Estrogen receptor α (ERα) is a member of a family of ligand-modulated transcription factors that have come to be known as nuclear receptors. ERα mediates the action of estrogens and plays an integral role in a wide range of physiological processes ranging from embryonic development and morphogenesis to reproduction to cardiovascular health. Not surprisingly, malfunction of the estrogen system is associated with a host of pathological conditions such as osteoporosis, heart disease and most notably breast cancer. Essential to its functioning as a transcription factor are specific protein-DNA interactions which are mediated by the binding of the DNA-binding (DB) domain of ERα to particular DNA sequences located within target gene promoters called estrogen response elements (EREs). Here, using a diverse array of biophysical techniques, including in particular isothermal titration calorimetry coupled with molecular modeling and semi-empirical analysis, I provide new insights into the ERα-DNA interaction in thermodynamic and structural terms. My data show that the binding of the DB domain of ERα to DNA is coupled to protonation at two specific amino acids, H196 and E203. Protonation of these residues is non-trivial and is required for high affinity binding. Amino acid sequence alignment of the DB domains of the NR family suggests that this may be a hallmark feature common to the functioning of all nuclear receptors. Furthermore, I demonstrate that the DB domain can tolerate all single nucleotide substitutions within the ERE and bind in the physiologically relevant nanomolar to micromolar range. Comparative thermodynamic analysis reveals that the DB domain binds to these ERE sequences utilizing a considerable range of energetic signatures such that any one thermodynamic component of binding is not predictive of associated affinity. In addition, it is shown that nucleotide substitution results in significant changes in secondary and three-dimensional features of the oligonucleotides and may impact binding affinity. Finally, I demonstrate that the zinc-finger of the DB domain of ERα is relatively promiscuous and can accommodate several heavy-metal divalent cations. Other than zinc, only DB domains reconstituted with cobalt, cadmium and mercury were capable of binding DNA. Incorporation of the metals resulted in a wide range of CD spectroscopic features which were found not to be predictive of DNA binding capacity. Thus, isostructure does not equate to isofunction in the case of metal reconstituted DB domain of ERα. This analysis suggests that metal coordination is not likely to be required for domain folding, but rather is required to bind DNA. Taken together, this thesis provides novel insights into the physicochemical basis of a key protein-DNA interaction essential to human health and disease. My studies bear the potential to impact the development of novel therapies harboring greater efficacy coupled with lower toxicity for the treatment of disease.

