Duygu Gizem Sentürk

• 03/05/2024
  
• 16.00 uur
• Locatie: Campus Groenenborger, US.024
• ​Online Doctoraatsverdediging​
• Promotoren: Sandra Van Aert & Annick De Backer
• Departement Fysica

Abstract

Nanomaterials play an essential role in modern technology from industry to life sciences. At the atomic scale, the properties and functionalities of materials strongly depend on their size and shape. Moreover, the functionalities of nanostructures are further enhanced when they are composed of multiple types of elements. Therefore, reliable characterisation of the atomic structure is essential to understand the structure-property relationship and to design nanostructures with tailored functionalities.

Scanning transmission electron microscopy (STEM) is one of the most powerful tools for characterising nanostructures. In STEM, electrons scattered from the sample are collected by an annular detector with predefined inner and outer angles, producing 2D atomic resolution image of a 3D nanostructure. Quantitative analysis of STEM images reveals the structural parameters such as the position, number and type of atoms. Until now, advanced statistics- and simulations-based methods have made it possible to count the number of atoms along the viewing direction for each atomic column in monotype crystalline nanostructures from a single STEM image. This allows the size and shape of nanomaterials to be estimated. However, for heterogeneous multi-element nanostructures, the atomic columns with varying thicknesses and elemental compositions often lead to indistinguishable measurements in the presence of noise. This complexity makes it challenging to determine the number of each type of atom. To overcome this problem, traditional quantification methods often rely on prior knowledge of the shape or size of the material, which is not always available. 

To avoid the need for prior knowledge, we propose to use a combination of multiple STEM images. These images are obtained from non-overlapping annular detector collection regions revealing unique information about the thickness and composition of the atomic columns. For this purpose, the 4D STEM technique, providing a rich electron diffraction dataset, is beneficial as it allows the generation of multiple STEM images with arbitrary annular detector settings. ​ ​

In this research, we explore the extension of both statistics- and simulations-based methodologies for such a multimode STEM imaging approach and achieve atom counting of each type of element in heterogeneous nanostructures. Moreover, strategies that would reveal these unknown atom counts with the highest attainable accuracy and precision are investigated by deriving optimal statistical experimental settings. This thesis demonstrates the possibilities and limitations of using additional signals resulting from multiple STEM images and ultimately from a 4D dataset when characterising multi-element nanostructures, offering a dose-efficient alternative.

Laurens Van Hoecke

• 02/05/2024
  
• 17.00 uur
• Locatie: Campus Drie Eiken, O.05
• ​Online Doctoraatsverdediging
• Promotoren: Patrice Perreault & Sammy Verbruggen
• Departement Bio-ingenieurswetenschappen

Abstract

Hydrogen (H₂) is expected to become a key molecule in the transition towards a society running on renewable energy. It can be used to store excess renewable energy at peak production moments and release this energy at a later stage when renewable energy production is less. However, storing H₂ is challenging due to the low density of this gas. As a solution, Liquid Organic Hydrogen Carriers or LOHC molecules have been proposed in the passed to increase volumetric energy density of H₂. LOHC are a class of molecules that have storage sites available, to which the H₂ gas can be chemically bounded. The LOHC molecule under investigation was dibenzyltoluene (DBT), which is an oil like liquid, that is easy to transport and poses little fire or explosion risks. To release the H₂ from the DBT carrier, via a so-called dehydrogenation reaction, efficient mass and heat transfer is required during the process, since a large volume increase is expected from H₂ release and the reaction is endothermic, i.e., a self – cooling process that takes place at temperatures around 300 °C. The heat has to be supplied specifically to the active sites of catalyst particles that are present inside the reactor and which enable the dehydrogenation to proceed. For heat transfer limited processes fluidized bed reactors are often used, which is a type of reactor where the particle phase is being agitated by the fluid flow. The research proposed in this work, was to explore via computational fluid dynamics (CFD) simulations the possibilities and challenges of using fluidized bed reactors for the dehydrogenation of LOHC. The model selection required for CFD simulations of a three-phase system was investigated in this work, with a main emphasis on the drag model selection. The CFD modelling study was focused on the use of swirling fluidized bed reactors, since it was hypothesised that the swirling effect could also aid in increased removal of the gas phase from the reaction medium to increase the efficiency of the process. Ultimately, it was shown that the main challenges in the design of fluidized bed reactors will be to create uniform particle distribution inside the reactor. A new design for a dehydrogenation reactor is proposed based on the insights gained in this thesis.

Hamid Ahmadi Eshtehardi

• 25/04/2024
  
• 10.00 uur
• Locatie: Campus Drie Eiken, R.R4
• ​Online Doctoraatsverdediging
• Promotoren: Annemie Bogaerts & Marie-Paule Delplancke
• Departement Chemie

Abstract

Despite the recent increasing interest in plasma technology for nitrogen fixation purposes, industrialization of this technology faces several challenges, including challenges of plasma catalysis for selective production of chemicals, the high energy cost of plasma-based nitrogen fixation compared to current industrial processes, and the design and development of scaled-up and energy-efficient plasma reactors for industrial purposes. In the framework of this thesis, we have tried to tackle these challenges and add to the state-of-the-art in plasma-based nitrogen fixation using a combination of experimental and modelling work.

Mees van Kampen

• 16/04/2024
  
• 13.30 uur
• Locatie: Stadscampus, S.M.003
• ​Online Doctoraatsverdediging​
• Promotoren: Francesco Hautmann & Pierre Van Mechelen
• Departement Fysica

Abstract

Studies on calculations for high-energy proton-proton collisions performed by the Parton Branching (PB) method for the evolution of transverse momentum dependent parton distribution functions (TMDs) will be presented. The PB method allows to perform both inclusive and exclusive calculations of collision final states by means of Monte Carlo techniques. Evolution of TMDs in the PB method allows for the resummation of soft gluons by the Sudakov form factor. The implementation of PB TMDs in the CASCADE Monte Carlo event generator allows for the calculation of a wide variety of particle collision processes in a wide kinematic range.

