Tailoring boron doped diamond surface properties for sensing applications

Boron doped diamond (BDD) has found numerous applications for electroanalysis in recent years. It’s material properties set it apart from other electrode materials due to its oft quoted wide solvent window and low background capacitances. However, the electrochemical performance has been shown to be highly dependent on the quality of the material, in particular it’s sp2 carbon content. For some applications, such as pH sensing, it has been shown that the inclusion of sp2 carbon impurities is advantageous. This can be achieved during diamond growth or by post-processing procedures, such as laser micromachining, as has been used in this thesis. Herein methods for electrochemically measuring surface sp2 carbon have been developed, and the functional groups on the electrode surface used for pH sensing applications and the underlying sp2 carbon component for dissolved oxygen sensing via the oxygen reduction reaction. To develop a pH sensor that works in unbuffered solutions laser micromachining, with control of the quinone surface coverage, was combined with pulsed voltammetric techniques to avoid perturbing the interfacial environment and control the local pH change. To further enhance pulsed voltammetric techniques, as used throughout this thesis, the raw current-time data was captured and post processed to extract information on the non-faradaic processes occurring, in addition to optimising the faradaic response. This work together advances the understanding of the effect of sp2 carbon in BDD electrodes and its use for electrochemical applications that requires optimisation of the material properties and electrochemical methods

On sequential Bayesian inference for continual learning

Sequential Bayesian inference can be used for continual learning to prevent catastrophic forgetting of past tasks and provide an informative prior when learning new tasks. We revisit sequential Bayesian inference and assess whether using the previous task’s posterior as a prior for a new task can prevent catastrophic forgetting in Bayesian neural networks. Our first contribution is to perform sequential Bayesian inference using Hamiltonian Monte Carlo. We propagate the posterior as a prior for new tasks by approximating the posterior via fitting a density estimator on Hamiltonian Monte Carlo samples. We find that this approach fails to prevent catastrophic forgetting, demonstrating the difficulty in performing sequential Bayesian inference in neural networks. From there, we study simple analytical examples of sequential Bayesian inference and CL and highlight the issue of model misspecification, which can lead to sub-optimal continual learning performance despite exact inference. Furthermore, we discuss how task data imbalances can cause forgetting. From these limitations, we argue that we need probabilistic models of the continual learning generative process rather than relying on sequential Bayesian inference over Bayesian neural network weights. Our final contribution is to propose a simple baseline called Prototypical Bayesian Continual Learning, which is competitive with the best performing Bayesian continual learning methods on class incremental continual learning computer vision benchmarks

Functional tests of the competitive exclusion hypothesis for multituberculate extinction

Multituberculate mammals thrived during the Mesozoic, but their diversity declined from the mid-late Paleocene onwards, becoming extinct in the late Eocene. The radiation of superficially similar, eutherian rodents has been linked to multituberculate extinction through competitive exclusion. However, characteristics providing rodents with a supposed competitive advantage are currently unknown and comparative functional tests between the two groups are lacking. Here, a multifaceted approach to craniomandibular biomechanics was taken to test the hypothesis that superior skull function made rodents more effective competitors. Digital models of the skulls of four extant rodents and the Upper Cretaceous multituberculate Kryptobaatar were constructed and used (i) in finite-element analysis to study feeding-induced stresses, (ii) to calculate metrics of bite force production and (iii) to determine mechanical resistances to bending and torsional forces. Rodents exhibit higher craniomandibular stresses and lower resistances to bending and torsion than the multituberculate, apparently refuting the competitive exclusion hypothesis. However, rodents optimize bite force production at the expense of higher skull stress and we argue that this is likely to have been more functionally and selectively important. Our results therefore provide the first functional lines of evidence for potential reasons behind the decline of multituberculates in the changing environments of the Paleogene.Peer reviewe

The shapes of bird beaks are highly controlled by nondietary factors

Bird beaks are textbook examples of ecological adaptation to diet, but their shapes are also controlled by genetic and developmental histories. To test the effects of these factors on the avian craniofacial skeleton, we conducted morphometric analyses on raptors, a polyphyletic group at the base of the landbird radiation. Despite common perception, we find that the beak is not an independently targeted module for selection. Instead, the beak and skull are highly integrated structures strongly regulated by size, with axes of shape change linked to the actions of recently identified regulatory genes. Together, size and integration account for almost 80% of the shape variation seen between different species to the exclusion of morphological dietary adaptation. Instead, birds of prey use size as a mechanism to modify their feeding ecology. The extent to which shape variation is confined to a few major axes may provide an advantage in that it facilitates rapid morphological evolution via changes in body size, but may also make raptors especially vulnerable when selection pressures act against these axes. The phylogenetic position of raptors suggests that this constraint is prevalent in all landbirds and that breaking the developmental correspondence between beak and braincase may be the key novelty in classic passerine adaptive radiations

