Tom Vermeyen

• 20/12/2023
  
• 4 p.m.
• Venue: Campus Drie Eiken, O.01
• Supervisors: Wouter Herrebout (UAntwerpen) & Patrick Bultinck (UGent)
• Department of Chemistry

Abstract

Determination of the so-called Absolute Configuration (AC) of a chiral compound is an important analytical step in research areas such as medicine and agrochemistry.

The AC of a chiral compound can be determined with Vibrational Circular Dichroism (VCD), which measures the difference in absorbance of left and right circularly polarised infrared radiation. VCD spectra exhibit substantial chiral sensitivity and contain an abundance of conformational information.

Unfortunately, there are no general empirical rules capable of linking a VCD spectrum to a specific AC or predicting the influence of the conformations on the VCD spectrum.

Therefore, in each VCD application one has to rely on expensive (DFT) calculations for the conformers of all possible AC's.

In this thesis, the added value of Machine Learning (ML) is explored for the AC determination workflow with VCD.

The presented results demonstrate that ML models are capable of directly extracting the AC from the VCD spectrum after training these models on a set of structurally similar compounds.

Neural Networks can successfully predict the influence of conformations on the spectrum from their geometries, as long as these conformations correspond to the same AC.

Additionally, the potential of linear ML models is tested to determine the composition of terpene mixtures and natural oils.

Wencong Xu

• 11/12/2023
  
• 10 a.m.
• Venue: Campus Drie Eiken, S.001
• ​Online PhD defence
• Supervisors: Annemie Bogaerts, Vladimir Galvita & Vera Meynen
• Department of Chemistry

Abstract

Plasma is considered one of the promising technologies to solve greenhouse gas problems, as it can activate CO₂ and CH₄ at relatively low temperatures. Among the various types of plasmas, the gliding arc plasmatron (GAP) is promising, as it has a high level of non-equilibrium and high electron density. Nevertheless, the conversion of CO₂ and CH₄ in the GAP reactor is limited. Therefore, combining the GAP reactor with catalysts and making use of the heat produced by the plasma to provide thermal energy to the catalyst, forming a post-plasma catalytic (PPC) system, is hypothesized to improve its performance. Previous studies have been reported on the PPC system, combining catalysts with other types of gliding arc plasmas, such as two-dimensional (2D) gliding arc plasma. However, the improvement in the conversion or selectivity was limited. Adding extra heating with high temperature can be a solution for this, while this will also increase the energy cost. Therefore, in this PhD research, we investigate important aspects of the PPC concept towards the use of the heat produced by GAP plasma to heat the plasma bed, without additional energy input.​ 

Aiming at this, based on a literature study (chapter 1), Ni-loaded layered double hydroxide (LDH) derived catalyst with good thermal catalytic DRM performance were chosen as the catalyst material. Before applying the LDH as a support material, the rehydration property of calcined LDH in moist and liquid environment was studied as part of chapter 2. The data indicated that after high temperatures calcination (600-900 °C), the obtained layered double oxides (LDOs) can rehydrate into LDH, although, the rehydrated LDH were different from the original LDH. In chapter 3, different operating conditions, such as gas flow rate, gas compositions (e.g. CH₄/CO₂ ratio and nitrogen dilution), and addition of H₂O were studied to investigate optimal conditions for PPC DRM, identifying possible differences in temperature profiles and exhaust gas compositions that might influence the catalytic performance. Subsequently, the impact of different PPC configurations, making use of the heat and exhaust gas composition produced by the GAP plasma, is shown in Chapter 4. Experiments studying the impact of adjusting the catalyst bed distance to the post-plasma, the catalyst amount, the influence of external heating (below 250 °C) and the addition of H₂O are discussed. As only limited improvement in the performance was achieved, a new type of catalyst bed was designed and utilized, as described in chapter 5. This improved configuration can realize better heat and mass transfer by directly connecting to the GAP device. The performance was improved and became comparable to the traditional thermal catalytic DRM results obtained at 800 °C, although obtained by a fully electrically driven plasma.

Daan Laméris

• 01/12/2023
  
• 3.15 p.m.
• Venue: Darwin Hall, ZOO Antwerpen
• ​Online PhD defence after registration
• Supervisors: Marcel Eens & Jeroen Stevens
• Department of Biology

Abstract

Emotions are an integral component of the daily lives of animals as they enable flexible responses to rewarding and aversive stimuli, thereby guiding behaviour. They are also major determinants of an animal’s welfare. Emotions are notoriously difficult to measure reliably, partly due to their species- and individual-specific nature. In this thesis, I explore animal emotions by focusing on the cognitive and behavioural components in zoo-housed bonobos (Pan paniscus). Using a combination of touchscreen and eye-tracking technology, I investigated attentional biases towards different stimuli. While completing a pictorial emotional Stroop task, I found that attention of the bonobos was attracted by non-social images such as leopards, food items, and flowers, alongside positive facial expressions, offering potential insights into the socio-ecological priorities of bonobos. Attention can, however, also be modulated by an animal’s own emotional state. To study such affect-congruent attention biases, I designed an eye-tracking study in which I primed emotions and subsequently studied preferential looking at competing facial expressions. Priming emotions using salient videos generally induced pupil dilation, although attention of the bonobos was captured by negative facial expressions, irrespective of the video type.

Shifting focus to behavioural outputs of emotions, I examined two indicators used to measure negative emotions across two studies: abnormal behaviours and self-directed behaviours. Factors such as sex, rearing history, and personality explained inter-individual variation in the performance of abnormal behaviours and revealed potential welfare implications. I furthermore identified two self-directed behaviours that were associated with negative emotional arousal. Not only the type of behaviour, but also how a behaviour is performed can inform us about emotions. As such, I developed a Qualitative Behavioural Assessment to study how humans perceive bonobo emotional expressivity. While expert knowledge proves crucial for rating expressive qualities, further validation and inclusion of caretaker knowledge are essential for continued tool development.

In the final study, I integrated cognitive and behavioural components of emotions within an animal welfare context. Managed fusion events between bonobo subgroups were characterised by increases in aggressive and socio-sexual interactions. Touchscreen testing also indicated cognitive signs of shifts towards negative emotions in the bonobos, although short-lasting. Correlates between cognitive and behavioural measures revealed additional emotional consequences of behaviours. In conclusion, this thesis offers a multifaceted exploration of animal emotions, emphasising the importance of species-specific measures and individual factors in understanding and assessing animal welfare.

Maruan Bracci

• 24/11/2023
  
• 9 a.m.
• ​Online PhD defence
• Supervisors: Sabine Van Doorslaer & Inés García-Rubio
• Joint PhD with the University of Zaragoza
• Department of Chemistry

Abstract

This work is focused on the in-depth spectroscopic analysis of horseradish peroxidase (HRP) and chloroperoxidase (CPO), proteins selected for their scientific and industrial relevance, with applications in biotechnology and pharmacology. The enzymatic cycle of both peroxidases goes via an oxidized intermediate state, called Compound I. Although abundantly studied, the exact description of the difference in the electronic structure of Compound I of various heme proteins remains challenging and forms the focus of this work in which this elusive state is being studied with Continuous-Wave and Pulsed Electron Paramagnetic Resonance (EPR), UV-Vis spectroscopy, and stopped-flow spectrophotometry. 

In order to realize this goal, different problems needed to be tackled. First of all, in an attempt to enhance CPO production, an innovative solid substrate method has been explored, promising potential for scalability. Furthermore, the author made crucial contributions to the developmental stages of three different rapid freeze quench apparatus used for trapping intermediate Compound I state from CPO immediately after the initiation of the catalytic cycle. Pulsed EPR techniques, such as HYSCORE and ENDOR, were utilized to investigate the resting state of both enzymes and their Compound I intermediate, providing insights into the electronic structure of their active centres and highlight their differences. To aid in the interpretation of HYSCORE spectra, a user-friendly graphical interface was developed, enabling researchers to manipulate experimental data and conduct simulations, even with minimal coding expertise. Moreover, a theoretical model of the electronic structure of Compound I was effectively utilized for the proteins under investigation in this study, highlighting the powerful interplay between theory and experiment. 

Robin Van Echelpoel

• 21/11/2023
  
• 4 p.m.
• Venue: Stadscampus, Promotiezaal van de Grauwzusters, Lange Sint-Annastraat 7, 2000 Antwerpen
• ​Online PhD defence
• Supervisor: Karolien De Wael
• Department of Bioscience engineering

Abstract

Illicit drugs are harmful substances, posing a threat to the health and safety of society. Each year, over half a million people die because of drug overdoses. The violence associated with the illicit drug trade disrupts communities across the globe, there is no region in the inhabited world that is spared from it. Policies, such as supply reduction and harm reduction, are in place to combat the illicit drug problem. Science can play a substantial role in this fight, by providing tools that enable these policies to be successfully enforced. One example are on-site detection tools, i.e. sensors that allow the on-site identification of an illicit drug in a sample of interest. Several technologies, such as color tests and portable spectroscopic techniques, are currently employed for this goal. Although these are valuable techniques, there is an opportunity for voltammetry, an electrochemical technique, to make an impactful addition to this repertoire of on-site detection tools.

Despite its attractive features (low-cost, portable, short analysis time, indifference to color,...), voltammetric illicit drug sensor have failed to make an impact in real scenarios. The work outlined in this PhD thesis aims to change this by bringing the technology from the lab to the field. Strategic choices, fueled by feedback from end-users, were made to further develop those specific aspects of the technology that previously haltered the technology to fulfill its potential. A detection algorithm was introduced that converts the voltammetric output into a clear-cut interpretation thereof, opening up the technology to end-users without prior knowledge of the technology. A sensor that allows qualitative and quantitative detection of the psychoactive drug MDMA was introduced, and importantly, validated on a large set of 212 confiscated samples. A state-of-the-art mobile application and adequate sampling methodology were developed, alongside other, often more practical studies and product developments, to evolve the technology into a product that truly creates value for end-users. Important steps towards multidrug detection were made with a festival sensor and a flowchart based on visual appearance that ties together a variety of voltammetric single sensors into a single multidrug sensing approach. Last but not least, multiple valorization aspects were researched, including a market study and an analysis to determine the optimal commercialization strategy. Overall, this PhD thesis has facilitated the transition of the voltammetric illicit drug sensing technology from lab to on-site application.

Chu-Ping Yu

• 20/11/2023
  
• 4 p.m.
• Venue: Campus Groenenborger, U.024
• ​Online PhD defence​
• Supervisors: Johan Verbeeck & Sandra Van Aert
• Department of Physics

Abstract

Transmission electron microscopy (TEM) is a technique that uses an electron beam to analyze materials. This analysis is based on the interaction between the electron beam and the sample, such as photon emission and electron diffraction pattern, to name a few. Sample damage, however, also occurs when such interaction alters the structure of the sample. To ensure information from the undamaged material can be acquired, the electron expense to probe the material is thus limited.

In this work, we propose efficient methods for acquiring and processing the information originating from the electron-sample interaction so that the study of the material and the conducting of the TEM experiment can be less hindered by the limited dose usage.

In the first part of the work, the relationship between the scattering of the electron and the local physical property of the sample is studied. Based on this relationship, two reconstruction schemes are proposed capable of producing high-resolution images at low-dose conditions. Besides, the proposed reconstructions are not restricted to complete datasets but instead work on pieces of data, therefore allowing live feedback during data acquisition. Such feature of the methods allows the whole TEM experiment to be carried out under low dose conditions and thus further reduces possible beam damage on the studied material.

In the second part of the work, we discuss our approach to modulating the electron beam and its benefits. An electrostatic device that can alter the wavefront of the passing electron wave is introduced and characterized. The beam-modulation ability is demonstrated by creating orthogonal beam sets, and applications that exploit the adaptability of the wave modulator are demonstrated with both simulation and experiments. ​ ​

Romy Poppe

• 17/11/2023
  
• 4 p.m.
• Venue: Campus Groenenborger, U.024
• Supervisor: Joke Hadermann
• Department of Physics

Abstract

Electrons, X-rays and neutrons that pass through a thin crystalline sample will be diffracted. Diffraction patterns of crystalline materials contain Bragg reflections (sharp discrete intensity maxima) and diffuse scattering (a weak continuous background). The Bragg reflections contain information about the average crystal structure (the type of atoms and the average atomic positions), whereas the diffuse scattering contains information about the short-range order (deviations from the average crystal structure that are ordered on a local scale). Because the properties of many materials depend on the short-range order, refining short-range order parameters is essential for understanding and optimizing material properties.

