Exhibiting the behaviour of time-delayed systems via an extension to qualitative simulation

I. Miguel and Q. Shen. Exhibiting the behaviour of time-delayed systems via an extension to qualitative simulation. IEEE Transactions on Systems, Man and Cybernetics, Part A: Systems and Humans, 35(2):298-305, 2005.

Stability of time-delay systems via Lyapunov functions

In this paper, a Lyapunov function candidate is introduced for multivariable systems with inner delays, without assuming a priori stability for the nondelayed subsystem. By using this Lyapunov function, a controller is deduced. Such a controller utilizes an input-output description of the original system, a circumstance that facilitates practical applications of the proposed approach.

Pinwheel Scheduling for Fault-tolerant Broadcast Disks in Real-time Database Systems

The design of programs for broadcast disks which incorporate real-time and fault-tolerance requirements is considered. A generalized model for real-time fault-tolerant broadcast disks is defined. It is shown that designing programs for broadcast disks specified in this model is closely related to the scheduling of pinwheel task systems. Some new results in pinwheel scheduling theory are derived, which facilitate the efficient generation of real-time fault-tolerant broadcast disk programs.

Energy storage systems for wave energy converters and microgrids

The thesis initially gives an overview of the wave industry and the current state of some of the leading technologies as well as the energy storage systems that are inherently part of the power take-off mechanism. The benefits of electrical energy storage systems for wave energy converters are then outlined as well as the key parameters required from them. The options for storage systems are investigated and the reasons for examining supercapacitors and lithium-ion batteries in more detail are shown. The thesis then focusses on a particular type of offshore wave energy converter in its analysis, the backward bent duct buoy employing a Wells turbine. Variable speed strategies from the research literature which make use of the energy stored in the turbine inertia are examined for this system, and based on this analysis an appropriate scheme is selected. A supercapacitor power smoothing approach is presented in conjunction with the variable speed strategy. As long component lifetime is a requirement for offshore wave energy converters, a computer-controlled test rig has been built to validate supercapacitor lifetimes to manufacturer’s specifications. The test rig is also utilised to determine the effect of temperature on supercapacitors, and determine application lifetime. Cycle testing is carried out on individual supercapacitors at room temperature, and also at rated temperature utilising a thermal chamber and equipment programmed through the general purpose interface bus by Matlab. Application testing is carried out using time-compressed scaled-power profiles from the model to allow a comparison of lifetime degradation. Further applications of supercapacitors in offshore wave energy converters are then explored. These include start-up of the non-self-starting Wells turbine, and low-voltage ride-through examined to the limits specified in the Irish grid code for wind turbines. These applications are investigated with a more complete model of the system that includes a detailed back-to-back converter coupling a permanent magnet synchronous generator to the grid. Supercapacitors have been utilised in combination with battery systems for many applications to aid with peak power requirements and have been shown to improve the performance of these energy storage systems. The design, implementation, and construction of coupling a 5 kW h lithium-ion battery to a microgrid are described. The high voltage battery employed a continuous power rating of 10 kW and was designed for the future EV market with a controller area network interface. This build gives a general insight to some of the engineering, planning, safety, and cost requirements of implementing a high power energy storage system near or on an offshore device for interface to a microgrid or grid.

