Environmental Research Institute - Doctoral Theses

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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.
From genotype to phenotype: characterising intraspecific variation in the three-spined stickleback (Gasterosteus aculeatus) in the Burrishoole aquatic ecosystem complex in western Ireland
(University College Cork, 2022-07) Leseur, Floriane; McGinnity, Philip; Reed, Thomas; Marine Institute
The stickleback Gasterosteus aculeatus is a resident of coastal marine and freshwaters throughout the temperate Holarctic and is a model species for evolutionary biology, particularly due to its recolonization events of freshwaters in previously glaciated catchments. This study concentrates on the species in Ireland, particularly in the Burrishoole system in the west coast of Ireland. The latter is an extensively studied catchment with freshwater streams and lakes running into a brackish lake over waterfalls largely impassable upstream to sticklebacks; then connecting to coastal waters. Previous genetic (using microsatellites), morphological and meristic studies in the Burrishoole catchment identified four statistically distinct populations; one in the major freshwater lake and three (completely-, partially- and low-plated forms) in the brackish lake. Here, a more extensive study was undertaken extending the geographic and temporal analyses of genetic aspects (using neutral and adaptive SNPs) and phenotypic traits including morphological and metabolic characters, and gut microbiome composition. Neutral SNPs showed largely the same population composition as previously suggested using microsatellites (i.e. isolation-by-adaptation reflective of time of divergence), though the partially-plated group in the brackish lake was not supported. This composition being temporarily stable and supported by morphological analysis. The confirmed adaptive SNPs suggest a different scenario with isolation-by-environment in relation to the two populations differentiated by ecomorph (plates, body shape, gill rakers and migratory behaviour) co-existing in Lough Furnace. Analysis of traits associated with metabolism and gut microbiome did not extend population differentiation, but yielded novel results individually. The individual results are discussed in four separate chapters, and the thesis then concludes with an overview chapter. Similarity or differences with other stickleback studies around the North Atlantic and Pacific are explored, and possible isolating mechanisms between the completely- and low-plated forms co-occurring during the spawning season in the brackish lake identified (migratory behaviour – anadromy - in the completely-plated form, absence of evidence of hybridisation in co-habitation, wash out from the freshwater population into the brackish lake). The rare physical characteristics observed in the Burrishoole system may allow clarification of the process of recolonization of freshwaters in this species.
The application of machine learning and 3D photogrammetry for cold-water coral habitat classification in the NE Atlantic
(University College Cork, 2023) de Oliveira, Larissa Macêdo Cruz; Wheeler, Andrew; Lim, Aaron; Conti, Luis Americo; Irish Research Council; Science Foundation Ireland; Marine Institute
Cold-water coral reefs are complex structural habitats that represent one of the most important deep marine ecosystems. As three-dimensional habitats with high structural complexity, they provide ecosystem services that influence species abundance and biodiversity, being indicators of ecosystem health. These habitats are considered hotspots of biodiversity around the globe, especially in cold and deep waters between 50 and 4000 metres depth. Similar to their tropical counterparts, these habitats are subject to several climate and anthropogenic threats. Over the last two decades, research efforts to identify, map and manage these environments have increased along with the advances in data acquisition. Technologies such as remotely underwater vehicles are equipped with high-resolution sensors that generate gigabytes to terabytes of data. However, data analysis methods are being outpaced by acquisition technologies and there is a latency in the extraction of meaningful information from large datasets. Furthermore, the fine-scale heterogeneity promoted by the three-dimensional scleractinian coral branching structure is often overlooked, being reduced to a two-dimensional scale. This thesis explores methods that can advance seabed mapping to further understand cold-water coral reef habitat features in the deep sea considering their natural, three-dimensional structure and posed data analysis demands given the current technologies. The key aims of the research were to: i) develop an unprecedented 3D imaging classification workflow for CWC habitats of Ireland whilst analysing the suitability and transferability of 2D and 3D data to represent these habitats in high-resolution; ii) quantify facies distribution and spatial variability; iii) link image data to processes driving CWC reef development; iv) develop new forms of visualisation