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The biopharmaceutical industry has long relied on the work of microbiologists to perform labour intensive experiments in bioprocess development. Real time information on the specific dynamics of each experiment would represent a major breakthrough in understanding bioprocesses. This would lead to higher productivity, shortened development cycles, ultimately resulting in cheaper drugs reaching the clinic faster with potentially improved safety and efficacy. The purpose of this thesis is to expedite the biopharmaceutical development by combining automation and near infrared spectroscopy in the early stages of bioprocess development. It develops the first automated spectroscopic system for automated smallvolume bioreactors. After describing the hardware, software, optimization and testing of this new tool, various advantages and challenges that come with such system are discussed. The advantages of automation when put to use into spectroscopy are quickly apparent. The automated approach can collect a - highly replicable - calibration dataset six times faster than the traditional approach, eliminating human error. Multivariate data analysis, including PCA and PLS, proved that valid real time measurements of analytes of interest in the fermentation media can be obtained. The use of the developed models for extrapolation showed limited success. Better results were obtained when an endogenous calibration dataset was prepared through means of automation. This exercise allowed the identification of critical success areas for developing a spectroscopy-based measuring system for small automated bioreactors. In the end, a roadmap for future implementation of an automated NIR system is provided that summarises the key lessons drawn from this thesis.

A promising scheme for plasma wakefield acceleration is the hybrid plasma acceleration mechanism, which is experimentally connected to worldwide programs at various accelerator facilities. This scheme may lead to extremely high-quality electron bunches, that can be used to drive ultrabright light sources such as free electron lasers. The big challenge for plasma acceleration is to produce electron bunches with high quality in terms of low emittance, energy spread, and high brightness. To overcome this challenge, the Trojan Horse "plasma photocathode" scheme is used to produce designer electron beams. This thesis explores the Trojan Horse mechanism in a systematic simulation based parametric study. Different interaction regimes are explored by variation of the injector laser pulse by normalised vector potential a0, spot size w0 and relative spatiotemporal synchronisation and alignment in the plasma wave at various densities. These parameters define the plasma photocathode process. The general motivation of this work is to investigate the generation of high quality electron beams for light source applications. Several factors and mechanisms impact the witness bunch, affect its beam emittance, and drive its growth. The main driver for emittance growth, particularly at increased witness beam charge levels, is space charge and intra-beam Coulomb repulsion. Although the laser-released electrons from the plasma photocathode are rapidly accelerated and focused by the plasma wakefields, increasing the charge, e.g., by means of increasing the background plasma density from which the plasma photocathode electrons are liberated, produced very strong electric fields inside the bunch and thus triggered and driven rapid emittance growth. The effect of evolving space charge in the formative phase of the witness beam production and acceleration is investigated using tailored particle-in-cell simulations, for example, by scanning the evolution of transverse phase space across different plasma densities, and the illumination of the process by analysis is not available to the experiment but only to high-resolution and high-fidelity simulations. These computational studies provide insight into the sensitivities and robustness of the scheme, which is important for upcoming experiments, e.g., at SLAC, FACET-II, and may allow pushing the emittance and brightness barrier of electron beams produced by the Trojan Horse process. This could dramatically impact applications such as ultrabright, hard x-ray free-electron lasers, particle and strongfield physics.

An emerging area of free electron laser development concerns tailoring the transverse and phase profile of the light, which can result in the radiation acquiring orbital angular momentum. This thesis studies the development of novel techniques for free electron lasers with consideration of the generation of higher-order orbital angular momentum modes acting as a starting point for this research. Three new techniques are presented in this thesis. The first examines altering mode competition in a free electron laser to induce radiation of a dominant orbital angular momentum mode. The next is a scheme to produce light with spatially varying states of polarisation - obtained through the overlap of different coherent transverse light distributions. The third technique produces trains of short radiation pulses where the properties of the pulses alternate. The goal of this research is to increase the diversity of radiation from free electron lasers in order to offer something new and unlock new areas of scientific research.