The homo and hetero dimerisation of two spectroscopically different chromophores were studied, namely: 4,4-difluoro-4-bora-3a,4a-diazas-indacene (g-BODIPY) and its 5-styryl-derivative (r-BODIPY). Various spectroscopic properties of the r-BODIPY in different common solvents were determined. It was shown that g- and r-BODIPY in the ground state can form homo- as well as hetero dimers. We demonstrate that the ganglioside GM1 in lipid bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) exhibits a non-uniform lateral distribution, which is an argument in favour of self-aggregation of GM1 being an intrinsic property of the GM1. This was concluded from energy transfer/migration studies of BODIPY-labelled gangliosides. An algorithm is presented that quantitatively accounts for donor–donor energy migration (DDEM) among fluorophore-labelled proteins forming regular non-covalent polymers. The DDEM algorithm is based on Monte Carlo (MC) and Brownian dynamics (BD) simulations and applies to the calculation of fluorescence depolarisation data, such as the fluorescence anisotropy. Thereby local orientations, as well as reorienting motions of the fluorescent groups are considered in the absence and presence of DDEM among them. A new method, in which a genetic algorithm (GA) was combined with BD and MC simulations, was developed to analyse fluorescence depolarisation data collected by the time-correlated single photon counting technique. It was applied to study g-BODIPY-labelled filamentous actin (F-actin). The technique registered the local order and reorienting motions of the fluorophores, which were covalently coupled to cysteine 374 (C374) in actin and interacted by means of electronic energy migration within the polymer. Analyses of F-actin samples composed of different fractions of labelled actin molecules revealed the known helical organiszation of F-actin, and demonstrated the usefulness of this technique for structure determination of complex protein polymers. The distance from the filament axis to the fluorophore was found to be considerably less than expected from the proposed position of C374 at a high filament radius. In addition, polymerisation experiments with BODIPY-actin suggest a 25-fold more efficient signal for filament formation than pyrene-actin.

Magnetic fields influence the rate and/or yield of chemical reactions that proceed via spin correlated radical pair intermediates. The field of spin chemistry centres around the study of such magnetic field effects (MFEs). This thesis is particularly concerned with the effects of the weak magnetic fields B₀ ~ 1mT relevant in the ongoing debates on the mechanism by which animals sense the geomagnetic field and on the putative health effects of environmental electromagnetic fields. Relatively few previous studies have dealt with such weak magnetic fields. This thesis presents several new theoretical tools and applies them to interpret experimental measurements. Chapter 1 surveys the development and theory of spin chemistry. Chapter 2 introduces the use of Tikhonov and Maximum Entropy Regularisation methods as a new means of analysing MARY field effect data. These are applied to recover details of the diffusive motion of reacting pyrene and N,N-dimethylaniline radicals. Chapter 3 gives a fresh derivation and appraisal of an approximate, semiclassical approach to MFEs. Monte Carlo calculations allow the elucidation of several "rules of thumb" for interpreting MFE data. Chapter 4 discusses recent optically-detected zero-field EPR measurements, adapting the gamma-COMPUTE algorithm from solid state NMR for their interpretation. Chapter 5 explores the role of RF polarisation in producing MFEs. The breakdown in weak fields of the familiar rotating frame approximation is analysed. Chapter 6 reviews current knowledge and landmark experiments in the area of animal magnetoreception. The origins of the sensitivity of European robins Erithacus rubecula to the Earth’s magnetic field are given particular attention. In Chapter 7, Schulten and Ritz’s hypothesis that avian magnetoreception is founded on a radical pair mechanism (RPM) reaction is appraised through calculations in model systems. Chapter 8 introduces quantitative methods of analysing anisotropic magnetic field effects using spherical harmonics. Chapter 9 considers recent observations that European robins may sometimes be disoriented by minuscule RF fields. These are shown to be consistent with magnetoreception via a radical pair with no (effective) magnetic nuclei in one of the radicals.

