A comparison of SAD and two‐wavelength MAD phasing for radiation‐damaged Se‐MET crystals

Although a case has been made that single‐wavelength anomalous dispersion (SAD) is the optimal strategy for data collection in the presence of radiation damage, two‐wavelength MAD experiments at the inflection and a high‐energy remote point of the absorption edge have been shown to be a potentially successful alternative method. In order to further investigate the performance of both data collection strategies, a comparison of SAD and MAD phasing was carried out for increasingly damaged data sets from three different seleno‐methionine protein samples collected under similar experimental conditions. In all but one example the MAD phases appeared to be less affected than SAD phases with increasing exposure to X‐rays, and had a better overall success rate, indicating that this method should be given serious consideration when dealing with radiation‐sensitive crystals. Simultaneous data collection in wedges at all wavelengths seems to be a very important factor in the success of MAD experiments; the decreased absorbed dose resulting from eschewing data collection at the maximum f ′′ wavelength may play a less important role. Specific radiation damage to the selenium atoms is found to be a minor effect compared with the effect on the anomalous dispersion signal, although potentially large enough to be a useful contribution to phasing in both SAD and MAD experiments.     

Phasing of lysozyme using one－wavelength anomalous scattering of sulphur atoms through the combination of direct methods and density modification

A new method of combining one-wavelength anomalous scattering (OAS) phasing and density modification has been described, in which the improved phases from density modification axe re-introduced into OAS phasing. In this way, the phases could be improved iteratively until convergence. The OAS phasing method is based on the previously established sign-probability formula, which breaks the phase ambiguity in the OAS phasing. The implementation of this method has been available in CCP4 as OASIS. This method, although based on direct-methods, could also incorporate known phases and figures of merit into its sign-probability formula. In the implementation of OASIS, the known phases axe from the positions of the anomalous scatters. In the current method, the known phases are from the density modification. The current method was tested on phasing a lysozyme crystal using anomalous scattering of sulphur atoms with diffraction data collected on an in-house x-ray source. The resulting map was well connected for the backbone atoms and clearly traceable, with an average map correlation coefficient of 0.6622 for the backbone atoms.     

交叉型波荡器软X射线自由电子激光极化控制的影响因素

 交叉型波荡器是一种实现软X射线自由电子激光极化控制的有效方式。以自放大自发辐射自由光电子激光为例,采用统计的方法系统地分析了交叉型波荡器软X射线自由电子激光极化控制的影响因素。通过对光场相干长度、光脉冲两分量之间相对滑移长度和光场分量平均功率差异等的分析,给出了优化交叉型波荡器极化控制方案遵循的原则,即：辐射场相干时间尽可能长,光场分量相对滑移长度尽可能短,辐射场分量功率差异尽可能小等。该原则为交叉型波荡器软X射线自由电子激光极化控制方案的优化提供了依据。     

Resonant "forbidden" reflections in magnetite

Resonant x-ray scattering was used to investigate electronic fluctuations of the octahedral iron atoms in magnetite. We measured the (002) and (006) "forbidden" x-ray diffraction reflections permitted by the anisotropy of the iron anomalous scattering factor. The energy and azimuthal angle dependencies of these reflections, and the polarization analysis, are shown and discussed. The results clearly show p and d iron empty states ordering in magnetite at room temperature. Moreover, the octahedral iron atoms are electronically equivalent in a time scale lower than 10(-16) sec. Therefore, magnetite should be considered as an itinerant magnet and not as a fluctuating mixed valence material.     

Lasing of middle-infrared free-election lasers using the storage ring NIJI-IV

We report for the first time to our knowledge the experimental realization of a storage ring free-electron laser (FEL) in the middle-infrared (MIR) region. A technique to adjust the optical cavity using higher harmonic FELs was developed for a fundamental FEL in the MIR region. The MIR FELs were oscillated in the wavelength region of 2475 to 2673 nm, and the relative linewidth was 5×10??. A quasi-monochromatic x-ray beam with an energy of 700 keV was generated using FEL Compton backscattering. We were able to realize a quasi-monochromatic x-ray beam, whose energy is difficult to generate even in advanced synchrotron radiation facilities.     

Multienergy anomalous diffuse scattering

A new approach to local structure determination is presented. A three-dimensional region of the reciprocal space of a SrTiO(3) single crystal was mapped by measuring x-ray diffuse scattering patterns at different sample orientations in order to reconstruct the local atomic structure. The phase problem was solved by means of anomalous scattering from strontium atoms at photon energies near their K absorption edge. Real-space reconstruction provides the average short-range order atomic arrangement in the vicinity of anomalous scatterers up to a distance of several unit cells.     

