Ensemble Transport Adaptive Importance Sampling

Markov chain Monte Carlo methods are a powerful and commonly used family of numerical methods for sampling from complex probability distributions. As applications of these methods increase in size and complexity, the need for efficient methods increases. In this paper, we present a particle ensemble algorithm. At each iteration, an importance sampling proposal distribution is formed using an ensemble of particles. A stratified sample is taken from this distribution and weighted under the posterior, a state-of-the-art ensemble transport resampling method is then used to create an evenly weighted sample ready for the next iteration. We demonstrate that this ensemble transport adaptive importance sampling (ETAIS) method outperforms MCMC methods with equivalent proposal distributions for low dimensional problems, and in fact shows better than linear improvements in convergence rates with respect to the number of ensemble members. We also introduce a new resampling strategy, multinomial transformation (MT), which while not as accurate as the ensemble transport resampler, is substantially less costly for large ensemble sizes, and can then be used in conjunction with ETAIS for complex problems. We also focus on how algorithmic parameters regarding the mixture proposal can be quickly tuned to optimise performance. In particular, we demonstrate this methodology's superior sampling for multimodal problems, such as those arising from inference for mixture models, and for problems with expensive likelihoods requiring the solution of a differential equation, for which speed-ups of orders of magnitude are demonstrated. Likelihood evaluations of the ensemble could be computed in a distributed manner, suggesting that this methodology is a good candidate for parallel Bayesian computations

Use of orbiting reflectors to decrease the technological challenges of surviving the lunar night

In this paper the feasibility of using lunar reflectors to decrease the technological challenges of surviving the lunar night is investigated. This is achieved by attempting to find orbits in the two-body problem where the argument of periapsis is constantly Sun-pointing to maximise the time spent by the reflectors over the night-side of the Moon. Using these orbits the ability of reflectors of varying sizes to provide sufficient illumination to a target point on the surface is determined for scenarios where a latitude band is constantly illuminated and a scenario where a specific point is tracked. The optimum masses required for these far-term scenarios are large. However, a nearer-term scenario using low altitude orbits suggest that the effective duration of the lunar night can be reduced by up to 50% using a set of 300 parabolic reflectors of 100m radius with a total system mass of 370 tonnes. A system is also demonstrated that will allow a partial illumination of the craters in the Moon’s polar region for a mass up to 700kg

The feasibility of using an L1 positioned dust cloud as a method of space-based geoengineering

In this paper a method of geoengineering is proposed involving clouds of dust placed in the vicinity of the L1 point as an alternative to the use of thin film reflectors. The aim of this scheme is to reduce the manufacturing requirement for space-based geoengineering. It has been concluded that the mass requirement for a cloud placed at the classical L1 point, to create an average solar insolation reduction of 1.7%, is 7.60x1010 kg yr−1 whilst a cloud placed at a displaced equilibrium point created by the inclusion of the effect of solar radiation pressure is 1.87x1010 kg yr−1. These mass ejection rates are considerably less than the mass required in other unprocessed dust cloud methods proposed and are comparable to thin film reflector geoengineering requirements. Importantly, unprocessed dust sourced in-situ is seen as an attractive scheme compared to highly engineered thin film reflectors. It is envisaged that the required mass of dust can be extracted from captured near Earth asteroids, whilst stabilised in the required position using the impulse provided by solar collectors or mass drivers used to eject material from the asteroid surface

Doctor of Philosophy

dissertationExtraintestinal pathogenic Escherichia coli (ExPEC) is a subset of E. coli that has evolved the ability to successfully colonize multiple host niches. It spends most of its time as a commensal within the gut as a frequent member of the microbiota. When ExPEC disperses to extraintestinal sites, it can cause diseases such as urinary tract infections (UTIs), bacteremia, and neonatal meningitis. The cumulative impact of ExPEC infections is quite high given the sheer prevalence of UTIs and the severity of bacteremia and neonatal meningitis. A deeper understanding of ExPEC host colonization could lead to innovative therapies that would reduce the disease and financial burden imposed by this pathogen. Here, we investigate the bacterial genetics that underpin host colonization, searching for ExPEC genes that are required for persistence in the gut and infection of extraintestinal sites. We employed three separate approaches, each uncovering a bacterial function critical for host colonization. (1) We studied how rqlI contributes to bacterial fitness in vivo, and found that in the absence of RqlI, the activity of the helicase RqlH is toxic, creating DNA lesions that trigger the bacterial DNA repair response, inhibit growth, and induce mutations. We propose that RqlH and RqlI function together to modify or repair DNA. (2) A high-throughput screen was employed to find ExPEC genes necessary for metabolism of intestinal mucus, which is thought to provide nutrients to commensal E. coli in the gut. The beta-oxidation pathway, which breaks down fatty acids, was found to be an important aspect of mucus metabolism. The beta-oxidation pathway was disrupted by misregulation of the glycerol degradation pathway, as observed in the glpG mutant, a strain that exhibited a defect in gut colonization. (3) To see if canonical extraintestinal virulence factors are important for gut colonization, several mutants were created and tested in vivo. A mutant in type 1 pili had reduced fitness, which was only partly attributable to an increase in flagellar expression. Hopefully our work, and similar future endeavors to understand the mechanisms of ExPEC colonization, will improve current therapies and create new treatment strategies

