Dissertations / Theses on the topic 'Biogeochemistry of extreme environments'

There is currently a considerable interest in characterising extreme environments, since they offer the opportunity to envision practical applications and to understand microbial diversity as an adaptive response that reflects environmental diversity. It is now well recognized that microorganisms thrive in extreme conditions such as contaminated soils/sediments and the pressurised depth of the Earth. Morphological, physiological, biochemical and genetic adaptations to extreme environments by these microorganisms have generated immense interest amongst scientists who continuously discover new occurrences and modes of microbial life on Earth. In this thesis, biogeochemical processes are investigated in two different extreme environments. (i) The deep biosphere, with a focus on shale gas basin and coal-bed methane (CBM). These environments are currently gaining momentum across the scientific community for the production of gaseous fuel. (i) [sic] Coal tar-contaminated soil and concentrated organic-phase coal tar, which was studied for bioremediation purposes. The core of this thesis consists of three articles dedicated to combination of different molecular and chromatographic methods of experimentation, analysis and interpretation. These include molecular tools such as DNA extraction techniques, PCR, 454-pyrosequencing and culturing-based approaches. The chemical experiments were metabolomic and isotopic chromatographic analyses. This study presented an extensive review of the biogeochemistry of unconventional gas systems, which provide an improved level of information of such environments. A robust culture-independent methodology was developed for the characterisation of microbial life in extreme environments, which was applied to describe, for the first time, the presence of bacteria in concentrated organic-phase coal tar. The deep sequencing methods were then used in combination with multidimensional compound specific isotope analysis (CSIA) to investigate community structure. The combined approach of deep sequencing methods with multidimensional CSIA was confirmed by statistics. Thus, high-throughput 16S rRNA gene sequencing and multidimentional CSIA, can be applied to investigate microbial community structure in extreme environments.

The proliferation of undesirable cyanobacteria within eutrophic freshwaters is now reported on a global scale, however the factors triggering cyanobacteria bloom formation were found to be especially complex. Even within a single water body, physical, chemical and biological factors all influence the assemblage of phytoplankton found. Notwithstanding the body of research conducted over the past 50 years, where concerted efforts have been applied to observing bloom patterns and the drivers of cyanobacteria blooms, substantial knowledge gaps were identified. An examination of field methods, the factors promoting the growth of cyanobacteria blooms in modified inland aquatic ecosystems, modelling to predict the onset of a bloom using a 7 day positive model, and consideration of the likely effects increasing atmospheric CO2 could have on the development of surface dwelling species were key themes addressed. The thesis represents a combination of field based and controlled experimental laboratory research. A three-year case study was undertaken at an inland freshwater impoundment where cyanobacteria blooms had become a burgeoning issue. Standard surface monitoring and in situ multi-parameter instruments were used to determine environmental stressors. Importantly the water body was characterised as a well-mixed system. A hypertrophic classification was attributed to the water body due to nutrient super saturation, high water temperatures and suspended sediment measured in all years. A discrepancy between the available analysis methods was found, as the molecular method detected a diversity of microorganisms including several cyanobacteria species, whereas microscopy detected only one species. Notably harmful colonies of picocyanobacteria were not observed using standard microscopy. The molecular data also showed cyanobacteria represented 30% of the total bacterial community yet; molecular analyses may be limited when cell counts are required for a comparison with the alert level framework. The case study found the adoption of multi-monitoring and analysis methods constitutes best practice, and should therefore be integral to early detection, risk mitigation and system characterisation. A controlled laboratory study was undertaken to measure the efficacy of emerging technology as a water quality-monitoring stratagem, with emphasis placed on the accuracy of fluorometry in turbid waters above 50 nephelometric turbidity units (NTUs). The results found in vivo fluorometry using a Manta 2 probe was useful for detecting Microcystis aeruginosa at concentrations consistent with the National Health and Medical Research Council’s alert framework (Green, Amber and Red). Phycocyanin was found to be a more reliable measure of cyanobacteria than chlorophyll a, and by using a calibrated instrument it was possible to accurately detect cyanobacteria in turbid waters up to 220 NTUs. Cyanobacteria are highly effective at CO2 assimilation, with a remarkable capacity to adapt to different CO2 conditions, however scant research had previously focused on understanding how freshwater species may respond to increasing atmospheric CO2. Controlled laboratory experiments were performed and diazotrophic and non-diazotrophic cultures were exposed to past and projected atmospheric CO2 concentrations. Both experimental species adapted to the ambient low and high CO2 conditions, however, significantly higher bio volume was measured in the elevated CO2 chambers. The ability of freshwater ecosystems to maintain steady state water chemistry or base-neutralizing capacity if atmospheric CO2 concentrations reach levels projected for the latter part of this century is questionable, and furthermore, the study provided empirical evidence to support the theoretical position that increasing CO2 may lead to changes in water chemistry, particularly a decrease in pH values.

Extreme work environments represent complex and challenging settings in which optimal performance is required rather than optional. This thesis advances knowledge of how demands and constraints within extreme work environments impact sustained human performance over time. This thesis establishes a theoretical framework of endurance that models ongoing human performance in extreme work-life systems; and provides empirical evidence on the different ways complex work demands can impact short- and long-term endurance in real-world extreme work environments.

With mankind’s ever increasing curiosity to explore the unknown, including a variety of hostile environments where we cannot tread, there exists a need for machines to do work on our behalf. For applications in the most extreme environments and applications silicon based electronics cannot function, and there is a requirement for circuits and sensors to be built from wide band gap materials capable of operation in these domains. This work addresses the initial development of silicon carbide circuits to monitor conditions and transmit information from such hostile environments. The characterisation, simulation and implementation of silicon carbide based circuits utilising proprietary high temperature passives is explored. Silicon carbide is a wide band gap semiconductor material with highly suitable properties for high-power, high frequency and high temperature applications. The bandgap varies depending on polytype, but the most commonly used polytype 4H, has a value of 3.265 eV at room temperature, which reduces as the thermal ionization of electrons from the valence band to the conduction band increases, allowing operation in ambient up to 600°C. Whilst silicon carbide allows for the growth of a native oxide, the quality has limitations and therefore junction field effect transistors (JFETs) have been utilised as the switch in this work. The characteristics of JFET devices are similar to those of early thermionic valve technology and their use in circuits is well known. In conjunction with JFETs, Schottky barrier diodes (SBDs) have been used as both varactors and rectifiers. Simulation models for high temperature components have been created through their characterisation of their electrical parameters at elevated temperatures. The JFETs were characterised at temperatures up to 573K, and values for TO V , β , λ , IS , RS and junction capacitances were extracted and then used to mathematically describe the operation of circuits using SPICE. The transconductance of SiC JFETs at high temperatures has been shown to decrease quadratically indicating a strong dependence upon carrier mobility in the channel. The channel resistance also decreased quadratically as a direct result of both electric field and temperature enhanced trap emission. The JFETs were tested to be operational up to 775K, where they failed due to delamination of an external passivation layer. ii Schottky diodes were characterised up to 573K, across the temperature range and values for ideality factor, capacitance, series resistance and forward voltage drop were extracted to mathematically model the devices. The series resistance of a SiC SBD exhibited a quadratic relationship with temperature indicating that it is dominated by optical phonon scattering of charge carriers. The observed deviation from a temperature independent ideality factor is due to the recombination of carriers in the depletion region affected by both traps and the formation of an interfacial layer at the SiC/metal interface. To compliment the silicon carbide active devices utilised in this work, high temperature passive devices and packaging/circuit boards were developed. Both HfO2 and AlN materials were investigated for use as potential high temperature capacitor dielectrics in metal-insulator-metal (MIM) capacitor structures. The different thicknesses of HfO2 (60nm and 90nm) and 300nm for AlN and the relevance to fabrication techniques are examined and their effective capacitor behaviour at high temperature explored. The HfO2 based capacitor structures exhibited high levels of leakage current at temperatures above 100°C. Along with elevated leakage when subjected to higher electric fields. This current leakage is due to the thin dielectric and high defect density and essentially turns the capacitors into high value resistors in the order of MΩ. This renders the devices unsuitable as capacitors in hostile environments at the scales tested. To address this issue AlN capacitors with a greater dielectric film thickness were fabricated with reduced leakage currents in comparison even at an electric field of 50MV/cm at 600K. The work demonstrated the world’s first high temperature wireless sensor node powered using energy harvesting technology, capable of operation at 573K. The module demonstrated the world’s first amplitude modulation (AM) and frequency modulation (FM) communication techniques at high temperature. It also demonstrated a novel high temperature self oscillating boost converter cable of boosting voltages from a thermoelectric generator also operating at this temperature. The AM oscillator operated at a maximum temperature of 553K and at a frequency of 19.4MHz with a signal amplitude 65dB above background noise. Realised from JFETs and HfO2 capacitors, modulation of the output signal was achieved by varying the load resistance by use of a second SiC JFET. By applying a negative signal voltage of between -2.5 and -3V, a 50% reduction in the signal amplitude and therefore Amplitude Modulation was achieved by modulating the power within the oscillator through the use of this secondary JFET. Temperature drift in the characteristics were also observed, iii with a decrease in oscillation frequency of almost 200 kHz when the temperature changed from 300K to 573K. This decrease is due to the increase in capacitance density of the HfO2 MIM capacitors and increasing junction capacitances of the JFET used as the amplifier within the oscillator circuit. Direct frequency modulation of a SiC Voltage Controlled Oscillator was demonstrated at a temperature of 573K with a oscillation frequency of 17MHz. Realised from an SiC JFET, AlN capacitors and a SiC SBD used as a varactor. It was possible to vary the frequency of oscillations by 100 kHz with an input signal no greater than 1.5V being applied to the SiC SBD. The effects of temperature drift were more dramatic in comparison to the AM circuit at 400 kHz over the entire temperature range, a result of the properties of the AlN film which causes the capacitors to increase in capacitance density by 10%. A novel self oscillating boost converter was commissioned using a counter wound transformer on high temperature ferrite, a SiC JFET and a SiC SBD. Based upon the operation of a free running blocking oscillator, oscillatory behaviour is a result of the electric and magnetic variations in the winding of the transformer and the amplification characteristics of a JFET. It demonstrated the ability to boost an input voltage of 1.3 volts to 3.9 volts at 573K and exhibited an efficiency of 30% at room temperature. The frequency of operation was highly dependent upon the input voltage due to the increased current flow through the primary coil portion of the transformer and the ambient temperature causing an increase in permeability of the ferrite, thus altering the inductance of both primary and secondary windings. However due its simplicity and its ability to boost the input voltage by 250% meant it was capable of powering the transmitters and in conjunction with a Themoelectric Generator so formed the basis for a self powered high temperature silicon carbide sensor node. The demonstration of these high temperature circuits provide the initial stages of being able to produce a high temperature wireless sensor node capable of operation in hostile environments. Utilising the self oscillating boost converter and a high temperature Thermoelectric Generator these prototype circuits were showed the ability to harvest energy from the high temperature ambient and power the silicon carbide circuitry. Along with appropriate sensor technology it demonstrated the feasibility of being able to monitor and transmit information from hazardous locations which is currently unachievable.

