Engineering Science - Doctoral Theses

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The potential role of optical guidance for bone-related biomedical applications in orthopedics and neurosurgery
(University College Cork, 2024) Li, Li Yao; Andersson-Engels, Stefan; Burke, Ray; Science Foundation Ireland
Optical sensing technology was explored as a means of intraoperative guidance for bone-related procedures in orthopedics and neurosurgery. Specifically, the feasibility of diffuse reflectance spectroscopy (DRS), a non-invasive and real-time optical technique that measures diffusely reflected light off samples of interest, was investigated in the thesis to differentiate biological tissue types and inform tissue boundaries as an intraoperative safety measure for revision total hip arthroplasty. Feature selection (FS) frameworks based on DRS measurements were developed utilizing machine learning techniques to determine wavelength features of optimal discriminative power for bone-related surgical procedures. Four FS frameworks, incorporating principal component analysis (PCA), linear discriminant analysis (LDA), backward interval partial least squares and an ensemble approach (biPLS), were designed with high adaptability to facilitate modifications and applications to other clinical scenarios. A feature subset of 10 wavelengths was generated from each FS framework yielding promising balanced accuracy scores for the one-vs-rest binary classification task. For cortical bone versus the rest class labels, PCA, LDA, biPLS and ensemble -based FS framework computed balanced accuracy scores of 94.8 ± 3.47%, 98.2 ± 2.02%, 95.8 ± 3.04% and 95.8 ± 3.16, respectively. For bone cement versus the rest, 100% balanced accuracy scores were generated from all FS frameworks. Subsequently, an in-house designed optical probe integrating DRS sensing was engineered and examined in ex vivo experiments. The most discriminative DRS wavelengths, selected by the FS frameworks including 1200 and 1450 nm, were incorporated as the illumination light sources. Furthermore, the performance of DRS to predict drilling depths in cranial bones was evaluated for craniotomy. Two models including partial least squares (PLS) regression and feedforward neural networks (FNN) were examined for prediction of skull thickness ranging from 1 to 5 mm away from the brain, yielding a root mean squared error regression loss of 0.08 and 0.06 mm from PLS, and 0.2 and 0.1 mm from FNN by using all versus selected features as model inputs, respectively. The predicted depths served as a safety protocol to indicate lookahead distances. On the other hand, the potential of ultrafast lasers in bone-related surgical applications was reviewed and explored from multiple perspectives. The advantages offered by ultrafast lasers over conventional laser systems (continuous wave or long-pulse lasers) included superior precision and minimized collateral thermal damage to surrounding tissues. However, clinical translation of ultrafast lasers to surgical applications had been constrained by limitations in pulse average power and material removal rate. In contrast, the use in implant surface texturing had advanced substantially, effectively enhancing bioactivation and osteointegration within bone matrices. At the end, ambient mass spectrometry, which employed a picosecond laser system for plume generation, was additionally assessed for tissue differentiation in a preliminary study. The classification model employed PCA for dimensionality reduction and LDA for multi-class classification. By using the reduced mass spectra dataset, bone cement was distinguished from biological tissue types with 100% in different classification metrics (precision, recall, F1 score). The highest misclassification rate occurred between trabecular and cortical bone with 18 instances where trabecular bone was classified as cortical bone. Overall, the research presented in the thesis has demonstrated promising results to advance basic science and consequently set the foundation for translational study of integrating optical sensing into surgical tools in bone-related procedures with valuable insights. This work was supported by Science Foundation Ireland (SFI), Grant No. SFI/15/RP/2828 and Grant No. SFI/22/RP-2TF/10293.
