Temperature dependence of the excitation spectrum in the charge-density-wave ErTe3_3 and HoTe3_3 systems

We provide optical reflectivity data collected over a broad spectral range and as a function of temperature on the ErTe$_3$ and HoTe$_3$ materials, which undergo two consecutive charge-density-wave (CDW) phase transitions at $T_{CDW1}$= 265 and 288 K and at $T_{CDW2}$= 157 and 110 K, respectively. We observe the temperature dependence of both the Drude component, due to the itinerant charge carriers, and the single-particle peak, ascribed to the charge-density-wave gap excitation. The CDW gap progressively opens while the metallic component gets narrow with decreasing temperature. An important fraction of the whole Fermi surface seems to be affected by the CDW phase transitions. It turns out that the temperature and the previously investigated pressure dependence of the most relevant CDW parameters share several common features and behaviors. Particularly, the order parameter of the CDW state is in general agreement with the predictions of the BCS theory

X-ray Absorption Linear Dichroism at the Ti K-edge of TiO2 anatase single crystal

Anatase TiO2 (a-TiO2) exhibits a strong X-ray absorption linear dichroism with the X-ray incidence angle in the pre-edge, the XANES and the EXAFS at the titanium K-edge. In the pre-edge region the behaviour of the A1-A3 and B peaks, originating from the 1s-3d transitions, is due to the strong $p$-orbital polarization and strong $p-d$ orbital mixing. An unambiguous assignment of the pre-edge peak transitions is made in the monoelectronic approximation with the support of ab initio finite difference method calculations and spherical tensor analysis in quantitative agreement with the experiment. It is found that A1 is mostly an on-site 3d-4p hybridized transition, while peaks A3 and B are non-local transitions, with A3 being mostly dipolar and influence by the 3d-4p intersite hybridization, while B is due to interactions at longer range. Finally, peak A2 which was previously assigned to a transition involving pentacoordinated titanium atoms exhibits a quadrupolar angular evolution with incidence angle. These results pave the way to the use of the pre-edge peaks at the K-edge of a-TiO2 to characterize the electronic structure of related materials and in the field of ultrafast XAS where the linear dichroism can be used to compare the photophysics along different axes.Comment: 43 pages, 19 figure

Coupled Electronic and Nuclear Motions during Azobenzene Photoisomerization Monitored by Ultrafast Electron Diffraction

Ultrafast electron diffraction is a powerful technique that can resolve molecular structures with femtosecond and angstrom resolutions. We demonstrate theoretically how it can be used to monitor conical intersection dynamics in molecules. Specific contributions to the signal are identified which vanish in the absence of vibronic coherence and offer a direct window into conical intersection paths. A special focus is on hybrid scattering from nuclei and electrons, a process that is unique to electron (rather than X-ray) diffraction and monitors the strongly coupled nuclear and electronic motions in the vicinity of conical intersections. An application is made to the cis to trans isomerization of azobenzene, computed with exact quantum dynamics wavepacket propagation in a reactive two-dimensional nuclear space

Time-sensitive autonomous architectures

Autonomous and software-defined vehicles (ASDVs) feature highly complex systems, coupling safety-critical and non-critical components such as infotainment. These systems require the highest connectivity, both inside the vehicle and with the outside world. An effective solution for network communication lies in Time-Sensitive Networking (TSN) which enables high-bandwidth and low-latency communications in a mixed-criticality environment. In this work, we present Time-Sensitive Autonomous Architectures (TSAA) to enable TSN in ASDVs. The software architecture is based on a hypervisor providing strong isolation and virtual access to TSN for virtual machines (VMs). TSAA latest iteration includes an autonomous car controlled by two Xilinx accelerators and a multiport TSN switch. We discuss the engineering challenges and the performance evaluation of the project demonstrator. In addition, we propose a Proof-of-Concept design of virtualized TSN to enable multiple VMs executing on a single board taking advantage of the inherent guarantees offered by TSN

Electronic correlations in iron-pnictide superconductors and beyond; what can we learn from optics