The refinement of short-range order parameters has previously been applied to the diffuse scattering in single-crystal X-ray and single-crystal neutron diffraction data but not yet to the diffuse scattering in single-crystal electron diffraction data. In this work, we will verify the possibility to refine short-range order parameters from the diffuse scattering in single-crystal electron diffraction data. Electron diffraction allows to acquire data on submicron-sized crystals, which are too small to be investigated with single-crystal X-ray and single-crystal neutron diffraction. ​ ​

In the first part of this work, we will refine short-range order parameters from the one-dimensional diffuse scattering in electron diffraction data acquired on the lithium-ion battery cathode material Li1.2Ni0.13Mn0.54Co0.13O2. The number of stacking faults and the twin percentages will be refined from the diffuse scattering using a Monte Carlo refinement. We will also describe a method to determine the spinel/layered phase ratio from the intensities of the Bragg reflections in electron diffraction data. ​ ​

In the second part of this work, we will refine short-range order parameters from the three-dimensional diffuse scattering in both single-crystal electron and single-crystal X-ray diffraction data acquired on Nb0.84CoSb. The correlations between neighbouring vacancies and the displacements of Sb and Co atoms will be refined from the diffuse scattering using a Monte Carlo refinement and a three-dimensional difference pair distribution function refinement. The effect of different experimental parameters on the spatial resolution of the observed diffuse scattering will also be investigated. Finally, the model of the short-range Nb-vacancy order in Nb0.84CoSb will also be applied to LiNi0.5Sn0.3Co0.2O2.

Tomáš Kello

• 16/11/2023
  
• 4 p.m.
• Venue: Campus Groenenborger, V.008
• ​Online PhD defence​
• Supervisors: Pierre Van Mechelen (UA) & Laurent Favart (ULB)
• Department of Physics
• Joint PhD Universiteit Antwerpen - Université Libre de Bruxelles
  
  

Abstract

This thesis presents constraints on the anomalous couplings (AC) of the Higgs boson (H) with vector bosons as obtained in analysis studying Higgs boson production and decay into the pair of W bosons. Various alternative Higgs spin-parity scenarios were considered, including CP violating effects. The study is performed on proton-proton collisions at a center-of-mass energy of 13 TeV, corresponding to 138 fb −1 of integrated luminosity, collected by the CMS detector at the LHC during the 2016-2018 period of data-taking. The analysis targets the dilepton different flavor (eμ) final state with up to two associated jets, providing additional kinematic information used in combination with the matrix element technique to increase sensitivity to anomalous contribution at the production vertex. In cases where the analysis phase space has limited kinematic information, we rely on decay kinematics, also affected by anomalous effects. Up to four anomalous couplings are studied both independently and simultaneously, within the standard model effective field theory framework assumed in the latter case. All measurements and the corresponding confidence intervals for their values we obtained were found to be consistent with the expectations for the Standard Model Higgs boson. These results significantly surpass previous AC constraints obtained in the H → W W∗ channel and are competitive with results obtained in other Higgs boson decay channels.

Fons Dingenen

• 27/10/2023
  
• 3 p.m.
• Venue: Campus Drie Eiken, R1
• Supervisors: Sammy Verbruggen & Silvia Lenaerts
• Department of Bioscience Engineering

Abstract

Seawater splitting is considered as a sustainable way of H2 production. While electrolysis is the more mature technology, the field of photocatalysis still holds tremendous promise due to its resistance towards seawater stability and selectivity issues. In order to increase the solar light activity of TiO2, the benchmark photocatalyst, this thesis explored the plasmonic rainbow concept. Here, TiO2 is modified with plasmonic gold-silver composites that allow the absorption of visible light. Cost-effective modification was demonstrated for pure water splitting. Unfortunately, these metal particles are prone to oxidation and hence need stabilization. Both insulating as conductive protective polymer shells were applied around the metal cores to effectively stabilize the nanoparticles in harsh environments. After promising results in saline solutions (0.5 M NaCl), aggregation occurred in actual seawater. To address this final problem, immobilization strategies using stereolithography 3D printing were investigated, showing significant activity and stability improvements in real seawater.

Gilles De Smet

• 26/10/2023
  
• 5 p.m.
• Venue: Campus Middelheim, G.010
• Supervisors: Bert Maes & Gwilherm Evano
• Department of Chemistry

Abstract

The increasing CO2 levels and associated climate change are drivers to move towards a circular chemical industry. Therefore, there is besides recyclable carbon an urgent need for means to access renewable carbon. Two main strategies have been put forward: (i) carbon capture and utilization (CCU) and (ii) use of biomass as feedstock. One particularly interesting biorenewable resource is lignin, part of lignocellulose biomass, giving access to phenolics, i.e. guaiacols, syringols, catechols and pyrogallols. These substrates are often referred to as platform molecules with the potential to serve as renewable feedstock for the production of commodity chemicals as an alternative to oil. However, lignin derived aromatics have a high oxygen content, which is in sharp contrast to benzene, toluene, xylene (BTX) obtained from current petroleum refining. Therefore, instead of an oxidative approach to introduce functional groups required for oil, a reductive approach is needed for bioaromatics. One way to allow a controlled decrease in oxygen content of lignin derived aromatics while maintaining aromaticity is chemoselective hydrodeoxygenation. A particular interesting subclass of HDO reactions is selective hydrodehydroxylation allowing removal of hydroxy groups in presence of methoxy groups. However, this transformation requires pre-activation of the hydroxy group by installment of a leaving group. Acetate is introduced as a renewable leaving group for selective hydrodeacetoxylation of aryl acetates using a homogeneous Ni0-NHC catalyst and pinacolborane reductant in green dimethyl carbonate solvent. Proof-of-concept for oil derived substrates was demonstrated using renewable 4-propylguaiacol obtained from pine wood via reductive catalytic fractionation (RCF). Furthermore, overcoming the limitations of air- and water-sensitive Ni0 catalysts, a heterogeneous Ni-catalyzed hydrodeoxygenation method was developed for methyl aryl carbonates and catechol carbonates. This methodology was also shown applicable to renewable 4-propylguaiacol and 4-propylcatechol obtained from RCF of pine wood. Next to aromatic substrates, hydrodeoxygenation of aliphatic hydroxy groups, pre-activated as methyl carbonates, using air-stable Ni0(cod)(dq) as catalyst giving the corresponding alkane products is also described.

Kamiel Janssens

• 24/10/2023
  
• 4 p.m.
• Venue: Campus Drie Eiken, O.02
• ​Online PhD defence
• Supervisors: Nick Van Remortel & Nelson Christensen
• Department of Physics

Abstract

Observing the gravitational-wave background (GWB) with Earth-based interferometric detectors will provide insights into astrophysical and cosmological processes in the early Universe. To confidently claim a detection in the future, a profound knowledge of the data quality and potential contamination by noise sources is of utmost importance. In this work a comprehensive study is presented on a wide variety of data quality issues that may arise in the search for an isotropic GWB with current and next generation Earth-based gravitational-wave (GW) interferometric detectors.

First of all, spectral artefacts are addressed during the third observing run by LIGO and Virgo. Secondly, one needs to understand the effect of noise sources which are correlated between the observing detectors. When not properly accounted for, these noise sources could bias future detections of a GWB in the Hz to kHz frequency band. Observations of Earth-scale correlations in magnetic field fluctuations are described between 1Hz and 1kHz. By using measurements of the coupling strength of magnetic fields to GW detectors, the effect of correlated magnetic noise on GW searches is predicted. Searches for an isotropic GWB could become contaminated by correlated magnetic noise when the detectors reach their design sensitivity in the second half of the 2020 decade.

Future projects such as the Einstein Telescope (ET) and Cosmic Explorer, should seriously consider the threat of magnetic noise. If not addressed, environmental magnetic noise will dominate the detectors' sensitivity below ~15Hz. The equilateral triangular configuration of three nested GW detectors of the ET brings certain advantages such as the sky-position-independent null channel, which is insensitive to GW signals from any direction. This would prove useful for the estimation of the detector noise, as the ET will have many overlapping signals at any given time. Within this context, this work includes a description how to take the effect of non-identical and correlated noise sources into account in the null channel framework.

However, the triangular detector configuration comes at a cost. The co-located placement of different detectors results in additional noise sources coupling coherently to multiple detectors. This could have a detrimental impact on the ET's capabilities in observing a GWB. Furthermore, the possibility of correlated seismic and Newtonian noise is investigated and shown to be problematic. More specifically, correlated Newtonian noise from seismic body waves has the potential to overwhelm a GWB signal up to ~40Hz by many orders of magnitude.

Eline Biscop

• 20/10/2023
  
• 11 a.m.
• Venue: Campus Drie Eiken, O.05
• ​Online PhD defence​
• Supervisors: Annemie Bogaerts, Evelien Smits & Abraham Lin
• Department of Chemistry

Abstract

Cancer, the second leading global cause of death, remains a formidable challenge despite advances in conventional therapies. The emergence of treatment resistance underscores the need for innovative approaches in the fight against this horrible disease. Over the past two decades, non-thermal plasma (NTP) has garnered attention as a novel addition to conventional treatments. NTP, a partially ionized gas, contains reactive oxygen and nitrogen species (RONS) that can induce oxidative stress in cells, ultimately leading to cell death. While oxidative stress therapies hold promise, their pro-oxidant nature requires careful consideration in therapy development. Chapter 1 introduces NTP, while Chapter 2 explores its potential as a selective treatment for glioblastoma and melanoma. The results reveal that various experimental factors can influence outcomes, making selectivity assessment challenging. However, lower NTP doses show promise in selectively targeting cancer cells. Chapter 3 investigates the stability of long-lived RONS in clinically relevant solutions, emphasizing the importance of understanding NTP-derived RONS behavior for reliable clinical applications. Chapter 4 delves into cell death pathways activated by NTP, demonstrating its potential to induce multiple forms of cell death, reducing the risk of resistance development. Chapter 5 shifts focus to the drawbacks of oxidative stress-inducing therapies, revealing that high NTP doses can enhance metastatic potential, while low doses have minimal impact on cancer cell migration. This underscores the need to optimize NTP parameters for effective treatment with minimal side effects. In summary, the thesis emphasizes the importance of optimizing NTP treatment parameters. While high NTP doses show strong cytotoxic responses, low repetitive NTP treatments have clinical potential by selectively targeting cancer cells without increasing metastatic potential. However, this approach may be limited to superficial tumors, requiring supplementary surgical interventions for deeper tumors. Chapter 6 concludes by highlighting challenges and future prospects for NTP treatment in cancer therapy.

Hannelore Peeters

• 20/10/2023
  
• 09.00 a.m.
• Venue: Stadscampus, Klooster van de Grauwzusters, Promotiezaal
• ​Online PhD defence
• Supervisors: Sammy Verbruggen & S. Lenaerts
• Department of Bioscience Engineering

Abstract

Surface fouling is an aesthetic and economic problem that can be helped by photocatalytic self-cleaning coatings. This research successfully develops and characterises a plasmon-embedded titania thin film that can act as a self-cleaning coating, effectively degrading organic fouling on construction materials such as window glass. Photocatalytic processes use light to enhance chemical reactions, in this case the oxidation of organic contaminants. Titania is a commonly used photocatalyst since it is abundantly available, well-characterised, cheap and non-toxic. However, it needs UV light to be activated, causing poor activity under sunlight as UV comprises <5% of the solar spectrum at the Earth's surface. Plasmonic nanoparticles (NPs) are nanosized metallic particles that interact with light of different wavelengths, depending on their size, shape and material. Here, gold, silver and bimetallic gold-silver NPs are used as they show surface plasmon resonance (SPR) under visible light. SPR enhances a photocatalyst in a variety of manners. (i) Near-field enhancement creates an enhanced magnetic field close to the NP, which improves charge carrier separation of the photocatalyst, preventing early recombination without a degradation reaction. (ii) The excited plasmonic electrons can be injected directly into the conduction band of the photocatalyst, activating the photocatalyst with visible light. Embedding the NPs in the photocatalytic layer establishes the close contact needed for these phenomena. It also protects the NPs from chemical corrosion and agglomeration. The novel coating method with different NPs of Au, AuAg (1:1) and Ag is tested using ISO standards for water, air purification, antibacterial and self-cleaning activity both under UV and simulated light. From these tests, it is clear that the novel coating outperforms commercial photocatalytic self-cleaning glass PilkingtonActivTM on all applications for both light sources. Benchmarking experiments show that the novel coating also outperforms industrial self-cleaning and hygienic surfaces. Despite the need for standardised tests to compare different materials, the executed ISO standards show some substantial drawbacks for testing different photocatalytic materials. The benefits and drawbacks of these standards are extensively discussed, including improvements and alternatives. To improve the compatibility of the coating with industrially relevant materials, the coating method was adapted to omit high temperature calcination. Low temperature acid crystallisation shows to be an interesting alternative to successfully coat heat-sensitive materials and activate them both with UV and solar light.

