Wetenschappen

Doctoraten 2024

Woon een doctoraat bij of raadpleeg de voorbije verdedigingen

Energy-Aware Design of Battery-Less IoT Devices - Adnan Sabovic (27/06/2024)

Adnan Sabovic

  • 27/06/2024
  • 16.00 uur
  • Locatie: Campus Middelheim, G.010
  • Promotoren: Jeroen Famaey & Eli De Poorter
  • Departement Informatica


Abstract

The Internet of Things is a concept used to connect embedded objects to the Internet, enabling billions of tiny devices to cooperate and communicate with each other while performing different application tasks. Currently, most of these devices rely on batteries as the main power source. These batteries can provide a stable power supply, but even when rechargeable, they are short-lived, lasting at most a few years. They contain toxic chemical components that can be harmful to the environment. Tiny battery-less IoT devices that depend on harvested energy from their environment provide a promising alternative for a more sustainable IoT vision. Using this approach, battery-less devices harvest available energy from different environmental sources (e.g., solar, kinetic, Radio Frequency (RF) energy) and store it in small capacitors. These capacitors act as energy storage, and compared to batteries, they are smaller and lost more than a decade, thanks to their ability to handle a large number of charge cycles. However, they have significantly lower energy density, storing less energy in a given volume, which can be critical for applications that require long-term energy supply and storage. Also, battery-less IoT devices operate in an unpredictable and dynamic energy harvesting environment, which together with the small energy storage, results in intermittent on-off behavior of the device. To effectively use battery-less IoT devices, the applications running on them should be able to properly handle their intermittency. Measuring and understanding the current consumption and execution time of different tasks of the application is one of the most important steps in achieving this. Conventional computing models and static sequential applications cannot handle such behavior, as they cannot guarantee forward progress, relying only on volatile memory, and assuming a stable energy supply during execution. This problem can be solved with task-based models, where each task performs some atomic function, and its output is saved in non-volatile memory after it successfully completes, including energy awareness as a most important factor in helping to avoid power failures and maintain forward progress.

Advancements in processor efficiency, sensors, as well as low-power communication and computing, unlock the possibility for direct deployment for a wide range of traditional and intelligent applications on battery-less devices, enabling them to play an important role as an extreme edge device in an IoT ecosystem.

Investigating the role of antimicrobial specialized metabolites and bacteriocins in the vaginal microbial community - Jelle Dillen (24/06/2024)

Jelle Dillen

  • 24/06/2024
  • 17.00 uur
  • Locatie: Campus Drie Eiken, O.01
  • Promotoren: Sarah Lebeer & Peter Bron
  • Departement Bio-ingenieurswetenschappen


Abstract

Urogenital infections are major contributors to antibiotic prescriptions, but treatment efficacy is compromised by antibiotic resistance. Additionally, antibiotics disrupt beneficial microbiota, increasing the risk of relapses and side effects. This highlights the urgent need for alternatives, such as microbiome-altering therapies. A vaginal microbiome dominated by lactobacilli, such as L. crispatus and L. jensenii, is associated with vaginal and urogenital health and is considered an "optimal" microbiome. A depletion of Lactobacillus species in the vagina has been linked to higher risks of bacterial, fungal, and viral infections in the vagina and other urogenital sites. While lactobacilli are known for their lactic acid production, their other antimicrobial compounds, including bacteriocins, nonribosomal peptides, and polyketides, remain understudied.

To enhance our understanding of their role, we utilized extensive data and samples from the Isala citizen science study, isolating over 900 Lactobacillaceae strains. Genomic analysis of 242 selected isolates revealed 514 biosynthetic gene clusters, mostly novel, including ribosomally-synthesized and post-translationally modified peptides, nonribosomal peptides, and polyketides. This genetic diversity highlights the untapped potential of Lactobacillaceae for specialized metabolite discovery. Further investigation into the diversity of L. crispatus isolates, coupled with their antimicrobial properties against common vaginal pathogens, revealed clear links between phylogeny, biosynthetic potential, activity, and vaginal community composition. One strain exhibited particularly high activity against tested pathogens, which correlated with the presence of a novel lanthipeptide cluster. This cluster's antifungal activity was validated through in silico characterization and heterologous expression in Escherichia coli. Additionally, we aimed to characterize a novel antimicrobial from L. jensenii, conserved across the species, which showed activity against the Gram-negative pathogen Klebsiella pneumoniae, a cause of adverse pregnancy outcomes and vaginal infections.