This thesis presents the development and redesign of a commercial electrochemical quartz crystal microbalance with dissipation (E–QCM–D). This was used to study factors affecting the efficiency of the four electron reduction catalysed by the fuel cell enzyme bilirubin oxidase from Myrothecium verrucaria immobilised on thiol modified gold surfaces. Within this thesis, the E–QCM–D was used to show that application of a constant potential to bilirubin oxidase adsorbed to thiol-modified gold surfaces causes activity loss that can be attributed to a change in structural arrangement. Varying the load by potential cycling distorts the enzyme by inducing rapid mass loss and denaturation. Attaching the enzyme covalently reduces the mass loss caused by potential cycling but does not mitigate activity loss. Covalent attachment also changes the orientation of the surface bound enzyme as verified by the position of the catalytic wave (related to the overpotential for catalysis) and reactive labelling followed by mass spectrometry analysis. The E–QCM–D was used to show how electrostatic interactions affect enzyme conformation where high pH causes a reduction in both mass loading at the electrode and a reduction in activity. At pH lower than the enzyme isoelectric point, there is a build up of multilayers in a clustered adsorption. When enzyme adsorbs to hydrophobic surfaces there is a rapid denaturation which completely inactivates the enzyme. Changing the surface chemistry from carboxyl groups to hydroxyl and acetamido groups shows that catalysis is shifted to more negative potentials as a result of an enzyme misorientation. Further to this, increasing the chain length of the thiol modifier indicates that an increased distance between surface and enzyme reduces activity, enzyme loading and results in a conformational rearrangement that permits electron transfer over longer distances.

In a time when microorganisms are controlling the world, research in biology is more relevant than ever and this requires some powerful instruments. Optical tweezers use a focused laser beam to manipulate and probe objects on the nano- and microscale. This allows for the exploration of a miniature world at the border between biology, chemistry and physics. New methods for biophysical and physicochemical measurements are continuously being developed and at Umeå University there is a need for a new system that combines several of these methods. This would truly be the new Swiss army knife of biophysical and biomechanical research, extending their reach in the world of optical tweezing. My ambition with this project is to design and construct a robust system that incorporates optical trapping with high-precision force measurements and Raman spectroscopy, as well as introducing the possibility of generating multiple traps by using a spatial light modulator (SLM). The proposed design incorporates four different lasers and a novel combination of signal detection techniques. To allow for precise control of the systems components and laser beams, I designed and constructed motorized opto-mechanical components. These are controlled by an in-house developed software that handles data processing and signal analysis, while also providing a user interface for the system. The components include, motorized beam blockers and optical attenuators, which were developed using commonly available 3D printing techniques and electronic controllers. By designing the system from scratch, I could eliminate the known weaknesses of conventional systems and allow for a modular design where components can be added easily. The system is divided into two parts, a laser breadboard and a main breadboard. The former contains all the equipment needed to generate and control the laser beams, which are then coupled through optical fibers to the latter. This contains the components needed to move the optical trap inside the sample chamber, while performing measurements and providing user feedback. Construction and testing was done for one sub-system at a time, while the lack of time required a postponement for the implementation of Raman and SLM. The system performance was verified through Allan variance stability tests and the results were compared with other optical tweezers setups. The results show that the system follows the thermal limit for averaging times (τ) up to ~1 s when disturbances had been eliminated, which is similar to other systems. However, we could also show a decrease in variance all the way to τ = 2000 s, which is exceptionally good and not found in conventional systems. The force-resolution was determined to be on the order of femtonewtons, which is also exceptionally good. Thus, I conclude that this optical tweezers setup could lie as a solid foundation for future development and research in biological science at Umeå University for years to come.

The presented work deals with the development of a monitoring system for monitoring the operation of the laboratory. The theoretical part of the work includes information on the safety of operation and work in biological laboratories, measured physical quantities and the principle of their measurement. The monitoring system is built on a compact ESP32-CAM camera and a WeMos D1 development board. The practical part consists of the design and implementation of a given system and the creation of a full-stack application for displaying live input from the laboratory for monitoring measured quantities in real time.

Sound localization is a vital aspect of hearing for safe navigation of everyday environments. It is also an important factor in speech intelligibility. This ability is facilitated by the interaural level difference (ILD) cue, which arises from binaural hearing: a sound will be more intense at the nearer ear than the farther. In a hearing-impaired listener, this binaural cue may not be available for use and localization may be diminished. While conventional, bilateral, wide dynamic range compression (WDRC) hearing aids distort the interaural level difference by independently altering sound intensities in each ear, wirelessly-linked devices have been suggested to benefit this task by matching amplification in order to preserve ILD. However, this technology has been shown to have varying degrees of success in aiding speech intelligibility and sound localization. As hearing impairment has wide-ranging adverse impacts to physical and mental health, social activity, and cognition, the task of localization improvement must be urgently addressed. Toward this end, neural modelling techniques are used to determine neural representations of ILD cues for linked and unlinked bilateral WDRC hearing aids. Findings suggest that wirelessly-linked WDRC is preferable over unlinked hearing aids or unaided, hearing-impaired listening, although parameters for optimal benefit are dependent on sound level, frequency content, and preceding sounds. / Thesis / Master of Applied Science (MASc)

