Many animals on earth need to navigate in their own environments for breeding and foraging. The ability to determine a correct heading and the current location for a migratory bird is critical for its survival. Animals that are sensitive to the Earth’s magnetic field can use it to obtain their direction of travel. In 2000, a paper suggested that radical pair reaction could form the basis for magnetoreception in migratory birds and a flavoprotein, cryptochrome, was proposed as the candidate for the radical pair precursor. Recent in vivo experimental results strongly support the hypothesis that radical pairs formed in the eyes of migratory birds are responsible for their magnetic compass sense. Cryptochrome has also been located in the UV-cones in the retinas of two different species of bird. Radical pairs in living cells are influenced mainly by Zeeman interaction, hyperfine interaction, rotational modulation, etc., and together they influence the recombination reactions of the radical pairs. This thesis considers the possible role of radical pairs in avian magnetoreception, using computer simulations of the quantum mechanical evolution of a radical pair under a variety of conditions. Chapter 1 contains the introductions to spin chemistry, avian magnetoreception, and the mathematical description of the quantum evolution of a radical pair. Chapter 2 describes the four different theoretical models for a general non-diffusion-controlled radical pair reaction and the product yields of a radical pair reaction predicted by these four models are analysed and compared. Chapter 3 introduces a model for avian magnetoreception that integrates photoselection with the radical pair reaction and the model is used to predict the retinal patterns that a bird may be able to use for magnetoreception. The anisotropic singlet product yields of a radical pair comprises the flavin chromophore and the tryptophan of a cryptochrome are also presented in this chapter. A paper based on some parts of this chapter is published [1] in the Journal of The Royal Society Interface. Chapter 4 describes a modified version of an algorithm that is used to calculate the product yields detected in a reaction yield detected magnetic resonance (RYDMR) experiment. The new algorithm is used to analyse the results of two sets of RYDMR experiments in which two radical pair systems, pyrene/1,3-dicyanobenzene and chrysene/1,4-dicyanobenzene, were used. The modulated detection technique used in the RYDMR experiments is also discussed in this chapter.

<strong>Chapter 1</strong> introduces the concept of spin, how spins interact, and how the spin state in a radical pair can affect the outcome of a chemical reaction between the unpaired electrons. The computational methodology for simulating such radical pairs is also discussed. <strong>Chapter 2</strong> discusses anisotropy in the singlet recombination yield of a radical pair in a carotenoid-porphyrin-fullerene triad, containing many hyperfine couplings. The singlet yield was calculated as a function of the direction of an applied magnetic field, using symmetry in the molecule to reduce the size of the problem. The symmetry reduction was partially successful, however it was not possible to include all the hyperfine couplings in the molecule. <strong>Chapter 3</strong> introduces a radical pair located on a flavin ligand and a tryptophan residue in the protein cryptochrome, and discusses the spin-relaxation mechanism of singlet-triplet dephasing. Magnetic field effect curves, describing the formation of a secondary radical pair as a function of applied magnetic field, were found to be broader in longer-lived radical pairs, due to dephasing caused by spin-selective recombination to the singlet ground state. Additional singlet-triplet dephasing may occur due to hopping of one of the unpaired electrons, between a zone of strong exchange interaction and a zone of negligible exchange interaction, although this is an incomplete description of the spin-relaxation. <strong>Chapter 4</strong> discusses the effect of rotational tumbling on spin-relaxation in the flavin-tryptophan radical pair in cryptochrome. Simulations indicated that the resulting modulation of anisotropic hyperfine couplings contributed modestly to spinrelaxation during transient absorption measurements, but was insufficient to explain the lack of an experimental low-field effect, or to explain the width of the experimental magnetic field effect curves as a function of magnetic field strength. <strong>Chapter 5</strong> discusses magnetic field effects on the mutual annihilation of a pair of triplet excitons in tetracene and anthracene crystals. The experimental singlet recombination yield was found, for the first time, to be modulated as a function of the direction of a applied magnetic field as weak as 2 mT. Simulations indicated that this anisotropy arose due to the zero field splitting of the electronic state in each triplet exciton. The direction of the external magnetic field altered the singlet component of the eigenstates of the Hamiltonian, and therefore altered the timeaverage of the singlet probability of a triplet exciton pair. This is different to the already established mechanism under a strong magnetic field, where the anisotropy arises from level crossings of eigenstates.