of 3D data of underwater environments; v) derive meaningful information from dense optical datasets. Here, CWC reef habitats in the Porcupine Bank Canyon and the Belgica Mound Province, in the Porcupine Seabight, SW of Ireland were reconstructed in 3D using Structure-from-Motion (SfM) photogrammetry. Point clouds, meshes, orthomosaics and digital elevation models (DEMs) were produced at sub-centimetric resolution. Four different classification workflows were developed and analysed, namely: Multiscale Geometrical Classification (MGC); Colour and Geometrical Classification (CGC); Object-Based Image Classification (OBIA) and; Machine Learning Multiclass classification (MLMC). These first three workflows provided a binary (coral, seabed) classification with accuracy ranging 56 to 74% and provided the analysis of the percentage class distribution for each habitat in 2D and 3D. Results show that there is an impact in mapping CWC in 3D and 2D of at least a tenth of order of magnitude. The MLMC method provided a multiclass (live coral, dead coral, coral rubble, and sediments and dropstones) classification of the 3D point cloud which achieved f1 scores of up to 95.1%. DEMs and classification results were used to assess local and regional CWC patterns in relation to terrain features, facies size and facies distribution. Further investigation revealed that CWC are not randomly distributed within CWC reefs, instead their distribution may be driven by local geomorphometric properties. Aiming to raise awareness and facilitate the interaction of humans with deep-water environments, an application for visualisation of 3D models of CWC in mobile phones was developed. This thesis demonstrates how SfM and machine learning can be used to quantify CWC facies and understand CWC reef habitats.
Understanding cold-water corals’ health and ecosystems on the Irish margin, NE Atlantic; a critical look into the ecology, geology, hydrodynamic processes and human impacts
(University College Cork, 2022-08) Appah, John; Wheeler, Andrew; Ramsay, Ruth; Lim, Aaron; Science Foundation Ireland
Cold-water corals (CWCs) have come under threat from climate change and anthropogenic activities such as fishing and marine litter pollution despite, being ecological engineers that support high biodiversity, and as a result are protected in Europe under the EU Habitats Directive with some designated as Special Areas of Conservation (SACs). Abiotic (low pH, macro and microplastics) and biotic (pathogens and harmful microbes) factors, due to climate change and human activities, can stress CWCs, disrupting the coral holobiont with dire consequences on the energy allocation processes, coral health and diseases, growth and survival, resilience as well as biodiversity in deep sea corals. CWCs are azooxanthellate, filter feed and exist withing temperature limits of 4-13 °C. Using a habitat mapping approach, coupled with CWC histology and studies of the coral microbiome, this PhD research investigates the CWCs’ ecosystem health and environmental processes that influence biodiversity in the two SACs, upper Porcupine Bank Canyon (uPBC) and the western Belgica Mound Province (wBMP), on the Irish continental margin, northeast Atlantic. Chapter one provides a general introduction to cold-water corals, the objectives of the research and the threats to ocean environmental health and consequent organismal health, while chapter two maps the spatial distribution of CWCs within one of the largest submarine canyons on the Irish margin, the uPBC, highlighting importantly habitat heterogeneity in reef habitats and the hydrographic factors that influence the pattern of CWCs distribution in the canyon. Chapter three mapped the distribution of marine litter in two special areas of conservation (PBC and BMP) on the Irish margin and its impact on CWCs’ distribution as well as to determine if the SACs are serving their purpose and their usefulness against litter entry. In chapter four, the study assessed the distribution and roles of the coral holobiont in the uPBC using molecular techniques whilst chapter five uses a combination of histological and molecular techniques to assess Haplosporidia and Vibrio spp. in main framework-forming corals in the uPBC. Chapter six synthesizes the data obtained and concludes on the distribution and status of the cold-water corals in the uPBC in the face of climate change and anthropogenic pressures. In the analysis, five different substrates were characterized in the uPBC and resolved into non-reef (sediment, sediment & dropstones and bedrock) and reef and rubble (live/dead coral and coral rubble) habitats, including the terrain features observed in the canyon, and these generally contributed to the high biodiversity. High benthic megafaunal diversity (higher number of taxa identified), although not significantly different from the Shannon’s diversity observed in reef and rubble habitats, was detected in the non-coral habitats compared to the reef and rubble habitats in the upper PBC. Percentage estimates of Shannon’s diversity for non-coral and reef and rubble habitats were (H’non-reef =2.38; H’reef