In summary, this PhD thesis provides an overview of specialized metabolite cluster prevalence and abundance across vaginal Lactobacillaceae, enhancing our understanding of their protective and beneficial roles, particularly focusing on L. crispatus and L. jensenii. By characterizing an antifungal from a specific L. crispatus isolate and a species-conserved antimicrobial from L. jensenii, we have laid the groundwork for developing novel probiotics, live biotherapeutic products, or specialized metabolites.

More persistent rainfall regimes: consequences and solutions for natural and managed grassland systems - Simon Reynaert (19/06/2024)

Simon Reynaert

  • 19/06/2024
  • 16.00 uur
  • Locatie: Campus Drie Eiken, O.07
  • Online Doctoraatsverdediging
  • Promotoren: Ivan Nijs, Hans De Boeck, Erik Verbruggen & Tommy D'Hose
  • Departement Biologie


Abstract

Global warming is changing the intra-annual variability of weather patterns around the world. Recent observations indicate that summer weather persistence is increasing in Europe, resulting in both longer dry and wet spells compared to historic averages. However, the consequences of these newly emerging climate regimes for terrestrial ecosystems have barely been studied. This thesis investigates how increasing weather persistence influences mesic grassland ecosystem functioning in a series of manipulation experiments with model grassland systems under different levels of management intensity. In addition, we explore several solutions for the observed consequences in terms of plant and soil remediation.

In unfertilized, species-rich systems, we found evidence that precipitation regimes with longer dry and wet spells reduce aboveground productivity and native plant diversity in the short-term (one to two years) (Chapters II, III & IV). These changes related to differences in species-specific responses to drought and more pronounced fluctuations in nutrient availability over time as well as shifting species interactions under drought. In particular, the length of the longest drought period throughout the growing season was the strongest determinant of short-term diversity and productivity declines. Moreover, the disproportionate loss of legumes and other forbs compared to graminoids likely negatively affected forage quality. Despite these adverse effects, ecosystems also showed acclimation to more extreme regimes through community reorganization and altered biochemistry, buffering productivity under recurrent and contrasting extreme soil conditions.

In fertilized monoculture systems, increased weather persistence reduced yield yet slightly improved forage digestibility (Chapters V & VI). Moreover, soils from permanent grasslands with elevated organic carbon (OC) showed declines in soil water availability. However, not all species and soil types were affected equally. Growing Festulolium, Festuca arundinacea or Dactylis glomerata led to significantly smaller yield losses compared to Lolium perenne cultivars. Regarding soil remediation, high OC soils with a permanent grassland history limited negative impacts on plant quality and yield in sandy-loam soils. Moreover, mixing basalt powder with the top soil layer improved yield in unfertilized monoculture systems under prolonged dry and wet spells.

To conclude, these findings indicate that increasing weather persistence will likely negatively affect grassland ecosystem service provisioning (i.e., plant diversity, productivity and soil water availability) by altering soil water and nutrient dynamics. However, choosing more drought resistant species and management practices that improve soil carbon sequestration shows potential to limit adverse effects on plant performance, ultimately making natural and managed grassland systems more climate resilient.

Ecological factors driving micro-geographic variation in tick-borne disease risk - Mats Van Gestel (18/06/2024)

Mats Van Gestel

  • 18/06/2024
  • 17.00 uur
  • Locatie: Campus Drie Eiken, O.05
  • Promotoren: Erik Matthysen (UA), Dieter Heylen (UA) & Kris Verheyen (UGent)
  • Departement Biologie