The objective of this work has been to study equilibrium and non equilibrium situations during high pressure gas processing operations with emphasis on utilization of the high reservoir pressure. The well stream pressures of some of the condensate and gas fields in the North Sea are well above 200 bar. Currently the gas is expanded to a specified processing condition, typically 40-70 bar, before it is recompressed to the transportation conditions. It would be a considerable environmental and economic advantage to be able to process the natural gas at the well stream pressure. Knowledge of thermodynamic- and kinetic properties of natural gas systems at high pressures is needed to be able to design new high pressure process equipment. Nowadays, reactive absorption into a methyldiethanolamine (MDEA)solution in a packed bed is a frequently used method to perform acid gas treating. The carbon dioxide removal process on the Sleipner field in the North Sea uses an aqueous MDEA solution and the operation pressure is about 100 bar. The planed carbon dioxide removal process for the Snøhvit field in the Barents Sea is the use of an activated MDEA solution. The aim of this work has been to study high-pressure effects related to the removal of carbon dioxide from natural gas. Both modelling and experimental work on high-pressure non-equilibrium situations in gas processing operations have been done. Few experimental measurements of mass transfer in high pressure fluid systems have been published. In this work a wetted wall column that can operate at pressures up to 200 bar was designed and constructed. The wetted wall column is a pipe made of stainless steel where the liquid is distributed as a thin liquid film on the inner pipewall while the gas flows co- or concurrent in the centre of the pipe. The experiments can be carried out with a well-defined interphase area and with relatively simple fluid mechanics. In this way we are able to isolate the effects we want to study in a simple and effective way. Experiments where carbon dioxide was absorbed into water and MDEA solutions were performed at pressures up to 150 bar and at temperatures 25 and 40°C. Nitrogen was used as an inert gas in all experiments. A general non-equilibrium simulation program (NeqSim) has been developed. The simulation program was implemented in the object-oriented programming language Java. Effort was taken to find an optimal object-oriented design. Despite the increasing popularity of object-oriented programming languages such as Java and C++, few publications have discussed how to implement thermodynamic and fluid mechanic models. A design for implementation of thermodynamic, mass transfer and fluid mechanic calculations in an object-oriented framework is presented in this work. NeqSim is based on rigorous thermodynamic and fluid mechanic models. Parameter fitting routines are implemented in the simulation tool and thermodynamic-, mass transfer- and fluid mechanic models were fitted to public available experimental data. Two electrolyte equations of state were developed and implemented in the computer code. The electrolyte equations of state were used to model the thermodynamic properties of the fluid systems considered in this work (non-electrolyte, electrolyte and weak-electrolyte systems). The first electrolyte equation of state (electrolyte ScRK-EOS) was based on a model previously developed by Furst and Renon (1993). The molecular part of the equation was based on a cubic equation of state (Scwarzentruber et.al. (1989)’s modification of the Redlich-Kwong EOS) with the Huron-Vidal mixing rule. Three ionic terms were added to this equation – a short-range ionic term, a long-range ionic term (MSA) and a Born term. The thermodynamic model has the advantage that it reduces to a standard cubic equation of state if no ions are present in the solution, and that public available interaction parameters used in the Huron-Vidal mixing rule could be utilized. The originality of this electrolyte equation of state is the use of the Huron-Vidal mixing rule and the addition of a Born term. Compared to electrolyte models based on equations for the gibbs excess energy, the electrolyte equation of state has the advantage that the extrapolation to higher pressures and solubility calculations of supercritical components is less cumbersome. The electrolyte equation of state was able to correlate and predict equilibrium properties of CO2-MDEA-water solutions with a good precision. It was also able to correlate high pressure data of systems of methane-CO2-MDEA and water. The second thermodynamic model (electrolyte CPA-EOS) evaluated in this work is a model where the molecular interactions are modelled with the CPA (cubic plus association) equation of state (Kontogeorgios et.al., 1999) with a classical one-parameter Van der Walls mixing rule. This model has the advantage that few binary interaction parameters have to be used (even for non-ideal solutions), and that its extrapolation capability to higher pressures is expected to be good. In the CPA model the same ionic terms are used as in the electrolyte ScRK-EOS. A general non-equilibrium two-fluid model was implemented in the simulation program developed in this work. The heat- and mass-transfer calculations were done using an advanced multicomponent mass transfer model based on non-equilibrium thermodynamics. The mass transfer model is flexible and able to simulate many types of non-equilibrium processes we find in the petroleum industry. A model for reactive mass transfer using enhancement factors was implemented for the calculation of mass transfer of CO2 into amine solutions. The mass transfer model was fitted to the available mass transfer data found in the open literature. The simulation program was used to analyse and perform parameter fitting to the high pressure experimental data obtained during this work. The mathematical models used in NeqSim were capable of representing the experimental data of this work with a good precision. From the experimental and modelling work done, we could conclude that the mass transfer model regressed to pure low-pressure data also was able to represent the high-pressure mass transfer data with an acceptable precision. Thus the extrapolation capability of the model to high pressures was good. For a given partial pressure of CO2 in the natural gas, calculations show a decreased CO2 capturing capacity of aqueous MDEA solutions at increased natural gas system pressure. A reduction up to 40% (at 200 bar) compared to low pressure capacity is estimated. The pressure effects can be modelled correctly by using suitable thermodynamic models for the liquid and gas. In a practical situation, the partial pressure of CO2 in the natural gas will be proportional to the total pressure. In these situations, it is shown that the CO2 capturing capacity of the MDEA solution will be increased at rising total pressures up to 200 bar. However, the increased capacity is not as large as we would expect from the higher CO2 partial pressure in the gas. The reaction kinetics of CO2 with MDEA is shown to be relatively unaffected by the total pressure when nitrogen is used as inert gas. It is however important that the effects of thermodynamic and kinetic non- ideality in the gas and liquid phase are modelled in a consistent way. Using the simulation program NeqSim – some selected high-pressure non-equilibrium processes (e.g. absorption, pipe flow) have been studied. It is demonstrated that the model is capable of simulating equilibrium- and non-equilibrium processes important to the process- and petroleum industry.

