In this thesis, the response of DNA and RNA to linear and torsional mechanical stress is studied using coarse-grained models. Inspired by single-molecule assays developed over the last two decades, the end-to-end extension, buckling and torque response behaviour of the stressed molecules is probed under conditions similar to experimentally used setups. Direct comparison with experimental data yields excellent agreement for many conditions. Results from coarse-grained simulations are also compared to the predictions of continuum models of linear polymer elasticity. A state diagram for supercoiled DNA as a function of twist and tension is determined. A novel confomational state of mechanically stressed DNA is proposed, consisting of a plectonemic structure with a denaturation bubble localized in its end-loop. The interconversion between this novel state and other, known structural motifs of supercoiled DNA is studied in detail. In particular, the influence of sequence properties on the novel state is investigated. Several possible implications for supercoiled DNA structures in vivo are discussed. Furthermore, the dynamical consequences of coupled denaturation and writhing are studied, and used to explain observations from recent single molecule experiments of DNA strand dynamics. Finally, the denaturation behaviour, topology and dynamics of short DNA minicircles is studies using coarse-grained simulations. Long-range interactions in the denaturation behaviour of the system are observed. These are induced by the topology of the system, and are consistent with results from recent molecular imaging studies. The results from coarse-grained simulations are related to modelling of the same system in all-atom simulations and a local denaturation model of DNA, yielding insight into the applicability of these different modelling approaches to study different processes in nucleic acids.

This dissertation attempts to understand how energy transfer in a molecular wire and a spherical organic assembly are affected by molecular structure. The molecular wire is a DNA-hybrid structure composed of a strand of thymine bases appended by a cyanine dye. Hydrogen bonded to each base is a naphthalene-derivative molecule. Using time-integrated photoluminescence and time-correlated single photon counting measurements, energy transfer from the naphthalene donors to the cyanine acceptors was confirmed, and its dependence on temperature and DNA-template length investigated. Donor-thymine bonding was disrupted at temperatures above about 25 degrees Celcius resulting in poor donor template decoration and low rates of energy transfer. Increasing numbers of donors attach to the scaffold, forming an orderly array, as the template length increases due to the stabilising effects of the donor-donor pi-stacking interactions. Conversely, modelled energy transfer rates fall as the scaffold length increases because of the longer donor-acceptor distances involved. Therefore, the energy transfer rate was greatest for a template built from 30 thymines. The spherical organic assemblies (nanoparticles) are formed by fast injection of a small volume of molecularly dissolved fluorene-derivative amphiphilic molecules into a polar solvent. The amphiphilic molecules contained either a naphthalene (donor) or a benzothiadiazole (acceptor) core. The donor-acceptor mixed nanoparticles resemble an amorphous polymer film and were modelled as such using the Foerster resonance energy transfer theory. The Foerster radii extracted from the measurements depends intricately on the donor-acceptor spectral overlap and distance. The latter effect was controlled by the stacking interactions between the molecules. Altering the morphology of the structural units is the key to optimising energy transfer in molecular structures. To achieve efficient organic molecule-based devices, the importance of this property needs to be fully appreciated and effectively exploited.

This thesis describes a portfolio of work aimed at the high field applications of superconductors and can be split into four main topics: The thermal stability of technical superconductors. This section investigates the effects of thermal perturbations on technical superconducting wire used in MRI scanner construction. The ultimate aim of this section is to predict how the architecture of the wire may affect its thermal stability. To this end a detailed finite element analysis model was constructed, verified by detailed experimental data, which could then be used to quickly and easily vary the wire’s parameters. Design of a high field pulsed electromagnetic coil for flux trapping in superconductors. This section details the design, construction and testing of a novel pulsed high field magnet. The design uses finite element analysis to predict the electromagnetic, thermal and structural properties of the coil. Explosive testing of high tensile fibres used in the construction of the high field coil. This section describes the refinement and use of a novel method for testing the mechanical properties of high tensile fibres in cylindrical geometries by using highly pressurized copper vessels. Pulsed field magnetization of bulk high temperature superconductors. This section discusses the process of magnetizing bulks of high temperature superconductors by using pulsed magnetic fields. It investigates how the trapped field varies with the magnitude and rise-time of the magnetizing field, sample temperature and time after magnetization.

