The influence of Hinode/SOT NFI instrumental effects on the visibility of simulated prominence fine structures in Hα

Context. Models of entire prominences with their numerous fine structures distributed within the prominence magnetic field use approximate radiative transfer techniques to visualize the simulated prominences. However, to accurately compare synthetic images of prominences obtained in this way with observations and to precisely analyze the visibility of even the faintest prominence features, it is important to take into account the influence of instrumental properties on the synthetic spectra and images. Aims. In the present work, we investigate how synthetic Hα images of simulated prominences are impacted by the instrumental effects induced by the Narrowband Filter Imager (NFI) of the Solar Optical Telescope (SOT) onboard the Hinode satellite. Methods. To process the synthetic Hα images provided by 3D Whole-Prominence Fine Structure (WPFS) models into SOT-like synthetic Hα images, we take into account the effects of the integration over the theoretical narrow-band transmission profile of NFI Lyot filter, the influence of the stray-light and point spread function (PSF) of Hinode/SOT, and the observed noise level. This allows us to compare the visibility of the prominence fine structures in the SOT-like synthetic Hα images with the synthetic Hα line-center images used by the 3D models and with a pair of Hinode/SOT NFI observations of quiescent prominences. Results. The comparison between the SOT-like synthetic Hα images and the synthetic Hα line-center images shows that all large and small-scale features are very similar in both visualizations and that the same very faint prominence fine structures can be discerned in both. This demonstrates that the computationally efficient Hα line-center visualization technique can be reliably used for the purpose of visualization of complex 3D prominence models. In addition, the qualitative comparison between the SOT-like synthetic images and prominence observations shows that the 3D WPFS models can reproduce large-scale prominence features rather well. However, the distribution of the prominence fine structures is significantly more diffuse in the observations than in the models and the diffuse intensity areas surrounding the observed prominences are also not present in the synthetic images. We also found that the maximum intensities reached in the models are about twice as high as those present in the observations–an indication that the mass-loading assumed in the present 3D WPFS models might be too large.

Ni cluster formation in low temperature annealed Ni50.6Ti49.4

Various low temperature treatments of Ni[Formula: see text]Ti[Formula: see text] have shown an unexpected effect on the martensitic start temperature. Periodic diffuse intensity distributions in reciprocal space indicate the formation of short pure Ni strings along the [Formula: see text]111[Formula: see text] directions in the B2 ordered lattice, precursing the formation of Ni4Ti3 precipitates formed at higher annealing temperatures.

Measuring and modeling diffuse scattering in protein X-ray crystallography

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.

Measuring and modeling diffuse scattering in protein X-ray crystallography

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations must be measured. Until now measurement of diffuse scattering from protein crystals has been scarce, due to the extra effort of collecting diffuse data. Here, we present three-dimensional measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested Translation-Libration-Screw (TLS), Liquid-Like Motions (LLM), and coarse-grained Normal Modes (NM) models of protein motions. The LLM model provides a global picture of motions and were refined against the diffuse data, while the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that NM-based refinement can generate dynamics-inspired structural models that simultaneously agree with both Bragg and diffuse scattering.SignificanceThe structural details of protein motions are critical to understanding many biological processes, but they are often hidden to conventional biophysical techniques. Diffuse X-ray scattering can reveal details of the correlated movements between atoms; however, the data collection historically has required extra effort and dedicated experimental protocols. We have measured three-dimensional diffuse intensities in X-ray diffraction from CypA and trypsin crystals using standard crystallographic data collection techniques. Analysis of the resulting data is consistent with the protein motions resembling diffusion in a liquid or vibrations of a soft solid. Our results show that using diffuse scattering to model protein motions can become a component of routine crystallographic analysis through the extension of commonplace methods.

Interpretation of electron diffraction patterns in the presence of oriented planar faults

The presence of high planar-fault densities in thin films,e.g.nanotwinned films, leads to peculiar diffraction effects. Frequently, the planar faults are oriented perpendicular to the growth direction. For the case of (nanosized) thin films of face-centered cubic (fcc) metals, often a {111}fccfiber texture prevails with the fiber axis parallel to the film normal. In diffraction patterns of cross-sectional transmission electron microscopy (TEM) samples of such films, as a consequence of twinning with (111) planes parallel to the surface as twinning planes, intensity streaks appear parallel to the growth direction. These intensity streaks are, however, invisible in diffraction patterns of top-view TEM samples. The latter diffraction patterns might be interpreted, at first sight, in terms of the diffraction pattern of a somehow textured fcc polycrystal. However, the diffraction-ring radii deviate from the expected radii. The consideration of intensity cylinders in reciprocal space formed by diffuse intensity streaks generated by the planar faults leads to a perfect match of the accordingly predicted radii with the observed intensity-ring radii.