Knowledge about the stability of phases and their relationships in the Fe-O system at high pressures and temperatures is essential in implications of the multifarious states of iron oxides for models of the evolution of the Earth. In this respect, the iron ferrite magnetite (FeFe2O4) plays a significant role since it participates in the control of geochemistry of ferric iron, and hence oxygen fugacity in the Earth`s deep interior. High-pressure experiments on Fe3O4 were performed using the diamond anvil cell technique combined with the laser and electrical resistive heating. The approach based on the combination of the synchrotron x-ray diffraction with Raman spectroscopic measurements benefited from the complementarity of the two methods originating from the different sensitivity to a range of structural order. High-pressure transformation of magnetite to a dense polymorph of the CaTi2O4-type structure proceeds via an intermediate step of the decomposition into a mixture of oxides on a microscopic scale. The kinetic hindrance of the reaction of the decomposition effectively prevents a phase separation controlled by diffusion and restricts the formation of the daughter products to locally ordered structures in the strained lattice of magnetite. Thermodynamic analysis of the observed phase transformations along with published results on the elastic properties and pressure-induced transitions of iron oxides has led to the reassessment of the phase diagram of Fe3O4. The pressure - temperature field of its stability with respect to the breakdown to a mixture of oxides FeO and Fe2O3, and to the transition to a high-pressure form, has been accordingly modified.

In the present work, the thermodynamic activites of ironoxide, denoted as "FeO" in the slag systems Al2O3-"FeO", CaO-"FeO", "FeO"-SiO2, Al2O3-"FeO"-SiO2, CaO-"FeO"-SiO2and "FeO"-MgO-SiO2were investigated by employing the gasequilibration technique at steelmaking temperatures. Thestrategy was to expose the molten slag mixtures kept inplatinum crucibles for an oxygen potential, determined by aCO/CO2-ratio. A part of the iron reduced from the "FeO"in the slag phase was dissolved into the Pt crucible. In order to obtain the activites of "FeO", chemical analysisof the quenched slag samples together with thermodynamicinformation of the binary metallic system Fe-Pt is required.Careful experimental work was carried out by employing asolid-state galvanic cell technique as well as calorimetricmeasurements in the temperature ranges of 1073-1273 K and300-1988 K respectively. The outcome of these experiments wasincorporated along with previous studies into a CALPHAD-type ofthermodynamic assessment performed with the Thermo-Calc™software. The proposed equilibrium diagram enabledextrapolation to higher temperatures. The experimentally obtained activites of "FeO" in thepresent work, along with earlier investigations were assessedwith the KTH slag model, THERMOSLAG©. New binaryparameters were evolved and incorporated in THERMOSLAG©.The present model calculations are compared with othercommercially available software such as F*A*C*T™andThermo-Calc™. The validity of the modified model wasinvestigated by measurements carried out in case of Al2O3-"FeO"-SiO2, CaO-"FeO"-SiO2and "FeO"-MgO-SiO2ternary slags. The potential of the model tocompute the activities in the case of multicomponent slags wasdemonstrated. A correlation between the activity of a metallic oxide in aternary slag system and the sulphide capacity of the slag wasinvestigated by using the solubility of sulphur in the binarysystems CaO-SiO2and Al2O3-CaO along with the sulphide capacity of the Al2O3-CaO-SiO2system. The estimated values of the activitieswere found to be in good agreement with the measured values.This correlation also gives the possibility to elucidate theapplicability of Henry's law to the activity of a metallicsulphide and to determine the order in the affinity of a cationto sulphur between two metallic oxides in a slag. Model calculations were performed with THERMOSLAG©, by using plant data from the ladle refiningprocess at OVAKO Steel, Hofors, Sweden. It was found thatoxygen estimations in the metal from the "FeO" analyses ofslags, obtained by conventional sampling and analysis methodwere less reliable. Reliable estimation of the oxygen levelsutilising the sulphur partition between the slag and the metalwere carried out using THERMOSLAG© software. <b>Keywords:</b>Thermodynamics, Activity, Galvanic cell,Calorimetry, Gas equilibration technique, Iron-platinum alloys,FeO, Slags, Modelling, Ladle

Hydrogen is abundant, uniformly distributed throughout the Earth's surface and its oxidation product (water) is environmentally benign. Owing to these features, it is considered as an ideal synthetic fuel for a new world energetic matrix (renewable, secure and environmentally friendly) that could allow a sustainable future development. However, for this prospect to become a reality, efficient ways to produce, transport and store hydrogen still need to be developed. In the present thesis, theoretical studies of a number of potential hydrogen storage materials have been performed using density functional theory. In NaAlH4 doped with 3d transition metals (TM), the hypothesis of the formation of Ti-Al intermetallic alloy as the main catalytic mechanism for the hydrogen sorption reaction is supported. The gateway hypothesis for the catalysis mechanism in TM-doped MgH2 is confirmed through the investigation of MgH2 nano-clusters. Thermodynamics of Li-Mg-N-H systems are analyzed with good agreement between theory and experiments. Besides chemical hydrides, the metal-organic frameworks (MOFs) have also been investigated. Li-decorated MOF-5 is demonstrated to possess enhanced hydrogen gas uptake properties with a theoretically predicted storage capacity of 2 wt% at 300 K and low pressure. The metal-hydrogen systems undergo many structural and electronic phase transitions induced by changes in pressure and/or temperature and/or H-concentration. It is important both from a fundamental and applied viewpoint to understand the underlying physics of these phenomena. Here, the pressure-induced structural phase transformations of NaBH4 and ErH3 were investigated. In the latter, an electronic transition is shown to accompany the structural modification. The electronic and optical properties of the low and high-pressure phases of crystalline MgH2 were calculated. The temperature-induced order-disorder transition in Li2NH is demonstrated to be triggered by Li sub-lattice melting. This result may contribute to a better understanding of the important solid-solid hydrogen storage reactions that involve this compound.