Ilenia Serra

• 18/10/2023
  
• 2 p.m.
• Venue: Campus Drie Eiken, R.109
• Supervisors: Sabine Van Doorslaer & Inés García-Rubio
• Department of Chemistry

Abstract

Chlorite dismutases (Clds) are heme b-containing oxidoreductases of bacterial origin which degrade chlorite to form chloride and molecular oxygen. This unique enzymatic activity was originally found in perchlorate- and chlorate-reducing bacteria, where Clds act as scavenging systems for the toxic chlorite produced during the respiration. In addition to their intriguing reactivity – the formation of an O-O bond was formerly described only for oxygenic organisms and in a methano-oxidizing bacterium – chlorite dismutases raised interest for their potential industrial applications, such as in the field of bioremediation, construction of biosensors and as a tool to improve aeration in bioreactors, to cite a few.

This work is principally focused on the study of the dimeric chlorite dismutase from Cyanothece sp. PCC7425 (CCld) to gain insights into different enzyme properties, including the role of key amino acids in the heme surroundings, modes of ligand binding and mechanistic details. The integration of different approaches, including site-directed mutagenesis, structure determination, activity and stability assays, was necessary to elucidate the investigated aspects. The project can be viewed as a combination of three main research questions: i) the role(s) of a conserved arginine residue situated at the distal side of the heme iron and the impact of its flexibility on different enzyme properties; ii) the mechanism of substrate binding and the influence of the arginine in this aspect; iii) the nature of the intermediate states formed during the catalytic cycle and their dependency on pH. Exploiting the paramagnetic nature of the ferric heme iron, either in the resting state of the enzyme, or upon ligand binding and in reaction with the substrate(s), electron paramagnetic resonance (EPR) spectroscopy was chosen in this work as a principal approach to address these questions. In addition to that, preliminary experiments of enzyme immobilization in different materials were performed, with the scope of expanding the chlorite dismutase potential for industrial usages.

Overall, this work aimed at gaining a comprehensive understanding of the molecular determinants of chlorite dismutases’ peculiar reactivity, using an integrative structural biology approach, where EPR spectroscopy proved to be a valuable technique to obtain information about the heme-containing active site of CCld. ​ ​

Wito Van Oijstaeijen

• 17/10/2023
  
• 3.30 p.m.
• Venue: Stadscampus, S.M.005
• Supervisors: Steven Van Passel & Jan Cools
• IMDO

Abstract

Climate change is an ever-increasing threat to our planet, with the urbanisation of previously open spaces exacerbating the issue. The loss of open space leads to a decrease in ecosystem services, which negatively impacts the liveability in urbanised environments, and beyond. The incorporation of green infrastructure (GI) into the built environment is acknowledged as an effective and multi-functional measure to make our living environment resilient and future-proof. ​ ​

Notwithstanding that the local level is essential for effective GI implementation, research into local decision making is very limited. This thesis therefore aims to address two significant gaps in the implementation of GI. The first objective is to bridge the science-policy gap by integrating scientific knowledge on ES and GI into local decision-making processes. In this context, the policy dimension within this thesis involves the process of translating overarching policy objectives into practical actions within local decision-making practices, abstracting from the intricacies of higher-level policymaking itself. The second objective focuses on the people-policy gap, which involves understanding stakeholders' perspectives and priorities regarding GI and its associated ecosystem services. Through stated preference valuation techniques (discrete choice experiments and a best-worst scaling experiment), multi-stakeholder GI perceptions are gathered. Finally, a novel tool to GI valuation is developed, acknowledging the different stakeholder views and building on the insights of collaborative tool development and design. By gaining insights into the demand, prioritisation, and provision of GI from the two most important stakeholder groups at the local level (residents and local decision-makers), this research aims to foster effective communication and alignment between public preferences and policy implementation. Ultimately, addressing these gaps will contribute to more informed planning and decision-making practices related to green infrastructure. The overall goal of this thesis is to enhance the uptake of GI knowledge in the local decision-making context, proposing pathways to facilitate and optimise investments in public GI. ​ ​

Matthias Hutsebaut-Buysse

• 11/10/2023
  
• 4 p.m.
• Venue: Campus Middelheim, A.143
• ​Online PhD defence
• Supervisor: Steven Latré
• Department of Computer Science

Abstract

Artificial Intelligence (AI) has seen tremendous successes in the past few years. These breakthroughs have, however, mainly been situated in the areas of Computer Vision (CV) and Natural Language Processing (NLP). Breakthroughs in these areas have been fuelled by the abundance of large internet datasets containing huge amounts of nicely labeled examples.

Unfortunately, this dataset approach is not very well suited for other types of tasks such as navigation tasks (e.g., navigating towards a set of coordinates, or searching for an object in an unknown environment). Navigation systems need to interact with often noisy environments which are often hard to model in terms of clean input/output labels. ​ ​

Reinforcement Learning (RL) offers an alternative learning paradigm, which allows an AI system to obtain its own dataset through direct interaction with the environment. Unfortunately, RL is still plagued with its own set of problems. One major limitation of RL is its sample inefficiency. Currently, an RL-based approach needs large amounts of interactions with its environment in order to learn a satisfying behaviour. This makes it impractical to utilise RL in real-world environments, and most often requires RL practitioners to train agents in simulated versions of the environment. It is however in most cases not straightforward how to utilise agents trained in simulation in the real world.

In this thesis, we propose a number of novel approaches which are able to increase the sample efficiency of RL approaches. This is done through working on multiple levels of abstraction, and through adapting prior related behaviours.

Abul Hasnat Rubel

• 10/10/2023
  
• 12 p.m.
• ​Online PhD defence
• Supervisor: Milorad Milosevic
• Department of Physics

Abstract

Using state-of-the-art simulation methods, we optimized the performance of nanoscale superconducting scanning probe tips for advanced spatial imaging of magnetic fields. The systematic studies of the tips’ static properties as a function of the tilted magnetic field, geometric parameters, and material parameters were carried out. The sensitivity of different superconducting quantum interference devices (SQUIDs) to the magnetic field emanating from the magnetic nanoparticle, where the location of a magnetic nanoparticle is considered below the primary loop's center, was examined as a function of the primary and secondary loop dimensions. The main objective of the research was to characterize and optimize the performance of a nano-sized SQUID-on-tip (SOT) device. Optimal SOT sensitivity was sought, for different loop sizes, arm linewidth, and lead dimensions. Moreover, we revealed that a constriction in the loop arms of the SOT can substantially improve the sensitivity of the device. Finally, the properties of the theta-SOT device were examined in the presence of in-plane and out-of-plane magnetic field components, enabling nanoscale imaging of 3D distributions of the magnetic field. Altogether, the obtained results deliver an engineering solution for the optimum performance of the SOT device in desired conditions.

Prakash Kumar Sahoo

• 02/10/2023
  
• 4.30 p.m.
• Venue: Campus Drie Eiken, Aula R2
• Supervisors: Shoubnik Das & Bert Maes
• Department of Chemistry

Abstract

The employment of costly, single-use catalysts, highly toxic reagents/reactants, and solvents is still a major problem within synthetic chemistry. Therefore, it becomes difficult for pharma industries to reduce the price as well as environmental toxicity. In this regard, ample attention needs to be given to the chemical community to replace them with inexpensive, abundant, benign, and reusable substitutes. The goal of this doctoral thesis was to contribute towards the sustainable development of novel synthetic methodologies for the synthesis and functionalization of pharmaceutical molecules and natural products using metal-free homogeneous and sustainable, single-atom-doped heterogeneous photocatalysis. ​ 

The research described in this thesis can be divided into four chapters. In the first chapter, we have shown the development of a robust, cost- and energy-efficient strategy to introduce diverse nucleophiles, including alcohols, carboxylic acids, and amines, via the functionalization of benzylic C−H bonds of simple aromatic building blocks as well as complex drug molecules and natural products. The second chapter demonstrates a redox-neutral decarboxylative radical polar crossover process for the synthesis of linear aliphatic amines using 4CzIPN as an organo-photocatalyst. The synthetic utility of this method is further demonstrated by the late-stage functionalization of pharmaceuticals as well as the synthesis of drug compounds. In the third chapter, a Mn metal-doped g-c3n4 heterogeneous photocatalyst has been developed to achieve the vicinal dichlorination of alkenes using N-Chlorosuccinamide as a chlorinating agent. Noteworthily, both unactivated and activated alkenes provide good to excellent yields with mild reaction conditions. Interestingly, nine pharmaceutical compounds have been functionalized with our system to prove the synthetic applicability of our method. Finally, the fourth chapter demonstrates a Mn metal-doped heterogeneous photocatalytic method for the selective para-chlorination of alkenes using N-chlorosuccinamide as a chlorinating agent. Mostly electron-rich aromatics worked in this system. ​ ​

Overall, the thesis contributes to the pharmaceutical industry by developing different methodologies that can selectively functionalize specific positions of complex pharmaceutical molecules with functional groups like amine, ether, ester, and chlorine in the presence of both homogeneous and single-metal-atom-doped heterogeneous photocatalysts using a mild photo-redox system. ​ ​

Kaimin Zhang

• 21/09/2023
  
• 4 p.m.
• Venue: Campus Drie Eiken, O.01
• ​Online PhD defence
• Supervisors: Vera Meynen & Sammy Verbruggen
• Department of Chemistry

Abstract

Grafting organophosphonic acids modification (PAs) on metal oxides has shown to be a flexible technology to tune the surface properties of metal oxides for various applications. Nevertheless, there are still puzzles that need to be addressed, such as the correlations between metal oxides properties (types of surface reactive sites) and the modification (modification degree), the correlations between metal oxides properties and the properties of modified surfaces. Moreover, the currently used liquid-phase method for the grafting has associated impeding effects of solvent on tailoring the modification degree, and also causes the formation of metal phosphonate side products. The solid-phase method can induce the unwanted changes in crystal phase of supports. Based on these questions, the three titania supports with divergent surface properties were selected as the metal oxides supports investigated, propylphosphonic acid (3PA) modification was carried out under the same synthesis conditions: four different concentration, two solvents (water or toluene), and one reaction time (4 h) and temperature (90 ℃). MeOH chemisorption was introduced to probe the surface (un)reactive sites for 3PA modification. On the other hand, MeOH chemisorption and inverse gas chromatography (IGC) were combined to characterize the changes in surface polarity and acidic properties induced by the modification. Next, a solid-phase method, manual grinding, was proposed to graft 3PA on titania, avoiding the impeding effects of solvent on improving modification degree and the formation of the titania phosphonate side products, as well as preserving the crystal phase. The results indicate that methanol chemisorption can qualitatively analysis the surface active sites that are consumed by 3PA modification, its chemisorption capacity shows the consistent trend with the maximum modification degree, hereby revealing the kinds of interactions that are important in controlling surface coverage. Titania supports is found to play an important role in changes in surface polarity and acidic properties by charactering the three modified titania samples at a similar modification degree using methanol chemisorption coupled with in-situ infrared and thermogravimetric-mass spectrometer, and IGC. Moreover, IGC provides additional information about the changes in binding modes. Furthermore, grafting 3PA modification on titania was achieved by manual grinding. Compared to the liquid-phase method, the maximum modification degree obtained by the manual grinding is 25 % higher while using 83.3 % or 75.0% lower amount of expensive 3PA and limiting the formation of titania phosphonate side products. Compared to the reactive milling method, the proposed manual grinding method preserves the crystal phases of titania.

Tess Ysebaert

• 20/09/2023
  
• 4 p.m.
• Venue: Campus Drie Eiken, O.02
• Supervisors: Siegfried Denys & Roeland Samson
• Department of Bioscience Engineering

Abstract

Exposure to air pollution, such as particulate matter (PM), causes adverse health effects. Particularly in cities, high levels of PM are measured, and urban green infrastructure is being considered as a solution. Plants hinder airflow and remove PM from the air by dry deposition on their leaves. Here, green walls offer significant advantages over other urban green infrastructure because they can grow on the large available wall surface without impeding natural air circulation. The objective of this PhD was to develop a method for assessing PM removal by green walls, based on predictive models and based on relevant parameters determined experimentally.

The aerodynamic effect of climbing plants was investigated with a wind tunnel and the aerodynamic resistance was found to depend on the plant species, leaf area density and wind speed. Plants with small, complex leaves exhibited more aerodynamic drag. The pressure and velocity measurements obtained were then used to optimise viscous and form drag resistance in a Computational Fluid Dynamics model. It showed that air resistance of plants should be modelled wind speed dependent. ​ ​

Next, PM deposition on green walls was studied in a wind tunnel setup with accurate devices for PM generation and measurement. The collection efficiency of Hedera helix was found to depend on particle size and wind speed, with larger particles being removed more efficiently and higher wind speeds being favourable. However, humidity and PM type had no significant influence. The research developed an optimised deposition model for PM, taking into account the different deposition mechanisms. The developed model allows mapping and even optimising the impact of green walls on PM concentrations at specific locations. ​ ​

In addition, Living Wall Systems (LWS) from different manufacturers were tested for their ability to retain PM. Some LWS systems were effective in reducing PM concentrations, while others increased concentrations. This emphasised the importance of careful selection of LWS plant species and supporting systems. In addition, the study included measurements of deposited PM on leaves and supporting system of LWS using the Saturation Isothermal Remanent Magnetization technique, which measures magnetisable PM. Plants with smaller and thicker leaves picked up more PM. ​ ​

The deposition model developed was tested in an urban model of a street canyon, in which a green wall was introduced. This model showed significant PM reduction, although it represented an optimal scenario. Overall, this research provides valuable insights for designing healthy and sustainable cities using green walls as a science-based solution for PM reduction.