Artefact detection and removal algorithms for EEG diagnostic systems

The electroencephalogram (EEG) is a medical technology that is used in the monitoring of the brain and in the diagnosis of many neurological illnesses. Although coarse in its precision, the EEG is a non-invasive tool that requires minimal set-up times, and is suitably unobtrusive and mobile to allow continuous monitoring of the patient, either in clinical or domestic environments. Consequently, the EEG is the current tool-of-choice with which to continuously monitor the brain where temporal resolution, ease-of- use and mobility are important. Traditionally, EEG data are examined by a trained clinician who identifies neurological events of interest. However, recent advances in signal processing and machine learning techniques have allowed the automated detection of neurological events for many medical applications. In doing so, the burden of work on the clinician has been significantly reduced, improving the response time to illness, and allowing the relevant medical treatment to be administered within minutes rather than hours. However, as typical EEG signals are of the order of microvolts (μV ), contamination by signals arising from sources other than the brain is frequent. These extra-cerebral sources, known as artefacts, can significantly distort the EEG signal, making its interpretation difficult, and can dramatically disimprove automatic neurological event detection classification performance. This thesis therefore, contributes to the further improvement of auto- mated neurological event detection systems, by identifying some of the major obstacles in deploying these EEG systems in ambulatory and clinical environments so that the EEG technologies can emerge from the laboratory towards real-world settings, where they can have a real-impact on the lives of patients. In this context, the thesis tackles three major problems in EEG monitoring, namely: (i) the problem of head-movement artefacts in ambulatory EEG, (ii) the high numbers of false detections in state-of-the-art, automated, epileptiform activity detection systems and (iii) false detections in state-of-the-art, automated neonatal seizure detection systems. To accomplish this, the thesis employs a wide range of statistical, signal processing and machine learning techniques drawn from mathematics, engineering and computer science. The first body of work outlined in this thesis proposes a system to automatically detect head-movement artefacts in ambulatory EEG and utilises supervised machine learning classifiers to do so. The resulting head-movement artefact detection system is the first of its kind and offers accurate detection of head-movement artefacts in ambulatory EEG. Subsequently, addtional physiological signals, in the form of gyroscopes, are used to detect head-movements and in doing so, bring additional information to the head- movement artefact detection task. A framework for combining EEG and gyroscope signals is then developed, offering improved head-movement arte- fact detection. The artefact detection methods developed for ambulatory EEG are subsequently adapted for use in an automated epileptiform activity detection system. Information from support vector machines classifiers used to detect epileptiform activity is fused with information from artefact-specific detection classifiers in order to significantly reduce the number of false detections in the epileptiform activity detection system. By this means, epileptiform activity detection which compares favourably with other state-of-the-art systems is achieved. Finally, the problem of false detections in automated neonatal seizure detection is approached in an alternative manner; blind source separation techniques, complimented with information from additional physiological signals are used to remove respiration artefact from the EEG. In utilising these methods, some encouraging advances have been made in detecting and removing respiration artefacts from the neonatal EEG, and in doing so, the performance of the underlying diagnostic technology is improved, bringing its deployment in the real-world, clinical domain one step closer.

A distributed architecture for the monitoring and analysis of time series data

It is estimated that the quantity of digital data being transferred, processed or stored at any one time currently stands at 4.4 zettabytes (4.4 × 2 70 bytes) and this figure is expected to have grown by a factor of 10 to 44 zettabytes by 2020. Exploiting this data is, and will remain, a significant challenge. At present there is the capacity to store 33% of digital data in existence at any one time; by 2020 this capacity is expected to fall to 15%. These statistics suggest that, in the era of Big Data, the identification of important, exploitable data will need to be done in a timely manner. Systems for the monitoring and analysis of data, e.g. stock markets, smart grids and sensor networks, can be made up of massive numbers of individual components. These components can be geographically distributed yet may interact with one another via continuous data streams, which in turn may affect the state of the sender or receiver. This introduces a dynamic causality, which further complicates the overall system by introducing a temporal constraint that is difficult to accommodate. Practical approaches to realising the system described above have led to a multiplicity of analysis techniques, each of which concentrates on specific characteristics of the system being analysed and treats these characteristics as the dominant component affecting the results being sought. The multiplicity of analysis techniques introduces another layer of heterogeneity, that is heterogeneity of approach, partitioning the field to the extent that results from one domain are difficult to exploit in another. The question is asked can a generic solution for the monitoring and analysis of data that: accommodates temporal constraints; bridges the gap between expert knowledge and raw data; and enables data to be effectively interpreted and exploited in a transparent manner, be identified? The approach proposed in this dissertation acquires, analyses and processes data in a manner that is free of the constraints of any particular analysis technique, while at the same time facilitating these techniques where appropriate. Constraints are applied by defining a workflow based on the production, interpretation and consumption of data. This supports the application of different analysis techniques on the same raw data without the danger of incorporating hidden bias that may exist. To illustrate and to realise this approach a software platform has been created that allows for the transparent analysis of data, combining analysis techniques with a maintainable record of provenance so that independent third party analysis can be applied to verify any derived conclusions. In order to demonstrate these concepts, a complex real world example involving the near real-time capturing and analysis of neurophysiological data from a neonatal intensive care unit (NICU) was chosen. A system was engineered to gather raw data, analyse that data using different analysis techniques, uncover information, incorporate that information into the system and curate the evolution of the discovered knowledge. The application domain was chosen for three reasons: firstly because it is complex and no comprehensive solution exists; secondly, it requires tight interaction with domain experts, thus requiring the handling of subjective knowledge and inference; and thirdly, given the dearth of neurophysiologists, there is a real world need to provide a solution for this domain