In the 50+ years since the discovery of magnetic compass orientation by migratory songbirds, evidence for the use of magnetic cues has been obtained for a range of taxonomic groups, including several classes of vertebrate and invertebrate taxa. Surprisingly, however, the biophysical mechanisms and biological substrate that underlie magnetic sensing are still not fully understood. Moreover, while use of magnetic cues for compass orientation is intuitive, the functional significance of other forms of behavioral responses mediated by magnetic cues, such as spontaneous magnetic alignment, is less clear. The following research was carried out to investigate the mechanisms underlying magnetic orientation in vertebrates and invertebrates. This involved the modification of existing experimental systems to characterize responses to magnetic cues in laboratory animals (flies, mice) and the development of novel techniques for studying the role of magnetic cues in the spatial behavior of free-living animals (red foxes). Chapter II examines magnetic orientation in wild-type Drosophila melanogaster larvae. We show that three strains of larvae reared under non-directional ultraviolet (UV) light exhibit quadramodal spontaneous orientation along the anti-cardinal compass directions (i.e. northeast, southeast, southwest, northwest) when tested in a radially symmetrical environment under UV light. Double-blind experiments cancelling the horizontal component of the magnetic field confirmed that the response is dependent on magnetic cues rather non-magnetic features of the test environment. Furthermore, we argue that the larval quadramodal pattern of response is consistent with properties of magnetic compass orientation observed in previous studies of adult Drosophila and laboratory mice, both of which have been proposed to be mediated by a light-dependent magnetic compass mechanism. Chapter III explores the use of novel biologging techniques to collect behavioral and spatial data from free-roaming mammals. Specifically, a previous observational study of free- roaming red foxes found a 4-fold increase in the success of predatory 'mousing' attacks when foxes were facing ~north-northeast, consistent with magnetic alignment responses reported for a range of terrestrial animals. The authors propose that the magnetic field may be used to increase accuracy of mousing attacks. Using tri-axial accelerometer and magnetometer bio-loggers fitted to semi-domesticated red foxes, we created ']magnetic ethograms' from behavioral and magnetic machine learning algorithms 'trained'] to identify three discrete behaviors (i.e. foraging, trotting, and mousing-like jumps) from raw accelerometer signatures and to classify the magnetic headings of mousing-like jumps into 45° sectors from raw magnetometer data. The classifier's ability to accurately identify behaviors from a separate fox not used to train the algorithm suggests that these techniques can be used in future experiments to obtain reliable magnetic ethograms for free-roaming foxes. We also developed the first radio-frequency emitting collar that broadcasts in the low MHz frequency range shown to disrupt magnetic compass responses in a host of animals. The radio-frequency collars coupled with biologgers will provide a powerful tool to characterize magnetic alignment responses in predatory red foxes and can be adapted for use in studies of magnetic alignment and magnetic compass orientation in other free-roaming mammals. Chapter 3 discusses findings from a magnetic nest building assay involving male labratory mice. Mice trained to position nests in one of four directions relative to the magnetic field exhibited both learned magnetic compass responses and fixed magnetic nest positioning orientation consistent with northeast-southwest spontaneous magnetic alignment behavior previously reported for wild mice and bank voles. This is the first mammalian assay in which both learned magnetic compass orientation and spontaneous magnetic alignment were exhibited in the same species, and suggests that the use of magnetic cues in rodents may be more flexible that previously realized. / Ph. D. / A variety of animals have been shown to use the Earth’s magnetic field to help guide diverse spatial behaviors, however, the underlying sensory mechanisms mediating this sense remain elusive. Evidence for two distinct sensory mechanisms has come from behavioral studies involving a wide