Abstract

The sheep tick (Ixodes ricinus) vectors, among others, Borrelia burgdorferi s.l., the causative agent of Lyme disease. Differences in its density and pathogen prevalence between forests have been attributed to climatological values, vegetation characteristics and the abundance of hosts. However, variation within forests has only been studied sporadically, whereas its understanding would greatly benefit forest management. This knowledge gap is addressed through a multi-year sampling campaign in recreational forests; Tick density, vegetation characteristics and local host abundance were measured and captured ticks were tested for pathogens. This was conducted near recreational infrastructure (benches and trails), as sharp changes in vegetation characteristics, microhabitat and the habitat use of tick hosts are expected here. This in turn was expected to affect tick density and pathogen prevalence. Additionally, the distinction was made between trails in the forest core and those at forest edges. In addition to the highest tick density being recorded in the forest interior, with lower values near infrastructure, an edge effect was observed with lower values at trails in forest edges. These differences within forest stands are attributed to differing vegetation characteristics and the habitat use of hosts. Density was higher in stands dominated by deciduous vegetation with dense canopy, compared to open, coniferous vegetation. The same was true for stands with a more developed shrub layer. Small, consistent differences in pathogen prevalence were also observed and attributed to varying drivers for different pathogens. These conclusions support the occurrence of amplification and inhibition mechanisms on a within-forest stand scale. I herein highlight that the effect of tick borne disease risk drivers may differ based on the considered spatial scale.

Additionally, experiments on the effect of herb layer vegetation on nymphal survival in summer and larval detachment patterns from wood mice were conducted, to estimate whether these processes may affect tick distribution. The experiment on survival implied that canopy and shrub layer vegetation determine microclimate buffering, and therefore also tick survival, to a larger degree than herb layer vegetation. The experiment on larval detachment offers a first indication that environmental factors can alter the detachment probability of larvae from wood mice, independent from temporal effects. The thesis is concluded by the translation of the fundamental findings to a forest management context. The contact rate between ticks and humans is outlined as a persistent knowledge gap with regards to the quantification of tick-borne disease risk.

Methane and Hydrogen Storage in Clathrate Hydrates - Nithin Bharadwaj Kummamuru (10/06/2024)

Nithin Bharadwaj Kummamuru

  • 10/06/2024
  • 15.30 uur
  • Locatie: Campus Drie Eiken, Q.002
  • Promotoren: Patrice Perreault & Sammy Verbruggen
  • Departement Bio-ingenieurswetenschappen


Abstract

In a world increasingly reliant on alternative energy sources, the quest for efficient and secure storage solutions is paramount. This thesis explores the exciting potential of a familiar material – water - to act as a vault for next-generation energy sources like hydrogen (H2) and methane (CH4). Nature offers a solution in the form of clathrate hydrates, fascinating cage-like structures formed from water molecules that can trap these gas molecules within their framework. This research investigates on improving the formation kinetics and gas storage capabilities of clathrate hydrates utilizing porous materials and the interstitial space between non-porous materials to augment the contact between gas and water thereby catalysing the growth of hydrates and unlocking their full potential as efficient and secure energy storage reservoirs. A key outcome of this research is the formulation of an empirical correlation, offering predictive insights into CH4 hydrate phase equilibrium conditions. Innovative approaches utilizing thermally conductive beads have yielded substantial enhancements in CH4 uptake. Furthermore, the identification of optimal water content within porous materials showcases a pathway to maximize CH4 storage capacity and hydrate growth kinetics. In the domain of hydrogen storage, attention is also directed towards unstirred systems, where the integration of functionalized porous materials has demonstrated a significant improvement in the rate of hydrate formation and the overall H2 storage capacity. A noteworthy achievement of this research lies in the successful storage of H2 within confined CH4 hydrates through a gas exchange process and the preliminary results show the potential for a safer and more sustainable method for H2 storage at mild thermodynamic conditions, offering promising prospects for future energy systems.

Per- and polyfluoroalkyl substances (PFAS) in private gardens: factors affecting accumulation in homegrown food and characterization of human exposure risk - Robin Lasters (06/06/2024)

Robin Lasters

  • 06/06/2024
  • 16.00 uur
  • Locatie: Campus Drie Eiken, O.01
  • Online Doctoraatsverdediging
  • Promotoren: Lieven Bervoets & Marcel Eens
  • Departement Biologie