Microorganisms are known to tolerate a variety of extreme environments, such as high and low pH, desiccation and a wide range of temperatures that would prove uninhabitable for most eukaryotic cells. However, extreme radiation exposure is a ubiquitous hazard to pro- and eukaryotic viability. Ionising and non-ionising radiation, and their associated high energies, cause damage to a cell in the form of DNA double-strand breaks, membrane deterioration, and lethal mutations. Radiation also induces secondary effects such as the production of reactive oxygen species, which attack and degrade organic compounds. It is therefore not surprising that radiation is considered by the scientific community to be one of the main influencing factors when regarding habitability on the early Earth, as well as other planets, such as present-day Mars. This thesis explores the response of select microbes that have been exposed to extreme radiation environments, i.e. both high and ultra-low radiation. Understanding how radiation affects the geochemical environment is key to the assessment of its potential to support life and to harbour molecules associated with life. The effect of radiation-induced photochemistry on the early terrestrial and present-day Martian surface is explored in conjunction with Fenton chemistry. Iron oxides are abundant on both Earth and Mars and act as catalysts in Photo-Fenton reactions, enabling the production of free radicals. The resulting consequences for habitability are shown to be antagonistic, with iron oxide enabling both the protection or destruction of cells, depending on the local geochemistry. In addition, the photo-reactivity of perchlorate is investigated. The UV-induced activation of the strong oxidant, and recently confirmed Martian surface constituent, is demonstrated, revealing its severe bacteriocidal effect on microbes. It is also shown to significantly reduce microbial viability when combined with further Martian soil constituents and components required for Photo-Fenton chemistry. In order to accurately analyse the effects of low earth orbit radiation on prokaryotic life, cyanobacterial samples were attached to the outside of the International Space Station as part of the EXPOSE-R2 mission for 1.5 years. The samples were subjected to various conditions, including exposure to a minimally filtered space radiation environment and simulated Mars conditions. The experiment is designed to test the protection that biogenic and non-biogenic substances may provide to cells. The results in this work present the post-flight analysis of the samples and demonstrate the ability of these substances to maintain cyanobacteria viability. They also show that the cyanobacterial cells themselves can effectively act as a shield for a secondary, co-cultured bacteria species. On the other end of the radiation dose scale, this work addresses the gaps in knowledge with regard to the little-understood effects of low, sub-background radiation on prokaryotes. Using the Boulby Underground Lab in the functioning Boulby Mine, Cleveland UK, microbes are cultivated under regulated, extremely low radiation environments to test multiple dose-response models. The results show no change in cell's growth rates or gradients in low radiation exposure when compared to surface-dose controls. They also fail to exhibit any enhanced susceptibility to stress factors, such as UV irradiation, as suggested by previous work in the field. These experiments mark the first extensive and tightly controlled research into microbial responses in the near-absence of radiation. This work illustrates the importance of understanding both primary and secondary effects of radiation on microbes and begins to bridge the knowledge gap from both ends of the dose axis. These approaches show the far-reaching influence radiation has on astrobiologically relevant topics, such as habitat geochemistry and life detection, and demonstrate the capacity of life to survive in extreme radiation environments.

The degradation of material surfaces is a 'valve' that has limited technological progress through the ages. Today's most challenging environments are those where component surfaces are exposed to the simultaneous or sequential actions of corrosion and mechanical wear. These phenomena can be mitigated by a better understanding of the interactions between the multiple degradation mechanisms and the systematic development of alternative material surfaces. In this work, PVD coatings based on the Fe-Cr-Ni, Cr-Ti, Cr-B-(N) and W-(B) material systems were developed using unbalanced magnetron sputtering and mainly applied to AISI 316L, Ti-6AI-4V and Ortron 90 substrates respectively. For Fe-Cr-Ni and Cr-Ti coatings, post deposition heat treatments were conducted to stimulate the formation of the cr-FeCrNi and Laves Cr2Ti intermetallic phases respectively. In all cases, the morphology, chemical composition, structure, mechanical properties, corrosion behaviour and damage tolerance of the various coated materials were investigated. Special emphasis was placed on the response of the coated materials and uncoated test-pieces to the simultaneous action of corrosion and mechanical wear that resulted from sliding an Ah03 ball against the coated and uncoated materials in a 0.9 wt%NaCI solution. For one case only, W-(B) coated AISI 52100, lubricated rolling/sliding contact durability was assessed. For the corrosion-wear tests, the removal and regeneration of the passive layer (type I corrosion-wear) dominated the material loss. A high coatings hardness for'Fe-Cr-Ni and CrTi coatings was often beneficial to reduce the mechanical wear but the corrosion due to wear frequently remained high. Partial post deposition oxidation of Fe-Cr-Ni coatings was very effective in reducing the latter. Also of importance was the roughening of the Ah03 counterface due to the formation of tribo/transfer films or grain pull out. The material loss for Cr-B-(N) coatings was dominated by a material transfer mechanism and Ah03 grain pull out resulted in high mechanical wear of amorphous Cr-Ti coating. W-(B) coatings generally had low material loss and their crystalline variants displayed a low p.. The latter became inappropriate for conditions which promote high W dissolution. In lubricated rolling/sliding tests W-(B) coated AISI 52100 performance was·dependent on coating crystal structure and boron supersaturation. The crystalline coatings with low boron supersaturation displayed the best rolling/sliding damage resistance.

The measurement of the surface temperature of many components in gas turbines has become increasingly important as the firing temperature raises to improve thermal efficiency and reduce CO2 emissions. Traditional methods to measure temperatures in real time, such as thermocouples or pyrometers, are sometimes not suitable and an alternative must be sought. Thermal history sensors record the maximum temperatures reached during operation, which can then be measured after the engine has cooled down. Currently, temperature sensitive paints are mainly used to obtain temperature profiles on gas turbine components but they present some limitations such as subjectivity of the measurement, poor resolution and toxicity. Permanent changes in the optical properties of thermographic phosphors have been proposed as an alternative to record temperatures and can potentially overcome some of the difficulties associated with traditional paints. The changes in the optical properties of some europium doped phosphors after oxidation can be used to sense temperatures up to 1400 °C. The oxidation mechanism of BaMgAl10O17:Eu are investigated in detail by means of standard material characterisation techniques and laser induced phosphorescence. Variations in the luminescence properties of the phosphor (intensity ratio and lifetime decay) are related to microstructural and chemical changes and permitted to measure temperatures in the range 700-1200 °C. The influence of practical factors that can affect the measurement accuracy and sensitivity are thoroughly characterised. These include the energy fluence used for excitation, duration of the exposure at high temperatures, dopant concentration, time spent during cooling down, composition of the atmosphere during the heat treatment and particle size. The reversibility of the changes in the optical properties of the phosphor is studied by applying a heat treatment in a reducing atmosphere, and thus reusability of the sensor demonstrated. The development of a coating made of this phosphor is explored for the first time with regards to its application as a sensor. The difficulties to manufacture such a coating are mainly related to the complex stoichiometry and high processing temperature of the phosphor material. BaMgAl10O17:Eu coatings onto metallic substrates are manufactured by the screen printing method. In these coatings, diffusion of elements from the substrate undesirably affects the optical properties of the sensor after exposure to high temperatures. The use of a diffusion barrier permits to perform temperature measurements at temperatures up to 1100 °C comparable to the powder material. Thermal gradients across the ceramic coating can drastically affect the accuracy of the temperature measurements performed by using luminescence. Investigations in thermal barrier coating sensors in controlled gradient conditions are performed that permit evaluation of the temperature error introduced by these gradients. Comparison of experimental data and a theoretical model indicates that significant temperature measurement errors can be expected in BAM:Eu coatings when a thermal gradient is present.

The military is a multifaceted organisation consisting of an extremely diverse workforce where multiple individual differences are found among personnel. Therefore, possessing knowledge of personality characteristics that are adaptive along with those that are maladaptive in training and combat situations would be very advantageous for the military, especially when recruiting and training new recruits. The present thesis contains five chapters with the intent to first explore individual differences that could account for recruits who pass or fail military basic training (MTB). A second purpose of the thesis was to develop a deeper understanding of the personality profiles of courageous actors who have been decorated for their acts of bravery. Chapter 1 offers brief empirical reviews on personalities and their relationship with performance in the military environment and identify certain gaps in the literature that needs to be addressed. In particular: (i) limited current empirical research is available on the effect that military basic training (MBT) may have on the personality of recruits under training; (ii) limited empirical evidence is available exploring the positive adaptation and functioning of psychoticism and psychopathy personality types within the military environment; (iii) limited research is available that explore the relationship between courageous soldiers and psychopathy; and (iv) limited empirical evidence is available on the positive effect of psychological attributes (i.e., punishment and reward sensitivity, mental toughness, effortful control, internalisation of core values) on performance of military recruits under training. The chapter concludes by proposing that the military creates an environment where individuals with some measure of psychoticism (Eysenck & Eysenck, 1976) and psychopathy (Lilienfeld & Widows, 2005) may flourish, provided that they are given appropriate training. The focus of Chapter 2 falls on psychological attributes and behaviours that British male Infantry recruits bring to the start of MBT and how those attributes influence retention and performance outcomes. Results indicated that at that start of MBT, high levels of psychoticism, mental toughness (MT), activation control and attention control, and low levels of neuroticism and punishment sensitivity successfully differentiated between recruits who successfully completed MBT first time from recruits who did not complete MBT first time. The results and theoretical implications are discussed in terms of what the Army may do to improve recruitment and retention. Chapter 3 is longitudinal in nature and explored the effect MBT has on the psychological attributes of military recruits during a 26 week MBT training programme. The same psychological attributes that were explored within Chapter 2 were investigated in Chapter 3. With relevance to personality, results indicated a significant increase in extraversion across training, whereas neuroticism and punishment sensitivity significantly decreased during MBT. With relation cognitive variables, only external regulation levels significantly decreased during MBT. The results and theoretical implications are discussed in terms of how training may (or may not) influence some deep-rooted characteristics of the recruit. Chapter 4 examines the ultimate expression of military performance; namely, the decorated courageous soldier. The chapter followed a multi-methodological approach involving qualitative and quantitative methods to explore the personality of courageous soldiers with specific reference, but not limited to: psychopathy, cognitive processes, motivation and behaviours. Findings indicated that decorated courageous soldiers are not psychopathic; however, decorated courageous soldiers share certain characteristics with psychopaths. The findings from Chapter 4 further suggest that courageous acts were performed as a result of the right person, with the right genetic-makeup, being in the right situation when it mattered. The results and theoretical implications are discussed in terms of individual differences in personality, behaviour, cognitions and motivation. Chapter 5 concludes the thesis by providing a summary of the empirical chapters, followed by a discussion of theoretical points of interest and applied implications. Some limitations and strengths of the thesis are highlighted; whereafter the thesis is concluded by forwarding future research questions in order to further understand personalities and their performance within the military environment.