Adaptive and convergent methods for large eddy simulation of turbulent combustion

textIn the recent past, LES methodology has emerged as a viable tool for modeling turbulent combustion. LES computes the large scale mixing process accurately, thereby providing a better starting point for small-scale models that describe the combustion process. Significant effort has been made over past decades to improve accuracy and applicability of the LES approach to a wide range of flows, though the current conventions often lack consistency to the problems at hand. To this end, the two main objectives of this dissertation are to develop a dynamic transport equation-based combustion model for large- eddy simulation (LES) of turbulent spray combustion and to investigate grid- independent LES modeling for scalar mixing. Long-standing combustion modeling approaches have shown to be suc- cessful for a wide range of gas-phase flames, however, the assumptions required to derive these formulations are invalidated in the presence of liquid fuels and non-negligible evaporation rates. In the first part of this work, a novel ap- proach is developed to account for these evaporation effects and the resulting multi-regime combustion process. First, the mathematical formulation is de- rived and the numerical implementation in a low-Mach number computational solver is verified against one-dimensional and lab scale, both non-reacting and reacting spray-laden flows. In order to clarify the modeling requirements in LES for spray combustion applications, results from a suite of fully-resolved direct numerical simulations (DNS) of a spray laden planar jet flame are fil- tered at a range of length scales. LES results are then validated against two sets of experimental jet flames, one having a pilot and allowing for reduced chemistry modeling and the second requiring the use of detail chemistry with in situ tabulation to reduce the computational cost of the direct integration of a chemical mechanism. The conventional LES governing equations are derived from a low-pass filtering of the Navier-Stokes equations. In practice, the filter used to derive the LES governing equations is not formally defined and instead, it is assumed that the discretization of LES equations will implicitly act as a low-pass filter. The second part of this study investigates an alternative derivation of the LES governing equations that requires the formal definition of the filtering operator, known as explicitly filtered LES. It has been shown that decoupling the filter- ing operation from the underlying grid allows for the isolation of subfilter-scale modeling errors from numerical discretization errors. Specific to combustion modeling are the aggregate errors associated with modeling sub-filter distribu- tions of scalars that are transported by numerical impacted turbulent fields. Quantities of interest to commonly-used combustion models, including sub- filter scalar variance and filtered scalar dissipation rate, are investigated for both homogeneous and shear-driven turbulent mixing.Aerospace Engineerin

Who Speaks for the River? Exploring Biodiversity Accounting using an Arena Approach

First paragraph: In confronting the unsustainability of human activity and attempting to define a ‘safe operating space’ for humanity, Rockstrom et al. (2009) estimate that biodiversity loss is one of nine planetary boundaries that have already been transgressed. The United Nations’ Millennium Ecosystem Assessment has extensively documented the extent to which ecosystems have been rapidly altered and global biodiversity has been subject to negative change (UNEP, 2005). Concerns over ecosystem degradation have led to the emergence of international agreements, including the Convention on Biological Diversity (1992). These agreements seek to establish policy frameworks for biodiversity and encourage recognition of ecosystem services and biodiversity within decision-making (for example TEEB, 2009). A range of ecological indicators and economic analyses are being developed as metrics to account for biodiversity and to engage with policy-makers and businesses (TEEB 2011; 2012), and forms of environmental reporting have been recognised as a potentially important means to recognise and measure the value of the natural environment (Thompson & Mackey 2010; Mackey & Galbraith 2011)

Effects of Ozone Levels on Climate Through Earth History

Molecular oxygen in our atmosphere has increased from less than a part per million in the Archean Eon, to a fraction of a percent in the Proterozoic, and finally to modern levels during the Phanerozoic. While oxygen itself has only minor radiative and climatic effects, the accompanying ozone has important consequences for Earth climate. Using the Community Earth System Model (CESM), a 3-D general circulation model, we test the effects of various levels of ozone on Earth's climate. When CO2 is held constant, the global mean surface temperature decreases with decreasing ozone, with a maximum drop of ~3.5 K at near total ozone removal. By supplementing our GCM results with 1-D radiative flux calculations, we are able to test which changes to the atmosphere are responsible for this temperature change. We find that the surface temperature change is caused mostly by the stratosphere being much colder when ozone is absent; this makes it drier, substantially weakening the greenhouse effect. We also examine the effect of the structure of the upper troposphere and lower stratosphere on the formation of clouds, and on the global circulation. At low ozone, both high and low clouds become more abundant, due to changes in the tropospheric stability. These generate opposing short-wave and long-wave radiative forcings that are nearly equal. The Hadley circulation and tropospheric jet streams are strengthened, while the stratospheric polar jets are weakened, the latter being a direct consequence of the change in stratospheric temperatures. This work identifies the major climatic impacts of ozone, an important piece of the evolution of Earth's atmosphere.</p

Geo-engineering using dust grains in heliotropic elliptical orbits

This paper examines the concept of a Saturn-like Earth ring comprised of dust grains to offset global warming. A new family of non-Keplerian periodic orbits, under the effects of solar radiation pressure and the Earth’s oblateness J2 perturbation, is selected to increase the lifetime of the passive cloud of particles and, thus, increase the efficiency of this geo-engineering strategy. An analytical model is used to predict the evolution of the dust due to solar-radiation pressure and the J2 effect. The attenuation of the solar radiation can then be calculated from the ring model. In comparison to circular orbits, eccentric orbits yield a more stable environment for small grain sizes and therefore achieve higher efficiencies when the orbital decay of the material is considered. Moreover, the special orbital dynamics experienced by high area-to-mass ratio objects, influenced by solar radiation pressure and the J2 effect, ensure the ring will maintain a permanent heliotropic shape, with dust spending the largest portion of time on the Sun facing side. It is envisaged that small dust grains can be released with an initial Δv to enter an eccentric orbit with Sun-facing apogee. Finally, an estimate of 5.94x1011 kg is computed as the total mass required to offset the effects of global warming