Full-Potential Multiple Scattering Theory with Space-Filling Cells for bound and continuum states

We present a rigorous derivation of a real space Full-Potential Multiple-Scattering-Theory (FP-MST), valid both for continuum and bound states, that is free from the drawbacks that up to now have impaired its development, in particular the need to use cell shape functions and rectangular matrices. In this connection we give a new scheme to generate local basis functions for the truncated potential cells that is simple, fast, efficient, valid for any shape of the cell and reduces to the minimum the number of spherical harmonics in the expansion of the scattering wave function. The method also avoids the need for saturating 'internal sums' due to the re-expansion of the spherical Hankel functions around another point in space (usually another cell center). Thus this approach, provides a straightforward extension of MST in the Muffin-Tin (MT) approximation, with only one truncation parameter given by the classical relation $l_{\rm max} = kR_b$, where $k$ is the excited (or ground state) electron wave vector and $R_b$ the radius of the bounding sphere of the scattering cell. It is shown that the theory converges absolutely in the $l_{\rm max} \to \infty$ limit. As a consequence it provides a firm ground to the use of FP-MST as a viable method for electronic structure calculations and makes possible the computation of x-ray spectroscopies, notably photo-electron diffraction, absorption and anomalous scattering among others, with the ease and versatility of the corresponding MT theory. Some numerical applications of the theory are presented, both for continuum and bound states.Comment: 48 pages, 6 figures, 2 table

A Critical Assessment of Multiple Scattering Expansions

We propose a comparative and critical assessment of multiple scattering expansions. The so-called multiple scattering series expansion is much used in the description of spectroscopies at higher energies. However, it is plagued with convergence problems when operated at lower energies. We compare this method to related methods that can be found in the literature, relying both on finite and infinite expansions. After discussing the pros and cons of these methods, we establish a simple alternative to multiple scattering series expansion which has a wider and faster range of convergence. [DOI: 10.1380/ejssnt.2012.599

X-ray absorption spectra of graphene and graphene oxide by full-potential multiple scattering calculations with self-consistent charge density

International audienceThe x-ray absorption near-edge structure of graphene, graphene oxide, and diamond is studied by the recently developed real-space full potential multiple scattering (FPMS) theory with space-filling cells. It is shown how accurate potentials for FPMS can be generated from self-consistent charge densities obtained with other schemes, especially the projector augmented wave method. Compared to standard multiple scattering calculations in the muffin-tin approximation, FPMS gives much better agreement with experiment. The effects of various structural modifications on the graphene spectra are well reproduced. (1) Stacking of graphene layers increases the peak intensity in the higher energy region. (2) The spectrum of the C atom located at the edge of a graphene sheet shows a prominent pre-edge structure. (3) Adsorption of oxygen gives rise to the so-called interlayer-state peak. Moreover, O K-edge spectra of graphene oxide are calculated for three types of bonding, C-OH, C-O-C, and C-O, and the proportions of these bondings at 800∘C are deduced by fitting them to the experimental spectru

A Nexafs Study of Nitric Oxide Layers Adsorbed from a nitrite Solution onto a Pt(111) Surface

NO molecules adsorbed on a Pt(111) surface from dipping in an acidic nitrite solution are studied by near edge X-ray absorption fine structure spectroscopy (NEXAFS), X-ray photoelectron spectroscopy (XPS), low energy electron diffraction (LEED) and scanning tunnelling microscopy (STM) techniques. LEED patterns and STM images show that no long range ordered structures are formed after NO adsorption on a Pt(111) surface. Although the total NO coverage is very low, spectroscopic features in N K-edge and O K-edge absorption spectra have been singled out and related to the different species induced by this preparation method. From these measurements it is concluded that the NO molecule is adsorbed trough the N atom in an upright conformation. The maximum saturation coverage is about 0.3 monolayers, and although nitric oxide is the major component, nitrite and nitrogen species are slightly co-adsorbed on the surface. The results obtained from this study are compared with those previously reported in the literature for NO adsorbed on Pt(111) under UHV conditions

Role of the exchange and correlation potential into calculating the x-ray absorption spectra of half-metallic alloys: the case of Mn and Cu K-edge XANES in Cu2_2MnM (M = Al, Sn, In) Heusler alloys

This work reports a theoretical study of the x-ray absorption near-edge structure spectra at both the Cu and the Mn K-edge in several Cu$_2$MnM (M= Al, Sn and In) Heusler alloys. Our results show that {\it ab-initio} single-channel multiple-scattering calculations are able of reproducing the experimental spectra. Moreover, an extensive discussion is presented concerning the role of the final state potential needed to reproduce the experimental data of these half-metallic alloys. In particular, the effects of the cluster-size and of the exchange and correlation potential needed in reproducing all the experimental XANES features are discussed.Comment: 15 pages, 5 figure

Effects of N,N-dimethyltryptamine on electrically evoked responses in the cat visual system and modification by neuroleptic agents,

The effects of N,N-dimethyltryptamine on electrically evoked potentials in the visual system of the cat and the interaction of selected neuroleptic agents with dimethyltryptamine were studied. Dimethyltryptamine caused a dose-dependent decrease in the amplitude of the response evoked by stimulation of the optic chiasm as recorded in the lateral geniculate nucleus and the visual cortex. Dimethyltryptamine had no significant effect on antidromically evoked potentials in the lateral geniculate nucleus or potentials in the visual cortex produced by optic radiation stimulation. A dose-dependent biphasic effect was found in animals pretreated with various doses of chlorpromazine, haloperidol, thiothixene, molindone, methiothepin and octoclothepin. Methiothepin and octoclothepin were the most potent antagonists of dimethyltryptamine, while molindone was essentially ineffective. Low doses of the neuroleptics, with the exception of molindone, potentiated the inhibitory action of dimethyltryptamine on evoked responses.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/21690/1/0000081.pd

