Alpha-hemolysin is a pore-forming toxin secreted by pathogenic Staphylococcus aureus. Its spontaneous oligomerization and assembly into a trans-bilayer beta-barrel pore is a model for the assembly of many other pore-forming toxins. It is studied here in vitro as a means to probe general membrane protein oligomerization and lipid bilayer insertion. This thesis details the results of experiments to develop and implement a novel in vitro lipid bilayer system, Droplet-on-Hydrogel Bilayers (DHBs) for the single-molecule imaging of alpha-hemolysin assembly. Chapter 2 describes the development of DHBs and their electrical characterization. Experiments show the detection of membrane channels in SDS-PAGE gels post-electrophoresis and DHBs use as a platform for nanopore stochastic sensing. Chapter 3 describes the engineering and characterization of fluorescently-labelled monomeric alpha-hemolysin for use in protein assembly imaging experiments described in Chapter 6. Chapter 4 describes the characterization of DHB lipid fluidity and suitability for single-molecule studies of membrane protein diffusion. In addition, a novel single-particle tracking algorithm is described. Chapter 5 describes experiments demonstrating simultaneous electrical and fluorescence measurements of alpha-hemolysin pores embedded within DHBs. The first multiple-pore stochastic sensing in a single-lipid bilayer is also described. Chapter 6 describes experiments studying the assembly of alpha-hemolysin monomers in DHBs. Results show that alpha-hemolysin assembles rapidly into its oligomeric state, with no detection of long-lived intermediate states.

Carbon-based materials are poised to be an important class of 21st century materials, for bio-medical, bio-electronic, and bio-sensing applications. Diamond and polymers are two examples of carbon-based materials of high interest to the bio-materials community. Diamond, in its conductive form, can be used as an electrochemical bio-sensor, whilst its nanoparticle form is considered a non-inflammatory platform to deliver drugs or to grow neuronal cells. Polymers, especially when chemically modified, have been used extensively in biological environments, from anti-microbial use to drug delivery. The large-scale use of either material for biological use is limited by two factors: ease of chemical modification and the paucity of knowledge of their surface chemistry in aqueous media. This thesis addresses aspects of both these issues. The first study reported is an in situ study of the adsorption dynamics of an exemplar globular protein (bovine serum albumin, BSA) on nanodiamond using the relatively novel quartz crystal microbalance with dissipation (QCM-D) technique. For the first time, QCM-D enabled the detailed study of protein dynamics (i.e. kinetics, viscoelastic properties, overlayer structure, etc.) onto nanodiamond thin films having various surface chemistry and roughness. The dynamics of protein adsorption is found to be sensitive to surface chemistry at all stages of adsorption, but it is only sensitive to surface roughness during initial adsorption phases. Our understanding of the nanodiamond-biology interface is enhanced by this study, and it suggests that QCM-D is useful for the study of the surface chemistry of nanoparticle forms of inorganic materials. A second study concerns a novel surface functionalization scheme, based on carbene and azo-coupling chemistry, which has been recently introduced as a practical, facile method for modifying the surfaces of polymers. Using modern surface characterization techniques, it is demonstrated that a chemical linker can be attached to polystyrene surfaces using carbene-based chemistry, and that further chemical functionality can be added to this chemical linker via an azo-coupling reaction. In situ studies of protein dynamics at these interfaces were conducted using QCM-D, thus enabling a link between specific protein behaviour and the polymer surface chemical termination chemistry to be made. A third area of study of investigates the use of diamond electrodes as a bio-sensor for dopamine under physiological conditions. For these conditions, ascorbic acid interferes with the dopamine oxidation signal, in ways that render the two signals irresolvable. Various modifications are used in attempts to reduce this interference, including: small and large cathodic treatments, grafting of electro-active polymers, addition of carbon nanotubes, and hydrogen plasma treatment. Those modifications leading to the hydrogen-termination of diamond are shown to work the best. Notably, hydrogen plasma treatment effects the complete electrochemical separation of dopamine and ascorbic acid at a diamond electrode. This is the first time this has been accomplished without adding non-diamond materials to the diamond electrode surface.