Niels Van Brempt

• 18/09/2023
  
• 4 p.m.
• Venue: Campus Groenenborger, U.025
• Supervisors: Sabine Van Doorslaer & Luc Moens
• Department of Physics

Abstract

Globins are versatile proteins widespread throughout life, with many biologically relevant functions aside from oxygen binding and transport, such as involvement in redox signaling, NO metabolism, and reproduction. This thesis primarily focuses on the globin domain of globin 33 (GLB-33GD) and globin 3 (GLB-3), which are among the 34 globin genes expressed in the nematode C. elegans. Additionally, the protoglobin of Methanosarcina acetivorans (MaPgb) is investigated. Special emphasizes was brought to the interaction between these globins and reactive nitrogen species.

Valuable information on ligand binding properties and different spin and ligation states is obtained by the in-depth analyses of a plethora of spectroscopic methods applied on globin solutions under varying experimental conditions. First, an in-depth spectroscopic study of GLB-33GD was conducted at varying pH levels, under nitrite-rich conditions. Additionally, a detailed investigation of the globin domain is presented using electron paramagnetic resonance (EPR) spectroscopy; first, in the absence of nitrite, in its ferric hydroxide-ligated state and secondly, in the ferrous NO-bound state, an important reaction product in the extremely fast nitrite reductase activity GLB-33GD is known to exhibit in vitro. The results from both chapters are linked with a discussion on the role of amino acid Arg E10 in the process and its impact on the nitrite binding mode at the heme iron. The focus then shifts to the ferric MaPgb, where its peculiar electronic state was shown spectroscopically, together with its NO-binding capacity. Kinetic analyses using UV-vis and spin-trap EPR spectroscopy reveal a high preference for NO binding over nitrite binding, with limited evidence of a potential nitrite dismutase activity of the globin. In a last chapter, attention is directed toward the first characterization study of the cysteine-rich GLB-3. The experimental optimization to determine the redox potential of this unique globin is outlined, along with initial enzymatic tests revealing limited reactivity towards small molecules and a strong bis-histidine coordination of GLB-3.

Overall, this thesis contributes to our understanding of globins and their interactions with nitrite and NO from a spectroscopic perspective, emphasizing the importance of the unique heme pocket structure on globin function and enhances our overall understanding of these crucial proteins and their biochemical properties.

Steven De Meyer

• 15/09/2023
  
• 4 p.m.
• Venue: Campus Middelheim, A.143
• Supervisor: Koen Janssens
• Department of Chemistry

Abstract

Scientific research into cultural heritage has significantly grown in importance over the past decades. The growing popularity of macroscopic imaging techniques such as X-ray fluorescence or Fourier transform infrared now means that conservators and restorers have access to highly objective information on the chemical composition of a painting without the necessity for destructive sampling. As many works of art are heterogeneous on the macroscopic scale, it is clear that solely relying on microscopic samples does not provide sufficiently representative information on the condition of a painting and that macroscopic imaging techniques should be considered a crucial part of the analytical toolkit for conservation science.

The goal of this research has been to investigate the added value of reflection-mode macroscopic X-ray powder diffraction (MA-XRPD) for scientific and art historical investigations of cultural heritage artefacts. A prototype scanner was developed after careful consideration of the individual components. This mobile instrument allows for the analysis of flat objects such as oil paintings with reflection MA-XRPD. In this manner images can be obtained that show the distribution of crystalline components present at the surface of the stratigraphy. These crystalline materials can originate from different sources and include original pigments and non-original pigments.

MA-XRPD offers novel insights into original pigments such as ultramarine, copper sulfates and lead white. In Girl with a Pearl Earring by Vermeer the MA-XRPD instrument was used to prove that Vermeer used multiple subtypes of lead white to achieve subtle optical effects while in the painting The Night Watch by Rembrandt the lead white composition was studied in detail; multiple rare lead-based compounds were identified that could be linked to the usage of specific driers in the oil paint. By investigating the presence of degradation products, MA-XRPD can be used to assess the conservation state of an artwork. Secondary alteration products were identified in paintings by Nellius and Mignon, explaining why the paintings had visually deteriorated over time. MA-XRPD registered the presence of lead arsenates which were formed from the original yellow arsenic-based orpiment. By combining microscopic and macroscopic analysis, a chemical degradation pathway for the conversion of the unstable orpiment pigment was proposed. In this manner, MA-XRPD can also be used to provide highly valuable information for conservators and restorers by pinpointing areas that have undergone degradation and to guide sampling campaigns. ​ ​

Ritam Raha

• 12/09/2023
  
• 2 p.m.
• Venue: Campus Middelheim, G.010
• Supervisors: Guillermo Perez & Nathanael Fijalkow
• Department of Computer Science

Abstract

 In the past decade, there has been an unprecedented rise in the incorporation of cyber-physical systems used to perform complex tasks. Verifying these systems is necessary to ensure their safety and reliability, especially in safety-critical scenarios. Formal verification has been proven to be a time-tested method to systematically verify these systems. In particular, it provides techniques for monitoring system executions against a formal specification. Temporal logic has gained popularity as a formal specification due to its mathematical rigour, human interpretability, and compatibility with various formal verification techniques. But, often, these specifications are hard to design manually, necessitating a need to automatically generate them from system executions. The objective of this thesis is twofold: (i) Develop algorithms to automatically learn temporal specifications from system executions; (ii) Apply formal verification techniques to assess the correctness of the system against the acquired specifications.

To achieve these objectives, in the learning part, we present two algorithms to learn specifications in temporal logics such as LTL, MTL, and STL. We present a dynamic programming-based algorithm for LTL specifications that leverages a normal form for a fragment of LTL and uses efficient enumeration techniques to learn concise formulas from system executions. For MTL and STL, we develop SMT-solver-based techniques to learn formulas that are not only concise but also efficient to be applied for formal verification of the system. Our algorithms are implemented in tools called SCARLET and TEAL, and their efficiency is demonstrated through experimental results. In the verification part, we focus on the LTL parameter-synthesis problems of one-counter automata, one of the fundamental formal models to represent complex systems, namely systems with discrete yet infinite state space.

One-counter automata are obtained by extending classical finite-state automata with a counter whose value can range over non-negative integers and be tested for zero. The updates and tests can be further made parametric by introducing a set of integer-valued variables called parameters. The LTL parameter-synthesis problem asks whether a valuation of the parameters exists such that all runs of the automaton satisfy an LTL specification. In this work, we show that (i) this problem is encodable into a decidable restriction of Presburger Arithmetic with Divisibility (PAD), (ii) the parameter synthesis problem is decidable, and in 3NEXP; (iii) the problem is in EXPSPACE where parameters can only be used in counter tests.

Guner Muarem

• 05/09/2023
  
• 5 p.m.
• Venue: Campus Middelheim, A.143
• Supervisors: Sonja Hohloch & David Eelbode
• Department of Mathematics

Abstract

The CCR (canonical commuting relation) and CAR algebras (canonical anticommuting relation) are fundamental algebras in theoretical physics used for the study of bosons and fermions. From a mathematical viewpoint, these algebras are named the Weyl algebra (or symplectic Clifford algebra) and Clifford algebra. These algebras can be constructed in a very analogous way. The Clifford algebra is constructed on a vector space equipped with a symmetric bilinear form, whereas the Weyl algebra requires an even dimensional vector space equipped with a skew-symmetric bilinear form (or symplectic form). There is, however, a fundamental difference: the Clifford algebra is finite-dimensional, whereas the Weyl algebra is infinite-dimensional. Using the generators of the Clifford (resp. Weyl) algebra, one can associate a natural first order spin (resp. metaplectic) invariant differential operator by contracting the Clifford algebra elements using the bilinear form (resp. the symplectic form) with derivatives. The theory which studies the solutions of the Dirac operator is known as Clifford analysis and can be seen as a hypercomplex function theory. In the first part of the thesis, we will study the symplectic Dirac operator, from an orthogonal point of view. By this we mean that we will focus on the subalgebra so(m), as this will allow us to derive branching rules for the space of k-homogeneous polynomial solutions for the symplectic Dirac operator. To arrive at this result we use techniques from representation theory, including the notion of transvector algebras and tensor products of (Verma modules). In addition, we provide the foundations of what we will call a 'hermitian variant' of symplectic Clifford analysis, where we incorporate the additional datum of a compatible complex structure and study the associated solution space using algebraic techniques and arrive at a Fischer decomposition.

In the second part of the thesis, we provide tools to study the dynamics of point vortex dynamics on the complex projective spaces and the six-dimensional flag manifold. These are the only Kähler twistor spaces arising from 4-manifolds. We give an explicit expression for Green's function on the projective space which enables us to determine the Hamiltonian (the energy of the system) and the equations of motions for the point vortex problem. Moreover, we determine the momentum map on the flag manifold, which is a key ingredient in understand the dynamics better.

Lingjuan Li

• 05/09/2023
  
• 3 p.m.
• Venue: Campus Drie Eiken, O.01
• ​Online PhD defence​
• Supervisors: Erik Verbruggen, Ivan Nijs & Gerrit Beemster
• Department of Biology

Abstract

Climate change is causing alterations in precipitation patterns, leading to adverse ecological consequences in many ecosystems. Recently, an increasingly persistent weather pattern has emerged, characterized by lengthening the duration of alternating dry and wet periods, which is more complex than exclusively drought or increasing precipitation. It is currently unclear how soil microbial communities respond to these new regimes in relation to their interactions with plants.

In this thesis, we explored responses of soil bacterial and fungal communities to increasing weather persistence in rainforests and grasslands, using high throughput sequencing technology. We investigated the resistance and resilience of microbial communities to prolonged drought in a mature seasonal tropical rainforest which experiences unusually intensive dry seasons in the current century. Rain exclusion prolonged the dry season by five months. Results show moderate resistance to prolonged drought, but quick recovery of microbial communities once the drought ended, indicating high resilience. To further investigate the ecological roles of soil microbial communities in response to increasing weather persistence, we set up grassland mesocosm experiments. In these experiments, precipitation frequency was adjusted along a series, ranging from 1 to 60 consecutive days alternating of dry and wet periods, while keeping the total precipitation constant. Our results show that microbial community assembly tended to be more stochastic processes at intermediate persistence while more deterministic processes dominated at low and high persistence within 120 days regime exposure. Moreover, more persistent precipitation reduced the fungal diversity and network connectivity but barely impacted that of bacterial communities. The soil microbial legacy induced by soil microbial communities subjected to prior persistent weather events was more enduring in subsequent fungal communities than bacterial communities, likely due to the slower growth of fungi compared to bacteria. However, a minor effect of soil microbial legacy was observed on plant performance. The dissimilarities of microbial communities between the first and second year were less with more persistent precipitation, potentially resulting in more vulnerable microbial communities due to some taxa disappearing and a reduction in functional redundancy under more persistent weather.

Low threshold translation: meaning/potential for society in English: This thesis offers a thorough theoretical grasp of how soil microbial communities react to both present and upcoming climate changes. It aids in forecasting and handling the impacts of future climate shifts on ecosystems guided by microbial communities.

Hamideh Hassani

• 04/09/2023
  
• 2.30 p.m.
• Venue: University of Liège, Amphithéâtre 142 (Petits amphithéâtres), Bât. B7b, au Sart Tilman
• ​Online PhD defence
• Supervisors: Bart Partoens (University of Antwerp) & Philippe Ghosez (University of Liège)
• Department of Physics

Abstract

This thesis concerns the fundamental understanding of polarons, which consist of quasiparticles emerging in materials from the interaction of extra charge carriers with the atomic lattice. Here, we focus on WO₃, an emblematic polaronic compound. Relying on first-principles calculations, we show that the intriguing medium-size polarons in its monoclinic phase do not fit with previous standard models but instead arise from the undoing of distortive atomic motions inherent to that phase, which lowers the bandgap through dynamical covalency effects. This finding leads us to introduce the new concept of anti-distortive polaron, further validated through a simple quantum-dot model. The study also delves into polaron-polaron interactions, revealing the formation of antiferromagnetic W⁵⁺-W⁵⁺ bipolaronic states with an energy lower than the W⁴⁺ state. This thesis does not only provide a comprehensive understanding of polarons in WO₃, which connects to its remarkable superconducting and chromic properties, but also opens new perspectives for the rational and fine tuning of the polaronic state. It also connects to the appearance of different kinds of polarons in multifunctional displacive perovskites and provides guidelines for tracking a similar behavior in other families of compounds.

