In Escherichia coli, the twin arginine translocase (Tat) is one of the major protein translocation mechanisms. The Tat system has the ability to transport folded proteins across the inner membrane. Therefore, it has the ability to discriminate between folding states. However, it is not well understood how the Tat system senses the folding state of a substrate. In this study we probed the Tat proofreading mechanism and we investigated whether Tat substrates in E. coli are translocated by the Tat system due to their rapid folding kinetics. We demonstrate that the E. coli Tat machinery can process a de-novo designed substrate (BT6 maquette). Moreover the Tat proofreading mechanism can discriminated between different folding states of this substrate. This data and the fact that this simple four helix artificial substrate offers a lot of engineering freedom, suggests that BT6 is an ideal candidate to study the Tat proofreading mechanism (chapter 3). In chapter 4, we focussed on the Tat system’s proofreading ability by substituting substrate surfaces of BT6 maquette. Mutants with substituted surface properties were expressed in order to understand what Tat senses as folded. Expression assays showed whether the mutants were accepted or rejected by Tat. We propose that the proofreading system does not sense a global unfolded state of the substrate but has the ability to sense localised unfolded regions. Finally, we tested whether Tat substrates fold co- or post-translationally to determine the speed of the folding kinetics by using an arrest peptide-mediated force measurements assay (chapter 5). This study was to increase our understanding about the rationale for using the Tat system.

Optical Coherence Tomography (OCT) is an imaging modality which has proven, since the early 1990s, its incredible potential. Nowadays, numerous fields of medical investigation, such as Ophthalmology, Dermatology or Cardiovascular imaging, would not be the same without the diagnostic tools bring by OCT. This tremendous development has been supported by industry support through improvement of dedicated components such as lasers, cameras and optics. A great example of this development is the evolution of Supercontinuum (SC) sources. Due to the extremely broad spectrum cover by SC sources, their high power density and high spatial coherence, it seems obvious to use them for driving OCT systems. However, an intensity noise issue arising from the SC sources has been reported as a limitation for OCT and needs to be addressed. The aim of the work presented in this thesis is to create a link between the world of Optical Coherence Tomography and Supercontinuum physics in order to understand the origins and the impact of SC source intensity noise into the OCT systems. This work is of importance as it helps to optimize the usefulness of the current generation of SC sources. Also, this work is a part of the work necessary for developing a new generation of SC sources which completely addresses the intensity noise limitations. More precisely, a part of the work presented deals with an optimization of the association SC source and OCT. The second part of the results is an attempt for improving this association by using a new SC source design.

This work covers the complete study of the properties of high quality nm-thick sputtered Yttrium iron garnet (Y3Fe5O12) films, with the discovery of interfacial diffusion and its effect on the magnetisation suppression. Here we report the structural and magnetic properties of YIG nano films deposited on Gadolinium gallium garnet (GGG) substrate by RF magnetron sputtering. The structural characterisation and morphology of the films were analysed using X-ray reflectivity (XRR), X-ray diffraction (XRD) and atomic force microscopy (AFM). The magnetic properties were investigated using VSM and SQUID magnetometer. The films in the 10 - 60 nm thickness range have surface roughness of 1-3 Å, and (111) crystalline orientation. The saturation magnetisation, coercive field and the Curie temperature observed in our YIG films are 144 ± 6 emu/cc, 0.30 ± 0.05 Oe and 559 K, respectively. The thickness dependence of the saturation magnetic moment shows the existence of a 6 nm dead layer. The temperature dependence of the magnetization M(T) in YIG reveals a reduction in magnetization at low temperature, below ~ 100 K. Through an extensive analysis using STEM, we discovered an interdiffusion zone of 4 - 6 nm at the YIG/GGG interface where Gd from the GGG and Y from the YIG diffuse. Analysis of XRR data also confirms the presence of Gd-rich diffused layer of 5 - 6 nm thick at the interface. This Gd-rich YIG layer having compensation temperature at 100 K corresponds to 40% Gd diffusion, that aligns antiparallel to the net moment of YIG, resulting in the magnetisation suppression in YIG at low temperature. Our polarised neutron reflectivity results also revealed the magnetization downturn in 80 nm YIG film. FMR results showed narrow FMR linewidth and a small Gilbert damping, for e.g. (2.6 ± 0.3) x 10−4 in 38 nm thick YIG. The temperature dependence of the Gilbert damping factor in YIG and YIG/Pt showed a linewidth broadening and increased damping below 50 K. Our current induced FMR results demonstrate the dominating role of Oersted field torque in driving the magnetization dynamics in YIG/Pt bilayer films. Our investigation on the effect of C60 molecules on the damping of YIG in YIG/C60 hybrid structures shows an increase in damping in thin YIG films, but it decreases between 80 - 160 nm. Our findings widen the applications of sputtered nm-thick epitaxial YIG films and YIG-based multilayers in magnonics, spin caloritronics and insulator-based spintronics devices.

