Vibrational excitation of the N2+ first negative (0,0), (1,0) and (2,0) bands by electron impact: a theoretical study using the R-matrix approach

Ab initio cross section calculations for vibronic excitation using the R -matrix approach have been performed on the N 2 + molecular ion complex. A three-state close-coupling expansion is used where the electronic target states; X 2 g + , A 2 u and B 2 u + of the molecular cation are represented by a valence configuration-interaction approximation. A non-adiabatic approximation is invoked to study vibronic excitation for the first three negative bands, (0,0), (1,0) and (2,0) of the X-B transition (B 2 u + v ´ X 2 g + v ´´ ) of N 2 + . Fixed-nuclei and non-adiabatic cross section results are compared with the available experimental data for the (0,0) band and the breakdown of the adiabatic fixed-nuclei approximation is clearly evident for the vibronic excitation of the (1,0) and (2,0) bands in this molecular ion complex.

Electron-impact ionization of argon using the R-matrix with a pseudo-states method

Electron-impact ionization cross sections for argon are calculated using both non-perturbative R-matrix with pseudo-states (RMPS) and perturbative distorted-wave methods. At twice the ionization potential, the 3p(61)S ground-term cross section from a distorted-wave calculation is found to be a factor of 4 above crossed-beams experimental measurements, while with the inclusion of term-dependent continuum effects in the distorted-wave method, the perturbative cross section still remains almost a factor of 2 above experiment. In the case of ionization from the metastable 3p(5)4s(3)P term, the distorted-wave ionization cross section is also higher than the experimental cross section. On the other hand, the ground-term cross section determined from a nonperturbative RMPS calculation that includes 27 LS spectroscopic terms and another 282 LS pseudo-state terms to represent the high Rydberg states, and the target continuum is found to be in excellent agreement with experimental measurements, while the RMPS result is below the experimental cross section for ionization from the metastable term. We conclude that both continuum term dependence and interchannel coupling effects, which are included in the RMPS method, are important for ionization from the ground term, and interchannel coupling is also significant for ionization from the metastable term

A radiation-damped R -matrix approach to the electron-impact excitation of helium-like ions for diagnostic application to fusion and astrophysical plasmas

Electron-impact excitation collision strengths for transitions between all singly excited levels up to the n = 4 shell of helium-Eke argon and the n = 4 and 5 shells of helium-like iron have been calculated using a radiation-damped R-matrix approach. The theoretical collision strengths have been examined and associated with their infinite-energy limit values to allow the preparation of Maxwell-averaged effective collision strengths. These are conservatively considered to be accurate to within 20% at all temperatures, 3 x 10(5)-3 x 10(8) K forAr(16+) and 10(6)-10(9) K for Fe24+. They have been compared with the results of previous studies, where possible, and we find a broad accord. The corresponding rate coefficients are required for use in the calculation of derived, collisional-radiative, effective emission coefficients for helium-like lines for diagnostic application to fusion and astrophysical plasmas. The uncertainties in the fundamental collision data have been used to provide a critical assessment of the expected resultant uncertainties in such derived data, including redistributive and cascade collisional-radiative effects. The consequential uncertainties in the parts of the effective emission coefficients driven by excitation from the ground levels for the key w, x, y and z lines vary between 5% and 10%. Our results remove an uncertainty in the reaction rates of a key class of atomic processes governing the spectral emission of helium-like ions in plasmas.

Valence and L-shell photoionization of Cl-like argon using R-matrix techniques

Photoionization cross-sections are obtained using the relativistic DiracAtomic R-matrix Codes (DARC) for all valence and L-shell energy ranges between 27 and 270 eV. A total of 557 levels arising from the dominant configurations 3s²3p⁴, 3s³p5, 3p⁶, 3s²3p³[3d, 4s, 4p], 3p⁵3d, 3s²3p²3d², 3s³p4³d, 3s³p3³d2 and 2s²2p⁵3s²3p⁵ have been included in the targetwavefunction representation of the Ar III ion, including up to 4p in the orbital basis. We also performed a smaller Breit-Pauli (BP) calculation containing the lowest 124 levels. Direct comparisons are made with previous theoretical and experimental work for both valence shell and L-shell photoionization. Excellent agreement was found for transitions involving the ²P^o initial state to all allowed final states for both calculations across a range of photon energies. A number of resonant states have been identified to help analyse and explain the nature of the spectra at photon energies between 250 and 270 eV.

