Abstract The correct three dimensional structures of proteins are essential for their ability to function properly. Proteins start to fold as soon as they are synthesized in the ribosomes from activated amino acids. Many secreted, cell-surface, secretory pathway and endoplasmic reticulum (ER) lumenal proteins have in their amino acid sequence cysteine residues which form intra- and intermolecular disulfide bridges that stabilize the overall fold of the proteins and protein complexes. The formation of correct disulfide bonds is a complex process which takes place within the ER. Protein disulfide isomerase (PDI) is the key enzyme in the formation and rearrangement of correct disulfide bonds in the ER. It is an archetypal and the best studied member of the PDI family, i.e. a group of ER proteins that resemble thioredoxin (TRX), a protein reductase, in their structure. PDI has a four domain a-b-b'-a' structure the a and a' domains having the catalytic activity and amino acid sequence similarity to TRX. In addition to its function as a thiol-disulfide oxidoreductase, PDI acts as the β subunit in two protein complexes: collagen prolyl 4-hydroxylase (C-P4H) and microsomal triglyceride transfer protein (MTP). The closest homologue of PDI is the multifunctional enzyme and chaperone ERp57 that functions in concert with two lectins, calnexin (CNX) and calreticulin (CRT) specifically in the folding of proteins that have sugar moieties linked to them. ERp57 is 56% similar to PDI in its amino acid sequence and has also the four-domain architecture. Despite the high similarity in their structures ERp57 cannot substitute for PDI as the β subunit of C-P4H. The minimum requirement for the C-P4H tetramer assembly is fulfilled by domains b' and a' of PDI, while domains a and b enhance this function and can be substituted in part by those of ERp57. Until very recently the structural information of any of the PDI family members, which contains the TRX active site was limited to solution structures of human PDI domains a and b. In this research the domain boundaries of the full length ERp57 were defined and the individual domains characterized. Furthermore the solution structures of the catalytically active domains a and a' of ERp57 were studied by nuclear magnetic resonance (NMR).

Abstract The triosephosphate isomerase (TIM) barrel superfamily is a broad family of proteins, most of which are enzymes. At the amino-acid-sequence level, many of the members of this family share little, if any, homology. Yet, they adopt the same three-dimensional (βα)8 fold. The TIM barrel fold seems to be a good framework for many different kinds of enzymes, providing unique possibilities for both natural and human-designed evolution, as the catalytic center and the stabilizing features are separated to different ends of the barrel. Indeed, in the light of most recent studies, it seems likely that at least most of the different TIM barrel enzymes, catalyzing a huge variety of reactions, have evolved from a common ancestor. TIM can be considered a real text-book enzyme — its catalytic properties and stucture-function relationships have been studied for decades. Still, at present, we are quite far from understanding the structural features that make TIM and other enzymes such superior catalysts in both efficiency and precision. TIM is a dimeric enzyme that consists of two identical subunits of 250 residues. It catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate in glycolysis. The basics of this reaction are well known, but there is ongoing discussion about the details of the proton transfer steps, and three alternative pathways have been suggested. In addition, it is a fascinating question how the enzyme succeeds in abstracting a highly stable proton from a carbon atom of the substrate. This study was undertaken to shed light on some of the questions concerning the structure-function relationships in TIM. The most important findings are the elucidation of the role of Asn11 as a catalytic residue and the meaning of the flexibility of both the catalytic Glu167 side chain as well as the substrate during catalysis, and the presence of a low-barrier hydrogen bond between Glu167 and a transition-state analogue, 2-phosphoglycolate. Furthermore, significant results were obtained on the importance of a conserved salt bridge, 20 Å away from the active site and the dimer interface, for the stability and folding of TIM as well as on the factors influencing the opening of the flexible loop 6 upon product release.

