### Tunable nano-plasmonic metamaterials at solid-liquid and liquid-liquid interfaces

Ye Ma
Metamaterials have demonstrated their unusual optical properties, ranging from negative refractive index to optical nonlinearity. Real-time adjustment of these properties becomes critical for the next generation of ‘smart’ optical devices. In this thesis, different methods for actively tuning the structure and output of metamaterials are demonstrated. These metamaterials consist of metallic nanoparticles (NPs) at solid-liquid interfaces (SLIs) and liquid-liquid interfaces (LLIs). Electrically, the assembly of gold NPs at a SLI is reversibly controlled by changing...

### Looking beyond the leaves and understanding the roots: sustainability assessment and monitoring of planted forests for biomass production in Brazil

Manuela De Moraes Czinar
Whereas most of the recent literature is concerned about the output legitimacy of planted forests, this thesis focus on the input legitimacy. The novel framework proposed in this thesis uses association membership and technical support as indicators of the sustainable expansion of planted forests from the lens of input legitimacy. This framework was based on the results of the grounded theory method applied to semi-structured interviews carried out with stakeholders in Brazil. Quantitative data were...

### Identifying host-pathogen interactions which cause severe malaria

Infectious diseases pathogenesis is dependent on the interactions between the host and the pathogen. Being able to simultaneously assess the transcriptomes of both host and pathogen as we have shown here, using dual RNA sequencing of whole blood from Plasmodium falciparum malaria patients, can reveal these crucial interactions. Using Gambian children samples we tried to unravel the mechanisms leading to severe malaria. The main finding was the clear involvement of neutrophil related genes in severe...

### Sensitivity analysis, uncertainty quantification and parameter estimation for a numerical tide and storm surge model

Simon Charles Warder
Storm surges pose a significant hazard to coastal communities worldwide. Accurate and reliable storm surge numerical models, combined with an understanding of model uncertainties, are therefore vital. In this work, an adjoint-capable numerical coastal ocean model, Thetis, is extended and used to perform a sensitivity analysis for a hindcast case study in the North Sea, revealing the spatial patterns of the sensitivity of modelled surges to three model inputs. These sensitivities are used to gain...

### The role of the general stress response in staphylococcal survival during exposure to host immune defences and antibiotics

Nishanthy Ranganathan
Persistent staphylococcal bacteraemia remains an important and frequent cause of morbidity and mortality, despite the availability of apparently effective antimicrobial therapy. Antibiotic tolerance is poorly characterised since despite bacteria being able able to survive prolonged antibiotic exposure without the acquisition of resistance mutations, they are found to be sensitive to antibiotics in vitro. SigB is a global regulator involved in the response of staphylococcal bacteria against acid, heat, salt and alcohol stresses. The majority of...

### Supporting data for the paper 'Small-scale capillary heterogeneity linked to rapid plume migration during CO2 storage' by S.J. Jackson and S. Krevor 2020

Samuel Jackson & Samuel Krevor
Herein lies the supporting data for the paper 'Small-scale capillary heterogeneity linked to rapid plume migration during CO2 storage'. We supply experimental, analytical and numerical simulation data used in the paper. The supplied zipped folders follow the same order as the main paper, with codes to reproduce each figure (and those in the supporting information PDF). There are also video files (in the 5_Field_scale_simulation zipped folder) showing the final CO2 plume evolution from the static...

### Investigating the CaMKKβ signalling pathway and its role in the regulation of blood pressure

Jiexin Zhao
Calcium/Calmodulin dependent protein kinase kinase beta (CaMKKβ) is a serine/threonine kinase involved in the Calcium/Calmodulin dependent protein kinase (CaMK) cascade. In 2005, CaMKKβ was shown to phosphorylate and activate AMP-activated protein kinase (AMPK), a master regulator of metabolism. Activation of AMPK has previously been reported to inhibit vascular smooth muscle myosin light chain (MLC) phosphorylation. The phosphorylation state of MLC in smooth muscle is known to directly control the contractility of blood vessels and the...

### Atomistic simulation of fission products in zirconia polymorphs

Alexandros Kenich
Zirconium alloys are used as a cladding material in most nuclear reactors worldwide due to properties uniquely suited to the operating environment of a reactor. In this thesis, density functional theory (DFT) simulations were conducted to investigate the behaviour of fission product dopants in the inner cladding oxide, and to examine the role this layer plays in limiting corrosion in the context of pellet-cladding interaction (PCI). Simulations in undoped monoclinic, tetragonal and cubic ZrO$_{2}$ yielded...

