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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

K-space algorithmic reconstruction (KAREN): a robust statistical methodology to separate Bragg and diffuse scattering

Diffuse scattering occurring in the Bragg diffraction pattern of a long-range-ordered structure represents local deviation from the governing regular lattice. However, interpreting the real-space structure from the diffraction pattern presents a significant challenge because of the dramatic difference in intensity between the Bragg and diffuse components of the total scattering function. In contrast to the sharp Bragg diffraction, the diffuse signal has generally been considered to be a weak expansive or continuous background signal. In this paper, using 1D and 2D models, it is demonstrated that diffuse scattering in fact consists of a complex array of high-frequency features that must not be averaged into a low-frequency background signal. To evaluate the actual diffuse scattering effectively, an algorithm has been developed that uses robust statistics and traditional signal processing techniques to identify Bragg peaks as signal outliers which can be removed from the overall scattering data and then replaced by statistically valid fill values. This method, described as a 'K-space algorithmic reconstruction' (KAREN), can identify Bragg reflections independent of prior knowledge of a system's unit cell. KAREN does not alter any data other than that in the immediate vicinity of the Bragg reflections, and reconstructs the diffuse component surrounding the Bragg peaks without introducing discontinuities which induce Fourier ripples or artifacts from underfilling `punched' voids. The KAREN algorithm for reconstructing diffuse scattering provides demonstrably better resolution than can be obtained from previously described punch-and-fill methods. The superior structural resolution obtained using the KAREN method is demonstrated by evaluating the complex ordered diffuse scattering observed from the neutron diffraction of a single plastic crystal of CBr 4 using pair distribution function analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2016

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. In conclusion, 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.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different translation–libration–screw refinement strategies produce unique diffuse intensity patterns. Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls-as-xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Spinteract: a program to refine magnetic interactions to diffuse scattering data

Magnetic diffuse scattering—the broad magnetic scattering features observed in neutron-diffraction data above a material's magnetic ordering temperature—provides a rich source of information about the material's magnetic Hamiltonian. However, this information has often remained under-utilised due to a lack of available computer software that can fit values of magnetic interaction parameters to such data. Here, an open-source computer program, Spinteract, is presented, which enables straightforward refinement of magnetic interaction parameters to powder and single-crystal magnetic diffuse scattering data. Here, the theory and implementation of this approach are summarised. Examples are presented of refinements to published experimental diffuse-scattering data sets for the canonical antiferromagnet MnO and the highly-frustrated classical spin liquid Gd 3 Ga 5 O 12 . Guidelines for data collection and refinement are outlined, and possible developments of the approach are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Neutron and x-ray scattering study of phonon dispersion and diffuse scattering in ( Na , Bi ) Ti O 3 - x BaTi O 3 single crystals near the morphotropic phase boundary

Neutron and x-ray scattering measurements were performed on (Na 1/2 Bi 1/2 )TiO 3-x at % BaTiO 3 (NBT-xBT) single crystals (x = 4, 5, 6.5, and 7.5) across the morphotropic phase boundary (MPB), as a function of both composition and temperature, and probing both structural and dynamical aspects. In addition to the known diffuse scattering pattern near the gamma points, our measurements revealed new, faint superlattice peaks, as well as an extensive diffuse scattering network, revealing a short-range ordering of polar nanoregions (PNR) with a static stacking morphology. Furthermore, in samples with compositions closest to the MPB, our inelastic neutron scattering investigations of the phonon dynamics showed two unusual features in the acoustic phonon branches, between the superlattice points, and between the superlattice points and gamma points, respectively. Finally, these critical elements are not present in the other compositions away from the MPB, which suggests that these features may be related to the tilt modes coupling behavior near the MPB.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

A Process for Modelling Diffuse Scattering from Disordered Molecular Crystals, Illustrated by Application to Monoclinic 9-Chloro-10-methylanthracene

Diffuse scattering from a crystal contains valuable information about the two-body correlations (related to the nanoscale order) in the material. Despite years of development, the detailed analysis of single crystal diffuse scattering (SCDS) has yet to become part of the everyday toolbox of the structural scientist. Recent decades have seen the pair distribution function approach to diffuse scattering (in fact, total scattering) from powders become a relatively routine tool. However, analysing the detailed, complex, and often highly anisotropic three-dimensional distribution of SCDS remains valuable yet rare because there is no routine method for undertaking the analysis. At present, analysis requires significant investment of time to develop specialist expertise, which means that the analysis of diffuse scattering, which has much to offer, is not incorporated thorough studies of many compounds even though it has the potential to be a very useful adjunct to existing techniques. This article endeavours to outline in some detail how the diffuse scattering from a molecular crystal can be modelled relatively quickly and largely using existing software tools. It is hoped this will provide a template for other studies. To enable this, the entire simulation is included as deposited material.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters

Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient ≥0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Intermolecular correlations are necessary to explain diffuse scattering from protein crystals

Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signal reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Integral X-ray diffuse scattering for studying irradiation-induced dislocation loops in single crystals

Numerical diffuse scattering cross-section calculations are used to establish a rigorous basis for determining the concentration and size distribution of dis­location loops in irradiated single crystals from integral X-ray diffuse scattering (XRDS) measurements. Differential XRDS intensities for prismatic {111} type dislocation loops are numerically calculated as a function of loop radius R and wavevectors q relative to Bragg reflections in tungsten. The results show the well known 1/q 2 Huang scattering form at small q that transitions to a ∼1/q 4 dependence associated with the Stokes–Wilson approximation for q ≳ 1/R. More importantly, they show further that the 1/q 4 falloff is not the asymptotic large-q form of the diffuse scattering for small loops (R < 200 Å) as has often been assumed. Rather, for loop sizes as small as R ≃ 5 Å with strong curvature, the calculations show definitively that the scattering transitions to a robust 1/q 5 falloff at larger q that arises due to the local strains near the dislocation core defining the circumference of the dislocation loops. The presence of this 1/q 5 asymptotic form for both small and large loops is experimentally confirmed using an integral XRDS measurement around the 110 reflection on self-ion-irradiated tungsten combined with numerically calculated integral XRDS cross-sections. Accordingly, the historical two-region theoretical treatment of the cross-sections for integral XRDS is extended to a three-region model that has direct sensitivity to the (first-moment) dislocation line lengths of dislocation loops. In conclusion, these developments enable the use of both numerical and analytically modeled cross-sections to make accurate integral XRDS determinations of dislocation loop sizes and concentrations using modest-intensity laboratory X-ray sources.

42 ENGINEERING↗
DOE OSTI2021

Multiphonon diffuse scattering in solids from first principles: Application to layered crystals and two-dimensional materials

Time-resolved diffuse scattering experiments have gained increasing attention due to their potential to reveal nonequilibrium dynamics of crystal lattice vibrations with full momentum resolution. Although progress has been made in interpreting experimental data on the basis of one-phonon scattering, understanding the role of individual phonons can be sometimes hindered by multiphonon excitations. In Ref. [M. Zacharias, H. Seiler, F. Caruso, D. Zahn, F. Giustino, P. C. Kelires, and R. Ernstorfer, Phys. Rev. Lett. 127, 207401 (2021)], we have introduced a rigorous approach for the calculation of the all-phonon inelastic scattering intensity of solids from first-principles. In the present work, we describe our implementation in detail and show that multiphonon interactions are captured efficiently by exploiting translational and time-reversal symmetries of the crystal. We demonstrate its predictive power by calculating the scattering patterns of monolayer molybdenum disulfide (MoS 2 ), bulk MoS 2 , and black phosphorus (bP), and we obtain excellent agreement with our measurements of thermal electron diffuse scattering. Remarkably, our results show that multiphonon excitations dominate in bP across multiple Brillouin zones, while in MoS 2 they play a less pronounced role. We expand our analysis for each system and examine the effect of individual atomic and interatomic vibrational motion on the diffuse scattering signals. We further demonstrate the high-throughput capability of our approach by reporting all-phonon scattering maps of two-dimensional MoSe 2 , WSe 2 , WS 2 , graphene, and CdI 2 , rationalizing in each case the effect of multiphonon processes. As a side point, we show that the special displacement method reproduces the thermally distorted configuration that generates precisely the all-phonon diffuse pattern. In conclusion, the present methodology opens the way for systematic calculations of the scattering intensity in crystals and the accurate interpretation of static and time-resolved inelastic scattering experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Dynamical Theory of X-Ray Diffraction for Restricted Beams: II. Diffuse Scattering by a Porous Crystal

A theory of X-ray diffuse scattering of restricted beams by a porous crystal is developed. Models of cylindrical and ellipsoidal pores, as well as the pores in the form of rectangular and triangular prisms, are considered. For these pores, the expressions for correlation eigenfunctions, static Debye—Weller factors, and correlation volumes are derived. The effect of the inclination and spatial correlation of pores on the equal-intensity diffuse-scattering contours is analyzed. The influence of the pore size fluctuation on the scattered intensity distribution is demonstrated.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Single Crystal Diffuse Neutron Scattering