I examine the PB method, focusing on the Sudakov form factor and the soft-gluon resolution scale. By extending the emission phase space with longitudinal splitting fractions z approaching one, we have achieved accurate perturbative resummation and a non-perturbative contribution to the evolution. A dynamical resolution scale separates resolvable and non-resolvable phase space regions, acting as a boundary between these perturbative and non-perturbative domains. We show that PB evolution with next-to-leading order (NLO) splitting functions achieves next-to-leading logarithmic accuracy in soft-gluon resummation. The implementation of the physical soft-gluon coupling enhances Sudakov resummation towards next-to-next-to-leading logarithmic accuracy. Non-perturbative contributions of the Sudakov are illustrated through the extraction of the Collins-Soper kernel.These extractions highlight the influence of both the emission phase space and the scale of the strong coupling in TMD evolution on the large-b behavior of the CS kernel.

Combining higher order matrix element calculations with PB TMDs and TMD shower is done through matching and merging techniques. Azimuthal correlations of high transverse momentum jets in di-jet production and boson-jet production are calculated using PB TMDs matched to NLO matrix elements. QCD predictions for final states with multiple jets in hadron collisions make use of multi-jet merging methods. These methods consistently combine the contributions from hard scattering matrix elements with different parton multiplicities and parton showers.

Calculations of jet transverse momentum and jet multiplicity distributions, as well as highly non-trivial jet event shapes, are performed with the recently developed TMD merging method. We investigate theoretical predictions for Z-boson plus jets production using multi-jet merging algorithms. Our analysis focuses on the differential jet rates and their discontinuities, which allows us to develop a method for quantitatively analyzing the merging algorithm and its dependence on the merging scale by varying invariant di-lepton masses.

Noelia Felipe Montiel

• 29/03/2024
  
• 15.00 uur
• Locatie: Stadscampus, Hof Van Liere, F. de Tassiszaal
• ​Online Doctoraatsverdediging
• Promotor: Karolien De Wael
• Departement Bio-ingenieurswetenschappen

Abstract

Illicit drug trafficking poses a significant threat to public health, safety and environment, requiring not only effective law enforcement measures, but also innovative harm reduction approaches. This PhD thesis aims to contribute to this multifaceted approach by developing electrochemical fingerprint (EF)-based sensors for the most prevalent illicit drugs and precursors. Throughout this thesis, the EF concept will be put to the test to ensure its practical applicability in real-world scenarios.

The lack of electroactivity in certain compounds may impose constraints on EF-based detection tools. This pivotal challenge is addressed by introducing a derivatization reaction to convert non-electrochemical active substances into electroactive ones. Specifically, BMK was used as a model due to its inherent inactive nature. This approach expands the scope of applicability of the EF also to non-electroactive species.

Recognizing that precursors are often exceptionally pure, the focus was then shifted to an opposite context, i.e. to heroin which is generally found together with cutting agents, impurities, and by-products from its manufacturing process. Oxidation signals of heroin were elucidated and further exploited to allow its detection in seizures. In this context, several analytical strategies were evaluated to enrich the EF of heroin. The development of these sensors makes clear the practical utility of the EF for highly impure substances in on-site settings.

Up to this point, the study of the EF focused exclusively on oxidative processes. However, reductive processes may also provide valuable insights on the target analytes. Therefore, the complete EF including oxidative and reductive processes was investigated to extract a richer and more detailed dataset, maximizing the information available. To achieve this, counterfeit Xanax emerged as a right candidate. This choice is based in the complex matrix of Xanax, which typically contains a diverse range of substances susceptible to both processes. By interrogating the complete EF, the research strives to disclose the full composition of complex matrixes.

When developing EF-based solutions for detecting illicit drugs, sensitivity arises as a critical point, especially in scenarios involving illicit drug smuggling. Consequently, the exploration of surfactants and nanomaterials on plant-based and synthetic cannabinoids becomes imperative to boost the analytical parameters.

Overall, by presenting electrochemical methods and practical solutions, this research paves the way for a more effective on-site EF-based devices to combat drug trafficking and associated challenges, positioning the electrochemical technology as a complementary tool to traditional devices.

Tom Eilers

• 29/03/2024
  
• 15.00 uur
• Locatie: Campus Drie Eiken, O.006
• Promotor: Sarah Lebeer
• Departement Bio-ingenieurswetenschappen

Abstract

Fermentation of foods and beverages has been an important biological preservation method for humanity for millennia. In this PhD project, we focused on lactic acid fermentation, and more specifically vegetable fermentations. In vegetable fermentations, a salt-brine is generally added to reduce the growth of spoilage organisms. In most salt-brine vegetable fermentations studied to date, lactic acid bacteria (LAB), particularly members of Lactobacillaceae are the most important fermentation bacteria.

This PhD explored three major aspects of LAB-dominated vegetable fermentations: (1) The effect of external factors studied, including vegetable type, salt concentration, and addition of CO₂, on the microbial community dynamics. (2) the genomic diversity of the Lactobacillaceae as determined by pangenome analysis. (3) The role of cellulase and carotenoid production by Lactobacillaceae as adaptation factors in vegetable fermentations and other environments.

Firstly, we found that most fermentations were characterized by a LAB-dominated community with the genus Leuconostoc as the most abundant genus. Root-associated vegetables, such as beet, carrot, parsnip, and sunroot had the most stable and robust fermentations. Additionally, lower salt concentrations was linked to the presence of less favorable genera of the Enterobacterales order. CO₂-addition could mitigate the effect of the low salt concentration, as most Enterobacterales disappeared faster.