Operation of SiGe BiCMOS Technology Under Extreme Environments Tianbing Chen 96 pages Directed by Dr. John D. Cressler "Extreme environment electronics" represents an important niche market and spans the operation of electronic components in surroundings lying outside the domain of conventional commercial, or even military specifications. Such extreme environments would include, for instance, operation to very low temperatures (e.g., to 77 K or even 4.2 K), operation to very high temperatures (e.g., to 200 C or even 300 C), and operation in a radiation-rich environment (e.g., space). The suitability of SiGe BiCMOS technology for extreme environment electronics applications is assessed in this work. The suitability of SiGe HBTs for use in high-temperature electronics applications is first investigated. SiGe HBTs are shown to exhibit sufficient current gain, frequency response, breakdown voltage, achieve acceptable device reliability, and improved low-frequency noise, at temperatures as high as 200-300 C. A comprehensive investigation of substrate bias effects on device performance, thermal properties, and reliability of vertical SiGe HBTs fabricated on CMOS-compatible, thin-film SOI, is presented. The impact of 63 MeV protons on these vertical SiGe HBTs fabricated on a CMOS-compatible SOI is then investigated. Proton irradiation creates G/R trap centers in SOI SiGe HBTs, creating positive charge at the buried oxide interface, effectively delaying the onset of the Kirk effect at high current density, which increases the frequency response of SOI SiGe HBTs following radiation. The thermodynamic stability of device-relevant epitaxial SiGe strained layers under proton irradiation is also investigated using x-ray diffraction techniques. Irradiation with 63 MeV protons is found to introduce no significant microdefects into the SiGe thin films, regardless of the starting stability condition of the SiGe film, and thus does not appear to be an issue for the use of SiGe HBT technology in emerging space systems. CMOS device reliability for emerging cryogenic space electronics applications is also assessed. CMOS device performance improves with cooling, however, CMOS device reliability becomes worse at decreased temperatures due to aggravated hot-carrier effects. The device lifetime is found to be a strong function of gate length, suggesting that design tradeoffs are inevitable.

The scope of extreme-environment diving defined within this work encompasses diving modes outside of the generally accepted no-decompression, open-circuit, compressed-air diving limits on selfcontained underwater breathing apparatus (scuba) in temperate or warmer waters. Extreme-environment diving is scientifically and politically interesting. The scientific diving operational safety and medical framework is the cornerstone from which diving takes place in the scientific community. From this effective baseline, as evidenced by decades of very low DCS incidence rates, the question of whether compressed air is the best breathing medium under pressure was addressed with findings indicating that in certain depth ranges a higher fraction of oxygen (while not exceeding a PC 2 of 1.6 ATA) and a lower fraction of nitrogen result in extended bottom times and a more efficient decompression. Extremeenvironment diving under ice presents a set of physiological. equipment, training and operational challenges beyond regular diving that have also been met through almost 50 years of experience as an underwater research tool. Diving modes such as mixed-gas, surface-supplied diving with helmets may mitigate risk factors that the diver incurs as a result of depth, inert gas narcosis or gas consumption. A close approximation of inert gas loading and decompression status monitoring is a function met by dive computers, a necessity in particular when the diver ventures outside of the single-dive profile into the realm of multi-level, multi-day repetitive diving or decompression diving. The monitoring of decompression status in extreme environments is now done exclusively through the use of dive computers and evaluations of the performance of regulators under ice have determined the characteristics of the next generation of life-support equipment for extreme-environment diving for science. These polar, deep and contaminated water environments require risk assessment that analyzes hazards such as cold stress, hydration, overheating, narcosis, equipment performance and decompression sickness. Scientific diving is a valuable research tool that has become an integral methodology in the pursuit of scientific questions in extreme environments of polar regions, in contaminated waters, and at depth.

Technological progress in recent decades has led to sensor networks and robotic explorers becoming principal tools for investigation of remote or "hostile" environments where it is difficult, if not impossible for humans to intervene. These situations include deep ocean and space environments where the devices can be subject to extreme pressures, temperatures and radiation levels. It is a costly enterprise to deploy an instrument in such settings and therefore reliable operation and ease of use are requisite features to build into the basic fabric of the machine. This thesis describes the design and implementation of a modular machine system based on a peer-to-peer, decentralised network topology where the power supply and electronic hardware resources are distributed homogeneously throughout a network of nodes. Embedded within each node is a minimal, low-power single board computer on which a real-time operating system and MicroCANopen protocol stack are operating to realise a standard interface to the network. The network is based on a grid paradigm where nodes act as resource producers and consumers, sharing information so that the machine system as a whole can perform tasks. The resulting architecture supports "plug-and-play" flexibility, to allow users or system developers to reconfigure or expand its capabilities by adding/removing nodes at a later time. An immediate application of this instrument is in-situ sampling of microbes in extreme aqueous habitats. The microbial sampler is targeted at providing improved sampling capabilities when performing physical, chemical and biological investigations in deep- ocean hydrothermal vent environments. At these depths the instrument is subject to immense pressures of many thousand pounds per square inch, where superheated, corrosive, mineral-loaded vent fluids mix with near-freezing seawater. In the longer term, it is anticipated that this flexible, open interface architecture on which the microbial sampler instrument is based will be applicable more generally to other sectors, including commercial and scientific markets.

Microelectrodes have been found to be a valuable tool in a variety of analytical studies. Their advantages over macro-sized electrodes are well known, including their enhanced mass transport properties (due to their ubiquitous hemispherical diffusion) which lead to steady state responses without external convection. They also exhibit high signal-to-noise ratios (greater sensitivities), furthering their analytical application. Microelectrode arrays are analytical devices with multiple electrodes. There are suitable for practical sensing with all the benefits of microelectrodes but with greater currents, leading to greater ease of measurement. To produce a reliable electroanalytical device the microelectrode response must be reproducible, a fundamental property based on the quality control of their production. Square microelectrode and array fabrication techniques have been developed for this purpose. This research discusses the fabrication and development of closely spaced arrays of square microelectrodes. Simulated and measured responses are compared and used to characterize electrode and array responses by cyclic voltammetry, electrical impedance spectroscopy and current-time transients. Measurements on variably spaced arrays allow insight into overlap of hemispherical diffusion from individual electrodes and the subsequent effect including peak current output on the array device. By studying these devices key insights into the mass transport properties of single square microelectrodes and microelectrode arrays were gained. This study also prepares and develops microelectrodes from materials appropriate for use in the extreme environments of molten salts and concentrated nitric acid solutions. These robust electrodes were developed for use in hydro- and pyro-chemical techniques for nuclear fuel reprocessing. These results demonstrate the practical uses for microelectrode systems across a wide range of chemical systems and in extreme conditions.

Wide bandgap semiconductor photodiodes were investigated for their suitability as radiation detectors for high temperature applications (≥ 20 °C), through measurements, calculations of key parameters of the devices, and relating the results back to the material, geometry of the detectors, environment under which the detectors were investigated, and previously published work. Three families of photodiodes were examined. 4H-SiC vertical Schottky UV photodiodes with Ni2Si interdigitated contacts were characterised for their response under dark and UV illumination. Electrical characterisation up to 120 °C and room temperature responsivity measurements (210 nm to 380 nm) suggested that the devices could operate at low UV light intensities, even at high visible and IR backgrounds without the use of filters, and at high temperatures. 4H-SiC Schottky photodiode detector arrays with planar thin NiSi contacts were investigated for X-ray (≤ 35 keV) detection and photon counting spectroscopy at 33 °C. The electrical characterisation of the devices up to 140 °C and subsequent analysis suggested that the devices are likely to operate as high temperature X-ray spectrometers. Results characterising GaAs p+-i-n+ mesa photodiode detectors for their room temperature visible and near infrared responsivity (580 nm to 870 nm), as well as their high temperature (≤ 60 °C) X-ray detection performance (at 5.9 keV) are presented. GaAs p+-i-n+ mesa photodiodes were also shown to be suitable for β- particle (electron) spectroscopy and X-ray fluorescence spectroscopy (≤ 21 keV) at 33 °C. The X-ray and electron spectroscopic measurements were supported by a comprehensive treatment of the noise components in charge sensitive preamplifiers. Calculations showed the potential benefits of using a SiC, rather than Si, JFET as the input transistor of such a preamplifier operating at high temperatures. The spectroscopic measurements, using both the 4H-SiC and GaAs photodiodes, are presented along with noise analysis to detangle the different noise components present in the reported spectrometers, identify the dominant source of noise, and suggest potential improvements for future spectrometers using the reported devices.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2011.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 270-275).
The controllable properties of magnetorheological (MR) fluids offer reliable and efficient actuation means to a number of far-ranging engineering applications. In this thesis we are motivated by the applications of MR fluids in oil & gas exploration and production. These applications also bring about a number of operational requirements for the fluid such as generating large magnetically induced shift in rheological properties with tolerance to elevated temperatures and low fluid density in order to maintain manageable hydrostatic downhole pressures. In this thesis we investigate a number of these fluid design constraints. Firstly, the evolution of the rheological properties of MR fluids over a wide range of magnetic field and temperature was investigated. A magnetorheometry fixture with a unique combination of high-field and high-temperature capability was manufactured. With the experimental measurements and the results from a numerical model of interparticle magnetic interaction, a scaling law was identified between the applied magnetic field and the resulting MR yield stress. The aggregation phenomena and the evolution of fluid microstructure were also investigated in microfluidic geometries with strong particle-wall interactions. The results of this study highlighted design features and operational techniques that can improve the performance of MR fluid valves. Investigation of fluid flow in non-uniform magnetic fields showed that in these regions the motion of the particle phase is governed by a balance between hydrodynamic and magnetophoretic forces. Finally, the flow of MR fluids in spatially-inhomogeneous magnetic and deformation fields was studied. A slit-flow magnetorheometer was manufactured to measure the bulk MR response of the fluid under non-uniform fields. In order to understand the parameters governing these flows and to develop a predictive tool for further investigations, a two-fluid suspension-balance constitutive model was developed which captures the key features of multi-phase flow and fluid anisotropy. The model was numerically implemented using the finite element method and was used to study the transport of MR fluids in spatially-inhomogeneous flows such as those encountered in contraction and expansion channels. This model provides insight into the design and optimization of MR fluid devices that can enhance the magnetically-controlled gain in flow resistance under downhole conditions.
by Murat Ocalan.
Ph.D.

