Modelling cytosolic flow and vesicle transport in the growing pollen tube

Scientific interest in the mathematical modelling of pollen tube growth has increased steadily over the last few decades. The highly localized and rapid nature of this growth necessitates large--scale actomyosin transport of cellular material throughout the cell cytoplasm. This directed movement of cellular material induces a flow in the cytosol, also known as 'cyclosis'. The extent to which inclusion of this flow is important to modelling the distribution of elements in the cytoplasm is currently unclear, with its effect often conflated with that of actomyosin transport. In this thesis, a finite volume method (FVM) is developed for the numerical evaluation of transport equations describing vesicle distribution in the pollen tube cytoplasm. This is coupled with a novel method of regularized ringlets, derived via analytical azimuthal integration of the regularized Stokeslet, for obtaining numerical solutions to axisymmetric Stokes flows. Using this method of regularized ringlets, we present an axisymmetric velocity profile for cytosolic flow in the pollen tube based on the drag induced by actomyosin vesicle transport. When used in the transport equation for vesicle distribution, we find that recreation of the apical `inverted vesicle cone' requires the use of an enlarged effective fluid viscosity amongst other results

The Ethynyl Hydrogen Bond

The nature and properties of the hydrogen bond are discussed with special reference to the ethynyl hydrogen bond. Proof is given of the electron accepting capacity of the C-H group and of the electron donating capacity of the "pi" electron system of aromatic rings. The theory of the calorimetries spectroscopic and diffraction methods of studying the hydrogen bond are discussed in detail especially as it applies to the investigations discussed in this thesis. An investigation of the ethynyl hydrogen bond was conducted in which the chief acatylenic electron acceptor used was benzoyl acetylene. Instruments were constructed for a calorimetric study of the ethynyl hydrogen bond, the apparatus being checked for accuracy by determining the heat of solution of potassium chloride in water. Heats of mixing of benzoyl acetylene in a variety of solvents were obtained and from these the enthalpy of hydrogen bond formation between the benzoyl acetylene and the active solvents was obtained. An infrared investigation of benzoyl acetylene and phenyl acetylene in a wide variety of solvents was carried out, the frequency shifts, half band widths and maximum intensities of the bands being noted. This indicated the wide range of compounds capable of hydrogen bonding and also provided evidence of bonding to the "pi" electron system of aromatic compounds as distinct from bonding to particular electronegative atoms. A quantitative study of benzoyl acetylene in benzene, various methylated benzenes and in n-butyl ether was carried out allowing the determination of association constants and degrees of association. This was repeated at a variety of temperatures allowing the calculation of hydrogen bond strengths. Results obtained using the infrared technique were found to be subject to considerable error. A quantitative study of benazoyl acetylene in the same solvents as above was carried out using the nuclear magnetic resonance method. This provided a very accurate method of determining association constants and degrees of association. It was intended to carry out temperature studies using this technique but this was impossible due to non-delivery of equipment. This method was also applied to the study of 1:4 dichlorobut-2-yne and propargyl chloride in benzene-cyclohexane mixtures and indicated the probable existence of hydrogen bonds between the methylene protons of these molecules and the "pi" electrons of benzene. An X-ray diffraction investigation of the ethynyl hydrogen bond was carried out with Dr. G. Ferguson. For this purpose ortho-bromobesasoylacetylene was prepared and photographed. A two-dimensional Fourier map of the molecule is shown and the first accurate measurement of a known C=H...O hydrogen bond is given