Secondly, the genomic diversity of the Lactobacillaceae was explored and various unique orthogroups for each species could be detected within their pangenome. These unique orthogroups were used to develop selective and specific strain-specific primers and were validated in situ by tracking starter cultures during carrot juice fermentations. Additionally, this exploration led to the discovery of a novel species called Lactiplantibacillus carotarum, isolated from fermented vegetables. Phenotypically, it was able to metabolize more different carbohydrates compared to the closest relatives, which can be highly present in some fermented vegetable substrates.

Lastly, the functional potential of cellulase and carotenoids by Lactobacillaceae isolated from fermented vegetables was explored. These factors were hypothesized to be important for adaptation of the fermented food microorganisms to the vegetable fermentation environment and were verified in vitro.

In conclusion, this PhD work contributed to a new understanding of the role of plant substrates, salt, and CO₂ in the microbial ecology of vegetable fermentations. We also revealed the potential of the pangenome for vegetable fermentation research. This work incrementally advances our understanding of these man-made ecosystems and might facilitate the development of novel functional foods in a more targeted approach.

Tim Leys

• 28/03/2024
  
• 16.00 uur
• Locatie: Campus Middelheim, G.010
• Promotor: Guillermo A. Pérez
• Departement Informatica

Abstract

In the present day, complex and dynamic systems have become ubiquitous. Their development remains intrinsically complex and, in safety-critical environments, verification of these systems is necessary to guarantee their safety and reliability. With the rise in popularity of generative software such as ChatGPT and GithubCopilot, there is a need for automatic fast verification of software.

Although counter automata are, generally speaking, a Turing complete model of computation, subclasses exist for which reachability (and its complement, safety) is decidable. Two such classes are one-counter automata, that limit the amount of counters to 1, and vector addition systems with states (VASS, for short), which have no conditions on the counter values besides that they have to be positive. In both cases, tight complexity bounds for the reachability problem have been proven: Reachability for one-counter automata is NP-complete and Ackermann-complete for VASS.

To provide more efficient solutions, we present conservative approximations for both classes. We present continuous one-counter automata, which allow partial updates to be scaled down before applying them to the counter. Then, we give a P-time algorithm for verifying reachability in continuous one-counter automata, as well as an NP algorithm for verifying reachability in parametric one-counter automata. These algorithms are even more powerful in that they compute the full set of reachable values. We present a geometrical interpretation of reachability sets for continuous VASS—here, again, counter updates can be scaled down. We prove that the reachability problem for so-called flat VASS and linear path schemes is in P and that linear path schemes of polynomial length are sufficient to witness reachability. Additionally, we provide an implementable algorithm by encoding the reachability sets of linear path schemes as a solution of set (in)equalities.

Finally, we look at a practical case study of verifying properties on stochastic compartment models. We establish that certain stochastic compartment models can be encoded as probabilistic counter machines where the configurations are bounded. 

Based on the latter, we obtain simple descriptions of the Markov chains induced by such models in the PRISM language. This enables the analysis of such compartmental models via probabilistic model checkers. We report on experimental results where we analyze the efficiency of probabilistic model checkers on a Belgian COVID-19 model.

Evgenii Vlasov

• 27/03/2024
  
• 16.00 uur
• Locatie: Campus Groenenborger, S.207
• ​Online Doctoraatsverdediging
• Promotoren: Sara Bals & Johan Verbeeck
• Departement Fysica

Abstract

Electron tomography (ET) is an indispensable tool for determining the three-dimensional (3D) structure of nanomaterials in (scanning) transmission electron microscopy ((S)TEM). ET enables 3D characterization of a variety of nanomaterials across different fields, including life sciences, chemistry, solid-state physics, and materials science down to atomic resolution. However, the acquisition of a conventional tilt series for ET is a time-consuming process and thus cannot capture fast transformations of materials in realistic conditions. Moreover, only a limited number of nanoparticles (NPs) can be investigated, hampering a general understanding of the average properties of the material. Therefore, alternative characterization techniques that allow for high-resolution characterization of the surface structure without the need to acquire a full tilt series in ET are required which would enable a more time-efficient investigation with better statistical value.

In the first part of this work, an alternative technique for the characterization of the morphology of NPs to improve the throughput and temporal resolution of ET is presented. The proposed technique exploits surface-sensitive secondary electron (SE) imaging in STEM employed using a modification of electron beam-induced current (EBIC) setup. The time- and dose efficiency of SEEBIC are tested in comparison with ET and superior spatial resolution is shown compared to conventional scanning electron microscopy. Finally, contrast artefacts arising in SEEBIC images are described, and their origin is discussed.

In the second part of my presentation, I will focus on real applications of the proposed technique and introduce a high-throughput methodology that combines images acquired by SEEBIC with quantitative image analysis to retrieve information about the helicity of gold nanorods. I will show that SEEBIC imaging overcomes the limitation of ET providing a general understanding of the connection between structure and chiroptical properties.

Irene Ramirez Rojas

• 22/03/2024
  
• 15.00 uur
• Locatie: Campus Drie Eiken, O.04
• Online Doctoraatsverdediging
• Promotoren: Erik Verbruggen & Heidy Schimann
• Departement Biologie

Abstract

Tropical rainforests host an exceptional biodiversity and play a fundamental role in the regulation of global climatic cycles. Soil fungi and bacteria are key players in the transformation and processing of nutrients in terrestrial ecosystems while having an essential role as tree mutualists or antagonists. Still, there are gaps in our understanding of the main variables driving soil microbes on these forests and it is unclear how future climate change scenarios may impact soil microbes and further affect the ecosystem.