range of organisms, including migratory birds, newts, mole rats, mice, and several classes of invertebrates. The following research was carried out to determine the underlying sensory mechanisms mediating magnetic sensing in larval fruit flies. Properties consistent with a light-dependent, photoreceptor-based mechanism were found to underlie innate magnetic alignment behavior in larval flies, similar to the proposed compass mechanism thought to mediate compass responses in migratory birds and newts. A reanalysis of two previous studies of learned magnetic compass responses in adult fruit flies and laboratory mice show similar behaviors when compared to that of larval flies, suggesting a common underlying light-dependent magnetic mechanism across these groups. Furthermore, we provide evidence for learned magnetic compass responses in laboratory mice, where the orientation of individuals appears to be dependent on properties of the local environment (e.g. electromagnetic, temperature, humidity) in training and testing. These data suggest that the use of magnetic cues in mammals is context-dependent and more flexible than previously recognized. We have also developed new technologies for studies of magnetic orientation in free-roaming animals. Specifically, bio-logging devices containing triaxial accelerometer and magnetometer sensors where used to create ‘magnetic ethograms’, where the behavior and magnetic alignment of an animal can be reliably and accurately extracted from raw sensor data. We also discuss possible field experiments that can be performed to provide a specific test of the underlying sensory mechanism mediating magnetic behavior in free-roaming animals. This work will likely be of interest to a broad range of disciplines including sensory ecology, ethology, quantum chemistry, biophysics, wildlife management, and conservation.

Organic semiconductors (OSCs) have already been shown to have great potential to play an important role in the future of clean energy generation (organic solar cells) and provide energy efficient lighting (organic light-emitting diodes, OLED). Prior research has found that the light-emission efficiency of OLED is severely limited by the magnetic state (technically the spin-configuration) of the light-emission process. In this thesis, we work on the processes using external magnetic fields that can overcome these magnetic limitations. A major focus of this research is to enhance the performance of OLED, while at the same time to unravel the scientific mechanisms by which magnetic fields act on OSCs devices. Thermally activated delayed fluorescence (TADF) is a next-generation OLED emission technology which enables nearly 100% light-emission efficiency without using heavy precious metals. TADF characteristics depend on the probability of reverse intersystem crossing (RISC) from the triplet excited states (T1) to singlet excited states (S1). The conversion (T1 to S1) process depends strongly on spin dynamics, thus we predict a dramatic magnetic field effects (MFEs) in such TADF OLED devices. In subsequent experiments we observed that changes in TADF devices due to various forms of electrical stress can lead to enormous increases in magnetic field effects (MFEs) on the current (> 1400%) and electroluminescence (> 4000%). Our work provides a flexible and inexpensive pathway towards magnetic functionality and field sensitivity in current organic devices. Such OLED pave the way for novel magnetic sensitive OSCs devices with integrated optical, electronic and magnetic characteristics. Organic magnetoresistance (OMAR) has been observed to alter the current and efficiency of OLED without any ferromagnetic components. Here we utilizes slight alterations to the device properties, the addition of a radical-doped functional layer, in which the spin-relaxing effects of localized nuclear spins and electronic spins interfere, to address the assumption about the importance of the hyperfine interaction and to attempt to differentiate between the different models for OMAR. A feature where the magnitude of OMAR exhibits a plateau over a wide range of doping fraction was observed at all temperatures investigated. This phenomenon is well explained by a theory in which a single dopant spin strongly interacts, by exchange, with one of the bottleneck sites. A similar can be used to explain the efficiency increases observed in organic solar cells for certain doping fractions.