Grasslands are one of the most important ecosystems on Earth, covering approximately one-third of the Earth’s surface. Grassland biodiversity is important as many services provided by such ecosystems are crucial for the human economy and well-being. Given the importance of grasslands ecosystems, in recent years research has been carried out on the potential to monitor them with novel remote sensing techniques. Improved detectors technology and novel sensors providing fine-scale hyperspectral imagery have been enabling new methods to monitor plant traits (PTs) and biodiversity. The aims of the work were to study different approaches to monitor key grassland PTs such as Leaf Area Index (LAI) and biodiversity-related traits. The thesis consists of 3 parts: 1) Evaluating the performance of remote sensing methods to estimate LAI in grassland ecosystems, 2) Estimating plant biodiversity by using the optical diversity approach in grassland ecosystems, and 3) Investigating the relationship between PTs variability with alpha and beta diversity for the applicability of the optical diversity approach in a subalpine grassland of the Italian Alps To evaluate the performance of remote sensing methods to estimate LAI, temporal and spatial observations of hyperspectral reflectance and LAI were analyzed at a grassland site in Monte Bondone, Italy (IT-MBo). In 2018, ground temporal observations of hyperspectral reflectance and LAI were carried out at a grassland site in Neustift, Austria (AT-NEU). To estimate biodiversity, in 2018 and 2019 a floristics survey was conducted to determine species composition and hyperspectral data were acquired at two grassland sites: IT-MBo and University of Padova’s Experimental Farm, Legnaro, Padua, Italy (IT-PD) respectively. Furthermore, in 2018, biochemistry analysis of the biomass samples collected from the grassland site IT-MBo was carried out to determine the foliar biochemical PTs variability. The results of the thesis demonstrated that the grassland spectral response across different spectral regions (Visible: VIS, red-edge: RE, Near-infrared: NIR) showed to be both site-specific and scale-dependent. In the first part of the thesis, the performance of spectral vegetation indices (SVIs) based on visible, red-edge (RE), and NIR bands alongside SVIs solely based or NIR-shoulder bands (wavelengths 750 - 900 nm) was evaluated. A strong correlation (R2 > 0.8) was observed between grassland LAI and both RE and NIR-shoulder SVIs on a temporal basis, but not on a spatial basis. Using the PROSAIL Radiative Transfer Model (RTM), it was demonstrated that grassland structural heterogeneity strongly affects the ability to retrieve LAI, with high uncertainties due to structural and biochemical PTs co-variation. In the second part, the applicability of the spectral variability hypothesis (SVH) was questioned and highlighted the challenges to use high-resolution hyperspectral images to estimate biodiversity in complex grassland ecosystems. It was reported that the relationship between biodiversity (Shannon, Richness, Simpson, and Evenness) and optical diversity metrics (Coefficient of variation (CV) and Standard deviation (SD)) is not consistent across plant communities. The results of the second part suggested that biodiversity in terms of species richness could be estimated by optical diversity metrics with an R2 = 0.4 at the IT-PD site where the grassland plots were artificially established and are showing a lower structure and complexity from the natural grassland plant communities. On the other hand, in the natural ecosystems at IT-MBo, it was more difficult to estimate biodiversity indices, probably due to structural and biochemical PTs co-variation. The effects of canopy non-vegetative elements (flowers and dead material), shadow pixels, and overexposed pixels on the relationship between optical diversity metrics and biodiversity indices were highlighted. In the third part, we examined the relationship between PTs variability (at both local and community scales, measured by standard deviation and by the Euclidean distances of the biochemical and biophysical PTs respectively) and taxonomic diversity (both α-diversity and β-diversity, measured by Shannon’s index and by Jaccard dissimilarity index of the species, families, and functional groups percent cover respectively) in Monte Bondone, Trentino province, Italy. The results of the study showed that the PTs variability metrics at alpha scale were not correlated with α-diversity. However, the results at the community scale (β-diversity) showed that some of the investigated biochemical and biophysical PTs variations metrics were associated with β-diversity. The SVH approach was also tested to estimate β-diversity and we found that spectral diversity calculated by spectral angular mapper (SAM) showed to be a better proxy of biodiversity in the same ecosystem where the spectral diversity failed to estimate alpha diversity, this leading to the conclusion that the link between functional and species diversity may be an indicator of the applicability of optical sampling methods to estimate biodiversity. The findings of the thesis highlighted that grassland structural heterogeneity strongly affects the ability to retrieve both LAI and biodiversity, with high uncertainties due to structural and biochemical PTs co-variation at complex grassland ecosystems. In this context, the uncertainties of satellite-based products (e.g., LAI) in monitoring grassland canopies characterized by either spatially or temporally varying structure need to be carefully taken into account. The results of the study highlighted that the poor performance of optical diversity proxies in estimating biodiversity in structurally heterogeneous grasslands might be due to the complex relationships between functional diversity and biodiversity, rather than the impossibility to detect functional diversity with spectral proxies.