In this thesis, we first explored the drivers of the microbial community composition in two pristine forests in French Guiana by using amplicon DNA sequencing. The neighboring tree species were found to be a crucial factor influencing the fungal and bacterial community composition at our sites regardless of the season. Additionally, within the environmental factors explored, soil moisture, phosphorus (P) and nitrogen (N) availability were consistently the main soil properties controlling the composition of soil microbial communities.

Secondly, as increased nutrient deposition due to anthropogenic activities are expected to affect tropical forests ecosystems N and P availability, a factorial N and P nutrient addition experiment in the same sites was used to assess the effects of changes in the soil nutrient stoichiometry on the soil microbial communities. These results showed that after 3 years of nutrient additions, the bacterial and fungal community composition was affected by both the N and P additions. Besides, the fungal community composition had a stronger response to the nutrient addition, especially when P was added. Moreover, when the nutrient addition effect was assessed in bacteria and fungi with different life strategies, we found different nutrient optima between them.

Furthermore, to study the effect of the connection to an existing mycorrhizal mycelium on tree seedlings, I established a mycelium exclusion experiment. Interestingly, we could not detect an effect of the mycorrhizal mycelium exclusion on the seedling N uptake, performance, or fungal community composition in roots after one year.

All together this work provides a deeper understanding of the factors influencing the soil microbial communities on these lowland tropical forests, demonstrating that the tree community composition exerts a higher influence on the soil microbial community composition than previously expected. Moreover, our results show that the fungal and bacterial community composition and its relationship with trees in the vicinity is highly dependent on the ecosystem nutrient availability.

Lize Delanghe

• 05/03/2024
  
• 17.00 uur
• Locatie: Campus Drie Eiken, O.01
• ​Online Doctoraatsverdediging
• Promotoren: Sarah Lebeer, Ingmar Claes, Julie Leysen & Margo Hagendorens
• Departement Bio-ingenieurswetenschappen

Abstract

The human skin microbiome is an open ecosystem that is influenced by external and personal factors and forms a key barrier against pathogens and other foreign substances. Different inflammatory skin conditions, such as atopic dermatitis (AD), are associated with a disturbed skin microbiome. The etiology of AD is complex, with roles for genetics, the immune system, environmental factors, and the skin microbiome, with a key role for Staphylococcus aureus as a skin pathogen. A high need for alternative treatments for AD has sparked the interest in probiotic interventions. This PhD thesis aimed to achieve in-depth insights into the relation between the skin microbiome and AD and to contribute to the development of a new probiotic product for AD. To develop microbiome-based treatments, we should first thoroughly understand the healthy skin microbiome. For this, we collected skin samples from the inner elbow of healthy volunteers and identified the core bacterial community. Age showed the be the major driver defining the skin microbiome composition and longitudinal stability. In addition, significant associations were found between specific skin taxa and season, hygiene, supplements, and the number of household member. Next, we compared the skin microbiome of our healthy cohort with AD patients. Here, we showed that S. aureus did not appear to have a prominent role in mild AD. We also assessed other taxa associated with mild AD and identified six skin species with an increased and 15 genera with a decreased abundance. To elucidate the potential of lactobacilli-based probiotics, we performed an exploratory study investigating the application of three lactobacilli strains on mild AD skin. The lactobacilli showed a good engraftment in the skin niche and the formulated creams reduced erythema and itch on the patients skin. These results already showed that probiotics have a high potential for AD, but there exists a large variety in strain-specific modes of action wherefore a careful selection of the most effective strains is important. Therefore, we selected 76 bacterial isolates and based on in vitro characterization of these strains, with the focus on safety, applicability and functional activity, we could finally select seven probiotic strains.

In conclusion, this work contributed to the microbiome research field and the development of new and effective treatments for AD by gaining insights into the skin microbiome in health and disease. In addition, we could select seven strains showing high promising modes of action, next to good safety and growth conditions.

Falk Mielke

• 01/03/2024
  
• 16.00 uur
• Locatie: Campus Drie Eiken, O.04
• Promotoren: Peter Aerts & Chris Van Ginneken
• Departement Biologie

Abstract

One crucial characteristic which sets animals apart from most other forms of life is the capability of quick locomotion.

Yet moving around does not always come easy: some animals are better at it than others, and common research tools in the field of locomotor biomechanics occasionally fail to quantify subtle differences.

For example, during early development, variability in locomotor patterns is high, faults and instabilities are common, but maturation is quick, which is a challenging context for comparative biomechanics.

In this project, I set out to expand our methodological capabilities for developmental, comparative biomechanics.

The thesis covers kinematics (how animals move) and kinetics (why they move). Based on the observation that locomotor patterns are often repetitive, and applying probabilistic, predictive models which incorporate variability, I spotlight the most fragile of newborn animals: those who are born with particularly low weight.

My primary model system are piglets, where low birth weight is common due to increasing litter sizes in commercial breeding.

The applied methods (Fourier analysis, probabilistic statistics) are exapted from other fields, thus not novel, but rarely applied to quantitative biomechanics to date.

I also highlight limitations and quantify commonly accepted inaccuracies of existing inverse dynamic methods. The case of piglet locomotion can demonstrate how the exapted tools enable unprecedented detail in the analysis of locomotor biomechanics.

In particular, I can confirm that low birth weight piglets are fully capable of normal locomotion, and I precisely quantify how their development is halted shortly after birth.

This provides some important constraints for the evaluation of coping strategies in commercial farming.

Besides, the methodological advances which I present in detail enable a whole new set of research questions for different contexts, within the field of locomotor biomechanics and beyond.

