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Structural, functional and mechanistic analysis of the Escherichia coli ammonium transporter AmtB
Get PDFThis thesis was previously held under moratorium from 28th June 2019 until 12th February 2024The exchange of ammonium across cellular membranes is an essential process in all kingdoms of life. Ammonium is a major source of nitrogen for bacteria, fungi, and plants, whereas in animal cells it is a cytotoxic waste metabolite, which must be excreted. The transport of ammonium is accomplished by the ubiquitous Ammonium transporter/Methylammonium permease/Rhesus (Amt/Mep/Rh) superfamily of membrane proteins. Inaddition to their fundamental role in facilitating the transport of metabolites, members of the Amt/Mep/Rh superfamily are important drivers of the virulence of infectious fungi. In humans, malfunctions of Rh proteins are linked toinherited haemolytic anaemia, stomatocytosis, and early onset depressive disorder, amongst many other human pathologies. Therefore, an improved understanding of the function of ammonium transporters has importantmedical implications alongside the elucidation of a central biological process. In spite of its general importance, a consensus on the pathway and mechanism of ammonium transport by this superfamily has not yet been achieved.The overall aim of this project is to use Escherichia coli AmtB, the paradigmatic, most intensely studied member of the Amt/Mep/Rh protein family and an integrative approach combining molecular genetics, biochemistry, biophysics and molecular dynamic simulations to gain valuable structural and functional information on this important protein family. A new in-solution structural approach combining Small Angle Neutron/X-ray Scattering with Molecular Dynamics simulation has been successfully developed providing a new tool to study membrane protein dynamics insolution. Moreover, a new mechanism for the deprotonation/translocation associated with ammonium transport through AmtB was suggested and demonstrated by using Solid Supported Membrane Electrophysiology (SSME)and Molecular Dynamics simulations on genetic variants. Furthermore, the influence of 1-palmitoyl-2-oleoyl phosphatidylglycerol (PG), a specific lipid known to structurally interact with AmtB, was assessed and it was suggested that this lipid is essential for translocation of ammonium across AmtB. Last but not least, the electrophysiological technique developed on AmtB has been extended to study the bacterial Rh and fungal Mep proteins to explore whetherthe mechanism I propose for AmtB is a common feature for the Amt/Mep/Rh protein family. Given the importance of this protein family in various fundamental biological processes and human diseases, this work may, in the long term, lead to the development of new therapeutic interventions.The exchange of ammonium across cellular membranes is an essential process in all kingdoms of life. Ammonium is a major source of nitrogen for bacteria, fungi, and plants, whereas in animal cells it is a cytotoxic waste metabolite, which must be excreted. The transport of ammonium is accomplished by the ubiquitous Ammonium transporter/Methylammonium permease/Rhesus (Amt/Mep/Rh) superfamily of membrane proteins. Inaddition to their fundamental role in facilitating the transport of metabolites, members of the Amt/Mep/Rh superfamily are important drivers of the virulence of infectious fungi. In humans, malfunctions of Rh proteins are linked toinherited haemolytic anaemia, stomatocytosis, and early onset depressive disorder, amongst many other human pathologies. Therefore, an improved understanding of the function of ammonium transporters has importantmedical implications alongside the elucidation of a central biological process. In spite of its general importance, a consensus on the pathway and mechanism of ammonium transport by this superfamily has not yet been achieved.The overall aim of this project is to use Escherichia coli AmtB, the paradigmatic, most intensely studied member of the Amt/Mep/Rh protein family and an integrative approach combining molecular genetics, biochemistry, biophysics and molecular dynamic simulations to gain valuable structural and functional information on this important protein family. A new in-solution structural approach combining Small Angle Neutron/X-ray Scattering with Molecular Dynamics simulation has been successfully developed providing a new tool to study membrane protein dynamics insolution. Moreover, a new mechanism for the deprotonation/translocation associated with ammonium transport through AmtB was suggested and demonstrated by using Solid Supported Membrane Electrophysiology (SSME)and Molecular Dynamics simulations on genetic variants. Furthermore, the influence of 1-palmitoyl-2-oleoyl phosphatidylglycerol (PG), a specific lipid known to structurally interact with AmtB, was assessed and it was suggested that this lipid is essential for translocation of ammonium across AmtB. Last but not least, the electrophysiological technique developed on AmtB has been extended to study the bacterial Rh and fungal Mep proteins to explore whetherthe mechanism I propose for AmtB is a common feature for the Amt/Mep/Rh protein family. Given the importance of this protein family in various fundamental biological processes and human diseases, this work may, in the long term, lead to the development of new therapeutic interventions
What attitudes about opium were driving the government of India's policies between 1857-1906?