Modelling of thin film oxide growth and etching
(University College Cork, 2023) Mullins, Rita; Nolan, Michael; Lam Research; Science Foundation Ireland
As integrated circuit technology follows Moore's Law and continues to shrink, conventional methods for depositing and etching thin films encounter numerous challenges. Moreover, the challenges intensify due to the expected widespread adoption of 'more-than-Moore' devices designed for non-conventional computing applications. Traditional deposition methods will struggle to deliver continuous films at increasingly thinner levels and on complex 3D structures. Moreover, traditional continuous-wave plasma etching faces problems in achieving precise critical dimension control, enhanced selectivity, and with minimal plasma damage, especially below the 10 nm scale. In response to these limitations, atomic-scale processing techniques have emerged; producing thin films tailored to meet the demands of smaller and more intricate structures crucial for future semiconductor devices. Atomic layer deposition (ALD) and atomic layer etching (ALE) offer uniform and conformal processing with precise thickness control and can be achieved using sequential, self-limiting thermal surface reactions. These are used in various applications, such as employing ALE for etching high dielectric metal oxides necessary for gate dielectrics in complex transistor structures such as Gate All-Around or Complementary FET, and utilizing ALD to deposit barrier/liner thin films within interconnects. Presently, ALD is widely used in the semiconductor industry whereas thermal ALE is in the early stage of development and is an emerging and promising frontier in thin film processing. It is difficult to investigate ALD and ALE reactions directly using experimental techniques. First principles density functional theory (DFT) can give deep insights into precursor chemistry and reaction mechanisms of ALD and ALE processes. In my thesis I studied the hydrogen fluoride (HF) pulse as the first step in thermal ALE of high dielectric metal oxides. A thermodynamic analysis is used to predict the temperature at which the targeted self-limiting (SL) reactions are favoured over continuous spontaneous etching (SE) in an ALE cycle. Furthermore, calculations of HF adsorption are performed on the oxide surfaces to understand the mechanistic details of the HF pulse and calculate theoretical etch rates. The results are compared between the metal oxides studied: monoclinic HfO2 and ZrO2, orthorhombic HfO2, amorphous HfO2 and ZnO. HCl is examined as an alternative to HF for crystalline HfO2, ZrO2 and ZnO. The second step in thermal ALE, the ligand exchange reaction is examined for crystalline HfO2 using HF and SiCl4 allowing us to determine how the target Hf species can be chlorinated before being eliminated as volatile Cl-containing species. A combined barrier and liner material incorporating Ru or Co into TaN has been proposed to replace the tri-layer stack of TaN/Ta/Cu for advanced interconnect technology. This will accommodate high aspect ratio trench structures with the continued miniaturization of devices and extend the use of Cu in interconnects for the next generation of electronic devices. Ruthenium and cobalt are also potential replacements for Cu in next-generation interconnects. In this thesis, DFT calculations are also used to explore the nature of N2/H2 terminated TaN surfaces that are produced after a plasma pulse (with H2 or N2/H2 plasma) in Plasma Enhanced ALD to incorporate Ru or Co into TaN. The reactivity of Ru and Co precursors is studied on stable NHx-terminated TaN surfaces. This work will help guide experimental PEALD for the incorporation of ruthenium or cobalt into TaN as a combined barrier and liner material. Finally the mechanism of Ru ALD using the novel precursor RuO4 and molecular H2 was investigated to elucidate the role of both reactants.
Micro cameras as adjunct tools in biomedical applications
(University College Cork, 2024) Niemitz, Lorenzo; Andersson-Engels, Stefan; Burke, Ray; Sorensen, Simon Toft; Science Foundation Ireland
Biomedical imaging is one of the most impactful periprocedural tools and is used across a wide range medical applications. The eyes of the clinician are a key component in surgical decision making, and an image is often the first step in both diagnostic and interventional procedures. With the miniaturisation of CMOS image sensors, micro-cameras are being investigated for use in biomedical imaging and the development of biomedically specific sensors has begun. This thesis makes several important contributions to the use of these micro-cameras as adjunct tools that meet a number of unmet clinical needs in a variety of interventional procedures. To achieve this integration capabilities are demonstrated and a micro-camera based technology platform is developed. The micro-camera is integrated at the tip of various devices, along with multi-spectral fibre illumination, automated readout, control, and image processing; into a compact format suitable for clinical use. The technology is then applied to a number of applications, with the system tailored to the specific use cases. The verification of procedural success in a cardiovascular intervention is investigated. A micro-camera based 2.30 mm catheter device is developed and tested on an animal model. It is shown to be able to image in the challenging environment of the blood field. Here the procedure can be recorded and we are able to extract physiological information in a step toward verification of device placement as well as success of ablation procedures in the heart. The dimensions are pushed to 1.19 mm to navigate into the peripheral lung. This achieves imaging deeper than with a traditional bronchoscope, while maintaining the ability to provide multi-spectral illumination via fibre optics. This is demonstrated on ex-vivo tissue. The micro-camera platform makes an impact on breast conserving surgery procedures, where for the first time the periprocedural imaging of micro-calcifications is investigated. This enables the intra-surgical detection of micro-calcifications up to 2.00 mm in the resection margin. To do this a multi-spectral diffuse optical imaging technique for surgical guidance is proposed, and used to detect micro-calcifications. A rigorous co-registration method is developed to validate the data, and image processing techniques proposed to aid the automated detection. Finally, polarisation resolved imaging is investigated using the microcamera. Here the platform offers a solution for flexible polarisation resolved imaging systems. An initial prototype of both a miniature and benchtop system is presented along with images on optical elements and bulk tissue samples. Line of sight to tissue imaging, and to investigate multi-spectral polarisation resolved imaging is discussed.