Jonas Schram

• 23/02/2024
  
• 16.00 uur
• Locatie: Campus Drie Eiken, O.4
• ​Online Doctoraatsverdediging
• Promotoren: Karolien De Wael & Marc Parrilla Pons
• Departement Bio-ingenieurswetenschappen

Abstract

Today, illicit drugs are omnipresent in society. Clandestine markets are growing faster than ever before, record amounts of cocaine are seized in seaports and airports, while the associated violence is spiralling out of control. In addition, drug monitoring centres worldwide are warning for the increasing complexity of the drug markets, as the traditionally popular drugs are joined by countless new synthetic variants, while medical drugs are also increasingly being abused. In order to provide services confronted with illicit drug samples (police, customs, forensic scientists, first responders, …) with important information on the identity of an unknown sample, suitable analytical tests are required. While these exist for laboratory environments, on-site applicable tests are important to accelerate the decision-making process. Electrochemical sensors have all the advantages required for such on-site tests: they are fast, portable, easy-to-use and reliable. Furthermore, they are not influenced by colours, which are frequently added to drug samples to deceive the existing tests.

Previous work has mainly focussed on the detection of a single drug per analysis. However, many drugs could be encountered due to the diversity of the drug markets. Therefore, this project developed electrochemical strategies for the detection of multiple drugs simultaneously. First, the electrochemical behaviour of the individual drugs was studied in different measuring conditions (assessing the influence of pH, concentration and temperature). Then, all findings and strategies were combined to detect multiple targets simultaneously. An electrochemical sensor was developed for the four most popular drugs at music festivals: cocaine, MDMA, amphetamine and ketamine. This sensor generates a so-called ‘superfingerprint’ of the sample, which is then automatically interpreted by a developed algorithm in order to produce a straightforward output.

Finally, a pill analysis sensor was developed in the context of drug checking services, where a consumer can anonymously have a sample chemically analysed to obtain information on the composition, dose and potentially harmful additives. The sensor achieved an outstanding accuracy in identifying the main component and provided the option to quantify, as well as an indication on the presence of other substances in the sample. The project’s findings demonstrate the potential for electrochemistry in illicit drug detection and provide a basis for the development of new sensors, targeting other drug combinations.

Fardokth Rezayi

• 22/02/2024
  
• 16.00 uur
• Locatie: Campus Drie Eiken, O.01
• ​Online Doctoraatsverdediging​​
• Inkomend dubbeldoctoraat Cardiff University - Universiteit Antwerpen
  
• Promotoren:  Sabine Van Doorslaer & Damien Murphy
• Departement Chemie

Abstract

Cu(II) coordination chemistry is of significant importance due to copper's widespread applications, particularly in chemical catalysis. This thesis explores the molecular structure, electronic properties, and variable coordination geometry of trigonal bipyramidal complexes of Cu(II) with tripodal ligands, more specifically different tripodal tetraamines. While square planar and square pyramidal Cu(II) complexes are commonly studied, less attention is given to trigonal bipyramidal Cu(II) centres. A variety of Electron Paramagnetic Resonance (EPR) techniques is used as a unique analytical tool to probe Cu(II) complex chemistry.

While the counter ions had only a negligible effect on coordination through outer sphere interactions, the effect of the type of tetraamine, pH and their concentration was significant, revealing subtle and strong variations in the coordination chemistry upon change of these conditions and thus emphasizing the importance of understanding the solution-based structures when aiming for specific applications.

The performance of different trigonal bipyramidal Cu(II)-tetraamine complexes for the selective oxidation of glycerol was further explored. The interest in glycerol oxidation is growing, since glycerol is a valuable bio-renewable compound formed during biomass conversion. Through a combination of different techniques, the catalytic behaviour could be fit to the faith of the Cu(II) complex during reaction. Attempts were made to heterogenise the Cu(II) complexes into Y zeolites in order to allow easy removal of the catalyst from the reaction mixture after glycerol oxidation. Though the correlation between Cu(II)-complex encapsulation, Si:Al ratio, and proton count in the zeolitic structure was identified, the heterogeneous material proved unsuitable for glycerol oxidation. Nevertheless, it holds promise for exploring alternative catalytic reactions.

Gunter Flipkens

• 19/02/2024
  
• 13.00 uur
• Locatie: Campus Drie Eiken, O.1
• ​Online Doctoraatsverdediging
• Promotoren: Ronny Blust & Raewyn Town
• Departement Biologie

Abstract

Drastic greenhouse gas emission reductions and gigaton-scale atmospheric carbon dioxide (CO2) removal are needed to keep global warming below 2°C. Silicate rock weathering has regulated climate on earth over geological time scales. Coastal enhanced silicate weathering (CESW) aims to accelerate this process by distributing gigatons of finely ground olivine-rich rock in dynamic coastal environments. Olivine is a proposed candidate mineral due to its abundance, relatively fast weathering rate, and theoretically high CO2 sequestration potential. However, the in situ CO2 sequestration potential remains uncertain and olivine’s high nickel (Ni) and chromium (Cr) content could be of potential ecological concern. This thesis aimed to advance our understanding of olivine dissolution and CO2 sequestration kinetics under the influence of hydrodynamics and assess potential ecotoxicological effects of CESW.

First, we investigated the effect of continuous grain-grain collisions on olivine weathering rates in seawater. Physical agitation enhanced olivine dissolution by 8 to 19 times compared to stagnant conditions, likely due to advective pore water flushing. Therefore, olivine should be supplied in coastal areas with sufficiently high bed shear stress and pore water exchange rates. Subsequently, a flume experiment was conducted to investigate the effect of current on olivine dissolution in permeable sediment. Olivine dissolution was more than one order of magnitude lower than expected, for reasons that could not be identified, highlighting the need for studies under environmentally realistic conditions.