Leonora Podvorica

• 30/08/2023
  
• 9-11 a.m.
• Venue: University of Torino
• ​Online PhD defence
• Supervisors: Sabine Van Doorslaer (University of Antwerp) & Mario Chiesa (University of Torino)
• Department of Chemistry

Marco Zaninelli

• 24/08/2023
  
• 4.30 p.m.
• Location: Campus Middelheim, G.010
• Supervisor: Karim Johannes Becher
• Department of Mathematics

Abstract

In this dissertation we develop algebraic techniques to compute upper bounds for the number of squares necessary to represent a sum of squares in a field. In particular, we obtain an upper bound for the number of squares necessary to represent products of positive definite real quadratic forms as sums of squares of fractions of forms. We also provide a wide range of methods to compute upper bounds for the Pythagoras number of a field, that is, the minimal number of squares necessary to represent all sums of squares in the field. Among these methods is a local-global principles for rational function fields, for which we give a new argument, and the real holomorphy ring of a field, which we study thoroughly. These provide alternative proofs to renowned results of Y. Pourchet and F. Pop's works about the Pythagoras number of function fields in one variable over the rational numbers. Finally, we provide a novel way to compute upper bounds for the Pythagoras number of a field possessing a finite number of valuations with certain properties, which applies to an ample range of situations.

Lennert Verboven

• 23/08/2023
  
• 3 p.m.
• Venue: Campus Drie Eiken, Q0.02
• Supervisors: Kris Laukens & Annelies Van Rie
• Department of Computer Science

Abstract

Information technology in health care aims to increase the quality of health services by digitizing patient data and automating and integrating health care applications. Clinical decision support systems aim to aid health care professionals in their decision-making process by combining all available patient data stored in their electronic health records with clinical knowledge to generate patient specific individualized recommendations informing treatment, diagnosis, and prognosis. Clinical decision support systems are becoming more prevalent in high income countries, but also hold the potential to facilitate treatment individualization in low- or middle- income settings with limited access to evolving medical knowledge at the primary point of care.

The application of information technology to the management of drug resistant tuberculosis is a prime example of the impact a clinical decision support system on the health care system given the high burden of drug resistant tuberculosis in low-income countries, the increasing usage of whole genome sequencing technologies for Mycobacterium tuberculosis (Mtb), the complexity in composing the optimal individualized treatment regimen, and the low level of training for many of the primary care health care workers caring for patients suffering from drug resistant tuberculosis. We first developed the XBS (complex Bacterial Samples) bioinformatics variant calling core, able to correctly and confidently identify variants in less than perfect clinical samples. Based upon the XBS variant calling core we developed the highly portable and comprehensive maximum accessible genome for Mtb analysis (MAGMA) pipeline. The MAGMA pipeline provides a wide range of analyses, facilitating precision medicine, drug resistance surveillance, and precision public health. The MAGMA pipeline therefore perfectly fills the need for a Mtb analysis pipeline useable high-burden, low-income clinical practice settings with limited (bio-)informatics experience.

Based upon a patient’s WGS based resistance profile, treatment should be individualized to ensure an effective treatment regimen. However, treatment individualization is a difficult process requiring up to date knowledge on drug toxicity, drug effectiveness, and drug-drug interactions. Given the scarcity of such knowledge at primary care facilities in high-burden, low-income countries treatment is rarely individualized. We therefore developed a user-friendly machine learning based hybrid data- and knowledge-driven treatment recommender clinical decision support system capable of recommending the optimal treatment for patients with complex resistance profiles, allowing the patients to benefit from the scientific advancements made.

Omar Biondo

• 03/07/2023
  
• 1.30 p.m.
• Venue: Atlas Building, room 0.710, TU/e campus, Eindhoven (NL)
• ​Online PhD defence
• Supervisors: Annemie Bogaerts & Gerard van Rooij
• Department of Chemistry

Abstract

Plasma-based CO2 conversion is worldwide gaining increasing interest. The aim of this work is to find potential pathways to improve the energy efficiency of plasma-based CO2 conversion beyond what is feasible for thermal chemistry. To do so, we use a combination of modeling and experiments to better understand the underlying mechanisms of CO2 conversion, ranging from non-thermal to thermal equilibrium conditions. Zero-dimensional (0D) chemical kinetics modelling, describing the detailed plasma chemistry, is developed to explore the vibrational kinetics of CO2, as the latter is known to play a crucial role in the energy efficient CO2 conversion. The 0D model is successfully validated against pulsed CO2 glow discharge experiments, enabling the reconstruction of the complex dynamics underlying gas heating in a pure CO2 discharge, paving the way towards the study of gas heating in more complex gas mixtures, such as CO2 plasmas with high dissociation degrees.

Energy-efficient, plasma-based CO2 conversion can also be obtained upon the addition of a reactive carbon bed in the post-discharge region. The reaction between solid carbon and O2 to form CO allows to both reduce the separation costs and increase the selectivity towards CO, thus, increasing the energy efficiency of the overall conversion process. In this regard, a novel 0D model to infer the mechanism underlying the performance of the carbon bed over time is developed. The model outcome indicates that gas temperature and oxygen complexes formed at the surface of solid carbon play a fundamental and interdependent role. These findings open the way towards further optimization of the coupling between plasma and carbon bed.

Experimentally, it has been demonstrated that “warm” plasmas (e.g. microwave or gliding arc plasmas) can yield very high energy efficiency for CO2 conversion, but typically only at reduced pressure. For industrial application, it will be important to realize such good energy efficiency at atmospheric pressure as well. However, recent experiments illustrate that the microwave plasma at atmospheric pressure is too close to thermal conditions to achieve a high energy efficiency. Hence, we use a comprehensive set of advanced diagnostics to characterize the plasma and the reactor performance, focusing on CO2 and CO2/CH4 microwave discharges. The results lead to a deeper understanding of the mechanism of power concentration with increasing pressure, typical of plasmas in most gases, which is of great importance for model validation and understanding of reactor performance.

Katlijn De Meulenaere

• 28/06/2023
  
• 4 p.m.
• Venue: Institute of Tropical Medicine Antwerp - Campus Rochus, Aula Janssens
• ​Registration form
• Supervisors: Kris Laukens & Anna Rosanas-Urgell

Abstract

Malaria is among the most impactful infectious diseases globally, and is caused by protozoan parasites of the genus Plasmodium. Plasmodium vivax is the second most important cause of human malaria, mainly affecting non-African countries. Despite the global health impact of P. vivax, our understanding of its unique biology is severely limited due to the lack of a long-term in vitro culture system. The goal of this thesis was to gain a better understanding of the P. vivax reticulocyte invasion process and the involved receptors and ligands, which are interesting targets for drug and vaccine development. To overcome the absence of a culture system, we combined several wet and dry lab approaches, and placed a particular focus on next-generation sequencing as a new avenue to study the invasion process.

First, we demonstrated that the red blood cell surface protein band 3 is a novel invasion receptor, through short-term culturing of field isolates from P. vivax patients in presence of band 3-blocking agents or Southeast Asian ovalocytosis red blood cells (mutated band 3). Transcriptome analysis of those same P. vivax isolates resulted in a list of potential band 3 ligand candidates, which was highly enriched in PvTRAg genes. In addition, we showed that presence of a PvTRAG38 peptide partially inhibited P. vivax invasion into reticulocytes. To further investigate the role of the PvTRAG38 in invasion, we made use of P. knowlesi models, as this species can be long-term cultured and is closely related to P. vivax. Using CRISPR/Cas9 genome editing, the PvTRAg38 ortholog (PkTRAg38.3) was tagged and knocked out to characterise its transcriptional timing and function. We found that PkTRAg38.3 was schizont-expressed, and that disruption of this gene resulted in an average growth defect of 15.5% over 2 blood cycles, supporting a role as invasion ligand. ​ ​

Finally, we developed tools and protocols to facilitate the generation and analysis of P. vivax sequencing data in future studies. Through low-input PacBio sequencing of a Peruvian P. vivax field isolate, the first high-quality reference genome for South-American isolates was assembled, called PvPAM. In addition, we successfully used the Nanopore adaptive sampling feature to enrich parasite DNA 4- to 6-fold during the sequencing run, thereby circumventing time-consuming and complex lab procedures to remove the predominant human DNA.

Wim Cuypers

• 23/06/2023
  
• 3.30 p.m.
• Venue: Campus Drie Eiken, O.02
• Supervisors: Kris Laukens & Sandra Van Puyvelde
• Department of Computer Science

Abstract

Salmonella is primarily known as a human pathogen responsible for gastroenteritis. Additionally, certain Salmonella strains pose a severe threat by causing life-threatening bloodstream infections. The emergence of antimicrobial resistance (AMR) in Salmonella has become a critical global concern.

The aim of this doctoral research was to investigate the genomic adaptations of Salmonella associated with AMR and explore the transcriptomic changes linked to host adaptation. Initially, we reviewed the literature on fluoroquinolone resistance (FQR) in Salmonella, and showed that the Salmonella Typhi H58 clade hampers the efficacy of fluoroquinolone treatment for typhoid fever in Asia. A greater diversity of plasmid-mediated quinolone resistance mechanisms was observed in non-typhoidal Salmonella compared to typhoidal Salmonella, likely due to the diverse host niche. Limited whole-genome sequencing (WGS) data on FQR in invasive non-typhoidal Salmonella (iNTS) were found, despite the high burden of iNTS in sub-Saharan Africa. ​ ​

Subsequently, we conducted a WGS study of Salmonella Concord (S. Concord). This pathogen is predominantly associated with gastroenteritis and bloodstream infections in individuals from Ethiopia and Ethiopian adoptees and exhibits remarkably high levels of AMR. By analysing the genomes of 284 historical and contemporary S. Concord isolates collected from 1944 to 2022, we revealed that S. Concord is a polyphyletic serovar, with isolates belonging to three Salmonella super-lineages. Within super-lineage A, eight lineages were identified of which four were linked to Ethiopia and demonstrated high levels of AMR to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. Using long-read sequencing, we uncovered a patchwork of horizontal gene transfer events in regions harboring AMR genes present on structurally diverse IncHI2 and IncA/C2 plasmids and/or chromosomal islands. ​ 

Finally, we re-implemented the iterative comparison of gene co-expression method using the R programming language to assess the extent of gene co-expression conservation between two gene expression datasets. We further investigated the gene co-expression patterns between two S. Typhimurium strains, including a strain representative of S. Typhimurium ST313 from sub-Saharan Africa. Minimal divergence in gene co-expression between the two strains was observed, but transcriptional rewiring likely occurred in the Type Three Secretion System 1 (T3SS-1) which is required for establishing infection in the gut. ​ ​

In conclusion, this PhD research aimed to investigate the genomic adaptations associated with AMR in Salmonella and explore the transcriptomic changes related to host adaptation. The resulting findings contribute to our understanding of AMR and host-adaptation in Salmonella.

Elise Vervloessem

• 20/06/2023
  
• 2 p.m.
• Venue: Campus Drie Eiken, R2
• ​Online PhD defence
• Supervisors: Annemie Bogaerts & Nathalie De Geyter
• Department of Chemistry

Abstract

Synthetic fertilizers (like ammonia/NH3) are of vital importance, however, their production process does not fit in the sustainable world we are trying to achieve. A potential alternative or complementary process is plasma, a partially ionized gas made up of a wide range of species types, which facilitates atypical chemistry while being compatible with current sustainability standards. ​ ​

The aim of this thesis is to elucidate (wet) plasma-based nitrogen fixation with a focus on (1) the role of pulsing in achieving low energy consumption, (2) the role of H2O as a hydrogen source in nitrogen fixation and (3) elucidation of nitrogen fixation pathways in humid air and humid N2 plasma in a combined experimental and computational study.

The main conclusions are as follows: (1) A quasi-1D chemical kinetics model reveals that the strong temperature drop in between pulses affects the NOx production and decomposition reactions (back – and forward reactions of the Zeldovich mechanism) positively, enabling efficient use of the power put into the plasma. (2) We show that the selectivity of plasma-based NF in humid air and humid N2 can be controlled by changing the humidity in the feed gas and suggest NH3 is mainly formed in the gas phase as opposed to the liquid phase, contrary to what is suggested predominantly in literature. (3) Lastly, we identify a significant loss pathway for HNO2 and NH3, where these molecules are synthesized simultaneously, i.e. downstream from the plasma, HNOx reacts with NH3 to form NH4NOx which decomposes into N2 and H2O or precipitates. To prevent ineffective nitrogen fixation, this pathway should be considered in future works aimed at optimizing nitrogen fixation. ​ ​

The thesis closes with a point of view on future research in the field of wet plasma-based nitrogen fixation. In short, (1) it would be important to validate our results further in other plasma setups and to attempt to apply the knowledge presented in this thesis for performance enhancement, (2) when the underlying chemistry of wet plasma-based NF has been more established and the advantages and disadvantages have been mapped, we can look for synergies with other NF fields, for example plasma-electrochemistry, and (3) wet plasma-based NF is in an earlier research stage compared to dry plasma-based NF, nonetheless is it important to also focus on the technological aspects of this application.

