<p>Osteoporosis is a major health care problem, by reason of its devastating consequences, in particular hip fractures. Worldwide it has been estimated that the incidence of hip fracture will increase to more than 6 million per year by 2050 compared to 1.7 million per year in 1990. Osteoporosis can be caused by various factors namely, genetic, lifestyle and environmental factors, and since the rising incidence of its consequences is not fully explained by the growing age of the population, there is an urgent need to identify individual causal factors of this condition. </p><p>The present research has focused on aluminium, one potential environmental factor of importance for bone disease, and its possible relation to osteoporosis, since it is known to cause osteoporosis-like bone disease and has been associated with induction of progressive central nervous system diseases.</p><p>Aluminium is the third most common element in the earth’s crust and the most abundant metal (8%). It is widely utilized industrially and it is also naturally present in many foods. Although aluminium is ubiquitous in the human environment, evolution has not given it an essential biological function.</p><p>The aluminium content of bone was measured by inductively coupled mass spectrometry in a large group of patients suffering from hip fractures, high energy fractures and osteoarthrosis. An exponential increase in aluminium content of bone with age was found (p=0.0004). However, no significant association of aluminium in bone with occurrence of hip fracture or dementia could be found, and no indirect evidence was obtained, e.g. through bone mineral density or biomechanical properties, that aluminium is involved in the pathogenesis of osteoporosis. Although we accumulate aluminium in bone throughout our lives, and there are experimental suggestions that aluminium induces premature cell death, the body content of this metal does not seem to influence the overall mortality risk. </p>

Algorithms and simulators comprised of SPICE3 as a circuit level simulator and two device simulators EOFLOW and PROPHET for accurate simulation of new types of devices are presented in this thesis. An integration of EOFLOW with SPICE3 creates a capability for efficient simulation of a system containing interconnected electroosmotic flow channels together with control electronics. Using this simulator, an accurate simulation of a complex interconnection of channels has been performed. In addition, various flow control schemes have been evaluated for their effectiveness. Coupling of PROPHET and SPTCE3 allows for the simulation of accurate semiconductor device models. This capability is necessary for critical RF and analog applications. The coupled SPICE3-HB-PROPHET simulator incorporates the harmonic balance algorithm for large-signal frequency domain analysis. Applications of this analysis are demonstrated in the noise coupling between devices sharing the same silicon substrate. / Graduation date: 2003

It has been shown that the amino terminus and second extracellular loop (EC2) of CXCR2 are crucial for ligand binding and receptor activation. The lack of an ionic lock motif in the third intracellular loop of CXCR2 focuses an investigation of the mechanism by which these two extracellular regions contribute to receptor recognition and activation. The first objective of this investigation was to predict the structure of CXCR2 based on known structures of crystallized GPCRs. Rhodopsin, β2-adrenergic receptor, CXCR4 were used for homology modeling of CXCR2 structure. Highly conserved motifs found in sequence alignments of the template GPCRs were helpful to generate CXCR2 models. We also studied solvent accessibility of residues in the EC2 of CXCR2 in the inactive state. Most of the residues in the EC2 were found to be solvent accessible in the inactive state, suggesting the residues might be involved in ligand recognition. Second, we studied the role of charged residues in the EC2 of CXCR2 in ligand binding and receptor activation using constitutively active mutants (CAM) of CXCR2, D9K and D9R. Combinatorial mutations consisting of the CAM in the amino terminus and single mutations of charged residues in the EC2 were generated to study two concepts including “attraction” and “repulsion” models. The mutant receptors were used to test their effects on cell surface expression, ligand binding, receptor activation through PLC-β3, and cellular transformation. All the mutations in the repulsion model result in CXCR2 receptors that are unable to bind ligand, suggesting that each of the Arg residues in the EC2 are important for ligand recognition. Interestingly, mutations in the attraction model partially inhibited receptor activation by the CAM D9K, suggesting that Glu198 and Asp199 residues in the EC2 are associated with receptor activation. Furthermore, a novel CAM, E198A/D199A, was identified in this study. These negatively charged residues are very close to a conserved disulfide bond linking the EC2 and the third transmembrane. In this sense, these current discoveries concerning the structural basis of CXCR2 and interdisciplinary approaches would provide new insights to investigate unknown mechanisms of interaction with its cognate ligands and receptor activation.