Next, a first assessment of the safe olivine deployment scale was made based on existing marine Ni and Cr environmental quality standards. Results indicated that 0.059 to 1.4 kg of olivine per m2 of seabed could be supplied without posing metal toxicity risks for benthic biota. Changes in sediment physicochemical properties may also lead to avoidance of olivine rich sediments by marine organisms. Short choice experiments with the gastropod Littorina littorea and amphipod Gammarus locusta indicated avoidance of pure olivine but tolerance to environmentally relevant olivine concentrations of 30% w/w and lower. Metal bioaccumulation and chronic olivine toxicity testing with Gammarus locusta further revealed concentration and grain size dependent effects, with adverse reproductive outcomes at olivine concentrations of 10% w/w and higher. These findings underscore the necessity for additional olivine toxicity data to derive accurate, site-specific olivine application guidelines. Overall, our work provides novel insights into the stimulating effect of hydrodynamics on olivine reactivity and shows possible trace metal-related adverse ecological impacts of CESW.

Mikhail Mychinko

• 12/02/2024
  
• 16.00 uur
• Locatie: Campus Groenenborger, US.024
• ​Online Doctoraatsverdediging​
• Promotor: Sara Bals
• Departement Fysica

Abstract

During the past decades, metallic nanoparticles (NPs) have attracted great attention in materials science due to their specific optical properties based on surface plasmon resonances. Because of these phenomena, plasmonic NPs (or nanoplasmonics) are very promising for application in biosensing, photocatalysts, medicine, data storage, solar energy conversion, etc. Currently, colloidal synthesis techniques enable scientists to routinely produce mono and bimetallic NPs of various shapes, sizes, composition, and elemental distribution, with superior properties for plasmonic applications. Two primary directions for further advancing nanoplasmonic-based technologies include synthesizing novel morphologies, such as highly asymmetric chiral NPs, and gaining deeper insights into the factors affecting the stability of produced nanoplasmonics. With the increasing complexity of nanoplasmonics’ morphologies and higher stability requirements, there is a pressing need for thorough investigations into their 3D structures and their evolution under different conditions, with high resolution. Electron tomography (ET) emerges as an ideal tool to retrieve shape and element-sensitive information about individual nanoparticles in 3D, achieving resolution down to the atomic level. Moreover, ET techniques can be combined with in situ holders, enabling detailed studies of processes mimicking real applications of nanoplasmonic-based devices. The first part of this defense will focus on structural and morphological characterization of chiral Au NPs, promising for spectroscopy techniques based on the differential absorption of left- and right-handed circularly polarized light. Specifically, I will discuss the primary strategies for wet-colloidal growth of the various types of intrinsically chiral Au NPs. Advanced ET methods will be demonstrated as powerful tools for characterizing the final helical morphologies of the produced Au NPs and for studying the chiral growth mechanisms by examining intermediate structures obtained during chiral growth.

The second part will focus on the stability under heating of various Au@Ag core-shell NPs. Operating in real conditions, such as elevated temperatures, may cause particle reshaping and redistribution of metals between the core and shell, gradually altering nanoplasmonics properties. Hence, a thorough understanding of the influence of size, shape, and defects on these processes is crucial for further developments. I will show how recently developed techniques, combining fast ET with in-situ heating holders, have allowed me to evaluate the influence of various parameters (size, shape, defect structure) on heat-induced elemental redistribution in Au@Ag core-shell nanoparticles qualitatively and quantitatively. Additionally, I will discuss the prospects of high-resolution ET for visualizing the diffusion of individual atoms within complex nanostructures.

Jan Clavel

• 05/02/2024
  
• 14.00 uur
• Locatie: Campus Drie Eiken, Q0.02
• Promotoren: Ivan Nijs, Erik Verbruggen & Jonas Lembrechts
• Departement Biologie

Abstract

Non-native species invasions are one of the most impactful drivers of biodiversity and ecosystem services loss worldwide and their occurrence is increasing rapidly as a consequence of ever-growing anthropogenic activities. One aspect of plant species invasion, which is only recently being recognized as a significant determinant of invasion success, is the symbiosis between plants and mycorrhizal fungi. Here, I focus on anthropogenic disturbance in mountain ecosystems and its impact on plant communities and mycorrhizal fungi to answer how these communities are impacted by said disturbance and whether non-native plants can benefit from these altered conditions. Therefore, I used three different approaches: 1) repeated surveys of plants and arbuscular mycorrhizal fungi along disturbed roadsides in the mountains of Norway, 2) combining a global plant dataset from along mountain roads with a database associating plants with their mycorrhizal types, and 3) an in-situ seed addition experiment measuring non-native plant success and changes in fungal community following different types of disturbance treatments. Through these methods, I assessed the effects of anthropogenic disturbance on mycorrhizal symbiosis and non-native plant species at multiple scales and resolutions.

I found that road disturbance has a globally consistent effect on mycorrhizal types in mountain systems: plants associated with arbuscular mycorrhizal (AM) fungi were more abundant following disturbance, and vegetation associated with ectomycorrhizal- or ericoid-mycorrhizal fungi was conversely less abundant. In the Norwegian regional study, AM fungi were similarly more abundant and diverse in the roots of plant communities affected by roadside disturbance. Experimental results found that physical disturbance and nutrient addition facilitate non-native plant success, have negative effects on EcM fungi and positive effects on fungal pathogens.

Our results show that anthropogenic disturbance has an effect on mycorrhizal fungi and in turn impacts the distribution of plant species in disturbed mountain systems. The resulting shift in mycorrhizal fungi towards AM can facilitate non-native plant success through disruption of the native fungal communities, especially so in high elevation and cold climate regions which are naturally less dominated by AM plants. I believe that these conclusions highlight the role of mycorrhizal symbiosis in understanding plant invasions trajectories and in turn emphasize the importance of closely monitoring sources of anthropogenic disturbance in mountain systems in order to prevent future establishment of non-native plants.