Hem desenvolupat aquesta tesi en el context d'intentar comprendre la interacció entre partícules d'alta energia i camps magnètics en escenaris astrofísics extrems, com púlsars i nebuloses. Per a això, hem emprat simulacions dutes a terme amb les eines en desenvolupament per a futures anàlisis de dades en raigs gamma i observacions de l'instrument LAT a bord del satèl·lit Fermi. En particular, ens concentrem en tres fonts; la nebulosa i el púlsar del Cranc, el romanent de supernova SNR G39.2-0.3, i el cúmul estel·lar Westerlund 2.
Hemos desarrollado esta tesis en el contexto de intentar comprender la interacción entre partículas de alta energía y campos magnéticos en escenarios astrofísicos extremos, como púlsares y nebulosas. Para ello, hemos empleado simulaciones llevadas a cabo con las herramientas en desarrollo para futuros análisis de datos en rayos gamma y observaciones del instrumento LAT abordo del satélite Fermi. En particular, nos concentramos en tres fuentes; la nebulosa y el púlsar del Cangrejo, el remanente de supernova SNR G39.2-0.3, y el cúmulo estelar Westerlund 2.
We developed this thesis in the context of understanding the interaction of high-energy particles and magnetic fields in extreme astrophysical environments, like pulsars and pulsar wind nebulae. We employed both simulations implemented with the tools currently in development for future gamma-ray data analysis and observations from the LAT instrument onboard the Fermi satellite. In particular, we focused on three sources, the Crab Nebula and pulsar, the supernova remnant SNR G39.2-0.3, and the Westerlund 2 stellar cluster.
Universitat Autònoma de Barcelona. Programa de Doctorat en Física

Thesis (Ph.D.)--Biology, Georgia Institute of Technology, 2008.
Committee Chair: Patricia Sobecky; Committee Member: Ellery Ingall; Committee Member: Jim Spain; Committee Member: Martial Taillefert; Committee Member: Thomas DiChristina.

A number of MIR sensing platforms and methods were developed in this research work demonstrating potential applicability of MIR spectroscopy for studying hydrocarbon systems in extreme environments. First of all, the quantitative determination of the diamondoid compound adamantane in organic media utilizing IR-ATR spectroscopy at waveguide surfaces was established. The developed analytical strategy further enabled the successful detection of adamantane in real world crude oil samples. These reported efforts provide a promising outlook for detection and monitoring of diamondoid constituents in naturally occurring crudes and petroleum samples. IR-ATR spectroscopy was further utilized for evaluating and characterizing distribution, variations, and origin of carbonate minerals within sediment formations surrounding a hydrocarbon seep site - MC 118 in the Gulf of Mexico. An analytical model for direct detection of 13C-depleted authigenic carbonates associated with cold seep ecosystems was constructed. Potential applicability of IR-ATR spectroscopy as direct on-ship - and in future in situ - analytical tool for characterizing hydrocarbon seep sites was demonstrated. MIR evanescent field absorption spectroscopy was also utilized to expand the understanding on the role of surfactants during gas hydrate formation at surfaces. This experimental method allowed detailed spectroscopic observations of detergent-related surface processes during SDS mediated gas hydrate formation. The obtained IR data enabled proposing a mechanism by which SDS decreases the induction time for hydrate nucleation, and promotes hydrate formation. Potential of MIR fiberoptic evanescent field spectroscopy for studying surface effects during gas hydrate nucleation and growth was demonstrated. Next, quantifying trace amounts of water content in hexane using MIR evanescent field absorption spectroscopy is presented. The improvement in sensitivity and of limit of detection was obtained by coating an optical fiber with layer of a hydrophilic polymer. The application of the polymer layer has enabled the on-line MIR detection of water in hexane at low ppm levels. These results indicate that the MIR evanescent filed spectroscopy method shows potential for in-situ detection and monitoring of water in industrial oils and petroleum products. Finally, quantification of trace amounts of oil content in water using MIR evanescent field absorption spectroscopy is reported. Unmodified and modified with grafted hydrophobic polymer layer silver halide optical fibers were employed for the measurements. The surface modification of the fiber has enabled the on-line MIR analysis of crude oil in water at the low ppb level. Potential application of MIR fiber-optic evanescent field spectroscopy using polymer modified waveguides toward in-situ low level detection of crude oil in open waters was demonstrated.

This thesis integrates physiological and evolutionary ecology to quantify effects of hypoxia (low oxygen) on the energetic and life-history traits of the mouth brooding African cichlid, Pseudocrenilabrus multicolor. A field survey of 10 populations in Uganda indicated that dissolved oxygen (DO) is a strong predictor of interdemic variation in life-history traits. Females from low-DO sites were characterized by smaller size at maturity, and more, smaller-sized offspring than females from high DO, supporting body-size surface area predictions under hypoxia. In lab rearing and acclimation experiments, embryos and juveniles held under hypoxia and normoxia did not differ in size or survival, suggesting genetic and/or maternal effects while the young are in the mouth. Once released, juvenile growth was slower under hypoxia. In adult P. multicolor, there was evidence for effects of long-term exposure to chronic hypoxia on energetics and mouth brooding. Critical oxygen tension, an index of hypoxia tolerance, was lower in fish reared under hypoxia and similarly plastic across populations. Estimates of resting routine metabolic rate and marginal metabolic scope in the same fish indicated both plastic and genetic components of metabolic response to hypoxia. Both acclimation and rearing studies demonstrated that mouth brooding is energetically expensive and more so under hypoxia. Standard metabolic rates were ~48% higher in brooding females compared to post-brooding females regardless of DO acclimation. However, the length of the brooding period (time in the mouth) was shorter and development faster for young brooded under hypoxia, a potential strategy for dealing with the expense of offspring care under hypoxia. An implicit optimality model created to predict optimal body size in response to the combined influences of oxygen and predator pressure supported our empirical findings for smaller body size under hypoxia. An integration of this work suggests that DO pl
L'hypoxie (un faible taux d'oxygène dissout dans l'eau - OD) constitue un stress environnemental de plus en plus présent auquel font face plusieurs organismes aquatiques à l'échelle planétaire. Cette thèse intègre à la fois l'écologie physiologique et évolutive afin de quantifier les effets de l'hypoxie sur les traits énergétiques et d'histoire de vie d'un cichlidé africain, Pseudocrenilabrus multicolor, une espèce avec un haut taux de plasticité phénotypique pratiquant la couvaison buccale. Un inventaire de terrain a révélé que l'OD est un bon indicateur de variation « inter-groupe » (interdemic) des traits de vie. Les femelles P. multicolor provenant de sites où le taux d'OD est faible se caractérisent par une plus petite taille à maturité, ainsi que par des portées plus abondantes mais constituées d'une progéniture de plus petite taille que les femelles provenant de sites à haute teneur en OD. Ceci supporte la prédiction, basée sur les principes physiologiques, que l'hypoxie engendre une taille plus petite. Lors d'élevages en laboratoire et d'expériences d'acclimatation, la taille et la survie des embryons et des juvéniles maintenus sous des conditions d'hypoxie et sous des concentrations normales en OD ne différaient pas. Ces résultats suggèrent que ces traits pourraient être influencés par la génétique et/ou par des effets maternels. Une fois les juvéniles relâchés par la mère, la croissance était plus lente sous un contexte d'hypoxie. Chez les individus adultes de P. multicolor, nous avons observé des preuves des effets de l'exposition à long-terme à l'hypoxie sur les flux et la distribution d'énergie, ainsi que sur la couvaison buccale. La tension critique en oxygène, un indice de tolérance à l'hypoxie, était plus basse chez les poissons élevés dans des conditions d'hypoxie, mais la plasticité y étant associée était semblable entre les populations. Les estimations du taux métabolique de l

Star clusters are fundamental building blocks of galaxies, and yet very little is known about young star clusters as they evolve unseen in the embedded phase. Using four band photometry of star clusters in NGC 3256 we are able to determine the chance of survival for star clusters over the course of the embedded phase, and combined with other data sets show a relationship between survivability and the star formation rate density. We also perform a detailed study of the XUV-disc phenomenon and their cluster population. Firstly we measure the broad properties of several XUV-disc galaxies in comparison to normal galaxies using surface photometry and individual object photometry. We reveal that these galaxies show a range of properties, some showing sharp edges in their Hα profiles whilst others do not, although all show a smoothly declining UV profile which extends beyond the optical edge of the disc. The HII regions in these outer discs appear to have luminosities consistent with single ionising O-type stars and have implied mass which suggest that the formation of the most massive stars is governed by stochastic processes. We also examine the spectra of HII regions in two XUV-disc galaxies, NGC 4625 and NGC 3621. Both galaxies show a shallower abundance gradient in the outer disc compared to the inner disc, yet NGC 4625 also shows a discontinuity close to the optical edge. This is of particular interest as NGC 3621 shows no sharp Hα and no discontinuity whilst NGC 4625 displays both of these features. The HII regions of both of these galaxies show properties different to bright inner disc HII regions, making abundance calculations less reliable.

Doctor of Philosophy
Department of Biology
Michael Tobler
Extremophiles are organisms with the ability to survive in environments characterized by strong physicochemical stressors lethal to most other organisms, providing excellent models to further our understanding of life's capacities and limitations to deal with far-from-average conditions. I studied how physiological processes varied among fish residing in starkly different environmental conditions to understand how organisms cope with extreme environments and disentangle the roles of short-term plastic responses and evolved population differences in shaping physiological responses. I used the Poecilia mexicana model, a series of extremophile fish populations that has colonized toxic hydrogen sulfide (H₂S) rich springs and caves, to address three major objectives: (1) I investigated the energetic consequences of life in extreme environments and tested whether predicted reductions in organismal energy demands evolved repeatedly along replicated environmental gradients. (2) I characterized variation in gene expression among populations and organs to test for interactive effects between different stressors and identify potential physiological mechanisms underlying adaptation to H₂S and cave environments. (3) I conducted common garden and H₂S-exposure experiments to test how evolutionary change and plasticity interact to shape variation in gene expression observed in nature. To address these objectives, I measured variation in metabolic physiology and quantified variation in physiological processes through genome-wide gene expression analyses. I found that adaptation to extreme environments directly impacts energy metabolism, with fish living in extreme environments consistently expending less energy overall. Reductions in energy demand have evolved in convergence and were primarily mediated through a life history shift (reduction in body mass). The quantification of gene expression across divergent habitats and organs revealed organ-specific physiological responses in H₂S-rich and cave habitats. Gene expression variation in the relevant genes was primarily shaped by evolutionary change in gene regulation, and ancestral plastic responses play a minor role in causing the observed expression differences between replicated sulfidic and nonsulfidic populations in nature. Overall, my research has implications for understanding the capacities and constraints that shape life in extreme environments and aids in our understanding of modifications in physiological pathways mediating adaptation to elevated H₂S and perpetual darkness.

Gas sensitive metal oxide semiconductor capacitors, utilising silicon carbide have been demonstrated for a range of applications, particularly in exhaust and combustion monitoring. As part of the control system, sensors play a pivotal role in the closed loop control of flue gas cleaning processes in power plants. Silicon Carbide Metal Oxide Semiconductor (SiC-MOS) gas sensors have previously demonstrated a response to a range of gas species including; H:, O2 and H2S. Because of the sensing mechanism responsible for the response of these sensors, these structures often limited to applications of sensing in a single gas ambient. For multiple gas species present in a mixture, it is not possible to uniquely identify the contribution from each individual gas species and so an array of sensors is required. This thesis concerns the fabrication of monolithic gas sensors and characterisation at harsh environments.

