Centre for Marine and Renewable Energy (MaREI) - Doctoral Theses

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    Development and implementation of a framework to aid the transition to proactive maintenance approaches on air handling units in the industrial setting
    (University College Cork, 2023) Ahern, Michael; Bruton, Ken; O'Sullivan, Dominic; Science Foundation Ireland
    This research explores the transition to proactive maintenance of HVAC equipment, specifically AHUs in industrial facilities, to make progress towards climate goals. HVAC systems account for 14% of global energy consumption, with the potential to increase efficiency by 20% by addressing energy-wasting faults according to Roth et al. However, these faults are difficult to detect due to their compensating control logic. This research highlights the potential of digitalisation techniques, particularly AI, to identify and rectify these faults, which would contribute to an approximate 2.8% global efficiency improvement. Notably, the study focuses on the nuances of industrial facilities, which have received limited attention compared to other building types. The research identifies several gaps in existing literature, including the knowledge gap between proactive data analysis and reactive engineering mind-sets, the data gap between high-quality experimental datasets and poor-quality industrial datasets, the operational gap between known baselines in experimental studies and unknown baselines in industrial settings, and the practice-theory gap between data-driven approaches in the literature and rule-based approaches in commercial tools. To address the knowledge gap, this thesis presents the IDAIC framework, a domain knowledge integration-type adaptation of the CRISP-DM process model. The implementation of the framework in an industrial facility to curate a dataset and develop a data assessment decision tree has contributed towards closing the data gap. Additionally, the study proposes extensions to the APAR ruleset and a practical data-driven fault detection method to address the operational gap. The deployment of the IDAIC framework as a tool leverages the UML modelling language to address practical considerations and demonstrate the approach's flexibility. Therefore, the main research outputs include the IDAIC framework, an industrial AHU dataset, a data assessment decision tree, an extension to the APAR ruleset, and a proactive maintenance decision support tool. Notably, this research unveils a fault in which the outside air damper is stuck in the fully open position, leading to estimated annual savings of €60,000. These findings validate the effectiveness of a human-centric, domain expertise-integrated approach that is resilient to industrial challenges, contributing to sustainable energy efficiency improvements and the achievement of climate targets using the best available solutions.
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    How seabirds respond to a changing oceanic environment: a biologging approach
    (University College Cork, 2023-05-17) Darby, Jamie; Jessopp, Mark John; Quinn, John; Irish Research Council; Petroleum Infrastructure Program
    Marine habitats are undergoing rapid change due to human influences. The intensity and diversity of human impacts on oceanic habitats are increasing with rising demand for energy and resources. For example, fisheries operate in over 90% of the ocean, harvesting marine life and directly affecting ecosystem functions and resilience. Climate change is also changing the physical and chemical properties of the ocean and altering storm frequency and intensity at a global scale. Seabirds are a group of marine predators that are sensitive to such changes, with impacts contributing to global population declines. We broadly understand how stressors affect different species through effects on life histories and physiological traits, and where seabirds are most impacted based on spatiotemporal overlap of seabirds with human activities. However, finer scale behavioural data are required to understand the functional response of seabirds to different stressors. Biologging devices are continuously improving and miniaturising, being applied to collect fine-scale behavioural information for smaller species and for more protracted durations. In this thesis, biotelemetry is used to investigate the at-sea behaviour of three North Atlantic seabird species in order to understand the drivers of distribution. A better understanding of such drivers sheds light on the challenges facing seabird species when far from land, susceptibility to stressors, and provides insights into more effective monitoring and conservation efforts. Chapter 1 provides a broad introduction to seabird ecology, the application of biologging, and identifies model species for investigating seabird responses to a range of environmental stressors. Chapter 2 investigates the diving behaviour of Manx shearwaters (Puffinus puffinus) and how this correlates with water clarity, which is predicted to deteriorate with increasing urbanisation, eutrophication, and climate impacts. Chapter 3 highlights the relative importance of commercial fisheries compared to other environmental variables in driving the foraging distribution and behaviour of northern fulmars (Fulmarus glacialis) during the breeding season. Chapter 4 expands on this by identifying fulmar-vessel encounters in the non-breeding season, showing how nocturnal vessel attendance is increasing over time, and the apparent relationship with migration effort and time-activity budgets. Chapter 5 identifies unusual levels of variability in the moult period of Atlantic puffins (Fratercula arctica), when they are flightless and more susceptible to climate impacts that may prevent them from foraging. Variability in moult strategy is tied to susceptibility of populations to risks posed by severe winter storms. Chapter 6 provides a synthesis of findings from previous chapters, highlighting how the methods and principles developed may be built upon to further improve our knowledge of seabird ecology and design appropriate conservation measures. Building on insights from previous chapters, I discuss how seabirds are likely to functionally respond to several stressors in the marine environment, including fisheries practices, climate change, and shifting prey availability. Several recommendations are made for further research, including exploring mitigative measures that can be employed to tackle the negative effects of changes to their environment.