Get PDFThis thesis will examine British Attitudes towards opium between 1857 to 1906 to analyse how they impacted policies of the Government of India. The research is presented thematically and draws upon numerous sources both from archives in Britain and the National Archives of India. The dominance of anti-opium and pro-opium positions have been the current focus of the literature rather than the complex middle ground where attitudes struggled to both condone or condemn the use of opium. Overall this will examine five main areas from high level state decisions, opium production, smuggling activities, the role of the Princely States, religious and missionary attitudes and finally medical attitudes. What this analysis will show is that there was no single objective or agenda that was driving British opium policy or ideas about the drug. Policies on opium operated at different levels and similarly they did not always relate to one another. They were affected by multiple ideas, local politics and subject to shifts and contradictions.This thesis will examine British Attitudes towards opium between 1857 to 1906 to analyse how they impacted policies of the Government of India. The research is presented thematically and draws upon numerous sources both from archives in Britain and the National Archives of India. The dominance of anti-opium and pro-opium positions have been the current focus of the literature rather than the complex middle ground where attitudes struggled to both condone or condemn the use of opium. Overall this will examine five main areas from high level state decisions, opium production, smuggling activities, the role of the Princely States, religious and missionary attitudes and finally medical attitudes. What this analysis will show is that there was no single objective or agenda that was driving British opium policy or ideas about the drug. Policies on opium operated at different levels and similarly they did not always relate to one another. They were affected by multiple ideas, local politics and subject to shifts and contradictions
Exploiting the potential of foam nests produced by Engystomops pustulosus
Get PDFFoams are formed of air trapped in a solid or liquid creating cell-like structures. They are attracting attention in the pharmaceutical industry as potential drug delivery systems. The Tungara frog, Engystomops pustulosus, constructs foam nests which act as incubation chambers protecting the developing eggs and tadpoles from predation and environmental damage. This foam is highly stable and does not harm the eggs, sperm ortadpoles. Amphibians produce a range of proteins and peptides that may have pharmaceutical utility, and this is a growing area of research. This work investigated the potential of the foam-nest produced by E. pustulosus as a novel drug release system. Bioinformatics were used to gain insight in to the six proteins that comprise the foam, the Ranaspumins (RSN), highlighting that many of the proteins have homology to uncharacterised amphibian proteins and that one protein, RSN-2, remains a unique surfactant protein. The foam was characterised as pharmaceutical foam revealing that it is low density, resistant to shear and is non-toxic to HaCaT cells. The foams drug release capabilities were tested by loading the foam with model hydrophilic and hydrophobic dyes and measuring their release profiles. The foam delivery potential was then tested with an antibiotic, rifampicin, demonstrating that the foam could successfully release an active drug with a release profile that shows promise for drug delivery. This work developed methodology to produce a synthetic foam using recombinant RSNs. A universal method was developed to clone each rsn gene into aplasmid vector which could be induced to overexpress each RSN in the bacterium Escherichia coli and subsequent purification. All six RSNs were cloned and overexpressed, but only RSN-2 could be purified successfully. The recombinant RSN-2 was investigated for its effect on mammalian and bacterial cells and was used to produce a stable foam, with release experiments showing that RSN-2 can be used to create a foam drug delivery system as the first step towards a completely synthetic foam. Overall, this work demonstrates that E. pustulosus foam has great potential as a drug release system.Foams are formed of air trapped in a solid or liquid creating cell-like structures. They are attracting attention in the pharmaceutical industry as potential drug delivery systems. The Tungara frog, Engystomops pustulosus, constructs foam nests which act as incubation chambers protecting the developing eggs and tadpoles from predation and environmental damage. This foam is highly stable and does not harm the eggs, sperm ortadpoles. Amphibians produce a range of proteins and peptides that may have pharmaceutical utility, and this is a growing area of research. This work investigated the potential of the foam-nest produced by E. pustulosus as a novel drug release system. Bioinformatics were used to gain insight in to the six proteins that comprise the foam, the Ranaspumins (RSN), highlighting that many of the proteins have homology to uncharacterised amphibian proteins and that one protein, RSN-2, remains a unique surfactant protein. The foam was characterised as pharmaceutical foam revealing that it is low density, resistant to shear and is non-toxic to HaCaT cells. The foams drug release capabilities were tested by loading the foam with model hydrophilic and hydrophobic dyes and measuring their release profiles. The foam delivery potential was then tested with an antibiotic, rifampicin, demonstrating that the foam could successfully release an active drug with a release profile that shows promise for drug delivery. This work developed methodology to produce a synthetic foam using recombinant RSNs. A universal method was developed to clone each rsn gene into aplasmid vector which could be induced to overexpress each RSN in the bacterium Escherichia coli and subsequent purification. All six RSNs were cloned and overexpressed, but only RSN-2 could be purified successfully. The recombinant RSN-2 was investigated for its effect on mammalian and bacterial cells and was used to produce a stable foam, with release experiments showing that RSN-2 can be used to create a foam drug delivery system as the first step towards a completely synthetic foam. Overall, this work demonstrates that E. pustulosus foam has great potential as a drug release system