Development and evaluation of tools and methodologies for estimating behaviour and predicting training outcome of working dogs
(University College Cork, 2023) Marcato, Marinara; Galvin, Paul; O'Flynn, Brendan; O'Mahony, Conor; Tedesco, Salvatore; INTERREG Programme (CALIN project); Science Foundation Ireland; Department of Agriculture, Food and the Marine, Ireland; European Regional Development Fund
Background: The average training success rate in different dog industries is as low as 50% and the cost of training a guide dog is as high as 53,00 in Ireland. The key to reducing costs is in the assessment of trainee dogs for identifying likely to fail at an early stage. Objectives: This thesis aims to improve behavioural assessment methods by including machine learning methods to (1) predict future outcomes in trainee assistance dogs based on ratings and test batteries, and (2) estimate canine posture based on a recognition system specifically designed for working dogs. Methods: (1) Two standardised ratings were used, in particular, the Canine Behavioral Assessment and Research Questionnaire (C-BARQ) was completed by puppy raisers and the Monash Canine Personality Questionnaire - Revised (MCPQ-R) was answered by dog trainers. Rating data were independently analysed to investigate their relationship with training outcomes. The novel Assistance Dog Test Battery (ADTB) was designed to assess the suitability of trainee assistance dogs for assistance work during training. The test was conducted at 3 weeks - Data Collection 1 (DC1) - and 10 weeks - Data Collection 2 (DC2) - after the start of formal training to investigate the optimal timing to predict working outcomes. (2) Three Inertial Measurement Units (IMUs) were placed on the dogs in different positions (neck, back and chest) and five postures (walking, standing, sitting, lying down and body shake) were annotated. Advanced machine learning techniques were applied for the first time in this field to improve state-of-the-art posture prediction performance. Results: (1) The machine learning models achieved an area under the ROC of 0.84 and 0.85 when using the ratings C-BARQ and MCPQ-R to predict training outcome; and 0.74 and 0.84 when using the DC1 and DC2 of the ADTB to predict working outcomes, respectively. (2) The optimal canine posture classifier achieved an f1-weighted of 0.90. Conclusions: (1) These novel machine learning models provided the most effective early prediction of suitability for assistance work. The MCPQ-R and ADTB were demonstrated for the first time to be a reliable canine behavioural assessment method for estimating future outcomes in trainee dogs. (2) Comparison with previous work reveals a superior performance of the new canine posture estimation system for working
A cross-disciplinary analysis of the materials used in the making of Irish works of art
(University College Cork, 2023) Biolcati, Veronica; Iacopino, Daniela; Ó Macháin, Pádraig; Irish Research Council
Nowadays, the fields of cultural heritage preservation and heritage science are experiencing a growing demand for non-invasive analytical methodologies. These approaches aim to minimize direct interaction with artefacts in order to minimize any potential damage. In fact, non-invasive analytical techniques, by virtue of their non-destructive nature, do not induce modifications in the physical or chemical constitution of the art objects, and they often obviate the need for sampling. Since decades, X-ray fluorescence spectroscopy (XRF) is routinely used as preliminary step in most analytical surveys of artworks. This publication-based thesis, under the auspices of the Inks & Skins project, presents three case studies which used XRF for the elemental characterization of the materials under analysis. XRF plaid a key role in all investigations, as it informed about material availability, artistic techniques, and manufacturing technologies among others. Following the introduction on the principle of XRF and a brief overview on inks and metals, chapter two presents the multi-analytical investigation of the Irish Gaelic manuscript on animal skin, the Book of Uí Mhaine. The presented publication was the culmination of an interdisciplinary analysis of the composing material and manufacturing techniques of the largest Gaelic Books surviving from the medieval vernacular period. XRF elucidated the elemental composition of inks, pigments, and parchment support. The extensive data collected in this study served as comparative tool for the undergoing research on the materials and techniques used in other (27 at the time of this thesis) medieval Irish manuscripts from different traditions. Chapter three presents the publication raising from the study of inks used to write nineteen satiric poems in Harward’s Almanac, a 17th century Dublin book. In this specific case XRF aided to establishing the original order in which the verses were written. Again, this work would have not been possible without a transdisciplinary approach which included paleography, codicology, material science, and statistical analysis. The fourth chapter offers a detailed description of an XRF-based analysis of three gold and silver medieval Irish chalices. This technical study was performed in order to put into historical contest a gilded silver chalice recently sold on auction as to be of medieval and Irish origin. This was done by comparing its materiality with two other late medieval silver-gilt chalices. The study helped to reveal their manufacturing technique, the nature of the decorating enamels and glass, and their story they went through. This work could have not been possible without the essential work and research of art historians. Finally, to highlight the enormous potential of XRF technique, all the analysis were performed on-site at partner institutions, libraries, and museums.

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