One of the most challenging tasks remaining in the field of biochemistry is the one of understanding how the information within the amino acid sequence of proteins translates into a unique structure. Solving this problem would lead to endless possibilities for application in the medical and biotechnology industry. Many decades ago scientists realized that the process that facilitates the folding of a polypeptide chain could not be random and happen by chance; there needs to be direction in the folding free energy landscape. This landscape is defined by the thermodynamic factors entropy and enthalpy. The contribution made by enthalpy i.e. the contact energies from intra- and intermolecular interactions have been extensively investigated by various mutational studies. The influence of entropy on the other hand, is less well understood. My work focuses on the effect of altering the entropic components of forming the various parts of a known protein scaffold. This is done by genetic engineering in combination with biophysical characterisation and analysis. The results show effects on protein folding rates as well as on the pathway for nucleation and emphasis the ability of the folding landscape to readjust to entropic variations. Proteins are therefore not required to fold along a unique route to their final structure but can do so in several ways. The folding pathways we observe today have hence likely evolved as an adaptation to biological demands.

The pathogenesis of Alzheimer’s disease (AD), the most common senile dementia, is a complex process. A crucial event in AD is the aggregation of amyloid-β protein (Aβ), a cleavage product from the Amyloid Precursor Protein (APP). Aβ40, a common component in amyloid plaques found in patients, aggregates in vitro at concentrations, much higher than the one found in vivo. But in the presence of charged lipid membranes, aggregations occurs at much lower concentration in vitro compared to the membrane-free case. This can be understood due to the ability of Aβ to get electrostatically attracted to target membranes with a pronounced surface potential. This electrostatically driven process accumulates peptide at the membrane surface at concentrations high enough for aggregation while the bulk concentration still remains below threshold. Here, we elucidated the molecular nature of this Aβ-membrane process and its consequences for Aβ misfolding by Circular Dichroism Spectroscopy, Differential Scanning Calorimetry and Nuclear Magnetic Resonance Spectroscopy. First, we revealed by NMR that Aβ40 peptide does indeed interact electrostatically with membranes of negative and positive surface potential. Surprisingly, it even binds to nominal neutral membranes if these contain lipids of opposite charge. Combined NMR and CD studies also revealed that the peptide might be shielded from aggregation when incorporated into the membrane. Moreover, CD studies of Aβ40 added to charged membranes showed that both positively and negatively membranes induce aggregation albeit at different kinetics and finally that macromolecular crowding can both speed up and slow down aggregation of Aβ.

This thesis presents a study of the effects of deep excavations on adjacent metro or utility tunnel in soft to medium soil. The main objective of the thesis is to develop a method of estimating these effects quantitatively. Extensive review of relevant literature published in the past four decades was conducted in order to understand the trends and the key developments in this area. It was revealed from the literature review that the concurrent use of the Observational Method and the finite element method for monitoring and controlling of ground deformations around the excavation has become a norm for deep excavation projects. Several design charts and guidelines for estimation of effects of deep excavations on adjacent raft foundations or pile foundations were found in the literature; however, no such charts or guidelines were found for estimation of effects of deep excavations on existing circular tunnels. Consequently, the development of these guidelines was established as one of the objectives of this study. <p>The initial phase of the research was focused on detailed study and analysis of two well-documented case studies the Chicago Subway Renovation Project, USA and the Tan Tock Seng Hospital Deep Excavation, Singapore. The back analyses of these two case studies were carried out using the finite element software PLAXIS. Exact site conditions and input parameters for the soil and the structural components were incorporated as much as possible. Appropriate adjustments in some of the input parameters were necessary to achieve good match between the computed and the observed results. <p> The back analyses were followed by parametric studies to identify important variables controlling the mechanisms of soil-structure interaction. The variables identified from the parametric studies of the two case studies were: soil stiffness, tunnel lining thickness, the depth of the excavation, and the location of tunnel. These variables were used to conduct a series of finite element analyses using simplified geometry and ground conditions for the purpose of formulating preliminary design charts. Results from these analyses were recorded in terms of in-plane and out-of-plane distortion of tunnel lining as well as additional shear forces and bending moments induced in the tunnel lining due to an adjacent deep excavation. The results were made non-dimensional before presenting them as contour plots. These contour plots constitute preliminary design charts, which can be used for the estimation of tunnel lining deformation caused by adjacent deep excavation.<p> Based on the results of this study, it can be concluded that a finite element program (such as PLAXIS) that is able to model construction processes associated with tunnelling and deep excavation in urban environment can be an invaluable tool in exploring the mechanism of ground deformation around the deep excavation and in quantifying the effects of ground deformation on existing adjacent structures. The modeller must, however, be aware of the fact that ways of modelling a particular construction process could be different for various finite element programs. It is important to interpret the instructions given in the manual of the program correctly. <p>Detailed back analyses of well-documented deep excavation case histories are vital from the point-of-view of building confidence in the selected finite element program. Such analyses also have the potential to identify key variables influencing the soil-structure interaction. <p> Preliminary design charts proposed in this thesis are very convenient for obtaining approximate values of tunnel lining deformation caused by adjacent deep excavation. Non-dimensional nature of these design charts makes it possible to be used for any depth of the deep excavation and for tunnels of any size, depth of cover, and distance from the vertical face of the excavation. These design charts can be used by engineers and contractors for initial estimation, selection and preliminary design of excavation support system, and are particularly useful during the planning phase. Town planners and project managers, who need to decide on the feasibility, damage control and risk management aspects of a deep excavation project, may also find these design charts equally useful. It should, however, be kept in mind that the estimates obtained from these design charts are highly approximate and as such, should be taken as guidelines for decision making processes. These estimates do not replace site specific detailed analysis and monitoring.