Research purpose The purpose of this study is to examine the extent to which both employees and leaders in extreme environments perceive the same levels of safety participation. Furthermore, this study examines the association between empowering leadership and team performance as well as empowering leadership and safety participation. Research design, approach and methods This study follows a quantitative approach as its main purpose is to establish relationships between constructs. As such, correlations and multiple regression analyses were conducted. Convenience sampling was applied to obtain the data. Firefighters and their immediate line officers (lieutenants) were surveyed. Five fire departments in small to medium cities were chosen in the Great Lakes and south-eastern regions in the United States (US). Questionnaires were distributed to 263 firemen, of which 186 were firefighters and 78 were their line officers/lieutenants. Main findings Results indicated that a positive association does not exist between firefighters' perceptions of safety participation and their leaders' perception of safety participation when control variables are added. Therefore, no significant relationship exists between firefighters' perceptions of safety participation and their leaders' perception of safety participation. Furthermore, the results also showed a positive association does not exist between empowering leadership and safety participation when control variables are added. Consequently, no significant relationship exists between firefighters' reports of empowering leadership and lieutenants' reports of safety participation. Lastly, regarding empowering leadership and team performance, the results did not support a direct relationship between these two constructs. Limitations The results should be interpreted bearing in mind that they are applicable to the United States of America and may not be generalised to the South African context. Additionally, very little research has been conducted on empowering leadership and safety behaviour in extreme environments, and therefore the literature review was limited to other organisational environments. Lastly, only three cultural groups (White, Black and Hispanic) and only men participated in this study, so results may not be generalisable to other demographic groups. The study was only positioned in extreme environments, specifically in firefighting, therefore it is unclear whether the results can be generalised to other work environments. Future Research It is suggested that this study is replicated, firstly because little research has been done in extreme environments but, secondly, that it also be specifically replicated in South Africa. Indicated by the data, a lieutenant's age has a positive association with how he perceives his team's safety participation. This could be due to various reasons. For example, the more experienced the lieutenant the more comfortable he gets towards the extreme environment. Lastly, it is suggested that research is conducted to determine other leadership styles which could be effective in extreme environments. Conclusion Insight was given into the empowering leadership style in terms of team performance and safety behaviour. Furthermore, the relation between firefighters' perceptions of safety participation and their leaders' perceptions of safety participation was not confirmed.
Dissertation (MCom)--University of Pretoria, 2017.
Human Resource Management
MCom
Unrestricted

Humans are motivated to explore, investigate, and learn about the world around them; in the process of doing so, some groups work and live in environments described as extreme and unusual. Using thematic content analysis, the goal of this dissertation was to better understand coping strategies (Folkman & Lazarus, 1980) and motive images (Winter, 1994) expressed in narratives of four highly skilled groups: astronauts, high-altitude mountaineers, search and rescue (SAR) crews, and small military combat units. Taken together, the findings provided insight into the similarities and differences among groups that work in extreme environments. All four teams relied on problem-focused compared to emotion-focused coping strategies. Soldiers were least likely to mention Planful Problem Solving and most likely to mention Supernatural Protection and Confrontation when compared to the other groups; on the other hand, mountaineers were least likely to mention Seeking Social Support and most likely to mention Self-Control. In relation to motive imagery, all four groups were primarily motivated by need for Achievement, followed by need for Affiliation and need for Power. Soldiers had the highest level of all three motives; astronauts and SAR crews do not differ on any of the three. Differences across occupational and environment type, leadership status, gender, and mission phases were examined. The study provided the first empirical evidence, across mission phases, on how high-altitude mountaineers and SAR crews cope with problems and express their motives. Implications of the research, limitations, and possible future directions were discussed.

SiGe BiCMOS technology has many advantageous properties that, when leveraged, enable circuit design for extreme environments. This work will focus on designs targeted for space system avioinics platforms under the NASA ETDP program. The program specifications include operation under temperatures ranging from -180 C to +125 C and with radiation tolerance up to total ionizing dose of 100 krad with built-in single-event latch-up tolerance. To the author's knowledge, this work presents the first design and measurement of a wide temperature range enabled, radiation tolerant as built, RS-485 wireline transceiver in SiGe BiCMOS technology. This work also includes design and testing of a charge amplification channel front-end intended to act as the interface between a piezoelectric sensor and an ADC. An additional feature is the design and testing of a 50 Ohm output buffer utilized for testing of components in a lab setting.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2011.
Cataloged from PDF version of thesis. Vita.
Includes bibliographical references (p. 52-55).
Neck and back pain is one of the most common musculoskeletal complaints in personnel in variable acceleration environments such as astronauts and military pilots. Ultrasound is known for dynamic imaging and diagnostic workup of the axial and appendicular skeleton, but is not currently used to image the cervical spine, the injury of which may change the biomechanics of the cervical vertebrae, which CT and MRI (the current gold standard in cervical spine imaging) are poor at capturing. To validate ultrasound as a modality for imaging dynamic motion of the cervical spine several experiments were performed in static and dynamic human and animal (ovine) models: 1. Static analysis of ex-vivo ovine cervical spines imaged by ultrasound, MRI, and CT demonstrated that the imaging modality affected the measured intervertebral disc height (p<0.01); similar evaluation was done in-vivo in Emergency Department patients who received a CT scan as part of their clinical course that showed that ultrasound could fit into existing clinical workflows. 2. Dynamic analysis of isolated ex-vivo ovine cervical spinal segments intervertebral disc displacement with a mounted ultrasound probe demonstrated a measurement uncertainty of ± 0.2 mm and no bias at low frequency sinusoidal spinal displacement. A similar evaluation in-vivo with humans with an ultrasound probe mounted on a cervical-collar found a 0.8-1.3 mm amount of cervical spine distraction from the C4-5 Functional Spinal Unit. In human cadavers subjected to passive flexion and extension of the cervical spine, ultrasound measurements of the relative flexion/extension angles between consecutive cervical vertebrae were similar to fluoroscopy. 3. Ultrasound was able to record dynamic motion of the cervical spine in-vivo in running on a treadmill, during parabolic flight, and traveling over a rough road in a military vehicle. The ultrasound methods developed and tested in this thesis could provide an inexpensive, portable and safe technique that can identify and characterize cervical spine anatomy and pathology.
Funding Acknowledgment: National Space Biomedical Research Institute, Army Research Office, Children's Hospital Orthopedic Surgery Foundation
by Daniel Miller Buckland.
Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2009.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 142-146).
The complex chemomechanical behavior of nanomaterials under extreme thermal and mechanical environments is of interest for a range of basic science and defense applications. By the limitation of experimental approaches for objects of nanometer, novel computational methods have been developed to investigate such phenomena in nanomaterials under extreme environments. In this thesis, novel continuum and atomistic mechanical modeling and simulations are implemented and constructed for the analysis of the chemomechanical behavior of the dissimilar nano-scale metals, Nickel and Aluminum under a variety of thermal and mechanical stimuli. These studies form the basis of preliminary research on the predictive design principles for reactive polymer nanocomposites.
by Hansohl Cho.
S.M.

This is a cross-disciplinary thesis consisting of both acoustics science research and practice-led research focused on improvised music performance. In very different ways, both types of research focus on how a person’s surrounding environment affects voice production. The thesis describes two experiments: a behavioural laboratory talking experiment and singing practice experiment with research outcomes including an original framework for singing practice and a recorded work of ensemble improvised music. Key aspects of both experiments are (i) vocal production response to the acoustic environment, (ii) acoustics that optimise the environment for a singer or talker, and (iii) the acoustic environment created by a retroreflective array whereby sound is reflected back to the person. The experiments can be summarised as follows: 1. A behavioural laboratory experiment A talking experiment that investigates how the sound of one’s own voice (autophony), with alterations in gain and spectral balance, influences conversational speech production. The experiment addressed the question: can acoustic treatments with a frequency bias, like a retroreflective array, influence voice production, optimising a room for comfortable conversing? 2. A practice-led singing experiment A singing experiment was completed in three stages. Stage one (i) was the design of a practice framework that facilitated the discovery and creative development of singing techniques and musical materials. The design incorporated empirical research about autophony and voice production response to room reflections and environment sound and an approach to skill acquisition based on the ecological dynamics theory called the constraints-led approach. Stage two (ii) was fifteen-months of recorded self-regulated singing practice within the practice framework. Stage three (iii) applied the vocal skills and musical materials discovered and developed in stage two to recorded ensemble improvisation.

I mari profondi comprendono oltre il 95 % della biosfera globale. La scoperta della porzione profonda degli oceani è ancora agli esordi, ed è considerata una delle attuali sfide scientifiche. Gli ambienti profondi sono considrati estremi, in quanto oscuri, tipicamente freddi e caratterizzati da elevate pressioni e forte scarsità di risorse trofiche. Il presente studio fornisce nuove informazioni sui fattori che controllano il funzionamento degli ecosistemi bentonici dei mari profondi a scala globale. I sedimenti oggetto di studio sono stati raccolti usando le più sofisticate tecnologie attualmente disponibili, coprendo un vasto range di aree e profondità oceaniche (range di profondità, 1000 - 10000 m). Un nuovo metodo molecolare è stato sviluppato ed ha permesso di quantificare per la prima volta l'impatto dei virus su diversi gruppi microbici. Nei sedimenti di mare profondo, a scala globale, i virus sono risultati infettare e uccidere preferenzialmente gli archaea, piuttosto che i batteri. Per lungo tempo si è ritenuto che gli archaea svolgessero un ruolo limitato nei cicli biogeochimici globali. Tuttavia, i risultati da noi ottenuti dimostrano che gli Archaea nelle profondità oceaniche contribuiscono notevolmente ai cicli biogeochimici globali di carbonio e azoto. Tra gli ecosistemi di mare profondo analizzati, le fosse oceaniche di profondità estreme hanno presentato caratteristiche peculiari, marcatamente differenti dalle circostanti piane abissali. Infatti, queste aree sono risultate agire come bioreattori di attività microbica, con accelerazione delle interazioni virus-ospite in grado di influenze la biodiversità e funzionamento degli ecosistemi bentonici adali. Nel complesso, i risultati discussi in questo lavoro rivelano nuovi ed inaspettati meccanismi di controllo delle dinamiche microbiche negli ecosistemi di mare profondo, che possono avere grande impatto sulla attuale concezione del funzionamento degli oceani. Inoltre, l’innovativa tecnica molecolare qui proposta, sviluppata specificamente per discriminare le infezioni virali su diversi target biologici, ha la possibilità di aprire nuovi filoni di ricerca nelle indagini sulle interazioni specifiche virus-ospite in diversi ecosistemi e in tutti i settori, non solo in campo ambientale.
The Deep Seas comprise more than 95% of the global Biosphere. The deep portion of the oceans is still largely unknown and its discovery is considered one of the last scientific challenges. Here the environmental conditions are extreme, as the deep sea is dark, typically cold and characterized by organic nutrient limitation and high pressures. The present work provides novel insights into the factors controlling the functioning of deep-sea benthic ecosystems at global scale. Deep-sea sediment samples were collected using the most sophisticated technologies available, across a wide range of oceanic regions and depths (depth range from 1000 down to ca. 10000 m). A new molecular method was developed and allowed investigating for the first time the selectivity of viral infection on different groups of microbial hosts. We report here that viruses preferentially infected and killed Archaea rather than Bacteria in deep-sea ecosystems worldwide. Archaea have been assumed for a long time to play a limited role in global biogeochemical cycles. However results reported here indicate that Archaea provide an important contribution to the global carbon and nitrogen cycling in the deep ocean interior. Among the deep-sea ecosystems investigated in the present study, hadal trenches were characterized by peculiar conditions, highly different from the surrounding abyssal plain. Indeed, they acted as bioreactors of microbial activity, with enhanced virus-host interactions significantly influencing benthic biodiversity and ecosystem functioning. Overall, the results of this investigation disclose new and unexpected mechanisms controlling microbial dynamics in the deep-sea ecosystems, which can have major impact on the current view of the functioning of the global oceans. Moreover, the novel molecular technique proposed here, specifically developed for discriminating the viral infections on different biological targets, has the potential to open new research perspectives in the investigation of the specific interactions between viruses and their hosts in a wide range of habitats and ecosystems, and not only in environmental studies.