Peridynamic analysis of fatigue crack growth in fillet welded joints
Get PDFFatigue assessment is one of the significant factors to be considered for a design life of structure and estimation of structural reliability during operation. Especially, for welded structures, various welding effects, such as stress concentration, residual stresses, weld geometry and weld quality, make the structure more vulnerable to fatigue failures. This requires more effective approaches for estimating fatigue performances of welded structures.Existing classical methods to predict the crack propagation under cyclic loadings have some difficulties in treating complicated patterns of crack growth. A peridynamic theory, however, has powerful advantage on discontinuities. A peridynamic fatigue model, which is a bond damage model of remaining life, is used to demonstrate two phases of fatigue failure, crack nucleation and crack growth. Two types of numerical tests are conducted to validate the peridynamic fatigue model. One is tensile test for the phase of crack nucleation and the other is compact tension test for the phase of crack growth. All results from numerical tests are compared with experimental test data to validate the peridynamic fatigue model.After validation of peridynamic fatigue model, numerical tests with peridynamic fatigue model are performed to investigate a weld effect of the length of unwelded zone on the fatigue performance of load-carrying fillet welded joint. Numerical results of fatigue performance and path of fatigue crack growth are compared with existing experimental data.In this thesis, the peridynamic fatigue model is validated by two different fatigue tests which are uniaxial tension-compression tests for the crack nucleation and ASTM E647 standard compact tests for the crack growth. After validation, the fatigue performance of the fillet welded joint is estimated with respect to the length of unwelded zone by simulating the fatigue crack growth under cyclic load conditions with the peridynamic fatigue model.Fatigue assessment is one of the significant factors to be considered for a design life of structure and estimation of structural reliability during operation. Especially, for welded structures, various welding effects, such as stress concentration, residual stresses, weld geometry and weld quality, make the structure more vulnerable to fatigue failures. This requires more effective approaches for estimating fatigue performances of welded structures.Existing classical methods to predict the crack propagation under cyclic loadings have some difficulties in treating complicated patterns of crack growth. A peridynamic theory, however, has powerful advantage on discontinuities. A peridynamic fatigue model, which is a bond damage model of remaining life, is used to demonstrate two phases of fatigue failure, crack nucleation and crack growth. Two types of numerical tests are conducted to validate the peridynamic fatigue model. One is tensile test for the phase of crack nucleation and the other is compact tension test for the phase of crack growth. All results from numerical tests are compared with experimental test data to validate the peridynamic fatigue model.After validation of peridynamic fatigue model, numerical tests with peridynamic fatigue model are performed to investigate a weld effect of the length of unwelded zone on the fatigue performance of load-carrying fillet welded joint. Numerical results of fatigue performance and path of fatigue crack growth are compared with existing experimental data.In this thesis, the peridynamic fatigue model is validated by two different fatigue tests which are uniaxial tension-compression tests for the crack nucleation and ASTM E647 standard compact tests for the crack growth. After validation, the fatigue performance of the fillet welded joint is estimated with respect to the length of unwelded zone by simulating the fatigue crack growth under cyclic load conditions with the peridynamic fatigue model
In the wake of a tidal turbine
Get PDFTidal energy is rapidly developing as a source of renewable energy. Horizontal axis tidal turbines are being installed in arrays, where device spacing is an important issue. Array performance will be affected as the flow from upstream devices (i.e. the wake) interacts with down-stream devices. Further experimental data is necessary to understand the characteristics of turbine wakes, in particular the wake far down-stream. This work describes a series of physical tests undertaken to characterise the wakes of scale model tidal turbines. An Acoustic Doppler Velocimeter (ADV) is used to profile the wakes of two turbines operating in six configurations: varying tip speed ratio, blade number, and including a device with contra rotating rotors. The wakes of various turbine configurations are mapped using velocity and turbulence data. Evidence of the wake can still be detected twenty five diameters downstream of the single rotor device, further than some literature suggests. If this is replicated on full scale devices in sea, this may impact the necessary spacing of devices within an array, or the performance of downstream devices. Evidence is found of rotational structure in the wake at eight diameters downstream. This is further than is suggested in most literature. The wake from the contra rotating device recovers faster than the wake from single rotor devices, and the rotational aspect of the near wake is diminished. Thus a contra rotating device could be used advantageously to give a smaller wake footprint for a given