Niels Van Putte

• 09/06/2023
  
• 4 p.m.
• Venue: Campus Drie Eiken, Q.002
• Online PhD defence
• Supervisors: Stijn Temmerman, Patrick Meire, Goedele Verreydt & Piet Seuntjens
• Department of Biology

Abstract

Tidal marshes take up and release certain elements from and to the river water. Hence, they act as a filter, improving the estuarine water quality. This filtering function depends on the interaction between the marsh soil and water that infiltrates into the marsh platform at high tide and seeps out of the creek banks at low tide. In the past centuries, many tidal marshes disappeared due to large scale land reclamations, together with their associated ecosystem services. Nowadays, tidal marshes are increasingly restored on formerly embanked agricultural areas to regain these ecosystem services. Here, we studied the effect of historical agricultural land use on the contribution of restored tidal marshes to water quality improvement, and we investigated several solutions to stimulate the water quality improving function in newly restored tidal marshes.

In restored tidal marshes, the soil is often compacted due to the historical agricultural land use, leading to a reduced organic matter content and micro- and macroporosity. In this compacted soil, groundwater flow is hindered, leading to a more waterlogged soil and reduced groundwater dynamics in the restored marsh as compared to a natural marsh.

The depth of groundwater drainage and the groundwater flow velocity have important implications for the processes that contribute to water quality improvement, e.g. removal of nitrogen, phosphorus retention and silica cycling. Where groundwater drains deeper, i.e. in the vicinity of tidal creeks and in a more porous soil, these processes are promoted.

We suggest that, in newly restored tidal marshes, the soil porosity can be increased by amending the soil (e.g. with organic matter), and the distance to the nearest tidal creek can be reduced by creek excavation. Numerical modelling showed that the largest gain in groundwater dynamics and seepage was attained when both measures were applied together. The effect of organic soil amendments on groundwater dynamics and nutrient cycling was further explored in a large scale in situ mesocosm experiment. Where the soil was amended, groundwater drained deeper and nitrogen removal increased.

For new tidal marsh restoration projects, we advise to conduct an explorative soil study. When the soil is heavily compacted, design measures, such as creek initiation and organic soil amendments can be applied to jumpstart the contribution to water quality improvement of newly restored tidal marshes.

Grzegorz Kielanski

• 08/06/2023
  
• 4 p.m.
• Venue: Campus Middelheim, G.010
• ​Online PhD defence
• Supervisor: Benny Van Houdt
• Department of Computer Science

Abstract

Queueing theory plays a crucial role in modelling systems with congestion. It has been long applied in analyzing and improving the performance of communication systems. As modern communication systems often are composed of multiple heterogeneous resources, the analysis of such large-scale systems using traditional queueing theory can be prohibitive. When analyzing such systems exactly, one usually comes across the problem of the, so called, state space explosion.

Large-scale systems are therefore often studied through mean field analysis: if a system consists of a large number of queues, it can be approximated by a system with infinitely many queues. The analysis of the model of the latter system, the mean field model, is generally more straightforward, as it circumvents the problem of the state space explosion.

The goal of this thesis is to analyze and gain insight in the performance of existing and novel large-scale load balancing policies through the use of mean field modelling. Each chapter of this thesis contains the mean field analysis of a family of systems with these policies. In the analysis, techniques from dynamical systems, stochastic modelling, probability theory, numerical analysis and simulations are used. ​ ​

The chapters are grouped into three parts. The first of these parts deals with monotone systems. These systems have an apparent ordering of states that is maintained over time. The next part deals with the analysis of systems with job stealing and multithreaded computing. In these systems parts of a job can be transferred between queues and can be thus worked on by different queues concurrently.

In the last part several hyperscalable policies with a single dispatcher are studied. These are policies where a central dispatcher distributes the jobs to the queues, based on their estimated queue lengths. The policies are called hyperscalable if the message overhead between the queues and the dispatcher is less than one message per job on average. ​ ​

For the systems in the last two parts, simulations are performed for finite number of queues to measure the accuracy of the mean field approximation.

Tim Elberfeld

• 06/06/2023
  
• 5 p.m.
• Venue: Campus Drie Eiken, Q.002
• ​Online PhD defence​
• Supervisors: Jan Sijbers & Jan De Beenhouwer
• Department of Physics

Abstract

Fiber-reinforced composites are an important part of modern material science. They are used in every area of our lives in some shape or form. Car manufacturers use them to make the car body lighter and give it better compression properties if there is an accident. Concrete mixed with fibers is now a widely used material not only in construction, but also in private home renovation and improvement. Wind turbines have blades made of plastic, reinforced with longer strands of glass fibers to make them lighter and stronger against the forces of the wind. The more the field progresses, the more the composites can be improved and their applications diversified. A fiber-reinforced composite consists of a base or matrix material that embeds some sort of fibrous material, which is the reinforcement component. This can be glass or carbon fibers, steel bars or natural fibers like bamboo. They can be added in layers, bundles, weaves or loosely dispersed within the material before its set.

A preferred method for investigating composites is X-ray computed tomography. This technique can generate a fully 3-dimensional image, that reveals the inside structure of the analyzed samples. As X-rays penetrate most materials easily, it is possible to acquire images of the attenuation of the incoming radiation when placing such a material sample between the source and the imaging device. Several of those so-called projections are collected over a large angular range, preferably 180 degrees or more. Using mathematical methods the volumetric image, the reconstruction, can then be computed from the projections. ​ ​

This work deals with the problem of the quantitative and statistical analysis of such composites, using X-ray computed tomography. More precisely, it shows approaches to detect the fibers in volumetric images of glass fiber-reinforced polymers and analyze their structure to give insight into their geometrical properties. After introducing the foundations for the work, a first framework for the extraction and analysis of straight fibers, called PARE, is introduced. This framework is then extended to also deal with fibers with arbitrary curvature. Parametric models for both straight and curved fibers are presented and it is shown how those parametric models can be improved using numerical optimization based on the information in the X-ray projection images.

Naomi Claeijs

• 02/06/2023
  
• 4.30 p.m.
• Venue: Campus Drie Eiken, Q.002
• Supervisor: Kris Vissenberg
• Department of Biology

Abstract

The main function of roots is to explore the soil for useful substances. Root hairs, tubular outgrowths of the root's outer cell layer, represent 70% of the root surface. They are pivotal for the absorption of water and nutrients, the anchoring of the plant in the soil, and the interaction with microorganisms. A lot of research has been conducted on root hair development in Arabidopsis thaliana, which is considered a model plant within the plant world. Mutations have shown that many genes are involved in this process of which our published mutant with shorter root hairs is an example. The expression of the gene that has been mutated, ERULUS, is controlled by auxin and normally encodes a kinase, a protein that regulates the activity of its targets through phosphorylation. Changes in the activity of specific cell wall enzymes that modify pectins cause highly impaired root hair growth in the mutant. During this project, I tried to elucidate the signal transduction pathway that starts with auxin, through ERULUS, and the control of cell wall metabolism which ultimately results in controlled root hair development. We expanded our knowledge regarding auxin and found that this plant hormone is involved in different stages of root hair development. It regulates the expression of multiple genes directly and indirectly through its auxin response factors 7 and 19. Moreover, the receptor-like kinases ERULUS and FERONIA are important since the entire protein needs to be active in order to develop normal root hairs. Although they belong to the same family, only their kinase domains can be swapped. Their extracellular domains are protein-specific and bind specific ligands. Without their kinase domain, both proteins lose part of their functionality, and growth, apoplastic pH and cytoplasmic calcium oscillation dynamics are affected. Furthermore, ERULUS is known to phosphorylate its downstream target proteins. Bio-informatics and a reverse genetic approach have shown that some of the genes related to those proteins are involved in root hair development as well. This project illustrates that root hair development is controlled by a complex network of hormones and genes, and that studying root hair growth is important to understand how plants grow.

Thomas Friedrich

• 01/06/2023
• 1 p.m.
• Venue: Campus Groenenborger, U.025
• ​Online PhD defence​
• Supervisor: Sandra Van Aert
• Department of Physics

Abstract

Nanoscience and nanotechnologies are of immense importance across many fields of science and for numerous practical applications. In this context, scanning transmission electron microscopy (STEM) and 4D-STEM are among the most powerful characterization methods at the atomic scale. Annular dark-field (ADF)-STEM can be used to quantify atomic structures in 3D by counting atoms based on a single projection image. In 4D-STEM a full diffraction pattern is recorded at each scan step, which enables more dose efficient imaging and the utilization of various advanced imaging modalities, which can however be complex and slow.

Both, STEM and 4D-STEM suffer from noise and distortions. In the first section of this work the most important of these distortions are discussed and it is shown how image restoration with a dedicated convolutional neural network (CNN) can be beneficial for atomic structure quantifications in ADF-STEM.

In the second part, a new 4D-STEM imaging method real-time-integrated-centre-of-mass (riCOM) is introduced, which is a very dose-efficient and fast algorithm that enables unprecedented live-imaging capabilities for 4D-STEM. It is based on the integrated centre-of-mass approach, but is reformulated with variable integration ranges and optional filters, which allows for a tunable contrast transfer function. This enables the imaging of light and heavy elements simultaneously at very low doses.

In the third part another new 4D-STEM method, coined AIRPI (AI-assisted rapid phase imaging) is introduced, which uses a CNN to retrieve a patch of the specimen's phase image for each scan position, based on the diffraction patterns in the probe's immediate surroundings. This allows also live imaging in principle and surpasses comparable state-of-the-art algorithms in terms of resolution also at low doses. Different atomic columns can be reliably distinguished over a wide range of atomic numbers, enabling a very good image interpretability. Further, AIRPI can recover low frequency image components, which preserves thickness information. This is a unique and important feature which could make quantitative 4D-STEM feasible. ​ ​

Enis Ukshini

• 26/05/2023
  
• 4 p.m.
• Venue: Campus Middelheim, G.010
• ​Online PhD defence
• Supervisor: Joris Dirckx
• Department of Physics

Abstract

The saxophone is a musical instrument which was created in the nineteenth century by Belgian inventor Adolphe Sax. It has since become a popular and versatile instrument used in various genres of music, including jazz, classical, and pop music. The mouthpiece and reed play a crucial role in this versatility as they significantly impact playing behaviour and sound. Even subtle changes in these parts (order of magnitude micrometres) can cause significant differences in the playability and sound of the instrument.

It is challenging to categorize reeds and mouthpieces in objective terms, and no clear set of parameters is available to classify and compare them.

Until now, mouthpieces are mainly categorized by tip opening (the space between the reed and the tip of the mouthpiece), facing length and internal shape. However, it is difficult to compare the artistic and acoustic performances of mouthpieces objectively. Musicians have to go through a lengthy process of trial and error before finding the right mouthpiece that suits their playing style and sound.

In this thesis, several aspects of these challenging problems were investigated to better understand saxophone reed dynamics and the influence of mouthpiece design.

On the level of apparatus development, the work resulted in a system which allows a fully automated measurement of reed vibrations and saxophone sound over all relevant settings of lip force, lip position, blowing pressure and notes. The apparatus made it possible to obtain full-field and time-resolved measurements of reed position and reed strain during the vibration cycle. The results showed that when the reed touches the mouthpiece, significant transversal strain develops, and the reed bends in the transversal direction so that its centre is below the level of the side rails.

New parameters were determined to define the combinations of lip force and blowing pressure for which the instrument will produce sound. With these parameters, a so-called playability range of different mouthpieces could be described objectively. The effect on the playability of even subtle design differences could be quantified.

Omid Ekrami

• 12/05/2023
  
• 4 p.m.
• Venue: Campus Drie Eiken, R1
• ​Online PhD defence
• Supervisors: Stefan Van Dongen & Peter Claes
• Department of Biology

Abstract

Judgement of attractiveness is often believed to be a cognitive adaptation, helping individuals to evaluate the biological fitness of their potential mates, consequently increasing their reproductive success. Two of the main factors generally believed to affect attractiveness are fluctuating asymmetry (FA) and masculinity/femininity. Lower FA is considered a sign of the body’s ability to block out environmental and genetic perturbations during development. Similarly, higher masculinity or femininity are attributed to higher steroid hormones, which are deemed to be immunosuppressants. Therefore, individuals with low FA and high masculinity/femininity are considered to have a high biological fitness. However, the scientific evidence behind this line of thought is ambiguous at best.

The main aim of this thesis is to try to overcome some of the shortcomings often attributed to the current literature on this subject, in order to provide reliable answers regarding the adaptive value of FA and masculinity. We developed an automated algorithm to measure these traits in high density 3D scans of human faces. This novel method is then used to study the possible correlations between FA, masculinity, attractiveness and biological fitness.