The Coulomb repulsion, impeding electrons' motion, has an important impact on the charge dynamics. It mainly causes a reduction of the effective metallic Drude weight (proportional to the so-called optical kinetic energy), encountered in the optical conductivity, with respect to the expectation within the nearly-free electron limit (defining the so-called band kinetic energy), as evinced from band-structure theory. In principle, the ratio between the optical and band kinetic energy allows defining the degree of electronic correlations. Through spectral weight arguments based on the excitation spectrum, we provide an experimental tool, free from any theoretical or band-structure based assumptions, in order to estimate the degree of electronic correlations in several systems. We first address the novel iron-pnictide superconductors, which serve to set the stage for our approach. We then revisit a large variety of materials, ranging from superconductors, to Kondo-like systems as well as materials close to the Mott-insulating state. As comparison we also tackle materials, where the electron-phonon coupling dominates. We establish a direct relationship between the strength of interaction and the resulting reduction of the optical kinetic energy of the itinerant charge carriers

A factorization of a super-conformal map

A super-conformal map and a minimal surface are factored into a product of two maps by modeling the Euclidean four-space and the complex Euclidean plane on the set of all quaternions. One of these two maps is a holomorphic map or a meromorphic map. These conformal maps adopt properties of a holomorphic function or a meromorphic function. Analogs of the Liouville theorem, the Schwarz lemma, the Schwarz-Pick theorem, the Weierstrass factorization theorem, the Abel-Jacobi theorem, and a relation between zeros of a minimal surface and branch points of a super-conformal map are obtained.Comment: 21 page

The neighbouring genes <i>AvrLm10A</i> and <i>AvrLm10B</i> are part of a large multigene family of cooperating effector genes conserved in Dothideomycetes and Sordariomycetes

Fungal effectors (small-secreted proteins) have long been considered as species or even subpopulation-specific. The increasing availability of high-quality fungal genomes and annotations has allowed the identification of trans-species or trans-genera families of effectors. Two avirulence effectors, AvrLm10A and AvrLm10B, of Leptosphaeria maculans, the fungus causing stem canker of oilseed rape, are members of such a large family of effectors. AvrLm10A and AvrLm10B are neighbouring genes, organized in divergent transcriptional orientation. Sequence searches within the L. maculans genome showed that AvrLm10A/AvrLm10B belong to a multigene family comprising five pairs of genes with a similar tail-to-tail organization. The two genes, in a pair, always had the same expression pattern and two expression profiles were distinguished, associated with the biotrophic colonization of cotyledons and/or petioles and stems. Of the two protein pairs further investigated, AvrLm10A_like1/AvrLm10B_like1 and AvrLm10A_like2/AvrLm10B_like2, the second one had the ability to physically interact, similarly to what was previously described for the AvrLm10A/AvrLm10B pair, and cross-interactions were also detected for two pairs. AvrLm10A homologues were identified in more than 30 Dothideomycete and Sordariomycete plant-pathogenic fungi. One of them, SIX5, is an effector from Fusarium oxysporum f. sp. lycopersici physically interacting with the avirulence effector Avr2. We found that AvrLm10A/SIX5 homologues were associated with at least eight distinct putative effector families, suggesting that AvrLm10A/SIX5 is able to cooperate with different effectors. These results point to a general role of the AvrLm10A/SIX5 proteins as “cooperating proteins”, able to interact with diverse families of effectors whose encoding gene is co-regulated with the neighbouring AvrLm10A homologue

Femtosecond X-ray emission study of the spin cross-over dynamics in haem proteins

In haemoglobin (consisting of four globular myoglobin-like subunits), the change from the low-spin (LS) hexacoordinated haem to the high spin (HS) pentacoordinated domed form upon ligand detachment and the reverse process upon ligand binding, represent the transition states that ultimately drive the respiratory function. Visible-ultraviolet light has long been used to mimic the ligand release from the haem by photodissociation, while its recombination was monitored using time-resolved infrared to ultraviolet spectroscopic tools. However, these are neither element- nor spin-sensitive. Here we investigate the transition state in the case of Myoglobin-NO (MbNO) using femtosecond Fe Kalpha and Kbeta non-resonant X-ray emission spectroscopy (XES) at an X-ray free-electron laser upon photolysis of the Fe-NO bond. We find that the photoinduced change from the LS (S = 1/2) MbNO to the HS (S = 2) deoxy-myoglobin (deoxyMb) haem occurs in ca. 800 fs, and that it proceeds via an intermediate (S = 1) spin state. The XES observables also show that upon NO recombination to deoxyMb, the return to the planar MbNO ground state is an electronic relaxation from HS to LS taking place in ca. 30 ps. Thus, the entire ligand dissociation-recombination cycle in MbNO is a spin cross-over followed by a reverse spin cross-over process