Magnetostriction in various metals has been known since 1842. Recently the focus has shifted away from ferrous metals, towards materials with a straightforward or exaggerated stress magnetostriction relationship. However, there is an increasing interest in understanding ferrous metal relationships, especially steels, because of its widespread use in building structures, transport and equipment and pipelines. The purpose of this PhD is to develop the relationship between stress and magnetisation for commercial steel, such that experimental determination and theoretical modelling will allow prediction and location of stress concentration zones, which can in turn be identified as defects within the material. Such defects are either expected, such as weld joints, or unexpected such as damage caused by pipeline corrosion or dents. This will serve to support a magnetic field measurement instrument, developed in University of Leeds Electrical Engineering, to allow non- invasive inspection of underground pipelines, and the detection of any defects using the technique of measuring Self Magnetic Flux Leakage (SMFL) from the pipe material. Extensive trials show reliable field performance, basic algorithms can estimate pipeline integrity. The prototype is being used commercially by the project sponsor, and is the subject of a patent. Experimental measurement of magnetic fields around stress concentration zones supports the development of a theoretical model which will enhance the operation of the prototype exploiting this magnetic technique. The hypothesis proposed is that the magnetic flux observed from SCZ (Stress Concentration Zone) in steel objects is because of a flux leakage mechanism from a SCZ, which could be due to a defect or anomaly. A simple magnetic model is proposed, where a pipeline is represented as a series of connected bar magnets, the joints or welds in the pipeline are discontinuities which create a magnetic field pattern in the pipe sections and at the weld joints. These areas can be modelled and located by characterizing each region as a dipole, with resulting characteristic magnetic field patterns, particularly when they are resolved into orthogonal components. Pipeline defects can be similarly modelled, and given this characteristic magnetic pattern, the SCZ area can be located by magnetometry. Analysis of the forward problem, predicting magnetic field from a given steel material stress state, has indicated that observed magnetic field from flux leakage is of the same magnitude as that calculated from the bulk flux of the steel object. This has led to the solution for the inverse problem of estimating material stress from the measured magnetic field from flux leakage of SCZ. Algorithms have been developed that allow the calculation of pipeline stress, the estimation of pipeline depth and correction for the direction of the pipeline. A simple depth algorithm is required to estimate the distance from the magnetic field measurement, to the SCZ, in this case the depth algorithm has been shown, by field trials, to have a standard error of +/- 40 cm with a 70 % confidence level. In addition, a stress algorithm has been developed, with an estimated standard error of +/- 15 MPa, and the algorithm is judged to be capable of estimating pipeline stress to +/- 20 % of the absolute value, whilst this is insufficient for a detailed determination of pipeline integrity, it is sufficient to indicate potential problem areas, which then can be evaluated with established techniques. Field trials carried out on industrial underground pipelines show the technique can locate welds in the pipeline and that 81\% of welds are located within +/- 3m of ILI (in line inspection) reference data with a POD (probability of Detection) of 75%. Unexpected defects were located, 83% being found < 2m compared to ILI data, with a mean error of +/- 1m. These features are demonstrated in surveys carried out in conjunction with National Grid. Work on the location of weld position has also demonstrated that there is a capability for this system to be used in this mode, which is of importance to pipeline operators, as they use weld positions to find pipeline sections that have defects. This then leads to the conclusions that the prototype system developed, can in principle identify and locate SCZ, the aspect to be developed is the characterisation and the determination of the severity of either a defect in the pipeline or an expected SCZ such as a weld, which is the subject of further work, beyond this PhD.

Semiconductor quantum dots (QDs) are a quintessential example of nanotechnology; their useful optoelectronic properties (including bright photoluminescence) that distinguish them from bulk semiconductors arise primarily due to their nanoscopic size, and the discrete, quantum mechanical nature of matter. The “redox environment”, defined as the general tendency of molecules to be reduced or oxidised in a given microenvironment, is one of the central concepts of the field of redox biology. Current methods of measuring the redox environment within living cells are unsatisfactory. To address this, a number QD-based redox sensors have been developed, however, there are still open questions about the physics of such sensors, particularly with respect to their excited-state electron dynamics. This thesis details the excited state dynamics of QD-based redox sensors, as well as their application to biology. Chapter 1 contains an overview of the photophysics of such QD biosensors, as well as a review of the relevant literature. Chapter 3 details electron microscopy-based studies of the internal structure of CuInS2 QDs, aimed at understanding their defect-related excited state dynamics, with a view to their application as less toxic biosensors. It was concluded that the emissive transition in CuInS2 QDs is associated to an electronic state that arises due to large, polydisperse defect clusters that exist within the CuInS2 lattice. Chapter 4 details ultrafast spectroscopic studies of a QD redox sensor that consists of a CdTe/CdS core/shell QD coupled with a quinone-derived electron acceptor (Q2NS), which acts as a redox-switching, photoluminescence-quenching electron acceptor. It was found that the comparatively efficient switchable quenching is due to an ultrafast trapping scheme, involving an electron energy state associated with a surface-based lattice defect. Application of the redox sensors to biological cells was then studied, particularly with respect to the mechanism by which cells internalise the QDs, and the resulting QD microenvironment. It arises that endocytosis and subsequent compartmentalisation of QDs by cells presents a significant challenge to the application of QDs as intracellular biosensors.