This thesis investigated the behaviour of cold-formed steel compression members under extreme temperature environments using experimental and numerical studies. It proposed both new and improved design models for (1) the elevated and sub-zero temperature mechanical properties of cold-formed steels and (2) the compression capacities of cold-formed steel members exposed to uniform and non-uniform elevated temperatures and uniform sub-zero temperatures. The proposed design models are likely to be adopted by the Australian and American cold-formed steel structures standards, while the new knowledge will enable increased applications of cold-formed steel members in the building industry.

Proglacial environments, formed by glacier retreat, exhibit distinct characteristics in discharge, water temperature, water residence time, and dissolved ion, carbon, and suspended sediment concentrations. The unnamed alpine glacier at the headwaters of the Wheaton River, Yukon, Canada, provides an ideal setting to compare deglaciation processes that result in three different proglacial environments. The glacier has evolved from occupying one large catchment (~4 km 2) to two smaller catchments (each ~2 km 2) via glacier thinning and net mass loss, forming two lobes separated by a medial moraine. Field observations revealed neither crevasses nor evidence of subglacial drainage outlets and suggested this glacier had a non-temperate thermal regime with meltwater predominantly flowing from supraglacial and ice marginal sources. Climate and bedrock geology were similar for the subcatchments, providing a natural laboratory to compare deglaciation processes. This study compared the hydrology and biogeochemistry of three outlet streams from this glacier: one stream drained a proglacial lake which is fed by meltwater from the lower west lobe, a second stream drained the upper west lobe, and a third stream was the major drainage outlet for the east lobe. Hydrologic monitoring over the 2006 melt season (June-August) and analyses of water samples for dissolved ion content and carbon indicated that the meltwaters are dominated by Ca 2+ and HCO 3-, which are derived from biogeochemical weathering of crustal materials. The study demonstrated that the presence of the proglacial lake, which acted as a meltwater reservoir, measurably modified meltwater residence time, water temperature, water chemistry, and bacterial biomass relative to the proglacial streams. Rock:water interaction between meltwater and medial morainal sediment and fine-grained, reactive glacial flour suspended in the streams and the lake water column also enhanced biogeochemical weathering within the catchment. Thus, this study provided a small-scale example for how differences in proglacial environments and water flow paths affect headwater hydrology and biogeochemistry. This study was the first of its kind in the Coast Mountains, Yukon, Canada, and results presented here aid in the understanding of how proglacial environments created by climate-induced glacier retreat affect hydrochemistry, hydrology, and carbon dynamics in remote high elevation environments.

The main part of the introduction illustrates the health care provision made in the past for workforces of the oil and gas industries functioning in remote places usually associated with an environmental hazard. Much of the past work has been carried out in the North Sea and the provision made there has been reviewed in some detail together with the gradual development of health care in the United Arab Emirates for both the offshore and the onshore oil-related workforces. There follows a short review of the provision made for two analogous situations - Newfoundland and Labrador and the British Antarctic Territories - since the developments there are of direct relevance to the Middle East situation. The main environmental hazard in the Middle East is heat and so the physiology and pathology of thermal balance in man are addressed in some detail. The first study is on the identification of the particular thermal problem which occurs in the offshore workings on the Abu Dhabi oil and gas companies, namely heat cramps. This problems had not been previously identified and the work done in determining its presence and its management is duly reported, indicating the problems of accepting health education material designed for one environment by another. In the development of systems of health care for both oil and non-oil related remote populations, the importance of training of the population at risk has been repeatedly emphasised. The perceived problems in that area are skill retention by laymen and the acceptance of the guidelines of the European and US Resuscitation Councils. A second study was therefore carried out to examine skill retention in laymen together with the feasibility of carrying out resuscitation manoeuvres in high temperatures.

The objective of this dissertation is the design, development, and experimental evaluation of novel algorithms and reconfigurable radio architectures for spectrally efficient cognitive networking in terrestrial, airborne, and underwater environments. Next-generation wireless communication architectures and networking protocols that maximize spectrum utilization efficiency in congested/contested or low-spectral availability (extreme) communication environments can enable a rich body of applications with unprecedented societal impact. In recent years, underwater wireless networks have attracted significant attention for military and commercial applications including oceanographic data collection, disaster prevention, tactical surveillance, offshore exploration, and pollution monitoring. Unmanned aerial systems that are autonomously networked and fully mobile can assist humans in extreme or difficult-to-reach environments and provide cost-effective wireless connectivity for devices without infrastructure coverage.

Cognitive radio (CR) has emerged as a promising technology to maximize spectral efficiency in dynamically changing communication environments by adaptively reconfiguring radio communication parameters. At the same time, the fast developing technology of software-defined radio (SDR) platforms has enabled hardware realization of cognitive radio algorithms for opportunistic spectrum access. However, existing algorithmic designs and protocols for shared spectrum access do not effectively capture the interdependencies between radio parameters at the physical (PHY), medium-access control (MAC), and network (NET) layers of the network protocol stack. In addition, existing off-the-shelf radio platforms and SDR programmable architectures are far from fulfilling runtime adaptation and reconfiguration across PHY, MAC, and NET layers. Spectrum allocation in cognitive networks with multi-hop communication requirements depends on the location, network traffic load, and interference profile at each network node. As a result, the development and implementation of algorithms and cross-layer reconfigurable radio platforms that can jointly treat space, time, and frequency as a unified resource to be dynamically optimized according to inter- and intra-network interference constraints is of fundamental importance.

In the next chapters, we present novel algorithmic and software/hardware implementation developments toward the deployment of spectrally efficient terrestrial, airborne, and underwater wireless networks. In Chapter 1 we review the state-of-art in commercially available SDR platforms, describe their software and hardware capabilities, and classify them based on their ability to enable rapid prototyping and advance experimental research in wireless networks. Chapter 2 discusses system design and implementation details toward real-time evaluation of a software-radio platform for all-spectrum cognitive channelization in the presence of narrowband or wideband primary stations. All-spectrum channelization is achieved by designing maximum signal-to-interference-plus-noise ratio (SINR) waveforms that span the whole continuum of the device-accessible spectrum, while satisfying peak power and interference temperature (IT) constraints for the secondary and primary users, respectively. In Chapter 3, we introduce the concept of all-spectrum channelization based on max-SINR optimized sparse-binary waveforms, we propose optimal and suboptimal waveform design algorithms, and evaluate their SINR and bit-error-rate (BER) performance in an SDR testbed. Chapter 4 considers the problem of channel estimation with minimal pilot signaling in multi-cell multi-user multi-input multi-output (MIMO) systems with very large antenna arrays at the base station, and proposes a least-squares (LS)-type algorithm that iteratively extracts channel and data estimates from a short record of data measurements. Our algorithmic developments toward spectrally-efficient cognitive networking through joint optimization of channel access code-waveforms and routes in a multi-hop network are described in Chapter 5. Algorithmic designs are software optimized on heterogeneous multi-core general-purpose processor (GPP)-based SDR architectures by leveraging a novel software-radio framework that offers self-optimization and real-time adaptation capabilities at the PHY, MAC, and NET layers of the network protocol stack. Our system design approach is experimentally validated under realistic conditions in a large-scale hybrid ground-air testbed deployment. Chapter 6 reviews the state-of-art in software and hardware platforms for underwater wireless networking and proposes a software-defined acoustic modem prototype that enables (i) cognitive reconfiguration of PHY/MAC parameters, and (ii) cross-technology communication adaptation. The proposed modem design is evaluated in terms of effective communication data rate in both water tank and lake testbed setups. In Chapter 7, we present a novel receiver configuration for code-waveform-based multiple-access underwater communications. The proposed receiver is fully reconfigurable and executes (i) all-spectrum cognitive channelization, and (ii) combined synchronization, channel estimation, and demodulation. Experimental evaluation in terms of SINR and BER show that all-spectrum channelization is a powerful proposition for underwater communications. At the same time, the proposed receiver design can significantly enhance bandwidth utilization. Finally, in Chapter 8, we focus on challenging practical issues that arise in underwater acoustic sensor network setups where co-located multi-antenna sensor deployment is not feasible due to power, computation, and hardware limitations, and design, implement, and evaluate an underwater receiver structure that accounts for multiple carrier frequency and timing offsets in virtual (distributed) MIMO underwater systems.

