Biomedical subjects

J J Rehr

Publications and source records attributed to J J Rehr.

18 recordsLinked to original sources

PubMed2006

Practical aspects of electron energy-loss spectroscopy (EELS) calculations using FEFF8.

We discuss the application of the ab initio program FEFF8 to calculations of electron energy-loss spectroscopy (EELS), focusing in particular on core-loss spectra. FEFF8 is based on a self-consistent, real space multiple scattering formalism. We focus on issues relevant to practical simulations, including the construction of well-converged potentials, the treatment of inelastic losses and exchange-correlation potentials and the core-hole. We also discuss how to account for experimental conditions, for example, sample orientation and finite temperature effects such as Debye-Waller factors. Finally we discuss the interpretation of the spectra in terms of electronic structure and local projected density of states (LDOS). As an explicit example, we illustrate various features of the code by application to the ionization edges of GaN.

Journal Article↗

PubMed2004

Bayes-Turchin approach to XAS analysis.

Modern analysis of X-ray absorption fine structure (XAFS) is usually based on a traditional least-squares fitting procedure. Here an alternative Bayes-Turchin method is discussed which has a number of advantages. In particular the method takes advantage of a priori estimates of the model parameters and their uncertainties and avoids the restriction on the size of the model parameter space or the necessity for Fourier filtering. Thus the method permits the analysis of the full X-ray absorption spectra (XAS), including both XAFS and X-ray absorption near-edge spectra (XANES). The approach leads to a set of linear equations for the model parameters, which are regularized using the 'Turchin condition'. Also, the method naturally partitions parameter space into relevant and irrelevant subspaces which are spanned by the experimental data or the a priori information, respectively. Finally we discuss how the method can be applied to the analysis of XANES spectra based on fits of experimental data to full multiple-scattering calculations. An illustrative application yields reasonable results even for very short data ranges.

Bayes Theorem↗

PubMed2004

Extended X-ray absorption fine structure measurements of laser-shocked V and Ti and crystal phase transformation in Ti.

Extended x-ray absorption fine structure (EXAFS), using a laser-imploded target as a source, can yield the properties of laser-shocked metals on a nanosecond time scale. EXAFS measurements of vanadium shocked to approximately 0.4 Mbar yield the compression and temperature in good agreement with hydrodynamic simulations and shock-speed measurements. In laser-shocked titanium at the same pressure, the EXAPS modulation damping is much higher than is warranted by the predicted temperature increase. This is shown to be due to the alpha-Ti to omega-Ti crystal phase transformation, known to occur below approximately 0.1 Mbar for slower shock waves.

Journal Article↗

PubMed2003

Properties of liquid silicon observed by time-resolved x-ray absorption spectroscopy.

Time-resolved x-ray spectroscopy at the Si L edges is used to probe the electronic structure of an amorphous Si foil as it melts following absorption of an ultrafast laser pulse. Picosecond temporal resolution allows observation of the transient liquid phase before vaporization and before the liquid breaks up into droplets. The melting causes changes in the spectrum that match predictions of molecular dynamics and ab initio x-ray absorption codes.

Journal Article↗

PubMed2003

Development of XAFS theory.

A major goal of theoretical simulations of X-ray absorption fine structure (XAFS) is to provide calculations for the interpretation and analysis of experimental data in terms of geometrical and electronic information. The extended region or EXAFS (50-2000 eV above an absorption edge) contains geometric information about the pair distribution function, i.e. distances to the nearest neighbors and their orientation. The theory of EXAFS is now well understood and has been recently reviewed [Rehr & Albers (2000). Rev. Mod. Phys. 72, 621-654]. The near-edge region (0-50 eV above the edge) or X-ray absorption near-edge structure (XANES) probes the states just above the Fermi level, and contains important electronic information, e.g. the electronic density of states (DOS). This data can be used to obtain the number of electrons or holes in the electronic configuration and spin and orbital moments on a particular atom via sum rules. XANES calculations with our ab initio code FEFF8 [Ankudinov et al. (1998). Phys. Rev. B, 58, 7565-7576] usually give semi-quantitative agreement with experiment, and permits the interpretation of XANES in terms of DOS. However, fully quantitative calculations remain a challenge. Several effects still need to be considered to treat the XANES region. These include non-spherical parts of the scattering potential and many-body effects such as multi-electron excitations, core-hole effects and local field effects (screening of the X-ray field).

Absorptiometry, Photon↗

PubMed2002

New developments in the theory and interpretation of X-ray spectra based on fast parallel calculations.

There has been dramatic progress over the past decade both in theory and in ab initio calculations of X-ray absorption fine structure. Significant progress has also been made in understanding X-ray absorption near-edge structure (XANES). This contribution briefly reviews the developments in this field leading up to the current state. One of the key advances has been the development of several ab initio codes such as FEFF, which permit an interpretation of the spectra in terms of geometrical and electronic properties of a material. Despite this progress, XANES calculations have remained challenging both to compute and to interpret. However, recent advances based on parallel Lanczos multiple-scattering algorithms have led to speed increases of typically two orders of magnitude, making fast calculations practicable. Improvements in the interpretation of near-edge structure have also been made. It is suggested that these developments can be advantageous in structural biology, e.g. in post-genomics studies of metalloproteins.

Absorptiometry, Photon↗

PubMed2001

Pt L-edge XANES as a probe of Pt clusters.