The dissolution of carbohydrates in Ionic liquids has received attention for many decades and still is to this day. Solutions of xylan and xylose in 1-ethyl-3-methylimidazolium acetate [C2mim] [OAc] were individually examined at various temperatures (20 °C-70 °C) using NMR spectroscopy, diffusion and the low field spin-lattice and spin-spin relaxation times (T1 and T2) as well as rheology measurements. The ratio of the diffusion coefficients for the anion to the cation remained constant upon the addition of xylan and xylose, showing that the anion and cation were equally affected by the presence of the carbohydrate. The activation energies for translational diffusion motion of both ions in the xylose solutions were similar to these found in published cellobiose. The addition of xylose and xylan individually have affected the mobility of the protons, with a decrease occurring with increasing carbohydrate concentrations. We are looking at the interactions between plant polymers, such as xylan with cellulose, with the aim to form biomimetic materials. A solution of cellulose and xylan in the ionic liquid 1-ethyl-3-methylimidazolium acetate [C2mim] [OAc] was examined using NMR diffusion, low field relaxometry and rheology measurements at various temperatures (20 °C-60 °C). We observed that the dissolving mechanism of xylan in the IL [C2mim] [OAc] is close to that for cellulose. The diffusion coefficient of the anion is preferentially more reduced by cellulose than by xylan. It is generally agreed that the anion is more active in the dissolution of carbohydrates than the cation. The dissolution mechanism of cellulose and xylan in the IL [C2mim] [OAc] can be examined via the mobility of the ions. We proposed that the number of accessible OH groups belonging to the carbohydrates are reduced at certain xylan-cellulose blend compositions, showing that at these concentrations there are significant interactions between the two biopolymers.

A supramolecular polymer is a complex assembly of molecules held together by noncovalent bonds, such as hydrogen bonding, host-guest interactions or coordinative bonds. The last few decades great developments have been made in the research and application of supramolecular polymers, and a wide variety of supramolecular polymers have been prepared. These supramolecular polymers have been applied within many application areas, especially for medical applications such as drug or DNA delivery into living cells, and controlled drug release. However, many fundamental aspects such as the relaxation dynamics and rheological properties over a wide temperature range as well as the detailed structure-properties relationships are still not well understood for supramolecular polymers. This thesis addresses this, and aims at a better understanding of how the supramolecular interactions affect the structure, relaxation dynamics and rheological properties of different supramolecular polymer systems over a wide timescale or temperature range ranging from the glassy to the melt states. The goal is to determine the structure-property relationships, and to provide guidelines for the design and synthesis of new supramolecular polymers. In this thesis, the dynamics of four different supramolecular polymers are investigated. The first system is based on a comb-like polymeric backbone of poly(2-ethylhexyl acrylate) (PEHA) to which a random distribution of 2-ureido-4[1H]-pyrimidinone (UPy) supramolecular side-groups are added. A series of polymers with varying side-group UPy contents have been synthesised using the reversible addition fragmentation chain transfer (RAFT) polymerization. The second system is based on poly(propylene glycol) (PPG) for which the chain ends were functionalised using supramolecular hydrogen-bonding UPy-groups. The unfunctionalized PPG is a viscous liquid at room temperature whereas the end-functionalised UPyPPG is a rubbery material due to the formation of long extended chains formed through multiple hydrogen bonds. For this supramolecular polymer system, we have investigated two possible application areas: (i) the use of blends of PPG and UPyPPG with lithium salts in polymer electrolytes for Li-ion batteries and (ii) the use together with UV curable components for self-healing coatings. The third system is based on hydroxyl-capped polytetrahydrofuran (PTHF) with varying molecular weights and the fourth is a set of alkane diols of different chain-length. For both these systems, intermolecular supramolecular hydrogen bond interactions via the chain-ends will become more important for shorter chains. Generally, the relaxation dynamics, thermodynamic response and rheological response were determined using a range of experimental techniques, including broadband dielectric relaxation spectroscopy, differential scanning calorimetry (both in the standard and modulated mode), shear and extensional rheology and nuclear magnetic resonance relaxometry.