Thèse produite en partenariat avec la Ferme d'hiver, centre de recherche industrielle pour l'agriculture en environnement contrôlé. / L’agriculture en environnement contrôlé (AEC) est une pratique agricole de haute technologie où la culture de plantes et son environnement sont soumis à une certaine forme de contrôle afin d’obtenir des rendements plus élevés et une efficacité de production accrue. L’AEC est essentielle en raison de son impact sur la disponibilité des terres arables, l’utilisation de l’eau et l’efficacité énergétique face à l’augmentation de l’insécurité alimentaire mondiale. Les systèmes de AEC sont contrôlés par le biais d’indicateurs de performance clés (IPC) complexes que les experts de plusieurs domaines, dont les ingénieurs et les agronomes, doivent optimiser. L’optimisation des IPC nécessite l’exploration de l’immense espace d’états du système d’AEC. Étant donné que ces systèmes sont complexes et hétérogènes, ils nécessitent une approche de modélisation et de co-simulation multi-paradigme dans laquelle les modèles utilisent les formalismes et les niveaux d’abstraction les plus appropriés. Nous proposons une architecture de co-simulation de AEC capable de capturer la dynamique des entités qui composent notre système à plusieurs niveaux d’abstraction. Nous présentons nos résultats démontrant la validité de notre approche / Controlled environment agriculture (CEA) is a high-tech agricultural practice where the crop and its environment are subject to some form of control to achieve higher yields and produc- tion efficiency. CEA is critical for its impacts on arable land availability, water usage, and energy efficiency amid the rise of global food insecurity. CEA systems are controlled through complex key performance indicators (KPI) that experts of multiple domains, including engi- neers and agronomists, must optimize. The optimization of KPI requires exploring the vast state space of the CEA system. As such systems are complex and heterogeneous, they re- quire a multi-paradigm modeling and co-simulation approach in which models use the most appropriate formalisms and levels of abstraction. We provide a co-simulation architecture for CEA to capture the dynamics of the entities that comprise our system at multiple levels of abstraction and present our results showing the validity of our approach.

Les performances du végétal et des arthropodes dont il constitue le microhabitat dépendent des températures de surface foliaire. Celles-ci peuvent dévier fortement de la température de l’air et présenter des niveaux d’hétérogénéité différents selon l'échelle spatiale considérée. La feuille atténue les températures extrêmes en rapprochant son amplitude de variation journalière de celle de la température de l’air. Cependant, cette réponse diminue l’hétérogénéité des températures de surface foliaire et les capacités de thermorégulation comportementale des arthropodes à l'échelle de la feuille. Les températures moyennes de surface foliaire atténuent peu le réchauffement, et déterminent localement la performance photosynthétique du végétal. De l’échelle de la feuille à celle de la canopée, les plantes montrent des réponses différentes au réchauffement. Ce type de changement d'échelle est primordial pour améliorer notre compréhension de l'impact des changements climatiques. / Plant performance and leaf-dwelling arthropods are impacted by leaf surface temperatures. Leaf surface temperatures can show important deviation from air temperature and present different levels of heterogeneity depending on the spatial scale. The leaf buffers temperature extremes by getting closer in amplitude to air temperature. However, this physiological response decreases the heterogeneity of temperatures at the leaf surface and the opportunities for arthropods to behavioraly thermoregulate in this microclimate. Mean temperatures at the leaf surface show low buffering abilities in response to warming and locally determine photosynthetic performance. From the leaf to the canopy scale, plants show different responses to warming and scaling is crucial to increase our understanding of the impact of global warming.

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