This thesis is concerned with studying the fascinating quantum properties of real-world nanostructures embedded in a noisy condensed matter environment. The interaction with light is used for controlling and manipulating the quantum state of the systems considered here. In some instances, laser pulses also provide a way of actively probing and controlling environmental interactions. The first two research chapters assess two different ways of performing all-optical spin qubit gates in self-assembled quantum dots. The principal conclusion is that an `adiabatic' control technique holds the promise of achieving a high fidelity when all primary sources of decoherence are taken into account. In the next chapter, it is shown that an optically driven quantum dot exciton interacting with the phonons of the surrounding lattice acts as a heat pump. Further, a model is developed which predicts the temperature-dependent damping of Rabi oscillations caused by bulk phonons, finding an excellent agreement with experimental data. A different system is studied in the following chapter: two electron spin qubits with no direct interaction, yet both exchange-coupled to an optically active mediator spin. The results of this study show that these general assumptions are sufficient for generating controlled electron spin entanglement over a wide range of parameters, even in the presence of noise. Finally, the Radical Pair model of the avian compass is investigated in the light of recent experimental results, leading to the surprising prediction that the electron spin coherence time in this molecular system seems to approach the millisecond timescale.

Quantum information processing (QIP), which inherently utilizes quantum mechanical phenomena to perform information processing, may outperform its classical counterpart at certain tasks. As one of the physical implementations of QIP, the electron-spin based architecture has recently attracted great interests. Endohedral fullerenes with unpaired electrons, such as N@C₆₀, are promising candidates to embody the qubits because of their long spin decoherence time. This thesis addresses several fundamental aspects of the strategy of engineering the N@C₆₀ molecules for applications in QIP. Chemical functionalization of N@C₆₀ is investigated and several different derivatives of N@C₆₀ are synthesized. These N@C₆₀ derivatives exhibit different stability when they are exposed to ambient light in a degassed solution. The cyclopropane derivative of N@C60 shows comparable stability to pristine N@C₆₀, whereas the pyrrolidine derivatives demonstrate much lower stability. To elucidate the effect of the functional groups on the stability, an escape mechanism of the encapsulated nitrogen atom is proposed based on DFT calculations. The escape of nitrogen is facilitated by a 6-membered ring formed in the decomposition of the pyrrolidine derivatives of N@C₆₀. In contrast, the 4-membered ring formed in the cyclopropane derivative of N@C₆₀ prohibits such an escape through the addends. Two N@C₆₀-porphyrin dyads are synthesized. The dyad with free base porphyrin exhibits typical zero-field splitting (ZFS) features due to functionalization in the solid-state electron spin resonance (ESR) spectrum. However, the nitrogen ESR signal in the second dyad of N@C₆₀ and copper porphyrin is completely suppressed at a wide range of sample concentrations. The dipolar coupling between the copper spin and the nitrogen spins is calculated to be 27.0 MHz. To prove the presence of the encapsulated nitrogen atom in the second dyad, demetallation of the copper porphyrin moiety is carried out. The recovery of approximately 82% of the signal intensity confirms that the dipolar coupling suppresses the ESR signal of N@C₆₀. To prepare ordered structure of N@C₆₀, the nematic matrix MBBA is employed to align the pyrrolidine derivatives of N@C₆₀. Orientations of these derivatives are investigated through simulation of their ESR spectra. The derivatives with a –CH3 or phenyl group derived straightforward from the N-substituent of the pyrrolidine ring are preferentially oriented based on their powder-like ESR spectra in the MBBA matrix. An angle of about is also found between the directors of fullerene derivatives and MBBA. In contrast, the derivatives with a –CH₂ group inserted between the phenyl group and the pyrrolidine ring are nearly randomly distributed in MBBA. These results illustrate the applicability of liquid crystal as a matrix to align N@C₆₀ derivatives for QIP applications.