amount of power captured. This could allow a more efficiently packed array, increasing the performance of the array over a given area.Tidal energy is rapidly developing as a source of renewable energy. Horizontal axis tidal turbines are being installed in arrays, where device spacing is an important issue. Array performance will be affected as the flow from upstream devices (i.e. the wake) interacts with down-stream devices. Further experimental data is necessary to understand the characteristics of turbine wakes, in particular the wake far down-stream. This work describes a series of physical tests undertaken to characterise the wakes of scale model tidal turbines. An Acoustic Doppler Velocimeter (ADV) is used to profile the wakes of two turbines operating in six configurations: varying tip speed ratio, blade number, and including a device with contra rotating rotors. The wakes of various turbine configurations are mapped using velocity and turbulence data. Evidence of the wake can still be detected twenty five diameters downstream of the single rotor device, further than some literature suggests. If this is replicated on full scale devices in sea, this may impact the necessary spacing of devices within an array, or the performance of downstream devices. Evidence is found of rotational structure in the wake at eight diameters downstream. This is further than is suggested in most literature. The wake from the contra rotating device recovers faster than the wake from single rotor devices, and the rotational aspect of the near wake is diminished. Thus a contra rotating device could be used advantageously to give a smaller wake footprint for a given amount of power captured. This could allow a more efficiently packed array, increasing the performance of the array over a given area
Mathematical methods for the modelling of cell migration and chemotaxis
No full textNumerical methods are developed for the study of cell migration and chemotaxis with specific focus on reaction-diffusion based models on moving domains. This thesis focuses building on the previous model of cell migration and chemotaxis introduced by Neilson et al [105]. It does this by introducing new and discussing existing numerical methods in a cell migration and chemotaxis context. A new approach to the solution of forced mean curvature flow is introduced in the form of a moving mesh partial differential equation (MMPDE). This MMPDE is split into two partial differential algebraic equations: one for the normal velocity and one for the tangential velocity. We examine curves moving with a prescribed normal velocity and this decoupling of the velocity components allows mesh adaption to be considered along the tangential component by means of a mesh adaption monitor function. This new method is not restricted to cell migration models and could be used in other contexts where mesh adaption of an evolving curve domain would be desired. A second-order conservative ALE-FEM scheme is also introduced for the solutions of reaction-diffusion equations on an evolving curve boundary and is subsequently used to derive the concentrations of various chemicals which lay on the model of the cell's membrane. The cell migration model is also extended to higher dimensions using a second ALE-FEM scheme which couples the solutions of reactions taking place on different domains together by means of a flux boundary condition and a two-dimensional mesh movement strategy which complements the new one-dimensional MMPDE approach for curves. This scheme is used to model diffusion of ligand molecules in the region exterior to the moving cell. Simulations are presented of this new two-dimensional model indicating the effect of cell movement and receptor-ligand binding dynamics on the cell micro-environment and research is currently underway to use this model to investigate biological theories [84, 86].Numerical methods are developed for the study of cell migration and chemotaxis with specific focus on reaction-diffusion based models on moving domains. This thesis focuses building on the previous model of cell migration and chemotaxis introduced by Neilson et al [105]. It does this by introducing new and discussing existing numerical methods in a cell migration and chemotaxis context. A new approach to the solution of forced mean curvature flow is introduced in the form of a moving mesh partial differential equation (MMPDE). This MMPDE is split into two partial differential algebraic equations: one for the normal velocity and one for the tangential velocity. We examine curves moving with a prescribed normal velocity and this decoupling of the velocity components allows mesh adaption to be considered along the tangential component by means of a mesh adaption monitor function. This new method is not restricted to cell migration models and could be used in other contexts where mesh adaption of an evolving curve domain would be desired. A second-order conservative ALE-FEM scheme is also introduced for the solutions of reaction-diffusion equations on an evolving curve boundary and is subsequently used to derive the concentrations of various chemicals which lay on the model of the cell's membrane. The cell migration model is also extended to higher dimensions using a second ALE-FEM scheme which couples the solutions of reactions taking place on different domains together by means of a flux boundary condition and a two-dimensional mesh movement strategy which complements the new one-dimensional MMPDE approach for curves. This scheme is used to model diffusion of ligand molecules in the region exterior to the moving cell. Simulations are presented of this new two-dimensional model indicating the effect of cell movement and receptor-ligand binding dynamics on the cell micro-environment and research is currently underway to use this model to investigate biological theories [84, 86]
Tele-rehabilitation platform : a total knee arthroplasty prototype study
