In this thesis, the effects of simple shear flow on macromolecular structure and interactions are investigated in detail via a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and rheology, namely Rheo-NMR. A specially designed NMR couette shear cell and benchtop shear cell, developed in-house, demonstrated that the direct measurement of the above phenomena is possible. First, to determine whether the shear cells were creating simple shear flow, results were reproduced from literature studies of liquid crystal systems which report shear effects on: Cetyl Trimethyl Ammonium Bromide (CTAB) in deuterium oxide, and Poly(gamma-benzyl-L-glutamate) (PBLG) in m-cresol. Next, the possible conformational changes to protein structure brought about by shear were investigated by applying shear to Bovine -lactogobulin ( -Lg). As the protein was sheared, a small, irreversible conformational change was observed by means of one-dimensional and two-dimensional 1H NMR with reasonable reproducibility. However, no observable change was detected by means of light scattering. A large conformational change was observed after shearing a destabilized -Lg sample containing 10% Trifluoroethanol (TFE) (v/v). From an NMR point of view, the sheared state was similar to the structure of -Lg containing large amounts of -helices and, interestingly, similar to the structure of -Lg containing -sheet amyloid fibrils. Gel electrophoresis tests suggested that the changes were caused by hydrophobic interactions. Unfortunately, this proved to be difficult to reproduce. The effect of shear on an inter-macromolecular interaction was investigated by applying shear during an enzyme reaction of pectin methylesterase (PME) on pectin. Experimental method and analysis developments are described in detail. It was observed that under the conditions studied, shear does not interfere with the de-esterification of pectin with two types of PME, which have different action mechanisms at average shear rates up to 1570 s-1.

<p>In this thesis, material properties have been examined under extreme conditions in computer-based calculations.</p><p>The research on iron (Fe), nickel (Ni), and ferropericlase (Mg_1-xFe_xO) are not only important for our understanding of the Earth, but also for an improved knowledge of these materials <i>per se</i>.</p><p>An embedded-atom model for Fe demonstrated to reproduce properties such as structure factors, densities and diffusion constants, and was employed to evaluate temperature gradients at Earth core conditions. A similar interaction together with a two-temperature method was applied for the analysis of shock-induced melting of Ni. For Mg_1-xFe_xO, the magnetic transition pressure was shown to increase with iron content. Furthermore, the C₄₄ softening with pressure and iron composition supports the experimentally observed phase transition for Mg_0.8Fe_0.2O at 35 GPa.</p><p>The properties of high density helium (He) is of great interest as the gas is one of the most abundant elements in the solar system. Furthermore, He and neon (Ne) are often used as pressure media in diamond anvil cells. The melting of He showed a possible fcc-bcc-liquid transition starting at T=340 K, P=22 GPa with a Buckingham potential, whereas the bcc phase was not seen with the Aziz form. For Ne, Monte Carlo calculations at ambient pressure showed very accurate results when extrapolating the melting temperatures to an infinite cluster limit. At high pressure, a one-phase <i>ab initio</i> melting curve showed a match with one-phase L-J potential results, which could imply a correspondence between <i>ab initio</i>/classical one-phase/two-phase calculations.</p><p>In the search for hard materials, <i>ab initio</i> calculations for four TiO₂ phases were compared. Just as imposed by experiment, the cotunnite phase was found to be very hard. The anomalous elastic behavior of the superconducting group-<i>V</i> metals V, Nb, Ta was found to be related to shrinking nesting vectors and the electronic topological transition (ETT).</p>