Molecular biophysics is a rapidly evolving field aimed at the physics-based investigation of the biomolecular processes that enable life. In this thesis, we explore two such processes: the thermodynamics of DNA bending, and the mechanism of the RecQ DNA helicase. A computational approach using a coarse-grained model of DNA is employed for the former; an experimental approach relying heavily on single-molecule fluorescence for the latter. There is much interest in understanding the physics of DNA bending, due to both its biological role in genome regulation and its relevance to nanotechnology. Small DNA bending fluctuations are well described by existing models; however, there is less consensus on what happens at larger bending fluctuations. A coarse-grained simulation is used to fully characterize the thermodynamics and mechanics of duplex DNA bending. We then use this newfound insight to harmonize experimental results between four distinct experimental systems: a 'molecular vise', DNA cyclization, DNA minicircles and a 'strained duplex'. We find that a specific structural defect present at large bending fluctuations, a 'kink', is responsible for the deviation from existing theory at lengths below about 80 base pairs. The RecQ DNA helicase is also of much biological and clinical interest, owing to its essential role in genome integrity via replication, recombination and repair. In humans, heritable defects in the RecQ helicases manifest clinically as premature aging and a greatly elevated cancer risk, in disorders such as Werner and Bloom syndromes. Unfortunately, the mechanism by which the RecQ helicase processes DNA remains poorly understood. Although several models have been proposed to describe the mechanics of helicases based on biochemical and structural data, ensemble experiments have been unable to address some of the more nuanced questions of helicase function. We prepare novel substrates to probe the mechanism of the RecQ helicase via single-molecule fluorescence, exploring DNA binding, translocation and unwinding. Using this insight, we propose a model for RecQ helicase activity.

Magnetic fields influence the rate and/or yield of chemical reactions that proceed via spin correlated radical pair intermediates. The field of spin chemistry centres around the study of such magnetic field effects (MFEs). This thesis is particularly concerned with the effects of the weak magnetic fields B₀ ~ 1mT relevant in the ongoing debates on the mechanism by which animals sense the geomagnetic field and on the putative health effects of environmental electromagnetic fields. Relatively few previous studies have dealt with such weak magnetic fields. This thesis presents several new theoretical tools and applies them to interpret experimental measurements. Chapter 1 surveys the development and theory of spin chemistry. Chapter 2 introduces the use of Tikhonov and Maximum Entropy Regularisation methods as a new means of analysing MARY field effect data. These are applied to recover details of the diffusive motion of reacting pyrene and N,N-dimethylaniline radicals. Chapter 3 gives a fresh derivation and appraisal of an approximate, semiclassical approach to MFEs. Monte Carlo calculations allow the elucidation of several "rules of thumb" for interpreting MFE data. Chapter 4 discusses recent optically-detected zero-field EPR measurements, adapting the gamma-COMPUTE algorithm from solid state NMR for their interpretation. Chapter 5 explores the role of RF polarisation in producing MFEs. The breakdown in weak fields of the familiar rotating frame approximation is analysed. Chapter 6 reviews current knowledge and landmark experiments in the area of animal magnetoreception. The origins of the sensitivity of European robins Erithacus rubecula to the Earth’s magnetic field are given particular attention. In Chapter 7, Schulten and Ritz’s hypothesis that avian magnetoreception is founded on a radical pair mechanism (RPM) reaction is appraised through calculations in model systems. Chapter 8 introduces quantitative methods of analysing anisotropic magnetic field effects using spherical harmonics. Chapter 9 considers recent observations that European robins may sometimes be disoriented by minuscule RF fields. These are shown to be consistent with magnetoreception via a radical pair with no (effective) magnetic nuclei in one of the radicals.

This thesis presents the development and redesign of a commercial electrochemical quartz crystal microbalance with dissipation (E–QCM–D). This was used to study factors affecting the efficiency of the four electron reduction catalysed by the fuel cell enzyme bilirubin oxidase from Myrothecium verrucaria immobilised on thiol modified gold surfaces. Within this thesis, the E–QCM–D was used to show that application of a constant potential to bilirubin oxidase adsorbed to thiol-modified gold surfaces causes activity loss that can be attributed to a change in structural arrangement. Varying the load by potential cycling distorts the enzyme by inducing rapid mass loss and denaturation. Attaching the enzyme covalently reduces the mass loss caused by potential cycling but does not mitigate activity loss. Covalent attachment also changes the orientation of the surface bound enzyme as verified by the position of the catalytic wave (related to the overpotential for catalysis) and reactive labelling followed by mass spectrometry analysis. The E–QCM–D was used to show how electrostatic interactions affect enzyme conformation where high pH causes a reduction in both mass loading at the electrode and a reduction in activity. At pH lower than the enzyme isoelectric point, there is a build up of multilayers in a clustered adsorption. When enzyme adsorbs to hydrophobic surfaces there is a rapid denaturation which completely inactivates the enzyme. Changing the surface chemistry from carboxyl groups to hydroxyl and acetamido groups shows that catalysis is shifted to more negative potentials as a result of an enzyme misorientation. Further to this, increasing the chain length of the thiol modifier indicates that an increased distance between surface and enzyme reduces activity, enzyme loading and results in a conformational rearrangement that permits electron transfer over longer distances.