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    The impact of UV radiation on the health and pathogen development of the Pacific oyster (Crassostrea gigas)
    (University College Cork, 2022-10-07) Kett, Gary; Culloty, Sarah C.; Lynch, Sharon A.; Jansen, Marcel A. K.; Horizon 2020 Framework Programme; European Regional Development Fund
    Pacific oysters Crassostrea gigas are cultured worldwide and play an important role in global food supply and the sustainable blue economy. Oyster culture sites in Europe, USA, Australasia, and Asia have been experiencing episodic summer mass mortality events. These mortality events can be severely damaging with significant impacts on stock reliability and profitability. Summer mass mortality events are believed to have a multifactorial aetiology driven by high water temperatures and the presence of pathogens, particularly Ostreid herpesvirus-1 and variants (OsHV-1 Var) and bacteria of the genus Vibrio such as V. aestuarianus. UV radiation (UVR) is an intertidal stressor which functions as an ecosystem regulator. UVR has disinfectant properties with the energetic potential to damage nucleic acids of microbes inhabiting surface waters. UVR can also have both positive and negative impacts on animal immune functioning by the activation or inactivation of certain biochemical pathways. Climate model predictions show UV levels changing globally due to changes in cloud cover, aerosols, ozone, and precipitation patterns. This study aimed to investigate the impact of UV radiation (UVR) on oyster health and pathogen performance. Firstly, a desk-based literature review study found that UVR predominantly hinders pathogens, although with varying efficacy, has mixed effects on aquatic invertebrates and has mixed effects on host-pathogen relationships. A clear knowledge gap was identified in that no study could be found which investigated the impact of UVR on bivalve health and survival. Vibrio bacteria are reported to be highly sensitive to UVR while herpesviruses either have high tolerance or can even be activated by solar UVR. UVR can be additive, synergistic, antagonistic, or neutral in outcomes of host-pathogen dynamics. Secondly, novel diagnostic methods for the detection and localisation of Vibrio bacteria within oyster tissues were designed, a generic conventional polymerase chain reaction PCR and a DIG-labelled in situ hybridisation (ISH) assay. These tools were designed to complement existing PCR and qPCR tools and allow for improved understanding of pathogen behaviour inside a C. gigas host exposed to UVR. Primers (VibF3/VibR3) were designed to amplify a 286 bp product from the 16S ribosomal RNA gene common to all Vibrio spp. and to form the ISH probe. ISH was carried out on C. gigas seed sourced from a V. aestuarianus endemic bay (n = 17) and on C. gigas juveniles sourced from a V. aestuarianus naive site (n = 12). Positive ISH signals were observed in PCR and qPCR positive C. gigas while no ISH signal was observed in uninfected samples from the naïve site. Direct Sangar sequencing of PCR products (n = 30), Blastn analysis and Clustal Omega alignments were used to confirm Vibrio sp. detection and assess similarity. Next, to examine the effect of supplemental UV-B on C. gigas seed, a set of laboratory-based experiments were constructed. Various size classes of C. gigas seed were exposed to two conditions: i) a short duration, high intensity UV-B exposure while immersed underwater or ii) a longer duration, low intensity UV-B exposure while emersed out of water. These experimental conditions were chosen to mimic tidal immersion and emersion. The intensity of exposure was lowered in the second trial in order to carry out the treatment over the length of a typical solar peak (midday) during low tide, with the total dose typical of what would be experienced in the south coast of Ireland on a clear summer day. The impact of UV exposure on oyster health was measured by monitoring survival daily, gill tissue DNA samples were used to monitor pathogen prevalence and intensity, and histological tissue cross-sections were examined for pathological damage. Results showed that UV-B exposure negatively impacted oyster survival, most notable in the smallest seed, reducing survival by up to 35%. UV-B also impeded the development of V. aestuarianus, although most effects were transitory and returned to pre-exposure infection levels within 1 - 3 days. Moribund oysters exposed to UV-B had significantly weaker V. aestuarianus infection intensities than moribund oysters in the control group. OsHV-1 Var was not detected in any sample throughout the experiment. These findings indicate that oyster mortality was caused by UV-B exposure rather than by pathogen infection. These data are the first reported impacts of UV-B on C. gigas health and the host-pathogen dynamic with V. aestuarianus. Results from this study suggest that UVR is likely to be a causative factor in C. gigas summer mass mortality episodes. Lastly, to bridge the prior findings to the natural environment, a field trial was designed on a commercial oyster culture cite to investigate the impact of shore grow-out height and the resulting emersion conditions including solar UVR on C. gigas and pathogen performance. Emersion has been shown to have mixed effects on C. gigas performance, though