Organic electrochemical transistors for neurotechnology

The organic electrochemical transistor is a device that has proven to provide a comprehensive insight into physiological activity. The burden of brain-related illnesses and the potential societal impact of enhancing human interaction and communication with computers motivates the advancement of technologies to provide greater insights into neural activity. This research focuses on the intersection of these fields through developing organic electrochemical transistors for neurotechnology. As such, this research reports the fabrication, characterisation, and operation of the devices to demonstrate their applicability in providing an accurate description of neural activity. In turn, pathways are offered on the optimisation and enhancement of transistor performance, informing the field on methods to maximise the efficacy of biosensing devices. This thesis opens with the motivations to develop neurotechnology in society by considering the burden of neurological disorders and the enhancement of human-machine communication. The roles that bioelectronics and organic electrochemical transistors could take in achieving such goals are then described. The literature on organic electrochemical transistors and their applications in neurotechnology is then examined. Foundational to this research was the design and fabrication of novel transistor architectures. As such, fabrication methods are then described which provide micrometre-scale resolutions, facilitating the production of biocompatible, high-performance devices. The thesis then describes an investigation with the aim to optimise the performance of organic electrochemical transistors for the maximisation of the range of electrophysiological signals that the devices can resolve and amplify. Devices are demonstrated with high amplification factors and bandwidths sufficient for transducing the full bioelectric spectrum. The devices efficaciously resolve electrophysiological inputs with a wide range of voltage and frequency characteristics, demonstrated through measuring the device response to pre-recorded signals and supported through noise quantification. Research is then presented with aims to employ organic electrochemical transistors in a linear amplifier topology that provides precise amplification control. Circuit parameters are identified for stable amplifier operation, and the transistors are physically implemented into amplifier circuits. An equation is then formulated which models the transistor current in the linear, non-linear and saturation regimes, and this equation is used to simulate the amplifier response. Through experimentation and simulation, the amplifier is extensively characterised, providing quantitative measures on amplifier gain, linearity, bandwidth, and noise. The amplifier is then inputted with pre-recorded bioelectric signals and the linear gain of the amplifier is experimentally demonstrated. The thesis then presents an investigation with the aim to determine the effect of electrode architecture on organic electrochemical transistor characteristics and bioelectric performance. The impacts of varying the interconnect resistance on the steady-state and transient characteristics are examined. Then, arrays of devices are fabricated, and the effects of varying the interconnect resistance and the interdigitated electrode geometry on bioelectric performance are quantified. The electrode architecture at the measurement site is then varied for a fixed site area to determine an optimal configuration for resolving bioelectric inputs. The investigation presents a pathway for the optimisation of electrode architecture for a given application. Finally, the thesis describes research that aims to determine the relationships between the morphological properties of the organic layer and the electrical characteristics relevant to biosensing performance. Electrical characterisations and resonant Raman spectroscopy are carried out on organic electrochemical transistors that are immersed in an aqueous solution over a period of 50 days, and the temporal changes in the derived parameters are presented. Then, the effects of varying the applied voltages on the active layer morphology and the device noise are investigated, providing an insight into how the structural changes of organic polymers correlate to variations in noise.Open Acces

Hierarchical strategies for efficient fault recovery on the reconfigurable PAnDA device

A novel hierarchical fault-tolerance methodology for reconfigurable devices is presented. A bespoke multi-reconfigurable FPGA architecture, the programmable analogue and digital array (PAnDA), is introduced allowing fine-grained reconfiguration beyond any other FPGA architecture currently in existence. Fault blind circuit repair strategies, which require no specific information of the nature or location of faults, are developed, exploiting architectural features of PAnDA. Two fault recovery techniques, stochastic and deterministic strategies, are proposed and results of each, as well as a comparison of the two, are presented. Both approaches are based on creating algorithms performing fine-grained hierarchical partial reconfiguration on faulty circuits in order to repair them. While the stochastic approach provides insights into feasibility of the method, the deterministic approach aims to generate optimal repair strategies for generic faults induced into a specific circuit. It is shown that both techniques successfully repair the benchmark circuits used after random faults are induced in random circuit locations, and the deterministic strategies are shown to operate efficiently and effectively after optimisation for a specific use case. The methods are shown to be generally applicable to any circuit on PAnDA, and to be straightforwardly customisable for any FPGA fabric providing some regularity and symmetry in its structure

A Hormone-Inspired Arbitration System For Self Identifying Abilities Amongst A Heterogeneous Robot Swarm

