Lattice models of pattern formation in bacterial dynamics

In this thesis I study a model of self propelled particles exhibiting run-and tumble dynamics on lattice. This non-Brownian diffusion is characterised by a random walk with a finite persistence length between changes of direction, and is inspired by the motion of bacteria such as Escherichia coli. By defining a class of models with multiple species of particle and transmutation between species we can recreate such dynamics. These models admit exact analytical results whilst also forming a counterpart to previous continuum models of run-and- tumble dynamics. I solve the externally driven non-interacting and zero-range versions of the model exactly and utilise a field theoretic approach to derive the continuum fluctuating hydrodynamics for more general interactions. I make contact with prior approaches to run-and-tumble dynamics of lattice and determine the steady state and linear stability for a class of crowding interactions, where the jump rate decreases as density increases. In addition to its interest from the perspective of nonequilibrium statistical mechanics, this lattice model constitutes an efficient tool to simulate a class of interacting run-and-tumble models relevant to bacterial motion. Pattern formation in bacterial colonies is confirmed to be able to stem solely from the interplay between a diffusivity that depends on the local bacterial density and regulated division of the cells, in particular without the need for any explicit chemotaxis. This simple and generic mechanism thus provides a null hypothesis for pattern formation in bacterial colonies which has to be falsified before appealing to more elaborate alternatives. Most of the literature on bacterial motility relies on models with instantaneous tumbles. As I show, however, the finite tumble duration can play a major role in the patterning process. Finally a connection is made to some real experimental results and the population ecology of multiple species of bacteria competing for the same resources is considered

A study of hydrous ethanol combustion in an optical central direct injection spark ignition engine

The aim of this experimental work was to improve understanding of the influence of hydrous ethanol on combustion in an engine demonstrating a tendency for biased flame migration towards the hotter exhaust walls as often reported for typical modern pent roof design IC engines. The work aimed to uncover the degree of residual water content that can be reasonably tolerated in terms of combustion characteristics in future ethanol SI engines (with the energy required to reduce water levels then potentially reduced). The experiments were performed in a single cylinder optical research engine equipped with a modern central direct injection combustion chamber and Bowditch type optical piston. Results were obtained under part-load engine operating conditions (selected to represent typical highway cruising conditions) with hydrous ethanol at 5%, 12% and 20% volume water. Baseline results were obtained using pure isooctane. High-speed cross-correlated particle image velocimetry was undertaken at 1500 rpm under motoring conditions with the intake plenum pressure set to 0.5 bar absolute. The horizontal imaging plane was fixed 10 mm below the combustion chamber “fire face”. Comparisons were made to CFD computations of the in-cylinder flow. Complimentary flame images were obtained via the “natural light” (chemiluminescence) technique over multiple engine cycles. The flame images revealed the tendency of an iso-octane fueled flame to migrate towards the exhaust side of the combustion chamber, with no complimentary bulk air motion apparent in this area in the horizontal imaging plane. The faster-burning ethanol offset this tendency of the flame to migrate towards the hotter exhaust walls. The fastest combustion rate occurred with pure ethanol, with higher water content (>5%) generally slowing down the flame speed rate to 10.64 m/s from 10.92 of ethanol and offsetting the flame speed/migration benefit (in good agreement with recent laminar burning velocity correlations for hydrous ethanol). When adding 20% water to ethanol the combustion rate was significantly slower (8.2 m/s) with a considerable increase in flame shape distortion as quantified by flame image shape factor values. The results demonstrate how the added water increases flame distortion and leads to higher flame centre displacement. Such flame centre displacement could potentially be offset in the future with a spark plug location biased further towards the intake side of the chamber (albeit sometimes practically constrained by the priorities given to intake valve sizing and local cooling jacket design). The results indicate that ethanol fuels offset such bias flame growth and allow residual water to be tolerated for an equivalent degree of biased flame migration. The implication is reduced fuel production energy and cost required to produce usable ethanol fuels

Cyclically resolved flame and flow imaging in an alcohol fuelled SI engine

The work was concerned with improving understanding of the interaction of the bulk in-cylinder flow with turbulent premixed flame propagation when using varied fuels including iso-octane, ethanol or butanol. The experiments were performed in a single cylinder research engine equipped with a modern central direct injection combustion chamber and Bowditch style optical piston. Results were obtained under typical part-load engine operating conditions. High speed cross-correlated particle image velocimetry was undertaken at 1500 rpm under motoring conditions with the plenum pressure set to 0.5 bar absolute, with the horizontal imaging plane fixed 10 mm below the combustion chamber “fireface”. Comparisons were made to CFD computations of the flow. Complementary flame images were then obtained via natural light (chemiluminescence) over multiple engine cycles. The flame images revealed the tendency of the flame to migrate towards the hotter exhaust side of the combustion chamber, with no complementary bulk air motion apparent in this area in the imaging plane. In terms of fuel effects, the addition of 16% butanol to iso-octane resulted in marginally faster combustion. Fastest combustion was observed with ethanol, in good agreement with laminar burning velocity correlations within the literature. The ethanol could be seen to offset the tendency of migration of the flame toward the exhaust walls under the fixed spark timing conditions. This exhaust migration phenomenon has been noted previously by others in optical pent-roofed engines but without both flow and flame imaging data being available. The results may imply that the spark plug should ideally be biased further towards the intake side of the chamber if the flame is to approach the intake and exhaust walls at similar times resulting in symmetrical flame propagation, reduced premature wall quenching and hence increase combustion stability and thermal efficiency. Such a layout is typically not preferred due to the priority given to the central fuel injector (and associated cooling jacket) location and maximizing the size of the inlet valves for improved volumetric efficiency