The biodiversity of two distinct marine environments was observed to describe the biogeocomplexity of these extreme ecological systems. A shallow-water hydrothermal vent in Papua New Guinea served as a study of a thermophilic ecosystem influenced by arsenic rich vent fluids while a 60 m deep offshore primarily anoxic karst sink served as a study of an anaerobic sulfur-influenced habitat. Both environments support unique biological communities that are influenced by the physical and chemical pressures imposed on them by the harsh conditions of these systems. In Tutum Bay, Ambitle Isle, Papua New Guinea, a transect was created from a shallow hydrothermal vent that extended 120 m away from the vent. Previous studies have shown that the geochemistry of the system is heavily influenced by arsenic which is toxic to most organisms. In this study, macro- and meiofauna were collected and scored and combined with bacterial sequence data collected along the length of the transect. It was found that near vent sites harbored biological communities more similar than sites further from the vent. Many species were found only at sites near the hydrothermal vent. Near-vent communities were less diverse than those away from the vent, and biodiversity generally increased as distance from the vent increased. Distinct correlations between thermophilic organisms and temperature were observed. The metabolic repertoire of the microbial communities suggests that many strategies are used to obtain energy and carbon. The relative abundance of bacteria containing genes to reduce arsenic was comparable to those able to reduce sulfur compounds. Primary production appeared to be a mix of chemo- and phototrophy. Food webs and association analysis suggest a complex interplay between macrofaunal, meiofaunal and bacterial communities. While the system is heavily influenced by arsenic, no specific correlation between the relative abundance of arsenic metabolizing organisms and the amount of arsenic in the system could be drawn. This is likely due to the fact that most of the arsenic produced by the system is readily adsorbed onto iron oxyhydroxides, reducing the arsenic's bioavailability. The anoxic conditions at Jewfish sink provide a different hurdle than the hot arsenic conditions found in Papua New Guinea. The anoxic conditions are shared by other pit features found in karst geography, but the metabolic processes between Jewfish sink and these other karst habitats are different. The blue holes and black holes of the Bahamas are some of the most well-studied of these karstic pits. In these features, which are large circular pits with diameters of over 300 m, light and sulfur are used as a means of energy acquisition. Jewfish sink, having an opening only 6 m in diameter, is light restricted compared to these systems. As a result, the strategy of organisms dwelling in the anoxic conditions of the sink is different than those found at the well-studied holes in the Bahamas. Geochemical measurements were recorded over two time periods spanning a combined total of 6 years. The anoxic bottom waters of Jewfish sink remain stable and contained high levels of sulfide throughout most of the seasons studies. Sequence analysis of prokaryotes within the sink showed that sulfur reducers had the highest relative abundance compared to other functional guilds. To monitor the changes of the microbial communities within the sink, bacterial communities were examined at 4 depths within the sink at 9 different intervals over a period of 685 days. Denaturing Gradient Gel Electrophoresis (DGGE) was used to fingerprint 16s rRNA bacterial communities and dissimilatory sulfite reducing communities by targeting the 16s rRNA bacterial gene and the dsr gene associated with dissimilatory sulfite reducing bacteria and archaea. The lowest depth studied within the sink (40 m) remained stable chemically and biologically until a turnover event occurred within the second winter of the study. This turnover event disrupted the biological communities at 40 m and led to a reestablished community comprised of different species that those found prior to the event. Upper waters within the sink show that clines establish themselves seasonally and partition zones that confine bacterial communities that are more similar to each other within these zones while excluding bacterial communities that are outside of these zones. Oxygenated water was shown to not contain prokaryotes containing the dsr gene. As the oxycline changed seasonally, dissimilatory sulfite reducing prokaryotes containing the dsr gene remained in the anoxic zone and required time to reestablish themselves whenever oxygenated water displaced them.

Astrobiology is a multidisciplinary topic that addresses the origin, distribution and evolution of life in the universe. One of the key questions relates to whether life could have evolved on other planetary bodies, and Mars has been the major focus. Biologists contribute to this question by studying the ecology of extreme environments on Earth that share closest analogy to Mars’ past or present environment. In this thesis, molecular-level interrogations were used to address some aspects of microbial biodiversity, ecology and stress tolerance in two such extreme environments. The high-altitude cold and intense UV irradiance of central Tibet was selected as an analogue for Mars surface today, whilst cold alkaline high-carbonate freshwater lakes were chosen as an analogue for Mars’ previous late wet phase. Biological soil crusts from central Tibet supported a diverse microflora and these were variously bacteria or eukarya dominated. The relatively well-developed eukarya-dominated crusts were characterized and showed they comprised of Stichococcus bacillaris, plus alphaproteobacteria, betaproteobacteria, bacteroidetes and gemmatimonadetes. In order to evaluate the diversity of radiation-tolerant taxa in these soils, samples were exposed to ionizing radiation and viability, physiology and phylogenetic identity determined. The most radio-tolerant taxa isolated and characterized were from the radiation tolerant phylum Deinococci (15kGy), whilst a relatively diverse range of Actinobacteria, Bacilli, Cyanobacteria and Proteobacteria were also recovered after exposure to doses up to 10kGy. This implies the high-radiation environment has selected for tolerance among diverse phyla, with tolerances that far exceed environmental exposure. It is not known at this stage if they all employ similar protective strategies. Microbial reefs that have developed in cold alkaline lakes in British Columbia were studied as analogues for a late-wet Mars environment. Molecular ecological analysis revealed that communities consisted largely of of Proteobacteria (alpha), Cyanobacteria (Leptolyngbya) and Acidobacteria, with similarities in community assembly to marine stromatolites. Microbial diversity varied spatially and temporally within microbialites, and indicated that geographically proximal structures can develop with different communities. Significant changes also occur between summer and winter when the lake surface is frozen. Investigation of other nearby lakes with similar geochemistry but not supporting microbialites revealed extensive microbial mats. These developed in the presence of relatively high concentrations of methane or sulfate, and their biodiversity reflected this with several putative methanotrophic and sulphate utilizing taxa identified. No obvious cues that inhibit or promote microbialite formation were observed in this study.
published_or_final_version
Biological Sciences
Doctoral
Doctor of Philosophy

Thesis (Ph. D.)--University of California, San Diego, 2007.
Title from first page of PDF file (viewed January 4, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.

Designing materials for fusion applications is a very challenging problem, requiring detailed understanding of the behaviour of materials under the kinds of extreme conditions expected in a fusion environment. During the lifetime of fusion-reactor components, materials will be subjected to high levels of neutron irradiation, but must still perform effectively at high operating temperatures and under significant loading conditions. Body-centred cubic (bcc) transition metals are some of the most promising candidates for structural materials in fusion because of their relatively high density, which allows for effective neutron-shielding with the minimum volume and mass of material. In this work we perform atomistic simulations on two of the most important of these, Fe and W. In this thesis we describe atomic-scale simulations of defects found in bcc systems. In part I we consider the vacancy and interstitial loop defects that are produced and accumulated as a result of irradiation-induced displacement cascades. We show that vacancy dislocation loops have a critical size below which they are highly unstable relative to planar void defects, and thus offer an explanation as to why they are so rarely seen in TEM observations of irradiated bcc metals. Additionally, we compare the diffusion rates of these vacancy loops to their interstitial counterparts and find that, while interstitial loops are more mobile, the difference in mobility is not as significant as might have been expected. In part II we study screw dislocations, which, as the rate limiting carriers of plastic deformation, are significantly responsible for the strength of materials. We present results from large-scale finite temperature molecular dynamics simulations of screw dislocations under stress and observe the thermally-activated kink-pair formation regime at low stress, which appears to be superseded by a frictional regime at higher stresses. The mobility functions fitted to the results are vital components in simulations of dislocation networks and other large-scale phenomena. Lastly, we develop a multi-string Frenkel-Kontorova model that allows us to study the core structure of screw dislocations. Subtle changes in the form of the interaction laws used in this model demonstrate the difference between the non-degenerate and degenerate core structures. We provide simple criteria to guarantee the correct structure when developing interatomic potentials for bcc metals.

Phylogeography aims to understand the processes that underlie the distribution of genetic variation within and among closely related species. Although the means by which this goal might be achieved differ considerably from those that spawned the field some thirty years ago, the foundation and conceptual breakthroughs made by Avise are nonetheless the same and are as relevant today as they were two decades ago. Namely, patterns of neutral genetic variation among individuals carry the signature of a species’ demographic past, and the spatial and temporal environmental heterogeneity across a species’ geographic range can influence patterns of evolutionary change. Aquatic systems throughout Mexico provide unique opportunities to study phenotypic plasticity and evolution in relation to climatic and environmental selective forces. There are several unique, often isolated aquatic environments throughout Mexico that have a history of geographic isolation and reconnection. The first study presented herein shows significant mitochondrial sequence divergence was also discovered between L. megalotis populations on either side of the Sierra de San Marcos that bisects the valley of Cuatro Ciénegas and that the populations in the valley are genetically distinct from those found outside of the valley. The second study recovered signals of two divergence events in Cuatro Ciénegas for six codistributed taxa, and reveals that both events occured in the Pleistocene during periods of increased aridity suggesting that climatic effects might have played a role in these species’ divergence. The final study presents an Illumina-based high-resolution species phylogeny for Astyanax mexicanus providing added support that there are multiple origins to cave populations and further clarifying the uniqueness of the Sabinos and Rio Subterráneo caves.

This research reviews and extends the impedance-based structural health monitoring technique in order to detect and identify structural damage on various complex structures. The basic principle behind this technique is to apply high frequency structural excitations (typically higher than 30 kHz) through the surface-bonded piezoelectric transducers, and measure the impedance of structures by monitoring the current and voltage applied to the transducers. Changes in impedance indicate changes in the structure, which in turn can indicate that damage has occurred. Several case studies, including a pipeline structure, a composite reinforced aluminum plate, a precision part (gear), a quarter-scale bridge section, and a steel pipe header, demonstrate how this technique can be used to detect damage in real-time. A method to process impedance measurements to prevent significant temperature and boundary condition changes registering as damage has been developed and implemented. Furthermore, the feasibility of using the technique for high temperature structures and for condition monitoring of critical facilities subjected to a severe natural disaster has been investigated. While the impedance-based structural health monitoring technique indicates qualitatively that damage has occurred, more information on the nature of damage is necessary for remote structures. In this research, two different damage identification schemes have been combined with the impedance method in order to quantitatively assess the state of structures. One is based on a wave propagation modeling, and the other is the use of artificial neural networks. A newly developed wave propagation model has been developed and combined with the impedance method in order to estimate the severity of damage. Numerical and experimental investigations on 1-dimensional structures were presented to illustrate the effectiveness of the combined approach. Furthermore, to avoid the complexity introduced by conventional computational methods in high frequency ranges, multiple sets of artificial neural networks were integrated with the impedance-based health monitoring technique. By incorporating neural network features, the technique is able to detect damage in its early stage and to determine the severity of damage without prior knowledge of the model of structures. The dissertation concludes with experimental examples, investigations on a quarter-scale steel bridge section and a space truss structure, in order to verify the performance of the proposed methodology.
Ph. D.