Haifa Rejeb Sfar

• 29/01/2024
  
• 14.00 uur
• Locatie: Campus Groenenborger, T.105
• ​Online Doctoraatsverdediging​
• Promotoren: Albert De Roeck & Nick Van Remortel
• Departement Fysica

Abstract

This thesis presents a search for long-lived heavy neutral leptons (HNLs) using proton-proton collision events, with a focus on the νMSM model for HNL production. The νMSM model is a theoretical framework that extends the Standard Model of particle physics to include right-handed neutrinos and provides a possible explanation for the observed neutrino masses and mixing angles. We have analyzed a data sample containing two leptons (electron or muon) and jets, with an integrated luminosity of 138 fb1 collected from 2016 to 2018, which corresponds to the full RunII dataset, and have developed a novel jet tagger based on a deep neural network to identify displaced jets from the HNL decay.

To estimate the contribution from background processes, we used an ABCD method, which is a data-driven technique that relies on the correlation between two independent variables to separate signal and background events. We applied this method to the data in sideband regions and determined the expected background in the signal region. No excess in data over the expected background is observed. Limits on the HNL production cross section are derived as a function of the HNL mass and the three coupling strengths (VlN ) to each lepton generation (l).

Our results provide the best limit on the coupling strength for pure muon coupling scenarios, excluding values of |VμN |2 > 5(4) × 107 for Dirac (Majorana) HNLs with a mass of 10 GeV at 95% CL. This has important implications for the viability of the νMSM model and other theoretical models that propose the existence of HNLs. Our methodology, including the use of the jet tagger and the ABCD method, can be applied to future searches for HNLs at higher energies and luminosities.

However, our study has limitations, such as the assumption of a specific HNL production mechanism and the use of simplified background models. Future research could focus on improving the sensitivity of the jet tagger, exploring alternative HNL production scenarios, developing more sophisticated background estimation techniques, and combining the results from existing HNL searches to improve the sensitivity and coverage of the parameter space.

Tong Zhang

• 26/01/2024
  
• 15.00 uur
• Locatie: Campus Groenenborger, V.008
• Promotoren: Shoubhik Das & Bert Maes
• Departement Chemie

Abstract

Due to the climate change, pollutions, energy shortage and other interrelated global crises, there is always an increasing demand for the development of environmentally friendly processes in the chemical industries. In the last two decades, the field of photochemistry has emerged as a potent methodology across diverse domains, enabling the synthesis of numerous intricate compounds through environmentally sustainable means. This thesis elucidates four distinct methodologies concerning the generation of valuable products across diverse domains through the utilization of photoredox and photochemical reactions. The thesis is divided into five chapters:

• Chapter 1: An overview and introductory exposition of the fundamental principles and concepts pertaining to photochemistry are provided.

• Chapter 2: We have enhanced the generation of hydrogen peroxide by introducing an aryl amino group in polymeric carbon nitrides via visible light-mediated photocatalysis. In addition to increasing the efficiency of photocatalytic system, the description of the whole reactive scenario for the polymeric carbon nitrides has been depicted by combining diverse characteristic methods and theoretical calculations. Futhermore, the possible active catalytic sites are identified with the aid of 15N and 19F solid state NMR without using any expensive labeling reagent.

• Chapter 3: We have developed a unique methodology for the generation of α-amino radicals under the irradiation of visible light under a metal-free condition. This strategy is induced by π–π stacking and ion-pairing interactions and facilitated the synthesis of functionalized amines through three-component coupling reactions.

• Chapter 4: We have designed an efficient method for the red light-mediated sulfonyltrifluoromethylation of olefins which provide remarkable regioselectivity. This reaction system has been thoughtfully designed, and excellent substrate compatibility and functional group tolerance exhibits the industrial potential, thus validating the significance of this strategy.

• Chapter 5: We have developed a metal-free photocatalytic system for the transformation of biomass into formic acid. Compared to previous strategies, our method can work efficiently at room temperature and atmospheric pressure. Notably, real biomass and even daily-life-based-materials such as waste papers and oak cork stoppers of wine bottles are also smoothly converted to formic acid.

Lin Zi

• 22/01/2024
  
• 09.00 uur
• Locatie: Campus Drie Eiken, Q.002
• Promotoren: Han Asard, Hamada Abd Elgawad & Kris Laukens
• Departement Biologie

Abstract

One aspect of climate change is the increased persistence of precipitation regimes (PRs), characterized by alternated longer dry and wet periods. While the ecological impacts of singular extreme events like drought and flood have been extensively studied, the immediate and legacy effects of the evolving more persistent PR, particularly at the molecular level in plants, remain underexplored.

This doctoral thesis aims to bridge this knowledge gap by conducting a large-scale outdoor experiment, applying a range of PR from short to long dry/wet cycles to grassland mesocosms. Ecometabolomics analysis revealed that the metabolome of a relatively sensitive species, Centaurea jacea, shifted under mild PR (10-day dry/wet cycle), while the metabolome of other less sensitive species changed only from a 20-day PR onwards. Accumulation of amino acids, lignin, and decreased non-structural sugar levels are universal responses across several species to increasing PR extremity, while changes in other metabolite classes are exhibited in a more species-specific manner. The sensitive species are less capable of inducing sufficient changes in important molecules such as lignin and phenylalanine, which may partly explain its sensitivity in PR responses.