In this thesis, fractured rock masses are treated asequivalent continua for large-scale analyses of rockengineering projects. Systematic developments are made for thedetermination of equivalent mechanical and hydraulic propertiesof fractured rock masses using a hybrid discrete fracturenetwork - distinct element method (DFN-DEM) approach. Thedetermined equivalent properties are then used for a far-fieldfinite element analysis of the thermo-mechanical impacts on thestress, deformation and permeability of fractured rockssurrounding a hypothetical geological repository of nuclearwaste. The geological data were extracted from the results ofan extensive site investigation programme at Sellafield, UK,conducted by Nirex UK Ltd. The scale dependencies of the hydraulic and mechanicalproperties were investigated by using multiple realizations ofthe fracture system geometry with increasing model sizes untilproperly defined hydraulic and mechanical representativeelementary volumes (REVs) were reached. The validity of thesecond order permeability tensor and the fourth-ordermechanical compliance tensor were tested for continuum analysesat larger scales. The REV was determined to be around 5 m formechanical and hydraulic data in this study. Analysis of the stress-dependent mechanical and hydraulicproperties shows that the effect of rock stresses is crucial.The elastic moduli increase significantly with the increase ofstress and an empirical equation of stress-dependent elasticmodulus is suggested based on results of numerical experiments.Calculations of the Poisson's ratios suggest greater valuesthan are normally assumed in practice. Depending on the stateof stress, permeability decreases or increases with increasingcompressive stress. Stress-induced flow channeling effect iscaptured by numerical modeling for the first time and detailedmechanisms of shear dilation of fractures are provided. Basedon the numerical experiments, a set of empirical equations wassuggested for the stress-dependent permeability, consideringboth normal deformation and shear dilation of fractures. Thermo-mechanical impact on the performance of ahypothetical repository at a far-field scale (5 km by 1 km) wasinvestigated with the stress-dependent equivalent propertiesdetermined at the REV scale. This analysis shows thatmechanical responses vary significantly depending on how themechanical properties were determined. The change ofpermeability due to the thermal loading is, however, notsignificant in this particular case. The thesis provides a framework for systematic analysis oflarge-scale engineering applications in fractured rock masses,such as geological repositories of nuclear wastes. Keyword:Fractured rock masses, Equivalent Continuum,Discrete Fracture Network (DFN), Distinct Element Method (DEM),Finite Element Method (FEM), Nuclear Waste Disposal, CoupledThermo-Hydro-Mechanical Processes

Neuropeptide Y (NPY) is known to influence a vast number of physiological and behavioral processes such as vasoconstriction, circadian rhythms, feeding, anxiety and memory. Peptides of the NPY family bind to five different cloned G-protein coupled receptor subtypes (Y1, 2, 4-6). The studies compiled in this thesis present inter-species comparisons of sequence similarities, binding properties and expression patterns among receptors of the NPY family. Cloning of Y1 and Y2 receptor subtypes from guinea pigs revealed strong binding profile similarity to the corresponding human receptors. Previously demonstrated atypical binding profiles in the caval vein of guinea pigs were concluded to result from other receptors than the cloned Y1 and Y2 receptors, or possibly combinations of distinct receptor subtypes. The guinea pig Y5 receptor was found to be expressed in regions of the brain that have been indicated as important for regulation of food intake. Expression in the hypothalamus, amygdala and brain stem was noticed, similar to studies in rats and humans. In other brain regions, such as the striatum and hippocampus, some species differences were observed. Mutagenesis studies of the human Y1 receptor indicated sites important for binding both of endogenous agonists and synthetic antagonists. Putative new sites of interaction with the Y1 antagonists BIBP3226 and/or SR120819A were recognized. The data were used to construct a three-dimensional structure model, based on a high-resolution bovine rhodopsin model. Cloning of the chicken (Gallus gallus) Y1, Y2 and Y5 receptors revealed high sequence similarities with mammalian receptors. Most endogenous ligands bound with similar affinities as to mammalian receptors. The strongest exception was the discovery of high-affinity binding to chicken Y2 of [Leu31, Pro34]NPY, which was previously considered to bind non-Y2 receptors only. The new human Y1 receptor model provides a basis for further investigations of ligand-receptor interactions which will be aided by information on NPY receptors from other taxa. Guinea pigs are concluded to be a good complement to rats and mice for studying NPY signaling. These results demonstrate the benefits of species comparisons for pharmacological studies.

