Abstract: In the biogeochemical flows on Earth, the reactive nitrogen (Nr) level has three times surpassed the safe boundary. The severe transgression of this boundary goes against sustainable planetary development. The modern food production process excessively relies on synthetic Nr fertilizers from the Haber– Bosch process. However, the massive loss of valuable nitrogen resources (i.e., 78-89%) from agriculture has been causing severe nitrogen cascade. Besides, the domestic wastewater in some local areas is discharged without proper treatment, making it a nonnegligible source of Nr pollution for local water bodies. Anthropogenic activities keep pumping out Nr pollution via point-source and non-point-source (NPS) emissions. Compared to the NPS emissions, point sources give visible and identified waste streams. It is vital to intervene the nitrogen cascade from point sources and facilitate humanity back to the safe Nr boundary. The collected and collectible Nr streams from food production, waste management, and recycling secondary raw materials can be used as waste-based fertilizers for agricultural cultivation. Besides the well-investigated recovery of inorganic Nr, organic Nr accounts for a massive Nr proportion on the Earth. Proper handling and treatment make these useful organic fertilizers for soil-based cultivation. However, these organic Nr fertilizers cannot directly apply to fertigation or hydroponic cultivation systems, and further biological conversion via nitrogen mineralization and nitrification to nitrate is essential. Besides the direct Nr cycling, the indirect Nr cycling ‘over the atmosphere’ should also be considered. In this way, the nitrogen cycle can be completed via converting the waste Nr back to nitrogen gas (i.e., Nr removal) and then synthesizing into Nr again. The municipal wastewater treatment plants receive a vast amount of low-strength Nr wastewater (mainly as ammonium) daily. Compared to the conventional nitrification/denitrification process, partial nitritation/anammox (PN/A) is considered a resource- and cost-effective technology for wastewater with a low COD/N ratio. Moreover, the novel autotrophic denitratation/anammox process could be a good Nr removal process for wastewater containing both ammonium and nitrate. This Ph.D. thesis aimed to develop Nr recovery, conversion, and removal bioreactor strategies for different types of waste streams and biomass. Nr recovery was investigated on high-strength Nr waste streams for fertigation or hydroponic applications in Chapters 2 and 3. On the other hand, Nr removal was studied on the medium- to low-strength Nr waste streams in Chapters 4 and 5. In Chapter 2, a novel mineralization and nitrification system was proposed, producing nutrient solutions from solid organic fertilizers for hydroponic systems. Batch tests showed that aerobic incubation at 35°C could realize the NO₃⁻-N production efficiency above 90% from a novel microbial fertilizer. Subsequently, in the stirred tank bioreactor test, NO₃⁻-N production efficiency stabilized in a range of 44-51% under the influent loading rate of 400 mg TN L⁻¹ d⁻¹ at a 5-day HRT. Using Ca(OH)₂ and Mg(OH)₂ as pH control reagents generated the nutrient solutions with different P, Ca, and Mg nutrient levels. After modeling the nutrient balancing process, the proportion of organic-sourced NO₃⁻-N in the Hoagland nutrient solution (HNS) of Ca(OH)₂ scenario was 92.7%, while only 37.4% in the Mg(OH)₂ scenario. Compared to commercial scenarios, the total costs of the organic-sourced HNS can be cost-competitive for hydroponic cultivation. In Chapter 3, the Nr recovery as nitrate (NO₃⁻-N) from diluted human urine (around 670 mg N L⁻¹) was explored in a trickling filter (TF) for the first time. A novel concept of in-situ integrating the TF system into hydroponic systems was proposed as meaningful progress towards sustainable agriculture. The difference between synthetic and real urine in nitrification efficiency was found to be negligible. The full nitrification of alkalinized real urine was realized in the pH-controlled TF by calcium hydroxide (Ca(OH)₂) at around pH 6. The TF could handle different urine collection batches and maintain relatively stable nitrification performance, with NO₃⁻-N production efficiency and rate of 88±3% and 136±4 mg N L⁻¹ d⁻¹, respectively. The optimal HLR to realize this nitrification performance was 2 m³ m⁻² h⁻¹, with energy consumption of 1.8 kWh electricity kg⁻¹ NO₃⁻-N production. Ca(OH)₂, as a cheap base, its triple advantages on urine alkalinization, full nitrification, and macronutrient supplementation were successfully demonstrated in our proposed concept. In Chapter 4, towards more sustainable wastewater treatment, the feasibility of one-stage partial nitritation/anammox (PN/A) was investigated in three parallel packed-bed trickling filters (TFs), with three types of carrier materials of different specific surface areas. Synthetic wastewater containing 100-250 mg NH₄⁺-N L⁻¹ was tested to mimic medium-strength household waste streams after carbon removal. Interestingly, the cheap carrier based on expanded clay achieved similar rates as commercially used plastic carrier materials. The top passive ventilation combined with an optimum hydraulic loading rate of 1.8 m³ m⁻² h⁻¹ could reach approximately 60% total nitrogen (TN) removal at a rate of 300 mg N L⁻¹ d⁻¹. A relatively low NO₃⁻-N production (13%) via PN/A was achieved in TFs. Most of the TN removal took place in the top compartment, where anammox activity was the highest. Energy consumption estimation (0.78 kWh electricity g⁻¹ N removed) suggested that the proposed process could be a suitable low-cost alternative for nitrogen removal. In Chapter 5, coupling sulfur-driven denitratation (SDN) with anammox was proposed to treat the wastewater containing both NO₃⁻-N and NH₄⁺-N, like the secondary effluents of mainstream PN/A processes. To explore the feasibility of sufficient and stable NO₂⁻-N accumulation via SDN in the long term, the effects of pH setpoints, residual NO₃⁻-N level, and biomass-specific NO₃⁻-N loading rate (BSNLR) were investigated. Alternating the pH setpoints between 7.0 and 8.5 could temporarily stimulate the NO₂⁻-N accumulation. Both the residual NO₃⁻-N and BSNLR showed highly positive correlations with the NO₂⁻-N accumulation efficiency. Under the control of pH 8.5, 1.0±0.8 mg NO₃⁻-N L⁻¹ and 150±42 mg NO₃⁻-N g⁻¹ VSS d⁻¹, SDN could produce 6.4±1.0 mg NO₂⁻-N L⁻¹ in the short term. Thiobacillus members may play a crucial role in managing the NO₂⁻-N accumulation, but the reduction of abundance and possible adaptation significantly impaired the efficacy of control strategies in the long run. Overall, novel technologies have been proposed to sustainably convert Nr in waste streams and biomass. The decision for Nr recovery versus removal and synthesis should be based on specific cases with the best environmental, economic, and human-health sustainability. In the future, the Nr management concepts should be further improved to make the nitrogen cycle more sustainable with higher resource use efficiency and less Nr emissions to the environment. Although the thesis is mainly focused on limited types of Nr waste streams, it pointed out the direction of sustainable Nr management and could facilitate the Nr back to the safe boundary in the long run.