This thesis primarily focuses on the electrochemical properties of the H₂/H⁺ redox couple, at various metallic electrodes in room temperature ionic liquids. Initially, a comprehensive overview of room temperature ionic liquids, RTILs, compared to conventional organic solvents is presented which identifies their favourable properties and applications, followed by a second chapter describing the basic theory of electrochemistry. A third chapter presents the general experimental reagents, instruments and measurements used in this thesis. The results presented in this thesis are summarized in six further chapters and shown as follows. (1) Hydrogenolysis, hydrogen loaded palladium electrodes by electrolysis of H[NTf₂] in a RTIL [C₂mim][NTf₂]. (2) Palladium nanoparticle-modified carbon nanotubes for electrochemical hydrogenolysis in RTILs. (3) Electrochemistry of hydrogen in the RTIL [C₂mim][NTf₂]: dissolved hydrogen lubricates diffusional transport. (4) The hydrogen evolution reaction in a room temperature ionic liquid: mechanism and electrocatalyst trends. (5) The formal potentials and electrode kinetics of the proton_hydrogen couple in various room temperature ionic liquids. (6) The electroreduction of benzoic acid: voltammetric observation of adsorbed hydrogen at a Platinum microelectrode in room temperature ionic liquids. The first two studies show electrochemically formed adsorbed H atoms at a metallic Pt or Pd surface can be used for clean, efficient, safe electrochemical hydrogenolysis of organic compounds in RTIL media. The next study shows the physicochemical changes of RTIL properties, arising from dissolved hydrogen gas. The last three studies looked at the electrochemical properties of H₂/H⁺ redox couple at various metallic electrodes over a range of RTILs vs a stable Ag/Ag⁺ reference couple, using H[NTf₂] and benzoic acid as proton sources. The kinetic and thermodynamic mechanisms of some reactions or processes are the same in RTILs as in conventional organic or aqueous solvents, but other remarkably different behaviours are presented. Most importantly significant constants are seen for platinum, gold and molybdenum electrodes in term of the mechanism of proton reduction to form hydrogen.

Nanomaterials have attracted great interest due to the unique physical properties and great potential in the applications of nanoscale devices. Two dimensional atomic crystals, which are atomic thickness, especially graphene, have triggered the gold rush recently due to the fascinating high mobility at room temperature for future electronics. The crystal structure of nanomaterials will have great influence on their physical properties. Thus, this thesis is focused on developing the methods to control the crystal structure of nanomaterials, namely quantum dots as semiconductor, boron nitride (BN) as insulator, graphene as semimetal, with low cost for their applications in photonics, structural support and electronics. In this thesis, firstly, Mn doped ZnSe quantum dots have been synthesized using colloidal synthesis. The shape control of Mn doped ZnSe quantum dots has been achieved from branched to spherical by switching the injection temperature from kinetics to thermodynamics region. Injection rates have been found to have effect on controlling the crystal phase from zinc blende to wurtzite. The structural-property relationship has been investigated. It is found that the spherical wurtzite Mn doped ZnSe quantum dots have the highest quantum yield comparing with other shape or crystal phase of the dots. Then, the Mn doped ZnSe quantum dots were deposited onto the BN sheets, which were micron-sized and fabricated by chemical exfoliation, for high resolution imaging. It is the first demonstration of utilizing ultrathin carbon free 2D atomic crystal as support for high resolution imaging. Phase contrast images reveal moiré interference patterns between nanocrystals and BN substrate that are used to determine the relative orientation of the nanocrystals with respect to the BN sheets and interference lattice planes using a newly developed equation method. Double diffraction is observed and has been analyzed using a vector method. As only a few microns sized 2D atomic crystal, like BN, can be fabricated by the chemical exfoliation. Chemical vapour deposition (CVD) is as used as an alternative to fabricate large area graphene. The mechanism and growth dynamics of graphene domains have been investigated using Cu catalyzed atmospheric pressure CVD. Rectangular few layer graphene domains were synthesized for the first time. It only grows on the Cu grains with (111) orientation due to the interplay between atomic structure of Cu lattice and graphene domains. Hexagonal graphene domains can form on nearly all non-(111) Cu surfaces. The few layer hexagonal single crystal graphene domains were aligned in their crystallographic orientation over millimetre scale. In order to improve the alignment and reduce the layer of graphene domains, a novel method is invented to perform the CVD reaction above the melting point of copper (1090 ºC) and using molybdenum or tungsten to prevent the balling of the copper from dewetting. By controlling the amount of hydrogen during the growth, individual single crystal domains of monolayer over 200 µm are produced determined by electron diffraction mapping. Raman mapping shows the monolayer nature of graphene grown by this method. This graphene exhibits a linear dispersion relationship and no sign of doping. The large scale alignment of monolayer hexagonal graphene domains with epitaxial relationship on Cu is the key to get wafer-sized single crystal monolayer graphene films. This paves the way for industry scale production of 2D single crystal graphene.