Enhancement of MAD/MIR phasing at low resolution and a new procedure for automatic phase extension

To achieve de novo protein structure determination of challenging cases, multi-wavelength anomalous diffraction(MAD) and multiple isomorphous replacement(MIR) phasing can be powerful tools to obtain low-resolution initial phases from heavy-atom derivative datasets, then phase extension is needed against high-resolution data to obtain accurate structures.In this context, we propose a direct-methods procedure here that could improve the initial low-resolution MAD/MIR phase quality.And accordingly, an automated process for extending initial phases to high resolution is also described.These two procedures are both implanted in the newly released IPCAS pipeline.Three cases are used to perform the test, including one set of 4.17 ? MAD data from a membrane protein and two sets of MAD/MIR data with derivatives truncated down to 6.80 ? and 6.90 ?, respectively.All the results have shown that the initial phases generated from the direct-methods procedure are better than that from the conventional MAD/MIR methods.The automated phase extensions for the latter two cases starting from 6.80 ? to 3.00 ? and 6.90 ? to 2.80 ? are proved to be successful, leading to complete models.This may provide convenient and reliable tools for phase improvement and phase extension in difficult low-resolution tasks.     

Coherent and transient states studied with extreme ultraviolet and X-ray free electron lasers: present and future prospects

The most recent light sources, extreme ultraviolet (EUV) and X-ray free electron lasers (FELs), have extended tabletop laser experiments to shorter wavelengths, adding element and chemical state specificity by exciting and probing electronic transitions from core levels. Through their unique properties, combining femtosecond X-ray pulses with coherence and enormous peak brightness, the FELs have enabled studies of a broad class of dynamic phenomena in matter that crosses many scientific disciplines and have led to major breakthroughs in the last few years. In this article, we review how the advances in the performance of the FELs, with respect to coherence, polarization and multi-color pulse production, have pushed the development of original experimental strategies to study non-equilibrium behavior of matter at the femtosecond–nanometer time–length scales. In this review, the emphasis is placed on the contribution of the EUV and soft X-ray FELs on three important subjects: (i) the new regime of X-ray matter interactions with ultrashort very intense X-ray pulses, (ii) the new potential of coherent imaging and scattering for answering questions about nano dynamics in complex materials and (iii) the unique possibility to stimulate and probe nonlinear phenomena that are at the heart of conversion of light into other forms of energy, relevant to photovoltaics, femtosecond magnetism and phase transitions in correlated materials.     

Electronic structure of metal nanoclusters

The electronic structure and the shape of the K absorption edge for small-sized clusters formed by transition metal atoms (titanium, nickel, and copper) are investigated using the quantum-mechanical multiple scattering method (FEFF8 code) and the molecular mechanics technique. It is shown that the x-ray photoelectron spectra and K x-ray absorption spectra of clusters containing 55 and more atoms are similar to the corresponding experimental spectra of macroscopic samples. The computer simulation of the electronic structure and the shape of the K absorption edge is performed for nanoclusters whose equilibrium geometric shape is determined by the molecular dynamics method.     

Philosophy of physics: quantum theory

A review has been made of the theories of the origin of x-ray satellite lines; the theories proposed since 1969 are dealt with in some detail. It seems certain that satellites are due to transitions in atoms which have an anomalous configuration of orbital electrons or are multiply ionized. The method of production of these configurations is the subject of all the theories. Recent results indicate that anomalous configurations and multiply ionized states can arise following a normal single ionization process.     

Clustering and polymerization of Li15C60

The structural and electronic properties of lithium intercalated fullerides (of which Li₁₅C₆₀ is the most representative) are still puzzling and unclear. Above 520 K, x-ray/neutron diffraction shows an fcc phase in which the 15 Li atoms clusterize in the octahedral interstices. However, at lower temperatures, a change in the crystalline symmetry and also in the electronic properties takes place as observed from ¹³C, ⁷Li/⁶Li NMR and x-ray diffraction measurements. X-ray diffraction data suggest the presence of two different stable structures: a tetragonal monomeric and an orthorhombic polymerised phase. Detailed ¹³C magic angle spinning NMR experiments in the latter phase indicate sp ³ bondings among the carbon atoms, whereas the relative (sp ²/sp ³) intensities, together with x-ray data, suggest the C₆₀ polymerization to be a [2+2] cycloaddition. Multiple quantum NMR experiments on ⁷Li confirm the presence of lithium clusters, as observed by x-ray diffraction in the high temperature phase, also at lower temperatures. However, the inferred cluster size is significantly smaller than that suggested by the stoichiometry. The distortion in the low-T structure of L₁₅C₆₀ is supposed to induce the migration of Li atoms from octahedral to tetrahedral voids, thus accounting for the lower number of Li atoms in the clusters. Further evidence of this scenario is obtained also from preliminary measurements of line shapes and T ₁ relaxation times, which exhibit a multiexponential recovery with very different constants that are hardly compatible with a single family of Li atom sites.     