### Revealing the disease dynamics of antigenically variable viruses

James Hay
Many viruses exhibit substantial antigenic variation, resulting in phenotypic differences between related variants of the same species. This variability poses a substantial public health burden, as hosts can be reinfected many times over their lifetime. In this thesis, I use mathematical models to capture unobserved biological processes in two antigenically variable systems: Zika and influenza. In Chapter 3, I develop a model linking Zika virus infection and the gestational risk of microcephaly. Through fitting this...

### Micro-environmental models of human exposure to air pollution

Gioia Mosler
Particulate air pollution (PM) has been shown by many studies to cause adverse health effects. Traditionally PM exposure was estimated using ambient concentrations. Lately, studies have revealed that this approach poorly reflects differences between individual’s exposures and as such results in exposure misclassification. This thesis aims to improve personal exposure predictions by building a model (MEPEX model), which takes into account the temporal and spatial variability of ambient PM, as well as visited microenvironments. For...

### Exposure to endocrine disrupting chemicals and other hormone-related variables, DNA methylation, and breast cancer

Catharina Maria Van Veldhoven
Introduction Breast cancer is the most common cancer in the world and environmental factors such as endocrine disrupting chemicals, as well as reproductive and hormone-related factors play a crucial role in the development of this disease. In order to assess causal pathways between these exposures and disease initiation, biomarkers based on DNA methylation measurements can be used. Methods The potential association between global and locus-specific DNA methylation and breast cancer risk was investigated in two...

### Evaluating integrated Neglected Tropical Disease (NTD) control strategies: cost, effectiveness and sustainability of the NTD control programme in Uganda

Fiona Fleming
The predicted costs and savings of integrated preventive chemotherapy (IPCT) for the Neglected Tropical Diseases (NTDs) have been proposed by a number of prior studies. The principle aims of the research presented in this thesis were to determine the cost, effectiveness and sustainability of the Ugandan integrated NTD Control Programme (NTDCP). Annual programme costs were prospectively and retrospectively collected at all levels of programme implementation in twelve districts over three years. Overall cost per person...

### On the theory and simulation of photonic condensates

Henry Hesten
Photons in a dye filled microcavity have been proven to form Bose-Einstein condensates both theoretically and experimentally. The system may also be placed in a fundamentally non- equilibrium state where multiple modes are condensed. This thesis theoretically examines some of the deviations from traditional Bose-Einstein condensate models which have been observed and which may be expected in future experiments. Unusual and potentially unseen condensed states are predicted, along with the unexpected non-critical slowing down of...

### Can routinely collected electronic health data be used to develop novel healthcare associated infection surveillance tools?

Carina King
Background: Healthcare associated infections (HCAI) pose a significant burden to health systems both within the UK and internationally. Surveillance is an essential component to any infection control programme, however traditional surveillance systems are time consuming and costly. Large amounts of electronic routine data are collected within the English NHS, yet these are not currently exploited for HCAI surveillance. Aim: To investigate whether routinely collected electronic hospital data can be exploited for HCAI surveillance within the...

### Photonic and electric control of single photon emission from individual quantum dots

Sergii Morozov
Modern single photon quantum technologies require on-demand and deterministic sources. Single photon emission has been observed from various solid state systems, such as individual molecules, defects and colour centres in diamond and 2D materials, and artificial atoms - quantum dots. However, the quantum emitters suffer from the slow radiation rate and omnidirectional emission, preventing their practical applications. First, this Thesis proposes to exploit the charged excitonic states in individual colloidal quantum dots for the enhancement...

### Mathematical modelling for assessing HIV epidemics and the impact of interventions in Latin America

Juan Fernando Vesga
Latin America is a region of diversity, inequality, poverty and an outstanding capacity to remain stable despite these challenges. The HIV epidemic in the region resembles these same characteristics, with a wide range of risk behaviours, a disproportionate burden in vulnerable groups and yet perhaps a highly effective response. Brazil and Colombia have extensively deployed prevention strategies and delivered antiretroviral treatment and there are still further expansions in sight. However, the likely impact of these...

### Development of diode pumped Alexandrite lasers

Xin Sheng
This thesis is focused on the development of diode-pumped Alexandrite lasers, especially in terms of understanding and optimizing their performance. Alexandrite possesses excellent physical properties and broad wavelength tunability (701-858 nm). Diode pumping of Alexandrite is a promising route to construct simple, compact and low-cost laser systems, which can enable a multitude of precision applications including remote sensing (LIDAR) light sources. This thesis work presents the first demonstration of a Q-switched Alexandrite laser under CW...