Abstract: Pretreatment is a critical step in the conversion of lignocellulose into biofuels and biochemicals. During pretreatment, the recalcitrance of lignocellulose is reduced, e.g. by removing lignin, thereby making the carbohydrates more accessible for enzymatic saccharification. Fungal delignification by white-rot fungi is a biotechnological alternative to chemical/physicochemical methods, which is carried out in solid-state fermentation with mild reaction conditions and without the formation of microbial inhibitors. However, fungal pretreatment presents some challenges, such as long pretreatment time, non-selective and low delignification, low enzymatic digestibility and feedstock sterilisation requirement, making its commercial implementation challenging compared to conventional methods. This study investigates the possibility of improving and characterising the solid-state fungal pretreatment of poplar wood by Phanerochaete chrysosporium. The individual and combined effects of MnSO4 and CuSO4 supplements on the delignification of sterilised wood are investigated using response surface methodology to improve the degree and selectivity of fungal delignification. Spore-inoculated solid-state fermentations are carried out for 4 weeks in sterile vented bottles. The mechanism of the concerted action of the metal ions on lignin degradation is then elucidated by relating fungal growth and ligninolytic enzyme activities to lignocellulose degradation as a function of pretreatment time. The optimised metal-supplemented system is then applied to the pretreatment of non-sterilised wood using different inoculation techniques (spores and pre-colonised substrate), nutrients (metal ions with or without glucose and sodium nitrate) and cultivation environments (sterile aerated bottles and open trays). The fermentations are then characterised using infrared spectroscopy, in particular NIR and ATR-FTIR spectroscopy, with the aim of developing rapid lignin quantification methods as an alternative to conventional wet chemical methods. Finally, the feasibility of producing fermentable sugars from sterilised and non-sterilised poplar wood using fungal pretreatment is evaluated through a techno-economic analysis. Supplementing the pretreatment system with 2.01 µmol CuSO4 and 0.77 µmol MnSO4 g-1 wood resulted in 1.9-fold higher lignin degradation, 2.3-fold higher delignification selectivity value and 2.9-fold higher glucose yield. The improved delignification could be explained by the concerted action of Mn2+ and Cu2+ ions, with Mn2+ ions inducing and Cu2+ prolonging manganese peroxidase production responsible for delignification. Fungal pretreatment at non-sterile conditions was obtained using trays in a simple solid-state fermentation set-up without sterile aeration. A 1:3 ratio of pre-colonised and untreated wood was applied for inoculation and only Cu2+, Mn2+ and sodium nitrate as supplements. Remarkably, this technology resulted in a comparably high glucose yield (28.51 ± 0.28%) to the traditional method using sterilised wood, sterile aeration and spores as inoculum, while reducing the amount of wood to be sterilised by 71.2%. Infrared spectroscopy-based methods with high coefficients of determination (R_CV