The current study is focused on the investigation of the spin and heat properties of a Permalloy/silver/Permalloy, Permalloy/silver (doped with Iron)/Permalloy and Vanadium/silver/Vanadium spin valves in a lateral geometry. The presence of a downturn in the spin-signal of these lateral spin valves at low temperatures, below 30 K, can be avoided by depositing the Ag at a faster rate. This will promote a better microstructure that seems to have a crucial role in systems with very low or no magnetic impurities. A small part of the report is dedicated to test the two different behaviours of the spin signal that have been suggested in the literature, in the case of spin transport through an oxidised normal metal channel. According to literature, it would either remove the downturn of the spin signal at low temperatures, or form one. Our devices exhibited no downturn below 30 K, but by oxidising them, did not lead to the creation of it. By doping the normal metal channel with a dust layer of magnetic impurities (MIL) one would expect that by increasing scattering centers the spin signal and spin diffusion length would decrease no matter where the MIL would be. Interestingly that was not confirmed, as not only the spin signal and diffusion length vary depending on the position of the MIL in the NM channel, but also in the occasion of the device where the MIL was place right in the middle of the NM channel. At temperatures above 70 K the spin signal presented was bigger than that of the reference device. Moreover, the spin diffusion length presented in the particular set of devices, exceeded that of the reference set of devices for temperatures higher than 140 K. Finally, thermal effects were also expected to get picked up during the measurements as in order to create the spin accumulation, a charge current of 500 μ A is driven through the resistive Permalloy injector. That would give rise to Joule heating and Peltier effect once it reaches the Permalloy/silver junction due to the mismatch of the Peltier coefficients. Heat would then diffuse along the silver channel and through the substrate and would be detected in the second silver/Permalloy junction. The latter acted as a thermocouple and due to the difference in their Seebeck coefficients the temperature difference that was picked up, was converted to potential difference. The Scanning Thermal Microscopy technique was employed to image these effects. Based on the results of the technique, an analytical model that can predict the injector and detector junction temperature increase from that of the substrate was developed. In addition to that, since the voltage output is proportional to the product of the effective Seebeck coefficient with the temperature difference, the detector voltage could be predicted. To test the model a simple system of V/Ag/V device was used to deconvolute the thermal effects avoiding having a spin accumulation in the detector signal. After that, the thermal effects arising in a Py/Ag/Py lateral spin valve were investigated. Finally, since the Peltier effect was present in the measurements, the non-local resistance, spin signal and baseline resistance were analysed as a function of current direction to find a so far not studied effect. There was a splitting in the non-local and baseline resistance across all different devices that had temperature and current dependence. To confirm that the effect was not an artefact, three cryostats, three transport sticks, two sample holders and two more systems (Py/Cu/Py and CoFe/Cu/CoFe) were studied.

The application of quantum cryptographic methods to existing communications infrastructures can be extremely difficult owing to the complex nature of quantum transmission methods. The premise of this thesis is an examination of methods to combine quantum-safe security with standard protocols, such as phase shift keying. Use is made of an algorithm previously presented by Ueli Maurer which allows for the distillation of a mutual symmetric cryptographic key from some shared secret information (Maurer, 1993). This algorithm is examined extensively and incorporated into a complete protocol which can be applied to pre-existing communications using phase shift keying. Primarily, one must consider the theoretical noise capabilities. In order to ensure the security of these communications the properties of microwaves are characterised and established as quantum-limited coherent states with a fractional excess noise on measurement. Side channel attacks are more prolific when one considers the quantum measurement attack vector, especially when one considers that the full extent of these attacks in not yet known. If the same security could be extracted from the distillation algorithm, without relying upon quantum mechanics as the resource, then a universal standard for widespread implementation could be produced. The properties of random numbers are shown to be a sufficent resource for the advantage distillation algorithm which provides a strong candidate for a possible post-quantum secure universal standard. The security of this (and various other protocols), however, relies upon the presence of an ‘impenetrable’ safe-house for trusted parties to prepare their cryptogrpahic resource (whether it be quantum or randomnumbers). A side channel attack is examined which is based on the possibility of signal leakage from a shielded room. The use of the vector potential elucidates a possible method for signals to be detected outside a Faraday shielded enclosure - methods for performing this detection are examined and a characterisation of the properties of the leakage is performed. Leakage is detected from a shielded room at the National Authority for Counter Eavesdropping. It is concluded that a threat exists from this. However, there are possibilities for counteracting this using certain dielectric materials which need to be explored further. Overall, it is established that advances have been made towards developing a post-quantum secure cryptographic method, which can be straight forwardly implemented in a variety of existing infrastructures using phase shift keying protocols, and even in a universal implementation using random numbers as a secure resource.

No description available.