We investigate systems comprising chains and rings of quantum dots, coupled to two metallic leads. Such systems allow to study the competition between orbital and spin degrees of freedom in a nanodevice, and the effect this subtle interplay has on two-channel Kondo (2CK) physics. We demonstrate that a rich range of strongly correlated electron behaviour results, with non-Fermi liquid 2CK phases and non-trivial phase transitions accessible. We employ physical arguments and the numerical renormalization group (NRG) technique to analyse these systems in detail, examining in particular both thermodynamic and dynamical properties. When leads are coupled to either end of a chain of dots, we show that the resulting behaviour on low temperature/energy scales can be understood in terms of simpler paradigmatic quantum `impurity' models. An effective low-energy single-spin 2CK model is derived for all odd-length chains, while the behaviour of even-length chains is related fundamentally to that of the classic `two-impurity Kondo' model. In particular, for small interdot coupling, we show that an effective coupling mediated though incipient single-channel Kondo states drives all odd chains to the 2CK fixed point (FP) on the lowest temperature/energy scales. A theory is also developed to describe a phase transition in even chains. We derive an effective channel-anisotropic 2CK model, which indicates that the critical FP of such models must be the 2CK FP. This physical picture is confirmed using NRG for various chain systems. We also examine the effect of local frustration on 2CK physics in mirror-symmetric ring systems. The importance of geometry and symmetry is demonstrated clearly in the markedly different physical behaviour that arises in systems where two leads are either connected to the same dot, or to neighbouring dots. In the latter case, we show for all odd-membered rings that two distinct 2CK phases, with different ground state parities, arise on tuning the interdot couplings. A frustration-induced phase transition thus occurs, the 2CK phases being separated by a novel critical point for which an effective low-energy model is derived. Precisely at the transition, parity mixing of the quasidegenerate local trimer states acts to destabilise the 2CK FPs, and the critical FP is shown to consist of a free pseudospin together with effective single-channel spin quenching. While connecting both leads to the same dot again results in two parity-distinct phases, a simple level-crossing transition now results due to the symmetry of the setup. The proposed geometry also allows access to a novel ferromagnetically-coupled two-channel local moment phase. Driven by varying the interdot couplings and occurring at the point of inherent magnetic frustration, such transitions in ring structures provide a striking example of the subtle interplay between internal spin and orbital degrees of freedom in coupled quantum dot systems, and the resulting effect on Kondo physics.

Superconducting qubits are a promising technology for building a scalable quantum computer. An important architecture employed in the field is called Circuit Quantum Electrodynamics (circuit QED), where such qubits are combined with high quality microwave cavities to study the interaction between artificial atoms and single microwave photons. The ultra-strong coupling achieved in these systems allows for control and readout of the quantum state of qubits to perform quantum information processing. The work on circuit QED performed in this thesis consisted of realizing an experimental setup for qubit experiments in a new laboratory, investigating the coherence and decay of higher energy levels of superconducting transmon qubits and finally demonstrating a novel coaxial form of circuit QED. Designing and building a 3D circuit QED setup involved the following main accomplishments: producing high quality 3D cavities; designing and installing the cryogenic microwave setup as well as the room temperature amplification and data acquisition circuitry; successfully developing a recipe for the fabrication of Josephson junctions; controlling and measuring superconducting 3D transmon qubits at 10mK. Several qubits were fully characterised and have shown coherence times of several microseconds and relaxation times up to 25μs. Superconducting qubits in fact possess higher energy levels that can provide significant computational advantages in quantum information applications. In experiments performed at MIT, preparation and control of the five lowest states of a transmon qubit was demonstrated, followed by an investigation of the phase coherence and decay dynamics of these higher energy levels. The decay was found to proceed mainly sequentially with relaxation times in excess of 20μs for all transitions. A direct measurement of the charge dispersion of these levels was performed to explore their characteristics of dephasing. This experiment was also reproduced on a 3D transmon fabricated and measured in Oxford, where due to a higher effective qubit temperature a multi-level decay model including thermal excitations was developed to explain the observed relaxation dynamics. Finally, a coaxial transmon, which we name the coaxmon, is presented and measured with a coaxial LC readout resonator and input/output coupling ports placed inline along the third dimension. This novel coaxial circuit QED architecture holds great promise for developing a scalable planar grid of qubits to build a quantum computer.