反常散射法同直接法的结合

对于某些类型的含重原子晶体结构,用通常的Patterson法、重原子法、乃至直接法,往往不易获得唯一的解。将由反常散射效应所得的部分相位信息同直接法结合起来有助于解决这个困难。本文用一个典型的已知晶体结构作试验,证明这样的结合可以收到良好的效果。 关键词：     

Modeling fast heavy ion induced amorphization in pure metals

Bombardment of metallic targets with heavy, GeV energy ions results in electronic excitation beyond a threshold value of stopping power. Due to the spatial homogeneity of ion tracks, the projectile homogeneously deposits its energy onto all atoms within a cylinder. The radius of such an ionization cylinder is calculated, thereafter the amount of energy transferred to each single atom in the cylinder is evaluated: n ionization events per atoms occur, which change the atomic configuration from (Z) to (Z-n). Ionized atoms are ejected out of the ionization cylinder, and they interact with matrix atoms inside a damage cylinder. Locally a starting compound [(Z) (Z-n)] is formed. Segregation at the matrix-damage cylinder interface of one component of the starting compound gives rise to a non-equilibrium compositional profile. Relaxation to metastable equilibrium of the associated non-equilibrium electronic density is simulated via charge transfer reactions, each of which involves a matrix atom and an ionized atom. The reaction product is a dimer, considered a nucleus of an effective compound. The energy cost to introduce in the matrix an effective compound dimer is calculated, together with the surface properties of starting and effective compounds. Qualitative differences are found between compounds which form in metals amorphized or, respectively crystallized under fast heavy ion irradiation.     

Low emittance, high brilliance relativistic electron beams from a laser-plasma accelerator

Progress in laser wakefield accelerators indicates their suitability as a driver of compact free-electron lasers (FELs). High brightness is defined by the normalized transverse emittance, which should be less than 1π mm mrad for an x-ray FEL. We report high-resolution measurements of the emittance of 125 MeV, monoenergetic beams from a wakefield accelerator. An emittance as low as 1.1±0.1π mm mrad is measured using a pepper-pot mask. This sets an upper limit on the emittance, which is comparable with conventional linear accelerators. A peak transverse brightness of 5×101? A m?1 rad?1 makes it suitable for compact XUV FELs.     

Nature of the high-pressure transition in Fe2O3 hematite

We present a new method to separate the crystallographic and electronic phase transitions in hematite using x-ray emission spectroscopy and x-ray diffraction. Our observations, based on the behavior of a metastable high-pressure phase in the stability domain of the low-pressure phase, show that the electronic transition is preempted by the crystallographic transition. The former occurs only afterwards in the high-pressure phase, possibly as a result of a Mott transition. The idea that the electronic transition drives the transition in hematite is therefore invalidated. Such methods should help elucidate the mechanics and the driving forces behind a number of first-order high-pressure phase transitions.     

Structure of quantum wires in Au/Si(557)

The structure of the Au/Si(557) surface is determined from three-dimensional x-ray diffraction measurements, which directly mandate a single Au atom per unit cell. We use a "heavy atom" method in which the Au atom images the rest of the structure. Au is found to substitute for a row of first-layer Si atoms in the middle of the terrace, which then reconstructs by step rebonding and adatoms. The structure is consistent with the 1D metallic behavior seen by photoemission.     

Time resolved spectroscopy with femtosecond soft-x-ray pulses

The most challenging application of time resolved spectroscopy is to directly observe the structural and electronic dynamics. Here we present the combination of x-ray absorption spectroscopy with laser driven x-ray sources, offering atomic spatial and temporal resolution. Our new approaches for optimization of laser driven x-ray sources resulted in the demonstration of spatially coherent sub-20 fs x-ray pulses in a range up to several keV. We excited polycrystalline silicon with an ultrashort laser pulse and characterized the collective motion of atoms with time resolved x-ray absorption spectroscopy at a temporal resolution of less than 20 fs. Finally, we have shown the feasibility of probing the dynamics of the electronic structure of silicon and carbon with near edge x-ray absorption spectroscopy.     

Generating optical orbital angular momentum in a high-gain free-electron laser at the first harmonic

A scheme to generate intense coherent light that carries orbital angular momentum (OAM) at the fundamental wavelength of an x-ray free-electron laser (FEL) is described. The OAM light is emitted as the dominant mode of the system until saturation provided that the helical microbunching imposed on the electron beam is larger than the shot-noise bunching that leads to self-amplified emission. Operating at the fundamental, this scheme is more efficient than alternate schemes that rely on harmonic emission, and can be applied to x-ray FELs without using external optical mode conversion elements.     

Modelling dynamics of samples exposed to free-electron-laser radiation with Boltzmann equations

We apply Boltzmann equations for modelling the radiation damage in samples irradiated by photons from free electron lasers (FELs). We test this method in a study case of a spherically symmetric xenon cluster irradiated with VUV FEL photons. Qualitative agreement between the model predictions and experimental data is found. The results obtained demonstrate the potential of the Boltzmann method for describing the complex and non-equilibrium dynamics of samples exposed to FEL radiation.