More than one-third of all Magnetic Resonance Imaging (MRI) scans employ image-enhancing contrast agents to increase the differential signal intensity between diseased and normal tissue. Because current clinical contrast agents exhibit low relaxivity (mM-1 s-1), low dose efficiency, and rapid secretion, we have designed a group of protein-based MRI contrast agents with multiple gadolinium binding sites. In this study, the developed purification method for Class ProCA-3 agents allows for a quick and cost-effective way to abstract up to 109 mg of pure, soluble protein from a 1L E. Coli cell pellet devoid of DNA or RNA “contamination” for extensive animal studies. Circular dichroism far-UV spectra ensure the metal stability of the agents, revealing maintenance of their native α-helical structure in the presence and absence of metal ions. Furthermore, substantial evidence supports the high dose efficiency of these agents, exhibiting up to five folds higher relaxivity than their analogous commercial competitors.

Voltage-dependent anion-selective channels (VDAC), or mitochondrial porins,regulate the flow of metabolites across the mitochondrial outer membrane. They presumably span the membrane as β-barrels, but the residues forming the individual β-strands are unknown. This information is essential for understanding the structure and function of the protein. Using Neurospora VDAC as a template, published data were reassessed to delineate a unified model for porin structure Bay and Court 2002, which was subsequently refined in collaboration with Greg Runke Runke et al. 2006. The focus of this work was the development and analysis of systems for maintaining high levels of folded porin for the acquisition of high resolution data needed for model testing. The conformation of hexahistidinyl-tagged Neurospora porin in detergent was probed by fluorescence, near-UV circular dichroism and ultraviolet absorption spectroscopy. Derivatives of tryptophan and tyrosine were also examined by fluorescence spectroscopy and UV absorbance spectroscopy to model the interactions between the detergents and the amino acid side chains in the protein. Detergent-specific levels of β-strand and tyrosine exposure were observed. In all cases, the two tryptophan residues reside in weakly asymmetric, hydrophobic environments, suggesting transient tertiary interactions. Porin solubilized in these detergents forms functional channels in liposomes and membrane insertion is accompanied by increased levels of β-strand and loss of protease sensitivity. These data were used to develop mixed detergent folding systems. A mixture of SDS and dodecyl-β-D-maltopyranoside (DDM)supports a β-strand rich conformation at high protein concentrations. The tertiary contacts and protease resistance of the SDS/DDM solubilized porin are very similar to those of the protein following reconstitution into liposomes. Finally, the role of sterols in porin folding was examined, as the addition of sterols to detergent-solubilized VDAC is required for channel formation in artificial membranes. Sterols do not alter the secondary structure of VDAC, and subtle alterations to tertiary interactions were detected, suggesting that sterols do not promote an insertion-competent structure, but rather facilitate insertion into artificial bilayers. In summary, this analysis of the folded states of detergent-solubilized porin has revealed a system that maintains high concentrations of mitochondrial porin in a state that is very promising for structural studies. / February 2007

Metal deposition is an additive layered manufacturing process that deposits molten metal droplets on a substrate and by repeating this process layer by layer, a complex shaped 3D geometry can be manufactured. In this thesis, the metal deposition process is performed by a robot with a wire feeder tool and a laser as energy source to melt the metal wire. The robot programming for robotized metal deposition process can be completely automated by computer aided robotics software. University West is currently developing an add-in application in a computer aided robotics software, Process Simulate, that is capable of programming the robotized metal deposition process. The first goal of this thesis was to verify the up to now developed software and the process from CAD drawing down to robot code. Another goal was to find and implement an algorithm that will reduce the number of locations on a circular arc to three locations. The algorithm to minimize the locations must be capable of changing all the different curvature paths to linear and circular arc motions which are easy to translate to robot code. The user should be able to decide the fitting precision of the approximated motion path to the original path. A real robot cell setup is modelled in Process Simulate. This lets Process Simulate generate the correct robot code for that specific cell.  Since each robot cell has its own unique setup, a custom script will be developed that changes the universal robot code, that Process Simulate generates, to the custom robot code required in this specific robot cell. The software is improved and tested from CAD drawing down to robot code but still needs to be debugged more and needs implementation of some non-existing features.