O complexo formado pela molécula de tetraciclina com o íon de magnésio é capaz de impedir a replicação do material genético no ribossomo bacteriano, tornando a tetraciclina um excelente antibiótico. Outra aplicação da tetraciclina, ligada ao íon európio, consiste em estimar a concentração de colesterol no sangue a partir das mudanças do espectro de emissão. Tal técnica apresenta uma resposta imediata e confiável, comparada às técnicas atuais. Emgeral, o espectro de absorção e emissão da tetraciclina é bastante sensível aos íons alojados e ao pH do solvente que o conjunto está imerso. Entretanto, o espectro de absorção teórico em solvente foi obtido com simples modelos contínuos que não consideram interações específicas impostas pelo ambiente no líquido, além da escassez de estudos teóricos para os complexos. Nossa proposta é obter o espectro de absorção eletrônica da tetraciclina e dos complexos formados com os íons Mg e Eu. Além disso, analisamos as mudanças de intensidade e deslocamentos dos máximos das bandas nos sistemas mencionados, em função do pH do solvente e do posicionamento do íon, estimando seu correto posicionamento. Realizamos a simulação clássica usando a técnica de Monte Carlo aplicando o potencial de Lennard-Jones mais Coulomb para cada átomo da molécula de tetraciclina e dos complexos em água. O espectro de absorção eletrônica foi obtido a partir da teoria funcional da densidade dependente do tempo considerando diversos modelos para descrição do solvente e do íon. Em geral, obtivemos uma boa descrição qualitativa dos espectros, quando comparado com os resultados experimentais. Os deslocamentos das bandas e mudanças de intensidades foram bem descritos pelos modelos que utilizaram a simulação clássica para gerar as configurações. Porém cada modelo privilegiou uma propriedade de um determinado sistema, tanto para as diferentes formas da tetraciclina quanto para a presença de íons. Palavras-chaves: tetraciclina, magnésio-tetraciclina, európio-tetraciclina, espectro de absorção, teoria do funcional da densidade dependente do tempo, simulação por Monte Carlo / The complex formed by the tetracycline molecule with the magnesium ion is able to avoid the replication of the genetic material in bacterial ribosome, making tetracycline an excellent antibiotic. Another application of tetracycline attached to the europium ion, is to evaluate the concentration of cholesterol in the blood from the changes in the emission spectrum. This technique presents an immediate and reliable response compared to current techniques. In general, the absorption and emission spectrum of tetracycline is sensitive to ions coupled and the pH of the solvent that the complex is immersed. However, the theoretical absorption spectrum in solvent was obtained with simple continuum models that do not consider specific interactions imposed by the liquid environment, and also the lack of theoretical studies for the complexes. Our proposal is to obtain the electronic absorption spectrum of tetracycline and complexes formed with the ions Mg and Eu. In addition, we analyze the changes in intensity and peak shifts of the bands in the systems mentioned as the function of pH of the solvent and the position of the ion, and estimating the correct position of the ion. We performed a simulation using the classical Monte Carlo technique applying the Lennard-Jones plus Coulomb potential for each atom of the molecule tetracycline and complexes in water. The electronic absorption spectrum was obtained with the time dependent density functional theory considering several models to describe the solvent and ion. In general, we obtained a good qualitative description of the spectra when compared to the experimental results. The shift of the bands and intensity changes were well described by the used models on classical simulation. However, each model favored one property of the system, both for the different forms of tetracycline and for the presence of ions. Keywords: tetracycline, magnesium-tetracycline, europium-tetracycline, absorption spectrum, time dependent density functional theory, Monte Carlo simulation

<p>The subject of this thesis is experimental studies of electron-transfer processes in ion-atom collisions at velocities significantly higher than typical orbital velocities of electrons in bound states of atoms or molecules. The experimental technique applied combines the high beam intensity of heavy-ion storage rings with a supersonic gas-jet target equipped with a recoil-ion-momentum spectrometer. In singleelectron capture to fast protons from helium atoms, we have for the first time achieved a complete separation of the kinematic and Thomas transfer mechanisms and are able to perform a quantitative comparison with the many theoretical results on a much more detailed level than what was previously possible. For the process of transfer ionization in proton-helium collisions we have determined the velocity dependence of the Thomas transfer ionization cross section to be the expected<i> v</i><i>p</i>^-11 when the projectile velocity, <i>v</i><i>p</i>, is sufficiently high. Further, we have determined the velocity-dependent probability for shake-off of the second electron from helium provided that the first one is transferred in a kinematic capture process. Finally, we have considered collisions between protons and hydrogen molecules. Here we have found a strong variation in the cross section for transfer and excitation processes when the angle between the direction of the incoming projectile and the internuclear axis of the target molecule is varied. The variation can be explained as a result of quantum mechanical interference related to the two indistinguishable atomic centers of the molecule.</p>

The subject of this thesis is experimental studies of electron-transfer processes in ion-atom collisions at velocities significantly higher than typical orbital velocities of electrons in bound states of atoms or molecules. The experimental technique applied combines the high beam intensity of heavy-ion storage rings with a supersonic gas-jet target equipped with a recoil-ion-momentum spectrometer. In singleelectron capture to fast protons from helium atoms, we have for the first time achieved a complete separation of the kinematic and Thomas transfer mechanisms and are able to perform a quantitative comparison with the many theoretical results on a much more detailed level than what was previously possible. For the process of transfer ionization in proton-helium collisions we have determined the velocity dependence of the Thomas transfer ionization cross section to be the expected vp-11 when the projectile velocity, vp, is sufficiently high. Further, we have determined the velocity-dependent probability for shake-off of the second electron from helium provided that the first one is transferred in a kinematic capture process. Finally, we have considered collisions between protons and hydrogen molecules. Here we have found a strong variation in the cross section for transfer and excitation processes when the angle between the direction of the incoming projectile and the internuclear axis of the target molecule is varied. The variation can be explained as a result of quantum mechanical interference related to the two indistinguishable atomic centers of the molecule.