Antisense Gene Silencing and Bacteriophages as Novel Disinfection Processes for Engineered Systems

The growth and proliferation of invasive bacteria in engineered systems is an ongoing problem. While there are a variety of physical and chemical processes to remove and inactivate bacterial pathogens, there are many situations in which these tools are no longer effective or appropriate for the treatment of a microbial target. For example, certain strains of bacteria are becoming resistant to commonly used disinfectants, such as chlorine and UV. Additionally, the overuse of antibiotics has contributed to the spread of antibiotic resistance, and there is concern that wastewater treatment processes are contributing to the spread of antibiotic resistant bacteria.

Due to the continually evolving nature of bacteria, it is difficult to develop methods for universal bacterial control in a wide range of engineered systems, as many of our treatment processes are static in nature. Still, invasive bacteria are present in many natural and engineered systems, where the application of broad acting disinfectants is impractical, because their use may inhibit the original desired bioprocesses. Therefore, to better control the growth of treatment resistant bacteria and to address limitations with the current disinfection processes, novel tools that are both specific and adaptable need to be developed and characterized.

In this dissertation, two possible biological disinfection processes were investigated for use in controlling invasive bacteria in engineered systems. First, antisense gene silencing, which is the specific use of oligonucleotides to silence gene expression, was investigated. This work was followed by the investigation of bacteriophages (phages), which are viruses that are specific to bacteria, in engineered systems.


For the antisense gene silencing work, a computational approach was used to quantify the number of off-targets and to determine the effects of off-targets in prokaryotic organisms. For the organisms of Escherichia coli K-12 MG1655 and Mycobacterium tuberculosis H37Rv the mean number of off-targets was found to be 15.0 + 13.2 and 38.2 + 61.4, respectively, which results in a reduction of greater than 90% of the effective oligonucleotide concentration. It was also demonstrated that there was a high variability in the number of off-targets over the length of a gene, but that on average, there was no general gene location that could be targeted to reduce off-targets. Therefore, this analysis needs to be performed for each gene in question. It was also demonstrated that the thermodynamic binding energy between the oligonucleotide and the mRNA accounted for 83% of the variation in the silencing efficiency, compared to the number of off-targets, which explained 43% of the variance of the silencing efficiency. This suggests that optimizing thermodynamic parameters must be prioritized over minimizing the number of off-targets. In conclusion for the antisense work, these results suggest that off-target hybrids can account for a greater than 90% reduction in the concentration of the silencing oligonucleotides, and that the effective concentration can be increased through the rational design of silencing targets by minimizing off-target hybrids.