FONZIE: An optimized pipeline for minisatellite marker discovery and primer design from large sequence data sets

<p>Abstract</p> <p>Background</p> <p>Micro-and minisatellites are among the most powerful genetic markers known to date. They have been used as tools for a large number of applications ranging from gene mapping to phylogenetic studies and isolate typing. However, identifying micro-and minisatellite markers on large sequence data sets is often a laborious process.</p> <p>Results</p> <p>FONZIE was designed to successively 1) perform a search for markers via the external software Tandem Repeat Finder, 2) exclude user-defined specific genomic regions, 3) screen for the size and the percent matches of each relevant marker found by Tandem Repeat Finder, 4) evaluate marker specificity (i.e., occurrence of the marker as a single copy in the genome) using BLAST2.0, 5) design minisatellite primer pairs via the external software Primer3, and 6) check the specificity of each final PCR product by BLAST. A final file returns to users all the results required to amplify markers. A biological validation of the approach was performed using the whole genome sequence of the phytopathogenic fungus <it>Leptosphaeria maculans</it>, showing that more than 90% of the minisatellite primer pairs generated by the pipeline amplified a PCR product, 44.8% of which showed agarose-gel resolvable polymorphism between isolates. Segregation analyses confirmed that the polymorphic minisatellites corresponded to single-locus markers.</p> <p>Conclusion</p> <p>FONZIE is a stand-alone and user-friendly application developed to minimize tedious manual operations, reduce errors, and speed up the search for efficient minisatellite and microsatellite markers departing from whole-genome sequence data. This pipeline facilitates the integration of data and provides a set of specific primer sequences for PCR amplification of single-locus markers. FONZIE is freely downloadable at: <url>http://www.versailles-grignon.inra.fr/bioger/equipes/leptosphaeria_maculans/outils_d_analyses/fonzie</url></p

Evolution of Linked Avirulence Effectors in Leptosphaeria maculans Is Affected by Genomic Environment and Exposure to Resistance Genes in Host Plants

Brassica napus (canola) cultivars and isolates of the blackleg fungus, Leptosphaeria maculans interact in a ‘gene for gene’ manner whereby plant resistance (R) genes are complementary to pathogen avirulence (Avr) genes. Avirulence genes encode proteins that belong to a class of pathogen molecules known as effectors, which includes small secreted proteins that play a role in disease. In Australia in 2003 canola cultivars with the Rlm1 resistance gene suffered a breakdown of disease resistance, resulting in severe yield losses. This was associated with a large increase in the frequency of virulence alleles of the complementary avirulence gene, AvrLm1, in fungal populations. Surprisingly, the frequency of virulence alleles of AvrLm6 (complementary to Rlm6) also increased dramatically, even though the cultivars did not contain Rlm6. In the L. maculans genome, AvrLm1 and AvrLm6 are linked along with five other genes in a region interspersed with transposable elements that have been degenerated by Repeat-Induced Point (RIP) mutations. Analyses of 295 Australian isolates showed deletions, RIP mutations and/or non-RIP derived amino acid substitutions in the predicted proteins encoded by these seven genes. The degree of RIP mutations within single copy sequences in this region was proportional to their proximity to the degenerated transposable elements. The RIP alleles were monophyletic and were present only in isolates collected after resistance conferred by Rlm1 broke down, whereas deletion alleles belonged to several polyphyletic lineages and were present before and after the resistance breakdown. Thus, genomic environment and exposure to resistance genes in B. napus has affected the evolution of these linked avirulence genes in L. maculans