Magnetoreception is the ability of some animals to use the weak magnetic field of the Earth for navigation over long-distance migrations. It is a well-known phenomenon, but its underlying biophysical mechanisms remain poorly understood. One proposal involves light-induced, magnetically sensitive chemical reactions occurring within cryptochrome proteins, rationalised via the radical pair mechanism (Chapter 1). The absence of evidence in support of this hypothesis is in part due to the lack of sufficiently sensitive techniques to measure magnetic field effects (MFEs) in biological samples. Cavity-enhanced detection, most commonly in the form of cavity ring-down spectroscopy (CRDS) or cavity-enhanced absorption spectroscopy (CEAS), is widely used in the gas phase to provide significant sensitivity gains over traditional single-pass measurements (Chapter 2). However, successful studies in the condensed phase are less prevalent due to the additional background losses inherent to the sample. This thesis reports on the application of broadband (i.e. monitoring > 100nm) variants of CRDS and CEAS to the study of MFEs on the radical recombination reactions of flavin-based systems in solution. The broadband CRDS (BBCRDS) instrument employed in Chapter 4 is able to monitor the spectral changes induced by magnetic fields with submicrosecond time resolution. However, the need to scan both the probe wavelength and time delay to construct time-resolved spectra leads to prohibitively long acquisition times, and hence exposure of sensitive samples to high numbers of photons. The broadband CEAS (BBCEAS) studies reported in Chapter 5 combine the high irradiance and spectral coverage of a supercontinuum radiation (SCR) source with a CCD detector to simultaneously acquire absorption spectra across the visible region (480–700nm). The CW nature of this technique precludes the possibility of following radical pair kinetics in real time. In an effort to combine the respective advantages of these two instruments, which individually have represented powerful advances in capability, a new cavity-enhanced technique is reported for the first time (Chapter 6). The result, optical cavity-enhanced transient absorption spectroscopy (OCTAS), is able to simultaneously monitor spectral evolution and associated MFEs on the microsecond timescale, with comparable sensitivity to the existing techniques. Magnetic responses in animal cryptochrome proteins have successfully been recorded using all three techniques, lending considerable weight to the hypothesis that these molecules are at the heart of the magnetic sense in animals.

This thesis describes the development and application of condensed-phase cavity-based spectroscopic techniques - namely cavity ring-down spectroscopy (CRDS); cavity enhanced absorption spectroscopy (CEAS); broadband cavity enhanced absorption spectroscopy (BBCEAS) and evanescent wave (EW) variants of all three. The recently-developed cavity technique of EW-broadband cavity enhanced absorption spectroscopy (EW-BBCEAS) has been used—in combination with a supercontinuum source (SC) and a sensitive, fast readout CCD detector—to record of the full visible spectrum (400–700 nm) of a silica-liquid interfacial layer (with an effective thickness ca. 1 µm), at rapid acquisition rates (> 600 Hz) that are sufficient to follow fast kinetics in the condensed phase, in real time. The sensitivity achieved (A_min= 3.9 x 10^-5) is comparable with previous EW-CRDS and EW-CEAS studies, but the spectral region accessed in this broadband variant is much larger. The study of liquid|air interfaces using EW cavity-based techniques is also illustrated for the first time. The first application of BBCEAS to the analysis of microfluidic samples, flowing through a microfluidic chip, is illustrated. Proof-of-principle experiments are presented, demonstrating the technique’s ability to provide full visible broadband spectral measurements of flowing microfluidic droplets, with both high detection sensitivity (α_min < 10^-2 cm^-1) and excellent spatial and temporal resolution: an SC light source and sensitive, fast readout CCD allowed measurement repetition rates of 273 Hz, whilst probing a very small sample volume (ca. 90 nL). A significant portion of this thesis is devoted to demonstrating the powerful capabilities of CEAS, CRDS and BBCEAS in monitoring radical recombination reactions and associated magnetic field effects (MFEs) in solution. The efficacy of CEAS as a high-sensitivity MFE detection method has been established in a proof-of-principle study, using narrow band CEAS in combination with phase-sensitive detection: MFE-induced absorbance changes of ca. 10^-6 could be detected using the modulated CEAS technique and the data are shown to be superior to those obtained using conventional transient absorption (TA) methods typically employed for MFE measurements. The powerful capabilities of CRDS in monitoring radical recombination reactions and associated MFEs are also demonstrated. In particular, a pump-probe CRDS variant allows not only high sensitivity (A_min on the order 10^-6), but also sub-microsecond time-resolution. Combined, these features represent significant advantages over TA. Finally, SC-BBCEAS is used to measure full visible spectra of photoinduced reactions and their MFEs. The applicability of this approach to in vitro MFE studies of Drosophila cryptochrome is demonstrated—the results mark the first in vitro observation of a magnetic field response in an animal cryptochrome, a key result supporting the hypothesis that cryptochromes are involved in the magnetic sense in animals.