Magister Scientiae Dentium - MSc(Dent) / The shift towards minimally invasive dentistry has meant that dental practitioners are now undertaking procedures that are conservative and preserve as much of the existing tooth structure as possible. Repairing composite is a more conservative way of managing damaged restorations when compared to their replacement. A number of different protocols for repairing composite restorations exist but there is little information as to which is the most effective method. Aim: The aim of this study was to evaluate the effect the following treatment procedures have on the shear bond strength of repaired composite: i. Five different repair protocols, ii. Two different types of repair composite materials and iii. Aging in artificial saliva prior to repairing. Materials and methods: Two hundred and forty composite cylinders of 5mm diameter and 5mm height made from Filtek Supreme XTE (3M ESPE, St. Paul, MN, USA) were prepared with the aid of a silicon matrix. They were then divided into two groups: a hundred and twenty of these cylinders were aged in a solution of artificial saliva for 28 days and the remaining samples were left unchanged with no aging. All the aged and non-aged composite cylinders were then randomly allocated to six groups of twenty each corresponding to the repair protocol applied. The first group from both of the aged and non-aged samples was treated by roughening the top surface with a diamond bur followed by an application of Scotchbond 1XT (3M ESPE, St. Paul, MN, USA). The second group received a surface roughening with a diamond bur,etching with 35% phosphoric acid and application of Scotchbond 1XT. The third group received an application of Scotchbond Universal (3M ESPE, St. Paul, MN, USA) and the fourth one had a single application of Tetric N-Bond Universal (Ivoclar Vivadent AG, Schaan, Liechtenstein) on its top surface. The fifth group was treated by blasting with COJET Sand (3M ESPE, St. Paul, MN, USA) particles together with an application of Scotchbond Universal. The final group was used as the control where no surface treatment was done. After the surface treatments, each of the composite samples was repaired by the addition of fresh composite in the shape of cylinders measuring 3mm in diameter and 4mm in height. This was done with the aid of a silicon matrix. Within each treatment sub-group (n=20), 10 cylinders were repaired using either Filtek Supreme XTE or Tetric N-Ceram. All two hundred and forty repaired samples were then subjected to shear bond strength testing on a Universal testing machine. Data analysis: The results of the shear bond strength tests expressed in megapascals (MPa) were recorded and analysed for the effect of three different factors under consideration. The effectiveness of the repair protocols, type of composite and aging in artificial saliva were compared using the analysis of variance. Differences within the groups were identified using a post hoc analysis. Results: The mean highest repair shear bond strength was observed when COJET Sand in conjunction with Scotchbond Universal was used to repair the aged composite blocks. There were no significant differences in the shear bond strength observed when either Filtek Supreme XTE or Tetric N-Ceram was used as the repair composites. Aging in artificial saliva led to a mean reduction of 18.08% in the repair bond strength across the six treatment groups. Conclusions: The application of a surface treatment and intermediate adhesive is crucial in improving bond strength in the composite repair interface. Repair with Filtek Supreme XTE and Tetric N-Ceram was equally effective. Aging in artificial saliva produced significantly reduced bond strength.

In this thesis, we analyse financial contagion between Southern European (Greek, Italian, Portuguese and Spanish) and Central Eastern European (Czech, Polish and Hungarian) stock markets respectively sovereign bond markets in the period from January 2001 to June 2016. A quantile regression framework is applied to analyse contagion based on measuring of occurrences and degrees of co-exceedances. We use conditional variance (volatility) of analysed markets to find direction of the contagion. Our results show that during the analysed period contagion between stock markets exists. Contagion between stock markets is stronger during the financial and sovereign debt crisis. Direction of contagion is from Southern European to Central Eastern European Countries. We do not find evidence of contagion between Sothern European and Central Eastern European sovereign bond markets. Our results show "flight to quality", but not "flight from quality".

This paper investigates the effect of bond market on economic growth in South Africa. Quarterly data for South Africa for the period 2003-2014 was used to develop a general- to- specific Auto-Regressive Distribution Lag (ARDL) approach. The empirical results confirm that there is a positive relationship between Bond market and economic growth in South Africa. A co-integrated relationship between economic growth, stock market and banking sector was noticed in both the long-run and short-runs.