Regarding the work with phages, the disinfection rates of bacteria in the presence of phages was determined. The disinfection rates of E. coli K12 MG1655 in the presence of coliphage Ec2 ranged up to 2 h-1, and were dependent on both the initial phage and bacterial concentrations. Increasing initial phage concentrations resulted in increasing disinfection rates, and generally, increasing initial bacterial concentrations resulted in increasing disinfection rates. However, disinfection rates were found to plateau at higher bacterial and phage concentrations. A multiple linear regression model was used to predict the disinfection rates as a function of the initial phage and bacterial concentrations, and this model was able to explain 93% of the variance in the disinfection rates. The disinfection rates were also modeled with a particle aggregation model. The results from these model simulations suggested that at lower phage and bacterial concentrations there are not enough collisions to support active disinfection rates, which therefore, limits the conditions and systems where phage based bacterial disinfection is possible. Additionally, the particle aggregation model over predicted the disinfection rates at higher phage and bacterial concentrations of 108 PFU/mL and 108 CFU/mL, suggesting other interactions were occurring at these higher concentrations. Overall, this work highlights the need for the development of alternative models to more accurately describe the dynamics of this system at a variety of phage and bacterial concentrations. Finally, the minimum required hydraulic residence time was calculated for a continuous stirred-tank reactor and a plug flow reactor (PFR) as a function of both the initial phage and bacterial concentrations, which suggested that phage treatment in a PFR is theoretically possible.

In addition to determining disinfection rates, the long-term bacterial growth inhibition potential was determined for a variety of phages with both Gram-negative and Gram-positive bacteria. It was determined, that on average, phages can be used to inhibit bacterial growth for up to 24 h, and that this effect was concentration dependent for various phages at specific time points. Additionally, it was found that a phage cocktail was no more effective at inhibiting bacterial growth over the long-term than the best performing phage in isolation.

Finally, for an industrial application, the use of phages to inhibit invasive Lactobacilli in ethanol fermentations was investigated. It was demonstrated that phage 8014-B2 can achieve a greater than 3-log inactivation of Lactobacillus plantarum during a 48 h fermentation. Additionally, it was shown that phages can be used to protect final product yields and maintain yeast viability. Through modeling the fermentation system with differential equations it was determined that there was a 10 h window in the beginning of the fermentation run, where the addition of phages can be used to protect final product yields, and after 20 h no additional benefit of the phage addition was observed.

In conclusion, this dissertation improved the current methods for designing antisense gene silencing targets for prokaryotic organisms, and characterized phages from an engineering perspective. First, the current design strategy for antisense targets in prokaryotic organisms was improved through the development of an algorithm that minimized the number of off-targets. For the phage work, a framework was developed to predict the disinfection rates in terms of the initial phage and bacterial concentrations. In addition, the long-term bacterial growth inhibition potential of multiple phages was determined for several bacteria. In regard to the phage application, phages were shown to protect both final product yields and yeast concentrations during fermentation. Taken together, this work suggests that the rational design of phage treatment is possible and further work is needed to expand on this foundation.

Flexible and robust run-time configuration for self-managing systems

This paper describes a methodology for deploying flexible dynamic configuration into embedded systems whilst preserving the reliability advantages of static systems. The methodology is based on the concept of decision points (DP) which are strategically placed to achieve fine-grained distribution of self-management logic to meet application-specific requirements. DP logic can be changed easily, and independently of the host component, enabling self-management behavior to be deferred beyond the point of system deployment. A transparent Dynamic Wrapper mechanism (DW) automatically detects and handles problems arising from the evaluation of self-management logic within each DP and ensures that the dynamic aspects of the system collapse down to statically defined default behavior to ensure safety and correctness despite failures. Dynamic context management contributes to flexibility, and removes the need for design-time binding of context providers and consumers, thus facilitating run-time composition and incremental component upgrade.

A run-time configurable software architecture for self-managing systems

This paper describes a highly flexible component architecture, primarily designed for automotive control systems, that supports distributed dynamically- configurable context-aware behaviour. The architecture enforces a separation of design-time and run-time concerns, enabling almost all decisions concerning runtime composition and adaptation to be deferred beyond deployment. Dynamic context management contributes to flexibility. The architecture is extensible, and can embed potentially many different self-management decision technologies simultaneously. The mechanism that implements the run-time configuration has been designed to be very robust, automatically and silently handling problems arising from the evaluation of self- management logic and ensuring that in the worst case the dynamic aspects of the system collapse down to static behavior in totally predictable ways.

Time-dependent modelling and experimental validation of the metal/flux interface in a continuous casting mould

A finite volume computer model of the continuous casting process for steel flat products has been developed. In this first stage, the model concentrates on the hydrodynamic aspects of the process and in particular the dynamic behavior of the metal/slag interface. The model was validated against experimental measurements obtained in a water model apparatus.