We study non-equilibrium and strongly-correlated dynamics in two contexts. We begin by analysing quantum many-body systems out of equilibrium through the lens of cold atomic impurities in Bose gases. Such highly-imbalanced mixtures provide a controlled arena for the study of interactions, dissipation, decoherence and transport in a many-body quantum environment. Specifically we investigate the oscillatory dynamics of a trapped and initially highly-localised impurity interacting with a weakly-interacting trapped quasi low-dimensional Bose gas. This relates to and goes beyond a recent experiment by the Inguscio group in Florence. We witness a delicate interplay between the self-trapping of the impurity and the inhomogeneity of the Bose gas, and describe the dissipation of the energy of the impurity through phononic excitations of the Bose gas. We then study the transport of a driven, periodically-trapped impurity through a quasi one-dimensional Bose gas. We show that placing the weakly-interacting Bose gas in a separate periodic potential leads to a phononic excitation spectrum that closely mimics those in solid state systems. As a result we show that the impurity-Bose gas system exhibits phonon-induced resonances in the impurity current that were predicted to occur in solids decades ago but never clearly observed. Following this, allowing the bosons to interact strongly, we predict the effect of different strongly-correlated phases of the Bose gas on the motion of the impurity. We show that, by observing the impurity, properties of the excitation spectrum of the Bose gas, e.g., gap and bandwidth, may be inferred along with the filling of the bosonic lattice. In other words the impurity acts as a probe of its environment. To describe the dynamics of such a strongly-correlated system we use the powerful and near-exact time-evolving block decimation (TEBD) method, which we describe in detail. The second part of this thesis then analyses, for the first time, the performance of this method when applied to simulate non-equilibrium classical stochastic processes. We study its efficacy for a well-understood model of transport, the totally-asymmetric exclusion process, and find it to be accurate. Next, motivated by the inefficiency of sampling-based numerical methods for high variance observables we adapt and apply TEBD to simulate a path-dependent observable whose variance increases exponentially with system size. Specifically we calculate the expected value of the exponential of the work done by a varying magnetic field on a one-dimensional Ising model undergoing Glauber dynamics. We confirm using Jarzynski's equality that the TEBD method remains accurate and efficient. Therefore TEBD and related methods complement and challenge the usual Monte Carlo-based simulators of non-equilibrium stochastic processes.

F₁-ATPase, the sector of ATP synthase where the synthesis of cellular ATP occurs, is a rotary molecular motor in its own right. Driven by ATP hydrolysis, direct observation of the rotation of the central axis within single molecules of F₁ is possible. Operating at close to 100% efficiency, F₁ from thermophilic Bacillus has been shown to produce ~40pN˙nm of torque during rotation. This thesis details the groundwork required for the direct measurement of the torque produced by F₁ using a rotary angle clamp, an optical trapping system specifically designed for application to rotary molecular motors. Proof-of-concept experiments will be presented thereby demonstrating the ability to directly manipulate single F₁ molecules from Escherichia coli and yeast mitochondria (Saccharomyces cerevisiae), along with activation of F₁ out of its inhibited state by the application of external torque. Despite in-depth knowledge of the rotary mechanism of F₁ from thermophilic Bacillus, the rotation of F₁ from Escherichia coli is relatively poorly understood. A detailed mechanical characterization of E.coli F₁ will be presented here, with particular attention to the ground states within the catalytic cycle, notably the ATP-binding state, the catalytic state and the inhibited state. The fundamental mechanism of E.coli F₁ appears to depart little from that of F₁ from thermophilic Bacillus, although, at room temperature, chemical processes occur faster within the E.coli enzyme, in line with considerations regarding the physiological conditions of the different species. Also presented here is the verification of the rotary nature of yeast mitochondrial F₁. The torque produced by F₁ from thermophilic Bacillus, E.coli and yeast mitochondria is the same, within experimental error, despite their diverse evolutionary and environmental origins.