<p>Laser-based absorption spectroscopy (AS) is a powerful technique for qualitative and quantitative studies of atoms and molecules. An important field of use of AS is the detection of species in trace concentrations, which has applications not only in physics and chemistry but also in biology and medicine, encompassing environmental monitoring, regulation of industrial processes and breath analysis. Although a large number of molecular species can successfully be detected with established AS techniques, there are some applications that require higher sensitivity, selectivity and accuracy, yet robust and compact instrumentation.</p><p>Various approaches have been made during the years to improve on the performance of AS, usually based on modulation spectrometry or external cavities. The most sensitive absorption technique of today is, however, noise-immune cavity-enhanced optical heterodyne molecular spectroscopy (NICE-OHMS). This technique elegantly combines several approaches: external cavities (for optical path length enhancement), modulation techniques (for noise reduction) and saturation spectroscopy (for enhanced selectivity). However, due to its complexity, the technique has so far not been applied to practical trace species detection.</p><p>This thesis provides the background for an understanding of NICE-OHMS and describes the construction of a first compact NICE-OHMS spectrometer based on a narrowband fiber laser. Moreover, it gives theoretical expressions for NICE-OHMS signal lineshapes, measured in various modes of detection, which can be fitted to the experimental data and thereby facilitate the assessment of species concentration. The sensitivity of the instrumentation is demonstrated by detection of acetylene (C₂H₂) and carbon dioxide (CO₂) in the 1.5 μm region. A fractional absorption sensitivity of 3*10^-9 (integrated absorption of 5*10^-11 cm^-1), could be achieved using a cavity with a finesse of 4800 and an acquisition time of 0.7 s. This results in a detection limit for C₂H₂ of 4.5 ppt (4.5*10^-12 atm).</p><p>In addition, the thesis revives the idea of using an accurate (frequency) measurement of the free-spectral-range (FSR) of an external cavity for sensitive and calibration-free concentration assessment. A theoretical description of the expected signal lineshapes is given, and in a first experimental demonstration the FSR could be measured with a resolution of 5 Hz, resulting in a fractional absorption sensitivity of 1*10^-7, and subsequently in a detection limit for C₂H₂ of 180 ppt (12.5 s acquisition time).</p><p>The thesis, finally, also contributes to the continuously ongoing development of conventional AS and wavelength modulated AS by addressing concepts related to when the light optically saturates the transition.</p>

Laser-based absorption spectroscopy (AS) is a powerful technique for qualitative and quantitative studies of atoms and molecules. An important field of use of AS is the detection of species in trace concentrations, which has applications not only in physics and chemistry but also in biology and medicine, encompassing environmental monitoring, regulation of industrial processes and breath analysis. Although a large number of molecular species can successfully be detected with established AS techniques, there are some applications that require higher sensitivity, selectivity and accuracy, yet robust and compact instrumentation. Various approaches have been made during the years to improve on the performance of AS, usually based on modulation spectrometry or external cavities. The most sensitive absorption technique of today is, however, noise-immune cavity-enhanced optical heterodyne molecular spectroscopy (NICE-OHMS). This technique elegantly combines several approaches: external cavities (for optical path length enhancement), modulation techniques (for noise reduction) and saturation spectroscopy (for enhanced selectivity). However, due to its complexity, the technique has so far not been applied to practical trace species detection. This thesis provides the background for an understanding of NICE-OHMS and describes the construction of a first compact NICE-OHMS spectrometer based on a narrowband fiber laser. Moreover, it gives theoretical expressions for NICE-OHMS signal lineshapes, measured in various modes of detection, which can be fitted to the experimental data and thereby facilitate the assessment of species concentration. The sensitivity of the instrumentation is demonstrated by detection of acetylene (C2H2) and carbon dioxide (CO2) in the 1.5 μm region. A fractional absorption sensitivity of 3*10-9 (integrated absorption of 5*10-11 cm-1), could be achieved using a cavity with a finesse of 4800 and an acquisition time of 0.7 s. This results in a detection limit for C2H2 of 4.5 ppt (4.5*10-12 atm). In addition, the thesis revives the idea of using an accurate (frequency) measurement of the free-spectral-range (FSR) of an external cavity for sensitive and calibration-free concentration assessment. A theoretical description of the expected signal lineshapes is given, and in a first experimental demonstration the FSR could be measured with a resolution of 5 Hz, resulting in a fractional absorption sensitivity of 1*10-7, and subsequently in a detection limit for C2H2 of 180 ppt (12.5 s acquisition time). The thesis, finally, also contributes to the continuously ongoing development of conventional AS and wavelength modulated AS by addressing concepts related to when the light optically saturates the transition.