Photoionization of Cl-like Argon using the Breit-Pauli R-matrix method

Here we present the photoionization cross sections for the ground and metastable states of Cl-like Argon by exploiting the fully relativistic Breit-Pauli R-matrix computer codes to determine these transitions of interest. We compare our work with previous theoretical and experimental results and present a detailed investigation into the model of Ar III, the resonant structure and identification process.

Comparison of Parallelised R-matrix codes for electron impact excitation of Cr II

A comparison of collision strengths and effective collision strengths has been undertaken for the Cr II ion based on the model of Wasson et al [2010 A & A. 524 A35]. Calculations have been completed using the Breit-Pauli, RMATRX II and DARC suites of codes.

Besov spaces and the Laplacian on fractal H-sets

Nesta tese são estudados espaços de Besov de suavidade generalizada em espaços euclidianos, numa classe de fractais designados conjuntos-h e em estruturas abstractas designadas por espaços-h. Foram obtidas caracterizações e propriedades para estes espaços de funções. Em particular, no caso de espaços de Besov em espaços euclidianos, foram obtidas caracterizações por diferenças e por decomposições em átomos não suaves, foi provada uma propriedade de homogeneidade e foram estudados multiplicadores pontuais. Para espaços de Besov em conjuntos-h foi obtida uma caracterização por decomposições em átomos não suaves e foi construído um operador extensão. Com o recurso a cartas, os resultados obtidos para estes espaços de funções em fractais foram aplicados para definir e trabalhar com espaços de Besov de suavidade generalizada em estruturas abstractas. Nesta tese foi também estudado o laplaciano fractal, considerado a actuar em espaços de Besov de suavidade generalizada em domínios que contêm um conjunto-h fractal. Foram obtidos resultados no contexto de teoria espectral para este operador e foi estudado, à custa deste operador, um problema de Dirichlet fractal no contexto de conjuntos-h.

Laplacian eigenvectors and eigenvalues and almost equitable partitions

Relations between Laplacian eigenvectors and eigenvalues and the existence of almost equitable partitions (which are generalizations of equitable partitions) are presented. Furthermore, on the basis of some properties of the adjacency eigenvectors of a graph, a necessary and sufficient condition for the graph to be primitive strongly regular is introduced. © 2006 Elsevier Ltd. All rights reserved.

Spectra of graphs obtained by a generalization of the join graph operation

Taking a Fiedler’s result on the spectrum of a matrix formed from two symmetric matrices as a motivation, a more general result is deduced and applied to the determination of adjacency and Laplacian spectra of graphs obtained by a generalized join graph operation on families of graphs (regular in the case of adjacency spectra and arbitrary in the case of Laplacian spectra). Some additional consequences are explored, namely regarding the largest eigenvalue and algebraic connectivity.

Endocrine regulation of extracellular matrix proteins in calcified tissue in teleost fish

Tese dout., Biologia, Universidade do Algarve, 2005

Evolution of the extracellular matrix in deuterostomes and the influence of calcitropic hormones

Tese de dout., Biologia (Biologia Molecular), Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2010

