No description available.

No description available.

No description available.

No description available.

No description available.

No description available.

The work of this thesis focuses on the interaction of high Rydberg states of hydrogen molecules and atoms with various doped Si semiconductor surfaces with the results compared with those obtained with an atomically flat gold surface. The major part of the thesis was carried out using para-H₂ molecular Rydberg states with principal quantum number n = 17 - 21 and core rotational quantum number N⁺ = 2. Subsequently, this study was continued using H atomic Rydberg states with principal quantum number n = 29 - 34. The high Rydberg states have been produced using two-step laser excitation. For close Rydberg surface separation (< 6 n² a.u.), the Rydberg states may be ionized due to an attractive surface potential experienced by the Rydberg electron, and the remaining ion core may be detected by applying an external electric field. An efficient ion detectability method is introduced to compare the many surface ionization profiles quantitatively. The p-type doped Si surfaces enhance the detected ion-signal more than the n-type doped Si surfaces due to the presence of widely distributed positive dopant charge fields in the p-type doped Si surfaces. As the dopant density increases, the area sampled by the resultant ions becomes effectively more neutral, and the decay rate of the potential from the surface dopant charge with distance from the surface becomes more rapid. Therefore, the minimum ionization distance is also reduced with increasing dopant density. It is found that the detected ion-signal decreases with increasing dopant density of both p- and n- type doped Si surfaces. The higher-n Rydberg states have shown higher ion detectability than that of lower-n Rydberg states and this variation also becomes smaller when increasing the dopant density. Experiments involving H2 Rydberg molecules incident on various doped Si surfaces in the presence of a Stark field at the point of excitation are also presented here. The surface ionization profiles produced via both electron and ion detection schemes are measured by changing the Stark polarization. Positive surface dopant charges oppose production of backscattered electrons and negative surface dopant charges enhance the electron-signal. For the electron detection scheme, lightly doped n-type Si surfaces show higher detectability but in the case of p-type Si surfaces the more heavily doped Si surfaces give a higher detected signal. This different behaviour of the detected ion or electron signal implies a different production mechanism. Theoretical trajectory simulations were also carried out based on a new 2D surface potential model. The results qualitatively agree with the experimental results and explain the changes of the surface ionization profiles between the various dopant types and dopant densities of the Si surfaces.

Single-molecule Förster resonance energy transfer (smFRET) has emerged as an important tool for studying biological reactions. This thesis describes smFRET investigations into the mechanism of bacterial transcription initiation. We developed protocols to immobilize RNAP-DNA initiation complexes using vesicles and antibodies. We used these techniques to show that the transcription bubble conformation in immobilized complexes exhibits inter-molecular heterogeneity. We observed large FRET changes that we attribute to transcription bubble opening and closing dynamics. We found that σ⁷⁰ region 3.2 (σR3.2) influences the kinetics of the bubble dynamics, which supports proposals that σR3.2 interacts with the transcription bubble template strand. We extended our investigations to RNA synthesis and were able to observe abortive initiation cycles directly. We observed RNAP pausing and backtracking for the first time in transcription initiation. We obtained data suggesting that σR3.2 stabilises short RNAs at the active centre and forms a barrier to the extension of RNAs longer than 5-nt in length. We extended our abortive initiation assay to observe signal changes that we attribute to promoter escape. Our data revealed the number of abortive cycles that occur prior to escape, the kinetics of promoter escape, and pausing events that may have some regulatory function. We investigated the conformational dynamics of the RNAP β clamp and observed dynamic conformational changes between clamp-open and clamp-closed states. Our work confirms proposals that the clamp remains stably closed once the open complex (RPO) is formed. We investigated what affect the antibiotics Myxopyronin and Lipiarmycin have on the clamp conformation. Our results revealed that Myxopyronin traps the clamp in a closed conformation, while Lipiarmycin traps it in an open conformation. Overall, we made a number of novel observations that we believe advance our understanding of the mechanism of transcription. We hope that the discoveries reported here will direct future research efforts into RNAP function.