In this thesis, material properties have been examined under extreme conditions in computer-based calculations. The research on iron (Fe), nickel (Ni), and ferropericlase (Mg1-xFexO) are not only important for our understanding of the Earth, but also for an improved knowledge of these materials per se. An embedded-atom model for Fe demonstrated to reproduce properties such as structure factors, densities and diffusion constants, and was employed to evaluate temperature gradients at Earth core conditions. A similar interaction together with a two-temperature method was applied for the analysis of shock-induced melting of Ni. For Mg1-xFexO, the magnetic transition pressure was shown to increase with iron content. Furthermore, the C44 softening with pressure and iron composition supports the experimentally observed phase transition for Mg0.8Fe0.2O at 35 GPa. The properties of high density helium (He) is of great interest as the gas is one of the most abundant elements in the solar system. Furthermore, He and neon (Ne) are often used as pressure media in diamond anvil cells. The melting of He showed a possible fcc-bcc-liquid transition starting at T=340 K, P=22 GPa with a Buckingham potential, whereas the bcc phase was not seen with the Aziz form. For Ne, Monte Carlo calculations at ambient pressure showed very accurate results when extrapolating the melting temperatures to an infinite cluster limit. At high pressure, a one-phase ab initio melting curve showed a match with one-phase L-J potential results, which could imply a correspondence between ab initio/classical one-phase/two-phase calculations. In the search for hard materials, ab initio calculations for four TiO2 phases were compared. Just as imposed by experiment, the cotunnite phase was found to be very hard. The anomalous elastic behavior of the superconducting group-V metals V, Nb, Ta was found to be related to shrinking nesting vectors and the electronic topological transition (ETT).

This thesis concerns methods for electronic structure calculations and some applications of the methods. The augmented planewave (APW) basis set and it’s relatives LAPW (linearised APW) and APW+lo (local orbitals) have been widely used for electronic structure calculations. Here a modification of the APW basis set based on a transformation of the basis functions from a curvilinear coordinate system. Applications to a few test systems show that the modified basis set may speed up electronic structure calculations of sparse systems. The local density approximation (LDA) is used in density functional theory. Although it is the simplest possible approximation possible for the unknown exchange-correlation energy functional, it has proven to give quite accurate results for a wide range of systems. LDA fails in systems where the non-local effects are important. By including non-local effects by adding an orbital dependent term to the energy functional, through for example the LDA+U method, the calculated properties of many materials are closer to experimental observations. In the thesis the most general formulation of the LDA+U method is presented and a new way of interpreting the results of a calculations by formulating the orbital dependent part of the energy functional in terms of multipole momentum tensors. Applications to some early actinide systems leads to a reformulations of Hund’s rules for polarisations associated with the spin and orbital magnetic moment and a suggestion for similar rules, Katt’s rules, valid in the strong spin orbit coupling regime.