Get PDFLong term conditions are the biggest challenge facing the NHS and a reablement paradigm shift is pursued as a solution. Rehabilitation services are to deliver this new way of doing things that focusses [sic] on prevention and restoration of lost function to keep care from becoming unaffordable. Unfortunately the rehabilitation services are already overburdened and cannot deliver sufficient rehabilitation to people with long term conditions. This insufficiency increases cost of care as it is part of a re-admission cycle. Breaking this cycle and also driving the paradigm shift would require a greatly increased amount of rehabilitation to be delivered. This could be accomplished by the use of tele-rehabilitation (TR), the use of ICT to deliver the service of rehabilitation by distance. This would save resources wasted ontravelling, but TR can also provide functions such as biofeedback, that enables patients to do exercises unsupervised, greatly increasing the amount of exercise they could do. For TR to be used in practice, a TR platform that can be used at a large scale is required. This technology had so far not been developed so the aim of this work was to develop a prototype and test if it meets all requirements for use at a large scale. For this prototype post total knee arthroplasty rehabilitation was chosen, although the platform has generic value thanks to its modularity and flexibility. Additional required properties and functions were uncovered, a development model chosen, a design method chosen and several versions of hardware and software developed as part of this iterative design method. Clinicians were interviewed, a new type of electro-goniometer was developed and its performance tested, and a usability study performed to confirm that the platform is easy to use for patients. It was found that the platform meets all demands and that it is therefore currently technologically possible to implement TR into practice. However, there are many more barriers before a TR service can be set up.Long term conditions are the biggest challenge facing the NHS and a reablement paradigm shift is pursued as a solution. Rehabilitation services are to deliver this new way of doing things that focusses [sic] on prevention and restoration of lost function to keep care from becoming unaffordable. Unfortunately the rehabilitation services are already overburdened and cannot deliver sufficient rehabilitation to people with long term conditions. This insufficiency increases cost of care as it is part of a re-admission cycle. Breaking this cycle and also driving the paradigm shift would require a greatly increased amount of rehabilitation to be delivered. This could be accomplished by the use of tele-rehabilitation (TR), the use of ICT to deliver the service of rehabilitation by distance. This would save resources wasted ontravelling, but TR can also provide functions such as biofeedback, that enables patients to do exercises unsupervised, greatly increasing the amount of exercise they could do. For TR to be used in practice, a TR platform that can be used at a large scale is required. This technology had so far not been developed so the aim of this work was to develop a prototype and test if it meets all requirements for use at a large scale. For this prototype post total knee arthroplasty rehabilitation was chosen, although the platform has generic value thanks to its modularity and flexibility. Additional required properties and functions were uncovered, a development model chosen, a design method chosen and several versions of hardware and software developed as part of this iterative design method. Clinicians were interviewed, a new type of electro-goniometer was developed and its performance tested, and a usability study performed to confirm that the platform is easy to use for patients. It was found that the platform meets all demands and that it is therefore currently technologically possible to implement TR into practice. However, there are many more barriers before a TR service can be set up
General perturbations methods for orbit propagation with particular application to orbit lifetime analysis
Get PDFThe average number of spacecraft launched per year has recently and rapidly increased, a trend largely the result of the increased use of small and micro-satellites, platforms such as the CubeSat. This growth trend is unlikely to reverse in the near-term. To mitigate the risk that spacecraft pose to the availability and accessibility of the space environment, space debris mitigation standards currently recommend that spacecraft be removed from low-Earth orbit within 25 years of end-of-mission. In order to prove compliance with these standards, spacecraft operators must demonstrate the evolution of their spacecraft's orbit through the use of orbit propagation software.;The aim of this thesis is to improve understanding and accuracy of general perturbations methods for orbit propagation. This thesis tackles this challenge from two different angles. Firstly, the general perturbations method itself is derived using modern mathematical toolsets. Secondly, the input parameters are addressed, these include atmospheric density and ballistic coefficient.;A new parameter is introduced, termed the density index, which enables the solar activity cycle to be captured in a new analytical atmospheric density model. Consequentially, a newsolar activity model is developed that uses a single independent variable per solar cycle to describe the solar activity across that cycle, as indicated by the F10.7 index. This density index is applied to a new analytical spherically-symmetrical model for atmospheric mass density.;When combined with the newly derived general perturbations method for orbit propagation, validation against historical data shows an improvement in orbit lifetime estimates from an average error of 50.44 percent with a standard deviation of 24.96 percent, to an average error of 3.46 percent with a standard deviation of 3.25 percent when compared with the method developed by King-Hele and co-authors including an averaged atmospheric mass