The dissociative and non-dissociative hydrogen uptake in carbon nanostructures and metallic films were investigated by measurements and analysis of solubility isotherms. The total, non-dissociative, uptake for multi-walled nano-barrels and amorphous nanoporous carbon was determined to be 6.2 and 4.2 wt. % respectively at 77 K and the adsorption energies (at lowest coverage) -7.2 and -4.2 kJ/mol. At 298 K the H-uptake was negligible. At low concentrations the H-uptake of Nb-films is strongly affected by the film thickness. For thicknesses less then about 31 nm, the absorption energy was found to be temperature dependent. Such changes have not been observed in Nb films before. The presence of multiple absorption energies was shown to limit the possibility to obtain relevant absorption and interaction energies by traditional Sievert's and van 't Hoff analysis. The Mg1-xNix system (0&lt;0.43) was investigated with respect to the hydrogen uptake. For Mg2Ni the hydrogen uptake, at an external hydrogen pressure of 1 bar, is close to 1.33 H/M (Mg2NiH4). The enthalpy of formation is smaller in the film as compared to bulk material. The changes in the absorption energy are caused by the adhesion to the substrate as well as the nanocrystallinity of the absorbing layers. The optical band gap of Mg2NiH4 was determined to be 2.4 eV. In Mg1-xYx (0&lt;0.17) it was found that the Y-concentration limits the hydrogen uptake at 1 bar. However, the kinetics of the uptake improves substantially with a minimum of 7 at.% of Y. For Mg-Y the optical band gap (3.6 eV) is independent of Y concentration within the concentration range investigated, while the transmittance decreases with increasing Y content.

Irreversible thermodynamics is a widely-applicable toolset that extends thermodynamics to describe systems undergoing irreversible processes. It is particularly useful for describing macroscopic flow of system components, whether conserved (e.g., particle number) or non-conserved (e.g., spin). We give a general introduction to this toolset and calculate the entropy production due to bulk and interfacial flow. We compare the entropy production and heating rate of bulk and interfacial transport, as well as interfacial charge and spin transport. We then demonstrate the power and applicability of this toolset by applying it to three systems. We first consider metal oxide growth, and discuss inconsistency in previous theory by Mott. We show, however, that Mott's solution is the lowest order of a consistent asymptotic solution, with the ion and electron concentrations and fluxes going as power series in t^-k/2, where k = 1, 2, .... We find that this gives corrections to the "parabolic growth law" that has oxide thickness going as t^1/2; the lowest order correction is logarithmic in t. We then consider the effect on spin of electric currents crossing an interface between a ferromagnet (FM) and non-magnetic material (NM). Previous theories for electrical potential and spin accumulation neglect chemical or magnetic contributions to the energy. We apply irreversible thermodynamics to show that both contributions are pivotal in predicting the spin accumulation, particularly in the NM. We also show that charge screening, not considered in previous theories, causes spin accumulation in the FM, which may be important in ferromagnetic semiconductors. Finally, we apply irreversible thermodynamics to thermal equilibration in a thin-film FM on a substrate. Recent experiments suggest that applying a thermal gradient across the length of the system causes a spin current along the thickness; this spin current is present much farther from the heat sources than expected. We find that, although the interaction between the separate thermal equilibration processes increases the largest equilibration length, thermal equilibration does not predict a length as large as the experimentally measured length; it does predict, however, a thermal gradient along the thickness that has the shape of the measured spin current.