New generations of ultrashort and intense laser pulses as well ashigh power synchrotron radiation sources and x-ray free electronlasers have promoted fast developments in nonlinear optics andx-ray spectroscopy.The new experimental achievements and the appearance of varieties of novelnonlinear phenomena call for further development of theories. The objective of this thesis is to develop and apply thetheories to explain existing experimental data and to suggest new experiments. The first part of the thesis is devoted to nonlinear propagation of optical pulses. It is shown that the vibrational levels can be selectively populated by varying the duration, shape and intensity of the pump pulse. We obtained a strict analytical solution for the resonant two-photon interaction in a multilevel system beyond rotating wave approximation. Simulations show that the polarization anisotropy of the two-photon excitation affects strongly the anisotropy of photobleaching.The two-photon area theorem is reformulated with taking into account the dynamical Stark shift and the contribution from the permanent dipole moments. In general the dynamical Stark shift does not allow complete population of the excited state, but it can be compensated by detunings in atoms. A dynamical theory of the sequential two-photon absorption of  microsecond pulses  is developed to explore the role of transverse inhomogeneity of the light beam on optical limiting properties.  The propagation of ultrashort laser pulses in nondipolar and dipolar media is investigated with special attention to the generation of superfluorescence and supercontinuum and the formation of attosecond pulses. The second part of the thesis addresses the interaction of molecules with x-ray radiation.  We explore here the role of nuclear dynamics in resonant Auger scattering. Multimode simulations of the Auger spectra of ethylene molecule explain the main spectral features of the experimental spectra and show that the spectral profiles are formed mainly due to six vibrational modes. We predict the Doppler splitting of the atomic peak in resonant Auger scattering from SF6 molecule for circularly polarized x-rays. This effect is confirmed by the recent experiment. A new scheme of x-ray pump-probe spectroscopy, namely, resonant inelastic x-ray scattering accompanied by core-hole hopping induced by strong laser fields is suggested. The laser-induced promotion of core holes opens the symmetry forbidden scattering channels and gives rise to new spectral lines in the x-ray scattering spectrum. The strength of the symmetry forbidden lines becomes strong when  the time of Rabi flopping is shorter than the lifetime of the core-excited state. We study the role of propagation of femtosecond x-ray free-electron pulses on the Auger process. Simulations show  that there exists a strong competition between Auger decay and stimulated emission. The Auger yield and Auger branching ratio are strongly suppressed in the course of pulse propagation. / QC 20100729

This thesis summarises experimental results on the molecular spectroscopy of gas phase molecules excited by synchrotron radiation in the VUV and soft X-ray regions. We have used three different detection techniques, photon induced fluorescence spectroscopy, photoionisation mass spectroscopy and near edge X-ray absorption fine structure spectroscopy to study molecular deuterium, hydrogen sulphide, ammonia, methanol, pyridine, pyridazine, pyrimidine, pyrazine, s-triazine, and 2-deoxy-D-ribose, the last one also known as the DNA sugar. Out of this variety of techniques and molecules we have shown that: (1) high resolution dispersed fluorescence allows us to identify vibrational and rotational bands in molecular deuterium, as well as to estimate the predissociation probability of the same molecule [paper I]; (2) the main species fluorescing after core excitation of methane, ammonia [paper III], hydrogen sulphide [paper II], pyridine, pyrimidine and s-triazine is H Balmer α, followed by fluorescence from ionised species, molecular bands and Balmer β, γ , δ; (3) the Rydberg enhancement seen in fluorescence measurements of water [Melero et al. PRL 96 (2006) 063003], corroborated later in H2S [paper II], NH3 [paper III] and CH4 [paper III] and postulated as general behaviour for molecules formed by low-Z atoms, is also seen in larger organic cyclic molecules, e.g. azabenzenes; (4) when dissociative ionisation of pyridine, pyridazine, pyrimidine, pyrazine, s-triazine and 2-deoxy-D-ribose occurs, concerted bond rearrangement and nuclear motion takes place as opposed to stepwise dissociation [papers V and VI]. / QC 20100916

A rigorous formalism for solving the Coulomb scattering problem is presented in this thesis. The approach is based on splitting the interaction potential into a finite-range part and a long-range tail part. In this representation the scattering problem can be reformulated to one which is suitable for applying exterior complex scaling. The scaled problem has zero boundary conditions at infinity and can be implemented numerically for finding scattering amplitudes. The systems under consideration may consist of two or three charged particles. The technique presented in this thesis is first developed for the case of a two body single channel Coulomb scattering problem. The method is mathematically validated for the partial wave formulation of the scattering problem. Integral and local representations for the partial wave scattering amplitudes have been derived. The partial wave results are summed up to obtain the scattering amplitude for the three dimensional scattering problem. The approach is generalized to allow the two body multichannel scattering problem to be solved. The theoretical results are illustrated with numerical calculations for a number of models. Finally, the potential splitting technique is further developed and validated for the three body Coulomb scattering problem. It is shown that only a part of the total interaction potential should be split to obtain the inhomogeneous equation required such that the method of exterior complex scaling can be applied. The final six-dimensional equation is reduced to a system of three dimensional equations using the full angular momentum representation. Such a system can be numerically implemented using the existing full angular momentum complex exterior scaling code (FAMCES). The code has been updated to solve the three body scattering problem. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Submitted. Paper 5: Manuscript.