The electromagnetic machines like the dc, induction, synchronous motor/generator and the transformer have an energy flow framework that is similar. All these machines deal with electrical energy in the electrical domain that is interfaced with the magnetic domain. Except for the transformer, the other machines also have one more energy interface i.e. with the mechanical domain. In all these machines, the magnetic domain acts as the silent energy manager. The electrical and the mechanical domain energies will have to pass through the magnetic domain and appropriately get routed. In recognition of the commonality of this pattern of energy flow, this thesis proposes a generalised model of a multiphase electromagnetic device wherein the dc machine, induction machine, synchronous machine and the transformers are special cases of the proposed generalised model. This is derived using bond graphs that is based on the underlining principle of Energy Flow rooted in the concept of Conservation of Energy. A model is a set of mathematical equations representing a physical system. A model is as good as a modeller understanding of the physical system and the underlying approximation he makes while writing down the equations describing the models behaviour to the stimulus. A modelling language tool, which can cut down the approximations made by using the power of identified analogous characteristics across the physical domain, can help make a model more close to real life situation. Bond Graph is such a modelling language which is powerful enough to model the non-linear, multi-disciplinary, hybrid continuous-discrete phenomena encountered in a real life physical system. Bond graphs as a modelling tool was introduced by Professor H.Paynter at Massachusetts Institute of Technology in 1959. The Bond Graph methodology is based on consideration of energy flows between the ports of the components of an engineering system. Bond Graph methodology enables one to develop a graphical model that is consistent with the first principle of energy conservation without having the need to start with establishing and reformulating equations. The derivation of a mathematical model from the graphical description is automated by software tools. As a consequence, a modeller using this methodology can focus on modelling of the physical system. In the graphical representation of bond graph the vertices of a bond graph denote subsystems, system components or elements, while the edges, called power bonds, represent energy flows between them. The nodes of a bond graph have power ports where energy can enter or exit. Bond graph models are developed in a hierarchical top-down or bottom-up approach by using component models or elements from model libraries. An electromagnetic machine is a black box having an assemblage of windings in iron resulting in a combination of input/output ports on shaft and electrical terminals. Abstraction of an machine model by a modeller matching the vision of the observer above is an ideal goal. Bond graph methodology is an appropriate tool for trying to reach this goal as it is based on object oriented modelling techniques. There have been few attempts to model electric machine in bond graph earlier. A well established DC motor bond graph has been widely used in all bond graph literature. But AC rotating machine being a higher order nonlinear system poses a tougher challenge. Here too, there have been few attempts in modelling AC machines. It is observed that majority of AC machine bond graph models have been built up from their mathematical models. But as the bond graph modelling technique is based on the unifying theory of energy exchange, better insight into the system is achievable if the model is conceptualised from its physical structure. This thesis starts from the basic theory of energy port to conceptualise the generalised model from physical correspondence. In this thesis a Rotating Electrical Machine is studied as a physical system. The energy ports inside this physical system is identified. When a physical system receives the energy through its energy port in one energy cycle, it processes this energy in one of the three ways. The received energy is converted into useful work or it is dissipated or stored. The storage can further be classified into two ways, either as kinetic energy or as potential energy. For a rotating electric machine the input-output port for energy exchange are either in electrical or mechanical domain depending on the class of the machine. The magnetic domain across all class of electromagnetic device acts as the energy manager. In order to capture the features of the energy jumping across the air gap in a rotating electrical machine, wherein the magnetic fields from spatially distributed windings of the stator and rotor interplay, an Axis Rotator (AR) element -a mathematical commutator, is introduced in this thesis as a new bond graph element. In a multiphase device, the energy from the various phases and spatial axes are transferred through the axis rotator element. The Axis Rotator is a critical element which helps distinguish between the various classes of electromagnetic devices. The defining features of the Axis Rotator helps in deriving the various special electromagnetic devices (such as the dc machine, induction machine, synchronous machine and the transformer) from the generalised model. The Axis Rotator exists in the magnetic domain. It naturally inherits the characteristics of the magnetic domain. The Axis Rotator as a bond graph element is complex. In a specific case of 3φ Induction Motor an alternative bond graph model with all integral elements is developed. By one to one correspondence with the AR bond graph model, the inner component of ’AR’ can be identified. Another advantage of using this model is that saturable and non-saturable magnetic permeance can be separated out, a useful feature in the nonlinear model discussed next. One of the most distinguishing features of the magnetic domain is the existence of Magnetic Hysteresis. Magnetic Hysteresis is a well understood and studied subject. But this physical process is wilfully ignored by the modelling community at large. The main reason for this is the difficulty of modelling a nonlinear phenomena. The bond graph modelling naturally allows the inclusion of such non-idealities within its framework. This thesis proposes the generalised model along with the inclusion of magnetic non-linearities and non-idealities into the model of the system. This inherent strength of bond graph model flows from the fact that the models in bond graph are developed from the first principles of energy conversation and the mathematical equations are derived later from the evolved graph. The tools that are available for bond graph simulation are not adequate for power electronics systems. The existing tools do not address space vectors and frame transformations. As a consequence it is difficult to simulate the electromagnetic device models developed in this thesis. The need for a bond graph tool to address vectors and frame transformations, a common occurrence in electric machines dynamic model study was acutely felt. This necessitated a support for handling complex data class from the underlying mathematical engine of the software. MATLAB/Simulink is the commonly available mathematical tool which has a support for complex variables. Therefore during the course of this research work a new software tool box was developed which meets the need of electromagnetic machines in particular and other engineering domains in general. For developing the new bond graph simulation software, the language extender approach was chosen, as it combines the capabilities of existing popular mathematical engine with its tested graphical frontend and the flexibility of combining different modelling technique like bond graph, block diagram, equations etc. It also ensures portability as they are compiled by interpreted language compiler of the mathematical engine and are thus independent of the computer operating system. C-MEX S-function methodology was used to develop the software as it has access to lower level functions and methods of the underlying mathematical engine. This helps in speeding up the software execution time alongwith the flexibility in defining new complex elements like the Nonlinear Axis Rotator. In conclusion, this thesis makes the following contributions: (i) The Axis rotator concept to handle space vectors and frame transformations, (ii) generalised model of the electromagnetic device, (iii) introduction of the saturation and hysteresis non-linearity in the magnetic domain, (iv) development of the bond graph toolbox to handle vector and frame transformations.