The focus of this research was the spontaneous magnetic alignment responses of animals. We show that snapping turtles (Chelydra serpentina) and crayfish (Cambarus sciotensis) spontaneously align their body axes relative to the magnetic field. In snapping turtles, this response is sensitive to low-level radio frequency fields, consistent with a mechanism involving a light-dependent radical pair mechanism. Findings from the turtle experiments also suggest that the Earth's magnetic field plays an important role in encoding spatial information in novel surroundings, and may help to organize multiple locales into a 'mental map' of familiar space. Given the importance of magnetic input in many aspects of spatial behavior, another important finding was that magnetic alignment of yearling turtles was disrupted by high levels of maternally transferred mercury, an industrial waste product found at high levels in some fresh water ecosystems. In crayfish, we investigated the effects of ectosymbionts (Annelida: Branchiobdellida) on magnetic alignment responses. Interestingly, the response of crayfish to magnetic cues parallels the complex symbiotic interaction between crayfish and their ectosymbiotic worms, which changes from mutualistic to parasitic with increasing worm density. Our working hypothesis was that these changes in spatial behavior may increase or decrease contact to other crayfish, and therefore increase or decrease transmission rates. Next, to address the ontogeny of the SMA, we attempted to replicate an earlier study showing a possible magnetic alignment response in chicken embryos. Although chicken embryos did show non-random alignment, we were not able to find a magnetic effect. Alignment is also an important feature of animal constructions and is very likely to have fitness consequences, which we explored in woodpecker cavity alignments in a meta-analysis of available global data. The latitudinal and continental pattern in 23 species of woodpeckers suggests that an alignment response can have the proximate function to regulate microclimate in the cavity and therefore, presumably, optimize incubation temperatures and increase hatching success. Overall, the presented findings show how experimental and observational studies of spontaneous alignment behavior can provide insight into the ecology and sensory biology of a wide range of animals. / Ph. D.

Cavity ring-down spectroscopy (CRDS) and cavity enhanced absorption spectroscopy (CEAS) are two well-established absorption spectroscopic techniques originally developed for gas-phase samples. Condensed-phase applications of these techniques still remain rare, complicated as they are by additional background losses induced by condensed-phase samples as well as the intracavity components in which the sample is constrained. This thesis is concerned with the development and application of optical-cavity-based techniques in the condensed phase. Polarization-dependent evanescent wave CRDS (EW-CRDS) has been used to study the molecular orientation at the solid/air and solid/liquid interfaces. An increase in average orientation angle with respect to the surface normal has been observed for both methylene blue and coumarin molecules as a function of coverage at the fused silica/air interface. An orientation-angle-dependent photobleaching of pyridin molecules at the fused silica/methanol interface have also been observed. EW-CRDS has also been used to monitor slow in situ photobleaching of thin dye films deposited on the prism surface. The photobleaching dynamics is interpreted as a combination of first- and second-order processes. A significant fraction of this thesis has been devoted to studying magnetic field effects (MFEs) on the kinetics of the radical pair (RP) reactions in solution, in an effort to understand the ability of animals to sense the geomagnetic field. Two novel optical-cavity-based techniques – broadband CEAS (BBCEAS) and CRDS have been developed for this purpose. BBCEAS uses a supercontinuum (SC) source as the cavity light source and a CCD camera as photodetector, enabling simultaneous acquisition of absorption spectrum across the whole visible region (400 – 800 nm). In CRDS, a tunable optical parametric oscillator has been used as the cavity light source. Combined with the switching of external magnetic field (SEMF) method, this technique allows the decay kinetics of the geminate RPs to be monitored, with nanosecond resolution. Both BBCEAS and CRDS provide sensitivity superior to single-pass transient absorption (TA), a technique traditionally used in the MFE studies. A series of photochemical systems have been studied by BBCEAS and CRDS, respectively, among which, the MFEs of drosophila melanogaster cryptochrome has been observed. Importantly, this is the first time an MFE has been observed in an animal cryptochrome, and provides key supporting evidence for the cryptochrome hypothesis of magnetoreception in animals. Besides the optical-cavity-based techniques, a novel fluorescence detection method of MFEs has also been demonstrated. This technique proved ultrahigh sensitivity when applicable.