Amino acid radicals are key redox intermediates in several natural enzymes including Cytochrome c peroxidase, DNA photolyase, ribonucletide reductase, cytochrome c oxidase and photosystem II. Electron transfer from amino acids is often coupled to deprotonation and this thesis concerns the coupling of electron transfer from tyrosine and tryptophan to trisbipyridineruthenium(III) with deprotonation in model complexes. Specifically the mechanisms for these proton coupled electron transfer reactions have been studied and the controlling parameters have been identified, the possible mechanisms being stepwise electron transfer followed by deprotonation and deprotonation followed by electron transfer or concerted electron transfer/deprotonation. Proton coupled electron transfer reactions have been studied using nano-second flash photolysis in water solution and the effect of pH, temperature, reaction driving force, deuteration and nature of the amino acid has been determined. I have shown that the rate constant for the concerted reaction depends intrinsically on the mixing entropy of the released proton and that the pH-dependence can be used as an experimental tool for mechanistic discrimination. Moreover I have shown that the concerted reaction inherently has a high reorganisation energy due to the coupling of the electron motion with deprotonation. Hydrogen bonding to the transferring proton however significantly reduces this reorganisation energy. The concerted reaction also has a relatively high driving force counteracting the high reorganisation energy in the competition between the concerted reaction and the stepwise electron transfer first reaction. The relative importance of the high reorganisation energy and the high driving force for the concerted reaction determines the mechanistic outcome of the reaction, the stepwise reaction being favoured by high over-all driving forces and the concerted reaction by high pH. By comparing my results from model complexes with tyrosineZ oxidation in photosystem II, I give strong evidence for a concerted electron transfer/deprotonation mechanism.

Atomic physics plays an important role in determining the evolution stages in a wide range of laboratory and cosmic plasmas. Therefore, the main contribution to our ability to model, infer and control plasma sources is the knowledge of underlying atomic processes. Of particular importance are reliable low temperature dielectronic recombination (DR) rate coefficients. This thesis provides systematically calculated DR rate coefficients of lithium-like beryllium and sodium ions via ∆n = 0 doubly excited resonant states. The calculations are based on complex-scaled relativistic many-body perturbation theory in an all-order formulation within the single- and double-excitation coupled-cluster scheme, including radiative corrections. Comparison of DR resonance parameters (energy levels, autoionization widths, radiative transition probabilities and strengths) between our theoretical predictions and the heavy-ion storage rings experiments (CRYRING-Stockholm and TSRHeidelberg) shows good agreement. The intruder state problem is a principal obstacle for general application of the coupled-cluster formalism on doubly excited states. Thus, we have developed a technique designed to avoid the intruder state problem. It is based on a convenient partitioning of the Hilbert space and reformulation of the conventional set of pairequations. The general aspects of this development are discussed, and the effectiveness of its numerical implementation (within the non-relativistic framework) is selectively illustrated on autoionizing doubly excited states of helium.