Diffuse neutron scattering has become a valuable tool for investigating local structure in materials ranging from organic molecular crystals containing only light atoms to piezo-ceramics that frequently contain heavy elements. Although neutron sources will never be able to compete with X-rays in terms of the available flux the special properties of neutrons, viz. the ability to explore inelastic scattering events, the fact that scattering lengths do not vary systematically with atomic number and their ability to scatter from magnetic moments, provides strong motivation for developing neutron diffuse scattering methods. Here, we compare three different instruments that have been used by us to collect neutron diffuse scattering data. Two of these are on a spallation source and one on a reactor source.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Magnetic Diffuse Scattering of YBaCo 4 O 7 and LuBaCo 4 O 7 on Kagome and Triangular Lattices

In this work, the magnetic diffuse scattering of YBaCo 4 O 7 and LuBaCo 4 O 7 with alternating kagome and triangular lattices has been studied through neutron scattering measurements on single-crystal samples. In YBaCo 4 O 7 , the line-shape-magnetic-diffuse scattering is observed around the magnetic transition temperature, which is consistent with the Monte Carlo simulation. In LuBaCo 4 O 7 , the line-shape-magnetic-diffuse scattering has not been detected. At low temperature, the propagation vectors of the observed magnetic reflections are different between YBaCo 4 O 7 and LuBaCo 4 O 7 . The structural distortion in RBaCo 4 O 7 is suggested to play a critical role for the magnetic properties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Synchrotron X-ray diffuse scattering from a stable polymorphic material: terephthalic acid, C 8 H 6 O 4

Terephthalic acid (TPA, C 8 H 6 O 4 ) is an industrially important chemical, one that shows polymorphism and disorder. Three polymorphs are known, two triclinic [(I) and (II)] and one monoclinic (III). Of the two triclinic polymorphs, (II) has been shown to be more stable in ambient conditions. This paper presents models of the local order of polymorphs (I) and (II), and compares the single-crystal diffuse scattering (SCDS) computed from the models with that observed from real crystals. TPA shows relatively weak and less-structured diffuse scattering than some other polymorphic materials, but it does appear that the SCDS is less well modelled by a purely harmonic model in polymorph (I) than in polymorph (II), according to the idea that the diffuse scattering is sensitive to anharmonicity that presages a structural phase transition. The work here verifies that displacive correlations are strong along the molecular chains and weak laterally, and that it is not necessary to allow the —COOH groups to librate to successfully model the diffuse scattering – keeping in mind that the data are from X-ray diffraction and not directly sensitive to H atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Methods for calculating X-ray diffuse scattering from a crystalline medium with spheroidal quantum dots

Two independent approaches to calculate the angular distribution of X-ray diffusion scattering from a crystalline medium with spheroidal quantum dots (QDs) have been proposed. The first method is based on the analytical solution involving the multipole expansion of elastic strain fields beyond QDs. The second approach is based on calculations of atomic displacements near QDs by the Green’s function method. An analysis of the diffuse scattering intensity distribution in the reciprocal space within these two approaches shows that both methods yield similar results for the chosen models of QD spatial distribution.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Femtosecond temperature measurements of laser-shocked copper deduced from the intensity of the x-ray thermal diffuse scattering

We present 50-fs, single-shot measurements of the x-ray thermal diffuse scattering (TDS) from copper foils that have been shocked via nanosecond laser ablation up to pressures above ∼135 GPa. We hence deduce the x-ray Debye–Waller factor, providing a temperature measurement. The targets were laser-shocked with the DiPOLE 100-X laser at the High Energy Density endstation of the European X-ray Free-Electron Laser. Single x-ray pulses, with a photon energy of 18 keV, were scattered from the samples and recorded on Varex detectors. Despite the targets being highly textured (as evinced by large variations in the elastic scattering) and with such texture changing upon compression, the absolute intensity of the azimuthally averaged inelastic TDS between the Bragg peaks is largely insensitive to these changes, and allowing for both Compton scattering and the low-level scattering from a sacrificial ablator layer provides a reliable measurement of $T/Θ^2_D$, where Θ D is the Debye temperature. We compare our results with the predictions of the SESAME 3336 and LEOS 290 equations of state for copper and find good agreement within experimental errors. We, thus, demonstrate that single-shot temperature measurements of dynamically compressed materials can be made via thermal diffuse scattering of XFEL radiation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