Engineering molecularly-active nanoplasmonic surfaces for DNA detection via colorimetry and Raman scattering

We report a novel nanophotonic biosensor surface capable of both colorimetric detection and Raman-scattered detection of DNA infection markers at extreme sensitivities. Combining direct-write lithography, dip-pen nanolithography based DNA patterning, and molecular self-assembly, we create molecularly-active plasmonic nanostructures onto which metallic nanoparticles are located via DNA-hybridization. Arraying these structures enables optical surfaces that change state when contacted by specific DNA sequences; shifting the surface color while simultaneously generating strong Raman-scattering signals. Patterning the DNA markers onto the plasmonic surface as micro-scale symbols results in easily identifiable color shifts, making this technique applicable to multiplexed lab-on-a-chip and point-of-care diagnostic applications

SERS enhancement of silver nanoparticles prepared by a template-directed triazole ligand strategy

Two advances in the development of a one-pot method to prepare silver nanoparticles (AgNPs) using the Tollens’ reagent are described. First, a template-directed process of AgNP synthesis using resorcinol triazole ligands bearing two pendent galactose sugars is shown. Second, the conversion of these AgNPs into SERS nanotags is demonstrated using malachite green isothiocyanate as the Raman reporter molecule

SERS enhancement of silver nanoparticles prepared by a template-directed triazole ligand strategy

Two advances in the development of a one-pot method to prepare silver nanoparticles (AgNPs) using the Tollens' reagent are described. First, a template-directed process of AgNP synthesis using resorcinol triazole ligands bearing two pendent galactose sugars is shown. Second, the conversion of these AgNPs into SERS nanotags is demonstrated using malachite green isothiocyanate as the Raman reporter molecule

Formation of a σ-alkane complex and a molecular rearrangement in the solid-State : [Rh(Cyp2PCH2CH2PCyp2)(η2:η2-C7H12)][BArF 4]

Addition of H2 to the precursor [Rh(Cyp2PCH2CH2PCyp2)(η2:η2- C7H8)][BArF 4] gives the σ-alkane complex [Rh(Cyp2PCH2CH2PCyp2)(η2:η2- C7H12)][BArF 4] by a single-crystal to single-crystal reaction, as characterized by Xray crystallography, SSNMR spectroscopy, and periodic DFT. An unexpected rearrangement of the {Rh(L2)}+ fragment is revealed

Eocene to Oligocene vegetation and climate in the Tasmanian Gateway region were controlled by changes in ocean currents and pCO2

Considered one of the most significant climate reorganizations of the Cenozoic period, the Eocene–Oligocene Transition (EOT; ca. 34.44–33.65) is characterized by global cooling and the first major glacial advance on Antarctica. In the southern high latitudes, the EOT cooling is primarily recorded in the marine realm, and its extent and effect on the terrestrial climate and vegetation are poorly documented. Here, we present new, well-dated, continuous, high-resolution palynological (sporomorph) data and quantitative sporomorph-based climate estimates recovered from the East Tasman Plateau (ODP Site 1172) to reconstruct climate and vegetation dynamics from the late Eocene (37.97 Ma) to the early Oligocene (33.06 Ma). Our results indicate three major climate transitions and four vegetation communities occupying Tasmania under different precipitation and temperature regimes: (i) a warm-temperate Nothofagus–Podocarpaceae-dominated rainforest with paratropical elements from 37.97 to 37.52 Ma; (ii) a cool-temperate Nothofagus-dominated rainforest with secondary Podocarpaceae rapidly expanding and taking over regions previously occupied by the warmer taxa between 37.306 and 35.60 Ma; (iii) fluctuation between warm-temperate–paratropical taxa and cool temperate forest from 35.50 to 34.49 Ma, followed by a cool phase across the EOT (34.30–33.82 Ma); and (iv) a post-EOT (earliest Oligocene) recovery characterized by a warm-temperate forest association from 33.55 to 33.06 Ma. Coincident with changes in the stratification of water masses and sequestration of carbon from surface water in the Southern Ocean, our sporomorph-based temperature estimates between 37.52 and 35.60 Ma (phase ii) showed 2–3 ∘C terrestrial cooling. The unusual fluctuation between warm and cold temperate forest between 35.50 to 34.59 Ma is suggested to be linked to the initial deepening of the Tasmanian Gateway, allowing eastern Tasmania to come under the influence of warm water associated with the proto-Leeuwin Current (PLC). Further to the above, our terrestrial data show the mean annual temperature declining by about 2 ∘C across the EOT before recovering in the earliest Oligocene. This phenomenon is synchronous with regional and global cooling during the EOT and linked to declining pCO2. However, the earliest Oligocene climate rebound along eastern Tasmania is linked to a transient recovery of atmospheric pCO2 and sustained deepening of the Tasmanian Gateway, promoting PLC throughflow. The three main climate transitional events across the studied interval (late Eocene–earliest Oligocene) in the Tasmanian Gateway region suggest that changes in ocean circulation due to accelerated deepening of the Tasmanian Gateway may not have been solely responsible for the changes in terrestrial climate and vegetation dynamics; a series of regional and global events, including a change in the stratification of water masses, sequestration of carbon from surface waters, and changes in pCO2, may have also played vital roles

Interoperability and FAIRness through a novel combination of Web technologies

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs