X-ray Fluorescence Holography Research Articles

New Structural Analysis Methods for Hemoglobin Crystals. Time-Resolved Cryogenic X-Ray Crystallography with Extended Pulsed-Laser Pumping and 3D Imaging by X-Ray Fluorescence Holography

Hemoglobin (Hb) has long served as a model for studying protein allostery in general. Static crystal structures of deoxy tense (T) state and oxy relaxed (R) state of Hb reveal multiple differences at both tertiary and quaternary levels. However, we still lack an adequate understanding of how these structural differences control ligand binding. Here we present two methods for Hb crystals to investigate the ligation-linked protein motion and the atomic details of the heme active site structure.The first method is time-resolved X-ray crystallography combined with high-repetition pulsed-laser pumping and cryogenic trapping. At cryogenic temperatures under 50 K, a photo-dissociated ligand molecule can move to only the limited range near the heme, and the protein moiety can undergo only small structural changes. By contrast, at 100-140 K under continuous pulsed-laser irradiation, we found that ligand migration and protein relaxation can be observed. We have succeeded in tracking the photo-dissociated ligand molecule that migrates along the pathway connecting inner cavities of Hb in a different direction in each subunit.The second method is atomic-resolution X-ray fluorescence holography (XFH), which utilizes fluorescing atoms as a wave source within a crystal sample. So far, XFH has generally been applied to inorganic materials to investigate the microscopic environments of trace metals. This is the first application of XFH for protein crystals. For Hb crystals, XFH can provide the three dimensional atomic images around the iron central atoms of the individual hemes. We have carried out XFH measurements at 100 K of CO-bound Hb crystals at BL6C, KEK, Japan. We will present our latest data and share with you the results and discussion of this work.

X-ray Fluorescence Holography for a Ti–Nb Binary Alloy Consisting of the Martensite, Austenite and Omega Phase

Abstract The local atomic structure near an Nb atom in a Ti–20 at. %Nb alloy single crystal, which consists of the β, α′′ and ω Ti phases, was investigated by means of X-ray fluorescence holography (XFH). The atomic images were reconstructed in the vicinity of an Nb atom, which is one of the typical β stabilizing elements in β Ti alloys. Most atoms in the β Ti primary phase were reconstructed clearly. The atoms in the α′′ Ti martensite phase could not be reconstructed, because the α′′ Ti martensite has the crystal structure with low symmetry. Some atoms in the ω Ti fine precipitates were reconstructed successfully, although the amount of the ω Ti phase was much smaller than that of the β phase. An Nb atom and its first nearest neighbors tend to keep the BCC structure even upon the ω Ti phase formation.

Atomic Image Reconstruction from Atomic Resolution Holography Using <i>L</i><sub>1</sub>-Regularized Linear Regression

Inverse x-ray fluorescence holography provides new knowledge about the local atomic structure around dopants in crystals. The three-dimensional atomic image is reconstructed from the inverse x-ray fluorescence hologram using a calculation. The performance of the algorithm used for this calculation is important. The Barton method, which is based on the Fourier transform, is typically used. However, images reconstructed by this method sometimes contain artifacts. I developed an algorithm (SPEA-L1) using an iterative method with L1 regularization and report its performance. [DOI: 10.1380/ejssnt.2016.158]

Fast Calculation Algorithm Using Barton's Method for Reconstructing Three-Dimensional Atomic Images from X-ray Fluorescence Holograms

Abstract A fast calculation algorithm for three-dimensional atomic image reconstruction from X-ray fluorescence holography (Barton's method) is described. This method employs HEALPix, an algorithm that is used to subdivide a spherical surface in which each pixel covers an identical surface area. Using this algorithm, the computing time for atomic image reconstruction is reduced by a factor of 14.5. The time can be reduced further by parallel processing and an optimization of the resolution parameter of HEALPix.

Matrix Effects in X-ray Fluorescence Holography: Samples of Arbitrary Thickness

Abstract The influence of matrix effects i.e. beam attenuation (BA) and indirect excitation (IE) on local structure imaging with multiple-energy x-ray fluorescence holography is studied using computer simulations. An analytic formalism is developed which allows for the description of BA and IE when the thickness of the sample is arbitrary. It is shown that beyond the thin-sample approximation, in specific cases, the measured holograms cannot be treated as entirely element sensitive. Consequently, it is demonstrated that due to the reduction of element sensitivity, spurious maxima can arise in the holographic reconstruction which can be misinterpreted as atomic images. The proposed formalism allows one to analyse BA and IE and to correct for them. It opens way for quantitative interpretation of x-ray fluorescence holograms.

On element-sensitive determination of local atomic structure with white-beam X-ray fluorescence holography

On element-sensitive determination of local atomic structure with white-beam X-ray fluorescence holography

Spontaneous formation of suboxidic coordination around Co in ferromagnetic rutile Ti0.95Co0.05O2 film

To evaluate local atomic structures around Co in high temperature diluted ferromagnetic semiconductor Co-doped TiO2, x-ray fluorescence holography and x-ray absorption fine structure experiments were carried out on rutile paramagnetic Ti0.99Co0.01O2 and ferromagnetic Ti0.95Co0.05O2 films. The Co atoms in the Ti0.99Co0.01O2 simply substituted for Ti sites in the rutile structure, whereas a suboxidic arrangement of CoO2Ti4 formed around Co in the Ti0.95Co0.05O2 films. A theoretical investigation based on a series of first-principles calculations indicated the stability of the aggregated suboxidic clusters in the rutile TiO2, supporting our hypothesis for the formation of suboxidic coordination in the highly Co-doped sample. The suboxidic coordination may be the source of strong exchange interaction, resulting in the high Curie temperature in Co-doped TiO2.

Structural studies on TlInSe thermoelectric material by X‐ray fluorescence holography, XAFS, and X‐ray diffraction

AbstractThe local structure around the Tl atoms in TlInSe thermoelectric material was investigated by X‐ray fluorescence holography (XFH), XAFS, and X‐ray diffraction (XD). The temperature dependent XAFS and XD data reveal that no distinct phase change features are found, and the position of the Tl atoms are fluctuated randomly in the Tl chain direction of the crystal, which is consistent with the XFH result at room temperature. Also, an interference between the positions of Tl and In atoms is suggested by all of these experiments.

Matrix effects in white-beam X-ray fluorescence holography

Recently, it has been shown that atomic structure determination with X-ray fluorescence holography (XFH) can be hindered by matrix effects,i.e.beam attenuation and indirect excitation. The analysis was limited to the monochromatic regime. In this work, the description of matrix effects is extended to the polychromatic case. It is shown that matrix effects affect the element sensitivity of white-beam XFH by introducing distortions in the holographic signal which may lead to spurious maxima in the reconstructed image. For high energies of the X-ray beam it is found that the effect of beam attenuation is very weak and indirect excitation mainly contributes to the distortions. A correction for matrix effects is proposed in the high-energy range, which allows one to remove the distortions and retrieve pure element-sensitive information. Numerical model calculations are performed to visualize the reduction of element sensitivity and its implications on local structure imaging.

Local Structure Analysis of Incommensurate Phase in Ti-42Ni-8Fe(at.%) Alloy by X-ray Fluorescence Holography

We have investigated local structures around Ni and Fe atoms by X-ray fluorescence holography (XFH) method in incommensurate (IC) phase of Ti-42Ni-8Fe(at.%) alloy and obtained the results as the followings; (i) The atomic distances between Ni atom and Fe atom and those 2nd nearest neighbor atoms are 0.27nm and 0.29nm, respectively. (ii) The atomic image intensities of 1st nearest neighbor atoms around Fe atoms are much weaker than those around Ni atoms. These results indicate that nanometer-sized heterogeneous strain exists and it is the cause of nanometer-sized domain in IC phase.

Local Structure Analysis of Lanthanum-Doped Strontium Titanate by Means of X-Ray Fluorescence Holography

Local Structure Analysis of Lanthanum-Doped Strontium Titanate by Means of X-Ray Fluorescence Holography

Local Clusters in a Distorted Rocksalt GeTe Crystal Found by X-ray Fluorescence Holography

A Ge Kα X-ray fluorescence holography (XFH) measurement was performed on a single-crystal GeTe film with a deformed rocksalt (rhombohedral) lattice, for which careful analyses and observations of the reconstructed atomic images were needed. The three-dimensional atomic images obtained around the central Ge atom were compared with the theoretical images obtained from a simulated hologram in the full sphere range and in the limited θ range (0 < θ < 74°), as in the experiment. It was found that reliable atomic images were realized only when neighboring atoms are located on the surface side of the central Ge atom. GeTe3 clusters were found by XFH, which cannot be easily detected by diffraction, and confirmed by ab initio molecular dynamics simulation.

Distorted and Undistorted Atomic Sites in a Ferromagnetic Semiconductor Ge0.6Mn0.4Te Film Determined by X-ray Fluorescence Holography

Local atomic structures around Ge and Mn atoms in a ferromagnetic semiconductor Ge0.6Mn0.4Te thin film were investigated by performing Ge and Mn Kα X-ray fluorescence holographic experiments. The obtained three-dimensional atomic images revealed that the local structure around Mn formed a rock salt lattice, whereas the lattice around Ge was strongly distorted, which is reflected by a rhombohedral structure of GeTe. The undistorted rock salt environment around the Mn atoms is considered to be a key factor allowing for this alloy to exhibit high-temperature ferromagnetism.

Atomic resolution holography.

Atomic resolution holography, such as X-ray fluorescence holography (XFH)[1] and photoelectron holography (PH), has the attention of researcher as an informative local structure analysis, because it provides three dimensional atomic images around specific elements within a range of a few nanometers. It can determine atomic arrangements around a specific element without any prior knowledge of structures. It is considered that the atomic resolution holographic is a third method of structural analysis at the atomic level after X-ray diffraction (XRD) and X-ray absorption fine structure (XAFS). As known by many researchers, XRD and XAFS are established methods that are widespread use in various fields. XRD and XAFS provide information on long-range translational periodicities and very local environments, respectively, whereas the atomic resolution holography gives 3D information on the local order and can visualize surrounding atoms with a large range of coordination shells. We call this feature "3D medium-range local structure observation".In addition to this feature, the atomic resolution holography is very sensitive to the displacement of atoms from their ideal positions, and one can obtain quantitative information about local lattice distortions by analyzing reconstructed atomic images[2] When dopants with different atomic radii from the matrix elements are present, the lattices around the dopants are distorted. However, using the conventional methods of structural analysis, one cannot determine the extent to which the local lattice distortions are preserved from the dopants. XFH is a good tool for solving this problem.Figure1 shows a recent achievement on a relaxor ferroelectric of Pb(Mg1/3Nb2/3)O3 (PMN) using XFH. The structural studies of relaxor ferroelectrics have been carried out by X-ray or neutron diffractions, which suggested rhombohedral distortions of their lattices. However, their true pictures have not been obtained, yet. The Nb Kα holograms showed four separate Pb images, as shown in Fig.1. Using these images, we could obtain acute and obtuse rhombohedral structures of the crystal unit cells. Moreover, the Pb-Pb correlated images reconstructed from Pb Lα holograms showed a local structure of body center-like 2a0 ×2a0 × 2a0 superlattice, proving a rigid 3D network structural model combining the two kinds of rhombohedrons. This superstructure are believed to play an important role in the relaxor behaviour of PMN at atomic level[3].jmicro;63/suppl_1/i13/DFU047F1F1DFU047F1Fig. 1.3D images of the nearest Pb and O atoms around Nb in Pb(Mg1/3Nb2/3)O3. The cube represents 1/8 of the unit cell.

Applications of X-ray fluorescence holography to determine local lattice distortions

X-ray fluorescence holography (XFH) is a method for investigating atomic order up to the medium ranges, and can provide 3D atomic images around specific elements within a radius of nm order. In addition to these characteristics, XFH is sensitive to positional fluctuations of atoms, and therefore it is useful for characterizing the local lattice distortions around specific elements. We have applied XFH to dopants and mixed crystals. We found interesting features in local lattice distortions, such as the displacements of first-neighbor atoms around dopants, far-sighted views of the atomistic fluctuations in mixed crystals, and the coexistence of distorted/undistorted sites in the same material.

Acute and obtuse rhombohedrons in the local structures of relaxor ferroelectric Pb(Mg1/3Nb2/3)O3

The local structures around Nb and Pb in the prototypical relaxor ferroelectric Pb(Mg${}_{1/3}$Nb${}_{2/3}$)O${}_{3}$ (PMN) were investigated by x-ray fluorescence holography. The separate atomic images of nearest Pb around Nb revealed acute and obtuse rhombohedral structures of the crystal unit cells. The Pb-Pb correlated images showed a local structure of body-center-like $2{a}_{0}\ifmmode\times\else\texttimes\fi{}2{a}_{0}\ifmmode\times\else\texttimes\fi{}2{a}_{0}$ superlattice, proving a rigid three-dimensional network structural model combining the two kinds of rhombohedrons. The Pb atoms in the networks are positionally stable, while the other Pb atoms are fluctuating. This superstructure and the fluctuating Pb and Nb atoms are believed to play an important role in the relaxor behavior of PMN at the atomic level.

Correction for beam attenuation and indirect excitation in x-ray fluorescence holography

The influence of beam attenuation (BA) and indirect excitation (IE) processes on atomic resolved imaging with x-ray fluorescence holography (XFH) is considered. It is shown that these processes can influence element sensitivity, the key feature of XFH. A model which allows one to correct for BA and IE is proposed and verified experimentally.

蛍光X線ホログラフィー： 回折実験による構造解析の矛盾とその解決

蛍光X線ホログラフィー： 回折実験による構造解析の矛盾とその解決

Direct extraction of quantitative structural information from x-ray fluorescence holograms using spherical-harmonic analysis

An x-ray fluorescence holograph contains information on both the amplitude and the phase of the x-ray scattering signal from a crystal structure. X-ray fluorescence holography is potentially a technique to directly extract atomic level structure information from crystal samples. We present here a reconstruction algorithm using a spherical-harmonic analysis that significantly improves the structure-resolving power of x-ray fluorescence holography over the widely used multiple energy Barton transform approach. Compared to the direct method for x-ray diffraction, this direct method has the advantages of full model independence and applicability to crystal systems with a large contrast in atomic numbers.

Local Structure around Mn Atoms in IV–VI Ferromagnetic Semiconductor Ge0.6Mn0.4Te Investigated by X-ray Fluorescence Holography

The local atomic structure around Mn atoms in Ge1-xMnxTe thin-film single crystal has been investigated by X-ray fluorescence holography (XFH) at room temperature. The obtained atomic image suggests that the Mn atoms replace the Ge atoms in the host GeTe, and the Mn position is stable in the exact positions of the anion fcc sublattice. The XFH result also suggests the fluctuation of the Ge positions or the cation vacancies.