Facet-resolved electrochemistry of polycrystalline boron-doped diamond electrodes : microscopic factors determining the aqueous solvent window in aqueous potassium chloride solutions

A systematic examination of the microscopic factors affecting the aqueous solvent (electrolyte) window of polycrystalline (p) boron-doped diamond (BDD) electrodes in chloride-containing salt solutions is undertaken using scanning electrochemical cell microscopy (SECCM), in conjunction with electron backscatter diffraction (EBSD) and Raman microscopy. A major focus is to determine the effect of local boron doping level, within the same orientation grains, on the solvent window response. EBSD is used to select the predominant (110) orientated areas of the surface with different boron-doped facets, thereby eliminating crystallographic effects from the electrochemical response. Voltammetric SECCM is employed, whereby a cyclic voltammogram (CV) is recorded at each pixel mapped by the meniscus-contact SECCM cell. The data obtained can be played as an electrochemical movie of potential-resolved current maps of the surface to reveal spatial variations of electroactivity, over a wide potential range, including the solvent (electrolyte) window. Local heterogeneities are observed, indicating that the solvent window is mainly linked to local dopant levels, with lower dopant levels leading to a wider window, i.e. slower electrode kinetics for solvent/electrolyte electrolysis. Furthermore, the effects of O- and H-surface termination of the BDD surface are investigated, for the same electrode (in the same area). The surface termination is a particularly important factor: the solvent window of an H-terminated surface is wider than for O-termination for similar boron dopant levels. Further, the anodic potential window of the O-terminated surface is greatly diminished due to chloride electro-oxidation. These studies provide new perspectives on the local electrochemical properties of BDD and highlight the importance of probing the electrochemistry of BDD at the level of a single crystalline grain (facet) in order to unravel the factors that control the solvent (aqueous) window of these complex heterogeneous electrodes

The multifactorial nature of beak and skull shape evolution in parrots and cockatoos (Psittaciformes)

Background The Psittaciformes (parrots and cockatoos) are characterised by their large beaks, and are renowned for their ability to produce high bite forces. These birds also possess a suite of modifications to their cranial architecture interpreted to be adaptations for feeding on mechanically resistant foods, yet the relationship between cranial morphology and diet has never been explicitly tested. Here, we provide a three-dimensional geometric morphometric analysis of the developmental and biomechanical factors that may be influencing the evolution of psittaciformes’ distinctive cranial morphologies. Results Contrary to our own predictions, we find that dietary preferences for more- or less- mechanically resistant foods have very little influence on beak and skull shape, and that diet predicts only 2.4% of the shape variation in psittaciform beaks and skulls. Conversely, evolutionary allometry and integration together predict almost half the observed shape variation, with phylogeny remaining an important factor in shape identity throughout our analyses, particularly in separating cockatoos (Cacatuoidea) from the true parrots (Psittacoidea). Conclusions Our results are similar to recent findings about the evolutionary trajectories of skull and beak shape in other avian families. We therefore propose that allometry and integration are important factors causing canalization of the avian head, and while diet clearly has an influence on beak shape between families, this may not be as important at driving evolvability within families as is commonly assumed

Diamond membrane production : the critical role of radicals in the non-contact electrochemical etching of sp2 carbon

Sub-micrometre single crystal diamond membranes are of huge importance for next generation optical, quantum and electronic device applications. Electrochemical etching has proven a critical step in the production of such membranes. Etching is used to selectively remove a very thin layer of sub-surface sp2 carbon, prepared by ion implantation in bulk diamond, releasing the diamond membrane. Due to the nanosized dimensions, etching is typically carried out using non-contact electrochemistry in low conductivity solutions (bipolar arrangement) which whilst effective, results in extremely slow etch rates. In this work, a new method of non-contact electrochemical etching is presented which uses high conductivity, high concentration, fully dissociated aqueous electrolytes. Careful choice of the electrolyte anion results in significant improvements in the sp2 carbon etch rate. In particular, we show both chloride and sulfate electrolytes increase etch rates significantly (up to × 40 for sulfate) compared to our measurements using the current state-of-the-art solutions and methodologies. Electron paramagnetic resonance experiments, recorded after the electrode potential has been switched off, reveal sizeable hydroxyl radical concentrations at timescales > 107 longer than their lifetime (≤μs). These measurements highlight the importance of electrochemically initiated, solution chemistry radical generation and regeneration pathways in high concentration sulfate and chloride solutions for nano-etching applications

Climate-informed stochastic hydrological modeling: Incorporating decadal-scale variability using paleo data