Evolution of matrix and bone gamma-carboxyglutamic acid proteins in vertebrates

The evolution of calcified tissues is a defining feature in vertebrate evolution. Investigating the evolution of proteins involved in tissue calcification should help elucidate how calcified tissues have evolved. The purpose of this study was to collect and compare sequences of matrix and bone γ-carboxyglutamic acid proteins (MGP and BGP, respectively) to identify common features and determine the evolutionary relationship between MGP and BGP. Thirteen cDNAs and genes were cloned using standard methods or reconstructed through the use of comparative genomics and data mining. These sequences were compared with available annotated sequences (a total of 48 complete or nearly complete sequences, 28 BGPs and 20 MGPs) have been identified across 32 different species (representing most classes of vertebrates), and evolutionarily conserved features in both MGP and BGP were analyzed using bioinformatic tools and the Tree-Puzzle software. We propose that: 1) MGP and BGP genes originated from two genome duplications that occurred around 500 and 400 million years ago before jawless and jawed fish evolved, respectively; 2) MGP appeared first concomitantly with the emergence of cartilaginous structures, and BGP appeared thereafter along with bony structures; and 3) BGP derives from MGP. We also propose a highly specific pattern definition for the Gla domain of BGP and MGP. Previous Section Next Section BGP1 (bone Gla protein or osteocalcin) and MGP (matrix Gla protein) belong to the growing family of vitamin K-dependent (VKD) proteins, the members of which are involved in a broad range of biological functions such as skeletogenesis and bone maintenance (BGP and MGP), hemostasis (prothrombin, clotting factors VII, IX, and X, and proteins C, S, and Z), growth control (gas6), and potentially signal transduction (proline-rich Gla proteins 1 and 2). VKD proteins are characterized by the presence of several Gla residues resulting from the post-translational vitamin K-dependent γ-carboxylation of specific glutamates, through which they can bind to calcium-containing mineral such as hydroxyapatite. To date, VKD proteins have only been clearly identified in vertebrates (1) although the presence of a γ-glutamyl carboxylase has been reported in the fruit fly Drosophila melanogaster (2) and in marine snails belonging to the genus Conus (3). Gla residues have also been found in neuropeptides from Conus venoms (4), suggesting a wider prevalence of γ-carboxylation.

Effect of polyunsaturated fatty acids (PUFAs) on the proliferation and extracellular matrix mineralization and gene expression of gilthead seabream skeletal cell lines

The aquaculture industry aims at replacing significant amounts of marine fish oil by vegetable oils in fish diet. Dietary lipids have been shown to alter the fatty acid composition of bone compartments, which would impact the local production of factors controlling bone formation. Knowledge on the mechanisms underlying the nutritional regulation of bone metabolism is however scarce in fish. Two in vitro bone-derived cell systems developed from seabream (an important species for aquaculture in the Mediterranean region) vertebra, capable of in vitro mineralization and exhibiting prechondrocyte (VSa13) and pre-osteoblast (VSa16) phenotype, were used to assess the effect of certain polyunsaturated fatty acids (PUFAs; arachidonic (AA), eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids) on cell proliferation, extracellular matrix (ECM) mineralization and gene expression. While all PUFAs promoted morphological changes in both cell lines, VSa16 cell proliferation appeared to be stimulated by PUFAs in a dose dependent manner until 100M, whereas proliferation of VSa13 cells was impaired at concentrations above 10M. AA, EPA and DHA inhibited VSa13 ECM mineralization, alone and in combination, while VSa16 ECM mineralization was only inhibited by AA and EPA. DHA had the opposite effect, increasing mineralization almost by 2 fold. When EFAs were combined, DHA apparently compensated for the inhibitory effect of AA and EPA. Expression of marker genes for bone and lipid metabolisms has been investigated by qPCR and shown to be regulated in pre-osteoblasts exposed to individual PUFAs. Our results show that PUFAs are effectors of fish bone cell lines, altering cell morphology, proliferation and mineralization when added to culture medium. This work also demonstrates the suitability of our in vitro cell systems to get insights into mineralization-related effects of PUFAs in vivo and to evaluate the replacement of fish oils by vegetable oil sources in fish feeds.

Higher order derivatives and norms of certain matrix functions

Tese de doutoramento, Matemática (Álgebra Lógica e Fundamentos), Universidade de Lisboa, Faculdade de Ciências, 2014