Reinforcement corrosion is the most common deterioration problem observed in reinforced concrete (RC) structures located at coastal or cold regions. The corrosion process can impact the performance of these structures by inducing damage on the bonding action between concrete and steel, either by the splitting of the concrete cover due to the volumetric expansion of corrosion products or the lubricant effect at the steel/concrete interface as the corrosion by-products accumulate. The current research aims at investigating corrosion-induced deterioration of bond between steel and concrete through finite element (FE) analysis of the flexural behaviour of corroded RC components. By treating the concrete cover as a thick-wall cylinder subjected to internal pressure, the analytical evaluation of impaired bond capacity is studied first and verified against published bonding tests. Then, the formulation of a numerical model is performed using ABAQUS, wherein a link element to simulate the bond behaviour is formulated and implemented through the ABAQUS user-subroutine (UEL) feature according to the validated analytical model. By introducing corrosion-induced damages, i.e., smaller cross-sectional area of reinforcement, splitting of concrete and bond deterioration, in the FE analyses, the results of the numerical model show good agreement with experimental observations. Upon validation of the analytical and FE models, a parametric investigation is conducted, wherein the effects of concrete strength, dimension of reinforcing bars, properties of oxide products, different corrosion damage mechanisms and the corrosion location along the longitudinal reinforcement on the flexural behaviour of RC beams are studied. The results show that the analytical evaluation for bond degradation is impacted by the selection of the post-cracking material model and the thickness of cover that determine the ‘holding capacity’ after cracking initiation. Also, the density of rust by-products affects the results of the analytical model at high corrosion levels. From the FE model results, it was observed that each damage mechanism due to corrosion contribute to different levels of flexural degradation, although the flexural strength degradation is mainly due to the loss of bonding action. The parametric study also demonstrates that flexural members which have reinforcement corrosion initiated near the supports suffer greater deterioration in flexural capacity than those with damages at mid span. Finally, based on these observations, suggestions for the application of both analytical and numerical models are made.