little is known about the impact of UVR in this host-pathogen-environment model. The field experiment in this study was carried out over 5 months, in July C. gigas seed (n = 570) were relayed in 6 replicate mesh bags split across two shore heights equating to a +4-hour emersion time in High Shore (HS) groups compared to the Low Shore (LS) cohort. Mortality (%) was counted in the field and samples (n = 30/shore height) were returned to the lab for pathogen screening for OsHV-1 Var and V. aestuarianus using PCR and qPCR. Increased oyster mortality was associated with emersion, particularly in periods of high UV exposure (>2.4 kJ/m2) and high air temperatures (>21 oC). Pathogen partitioning was observed, OsHV-1 Var was detected more in high shore cohorts while a higher prevalence of V. aestuarianus was detected in low shore C. gigas. Results indicate that environmental conditions impacted spat survival more so than pathogen infection. These findings further demonstrate that oyster mortality and infection levels are influenced by shore height and emersion time. Results from this study can be applied in husbandry practices to reduce losses during summer mass mortality events. Research outcomes are discussed in terms of the wider framework of theoretical knowledge and global development goals, future research questions are posed and recommendations for experimental design are offered. In terms of commercial application, specific husbandry practices are suggested based on the findings of this study, however additional research should be carried out to support or improve upon these recommendations.
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    The application of object-based image analysis to geomorphological seabed mapping
    (University College Cork, 2023-02) Summers, Gerard; Wheeler, Andrew; Lim, Aaron; European Commission; Interreg; Irish Research Council; Geological Survey of Ireland
    Increasing anthropogenic pressures on marine ecosystems due to the reliance on marine resources and the intense development of the marine realm within the last 10 years has threatened the effective functioning of many unique and fragile marine habitats. These environmental stresses warrant effective monitoring and management practices to ensure the preservation of good environmental status. In situ monitoring of marine environmental processes, such as current flow analysis through Acoustic Doppler Current Profilers, provide data with a high temporal resolution at distinct points on the seafloor. However, extensive spatial coverage of seafloor environmental requires a more efficient strategy to quantify these processes. Seabed mapping has long been established as an essential implement in the effective administration of marine ecosystems. Furthermore, in recognition of the significance of seabed mapping in the successful governance of the marine realm, several international seabed mapping initiatives and national seabed mapping programmes have been established with the goal to achieve complete mapping coverage of the seafloor by 2030. Such a significant volume of data evokes the necessity for an objective and repeatable approach to extract meaningful information from the seabed. Geomorphological seafloor features, including current induced seabed sedimentary bedforms (SSBs), are important indicators of habitat, and are readily apparent in seabed mapping data. Moreover, SSBs are common to many marine habitats and spatial scales and are the physical expression of seafloor hydrodynamics, thus these features are appropriate for a standardised approach designed to ascertain objective information on seabed hydrodynamics. This thesis develops a scale robust object-based image analysis (OBIA) approach that is created to classify SSBs as depicted in multibeam echosounder (MBES) bathymetry and derive hydrodynamic information from their morphometrics. This OBIA approach was applied to SSBs occurring in two spatial resolutions of MBES data. Here, four machine learning classifiers support vector machines, two multi-layer perceptrons, and voting ensemble were assessed on their ability to classify SSBs in these two resolutions of data. The results show that the voting ensemble classifier provided the most accurate results for both datasets. The OBIA framework was applied to SSBs depicted in MBES data acquired in a cold-water coral (CWC) habitat in the “downslope Moira Mounds” in the Porcupine Seabight. The SSB attributes of wave height and wavelength were derived from the SSBs classified in these data were used as an input to a multiple linear regression that predicted the seabed current velocity. These predictions illustrated the variable influence of topographic steering occurring at regional-, local-, and micro-spatial scales on regional hydrodynamics. This workflow presented the first estimation of current flow velocity and direction from SSBs in MBES data. Finally, this OBIA approach was used to assess SSBs occurring in multiple resolutions of data within the same region, altering the resolution of observation to evaluate the effect of spatial resolution on the temporal resolution of seabed current hydrodynamics. Moreover, this study determined that the coarse spatial resolution MBES data prevented the assessment of short-term variations in seabed benthic habitat hydrodynamics.