Current exploration of adaptation in robot swarms requires the swarm or individuals within that swarm to have knowledge of their own capabilities. Across long term use a swarms understanding of its capabilities may become inaccurate due to wear or faults in the system. In addition to this, systems capable of self designing morphologies are becoming increasingly feasible. In these self designing examples it would be impossible to have accurate knowledge of capability before executing a task for the first time. We propose an arbitration system that requires no explicit knowledge of capability but instead uses hormone-inspired values to decide on an environmental preference. The robots in the swarm differ by wheel type and thus how quickly they are able to move across terrain. The goal of this system is to allow robots to identify their strengths within a swarm and allocate themselves to areas of an environment with a floor type that suits their ability. This work shows that the use of a hormone-inspired arbitration system can extrapolate robot capability and adapt the systems preference of terrain to suit said capability.</p

Conodont (U-Th)/He thermochronology of the Mormon Mountains, Tule Spring Hills, and Beaver Dam Mountains, southeastern Nevada and southwestern Utah

ABSTRACT Although (U-Th)/He thermochronology is a well-established dating technique used to understand the temperature-time histories of rocks, the method is restricted to rocks that contain specific accessory minerals such as apatite or zircon. Marine carbonates and shales typically lack these accessory phases, and thus present a challenge for application of the method. Here, we explore the utility of biogenic apatite from conodonts as a (U-Th)/He thermochronometer at a well- studied calibration site located in eastern Nevada and southwestern Utah. We perform (U-Th)/He thermochronometry, laser ablation inductively coupled plasma mass spectrometry, X-ray micro-computed tomography, and scanning electron microscopy on specimens with conodont color alteration indices (CAI) of 1.5 – 3 extracted from carbonate rocks in the footwalls of low-angle normal faults in the Mormon Mountains, Tule Spring Hills, and Beaver Dam Mountains. (U-Th)/He (CHe) dates have high scatter; dates are commonly reproducible to 20% of sample means, but can deviate up to 150%. All CAI 1.5 – 2.5 conodonts produce CHe dates younger than 193 Ma, consistent with thermal resetting of samples; however, most CAI 3 conodonts give ages 2 – 3x older than Mississippian and Permian deposition. Average U, Th, and rare earth element (REE) concentrations depend on porosity and permeability differences between albid and hyaline conodont tissue and range from <10 to 100s of ppm in concentration. Parent isotope concentrations are especially low in CAI 3 conodonts, commonly <1 ppm, and there is an inverse relationship between these concentrations and CHe dates. The majority of parent U, Th, and Sm, and REEs are concentrated within the outer 5 μm of the conodont elements and consistently show 5 – 10x enrichment relative to cores. Margin enrichment is also depressed with increasing CAI. SEM imaging shows a shift in the orientation of apatite microcrystallites from perpendicular to parallel to the major axis of the conodont elements at CAI 3, and corrosion and recrystallization features on the surfaces of some CAI 2.5 and 3 conodonts. We propose these microstructural changes associated with increasing CAI influence CHe dates. Parent isotope loss occurs during the post-cooling stage, either in the outcrop or in the laboratory. Our hypothesis is that the double-buffered formic acid procedure for dissolving dolomitized carbonates may accelerate this loss in higher CAI conodonts

Game Tutorial Analysis

In this study we observed players from two groups playing the game Thief: Deadly Shadows. By having one group play the tutorial level and the other group not play it, we were able to examine the effects that the tutorial level had on the performance of the players. We concluded that the tutorial was effective in teaching players the basic style of game play, as well as some of the game play techniques unique to the game

High-Sigma Performance Analysis using Multi-Objective Evolutionary Algorithms

Semiconductor devices have rapidly improved in performance and function density over the past 25 years enabled by the continuous shrinking of technology feature sizes. Fabricating transistors that small, even with advanced processes, results in structural irregularities at the atomic scale, which affect device characteristics in a random manner. To simulate performance of circuits comprising a large number of devices using statistical models and ensuring low failure rates, performance outliers are required to be investigated. Standard Monte Carlo analysis will quickly become intractable because of the large number of circuit simulations required. Cases where the number of samples exceeds are known as “high-sigma problems”. This work proposes a highsigma sampling methodology based on multi-objective optimisation using evolutionary algorithms. A D-type Flip Flop is presented as a case study and it is shown that higher sigma outliers can be reached using a similar number of SPICE evaluations as Monte Carlo analysis