Beyond immediate effects, my research found that previous exposure to more persistent PR resulted in acclimated grassland communities in the following year. These communities showed increased aboveground productivity and structural sugar content, reduced molecular stress responses and reduced diversity. Furthermore, soil inoculum from more persistent PR promoted the upregulation of several pathways, such as hormone synthesis (e.g., jasmonic acid, abscisic acid, salicylic acid, ethylene), oxidative stress, cell wall modification (e.g., lignin deposition, callose synthesis, cell wall thickening, pectin metabolic process), and chitin catabolic processes, which may provide potential beneficial effects for plants.

In conclusion, this thesis demonstrates that more persistent PR induces significant changes in plant biochemical and transcriptional levels. While these changes may enhance the acclimation of grassland species, they may also decrease nutritive value, potentially altering their role in the feeding of organisms. Species or individuals unable to induce sufficient protective changes may be excluded from the community, leading to a loss of diversity in the ecosystem.

Nathanaël Six

• 18/01/2024
  
• 16.00 uur
• Locatie: Campus Drie Eiken, S1
• Promotoren: Jan Sijbers & Jan De Beenhouwer
• Departement Fysica

Abstract

X-ray computed tomography (CT) is a powerful and non-invasive technique to visualise the internal structure of an object from a set of X-ray radiographs. Reconstruction algorithms are used to map projection data to a 3D volume. A model of the X-ray acquisition process is used by reconstruction algorithms and the algorithms require a large number of projections to function well. However, in certain applications, the number of projections has to be limited, to reduce total delivered dose, lower acquisition time or because of geometrical constraints. Furthermore, the most commonly used algorithms have a simple linear forward model for X-ray attenuation that does not model the real acquisition accurately. Finally, conventional reconstruction algorithms in CT are not efficient with respect to computation time. In this thesis, we will develop improved reconstruction algorithms for CT by investigating more accurate non-linear forward models, and different numerical optimisation approaches for these models.

Eline Cauwenberghs

• 16/01/2024
  
• 17.00 uur
• Locatie: Campus Drie Eiken, Q0.02
• Promotoren: Sarah Lebeer & Kim van Hoorenbeeck
• Departement Bio-ingenieurswetenschappen

Abstract

For several decades, it was widely believed that the healthy respiratory tract was sterile. However, advancements in next-generation sequencing techniques have enabled us to unveil the microbial communities residing within the respiratory tract, both in health and disease. However, there is a lack of in-depth functional insights into these communities to design innovative microbiome therapies for the respiratory tract. Nevertheless, such therapies show great promise as they can act via multifactorial mechanism of action improving respiratory health. Specifically for people with cystic fibrosis (CF), microbiome therapies could complement current treatments by preventing chronic colonization of pathogens at early age and by enhancing the effectiveness of therapies such as antibiotics and modulators through creation of a more stable microbial ecosystem. This PhD thesis aimed to expand the knowledge on the microbial communities within various respiratory tract niches and explore the potential of microbiome therapies as a preventive or complementary treatment strategy for CF. First, we studied the salivary microbiome of 246 women using 16S rRNA amplicon sequencing to investigate whether we could detect bacterial biomarkers linked with respiratory disease. We found that the salivary microbiome was highly preserved among healthy women and lifestyle and host-related parameters had only subtle effects on specific taxa. For the detection of bacterial biomarkers linked with respiratory disease, more targeted sampling methods and insights at a lower taxonomic level were needed. Therefore, we next performed shallow metagenomic shotgun sequencing on respiratory tract samples, including nasopharyngeal, oropharyngeal and sputum samples. The host DNA depletion step was found to reduce the presence of Gram-negative taxa, which play an important role in the human airways. Taken this bias into account, we could show the potential of shallow shotgun sequencing in a clinical setting by identifying important CF pathogens at species level in oropharyngeal and sputum samples providing valuable information about the patient’s disease status. Lastly, we aimed to evaluate the potential of probiotics for CF. Lacticaseibacillus casei AMBR2 demonstrated important adaptation and multifactorial probiotic characteristics in vitro with a focus on CF pathogenesis. Moreover, we identified four putative bacteriocin gene clusters in the genome of AMBR2 of which one exhibited high activity against Gram-negative pathogens.

This work combined microbiome research (16S rRNA amplicon and shallow metagenomic shotgun sequencing) with functional studies to achieve the research goals. It has enriched the understanding regarding microbe-microbe and microbe-host interactions in the context of CF, paving the way for future therapeutic applications.

Lennart Fernandes

• 10/01/2024
  
• 16.00 uur
• Locatie: CST, Promotiezaal van de Grauwzusters, Lange Sint-Annastraat 7, 2000 Antwerpen
• ​Online Doctoraatsverdediging
• Promotoren: Michiel Wouters & Jacques Tempere
• Departement Fysica

Abstract

In this thesis the behaviour of quantum fluids out of equilibrium is studied. These are ultracold gases in which quantum mechanical effects - usually only visible at the atomic scale - determine the macroscopic properties. The work is composed of several related projects, in which the central role of quantum fluctuations is highlighted.

In the Gaussian theory for quantum systems, fluctuations are approximated as corrections to a classical description of the fluid. A central contribution of this work is the development and application of a new approach that enables this established method to describe quantum states with large, nonlinear fluctuations. Inspired by the study of open quantum systems, we do this by introducing a virtual environment, which continuously measures the system to suppress the growth of quantum fluctuations. This method is successfully applied to the dynamics of a spinor fluid, in which restrictions on the interactions between atoms lead to the formation of a non-equilibrium state with a high degree of quantum entanglement.

Finally, the acquired knowledge on spinor fluids is used for their application as a platform for analog gravity. We introduce Hawking radiation emitted by black holes, show that the underlying mechanism is a general property of quantum fields in a flowing background, and apply this analogy to spin waves in a spinor gas.