The sensitivity of Pt L-edge XANES to local geometric and electronic structure in various Pt(n) clusters is investigated using the ab initio self-consistent FEFF8 code. Calculations based on FEFF8 are found to be in good agreement with experiment. For pure Pt clusters the XANES can distinguish between 2- and 3-dimensional clusters. Self-consistency is important in determining the variation of XANES with cluster size. The effect of a support is also studied. In Pt-Cl(x) clusters the presence of a Cl-Pt bond leads to a "hybridization peak," i.e., a peak in the Cl d-density of states (d-DOS) mixed with Pt d-states. For Pt-H clusters hydrogen addition is well correlated with the growth of a broad shoulder on the white line. This change is attributed largely to AXAFS, i.e., to a corresponding change in the atomic background absorption.

Journal Article↗

PubMed2001

Progress and challenges in the theory and interpretation of X-ray spectra.

There has been dramatic progress over the past decade both in theory and in ab initio calculations of X-ray absorption fine structure (XAFS). Rapid progress is now being made in understanding X-ray absorption near-edge structure (XANES). This presentation reviews the developments in this field by many groups leading up to the current state of the art. These developments have led to several ab initio codes, such as FEFF, which yield results comparable to experimental results for XAFS, and permit an interpretation of the spectra in terms of geometrical and electronic properties of a material. The review begins with a summary of the key theoretical developments that are essential for achieving a quantitative agreement with experiment for XAFS. The same high-order multiple-scattering (MS) theory of XAFS can also give an approximate treatment of XANES, but this approach can fail close to an edge, where full MS calculations are often necessary. However, a fully quantitative treatment of XANES remains challenging, largely as a result of a number of many-body effects, e.g. the approximate treatment of the core-hole, multiplet effects, the photoelectron self energy and inelastic losses. Finally, natural extensions of the theory to other spectroscopies, such as anomalous X-ray scattering, DAFS (diffraction anomalous fine structure) and XMCD (X-ray magnetic circular dichroism) are briefly discussed. These developments are illustrated with a number of applications.

Journal Article↗

PubMed2001

Hole counts from X-ray absorption spectra.

The interpretation of X-ray absorption spectra in terms of electronic structure has long been of interest. Hole counts derived from such spectra are often interpreted in terms of free-atom occupation numbers or Mülliken counts. It is shown here, however, that renormalized-atom (RA) and cellular counts are better choices to characterize the configuration of occupied electron states in molecules and condensed matter. A projection-operator approach is introduced to subtract delocalized states and to determine quantitatively such hole counts from X-ray absorption spectra. The described approach is based on multiple-scattering theory (MST) and on atomic calculations of a smooth transformation relating the X-ray absorption spectra to local projected densities of states (LDOS). Theoretical tests for the s and d electrons in transition metals show that the approach works well.

Journal Article↗

PubMed2001

The use of the FEFF8 code to calculate the XANES and electron density of states of some sulfides.

The FEFF8 was used to calculate x-ray absorption spectra (XANES) and the local partial electron density of states (LDOS) for several sulfides: InPS4 (twice defective chalcopyrite), CdIn2S4 (normal spinel) and Tl3AsS3 (space group R3m). The calculated XANES are compared with experimental spectra. The self-consistent MT-potentials found for clusters of about 35 atoms were used to calculate XANES and LDOS for clusters of 87 atoms in the approach of full multiple scattering. In all cases the agreement of the simulated XANES and experimental ones is quite good. The theoretical LDOS agree well with the experimental x-ray emission K- and L2,3-spectra.

Journal Article↗

PubMed2001

Effect of hydrogen adsorption on the x-ray absorption spectra of small Pt clusters.

Hydrogen adsorption on Pt(6)H(n) clusters leads to striking changes in the Pt L(2,3) x-ray absorption spectra. These effects are interpreted using a self-consistent real space Green's function approach. Calculations show that they are due largely to changes in the atomic background contribution to x-ray absorption (i.e., atomic x-ray absorption fine structure) and to reduced Pt-Pt scattering at the edge, while Pt-H multiple scattering is relatively weak. The origin of both effects is traced to the change in the local Pt potential due to Pt-H bonding.

Journal Article↗

PubMed2000

Importance of multiple-scattering phenomena in XAS structural determinations of [Ni(CN)4]2- in condensed phases.

A quantitative analysis of the XAS spectra of the tetracyanonickelate complex [Ni(CN)4]2- has been carried out. The simultaneous study of the EXAFS and XANES regions yielded complementary information regarding the geometric and electronic structures of the complex. XANES spectra were modeled by applying recently developed self-consistent, full multiple-scattering algorithms in the FEFF8 code (version 8 x 34). XANES spectra for clusters of different sizes (from 9 to 125 atoms) were computed and compared with experimental spectra. This region of the spectra was proportional to a broadened Ni p-density of states diagram above the Fermi level. Although the main features of the XANES spectra were reasonably reproduced by computations, the weak dependence of the theoretical spectra on cluster size contrasts with the close similarity between the experimental spectra of the solid and solution systems. Because of the special geometry of the complex, calculations with polarized light parallel and perpendicular to the molecular plane were carried out, yielding a reasonable reproduction of the experimental data from another report for cluster sizes equal to or higher than 45 atoms. The highly symmetric square planar structure of the complex was found to be responsible for the unusual amplitude of the multiple-scattering (MS) contributions to the EXAFS spectra. Spectra in this region were fitted using the FEFFIT EXAFS analysis program, taking into account only the MS paths that simultaneously have both a high amplitude, as calculated with the ab initio code FEFF, and a small Debye-Waller factor, as estimated by the independent-vibration approximation model. Fitting results yielded very similar structures for the Ni2+ complex in the solid state and in solution, though the larger Debye-Waller factors found for the solid suggest higher static disorder in this state.

Journal Article↗

PubMed1999