Babette Muyshondt

• 25/04/2023
  
• 4 p.m.
• Venue: Campus Drie Eiken, Q.002
• ​Online PhD defence​
  
• Supervisors: Roeland Samson, Karen Wuyts & Sarah Lebeer
• Department of Bioscience engineering

Abstract

In this PhD thesis the ecology of phyllosphere bacterial communities is investigated through both observational and experimental studies. In the first part, we aimed to assess the impact of urbanization on phyllosphere bacteria communities on a broad scale, and for that we determined the composition and diversity along a fragmentation and urbanization gradient in cities across Europe. More specifically, we investigated the relationship of urban phyllosphere bacterial community composition and diversity with different urban variables including particulate matter pollution, microclimate and landscape characteristics such as green infrastructure cover in the surroundings and green area size. To do so, we sampled the phyllosphere bacterial communities of Platanus x acerifolia and Acer pseudoplatanus in 77 UGAs distributed over six European cities and determined their composition and diversity using 16S rRNA gene sequencing. In the second part, we aimed to identify and compare the seasonal variation in the bacterial composition and diversity of leaves, twigs and buds on five different tree species in identical environmental conditions. In addition, we investigated the contribution of the twig and bud phyllosphere to the leaf phyllosphere. Therefore, we followed-up the bacterial communities of five tree species in a common-garden setting, using 16S rRNA sequencing, from budburst over leaf emergence to leaf shedding from March to October. In a third part, the effect of traffic-derived air pollution exposure on the phyllosphere bacterial community is studied, either directly or indirectly via the effect of the leaf traits including leaf wettability, stomatal density and specific leaf area. Differences in air pollution exposure were created by planting Betula pendula trees along a transect at different distances from heavy-trafficked highways at four locations. To do so, we followed the phyllosphere bacterial communities and leaf traits monthly of these 58 Betula pendula trees from May to September. As a last part, we investigated the effect of ammonium fertilization and dosage on phyllosphere bacterial communities and leaf traits of Hedera hiberica plant in an controlled environment. Weekly leaf samples were collected for five weeks and one more after eight weeks. With these experiments we want to gather new and more knowledge about phyllosphere bacterial communities and their relation to urban stressors, which will be essential for their management and potential application potential in the future.

Robin Verachtert

• 24/04/2023
  
• 4 p.m.
• Venue: Campus Drie Eiken, O.01
• Supervisors: Bart Goethals & Koen Verstrepen
• Department of Computer Science

Abstract

In this thesis, we describe several methods to handle temporal dynamics in recommender systems.

Recommender systems are often deployed in highly dynamic environments such as news websites or retail pages. When a new article is published, it is important that the recommender system is able to quickly recommend it, otherwise, the users will fail to find utility in the recommendations. Utilising temporal information proves to be a crucial factor to make sure these systems perform well and generate the right recommendations for users browsing news or retail websites.

First, we look at how to keep models up to date, such that they can deal with the constantly changing online environments, and recommend new items quickly.

Next, we show that using only more recent data or giving more recent data additional weight, makes baseline algorithms perform impressively well.

This finding, going against the common knowledge that more data is better, indicates that the quality of data is a fundamental part of making good recommendations.

Finally, we investigate the effects popularity has on recommendation quality, and find that a balance needs to be found between popularity and relevance in order to give the best possible recommendations.

Sten Vercammen

• 11/04/2023
• 5 p.m.
• Venue: Campus Middelheim, G.010
• Supervisors: Serge Demeyer, Görel Hedin & Markus Borg
• Department of Computer Science

Abstract

The growing reliance on automated software tests raises a fundamental question: How trustworthy are these automated tests? Today, mutation testing is acknowledged within academic circles as the most promising technique for assessing the fault-detection capability of a test suite. The technique deliberately injects faults (called mutants) into the production code and counts how many of them are caught by the test suite.

Mutation testing shines in systems with high statement coverage because uncaught mutants reveal weaknesses in code which is supposedly covered by tests. Safety-critical systems –where safety standards dictate high statement coverage– are therefore a prime candidate for mutation testing. In safety-critical software, C and C++ dominate the technology stack. Yet this is not represented in the mutation testing community: a systematic literature review on mutation testing from 2019 analysed 502 papers and reported that from the 190 empirical studies, 62 targeted the C language family and out of the 76 mutation testing tools, only 15 targeted the C language family. Despite the apparent potential, mutation testing is difficult to adopt in industrial settings, because the technique —in its basic form— requires a tremendous amount of computing power. Without optimisations, the entire code base must be compiled and tested separately for each injected mutant. Hence for medium to large test suites, mutation testing without optimisations becomes prohibitively expensive. ​ ​

To make mutation testing effective in an industrial setting, we set three objectives: (1) generate fewer mutants, (2) process them smarter and (3) execute them faster. To meet our objectives, we investigate the most promising techniques from the current state-of-the-art. This ranges from leveraging cloud technology to compiler integrated techniques using the Clang front-end. These optimisation strategies allow to eliminate the compilation and execution overhead in order to to support efficient mutation testing for the C language family. ​ ​

As a final step, we perform an empirical study on the perception of mutation testing in industry. The aim is to investigate whether the advances are sufficient to allow industrial adoption and to identify any remaining barriers preventing industrial adoption. ​ ​

In this Ph.D. thesis we show that a combination of mutation testing optimisation techniques from the do fewer, do faster, and do smarter are needed to perform mutation testing in a continuous integration setting. Furthermore, the industrial perception of mutation testing is evolving as additional organisations recognise its potential.

Senne Van Alphen

• 17/03/2023
  
• 11 a.m.
• Venue: Campus Drie Eiken, Building O, O.01
• ​Online PhD defence
• Supervisors: Annemie Bogaerts & Rony Snyders
• Department of Chemistry

Abstract

200 years ago, humanity started the industrial revolution by discovering fossil fuels, which lead to unprecedented technological advancements. However it has become alarmingly clear that the major environmental concerns associated with fossil fuels require a short-term transition from a carbon-based energy economy to a sustainable one based on green electricity. A key step concerning this transition exists in developing electricity-driven alternatives for chemical processes that rely on fossil fuels as a raw material. A technology that is gaining increasing interest to achieve this, is plasma technology.

Using plasmas to induce chemical reactions by selectively heating electrons in a gas has already delivered promising results for gas conversion applications like CO2 conversion and N2 fixation, but plasma reactors still require optimization to be considered industrially competitive to existing fossil fuel-based processes and emerging other electricity-based technologies. In this thesis I develop computational models to describe plasma reactors and identify key mechanisms in three different plasma reactors for three different gas conversion applications, i.e. N2 fixation, combined CO2-CH4 conversion and CO2 splitting.

I first developed models to describe a new rotating gliding arc (GA) reactor operating in two arc modes, which, as revealed by my model, are characterized by distinct plasma chemistry pathways. Subsequently, my colleague and I study the quenching effect of an effusion nozzle to this rotating GA reactor, reaching the best results to date for N2 fixation into NOx at atmospheric pressure, i.e., NOx concentrations up to 5.9%, at an energy cost down to 2.1 MJ/mol.

Afterwards, I investigate the possible improvement of N2 admixtures in plasma-based CO2 and CH4 conversion, as significant amounts of N2 are often found in industrial CO2 waste streams, and gas separations are financially costly. Through combining my models with the experiment from a fellow PhD student, we reveal that moderate amounts of N2 (i.e. around 20%) increase both the electron density and the gas temperature to yield an overall energy cost reduction of 21%.

Finally, I model quenching nozzles for plasma-based CO2 conversion in a microwave reactor, to explain the enhancements in CO2 conversion that were demonstrated in experiments. Through computational modelling I reveal that the nozzle introduces fast gas quenching resulting in the suppression of recombination reactions, which have more impact at low flow rates, where recombination is the most limiting factor in the conversion process.

Reyes Salas

• 24/02/2023
  
• 4 p.m.
• Venue: Campus Drie Eiken, Q.002
• ​Online PhD defence
• Supervisors: Wendt Müller, Luc Lens & Jan Mees
• Department of Biology

Abstract

The world is witnessing unprecedented rates of habitat degradation due to anthropogenic activities, especially urbanisation. Yet, some species are commonly believed to have successfully adapted to breed in urban areas. However, we have still a poor understanding of the actual fitness consequences. The fact that animals are attracted to an urban environment might conceal that urban landscapes can act as ecological traps, since even highly opportunistic species might have difficulties to keep up with the high rate of environmental change. This dissertation tackles this question by exploring the capacities to breed in changing environments along with in depth studies on the drivers of territoriality and on the role of the early life social environment for the offspring in order to deduce potential consequences of reproducing in urban landscapes. To this end, a colonial breeding seabird species, the lesser black-backed gull (Larus fuscus), which is thought to thrive in highly anthropogenic environments, is used as model species.

First, I explored whether nesting site relocations, as frequently occurring in rapidly changing urban environments, impact on reproductive success, and I could show that individuals that lost their breeding site due to anthropogenic activities laid smaller eggs and that the likelihood of skipping a breeding season increased. In a next step and by using GPS tracking devices, I then showed that investing time in territoriality imposes a carry-over effect on reproductive investment. While not measured explicitly, it can be assumed that time costs increase after a relocation and might be the cause of the observed negative reproductive investment in relocated birds.

Moreover, we currently lack a profound understanding of the importance of a territory for the chicks, even though it is known that the social early-life environment can shape an individual’s (behavioural) phenotype. This is particularly relevant in lesser black-backed gulls, because here chicks experience high levels of aggression when crossing into a neighbouring territory. I indeed found that chicks raised in dense areas where territories are closer together showed the lowest exploration activity. In a final step, I deployed a novel tracking technology to study the movement behaviour of the chicks in the colony, and I could show that the social environment also affected the movement activity, territory size and social associations among chicks from neighbouring nests.

Kasra Rafiezadeh Shahi

• 24/02/2023
  
• 4 p.m.
• Venue: Stadscampus, Building C, C.002
• ​Online PhD defence
• Supervisors: Paul Scheunders, Pedra Ghamisi & Richard Gloaguen
• Department of Physics

Abstract

In recent years, there has been an explosive growth in remotely sensed (RS) data usage in geoscience and Earth observation applications. The recent technical advancements allow users to acquire various types of rich information. A quintessential example of RS data is hyperspectral imagery. A hyperspectral image (HSI) provides rich spectral data over a wide range of the electromagnetic spectrum. Such information enables users to identify, track and distinguish different materials and objects. Another RS data example is light detection and ranging (LiDAR). LiDAR yields information on the altitude of the observed objects. Hence, it allows distinguishing objects that might share common spectral characteristics but have different altitudes (e.g., tree species). ​ 

Although RS data have high potential for material characterization, the processing of such data poses challenges, for example, on the high dimensional nature of the datasets or an efficient fusion of multiple data sources. Machine learning approaches march as the pioneer solutions to the aforementioned issues. ​ ​

Among machine learning approaches, supervised learning approaches perform accurately in various tasks (e.g., classification and regression). Nevertheless, such approaches demand an immense number of training samples during their process. Specifically, in geoscience and Earth observation applications, acquiring training samples is a labor-intensive, time-consuming, and expensive task. Moreover, in some cases, it is not possible to generate training samples due to limited accessibility. Therefore, supervised approaches constitute a shortcoming with respect to the availability of training samples. ​ ​

On the contrary, unsupervised learning approaches accomplish different tasks (e.g., feature extraction and clustering) by merely analyzing the data itself. To be more specific, the clustering problem refers to grouping similar pixels into clusters. In general, clustering approaches can be split into two categories: (1) Conventional shallow learning (CSL) and (2) Deep learning (DL)-based approaches. This study is devoted to the development of unsupervised CSL and DL approaches for single- and multi-sensor remote sensing data clustering.

Jinxin Wang

• 09/02/2023
  
• 2 p.m.
• Venue: Campus Drie Eiken, O.03
• Supervisors: Vera Meynen & Annemie Bogaerts
• Department of Chemistry

Abstract

The plasma-based dry reforming in a dielectric barrier discharge (DBD) reactor is important to achieve sustainable goals, but many challenges remain. For example, the conversion and energy yield of DBD reactors are relatively low, and the catalysts or packing materials used in existing studies cannot improve them, possibly due to the unsuitable properties and structures of catalysts or packing materials for plasma processes.