This thesis aims to investigate the possibility of developing spectroscopic techniques for trace gas detection, with particular emphasis on their applicability to breath analysis and medical diagnostics. Whilst key breath molecules such as methane and carbon dioxide will feature throughout this work, the focus of the research is on the detection of breath acetone, a molecule strongly linked with the diabetic condition. Preliminary studies into the suitability of cavity enhanced absorption spectroscopy (CEAS) for the analysis of breath are carried out on methane, a molecule found in varying quantities in breath depending on whether the subject is a methane-producer or not. A telecommunications near-infrared semiconductor diode laser (1.6 µm) is used with an optical cavity based detection system to probe transitions within the vibrational overtone of methane. Achieving a minimum detectable sensitivity of 600 ppb, the device is used to analyse the breath of 48 volunteers, identifying approximately one in three as methane producers. Following this, a second type of laser source, the novel and widely tunable Digital Supermode Distributed Bragg Reflector (DS-DBR) laser, is characterised and the first demonstration of its use in spectroscopy documented. Particular emphasis is given to its application to CEAS and to probing the transitions of the two Fermi resonance components of the CO_2 3ν_1 + ν_3 combination bands found within the spectral range (1.56 - 1.61 µm) of the laser, providing the means to determine accurate ^{13}CO_2/^{12}CO_2 ratios for use in the urea breath test. Not all molecules exhibit narrow, well-resolved ro-vibrational transitions and the next section of the thesis focuses on the detection of molecules, such as acetone, with broad, congested absorption features which are not readily discernible using narrowband laser sources. To provide the necessary specificity for these molecules, two types of broadband source, a Superluminescent Light Emitting Diode (SLED) and a Supercontinuum source (SC), both emitting over the 1.6 - 1.7 µm region, are used in the development of a series of broadband cavity enhanced absorption (BB-CEAS) spectrometers. The three broadband absorbers investigated here, butadiene, acetone and isoprene, all exhibit overtone and combination bands in this spectral region and direct absorption measurements are taken to determine absorption cross-sections for all three molecules. The first BB-CEAS spectrometer couples the SLED device with a dispersive monochromator, attaining a minimum detectable sensitivity of 6 x 10^{-8} cm^{-1}, which is further enhanced to 1.5 x 10^{-8} cm^{-1} on replacing the monochromator with a Fourier Transform interferometer. The spectral coverage is then extended to 1.5 - 1.7 µm by coupling the first SLED with a second device, providing a demonstration of simultaneous multiple species detection. Finally, a SC source is used to provide greater power and uniform spectral intensity, resulting in an improved minimum detectable sensitivity of 5 x 10^{-9} cm^{-1}, or 200 ppb, 400 ppb and 200 ppb for butadiene, acetone and isoprene respectively. This device is then applied to acetone-enriched breath samples; the resulting spectra are fitted with a simulation to return the acetone levels present in the breath-matrix. Following this, the development of a prototype breath acetone analyser, carried out at Oxford Medical Diagnostics Ltd. (OMD), is described. To fulfill the requirements of a compact and commercially-viable device, a diode laser-based system is used, which necessitates a thorough investigation into all possible sources of absorption level change. Most notably, this includes a study into the removal and negating of interfering species, such as water vapour, and to a lesser extent, methane. A novel solution is presented, utilising a water-removal device in conjunction with molecular sieve so that each breath sample generates its own background, which has allowed breath acetone levels to be measured within an uncertainty of 200 ppb. Spectroscopic detection then moves to the mid-infrared with the demonstration of a continuous wave 8 µm quantum cascade laser, which allows the larger absorption cross-sections associated with fundamental vibrational modes to be probed. Following the laser's characterisation using methane, including a wavelength modulation spectroscopy study, the low effective laser linewidth is utilised to resolve rotational structure in low pressure samples of pure acetone. Absorption cross-sections are determined before the sensitivity of the system is enhanced for the detection of dilute concentrations of acetone using two types of multipass cells, firstly a White cell and secondly a home-built Herriott cell. This allows an acetone minimum detectable absorption of 350 ppb and 20 ppb to be attained, respectively. Following this, an optical cavity is constructed and, on treating breath samples in a water-removal device prior to analysis, breath acetone levels determined and corroborated with a mass spectrometer. Finally, a preliminary study probing acetone in the ultraviolet is presented. Utilising an LED centred at 280 nm with a low finesse optical cavity and an imaging spectrograph, detection of 25 ppm of acetone is demonstrated and possible vibronic structure resolved. Combining large absorption cross-sections with the potential to be compact and commercially viable, further development of this arrangement could ultimately represent the optimum solution for breath acetone detection.

Imaging mass spectrometry (IMS) in microscope mode allows the spatially resolved molecular constitution of a large sample section to be analysed in a single experiment. If performed in a linear mass spectrometer, the applicability of microscope IMS is limited by a number of factors: the low mass resolving power of the employed ion optics; the time resolution afforded by the scintillator screen based particle detector and the multi-hit capability, per pixel, of the employed imaging sensor. To overcome these limitations, this thesis concerns the construction of an advanced ion optic employing a pulsed extraction method to gain a higher ToF resolution, the development of a bright scintillator screen with short emission lifetime, and the application of the Pixel Imaging Mass Spectrometry (PImMS) sensor with multi-mass imaging and time stamping capabilities. Initial experimental results employing a three electrode ion optic to spatially map ions emitted from a sample surface are presented. By applying a static electric potential a time-of-flight resolution of t/2Δt=54 and a spatial resolution of 20 μm are determined across a field-of-view of 4 mm diameter. While the moderate time-of-flight resolution only allows particles separated by a few Dalton to be distinguished, the instrument is used to demonstrate the multi-mass imaging capabilities of the PImMS sensor when being applied to image grid structures or tissue samples. An improved time-of-flight resolution is achieved by post extraction differential acceleration of a selected range of ions (up to 100 Da) using a newly developed five electrode ion optic. This modification is shown to correct the initial velocity spread of the ions coming off the sample surface, which yields an enhanced time-of-flight resolution of t/2Δt=2000 . The spatial resolution of the instrument is found to be 20 μm across a field-of-view of 4 mm. Adjusting the extraction field strength applied to the ion optic of the constructed mass spectrometer allows the optimised mass range to be tuned to any mass of interest. Ion images are recorded for various samples with comparable spatial and ToF resolution. Hence, studies on tissue sections and multi sample arrays become accessible with the improved design and operational principle of the microscope mode IMS instrument. A fast and efficient conversion of impinging ions into detectable flashes of light, which can consequently be recorded by a fast imaging sensor, is essential to maintain the achievable time-of-flight and spatial resolution of the IMS instrument constructed. In order to find a suitable fast and bright scintillator to be applied in a microchannel based particle detector, various inorganic and organic substances are characterised in terms of their emission properties following electron excitation. Poly-para-phenylene laser dye screens are found to show an outstanding performance among all substances analysed. An emission life time of below 4 ns and a brightness exceeding that of a P47 screen (industry standard) by a factor 2× is determined. No signal degradation is observed over an extended period, and the spatial resolution is found to be comparable to commercial imaging detectors. Hence, these scintillator screens are fully compatible with any ion imaging application requiring a high time resolution. In a further series of mass spectrometric experiments, ions are accelerated onto a scintillator mounted in front of a multi pixel photon counter. The charged particle impact stimulated the emission of a few photons, which are collected by the fast photon counter. Poly-para-phenylene laser dyes again show an outstanding efficiency for the conversion of ions into photons, resulting in a signal enhancement of up to 5× in comparison to previous experiments, which employed an inorganic LYSO scintillator.