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Abstract: In this thesis, we report the ability to fabricate hydrogels using low molecular weight gelators (LMWGs) and the subsequent characterisation of their mechanical properties over a variety of different length scales. These materials have been investigated due to their potential use in a wide range of biomedical applications including drug delivery, tissue engineering, cell culture and wound healing. We describe the localised gelation of LMWGs on electrode surfaces via electrochemically generated pH gradients. The electrofabrication of hydrogels on electrode surfaces has shown great potential in the field of biomedicine, with applications ranging from antimicrobial wound dressings, tissue engineering scaffolds and biomimetic materials. First, we describe the largest reported di- and tri-peptide-based hydrogels on electrode surfaces via the electrochemical oxidation of hydroquinone. Expanding upon previous work which focuses on the fabrication of hydrogels on the nanometre to millimetre scale, we deposit hydrogels around 3 cm3 in size. Furthermore, we demonstrate that there is an upper limit to how large the hydrogels can grow which is determined by the size of the pH gradient from the electrode surface. To grow hydrogels of this size, much longer deposition times of two to five hours are required than in previous reports. When the gelator/hydroquinone solution is left exposed to the open atmosphere for this amount of time, the hydroquinone in solution oxidises to benzoquinone/quinhydrone before it can be consumed electrochemically. This inhibits the electrochemical reaction and reduces gelation efficiency. To prevent this, we build a system that can perform the fabrication process under an inert nitrogen atmosphere. Using this system, we show how the choice of gelator affects the mechanical properties of the hydrogel and the resulting material phenomena that cause these changes. As well as this, we show how this approach can be used to grow multi-layered hydrogels, with each layer presenting different chemical and mechanical properties. Secondly, we report the first known example of electrodeposition for a LMWG molecule using an electrochemically generated basic pH gradient at electrode surfaces. This approach has previously been used to fabricate hydrogels of the biopolymer chitosan using the galvanostatic reduction of hydrogen peroxide. During the electrochemical reduction of hydrogen peroxide, hydroxide ions are produced. As a result, a basic pH zone is generated at the electrode, triggering solutions of chitosan to form immobilised hydrogels on the electrode surface. Using this approach, we show how electrodeposition at high pH can be applied to our LMWG system. We then show that we can electrochemically form hydrogels at high pH, with the gel properties being greatly improved by the addition and increased concentration of hydrogen peroxide. Following from this, we then show the simultaneous formation of two low molecular weight hydrogels at acidic and basic pH extremes. To achieve this, we couple the electrochemical reduction of hydrogen peroxide and the electrochemical oxidation of hydroquinone described in the previous chapter. Finally, we report the electrodeposition of five carbazole-protected amino acid hydrogels on electrode surfaces via the electrochemical oxidation of hydroquinone. As well as this, we report the full to partial electropolymerisation of the pre-assembled hydrogels in perchloric acid. For the less bulky carbazole-protected amino acids, the full collapse of the hydrogel to form electrochromic polymers on the electrode surface is achieved. However, for the bulkier gelators, little to no evidence of polymerisation occurs. We believe this is due to the bulky side chain on the gelator backbone preventing the molecular reorganization required for polymerization to occur.

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Abstract: The epitaxial growth of anatase (001) films deposited by pulsed laser deposition (PLD) and molecular beam epitaxy (MBE) on SrTiO3 (001) (STO) single crystals has been studied using X-ray diffraction and surface sensitivity UHV techniques. The evolution of the strain represented by the microstrain and the change of the in-plane and out-of-plane lattice parameters with film growth temperature, the effect of the annealing temperature and the influence of the oxygen content of the film have been investigated. The out-of-plane lattice strain shows a compressive (-0.2%) or expansive (+0.3%) behavior, in the range 600 - 900°C, for temperatures below or above 700°C, respectively. The in-plane lattice parameters, as well as the cell volume of the film, remain under compression over the entire temperature range explored. PLD films grow into square islands that align with the surface lattice directions of the STO substrate. The maximum size of these islands is reached at growth temperatures close to 875-925°C. Film annealing at temperatures of 800°C or higher melts the islands into flat terraces. Larger terraces are reached at high annealing temperatures of 925°C for extended periods of 12 hours. This procedure allows flat surface terrace sizes of up to 650 nm to be achieved. The crystalline quality achieved in anatase films prepared by PLD or MBE growth methods is similar. The two-step anatase growth process used during the synthesis of the films with both methods: film growth and post-annealing treatment in oxygen or air at ambient pressure, using temperature and time as key parameters, allows to control the surface terrace size and stoichiometry of the films, as well as the anatase/rutile intermixing rates at sufficiently high temperatures. This growth process could allow the substitution of their equivalent single crystals. The range of applicability of these films would include their use as structural and electronic model systems, or in harsh experimental conditions due to their low production cost.

