On the generation and analysis of program transformations

This thesis discusses the idea of using domain specific languages for program transformation, and the application, implementation and analysis of one such domain specific language that combines rewrite rules for transformation and uses temporal logic to express its side conditions. We have conducted three investigations. - An efficient implementation is described that is able to generate compiler optimizations from temporal logic specifications. Its description is accompanied by an empirical study of its performance. - We extend the fundamental ideas of this language to source code in order to write bug fixing transformations. Example transformations are given that fix common bugs within Java programs. The adaptations to the transformation language are described and a sample implementation which can apply these transformations is provided. - We describe an approach to the formal analysis of compiler optimizations that proves that the optimizations do not change the semantics of the program that they are optimizing. Some example proofs are included. The result of these combined investigations is greater than the sum of their parts. By demonstrating that a declarative language may be efficiently applied and formally reasoned about satisfies both theoretical and practical concerns, whilst our extension towards bug fixing shows more varied uses are possible

Fabrication of mirror templates in silica with micron-sized radii of curvature

We present the fabrication of exceptionally small-radius concave microoptics on fused silica substrates using CO2 laser ablation and subsequent reactive ion etching. The protocol yields on-axis near-Gaussian depressions with radius of curvature $\lesssim5$ microns at shallow depth and low surface roughness of 2 angstroms. This geometry is appealing for cavity quantum electrodynamics where small mode volumes and low scattering losses are desired. We study the optical performance of the structure within a tunable Fabry-Perot type microcavity, demonstrate near-coating-limited loss rates (F = 25,000) and small focal lengths consistent with their geometrical dimensions.Comment: 5 pages, 4 figure

Spin-Polarized Electrons in Monolayer MoS2_2

The optical susceptibility is a local, minimally-invasive and spin-selective probe of the ground state of a two-dimensional electron gas. We apply this probe to a gated monolayer of MoS$_2$. We demonstrate that the electrons are spin polarized. Of the four available bands, only two are occupied. These two bands have the same spin but different valley quantum numbers. We argue that strong Coulomb interactions are a key aspect of this spontaneous symmetry breaking. The Bohr radius is so small that even electrons located far apart in phase space interact, facilitating exchange couplings to align the spins

A microbiological assessment of the human biliary tract in health and disease

The gastrointestinal tract in humans is home to 100 trillion bacteria, collectively referred to as the gut microbiota. This ‘bacterial organ’ has a vital role to play in both health and disease. Conventional wisdom dictates that bile in normal biliary systems is sterile. However, the liver is continually exposed to gut bacteria and their metabolites via the portal vein. Recent studies have identified bacterial populations within the biliary system of symptomatic patients undergoing cholecystectomy or biliary intervention. In this study we identified that there is a complex biliary microbiota within a normal biliary tract. Many bacterial species were isolated from the bile of patients undergoing hepatic resection or cholecystectomy and their identity established through sequencing their 16S ribosomal RNA gene. These included Staphylococcus, Micrococcus, Enterococcus and Bacillus sp. Isolated bacteria were examined for their resistance to bile salts and the results suggested that all the isolates were able to survive under physiologically relevant bile concentrations with some isolates expressing bile salt hydrolase activity. An in-depth analysis of the biliary microbiome using 16S-based metataxonomics was performed. Results suggested that human bile has a diverse and varied microbiota, a large proportion of which were unculturable. 34 different genera were identified with Pseudomonas being the most prevalent. Dysbiosis was noted between diseased (e.g. gallstone and biliary obstruction) and normal samples. The gut microbiota of the two most common chronic biliary conditions, Primary Sclerosing Cholangits and Primary Biliary Cholangitis, were also examined to see if dysbiosis was present. There is an emerging dysbiosis in patients with chronic cholestatic liver disease, although these results were possibly restricted through patient treatment with ursodeoxycholic acid. This study is the first to describe a complex biliary microbiota in normal human bile and in the future a detailed understanding of the function of this microbiota may provide a therapeutic target for biliary disease

Quantum confined Stark effect in a MoS2_2 monolayer van der Waals heterostructure

The optics of dangling-bond-free van der Waals heterostructures containing transition metal dichalcogenides are dominated by excitons. A crucial property of a confined exciton is the quantum confined Stark effect (QCSE). Here, such a heterostructure is used to probe the QCSE by applying a uniform vertical electric field across a molybdenum disulfide (MoS$_2$) monolayer. The photoluminescence emission energies of the neutral and charged excitons shift quadratically with the applied electric field provided the electron density remains constant, demonstrating that the exciton can be polarized. Stark shifts corresponding to about half the homogeneous linewidth were achieved. Neutral and charged exciton polarizabilities of (7.8~\pm~1.0)\times 10^{-10}~\tr{D~m~V}^{-1} and (6.4~\pm~0.9)\times 10^{-10}~\tr{D~m~V}^{-1} at relatively low electron density (8 \times 10^{11}~\tr{cm}^{-2}) have been extracted, respectively. These values are one order of magnitude lower than the previously reported values, but in line with theoretical calculations. The methodology presented here is versatile and can be applied to other semiconducting layered materials as well

Simple atomic quantum memory suitable for semiconductor quantum dot single photons