Abstract: Gielis transformations are a generalization of Lame curves. To combine domains, we can make use of the natural alliance between Lame's work and Rvachev's R-functions. A logical next step is the extension to n-valued logic dening dierent partitions.

Abstract: The interaction of diatoms with sunlight is fundamental in order to deeply understand their role in terrestrial ecology and biogeochemistry, essentially due to their massive contribution to global primary production through photosynthesis and its e↵ect on carbon, oxygen and silicon cycles. Following the journey of light through natural waters, its propagation through the intricate frustule micro- and nano-structure and, finally, its fate inside the photosynthetic machinery of the living cell requires several mathematical and computational models in order to accurately describe all the involved phenomena taking place at di↵erent space scales and physical regimes. In this chapter, we review the main analytical models describing the underwater optical field, the essential numerical algorithms for the study of photonic properties of the diatom frustule seen as a natural metamaterial, as well as the principal models describing photon harvesting in diatom plastids and methods for complex EM propagation problems and wave propagation in dispersive materials with multiple relaxation times. These mathematical methods will be integrated in a unifying geometric perspective.

Abstract: ​In this thesis, microalga Dunaliella salina is highlighted as a novel source of protein to sustain the human needs. As demonstrated in this thesis, the biochemical composition of D. salina is not fixed, and can be substantially influenced by internal and external conditions. In order to comply with the human requirement of protein, various important factors affecting the protein quantity and quality of D. salina have been evaluated in this thesis for an optimized production strategy. All tested parameters, namely salinity, pH, light regimes (continuous light and light/dark cycle), light intensity, nutrient levels and growth phases can contribute to significant variations of protein content and essential amino acid (EAA) level in D. salina. Ultimately, D. salina is capable of producing high amount of superior quality protein, complying with the FAO reference for human consumption. Even better, such protein of superior quality can be accompanied by unique β-carotene accumulation in D. salina, a pigment with anti-oxidant pro-vitamin A effect. In the end, according to the techno-economic analysis (TEA), it is economically feasible to produce D. salina biomass for human nutrition.