### Role of Cnot3 in gene regulation and cell cycle progression

Matteo Martufi
Gene expression is a process that is tightly regulated by many factors. Different genes are transcribed not only in a cell specific manner but are also differentially expressed at different stages of the cell cycle. Cnot3 is part of the CCR4-NOT deadenylation complex, which is involved in the turnover of mRNAs in the cytoplasm and has also been shown to have roles in regulating transcription and cell proliferation and in maintaining ES cell pluripotency. Previous...

### Mechanism of noble gas neuroprotection in an in vitro model of traumatic brain injury

Katie Harris
Background: The noble gases xenon and argon are neuroprotective in models of brain injury. This thesis investigated the neuroprotective mechanisms of the inert gases xenon, argon, krypton, neon and helium in in vitro models of traumatic brain injury and ischemia. Methods: This study used an in vitro model of focal mechanical trauma and oxygen and glucose deprivation using mouse organotypic hippocampal brain slices. Injury was quantified by propidium iodide fluorescence. Results: Xenon (50.6 kPa) and,...

### Mechanisms of Colorectal Cancer Pathogenesis: Role of Hypoxia

Ngayu Munga Thairu
Colorectal cancer (CRC) is the third most common cancer worldwide Hypoxia plays a pivotal role in cancer, regulating cellular processes such as angiogenesis via the Hypoxia Inducible Factor (HIF) pathway. HIF-1α and HIF-2α, isoforms of the α-subunit, were previously thought to be functionally redundant, but mounting evidence supports their divergent roles in many cancers. In CRC their relative roles remain unclear. This study aimed to elucidate their relative contribution to hypoxic regulation of CRC using...

### Novel strategies for the identification of biomarkers of non-Hodgkin lymphoma: evidence from the European Prospective Investigation into Cancer (EPIC)

Rachel Kelly
Non-Hodgkin’s Lymphomas (NHL) represent the eighth most common cancer in Western Europe. Yet despite their widespread prevalence and high mortality rate relatively little is known about the aetiology of these hematological malignancies. Consequently NHL represents an ideal candidate for the discovery of biomarkers lying along the causal pathway. Such biomarkers would allow the improved identification of risk factors and high risk individuals, as well as an enhanced understanding of lymphomageneisis. However, to date there has...

### Magnetic Resonance Imaging of the Neonatal Cardiovascular System : Impact of Patent Ductus Arteriosus

The incidence of premature birth is increasing in absolute number and as a proportion of all births around the world. Many pathologies seen in this cohort are related to abnormal blood supply. Fetal and premature cardiovascular systems differ greatly as to maintain adequate blood flow to the developing organs in the uterine and extra-uterine environments require very different circulations. Subsequently following preterm birth the immature cardiovascular system undergoes abrupt adaptations, often resulting in the prolonged...

### Characterisation of the Haemodynamic Response Function (HRF) in the neonatal brain using functional MRI

Tomoki Arichi
Background: Preterm birth is associated with a marked increase in the risk of later neurodevelopmental impairment. With the incidence rising, novel tools are needed to provide an improved understanding of the underlying pathology and better prognostic information. Functional Magnetic Resonance Imaging (fMRI) with Blood Oxygen Level Dependent (BOLD) contrast has the potential to add greatly to the knowledge gained through traditional MRI techniques. However, it has been rarely used with neonatal subjects due to difficulties...

### The characterisation of a functional interaction between Ikaros and Foxp1 in pre-B-cells and acute lymphoblastic leukaemia

Jonathan Bond
B-lymphopoiesis is characterised by orderly progression through a series of stages of differentiation, each of which is associated with specific patterns of protein expression and cellular proliferation. These processes require a high degree of regulation by the coordinated action of a series of transcription factors that are critical for appropriate stage-specific gene expression. We describe a novel interaction between Ikaros and Foxp1, two transcription factors that are essential for normal B-lymphopoiesis, and which frequently exhibit...

### Examining the charge storage mechanisms of nanoscale nickel hydroxide

Joseph H. L. Hadden
The aim of this work was to develop mechanistic understanding, as well as techniques to study the charging and discharging behaviour of a material which has controversially been described as either a battery or a pseudocapacitor electrode material. Nickel hydroxide, Ni(OH)2, was chosen as the material of choice due to its long history as a secondary battery cathode material, as well as recent interest in it as a high rate supercapacitor. This recent interest is...

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#### Affiliations

• Imperial College London
2,087
• University of Oxford
10
• University of Exeter
5
• University of Cambridge
4
• University of Southampton
3
• University of Leeds
3
• University of Birmingham
3
• Shell (Netherlands)
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• Durham University
2
• Queen Mary University of London
2