The substrate selectivities for different serine hydrolases were utilized in various applications, presented in papers I-VI. The articles are discussed in the thesis in view of the kinetics of the enzyme catalysis involved. In paper I the enantioselectivities towards a range of secondary alcohols were reversed for Candida antarctica lipase B by site directed mutagenesis. The thermodynamic components of the enantioselectivity were determined for the mutated variant of the lipase. In papers II-III Candida antarctica lipase B was engineered for selective monoacylation using two different approaches. A variant of the lipase created for substrate assisted catalysis (paper II) and three different variants with mutations which decreased the volume of the active site (paper III) were evaluated. Enzyme kinetics for the different variants were measured and translated into activation energies for comparison of the approaches. In papers IV and V three different enzymes were used for rapid analysis of enantiomeric excess and conversion of O-acylated cyanohydrins synthesized by a defined protocol. Horse liver alcohol dehydrogenase, Candida antarctica lipase B and pig liver esterase were sequentially added to a solution containing the O-acylated cyanohydrin. Each enzyme caused a drop in absorbance from oxidation of NADH to NAD+. The product yield and enantiomeric excess was calculated from the relative differences in absorbance. In paper VI a method for C-terminal peptide sequencing was developed based on conventional Carboxypeptidase Y digestion combined with matrix assisted laser desorption/ionization mass spectrometry. An alternative nucleophile was used to obtain a stable peptide ladder and improve sequence coverage. / QC20100629

The aim of this thesis work is to increase the knowledge of phenomena taking place during the initial stage in a top blown converter. The work has been done in a few steps resulting in four different supplements. Water model experiments have been carried out using particle image velocimetry (PIV) technology. The system investigated was a fundamental top blown converter where an air jet was set to impinge on a water surface. The flow field of the combined blown case, where an air jet was introduced through a bottom nozzle, was also captured by the PIV. The work clearly showed that the flow field caused by an impinging top blown jet alone could not match that of the bottom blown case. The main re-circulation loop (or vortex) was investigated with respect to position and it was found that an increased flow rate pushes the center of the re-circulation loop downwards into the bath. However, for the top-blown case there is a point when the flow rate is too large to cause a distinguishable re-circulation loop since the jet becomes more plunging (i.e. penetrates deep into the bath) than impinging, with large surface agitation and splashing as a result.A numerical model with the same dimensions as the experimental system was then created. Three different turbulence models from the same family were tested: standard-, realizable- and a modified-(slight modification of one of the coefficients in order to produce less spreading of the air jet) k-ε turbulence model. It could be shown that for the family of k-ε turbulence models the difference in penetration depth was small and that the values corresponded well to literature data. However, when it comes to the position of the re-circulation loop it was shown that the realizable k-ε model produced better results when comparing the results to the experimental data produced from the PIV measurements, mentioned earlier.It was then shown how the computational fluid dynamics (CFD) model could be coupled to thermodynamics databases in order to solve for both reactions and transport in the system. Instead of an air-water system, a gas-steel-slag system was created using the knowledge obtained in the previous simulation step described above. Reactions between gas-steel, gas-slag, steel-slag and gas-steel-slag were considered. Extrapolation of data from a few seconds of simulation was used for comparison to experimental data from the literature and showed reasonable agreement. The overall conclusion was that it is possible to make a coupling of the Thermo-Calc databases and a CFD software to make dynamic simulations of metallurgical processes such as a top-blown converter.A parametric study was then undertaken where two different steel grades were tested; one with high initial carbon content (3.85 mass-%) and one with lower carbon content (0.5 mass-%). The initial silicon content was held constant at 0.84 mass-%. Different initial temperatures were tested and also some variation in initial dissolved oxygen content was tried. It was found that the rate of decarburization/desiliconization was influenced by the temperature and carbon concentration in the melt, where a high temperature as well as a high carbon concentration favors decarburization over desiliconization. It was also seen that the region affected by a lower concentration of alloys (or impurities) was quite small close to the axis where the impinging jet hits the bath. Add the oscillating nature of the cavity and it was realized that sampling from this region during an experiment might be quite difficult. / QC 20100720

An optimally designed thermosiphon for power electronics cooling is developed. There exists a need for augmented grid assets to facilitate power routing and decrease line losses. Power converter augmented transformers (PCATs) are critically limited thermally. Conventional active cooling system pumps and fans will not meet the 30 year life and 99.9% reliability required for grid scale implementation. This approach seeks to develop a single-phase closed-loop thermosiphon to remove heat from power electronics at fluxes on the order of 10 - 15 W/cm2. The passive thermosiphon is inherently a coupled thermal-fluid system. A parametric model and multi-physics design optimization code will be constructed to simulate thermosiphon steady state performance. The model will utilize heat transfer and fluid dynamic correlations from literature. A particle swarm optimization technique will be implemented for its performance with discrete domain problems. Several thermosiphons will be constructed, instrumented, and tested to verify the model and reach an optimal design.