Abstract: Het gebruik van plasmon-actieve nanodeeltjes heeft de laatste 10 jaar zeer veel interesse gewekt bij onderzoekers in verschillende toepassingsdomeinen zoals fotokatalyse of oppervlakte versterkte Raman spectroscopie. Er is echter een grote limiterende factor bij het gebruik van edelmetaal nanodeeltjes zoals goud en zilver en dat is de stabiliteit. Deze oxideren en aggregeren snel, zeker in oxidatieve omgeving zoals in lucht. Een interessante aanpak om plasmon-actieve nanodeeltjes te stabiliseren, is om ze te omgeven in een schil, met andere woorden om een kern-schil nanodeeltje te vormen. Er zijn een heel aantal verschillende manieren waarop kern-schil nanodeeltjes gesynthetiseerd kunnen worden. In eerste instantie werden metaal nanodeeltjes omgeven door een (dunne) TiO2 laag. Afhankelijk van de hoeveelheid TiO2 precursor kon de dikte van de laag gecontroleerd worden tot enkele nanometers dik. De stalen werden getest voor de fotokatalytische afbraak van een vaste laag stearinezuur waarbij toevoeging van 2 wt% metaal@TiO2 op P25 leidde tot een significante verbetering in afbraakefficiëntie in vergelijking met zuiver P25. Een andere manier voor het stabiliseren van metaal nanodeeltjes is door ze te omgeven met een polymeerschil. Op deze manier kon de laagdikte gecontroleerd worden met sub-nanometer controle wat een zeer belangrijke factor is voor de hoeveelheid near-field versterking dat buiten de polymeer schil kan gaan. Een XTT test werd uitgevoerd om te bepalen wat de zuurstofactivatie snelheid was van goud en zilver (en goud-zilver bimetallische) nanodeeltjes, al dan niet omgeven door een (niet-)geleidende polymeer laag. Wanneer de stalen gecoat werden met vier niet-geleidende polymeerlagen zakte de zuurstofactivatie nagenoeg tot nul. Aan de andere kant, als goud nanodeeltjes werden omgeven door een geleidende schil was er nog steeds zuurstofactivatie, hoewel lager dan in het geval van goud zonder laag. Het laatste deel van deze thesis focuste meer op mogelijke toepassingen in luchtzuivering. In dit werk werd een glazen buis, gecoat aan de binnenkant met (Ag@polymer gemodificeerd) TiO2, als een spiraal rond een UVA lamp gewikkeld. De geoptimaliseerde spiraalreactor werd dan vergeleken met een conventionele cilindervormige fotoreactor, met dezelfde dimensies en totale katalysatorbelading, over een grote range aan experimentele condities. Uit de resultaten bleek dat de spiraalreactor significant betere afbraakefficiënties vertoonde in vergelijking met de conventionele cilindervormige reactor over een grote range aan debieten. Een adsorptiestap in combinatie met de geoptimaliseerde spiraalreactor zou kunnen leiden tot een zeer krachtige luchtzuiveringstechnologie.

Abstract: Electromagnetic design problems involve optimizing multiple parameters that are nonlinearly related to objective functions. Traditional optimization techniques require significant computational resources that grow exponentially as the problem size increases. Therefore, a method that can produce good results with moderate memory and computational resources is desirable. Bioinspired optimization methods, such as particle swarm optimization (PSO), are known for their computational efficiency and are commonly used in various scientific and technological fields. In this article we explore the potential of advanced PSO-based algorithms to tackle challenging electromagnetic design and analysis problems faced in real-life applications. It provides a detailed comparison between conventional PSO and its quantum-inspired version regarding accuracy and computational costs. Additionally, theoretical insights on convergence issues and sensitivity analysis on parameters influencing the stochastic process are reported. The utilization of a novel quantum PSO-based algorithm in advanced scenarios, such as reconfigurable and shaped lens antenna synthesis, is illustrated. The hybrid modeling approach, based on the unified geometrical description enabled by the Gielis Transformation, is applied in combination with a suitable quantum PSO-based algorithm, along with a geometrical tube tracing and physical optics technique for solving the inverse problem aimed at identifying the geometrical parameters that yield optimal antenna performance.

Abstract: Monitoring and modelling tools may improve irrigation strategies in precision agriculture. We used non-invasive soil moisture monitoring, a crop growth and a soil hydrological model to predict soil water content fluctuations and crop yield in a heterogeneous sandy grassland soil under supplementary irrigation. The sensitivity of the soil hydrological model to hydraulic parameters, water stress, crop yield and lower boundary conditions was assessed after integrating models. Free drainage and incremental constant head conditions were implemented in a lower boundary sensitivity analysis. A time-dependent sensitivity analysis of the hydraulic parameters showed that changes in soil water content are mainly affected by the soil saturated hydraulic conductivity K-s and the Mualem-van Genuchten retention curve shape parameters n and alpha. Results further showed that different parameter optimization strategies (two-, three-, four- or six-parameter optimizations) did not affect the calculated water stress and water content as significantly as does the bottom boundary. In this case, a two-parameter scenario, where K-s was optimized for each layer under the condition of a constant groundwater depth at 135-140 cm, performed best. A larger yield reduction, and a larger number and longer duration of stress conditions occurred in the free drainage condition as compared to constant boundary conditions. Numerical results showed that optimal irrigation scheduling using the aforementioned water stress calculations can save up to 12-22 % irrigation water as compared to the current irrigation regime. This resulted in a yield increase of 4.5-6.5 %, simulated by the crop growth model.