density (not including solar activity effects). Furthermore, the new method with the new analytical spherically-symmetrical atmospheric model and solar activity models applied is found to compare favourably against other general and special perturbations methods, including thirdparty, and commercial software, the most accurate of which was found to have an average error of 6.63 percent and standard deviation of 7.00 percent.;The spherically-symmetrical atmospheric model is also extended to include an analytical non-spherically-symmetrical atmospheric density companion model. This improvement allows the method to be applied with confidence to highly inclined orbits and special cases such as sun-synchronous orbits where the inclusion of the effects of atmospheric oblateness and the diurnal bulge will be particularly significant.;Using a case study of a sun-synchronous satellite a comparison is drawn between the models, showing that by capturing the effects of a non-spherically-symmetrical atmosphere the orbit lifetime predicted could be up to 10 percent different than when using the spherically-symmetrical model. It is noted that the inclusion of the non-spherically-symmetrical model is less important than the inclusion of the solar activity model.;A new method of determining the average projected area of a randomly tumbling CubeSat is presented, which improves on the accuracy of the method recommended in Section 6.3 of the ISO standard 27852:2010(E). For the range of CubeSat configurations presented it can be seen that the new method improves the error in the average projected area from, approximately 27 percent to within 5 percent. It is of particular note that the ISO standard is found to consistently overestimate the average projected area when considering noncuboid spacecraft configurations, meaning that when applied to an orbit decay model it will consistently underestimate the orbit lifetime.;A further improvement to the general perturbations method is suggested, using spacecraft orbit decay tracking data to inform orbit predictions. The decay data is used to derive the ballistic coefficient input parameter in order to make the method independent from error inthis input. The accuracy of the method including decay data is validated against the original method using historical data.;Finally, some applications of the developed methods are presented, including launch window selection, and post operations predictions. The most notable result of the presented applications is, however, in collision risk analysis. A popular de-orbit concept due to its simplicity is drag augmentation, the use of a deployable surface to increase atmospheric friction. Such concepts have received notable attention, with various funding bodies and licensing authorities supporting technology and flight demonstrations, as well as in the specialist and popular media.;However, studies lack a full analysis of the implications of increasing projected area on collision risk, focusing principally on time to de-orbit and assuming a direct correlation with collision risk. Using the volume swept (equivalent to area-time product) during de-orbit as a metric for collision risk it is shown that, contrary to the widely held belief, drag augmentation typically increases collision risk. It is shown that if applied in the worst-case scenario, specifically at the wrong time during the solar activity cycle, drag augmentation can increase the collision risk by an order of magnitude.;The legal implications of this are briefly considered, and it is shown that spacecraft operators who inappropriately deploy a drag augmentation device could be argued liable for any subsequent on-orbit collision. As such the viability of drag augmentation as a simple, low-cost end-of missionspacecraft removal device is diminished and it is anticipated that licensing authorities need to reconsider future and prior approval to deploy such devices.The average number of spacecraft launched per year has recently and rapidly increased, a trend largely the result of the increased use of small and micro-satellites, platforms such as the CubeSat. This growth trend is unlikely to reverse in the near-term. To mitigate the risk that spacecraft pose to the availability and accessibility of the space environment, space debris mitigation standards currently recommend that spacecraft be removed from low-Earth orbit within 25 years of end-of-mission. In order to prove compliance with these standards, spacecraft operators must demonstrate the evolution of their spacecraft's orbit through the use of orbit propagation software.;The aim of this thesis is to improve understanding and accuracy of general perturbations methods for orbit propagation. This thesis tackles this challenge from two different angles. Firstly, the general perturbations method itself is derived using modern mathematical toolsets. Secondly, the input parameters are addressed, these include atmospheric density and ballistic coefficient.;A new parameter is introduced, termed the density index, which enables the solar activity cycle to be captured in a new analytical atmospheric density model. Consequentially, a newsolar activity model is developed that uses a single independent variable per solar cycle to describe the solar activity across that cycle, as indicated by the F10.7 index. This density index is applied to a new analytical spherically-symmetrical model for atmospheric mass density.;When combined with the newly derived general perturbations method for orbit propagation, validation against historical data shows an improvement in orbit lifetime estimates from an average error of 50.44 percent with a standard deviation of 24.96 percent, to an average error of 3.46 percent with a standard deviation of 3.25 percent when compared with the method developed by King-Hele and co-authors including an averaged atmospheric mass density (not including solar activity effects). Furthermore, the new method with the new analytical spherically-symmetrical atmospheric model and