses for uniaxially and biaxially pre-stretched samples. Finally, the model is effi-ciently tested on several materials and proves to provide a quantitative estimate of the anisotropy induced by the Mullins softening for a wide range of filled rubbers

Simulation of diffuse scattering in DL-norleucine

The diffraction patterns of DL-norleucine (SR-2-aminohexanoic acid, DL-Nle) crystals may show obvious diffuse scattering, usually described as `streaking', between the Bragg peaks. This phenomenon is obviously related to the non-ideal behaviour of the crystal. The normal interpretation is disorder in the stacking of weakly interacting 2D layers, known also for a number of other racemates of amino acids with linear hydrophobic side chains, as well as 1:1 complexes between different L- and D-enantiomers (quasi-racemates). Presented here is the first attempt to extract the information hidden in the diffuse scattering for this group of compounds by applying Monte Carlo simulations to the site distributions of two polymorphs in a block of 48 × 48 × 48 unit cells (four sites in each unit cell, 442 368 in total). The results demonstrate that it is indeed possible to model the diffuse scattering and relate it to processes expected to take place during phase transitions, characterized by slipping of molecular bilayers (or parts of them) relative to their neighbours. The understanding of the (intermediate) mixed phases in terms of domain size and defect density is consequently brought to a new level

Local structure of relaxor ferroelectric SrxBa1-xNb2O6 from a pair distribution function analysis

Pair distribution function analysis of neutron-scattering data and of ab initio molecular dynamics results have been employed to study short-range structural correlations and their temperature dependence in a heavily disordered dielectric material SrxBa1-xNb2O6 (x = 0.35, 0.5, and 0.61). Intrinsic disorder caused by a partial occupation of the cationic sites by differently sized Sr and Ba atoms and their vacancies introduces important local strains to the structure and directly influences the Nb-O-6 octahedra tilting. The resulting complex system of tilts is found to be both temperature and Sr-doping sensitive with the biggest tilt magnitudes reached at low temperatures and high strontium contents, where ferroelectric relaxor behavior appears. We find evidence for two Nb-O-6 subsystems with different variations of niobium-oxygen bond lengths, distinct dynamics, and disparate levels of deviation from macroscopic polarization direction. These findings establish a detailed picture of the local structure of SrxBa1-xNb2O6 and provide a deeper insight into the origins of the materials dielectric properties.This work was supported by the Czech Science Foundation (Project No. 16-09142S). The computational part of this research was undertaken on the NCI National Facility in Canberra, Australia, which is supported by the Australian Commonwealth Government.

An analysis of the impact of pre-analytical factors on the urine proteome: Sample processing time, temperature, and proteolysis

Purpose: We have examined the impact of sample processing time delay, temperature, and the addition of protease inhibitors (PIs) on the urinary proteome and peptidome, an important aspect of biomarker studies. Experimental design: Ten urine samples from patients with varying pathologies were each divided and PIs added to one-half, with aliquots of each then processed and frozen immediately, or after a delay of 6 h at 4°C or room temperature (20–22°C), effectively yielding 60 samples in total. Samples were then analyzed by 2D-PAGE, SELDI-TOF-MS, and immunoassay. Results: Interindividual variability in profiles was the dominant feature in all analyses. Minimal changes were observed by 2D-PAGE as a result of delay in processing, temperature, or PIs and no changes were seen in IgG, albumin, β2-microglobulin, or α1-microglobulin measured by immunoassay. Analysis of peptides showed clustering of some samples by presence/absence of PIs but the extent was very patient-dependent with most samples showing minimal effects. Conclusions and clinical relevance: The extent of processing-induced changes and the benefit of PI addition are patient- and sample-dependent. A consistent processing methodology is essential within a study to avoid any confounding of the results

Diffuse X-ray scattering and disorder in p-methyl-N-(p-chlorobenzylidene)aniline, C14H12ClN (ClMe): analysis via automatic refinement of a Monte Carlo model

A recently developed method for fitting a Monte Carlo computer simulation model to observed single-crystal diffuse X-ray scattering has been applied to (hOl) scattering data obtained for the disordered compound p-methyl-N-(p-chlorobenzylidene)aniline, C14H12ClN (ClMe), at 295 K. Each molecular site is occupied by a molecule in one of four basically different orientations defined by combinations of a side-to-side and an end-to-end flip. These different orientations were represented in the model by two sets of binary random variables. In addition to these occupancy variables, the model also allowed local orientational and centre-of-mass translational displacements. The disordered structure was modelled using rigid-body molecules linked by harmonic springs to represent 'effective' intermolecular interactions. The refined model included 4 parameters describing the correlation of neighbouring occupational variables and 28 parameters describing the force-constant and 'size-effect' parameters on seven symmetry-inequivalent types of intermolecular vectors. The model refined to an overall agreement factor, R = [∑ w(ΔI)2/∑ wIobs/2]1/2, of 32.8% for 28500 data points. It was found that the SRO correlation structure observed within the layers of molecules in the ab plane is typical of a frustrated lattice, where nearest- and second-nearest-neighbour effects oppose each other. This appears to be the main difference between this compound and the sister compound, p-chloro-N-(p-methylbenzylidene)aniline (MeCl), studied previously. The local relaxational displacements that result from local 'size-effect' strains operating on different intermolecular vectors generally reflect the tendency for distances involving Cl-Cl interactions to be longer than the observed average distances

One hundred years of diffuse X-ray scattering

It is not generally appreciated that X-ray diffuse scattering has been known for almost as long as the Bragg scattering that is used in crystal structure determination. While we are celebrating the centenary of the birth of crystallography, marked by th

Hexagonal paracrystals

Spatially interacting Gaussian random variables arranged on a hexagonal lattice are used to construct examples of hexagonal paracrystals. As for previously described paracrystals on a square lattice the distributions may be specified by a variance, σL 2