Cost-effectiveness comparison between palpation- and ultrasound-guided thyroid fine-needle aspiration biopsies

<p>Abstract</p> <p>Background</p> <p>The aim of this study is to perform a cost-effectiveness comparison between palpation-guided thyroid fine-needle aspiration biopsies (P-FNA) and ultrasound-guided thyroid FNA biopsies (USG-FNA).</p> <p>Methods</p> <p>Each nodule was considered as a case. Diagnostic steps were history and physical examination, TSH measurement, Tc^99mthyroid scintigraphy for nodules with a low TSH level, initial P-FNA versus initial USG-FNA, repeat USG-FNA for nodules with initial inadequate P-FNA or USG-FNA, hemithyroidectomy for inadequate repeat USG-FNA. American Thyroid Association thyroid nodule management guidelines were simulated in estimating the cost of P-FNA strategy. American Association of Clinical Endocrinologists guidelines were simulated for USG-FNA strategy. Total costs were estimated by adding the cost of each diagnostic step to reach a diagnosis for 100 nodules. Strategy cost was found by dividing the total cost to 100. Incremental cost-effectiveness ratio (ICER) was calculated by dividing the difference between strategy cost of USG-FNA and P-FNA to the difference between accuracy of USG-FNA and P-FNA. A positive ICER indicates more and a negative ICER indicates less expense to achieve one more additional accurate diagnosis of thyroid cancer for USG-FNA.</p> <p>Results</p> <p>Seventy-eight P-FNAs and 190 USG-FNAs were performed between April 2003 and May 2008. There were no differences in age, gender, thyroid function, frequency of multinodular goiter, nodule location and diameter (median nodule diameter: 18.4 mm in P-FNA and 17.0 mm in USG-FNA) between groups. Cytology results in P-FNA versus USG-FNA groups were as follows: benign 49% versus 62% (p = 0.04), inadequate 42% versus 29% (p = 0.03), malignant 3% (p = 1.00) and indeterminate 6% (p = 0.78) for both. Eleven nodules from P-FNA and 18 from USG-FNA group underwent surgery. The accuracy of P-FNA was 0.64 and USG-FNA 0.72. Unit cost of P-FNA was 148 Euros and USG-FNA 226 Euros. The cost of P-FNA strategy was 534 Euros and USG-FNA strategy 523 Euros. Strategy cost includes the expense of repeat USG-FNA for initial inadequate FNAs and surgery for repeat inadequate USG-FNAs. ICER was -138 Euros.</p> <p>Conclusion</p> <p>Universal application of USG-FNA for all thyroid nodules is cost-effective and saves 138 Euros per additional accurate diagnosis of benign versus malignant thyroid nodular disease.</p> <p>Trial registration</p> <p>ClinicalTrials.gov, NCT00571090</p

A Rapid FACS-Based Strategy to Isolate Human Gene Knockin and Knockout Clones

Gene targeting protocols for mammalian cells remain inefficient and labor intensive. Here we describe FASTarget, a rapid, fluorescent cell sorting based strategy to isolate rare gene targeting events in human somatic cells. A fluorescent protein is used as a means for direct selection of targeted clones obviating the need for selection and outgrowth of drug resistant clones. Importantly, the use of a promoter-less, ATG-less construct greatly facilitates the recovery of correctly targeted cells. Using this method we report successful gene targeting in up to 94% of recovered human somatic cell clones. We create functional EYFP-tagged knockin clones in both transformed and non-transformed human somatic cell lines providing a valuable tool for mammalian cell biology. We further demonstrate the use of this technology to create gene knockouts. Using this generally applicable strategy we can recover gene targeted clones within approximately one month from DNA construct delivery to obtaining targeted monoclonal cell lines

Significantly Longer Envelope V2 Loops Are Characteristic of Heterosexually Transmitted Subtype B HIV-1 in Trinidad

In Trinidad and the wider Caribbean, subtype B Human Immunodeficiency Virus-type 1 (HIV-1B) overwhelmingly accounts for HIV infection among heterosexuals; this contrasts with the association of HIV-1B with homosexual transmission and injecting drug use globally. The HIV envelope contains genetic determinants of cell tropism and evasion from immune attack. In this study we investigate the genetic properties of the env V1-C4 of HIV-1B soon after transmission to Trinidadian heterosexuals. This will reveal distinctive genetic features of the strains that cause the HIV-1B epidemic in Trinidad and generate insights to better understand their properties.Quasispecies sampling was performed on the env V1-C4 of HIV-1B strains soon after transmission to heterosexual Trinidadians in a cohort of seroconverters. Phylogenetic relationships were determined for these quasispecies and the length and number of asparagine (N) linked glycosylation sites (NLGS) in their variable loops compared to that for HIV-1B globally. Signature amino acids within the constant domains of the env V1-C4 were identified for heterosexually transmitted HIV-1B from Trinidad relative to HIV-1B globally. HIV-1B obtained from Trinidadian heterosexuals soon after seroconversion had significantly longer V2 loops with one more glycosylation site, shorter V3 loops and no significant difference in V1 or V4 when compared to HIV-1B obtained soon after seroconversion from infected individuals in the rest of the world. HIV-1B soon after seroconversion and during chronic infection of Trinidadians was not significantly different, suggesting that distinctly long V2 loops are characteristic of HIV-1B in Trinidad. A threonine deletion at position 319 (T319-) along with the substitutions R315K and S440R were found to be distinctly associated with HIV-1B from Trinidad compared to HIV-1B globally.This finding of distinctive genetic features that are characteristic of HIV-1B strains from Trinidad is consistent with the Trinidad epidemic being established by a founder strain or closely related founder strains of HIV-1B