solar activity models applied is found to compare favourably against other general and special perturbations methods, including thirdparty, and commercial software, the most accurate of which was found to have an average error of 6.63 percent and standard deviation of 7.00 percent.;The spherically-symmetrical atmospheric model is also extended to include an analytical non-spherically-symmetrical atmospheric density companion model. This improvement allows the method to be applied with confidence to highly inclined orbits and special cases such as sun-synchronous orbits where the inclusion of the effects of atmospheric oblateness and the diurnal bulge will be particularly significant.;Using a case study of a sun-synchronous satellite a comparison is drawn between the models, showing that by capturing the effects of a non-spherically-symmetrical atmosphere the orbit lifetime predicted could be up to 10 percent different than when using the spherically-symmetrical model. It is noted that the inclusion of the non-spherically-symmetrical model is less important than the inclusion of the solar activity model.;A new method of determining the average projected area of a randomly tumbling CubeSat is presented, which improves on the accuracy of the method recommended in Section 6.3 of the ISO standard 27852:2010(E). For the range of CubeSat configurations presented it can be seen that the new method improves the error in the average projected area from, approximately 27 percent to within 5 percent. It is of particular note that the ISO standard is found to consistently overestimate the average projected area when considering noncuboid spacecraft configurations, meaning that when applied to an orbit decay model it will consistently underestimate the orbit lifetime.;A further improvement to the general perturbations method is suggested, using spacecraft orbit decay tracking data to inform orbit predictions. The decay data is used to derive the ballistic coefficient input parameter in order to make the method independent from error inthis input. The accuracy of the method including decay data is validated against the original method using historical data.;Finally, some applications of the developed methods are presented, including launch window selection, and post operations predictions. The most notable result of the presented applications is, however, in collision risk analysis. A popular de-orbit concept due to its simplicity is drag augmentation, the use of a deployable surface to increase atmospheric friction. Such concepts have received notable attention, with various funding bodies and licensing authorities supporting technology and flight demonstrations, as well as in the specialist and popular media.;However, studies lack a full analysis of the implications of increasing projected area on collision risk, focusing principally on time to de-orbit and assuming a direct correlation with collision risk. Using the volume swept (equivalent to area-time product) during de-orbit as a metric for collision risk it is shown that, contrary to the widely held belief, drag augmentation typically increases collision risk. It is shown that if applied in the worst-case scenario, specifically at the wrong time during the solar activity cycle, drag augmentation can increase the collision risk by an order of magnitude.;The legal implications of this are briefly considered, and it is shown that spacecraft operators who inappropriately deploy a drag augmentation device could be argued liable for any subsequent on-orbit collision. As such the viability of drag augmentation as a simple, low-cost end-of missionspacecraft removal device is diminished and it is anticipated that licensing authorities need to reconsider future and prior approval to deploy such devices
Applications of principal modes to imaging, control and surface enhancement in nanoparticles
Get PDFThe theory of principal modes allows a computationally efficient generalisation of Mie's analytical approach for the sphere to obtain semi-analytical solutions for general geometries with smooth surfaces. In this thesis, we apply this method to investigate a range of single and multiple particle metallic structures in the linear, non-linear and non-local response regimes outside of the quasi-static limit. We propose schemes for the coherent control of light waves and currents in metallic nanospheres, using conventional laser sources, in all three of these regimes.;The conditions on the external control field we derive lead to a reduction of absorption, suppression of radiative losses and high sensitivity to small variations in the local environment, including subwavelength spatial shifts. As part of an international collaboration with researchers from Waseda University and the Institute for Molecular Science in Japan, the optical properties of single gold nanodiscs were studied by scanning near-field optical microscopy.;The modal analysis indicates that the complex spatial features observed in the transmission images originate mainly from a few fundamental plasmon modes of the discs. By reformulating the principal modes in terms of Green's functions we are able to describe systems containing multiple particles, in which both particles and host medium may be inhomogeneous. Using this formalism, the enhancement of the rates of both the emission and far field radiation of dipoles placed in the gap between metallic nanorods, nanospheres, and substrates are investigated numerically.;For aluminium structures, bright mode resonances are tunable over tens or hundreds of nanometres in the ultraviolet by changing the size of the nanoparticles, with far field radiative enhancements of up to three orders of magnitude. These results show that aluminium nanostructures are ideal for applications to nano lasing and label-free detection of weakly fluorescent DNA bases and proteins in the ultraviolet.The theory of principal modes allows a computationally efficient generalisation of Mie's analytical approach for the sphere to obtain semi-analytical