Abstract: In the present work, multiphysics modeling was used to investigate the feasibility of a photocatalysis-based outdoor air purifying solution that could be used in high polluted streets, especially street canyons. The article focuses on the use of a semi-active photocatalysis in the surfaces of the street as a solution to remove anthropogenic pollutants from the air. The solution is based on lamellae arranged horizontally on the wall of the street, coated with a photocatalyst (TiO2), lightened with UV light, with a dimension of 8 cm × 48 cm × 1 m. Fans were used in the system to create airflow. A high purification percentage was obtained. An artificial neural network (ANN) was used to predict the optimal purification method based on previous simulations, to design purification strategies considering the energy cost. The ANN was used to forecast the amount of purified with a feed-forward neural network and a backpropagation algorithm to train the model.

Abstract: Preston's equation is a general model describing the egg shape of birds. The parameters of Preston's equation are usually estimated after re-expressing it as the Todd-Smart equation and scaling the egg's actual length to two. This method assumes that the straight line through the two points on an egg's profile separated by the maximum distance (i.e., the longest axis of an egg's profile) is the mid-line. It hypothesizes that the photographed egg's profile is perfectly bilaterally symmetrical, which seldom holds true because of photographic errors and placement errors. The existing parameter estimation method for Preston's equation considers an angle of deviation for the longest axis of an egg's profile from the mid-line, which decreases prediction errors to a certain degree. Nevertheless, this method cannot provide an accurate estimate of the coordinates of the egg's center, and it leads to sub-optimal parameter estimation. Thus, it is better to account for the possible asymmetry between the two sides of an egg's profile along its mid-line when fitting egg-shape data. In this paper, we propose a method based on the optimization algorithm (optimPE) to fit egg-shape data and better estimate the parameters of Preston's equation by automatically searching for the optimal mid-line of an egg's profile and testing its validity using profiles of 59 bird eggs spanning a wide range of existing egg shapes. We further compared this method with the existing one based on multiple linear regression (lmPE). This study demonstrated the ability of the optimPE method to estimate numerical values of the parameters of Preston's equation and provide the theoretical egg length (i.e., the distance between two ends of the mid-line of an egg's profile) and the egg's maximum breadth. This provides a valuable approach for comparing egg shapes among conspecifics or across different species, or even different classes (e.g., birds and reptiles), in future investigations.

Abstract: Many natural radial symmetrical shapes (e.g., sea stars) follow the Gielis equation (GE) or its twin equation (TGE). A supertriangle (three triangles arranged around a central polygon) represents such a shape, but no study has tested whether natural shapes can be represented as/are supertriangles or whether the GE or TGE can describe their shape. We collected 100 pieces of Koelreuteria paniculata fruit, which have a supertriangular shape, extracted the boundary coordinates for their vertical projections, and then fitted them with the GE and TGE. The adjusted root mean square errors (RMSEadj) of the two equations were always less than 0.08, and >70% were less than 0.05. For 57/100 fruit projections, the GE had a lower RMSEadj than the TGE, although overall differences in the goodness of fit were non-significant. However, the TGE produces more symmetrical shapes than the GE as the two parameters controlling the extent of symmetry in it are approximately equal. This work demonstrates that natural supertriangles exist, validates the use of the GE and TGE to model their shapes, and suggests that different complex radially symmetrical shapes can be generated by the same equation, implying that different types of biological symmetry may result from the same biophysical mechanisms.

Abstract: Many natural shapes exhibit surprising symmetry and can be described by the Gielis equation, which has several classical geometric equations (for example, the circle, ellipse and superellipse) as special cases. However, the original Gielis equation cannot reflect some diverse shapes due to limitations of its power-law hypothesis. In the present study, we propose a generalized version by introducing a link function. Thus, the original Gielis equation can be deemed to be a special case of the generalized Gielis equation (GGE) with a power-law link function. The link function can be based on the morphological features of different objects so that the GGE is more flexible in fitting the data of the shape than its original version. The GGE is shown to be valid in depicting the shapes of some starfish and plant leaves.