A modulation wave approach to the order hidden in disorder

The usefulness of a modulation wave approach to understanding and interpreting the highly structured continuous diffuse intensity distributions characteristic of the reciprocal spaces of the very large family of inherently flexible materials which exhibit ordered `disorder' is pointed out. It is shown that both longer range order and truly short-range order are simultaneously encoded in highly structured diffuse intensity distributions. The long-range ordered crystal chemical rules giving rise to such diffuse distributions are highlighted, along with the existence and usefulness of systematic extinction conditions in these types of structured diffuse distributions.

Energy-filtered electron diffuse scattering of ferroelectrics PMN and PMN-xPT

PbMb1/3Nb2/3O3 (PMN) and its solid solution (1-x)PbMb1/3Nb2/3O3-(x)PbTiO3 (PMN-xPT) are relaxor ferroelectrics which have attracted attention in the last few decades because of their very interesting dielectric and piezoelectric properties and have since be two of the most extensively studied. All the previous studies emphasized the role of the local structural fluctuations leading to local changes in symmetries [1] due to displacements of ions in the unit-cell. We studied PMN and PMN-xPT by electron diffuse scattering using an in-column energy filter and Imaging-Plates as detector. We found evidences for streaks of intensity along the [110]* direction as previously found in PbZn1/3Nb2/3O3 (PZN) with neutron diffraction [2]. Moreover, weak diffuse scattering sheets can be observed along (111)* reciprocal planes showing the existence of correlations along the [111] directions of the direct lattice. Figure 1 shows a diffraction pattern taken along [02-1] zone axis presenting both diffuse features. This can be related to the displacement of Pb ions along the diagonals of the cube found by simulation [3] but greatly complexify the analysis of the shape of the diffuse intensity. Compared to the neutron, electron diffraction has the advantage of two dimensional recording of diffuse scattering and eventually sensitivity to charge ordering but quantitative analysis is limited due to the complication of multiple scattering and the lack of sufficient energy resolution for the study of inelastic phonon scattering.

A modulation wave approach to the long range order hidden in nominal 'disorder'

While the definition of a crystal in terms of pure point diffraction/sharp Bragg reflections only is undoubtedly an excellent approximation for many crystalline materials, there exists a large and growing family of phases for which such a description is grossly inadequate: namely crystalline materials whose reciprocal spaces exhibit highly structured, continuous, diffuse intensity distributions which are essentially long range ordered in at least one or more dimensions (see e.g. Fig.1). To gain insight into both the local order, as well as the long range order, hidden in disordered materials of this type it is very helpful, if not essential, to use the language of modulated structures. An approach of this type automatically emphasizes the close relationship between the crystallography of disordered structures and aperiodic crystallography in general. In this contribution, the use of such an approach to understand the often highly structured shapes of such diffuse distributions, the characteristic extinction conditions frequently associated with them and the long range crystal chemical rules underlying their existence will be highlighted. Fig.1: <11-2> and <-110> zone axis electron diffraction patterns of (a) β-cristobalite and (b) SiO2-tridymite.

SHORT RANGE ORDERING AND LOCAL DISPLACEMENT OF ALLOYS STUDIED BY CVM

Cluster Variation Method (CVM) is a powerful statistical mechanics means to investigate phase equilibria of an alloy. The advantageous feature of the CVM stems from the fact that wide range of atomic correlations which play an important role at the phase transition is efficiently incorporated into the free energy formula. Hence, configurational fluctuation can be systematically studied through the calculations of correlation functions in the real space and short range order diffuse intensity spectrum in the k-space. However, one of the deficiencies of the conventional CVM is the fact that local lattice distortion (local atomic displacement) is not correctly dealt with. In order to improve such shortcomings, Continuous Displacement Cluster Variation Method (CDCVM) has been developed. In the CDCVM, local lattice distortion is mapped onto the configurational freedom of a multi-component alloy on a rigid (uniformly deformable) lattice. With CDCVM, the applicability of CVM is enlarged and the calculations of diffuse intensity spectrum originating from local lattice distortion can be performed.

On the Stability of 3C-SiC Single Crystals at High Temperatures

The 3C-6H polytypic transition in 3C-SiC single crystals is studied by means of diffuse X-ray scattering (DXS) coupled with transmission electron microscopy (TEM). TEM reveals that the partially transformed SiC crystals contain regions of significantly transformed SiC (characterized by a high density of stacking faults) co-existing with regions of pure 3C-SiC. The simulation of the diffuse intensity allows to determine both the volume fraction of transformed material and the transformation level within these regions. It is further shown that the evolution with time and temperature of the transition implies the multiplication and glide of partial dislocations, the kinetics of which are quantified by means of DXS.