solutions for general geometries with smooth surfaces. In this thesis, we apply this method to investigate a range of single and multiple particle metallic structures in the linear, non-linear and non-local response regimes outside of the quasi-static limit. We propose schemes for the coherent control of light waves and currents in metallic nanospheres, using conventional laser sources, in all three of these regimes.;The conditions on the external control field we derive lead to a reduction of absorption, suppression of radiative losses and high sensitivity to small variations in the local environment, including subwavelength spatial shifts. As part of an international collaboration with researchers from Waseda University and the Institute for Molecular Science in Japan, the optical properties of single gold nanodiscs were studied by scanning near-field optical microscopy.;The modal analysis indicates that the complex spatial features observed in the transmission images originate mainly from a few fundamental plasmon modes of the discs. By reformulating the principal modes in terms of Green's functions we are able to describe systems containing multiple particles, in which both particles and host medium may be inhomogeneous. Using this formalism, the enhancement of the rates of both the emission and far field radiation of dipoles placed in the gap between metallic nanorods, nanospheres, and substrates are investigated numerically.;For aluminium structures, bright mode resonances are tunable over tens or hundreds of nanometres in the ultraviolet by changing the size of the nanoparticles, with far field radiative enhancements of up to three orders of magnitude. These results show that aluminium nanostructures are ideal for applications to nano lasing and label-free detection of weakly fluorescent DNA bases and proteins in the ultraviolet
Development of small molecule colorimetric sensors for the determination of mercury in aqueous media
Get PDFWhile a number of colorimetric sensors are available for the detection of Hg2+, lack of sensitivity or selectivity, complicated synthetic routes and difficulty in adaptation for field application, are common drawbacks. Consequently, this thesis describes the development of readily synthesised, robust, selective, sensitive, cost-effective, small molecule colorimetric sensors for Hg2+ detection in water.;The reaction between Hg2+ and off-the-shelf chromogenic reagents, cuprous iodide (CuI), diphenylcarbazone (DPC) and rhodamine 6G (R6G), was studied in solution; in spot test mode (as wet reagents and dried onto filter papers); and in a Hg-bubbler apparatus. Both DPC and R6G produced a colorimetric response in solution and wet spot test mode, but bleaching and oxidation affected the response in dry spot mode. The Hg-bubbler apparatus was found applicable to R6G and CuI. However, reduction of reagents in the field is proved difficult.;Rhodamine B thiolactone (RBT) was synthesised. It exhibited high selectivity for Hg2+, with reasonable visual and spectrophotometric detection limits. A disadvantage was that the solid was undergo ring-opening reaction unless stored at low temperature away from light. The RBT was immobilised in sol-gel and agar-agar matrixes with filter paper substrate. Pumping Hg2+ solutions through these membranes changed their colour. Images of the membranes were recorded and analysed using a flatbed scanner and ImageJ software. Based on the grayscale intensity in the green channel, the detection limits were 0.4 and 0.2 μg/L for the sol-gel and agar-agar membranes, respectively. The method was used to quantify Hg2+ in real water samples. Interference due to the presence of Cl- was noted.;Finally, a portable platform was developed. Images of RBT doped agar-agar membranes were captured using the camera of a mobile phone, together with a homemade lightproof box, and a bespoke 'Hg-Sense' app. Results were generally acceptable and can be applied by regulation authorities.While a number of colorimetric sensors are available for the detection of Hg2+, lack of sensitivity or selectivity, complicated synthetic routes and difficulty in adaptation for field application, are common drawbacks. Consequently, this thesis describes the development of readily synthesised, robust, selective, sensitive, cost-effective, small molecule colorimetric sensors for Hg2+ detection in water.;The reaction between Hg2+ and off-the-shelf chromogenic reagents, cuprous iodide (CuI), diphenylcarbazone (DPC) and rhodamine 6G (R6G), was studied in solution; in spot test mode (as wet reagents and dried onto filter papers); and in a Hg-bubbler apparatus. Both DPC and R6G produced a colorimetric response in solution and wet spot test mode, but bleaching and oxidation affected the response in dry spot mode. The Hg-bubbler apparatus was found applicable to R6G and CuI. However, reduction of reagents in the field is proved difficult.;Rhodamine B thiolactone (RBT) was synthesised. It exhibited high selectivity for Hg2+, with reasonable visual and spectrophotometric detection limits. A disadvantage was that the solid was undergo ring-opening reaction unless stored at low temperature away from light. The RBT was immobilised in sol-gel and agar-agar matrixes with filter paper substrate. Pumping Hg2+ solutions through these membranes changed their colour. Images of the membranes were recorded and analysed using a flatbed scanner and ImageJ software. Based on the grayscale intensity in the green channel, the detection limits were 0.4 and 0.2 μg/L for the sol-gel and agar-agar membranes, respectively. The method was used to quantify Hg2+ in real water samples. Interference due to the presence of Cl- was noted.;Finally, a portable platform was developed. Images of RBT doped agar-agar membranes were captured using the camera of a mobile phone, together with a homemade lightproof box, and a bespoke 'Hg-Sense' app. Results were generally acceptable and can be applied by regulation authorities
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