Ab-initio determination of x-ray absorption near edge structure (xanes) spectra in an ultrasoft and norm conserving pseudopotentials scheme

X-ray absorption spectroscopy (XAS) is a powerful means of investigation of structural and electronic properties in condensed -matter physics. Analysis of the near edge part of the XAS spectrum, the so – called X-ray Absorption Near Edge Structure (XANES), can typically provide the following information on the photoexcited atom: - Oxidation state and coordination environment. - Speciation of transition metal compounds. - Conduction band DOS projected on the excited atomic species (PDOS). Analysis of XANES spectra is greatly aided by simulations; in the most common scheme the multiple scattering framework is used with the muffin tin approximation for the scattering potential and the spectral simulation is based on a hypothetical, reference structure. This approach has the advantage of requiring relatively little computing power but in many cases the assumed structure is quite different from the actual system measured and the muffin tin approximation is not adequate for low symmetry structures or highly directional bonds. It is therefore very interesting and justified to develop alternative methods. In one approach, the spectral simulation is based on atomic coordinates obtained from a DFT (Density Functional Theory) optimized structure. In another approach, which is the object of this thesis, the XANES spectrum is calculated directly based on an ab – initio DFT calculation of the atomic and electronic structure. This method takes full advantage of the real many-electron final wavefunction that can be computed with DFT algorithms that include a core-hole in the absorbing atom to compute the final cross section. To calculate the many-electron final wavefunction the Projector Augmented Wave method (PAW) is used. In this scheme, the absorption cross section is written in function of several contributions as the many-electrons function of the finale state; it is calculated starting from pseudo-wavefunction and performing a reconstruction of the real-wavefunction by using a transform operator which contains some parameters, called partial waves and projector waves. The aim of my thesis is to apply and test the PAW methodology to the calculation of the XANES cross section. I have focused on iron and silicon structures and on some biological molecules target (myoglobin and cytochrome c). Finally other inorganic and biological systems could be taken into account for future applications of this methodology, which could become an important improvement with respect to the multiscattering approach.

The effect of temperature on pressure tolerance of the shallow-water shrimp Palaemon serratus

Tolerance to low temperature and high pressure may allow shallow-water species to extend bathymetric range in response to changing climate, but adaptation to contrasting shallow-water environments may affect tolerance to these factors. The brackish shallow-water shrimp Palaemon varians demonstrates remarkable tolerance to elevated hydrostatic pressure and low temperature, but inhabits a highly variable environment: environmental adaptation may therefore make P. varians tolerances unrepresentative of other shallow-water species. Critical thermal maximum (CTmax), critical hydrostatic pressure maximum (CPmax), and acute respiratory response to hydrostatic pressure were assessed in the shallow-water shrimp Palaemon serratus, which inhabits a more stable intertidal habitat. P. serratus’ CTmax was 22.3°C when acclimated at 10°C, and CPmax was 5.9, 10.1, and 14.1 MPa when acclimated at 5, 10, and 15°C respectively: these critical tolerances were consistently lower than P. varians. Respiratory responses to acute hyperbaric exposures similarly indicated lower tolerance to hydrostatic pressure in P. serratus than in P. varians. Contrasting tolerances likely reflect physiological adaptation to differing environments and reveal that the capacity for depth-range extension may vary among species from different habitats.