Despite the on-going intensity of research in the field of protective structural design, one topic that has been largely ignored in the literature is the effect of high strain rates on the bond between reinforcing steel and the surrounding concrete. Therefore, a comprehensive research program was undertaken to establish the effect of high strain rates on reinforced concrete bond. The experimental research consisted of the construction and testing of fourteen flexural beam-end bond specimens and twenty-five lap-spliced reinforced concrete beams. The physical and material properties of the specimens were selected based on a range of design parameters known to significantly influence bond strength. In order to establish a baseline for comparison, approximately half of the total number of specimens were subjected to static testing, while the remainder were subjected to dynamic loading generated using a shock tube. The strain rates generated using the shock tube were consistent with those obtained for mid- and far-field explosive detonation. Results of the beam-end and lap splice beam tests showed that the flexural behaviour of reinforced concrete was significantly stronger and stiffer when subjected to dynamic loading. Furthermore, the high strain rate bond strength was always greater than the corresponding low strain rate values, yielding an average dynamic increase factor (DIF) applied to ultimate bond strength of 1.28. Analysis of the low and high strain rate test results led to the development of empirical expressions describing the observed strain rate sensitivity of reinforced concrete bond for spliced and developed bars with and without transverse reinforcement. The predictive accuracy of the proposed DIF expressions was assessed against the experimental results and data from the literature. It was found that the dynamic bond strength of reinforced concrete can be predicted with reasonably good accuracy and that the proposed DIF expressions can be used for analysis and design of protective structures. An analytical method was also developed to predict the flexural load-deformation behaviour of reinforced concrete members containing tension lap splices. The analysis incorporated the effect of reinforcement slip through the use of pseudo-material stress-strain relationships, in addition to giving consideration to the effect of high strain rates on bond-slip characteristics and on the material properties of concrete and steel. A comparison of the analytical predictions with experimental data demonstrated that the proposed analysis technique can reasonably predict the flexural response of beams with tension lap splices. The results also demonstrated that the model is equally applicable for use at low- and high-strain rates, such as those generated during blast and impact.

This thesis covers detailed analysis of bond pricing function. It focuses on connections between mathematical definitions and financial practice and it points out advantages and drawbacks of currently used function. Well known properties of this function are extended to negative internal rate of return values. This topic is further discussed with internal rate of return polynomial equations solving. Taylor series approximation is also shown regarding duration and convexity of bonds.

Abstract  Aim: To determine the shear bond strength of two commercially available self-adhesive resin cements on four different materials and to analyse the degree of conversion (DC) of those resin cements.  Materials and Methods: A total of 45 embedded specimens made of four different materials were prepared for the notched-edge shear bond strength test. Ten specimens each of resin composite, glass-ionomer, zirconia and 15 of human dentine. Pillars of two different self-adhesive resin cements were luted onto these specimens. Five of the dentine specimens were treated with Katana Cleaner before being luted with Panavia. A single sample from each self-adhesive resin cement was used to determine the DC using ATR-FTIR Spectroscopy. The samples were measured uncured, right after being light cured and 10 min thereafter. Results: The highest shear bond strength values were seen for RelyX, irrespective of the material tested. This difference was statistically significant. No statistically significant difference was seen between the dentine specimens pre-treated with Katana Cleaner and luted with Panavia, compared to no pre-treatment. No statistically significant differences were found regarding DC between Panavia and RelyX.  Conclusion: The bond between the dental materials and the tooth structure is extremely important for the longevity of the restoration. The bond strength of RelyX for all materials tested were 2.1 to 37.5 times higher than that for Panavia and the differences were statistically significant. Panavia had virtually no bonding to the dentine in this study which might be due to the treatment of the dentine. The differences regarding the degree of conversion between the two resin cements were not statistically significant. However, the DC 10 min after curing was 1.3 times higher than directly after curing for both resins.