Quantum memories matched to single photon sources will form an important cornerstone of future quantum network technology. We demonstrate such a memory in warm Rb vapor with on-demand storage and retrieval, based on electromagnetically induced transparency. With an acceptance bandwidth of $\delta f$ = 0.66~GHz the memory is suitable for single photons emitted by semiconductor quantum dots. In this regime, vapor cell memories offer an excellent compromise between storage efficiency, storage time, noise level, and experimental complexity, and atomic collisions have negligible influence on the optical coherences. Operation of the memory is demonstrated using attenuated laser pulses on the single photon level. For 50 ns storage time we measure $\eta_{\textrm{e2e}}^{\textrm{50ns}} = 3.4(3)\%$ \emph{end-to-end efficiency} of the fiber-coupled memory, with an \emph{total intrinsic efficiency} $\eta_{\textrm{int}} = 17(3)\%$. Straightforward technological improvements can boost the end-to-end-efficiency to $\eta_{\textrm{e2e}} \approx 35\%$; beyond that increasing the optical depth and exploiting the Zeeman substructure of the atoms will allow such a memory to approach near unity efficiency. In the present memory, the unconditional readout noise level of $9\cdot 10^{-3}$ photons is dominated by atomic fluorescence, and for input pulses containing on average $\mu_{1}=0.27(4)$ photons the signal to noise level would be unity

Transform-limited single photons from a single quantum dot

A semiconductor quantum dot mimics a two-level atom. Performance as a single photon source is limited by decoherence and dephasing of the optical transition. Even with high quality material at low temperature, the optical linewidths are a factor of two larger than the transform-limit. A major contributor to the inhomogeneous linewdith is the nuclear spin noise. We show here that the nuclear spin noise depends on optical excitation, increasing (decreasing) with increasing resonant laser power for the neutral (charged) exciton. Based on this observation, we discover regimes where we demonstrate transform-limited linewidths on both neutral and charged excitons even when the measurement is performed very slowly

A catchment scale assessment of patterns and controls of historic 2D river planform adjustment

The supply, transfer and deposition of sediment from channel headwaters to lowland sinks, is a fundamental process governing upland catchment geomorphology, and can begin to be understood by quantifying 2D river planform adjustments over time. This paper presents a catchment scale methodology to quantify historic patterns of 2D channel planform adjustment and considers geomorphic controls on 2D river stability. The methodology is applied to 18 rivers (total length = 24 km) in the upland headwaters of the previously glaciated Wasdale catchment (45 km2), Lake District, northwest England. Planform adjustments were mapped from historic maps and air photographs over six contiguous time windows covering the last 150 yr. A total of 1048 adjustment and stable reaches were mapped. Over the full period of analysis (1860–2010) 32% (8 km) of the channels studied were adjusting. Contrasts were identified between the geomorphic characteristics (slope, catchment area, unit specific stream power, channel width and valley bottom width) of adjusting and stable reaches. The majority of adjustments mapped were observed in third and fourth order channels in the floodplain valley transfer zone, where the channels were laterally unconfined (mean valley bottom widths of 230 ± 180 m), with low sediment continuity. In contrast, lower order channels were typically confined (mean valley bottom widths of 31 ± 43 m) and showed relative 2D lateral stability. Hence, valley bottom width was found to be important in determining the available space for rivers to adjust. Over the full period of analysis 38% of planform adjustments involved combined processes, for example, as bar and bend adjustments. The study demonstrates the importance of stream network hierarchy in determining spatial patterns of historic planform adjustments at the catchment scale. The methodology developed provides a quantitative assessment of planform adjustment patterns and geomorphic controls, which is needed to support the prioritisation of future river management and restoration

Deterministic enhancement of coherent photon generation from a nitrogen-vacancy center in ultrapure diamond

The nitrogen-vacancy (NV) center in diamond has an optically addressable, highly coherent spin. However, an NV center even in high quality single-crystalline material is a very poor source of single photons: extraction out of the high-index diamond is inefficient, the emission of coherent photons represents just a few per cent of the total emission, and the decay time is large. In principle, all three problems can be addressed with a resonant microcavity. In practice, it has proved difficult to implement this concept: photonic engineering hinges on nano-fabrication yet it is notoriously difficult to process diamond without degrading the NV centers. We present here a microcavity scheme which uses minimally processed diamond, thereby preserving the high quality of the starting material, and a tunable microcavity platform. We demonstrate a clear change in the lifetime for multiple individual NV centers on tuning both the cavity frequency and anti-node position, a Purcell effect. The overall Purcell factor $F_{\rm P}=2.0$ translates to a Purcell factor for the zero phonon line (ZPL) of $F_{\rm P}^{\rm ZPL}\sim30$ and an increase in the ZPL emission probability from $\sim 3 \%$ to $\sim 46 \%$. By making a step-change in the NV's optical properties in a deterministic way, these results pave the way for much enhanced spin-photon and spin-spin entanglement rates.Comment: 6 pages, 4 figure

GHz bandwidth electro-optics of a single self-assembled quantum dot in a charge-tunable device

The response of a single InGaAs quantum dot, embedded in a miniaturized charge-tunable device, to an applied GHz bandwidth electrical pulse is investigated via its optical response. Quantum dot response times of 1.0 \pm 0.1 ns are characterized via several different measurement techniques, demonstrating GHz bandwidth electrical control. Furthermore a novel optical detection technique based on resonant electron-hole pair generation in the hybridization region is used to map fully the voltage pulse experienced by the quantum dot, showing in this case a simple exponential rise.Comment: 7 pages, 4 figure