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    Improving the ability of energy systems optimisation modelling to inform national energy policymaking
    (University College Cork, 2023-04-27) Aryanpur, Vahid; O'Gallachoir, Brian; Glynn, James; Daly, Hannah E.; Science Foundation Ireland
    Energy Systems Optimisation Models (ESOMs) are extensively used to inform energy and environmental policymaking. They generate valuable insights into the possible pathways that reduce our reliance on fossil fuels and achieve ambitious clean energy transition goals. However, the academic literature identifies a number of priority areas for development with ESOMs to improve their ability to generate useful insights applicable to the energy transition. This thesis explores and delivers key developments in several of these dimensions: spatial resolution, energy-economy linkage, significance of model skill, and heterogeneity of consumers. From a policy perspective, this thesis seeks to improve the model-based analysis in the context of national-level energy sector decarbonisation and thus, mitigation policies are critically investigated. Moreover, the impacts of the mitigation actions on local air pollution levels and promoting energy security are also explored. Accordingly, the main contributions of this thesis are improvements to the state-of-the-art energy modelling methods and applications of the enhanced models to answer key policy questions with convincing evidence. The improvements are demonstrated via two well-established energy systems modelling tools in Ireland and Iran. The thesis concludes with several modelling and policy insights and suggestions on interesting areas for further investigation to strengthen the contribution of ESOMs to ensure improved climate mitigation and energy policies. The first weakness is the limited spatial and consumer granularity in ESOMs which constrains their ability to analyse region-specific energy transition pathways. This thesis develops a multi-regional representation of the transport sector within the TIMES-Ireland Model (TIM), an ESOM used to develop ambitious mitigation pathways for Ireland’s energy system. The multi-regional approach captures region-specific characteristics of transport technologies and infrastructures across 26 counties. It also incorporates the heterogeneity of the impact of air pollution in sub-national regions and estimates the ancillary pollution benefits of the mitigation targets in those regions. The spatially explicit modelling approach also reveals higher economic co-benefits than single region modelling. The single-region method masks the higher damage costs in medium and large cities, thus underestimating total benefits. This thesis also develops a multi-consumer approach, more accurately capturing consumer heterogeneity. Having homogeneous consumers in ESOMs tends to oversimplify purchase decisions, especially for capital-intensive technology adoption. TIM simulates vehicle purchase decisions using hurdle rates. This thesis disaggregates consumers into five groups, ranging from low- to high-income families, to incorporate a more realistic representation of their behaviour in vehicle purchasing decisions. The results demonstrates that the model with heterogenous consumers offers higher Electric Vehicle (EV) adoption than a single region model calibrated with average national data and identical consumers. Spatially explicit analysis presents valuable insights into regional EVs diffusion and their electricity consumption at a subnational level which are usually challenging to achieve through an aggregated national model. Secondly, ESOMs often ignore the effects of changes in energy costs on energy service demands, despite their key ability to balance supply and demand. The thesis addresses this by developing a comprehensive representation of the power sector within the MESSAGE model, an ESOM used to explore the impacts of different subsidy reform scenarios in Iran. The thesis develops a soft-linked framework combining MESSAGE with an economic model and analyses both supply and demand sides under harmonised assumptions. The novel soft-linking addresses the structural weakness of ESOMs in capturing the effects of energy price on demand. The hybrid model is used to investigate the impacts of subsidy removal on power demand and the required generation mix. The findings reveal that under an early and steady reform scenario, the system avoids lock-in effect, and thus the development of renewable energy technologies and energy efficiency plans become cost-competitive. By contrast, the late subsidy reform path even with radical removal fails to tackle the lock-in effect’s risk. On the other hand, the long-term energy system transition is deeply uncertain. The hybrid modelling framework in this research is also used to conduct an ex-post analysis exploring the extent to which electricity subsidy reform could have reduced Iran’s energy demand during the last three decades. To minimise the uncertainties, both energy and economic models are calibrated with three decades of historical data. The cost-optimal modelling results are then compared with the real-world transition, revealing a 50% lower cumulative cost in the subsidy removal scenario compared with the real-world transition. This deviation highlights what could have been achieved through the implementation of different policies in the absence of uncertainties, providing valuable insights for informing future policy initiatives. Finally, this hybrid framework is also used to show how synergies and efficiencies from Iran’s energy subsidy reforms and lifting its sanctions could enhance global energy security, with a focus on natural gas. It demonstrates that significant opportunities could be realised through a combination of national energy policy reforms and cross border cooperation in a favourable international environment.