Abstract

In the past decade, homegrown food consumption has surged in rural, urban, and industrial areas. However, organic pollutants in private gardens, including per- and polyfluoroalkylated substances (PFAS), pose health risks by entering the food chain through bioaccumulation. Very little is known about the driving factors of PFAS accumulation in homegrown food. Therefore, this thesis project aimed to assess PFAS accumulation in various homegrown food categories and related human exposure risks, exploring factors affecting PFAS bioavailability. The results showed that multiple PFAS are omnipresent in homegrown food and can accumulate to concentrations that frequently exceed available health guidelines, even under modest consumption scenarios, especially with regard to egg intake. Within the crop category, higher accumulation was noticed in annual crops in comparison to perennial crops, potentially linked with differences in terms of life-history strategies between these two plant taxa. Large spatial and temporal differences in soil PFAS profile and concentrations were found within private gardens, suggesting that site-specific characteristics and functional usage play a major role in shaping local PFAS contamination. Predictive models could be constructed for some major PFAS in eggs, which show promising potential for applicability in risk assessment by policy makers. Moreover, mitigation and remediation measures could be formulated that should be readily usable for private gardeners to ultimately lower PFAS exposure via homegrown food.

PFAS pollution in gardens within ± 4 km from the fluorochemical plant in Antwerp could be strongly linked with both historical and recent fluorochemical emissions. On the other hand, diffusive mechanisms (e.g. atmospheric transport) and site-specific soil management may be mainly affecting levels at gardens further away from point sources. The accumulation in chicken eggs was generally higher closer to the major fluorochemical plant, although soil characteristics (e.g. organic matter, clay content and pH) could strongly affect this pattern. Conversely, the PFAS accumulation in the crops was not affected by the distance from the plant site and soil characteristics played only a minor role in governing crop accumulation. Long-term declining concentrations in soil and eggs could be observed for some PFAS, although this trend stagnated over recent years. Short-term increases of short-chain and long-chain PFAS concentrations could be observed, mainly in the soil from the chicken enclosure. These findings underpin that homegrown food cannot be neglected as a relevant human exposure source to PFAS and show the urgent necessity for further regulation steps and monitoring efforts.


Comparative analysis of metal toxicity responses in aquatic invertebrate and vertebrate model organisms - Sanah Majid (03/06/2024)

Sanah Majid

  • 03/06/2024
  • 16.30 uur
  • Locatie: Campus Groenenborger, T129
  • Promotoren: Ronny Blust & Karen Smeets
  • Departement Biologie


Abstract

The presence of metals in the environment has often been associated with various adverse effects to living systems, including humans. Given their ubiquitous nature, metals are commonly accepted to occur as complex mixtures and have therefore always been of concern. Despite the considerable attention given to this issue, there remains a lack of sufficient knowledge of the mechanisms underlying toxicological outcomes specific to each metal and/or each mixture. In addition, knowledge of the toxicity of metal mixtures in taxonomically distinct species is inadequately explored. Addressing these key questions is important for gaining a better understanding of the magnitude and mechanisms of toxicity in biological systems. In this context, our study aims to explore how exposures in a single and binary metal pollution scenario differentially affect aquatic vertebrate and invertebrate organisms across various biological levels. The study focuses on copper (Cu) and cadmium (Cd) as metal toxicants in three animal models: the zebrafish (Danio rerio), the water flea (Daphnia magna) and the planarian flatworm (Schmidtea mediterranea). Our study contributes to a better understanding of the interactive effects of metal toxicity across different biological levels and emphasises the importance of an in-depth approach in assessing the risks associated with metal pollution. The findings presented in this work show a stronger action of Cu and Cd as a mixture in different aquatic organisms under controlled conditions. In particular, our study reveals important developmental, behavioural, and molecular changes with some effects more manifested in mixtures compared to single metal exposures. Furthermore, our study highlights that relying solely on metal accumulation levels as a reliable predictor of toxicity is insufficient; however, it can still serve as a valuable biomarker of exposure. The absence of a clear relationship between metal concentrations in tissues and observed effects emphasises the influence of internal compartmentalisation and the intricate molecular defence mechanisms involved in damage control and repair processes.