and ruble = 2.16) and Pielou’s evenness (J’non--reef =0.71; J’ reef and ruble = 0.65) respectively whilst density estimates of Shannon’s diversity for non-coral and reef and rubble habitats were (H’non-reef =1.72; H’reef and ruble = 1.14) and Pielou’s evenness (J’non--reef =0.54; J’ reef and ruble = 0.43) respectively. Geomorphology and hydrography were noted to affect the distribution of litter in the SACs. Another striking finding was that fishing gear (uPBC=80.7%, wBMP = 14.3% buoys) and plastics (uPBC = 11.3%, wBMP = 55.1%) were detected in relatively high abundance, suggesting that anthropogenic activities such as fishing (>60% vessels) are ongoing in the PBC and BMP despite being a SACs. It is unclear, however, if the observed fishing gear in the uPBC and wBMP may have drifted into them by deep-sea currents or were dumped before they were designated an SAC, as the SACs are closed to fishing. Additionally, the results reveal the upper canyon as a high energy environment with sufficient mixing of materials and community composition among the corals, water and sediment samples. Shannon’s index (H = 2.19, P = 0.33) and species evenness (J’ = 1.66, P = 0.43) among the groups of samples, respectively, were not significantly different. A positive note is that the corals generally appear to be in good health with low Haplosporidia (0.03%) and Vibrio (0.03%) infections in a single L. pertusa individual from the canyon head respectively, although we risk losing the corals due to bottom fishing and the current trend of climate change. A total of 40% Rickettsiales-like organisms (RLOs), with 26.7% observed in the south branch and 13.3% observed in the canyon head were detected. Despite the many threats and pressures such as marine litter pollution, changing pH, sedimentation and bottom trawling, the CWCs on the Irish margin, are associated with high biodiversity and appear to be resilient, well adapted to the deep-sea environment. However, regular monitoring campaigns and health screening studies are advocated. Although continuous monitoring through research and management activities would be the way forward, it is recognised that the cost of such deep-sea surveys/expeditions are huge and require sufficient funding from the various funding bodies. It is believed that the findings of this research will inform policy makers and management on how to effectively protect the vulnerable ecosystems of these deep seas.
Understanding future power system challenges with higher renewables and electrification
(University College Cork, 2022-01) Mehigan, Laura; Deane, Paul; O'Gallachoir, Brian; Bertsch, Valentin; Science Foundation Ireland
Urgent action to reduce global greenhouse gas emissions is needed to prevent irreversible damage to the world’s climates. An opportunity exists to decarbonise electricity systems and to aid decarbonisation of heat and transport through electrification. This can only be achieved if electricity systems incorporate significantly higher levels of renewables and can cope with higher electrification. However, achieving this is not without its challenges particularly in the decade to 2030. Failure to make meaningful progress in this crucial decade will reduce the likelihood of meeting the commitments under the Paris Climate Agreement. To solve these challenges, they must first be understood. The central focus of this thesis is to improve the understanding of the challenges faced by future electricity systems with higher Renewable Energy Sources (RES) and higher electrification with an emphasis on the European power sector for the year 2030. The thesis investigates the role of Distributed Generation (DG) in future electricity systems and acknowledges that while the role of DG is important it is not the key determinant of the challenges faced in future electricity systems. The challenge of declining rotational inertia from synchronous generators is investigated and the impact of managing rather than solving this challenge is quantified for every synchronous area in the pan European power system. An exploration of how carbon price influences the role of flexibility providers (batteries and interconnection) in decarbonisation of the European power system for a policy relevant scenario reveals new insights. These insights include the importance of a high carbon price to ensure that flexibility providers reduce emissions while fossil fuels remain in the generation mix, batteries reduce solar curtailment more than interconnection, and interconnection reduces wind curtailment more than batteries. The main contributions of the thesis are the methodological contributions and insights gained into the future challenges from both a synchronous area level and a broader European perspective. The work undertaken as part of this thesis has accelerated discussions on the challenges that will be faced to achieve renewable ambitions in 2030. In particular, this research has contributed to a recent policy decision in Ireland on the need for backup generation in 2030 and during the transition to a decarbonised system.

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