Continuous Plankton Records - Persistence In Time-Series And The Population-Dynamics Of Pseudocalanus-Elongatus And Acartia-Clausi

Rates of population increase in early spring and the sizes of overwintering stocks were calculated for the planktonic copepods Pseudocalanus elongatus and Acartia clausi for a set of areas covering the open waters of the north-east Atlantic Ocean and the North Sea for the period 1948 to 1979. For both species, the rates of population increase were higher in the open ocean than in the North Sea and appear to be related to temperature. The overwintering stocks in the North Sea were larger than those in the open ocean and are probably related to phytoplanton concentration. P. elongatus shows higher overwintering stocks and lower rates of population increase than A. clausi, resulting in different levels of persistence in the stocks of the two species. It is suggested that this difference in persistence is responsible for differences between the two species with respect to geographical distribution in summer and different patterns of year-to-year fluctuations in abundance.

Continuous Plankton Records - Persistence In Time-Series Of Annual Means Of Abundance Of Zooplankton

Time-series of annual means of abundance of zooplankton of the north-east Atlantic Ocean and the North Sea, for the period 1948 to 1977, show considerable associations between successive years. The seasonal dynamics of the stocks appear to be consistent with at least a proportion of this being due to inherent persistence from year-to-year. Experiments with a simple model suggest that the observed properties of the time-series cannot be reproduced as a response to simple random forcing. The extent of trends and long wavelength variations can be simulated by introducing fairly extensive persistence into the perturbations, but this underestimates the extent of shorter wavelength variability in the observed time-series. The effect of persistence is to increase the proportion of trend and long wavelength variability in time-series of annual means, but stocks can respond to short wavelength perturbations provided these have a clearly defined frequency.

Biodiversity as a dynamic variable in the Gulf of Maine continuous plankton recorder transect

Studies relating biodiversity to ecosystem processes typically do not take into account changes in biodiversity through time. Marine systems are highly dynamic, with biodiversity changing at diel, seasonal and inter-decadal timescales. We examined the dynamics of biodiversity in the Gulf of Maine pelagic zooplankton community. Taxonomic data came from the Gulf of Maine continuous plankton recorder (CPR) transect, spanning the years 1961–2006. The CPR transect also contains coincident information on temperature and phytoplankton biomass (measured by the phytoplankton color index). Taxonomic richness varied at all timescales considered. The relationships between temperature and richness, and between phytoplankton and richness, also depended on temporal scale. The temperature–richness relationship was monotonic at the multi-decadal scale, and tended to be hump-shaped at finer scales; the productivity–richness relationship was hump-shaped at the multi-decadal scale, and tended to be monotonic at finer scales. Seasonal biodiversity dynamics were linked to temperature; inter-decadal biodiversity dynamics were linked to phytoplankton.

Organisational controls, typologies and time scales of paraglacial gravel-dominated coastal systems

The fundamental controls on the initiation and development of gravel-dominated deposits (beaches and barriers) on paraglacial coasts are particle size and shape, sediment supply, storm wave activity (primarily runup), relative sea-level (RSL) change, and terrestrial basement structure (primarily as it affects accommodation space). This paper examines the stochastic basis for barrier organisation as shown by variation in gravel barrier architecture. We recognise punctuated self-organisation of barrier development that is disrupted by short phases of barrier instability. The latter results from positive feedback causing barrier breakdown when sediment supply is exhausted. We examine published typologies for gravel barriers and advocate a consolidated perspective using rate of RSL change and sediment supply. We also consider the temporal variation in controls on barrier development. These are examined in terms of a simple behavioural model (BARCH) for prograding gravel barrier architecture and its sensitivity to such controls. The nature of macroscale (102–103 years) gravel barrier development, including inherited characteristics that influence barrier genesis, as well as forcing from changing RSL, sediment supply, headland control and barrier inertia, is examined in the context of long-surviving barriers along the southern England coastline.