In order to study the effect of catalyst structure on plasma-based dry reforming, a controllable synthesis of the catalyst supports or templates was explored. In Chapter 2, an initially immiscible synthesis method was proposed to synthesize uniform silica spheres, which can replace the organic solvent-based Stöber method to successfully synthesize silica particles with the same size ranges as the original Stöber process without addition of organic solvents. Using the silica spheres as templates, 3D porous Cu and CuO catalysts with different pore sizes were synthesized in Chapter 3 to study the effect of catalyst pore size on the plasma-catalytic dry reforming. In most cases, the smaller the pore size, the higher the conversion of CH4 and CO2 due to the reaction of radicals and ions formed in the plasma. An exception are the samples synthesized from 1 μm silica, which show better performance due to the electric field enhancement for pore sizes close to the Debye length. Besides the pore size, the particle diameter of the catalyst or packing is also one of the important factors affecting the interaction between plasma and catalyst. In Chapter 4, SiO2 spheres (with or without supported metal) were used to study the effect of different support particle sizes on plasma-based dry reforming. We found that a uniform SiO2 packing improves the conversion of plasma-based dry reforming. The conversion of plasma-based dry reforming first increases and then decreases with increasing particle size, due to the balance between the promoting and hindering effect of the particle filling on the plasma discharge. Chapter 5 is to improve the design of the DBD reactor itself, in order to try to increase its low energy yield. Some stainless steel rings were put over the inner electrode rod of the DBD reactor. The presence of rings increases the local electric field, the displaced charges and the discharge fraction, and also makes the discharge more stable and with more uniform intensity. The placement of the rings improves the performance of the reactor at 30 W supplied power. ​ ​

Brent van Bladel

• 02/02/2023
  
• 5 p.m.
• Venue: Campus Middelheim, G.010
• Supervisor: Serge Demeyer
• Department of Computer Science

Abstract

As software has become ever important in our lives, all that code needs to be of a high quality. A common way to achieve this is via software testing, where additional "test code" is written with the sole purpose of finding mistakes in the original code, or "production code". As test code has the large responsibility of ensuring qualitative software, it is critical that the test code itself is of high quality as well. However, while the quality of test code is often synonymous with its ability to find bugs, it is equally important to ensure readability and maintainability of test code to allow agile teams working incrementally to update, extend, and maintain the test code each iteration. ​ ​

The presence of code duplication, or "code clones", can affect the readability and maintainability of code. While code clones have already been extensively researched in production code, research on test code duplication is limited. And yet, duplicate tests are a common occurrence, as the quickest way for a developer to test a new feature is to copy, paste, and modify an existing test. In this thesis, we address this gap in the literature by answering two research questions. First, we investigate whether the structure of test code can be exploited to detect semantic code clones. Second, we investigate whether test code duplication should be considered independently of production code duplication. ​ 

In the end, we show that test code is a rich source for studying clones and that further investigation is warranted.

Sarah Ahannach

• 24/01/2023
• 5 p.m.
• Venue: Campus Drie Eiken, O.03
• ​Online PhD defence​
  
• Supervisors: Sarah Lebeer & Gilbert Donders
• Department of Bioscience Engineering

Abstract

Women’s health and safety is receiving increased global attention in the last decennia, which - some may say - is long overdue. Science is unfortunately still not filling society’s needs when it comes to women’s health and particularly vaginal health. For instance, in the last 40 years no significant breakthroughs have been made on managing bladder and vaginal infections, despite important implications for physical and mental health of women, their children and partners. Yet, the field is moving forward and women’s health is now subject to a growing interest in the global microbiome research field. In particular, the vaginal microbiome has already been suggested to be crucial for vaginal disease prevention, successful fertilization and healthy pregnancies. Nevertheless, despite the growing understanding of the female microbiome and its importance, large-scale studies on the healthy women and the link to various lifestyle factors are generally lacking. Such knowledge on factors affecting the microbiome is needed when microbiome analyses are explored for forensic applications, such as to provide trace evidence helping reconstruct a crime event. This PhD work aims to lay cornerstones that will ultimately help all women achieve the best possible health and safety through microbial management and cutting-edge microbiome analyses. To this end, three research objectives were formulated: (i) to benchmark the female microbiome in Belgium and the main associating factors on its composition using a citizen science approach; (ii) to come to a better mechanistic and ecological understanding of the benefits of vaginal lactobacilli to the host and their potential as pre- and probiotics; and (iii) to explore microbiome analysis as a tool to investigate trace evidence in forensic casework. To support and enable the completion of these research objectives a citizen science project on women’s health with scientific and societal objectives named Isala (https://isala.be/en/) was set up, and a daughter project studying the application of microbial fingerprinting in sexual assault investigations, named GeneDoe. Overall, this PhD thesis contributes to a new understanding of women’s microbiome and how citizen science facilitates microbiome research while breaking the taboo on sensitive topics. It opens new research directions into the inner workings of the vaginal ecosystem, vitamin-producing bacteria, and applying microbiome analysis to forensics. This work will improve knowledge of the female microbiome stability and dynamics by presenting novel findings for clinical trials to unravel underlying mechanisms; the development of novel biotherapeutics; and the design of novel tools for diagnostics and criminal investigations.

Jeroen Van Houtte

• 19/01/2023
• 3 p.m.
• Venue: Campus Middelheim, G.010
• ​Online PhD defence​
• Supervisors: Jan Sijbers & Toon Huysmans
• Department of Physics

Abstract

Over the past decade, digital data generation and collection has become increasingly important in biomedicine. Surgeons heavily rely on biomedical data for diagnoses, pre-operative planning, follow-up, etc. Learning from large collections of data, such as optical surface scans and images, can help us in automating diagnoses and reducing human subjectivity. The knowledge of shape variability in a large dataset can be a guide for product development for example. Letting a computer “understand” images based on past examples enables computer-assisted robotic surgeries. ​ ​

This thesis provides data-driven solutions for biomedical problems. On a first level, we present a framework to combine the shape information of different patients into one digital model. On a second level, these digital models serve as prior knowledge for computers to automatically “understand” new data. A crucial step on both, the modeling and the application level, is the anatomical alignment of data. This step, known as “registration”, involves the identification of corresponding points between different data which remains a challenging task to computers.

The manuscript is divided into three parts. Part I provides an introduction to geometry and image processing, X-ray imaging and deep-learning. ​ ​

Part II presents the contributions of this thesis to (statistical) shape modeling of articulating bodies. Articulating statistical shape models (SSM) describe any individual up to a certain accuracy, while maintaining the possibility to be articulated into different poses. Hence, the acquisition of person-specific 3D models is no longer required. Two different articulating SSM’s have been constructed: a SSM of the human hand for splint design based on low quality 3D-scans, and a SSM of a horse limb for veterinary applications. The ability of SSM’s to describe many individuals also allows it to generate virtual data to train deep-learning models on. ​ ​

Part III of the thesis focuses on solving a specific registration problem in X-ray imaging. X-ray imaging or radiography is the most common imaging procedure for many orthopedic interventions thanks to its ability to visualize internal structures with a relatively low radiation dose and low acquisition cost. However, interpretation from 2D radiographs can be hampered by overlapping structures, magnification effects and the patient’s positioning. To avoid the difficulties associated with 2D projections, we developed two deep-learning methods, with and without statistical prior, to register a 3D model to a pair of radiographs. The registered model enables a 3D-interpretation, while keeping the benefits of RX over CT, in terms of costs and radiation dose. ​ ​

Shahid Ullah Khan

• 19/01/2023
• 2 p.m.
• Venue: Campus Drie Eiken, Q.002
• ​Online PhD defence​
• Supervisors: Karolien De Wael & Sammy Verbruggen
• Department of Chemistry

Abstract

Singlet molecular oxygen (1O2) has continuously attracted researchers' interest because of its involvement in various processes, such as in photodynamic reactions in biological and chemical systems. 1O2 is an effective electrophile and potent oxidizing agent and can be easily generated by photosensitization via the illumination of organic dyes with visible light. As described in Chapter 1, 1O2 has gained prominence in various applications such as wastewater treatment, photodynamic therapy of cancer, organic synthesis, and recently developed 1O2-based photoelectrochemical (PEC) sensing of phenolic compounds. Phenolic compounds are a potential source of contaminants that originates from industrial effluents and waste products of chemical and pharmaceutical industries. These phenolic compounds pose severe threats to humans and aquatic life after reaching the environment. Therefore, it is imperative to develop photoactive materials that efficiently generate 1O2 and oxidize phenolic compounds and antibiotics. The existing 1O2 generating photosensitizers (PSs) include porphyrins, phthalocyanines (Pcs), subphthalocyanines (SubPcs), and other dyes such as derivatives of xanthene (e.g., Rose Bengal (RB)), and fluorinated boron-dipyrromethene (BODIPYs), and phenothiazinium dyes (e. g. Methylene Blue) which display long-lived triplet excited state and can be used in 1O2-based applications. This thesis focuses on preparing efficient hybrid materials based on newly synthesized Pcs, different surface area titanium dioxide (TiO2) and plasmonic gold nanoparticles (AuNPs) for their use in the PEC detection of phenolic compounds.

The first focus was on developing a fast amperometric method to test the photo-electrocatalytic activity of 1O2 producing PSs dissolved in MeOH based on the redox cycling of an electroactive phenolic compound, hydroquinone (HQ) (Chapter 2). This method of testing PSs does not require the accumulation of a reaction product since the amperometric signal develops near instantly when the light is on, which enables dynamic monitoring of a PSs activity at varying conditions in a single experiment. This method was crucial to measure high 1O2 quantum yield and low yield in the same experimental conditions. Moreover, the obtained results revealed a range of working parameters affecting the PEC activity of PSs. ​ ​

The next goal was to immobilize tert-butyl substituted aluminum Pc (t-BuPcAlCl) on the solid support, which showed a high 1O2 quantum yield. However, before immobilizing Pc on a solid support such as TiO2, it is essential to know the electronic energy level of Pcs for the possible electron transfers from Pcs to TiO2. Therefore, Chapter 3 explored the (spectro)electrochemical properties of t-BuPcAlCl Pc. Next, in Chapter 4, t-BuPcAlCl Pc and other tert-butyl substituted Pcs with Zn central metal, t-BuPcZn, and its metal-free derivative t-BuPcH2 were immobilized on different surface area TiO2. The PEC activity of immobilized Pcs on TiO2 toward different phenols and antibiotics was studied, and the action mechanism was revealed and compared with sterically hindered fluorinated Pc F64PcZn. ​ ​

In the final part of this thesis plasmonic AuNPs were introduced combined with trimethylsilane-protected acetylene functionalized ZnPc (TMSZnPc) to study the synergistic effect that boosts the overall activity toward the detection of phenols under visible light illumination (Chapter 5) . The TMSZnPc was coupled with AuNPs via a click chemistry approach. The 1O2 quantum yield of TMSZnPc improved significantly after conjugating with AuNPs, and, subsequently, the PEC activity for detecting HQ. The theoretical and experimental investigation demonstrated that the plasmonic enhancement of TMSZnPc is driven by the near-field mechanism. This shows the importance of plasmonic AuNPs with other photoactive species for their use in 1O2-based applications. ​ ​

The fundamental knowledge obtained in this doctoral study will ultimately deepen the understanding of developing 1O2-based PEC sensors for detecting phenolic compounds and pharmaceuticals in the wastewater stream, helping to choose efficient materials and, in the last instance, a more sustainable future especially access to clean water for everyone.

Joaquim Sanctorum

• 12/01/2023
  
• 4.30 p.m.
• Venue: Campus Groenenborger, U.025
• ​Online PhD defence
• Supervisor: Joris Dirckx
• Department of Physics

Abstract

Birth is the most critical event in the early ontogenesis of mammals, of which we humans are also a part. Unfortunately, for a considerable percentage of newborns, this event can occur prematurely. According to the World Health Organization (WHO), preterm birth (before 37 weeks of pregnancy) occurs in 5% to 18% of annual births across 184 countries, representing about 15 million babies per year.

Modern advances in medicine have drastically increased the survival rates of premature babies, yet, many survivors are prone to developing lifetime disabilities. It was estimated that motoric deficits might develop in 5% to 27% of premature infants, of which celebral palsy is the most severe. To this day, there are no established therapies to overcome these issues due to the lack of fundamental knowledge on the connection between growth retardation at birth and the further development of the infant. ​ ​

Fundamental insights can be gained by studying the development of the movement apparatus and the related motoric defects during a longer period of time (longitudinal study) using X-ray imaging techniques. Movement patterns can be analyzed using X-ray stereofluoroscopy (XRSF), which provides 3D information on the movements of bones and joints. X-ray computed tomography (CT), on the other hand, yields structural information on the bones and the muscles. Repeated application of these two X-ray techniques and a combination of the data types can provide essential information to study the movement apparatus over time. ​ ​

Due to their hazardous nature, these techniques are to be avoided in infant-related research. However, low-birth-weight piglets exhibit a high degree of physiological similarity to human babies and therefore are a clinically relevant model. Yet, piglets develop rather quickly (a matter of days or even hours), posing profound time constraints on the envisaged longitudinal research approach, as XRSF and CT are not available in the same facility. ​ ​

The work presented in this dissertation is aimed at combining XRSF and CT in the same set-up to make longitudinal studies on the motoric development in rapidly developing animals possible. The main research topics discussed in this manuscript are image distortion correction, geometry calibration of the modular set-up, extended field-of-view tomography and the use of multi-exposure fusion techniques. The dissertation thus covers a broad range of challenges that may arise when transforming a standard XRSF set-up to a high-speed tomograph, and may serve as a guide to face these.