From winter sleep to spring wake-up: elucidating how temperature and daylength affect dormancy and budburst in temperate deciduous trees - Romain Garrigues (27/05/2024)

Romain Garrigues

  • 27/05/2024
  • 10.00 uur
  • Locatie: Campus Drie Eiken, Q.002
  • Promotoren: Matteo Campioli, Han Asard & Hamada Abd-Elgawad
  • Departement Biologie


Abstract

This thesis investigates the timing of phenological stages, the influence of environmental factors (temperature and daylength), and the molecular mechanisms underlying winter dormancy (endodormancy) in deciduous trees. The focus is on two deciduous species: Populus nigra (black poplars) and Fagus sylvatica (European beech). Three field experiments examine responses to current climate conditions, late fall warming, and modified winter-spring daylength. Transcriptome analysis sheds light on gene expression changes during endodormancy. While early successional species exhibit earlier phenological events, temperature variations play a significant role. Lack of chilling accumulation during late autumn affects dormancy depth and spring phenology, with elevated temperature treatments showing varied responses across years. Late autumn temperatures and daylength interaction affect bud dormancy and spring phenology in European beech and are showing that daylength is the last guardian to avoid early budburst. Transcriptome analysis identifies genes associated with dormancy transition, emphasizing DNA binding, cell cycle regulation, and phytohormone pathways. Overall, the thesis contributes to understanding deciduous tree behavior and implications for forest responses to climate change, offering insights into phenological events (dormancy depth and spring budburst) while presenting novel data on molecular mechanisms during endodormancy.

Unscrambling complex heterogeneous nanostructures by using quantitative 4D scanning transmission electron microscopy - Duygu Gizem Sentürk (03/05/2024)

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.


CFD – Assisted Design of Fluidized Reactors for Hydrogen Release from LOHC - Laurens Van Hoecke (02/05/2024)

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.

Combined computational-experimental study on plasma and plasma catalysis for N2 fixation - Hamid Ahmadi Eshtehardi (25/04/2024)

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.

Improving the Accuracy of Transverse Momentum Dependent Parton Branching Methods for Collider Physics - Mees van Kampen (16/04/2024)

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.

Voltage against illicit drug trafficking. Capabilities of electrochemical fingerprinting to detect illicit drugs - Noelia Felipe Montiel (29/03/2024)

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.

Functional potential and ecology of Lactobacillaceae in vegetable fermentations - Tom Eilers (29/03/2024)

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.

Efficient Algorithms for Reachability in Infinite State Space Systems - Tim Leys (28/03/2024)

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.

Exploiting secondary electrons in transmission electron microscopy for 3D characterization of nanoparticle morphologies - Evgenii Vlasov (27/03/2024)

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.

Underground connections: the interplay between tropical rainforest trees and soil microbial communities - Irene Ramirez Rojas (22/03/2024)

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.

Study of the skin microbiome and the potential of topical probiotics for atopic dermatitis - Lize Delanghe (05/03/2024)

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.

Methodological Advances in Studying Postnatal Locomotor Development - Falk Mielke (01/03/2024)

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.

Electrochemical sensing strategies for multiple illicit drugs - Jonas Schram (23/02/2024)

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.

An Advanced EPR Investigation of Copper Complexes in Catalysis - Fardokht Rezayi (22/02/2024)

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.

Coastal enhanced olivine weathering for climate change mitigation: investigating the CO2 sequestration potential and ecotoxicological risks - Gunter Flipkens (19/02/2024)

Gunter Flipkens


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.

Advanced Electron Tomography to Investigate the Growth and Stability of Complex Metal Nanoparticles - Mikhail Mychinko (12/02/2024)

Mikhail Mychinko


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.

The potential for upward range expansion of alien plant species in cold-climate mountains in a warming world - Jan Clavel (05/02/2024)

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.

Search for longlived Heavy Neutral Leptons using a displaced jet tagger in the CMS experiment - Haifa Rejeb Sfar (29/01/2024)

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.


Applications of Photoredox Chemistry for the Generation of Valuable Products - Tong Zhang (26/01/2024)

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.

Elucidating the molecular mechanisms underlying grassland species in response to more persistent precipitation regimes - Lin Zi (22/01/2024)

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.

Improved X-ray CT reconstruction techniques with non-linear imaging models - Nathanaël Six (18/01/2024)

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.


Exploring the potential and molecular mechanisms of beneficial lactic acid bacteria in respiratory mucosal disorders - Eline Cauwenberghs (16/01/2024)

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.


Fluctuations in multicomponent quantum fluids - Lennart Fernandes (10/01/2024)

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.