A hierarchical framework for incorporating modes of climate variability into stochastic simulations of hydrological data is developed, termed the climate-informed multi-time scale stochastic (CIMSS) framework. A case study on two catchments in eastern Australia illustrates this framework. To develop an identifiable model characterizing long-term variability for the first level of the hierarchy, paleoclimate proxies, and instrumental indices describing the Interdecadal Pacific Oscillation (IPO) and the Pacific Decadal Oscillation (PDO) are analyzed. A new paleo IPO-PDO time series dating back 440 yr is produced, combining seven IPO-PDO paleo sources using an objective smoothing procedure to fit low-pass filters to individual records. The paleo data analysis indicates that wet/dry IPO-PDO states have a broad range of run lengths, with 90% between 3 and 33 yr and a mean of 15 yr. The Markov chain model, previously used to simulate oscillating wet/dry climate states, is found to underestimate the probability of wet/dry periods >5 yr, and is rejected in favor of a gamma distribution for simulating the run lengths of the wet/dry IPO-PDO states. For the second level of the hierarchy, a seasonal rainfall model is conditioned on the simulated IPO-PDO state. The model is able to replicate observed statistics such as seasonal and multiyear accumulated rainfall distributions and interannual autocorrelations. Mean seasonal rainfall in the IPO-PDO dry states is found to be 15%-28% lower than the wet state at the case study sites. In comparison, an annual lag-one autoregressive model is unable to adequately capture the observed rainfall distribution within separate IPO-PDO states. Copyright © 2011 by the American Geophysical Union.Benjamin J. Henley, Mark A. Thyer, George Kuczera and Stewart W. Frank

Climate-informed stochastic hydrological modeling: Incorporating decadal-scale variability using paleo data

A hierarchical framework for incorporating modes of climate variability into stochastic simulations of hydrological data is developed, termed the climate-informed multi-time scale stochastic (CIMSS) framework. A case study on two catchments in eastern Australia illustrates this framework. To develop an identifiable model characterizing long-term variability for the first level of the hierarchy, paleoclimate proxies, and instrumental indices describing the Interdecadal Pacific Oscillation (IPO) and the Pacific Decadal Oscillation (PDO) are analyzed. A new paleo IPO-PDO time series dating back 440 yr is produced, combining seven IPO-PDO paleo sources using an objective smoothing procedure to fit low-pass filters to individual records. The paleo data analysis indicates that wet/dry IPO-PDO states have a broad range of run lengths, with 90% between 3 and 33 yr and a mean of 15 yr. The Markov chain model, previously used to simulate oscillating wet/dry climate states, is found to underestimate the probability of wet/dry periods >5 yr, and is rejected in favor of a gamma distribution for simulating the run lengths of the wet/dry IPO-PDO states. For the second level of the hierarchy, a seasonal rainfall model is conditioned on the simulated IPO-PDO state. The model is able to replicate observed statistics such as seasonal and multiyear accumulated rainfall distributions and interannual autocorrelations. Mean seasonal rainfall in the IPO-PDO dry states is found to be 15%-28% lower than the wet state at the case study sites. In comparison, an annual lag-one autoregressive model is unable to adequately capture the observed rainfall distribution within separate IPO-PDO states. Copyright © 2011 by the American Geophysical Union.Benjamin J. Henley, Mark A. Thyer, George Kuczera and Stewart W. Frank

Unique Type I Interferon Responses Determine the Functional Fate of Migratory Lung Dendritic Cells during Influenza Virus Infection

Migratory lung dendritic cells (DCs) transport viral antigen from the lungs to the draining mediastinal lymph nodes (MLNs) during influenza virus infection to initiate the adaptive immune response. Two major migratory DC subsets, CD103+ DCs and CD11bhigh DCs participate in this function and it is not clear if these antigen presenting cell (APC) populations become directly infected and if so whether their activity is influenced by the infection. In these experiments we show that both subpopulations can become infected and migrate to the draining MLN but a difference in their response to type I interferon (I-IFN) signaling dictates the capacity of the virus to replicate. CD103+ DCs allow the virus to replicate to significantly higher levels than do the CD11bhigh DCs, and they release infectious virus in the MLNs and when cultured ex-vivo. Virus replication in CD11bhigh DCs is inhibited by I-IFNs, since ablation of the I-IFN receptor (IFNAR) signaling permits virus to replicate vigorously and productively in this subset. Interestingly, CD103+ DCs are less sensitive to I-IFNs upregulating interferon-induced genes to a lesser extent than CD11bhigh DCs. The attenuated IFNAR signaling by CD103+ DCs correlates with their described superior antigen presentation capacity for naïve CD8+ T cells when compared to CD11bhigh DCs. Indeed ablation of IFNAR signaling equalizes the competency of the antigen presenting function for the two subpopulations. Thus, antigen presentation by lung DCs is proportional to virus replication and this is tightly constrained by I-IFN. The “interferon-resistant” CD103+ DCs may have evolved to ensure the presentation of viral antigens to T cells in I-IFN rich environments. Conversely, this trait may be exploitable by viral pathogens as a mechanism for systemic dissemination