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Abstract: The understanding of antiferromagnetic domain walls, which are the interface between domains with different Néel order orientations, is a crucial aspect to enable the use of antiferromagnetic materials as active elements in future spintronic devices. In this work, we demonstrate that in antiferromagnetic NiO/Pt bilayers arbitrary-shaped structures can be generated by switching driven by electrical current pulses. The generated domains are T domains, separated from each other by a domain wall whose spins are pointing toward the average direction of the two T domains rather than the common axis of the two planes. Interestingly, this direction is the same for the whole domain wall indicating the absence of strong Lifshitz invariants. The domain wall can be micromagnetically modeled by strain distributions in the NiO thin film induced by the MgO substrate, deviating from the bulk anisotropy. From our measurements we determine the domain-wall width to have a full width at half maximum of Δ = 98 ± 10 nm, demonstrating strong confinement.

Open Access

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Abstract: Over the past few years, many machine learning-based scoring functions for predicting the binding of small molecules to proteins have been developed. Their objective is to approximate the distribution which takes two molecules as input and outputs the energy of their interaction. Only a scoring function that accounts for the interatomic interactions involved in binding can accurately predict binding affinity on unseen molecules. However, many scoring functions make predictions based on data set biases rather than an understanding of the physics of binding. These scoring functions perform well when tested on similar targets to those in the training set but fail to generalize to dissimilar targets. To test what a machine learning-based scoring function has learned, input attribution, a technique for learning which features are important to a model when making a prediction on a particular data point, can be applied. If a model successfully learns something beyond data set biases, attribution should give insight into the important binding interactions that are taking place. We built a machine learning-based scoring function that aimed to avoid the influence of bias via thorough train and test data set filtering and show that it achieves comparable performance on the Comparative Assessment of Scoring Functions, 2016 (CASF-2016) benchmark to other leading methods. We then use the CASF-2016 test set to perform attribution and find that the bonds identified as important by PointVS, unlike those extracted from other scoring functions, have a high correlation with those found by a distance-based interaction profiler. We then show that attribution can be used to extract important binding pharmacophores from a given protein target when supplied with a number of bound structures. We use this information to perform fragment elaboration and see improvements in docking scores compared to using structural information from a traditional, data-based approach. This not only provides definitive proof that the scoring function has learned to identify some important binding interactions but also constitutes the first deep learning-based method for extracting structural information from a target for molecule design.

Open Access

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Abstract: Tetragonal CuMnAs is a room temperature antiferromagnet with an electrically reorientable Néel vector and a Dirac semimetal candidate. Direct measurements of the electronic structure of single-crystalline thin films of tetragonal CuMnAs using angle-resolved photoemission spectroscopy (ARPES) are reported, including Fermi surfaces (FS) and energy-wavevector dispersions. After correcting for a chemical potential shift of ≈− 390 meV (hole doping), there is excellent agreement of FS, orbital character of bands, and Fermi velocities between the experiment and density functional theory calculations. In addition, 2×1 surface reconstructions are found in the low energy electron diffraction (LEED) and ARPES. This work underscores the need to control the chemical potential in tetragonal CuMnAs to enable the exploration and exploitation of the Dirac fermions with tunable masses, which are predicted to be above the chemical potential in the present samples.