This thesis is based on five papers addressing variance reduction in different ways. The papers have in common that they all present new numerical methods. Paper I investigates quantitative structure-retention relationships from an image processing perspective, using an artificial neural network to preprocess three-dimensional structural descriptions of the studied steroid molecules. Paper II presents a new method for computing free energies. Free energy is the quantity that determines chemical equilibria and partition coefficients. The proposed method may be used for estimating, e.g., chromatographic retention without performing experiments. Two papers (III and IV) deal with correcting deviations from bilinearity by so-called peak alignment. Bilinearity is a theoretical assumption about the distribution of instrumental data that is often violated by measured data. Deviations from bilinearity lead to increased variance, both in the data and in inferences from the data, unless invariance to the deviations is built into the model, e.g., by the use of the method proposed in paper III and extended in paper IV. Paper V addresses a generic problem in classification; namely, how to measure the goodness of different data representations, so that the best classifier may be constructed. Variance reduction is one of the pillars on which analytical chemistry rests. This thesis considers two aspects on variance reduction: before and after experiments are performed. Before experimenting, theoretical predictions of experimental outcomes may be used to direct which experiments to perform, and how to perform them (papers I and II). After experiments are performed, the variance of inferences from the measured data are affected by the method of data analysis (papers III-V).

Osteoporosis is a major health care problem, by reason of its devastating consequences, in particular hip fractures. Worldwide it has been estimated that the incidence of hip fracture will increase to more than 6 million per year by 2050 compared to 1.7 million per year in 1990. Osteoporosis can be caused by various factors namely, genetic, lifestyle and environmental factors, and since the rising incidence of its consequences is not fully explained by the growing age of the population, there is an urgent need to identify individual causal factors of this condition. The present research has focused on aluminium, one potential environmental factor of importance for bone disease, and its possible relation to osteoporosis, since it is known to cause osteoporosis-like bone disease and has been associated with induction of progressive central nervous system diseases. Aluminium is the third most common element in the earth’s crust and the most abundant metal (8%). It is widely utilized industrially and it is also naturally present in many foods. Although aluminium is ubiquitous in the human environment, evolution has not given it an essential biological function. The aluminium content of bone was measured by inductively coupled mass spectrometry in a large group of patients suffering from hip fractures, high energy fractures and osteoarthrosis. An exponential increase in aluminium content of bone with age was found (p=0.0004). However, no significant association of aluminium in bone with occurrence of hip fracture or dementia could be found, and no indirect evidence was obtained, e.g. through bone mineral density or biomechanical properties, that aluminium is involved in the pathogenesis of osteoporosis. Although we accumulate aluminium in bone throughout our lives, and there are experimental suggestions that aluminium induces premature cell death, the body content of this metal does not seem to influence the overall mortality risk.

Proton-coupled electron transfer (PCET) is one of the elementary reactions occurring in many chemical and biological systems, such as photosystem II where the oxidation of tyrosine (TyrZ) is coupled to deprotonation of the phenolic proton. This reaction is here modelled by the oxidation of a phenol covalently linked to a Ru(bpy)32+-moitey, which is photo-oxidized by a laser flash-quench method. This model system is unusual as mechanism of PCET is studied in a unimolecular system in water solution. Here we address the question how the nature of the proton accepting base and its hydrogen bond to phenol influence the PCET reaction. In the first part we investigate the effect of an internal hydrogen bond PCET from. Two similar phenols are compared. For both these the proton accepting base is a carboxylate group linked to the phenol on the ortho-position directly or via a methylene group. On the basis of kinetic and thermodynamic arguments it is suggested that the PCET from these occurs via a concerted electron proton transfer (CEP). Moreover, numerical modelling of the kinetic data provides an in-depth analysis of this CEP reaction, including promoting  vibrations  along the O–H–O coordinate that are required to explain the data. The second part describes the study on oxidation of phenol where either water or an external base the proton acceptor. The pH-dependence of the kinetics reveals four mechanistic regions for PCET within the same molecule when water is the base. It is shown that the competition between the mechanisms can be tuned by the strength of the oxidant. Moreover, these studies reveal the conditions that may favour a buffer-assisted PCET over that with deprotonation to water solution.