In this Thesis the magnetic and structural properties of thin epitaxial Fe, Co, and Ni films are discussed. Some of the in-situ prepared samples were used to characterize the degree of circular polarization of the newly installed beamline D1011 at MAX-lab. By means of x-ray magnetic circular dichroism (XMCD) and utilizing the associated magneto optic sum rules, the orbital (ml) and spin (ms) moments are determined directly in mB/atom with elemental specificity. The extended x-ray absorption fine structure (EXAFS) measurements yield site specific information on the local crystallographic structure. These measurements were performed using the circular x-rays of several beamlines. The influence of the degree of spatial source coherence lspat of the x-rays was characterized by means of Fresnel diffractometry. A correlation between enhanced XAS white line intensities and higher values of lspat was established for 20 ML Fe, Co, and Ni films on Cu(100). The degree of circularly polarized x-rays (Pc) at beamline D1011 at MAX-lab was characterized by studying Fe films on Cu(100) by means of XMCD. The maximum value of Pc is experimentally determined to Pc =0.85. The Au/Co/Au trilayer system was studied as a function of Co thickness, temperature, and Au cap thickness. A 10 mono-layer (ML) Co film, with an Au cap of 20 Å, shows a spin reorientation transition (SRT) from an in-plane to an out-of-plane easy direction as the temperature is lowered from 300 K to 200 K. The magnetic properities of these Co films are very different to what is found for bulk samples due to, in particular, the broken symmetry at the interfaces. The thickness dependent spin reorientation transition in the Fe/Ag(100) system was characterized by means of XMCD and EXAFS measurements. 3 ML Fe films show an out-of-plane easy direction with an 125% enhanced orbital moment as compared to the 25 ML Fe in-plane film. Simulations of the Fe L-edge EXAFS indicate the bulk Fe bcc structure for film thicknesses of 6-25 ML Fe. For 3 ML Fe strong deviations from this bcc phase is observed. Ultrathin Co films deposited on flat and vicinal Cu(111) in the thickness region 1-25 ML were studied by means of XMCD and scanning tunneling microscopy (STM). The vicinal Cu(111) Co deposition leads to the formation of elongated islands preferentially oriented along the step edges. In connection to this particular Co growth mode we observe an increase of both the orbital and the spin moment on the vicinal Cu(111) of about 25% relative to what was observed for Co on flat Cu(111).

This work presents first-principles calculations of long-range intermolecular dispersion energies between two atoms or molecules and of electronic circular dichroism spectra of chiral molecules. The former is expressed in terms of the C6 dipole-dipole dispersion coefficients Δε, and the latter is given in terms of the extinction coefficient. In a series of publications, the complex linear polarization propagator method has been shown to be a powerful tool to provide accurate ab initio and first-principles density functional theory results. This was the case not only for the C6 dispersion coefficients but also for the electronic circular dichroism at an arbitrary wavelength ranging from the optical to the X-ray regions of the spectrum. The selected samples for the investigation of dispersion interactions in the electronic ground state are the noble gases, n-alkanes, polyacenes, azabenzenes, alkali-metal clusters, and C60. It is found that the values of C6 for the sodium-cluster-to-fullerene interactions are well within the error bars of the experiment. The proposed method can also be used to determine dispersion energies for species in their respective excited electronic states. The C6 dispersion coefficients for the first π → π* excited state of the azabenzene molecules have been obtained with the adopted method in the multiconfiguration self-consistent field approximation. The dispersion energy of the π → π* excited state is smaller than that of the ground state. It is found that the characteristic frequencies ω1 defined in the London approximation of n-alkanes vary in a narrow range which makes it possible to construct a simple structure-to-property relationship based on the number of π-bonds for the dispersion interaction in these saturated compounds. However, this simple approach is not applicable to the interactions of the π-conjugated systems since, depending on the systems, their characteristic frequencies ω1 can vary greatly. In addition, an accomplishment of calculations of the electronic circular dichroism spectra in the near-edge X-ray absorption has been demonstrated.

This thesis evaluates decommissioning strategies for the International Space Station ISS. A permanent solution is attempted by employing energy efficient invariant manifolds that arise in the circular restricted three body problem CRTBP to transport the ISS from its low Earth orbit LEO to a lunar orbit. Although the invariant manifolds provide efficient transport, getting the the ISS onto the manifolds proves quite expensive, and the trajectories take too long to complete. Therefore a more practical, although temporary, solution consisting of an optimal re-boost maneuver with the European Space Agency's automated transfer vehicle ATV is proposed. The optimal re-boost trajectory is found using control parameterization and the sequential quadratic programming SQP algorithm. The model used for optimization takes into account the affects of atmospheric drag and gravity perturbations. The optimal re-boost maneuver produces a satellite lifetime of approximately ninety-five years using a two ATV strategy.

The aim of this project is to design a microstrip phase array antenna in ADS (Advance Design System) Momentum. The resonant frequency of which is 10 GHz. Two circular patches with a radius of 5.83 mm each are used in designing the array antenna. RT-DURROID 5880 is used as a substrate for this microstrip patch array design. These circular patches are excited using coaxial probe feed and transmission lines of particular lengths and widths. These transmission lines perfectly match the impedance of the circular patches. Various parameters, for example the S-parameters, two dimensional and three dimensional radiation patterns, excitation models, gain, directivity and efficiency of the designed antenna are obtained from ADS Momentum.