During the last decades many studies have been undertaken to investigate life in extreme environments, leading to the discovery of novel organisms and novel habitats previously though to be unapproachable for life. Microbes are key players in a number of ecological processes such as mineral dissolution, soil genesis, plant growth promotion (PGP) and bioremediation of polluted sites and they are the main responsibles for element cycles both in conventional and extreme ecosystems. The biotechnological potential of extremophiles is well recognized, and the aim of this PhD project was to give further insight on the possible exploitation of the microbiome naturally adapted to cope with extreme values of one or more environmental parameters to develop sustainable strategies in agriculture and ecosystem management with a particular focus on arid and saline lands. Mineral-microbe interactions have been studied in detail, particularly regarding the importance of bioweathering bacteria in the ambit of soil fertility promotion in arid lands. Specific sites within the Midtre Lovénbreen glacier moraine (Svalbard, Norway), where pyritic rocks were present, hosted an active acidophilic iron-oxidizing bacterial community involved in the bioweathering of pyrite supplied by the rock disaggregation due to winter freezing. A decreased iron concentration and acidification were observed along the wheathered area departing form the pyrite-rich rock, where the oxidation of ferrous iron led to the accumulation of ferric oxy-hydroxides in the above soil. These ferric compounds were linked to the increase of soil physico-chemical properties that in turn determined a higher water holding capacity (WHC) and nutrient content in the surrounding vegetated area, densely colonized by mosses and small vascular plants. At the outer border of the vegetated area, the rest of the moraine hosted typical first colonizer bacteria, mainly belonging to the class Cyanobacteria, that are capable of nitrogen and carbon fixation. Thus, compared to the rest of the moraine, the enhancement of soil formation processes and plant colonization in the vegetated area was driven by the synergy between acidification and leaching activity of a chemolitotrophic community and the cyanobacteria-mediated primary productivity. A detailed description of the bacterial communities colonizing the weathered area, the vegetated area, and the barren moraine was obtained through the construction of 16S rRNA gene libraries. The statistical ∫-Libshuff analysis indicated these areas as three different ecological niches. The microbiome of the weathered area was dominated by few bacterial taxa due to the low pH value of the biological soil crust (BSC) whereas the vegetated area and the moraine displayed higher biodiversity. The most abundant phylogenetic groups in these BSCs were nevertheless different and in the case of the vegetated area they corresponded to those typical of mature and rhizospheric soils. The ability of microorganisms to interact with minerals is an essential factor that influence plant nutrition by providing nutrients, such as phosphorous, that are generally present in the soils as insoluble forms. The capability to solubilize poorly bioavailable nutrients is one of the PGP activities that have been investigated in the microbiome associated to different plant species living in arid hypersaline soils in Central and South Tunisia (Olea europea and Salicornia spp.) or acid soils located in a volcanic area in Mexico. A large collection of bacterial isolates has been constituted, identified and characterized for the in vitro PGP potential. Halophilic bacteria were isolated from the rhizosphere of Salicornia plants on oligotrophic media enriched with NaCl. The isolates obtained from 15% NaCl enriched media mainly belonged to the Halomonas genus, whereas the bacteria isolated at 10% NaCl showed a higher phylogenetic diversity at the genus level. Most of the bacteria comprised in the halophiles collection exhibited high resistance to drought, temperature and salt stresses. PGP activities were also widespread, especially the ability to produce indol-3-acetic acid (IAA), which promotes lateral roots developement. Furthermore, high percentage of the halophilic bacteria produced ammonium (94%) and were able to solubilize phosphate (64%) while the ability to produce protease, an activity involved in biocontrol processes, was less frequent. The comprehensive study realized on the culturable halophilic fraction of the rhizospheric bacteria associated to Salicornia spp. allowed the identification of 20 isolates as suitable candidate for developing a bacterial inoculum aimed to promote plant growth under saline stress. The diversity of the microbiome inhabiting different fractions of the Olea europea root system was investigated by applying a cultivation-independent method (Denaturing Gradient Gel Electrophoresis). The interior root tissues, the rhizosphere, the root surrounding soil and the bulk soil were colonized by a rich and diverse microbiome, shaped both by interaction with the plant and the environmental parameters of the collection site. Moreover, from these four fractions a bacterial collection was obtained for the screening of ecological and PGP features of culturable bacteria associated to olive tree growing under drought stress. In addition to the abiotic stress resistance, bacterial isolates displayed a variety of PGP activities, such as potential nitrogen fixation, siderophores and exopolysaccharides production and phosphate solubilization. Overall, the obtained dataset highlighted the possibility to use the investigated PGP bacteria associated to olive tree as biofertilizer for supporting olive growth under drought stress. An extremophile plant living at high T (42°C) and low pH (4.1) was collected at El Chichón volcanic system (Mexico). The PGP activities of a collection of rhizobacteria isolated from the plant were explored through in vitro tests. Several strains were able to affect phytohormones balance by the production of indole-3-acetic acid and 1-aminocyclopropane-1-carboxylate (ACC)-deaminase, the latter being involved in the decrease of ethylene level in plants. Remarkable percentage of the isolated bacteria displayed also additional potential PGP activities based on weathering activity. Volcanic habitats can hence be estimated as source of extremophile rhizobacteria potentialy able to help pioneer plants to cope with the severe condition of acidic soils. Microbe-environment interactions have been investigated also in deep hypersaline anoxic basins (DHABs) located in the eastern Mediterranean Sea, model environments to look for bacterial phylotypes specifically adapted to high salinity conditions. Mediterranean DHABs are far below the photic zone and contain brines originated by the dissolution of Messinian evaporites. Compared to other DHABs, Urania has very high concentrations of methane (5.56 mM) and levels of sulfide (up to 16 mM) that make it one of the most sulfidic marine water bodies on Earth. The interface between seawater and the anoxic hypersaline brine of DHABs is an oxic-anoxic interface containing an halocline with layers from seawater to brine typical salinity and is a hot-spot of microbial activity. Methanogenesis activity was detected along the first of the two environmental chemoclines present in the Urania basin and 16S rRNA gene libraries indicated the Euryarchaeota group MSBL1 as the primary candidates for methane production. Cultivation-independent analyses proved that sulfur cycling is a major driver in shaping the microbial communities, though other chemolithoautotrophic processes like manganese oxidation and anaerobic ammonium oxidation (ANAMMOX) are involved. The occurrence of ANAMMOX reaction was verified in other DHABs, namely L’Atalante and Bannock. Labelled dinitrogen gas production in 15N activity test demonstrated that anammox bacteria were active in the chemoclines of both the basins. Fluorescence in situ hybridization and 16S rRNA gene libraries using anammox-specific PCR primers unveiled the presence of the known marine anammox genus ‘Scalindua’, together with putatively novel operational taxonomic units (OTUs) closely affiliated to sequences retrieved in other marine environments where anammox activity were detected. Real Time PCR assay allowed to quantify anammox-related 16S rRNA genes in Bannock basin, which were highly abundant in correspondence of the oxic-anoxic boundary in the salinity range comprised between 6.4 and 12.1%. Cluster analysis of 16S rRNA gene libraries showed that chemoclines of Bannock and L’Atalante basins, having diverse geochemical settings, selected for different anammox phylotypes and that a shift in anammox population could be observed at increasing salinity values. The detection of putative novel phylotypes specifically adapted to peculiar salinity levels represent a key step for designing ad hoc inocula to be used in the remediation of saline wastewaters originated by industrial and agricultural processes. Actually the known freshwater anammox populations could only adapt to salt concentrations up to 3% if salinity is slowly increased, thus the selection of naturally adapted anammox strains would be of primary importance to enhance the exploitation of this process during the removal of nitrogen compounds from wastewater. The occurrence of microbe-plant positive associations was proved in different stressed soils, and their exploitation is likely the most promising approach to avoid or reduce the use of chemical fertilizer and to boost plant growth and crop productivity whitout the use of genetically modified organisms (GMO) in respect of the biodiversity. Similarly, the discovery of novel anammox phylotypes in hypersaline ecosystems shed a new light on the utilization of this functional group of bacteria for the removal of nitrogen from saline wastewaters, a critical step of treatment processes due to the environmental impact of nitrogen compounds and the severe legislation on wastewater discharges.

Many legacy nuclear facilities exist with the number of such facilities due to increase in the future. For a variety of reasons, some of these facilities have poorly documented blueprints and floor plans. This has led to many areas within such facilities being left unexplored and in an unknown state for some considerable time. The risk to health that these areas might pose has in some cases precluded human exploration and facilities have been maintained in a containment state for many years. However, in more recent years there has been a move to decommission such facilities. The change of strategy from containment to decommissioning will require knowledge of what it is that needs to be decommissioned. It is hoped that an autonomous or semi- autonomous robotic solution can satisfy the requirement. For successful mapping of such environments, it is required that the robot is capable of producing complete scans of the world around it. As it moves through the environment the robot will not only need to map the presence, type and extent of radioactivity, but do so in a way that is economical from the perspective of battery life. Additionally, the presence of radioactivity presents a threat to the robot electronics. Exposure to radiation will be necessary but should be minimised to prolong the functional life of the robot. Some tethered robots have been developed for such applications, but these can cause issues such as snagging or the tether inadvertently spreading contamination, due to being dragged along the floor. Nuclear environments have very unique challenges, due to the radiation. Alpha and beta radiation have a short emission distance and therefore cannot be detected until the robot is in very close proximity. Although the robot will not become disabled by these forms of radiation, it may become contaminated which is undesirable. Radiation from gamma sources can be detected at range, however pinpointing a source requires sensors to be taken close to the emitter, which has adverse effects on the robot's electronics, for example gamma radiation damages silicon based electronics. Anything entering these environments is deemed to be contaminated and will eventually require disposal. Consequently the number of entries made should ideally be minimised, to reduce the production and spread of potential waste/contamination. This thesis presents results from an investigation of ways to provide complete scans of an environment with novel algorithms which take advantage of common features found in industrial environments and thereby allow for gaps in the data set to be detected. From this data it is then possible to calculate a minimum set of way points required to be visited to allow for all of the gaps to be filled in. This is achieved by taking into account the sensor's parameters such as minimum and maximum sensor range, angle of incidence and optimal sensor distance, along with robot and environmental factors. An investigation into appropriate exploration strategies has been undertaken looking at the ways in which gamma radiation sources affect the coverage of an environment. It has discovered undesired behaviours exhibited by the robot when radiation is present. To overcome these behaviours a novel movement strategy has been presented, along with a set of linear and binary battery modifiers, which adapt common movement strategies to help improve overall coverage of an unknown environment. Collaborative exploration of unknown environments has also been investigated, looking into the specific challenges radiation and contamination offer. This work has presented new ways of allowing multiple robots to independently explore an environment, sharing knowledge as they go, whilst safely exploring unknown hazardous space where a robot may be lost due to contamination or radiation damage.

Biogeochemical extreme events are analysed for the special case of the surface chlorophyll in the Mediterranean open sea. The extremes are defined statistically as values over the 99th percentile threshold that are connected in space and time. A multidecadal simulation with daily output (1979-2012) was run to collect the statistics needed to carry out the study. The online coupled hydrodynamic-biogeochemical (MITgcm-BFM) model has a spatial resolution of 1/12°, with 75 vertical levels. The model was corroborated with available observations and other validated models. To account for the heterogeneity of the chlorophyll features and dynamics across the Mediterranean area, the definition of the extremes as peaks over the threshold was initially applied at each grid point and then refined to include in one extreme event all the points near in space with extremes at the same time. The macro-events were then characterized by a set of indexes, related to their spatio-temporal localisation, shape and impact on the local marine ecosystem due to their supply of high and/or anomalous biomass production. Following, the macro-events occurred in the Mediterranean area in the winter-spring months of the 1994-2012 period were described and classified using the introduced set of indexes. Overall, the macro-events occurred in each year during the winter months, especially in the northern part of the Mediterranean Sea. They have a wide spectrum of possible shapes, mainly corresponding to a duration shorter than 20 days and a radius contained within the larger Mediterranean mesoscale (200 km). The most persistent macro-events (uniformity index higher than 60%) are relatively small and short within the total spectrum, with an inverse proportionality between area and duration. The most severe macro-events (mean severity higher than 1.1 kgChl/km2/day in the first meter of depth) have intermediate area and duration; generally they are not very persistent, but sometimes they are very anomalous (anomaly higher than 15%). The most anomalous macro-events have typically medium or long duration (up to 84 days) and they can be also very large (up to the whole sub-basin scale), but not very persistent. In agreement with literature, no significant trends are observed in the macro-events indexes on the basin-scale. Some subdomains were analysed in detail: the North Western Mediterranean Sea (NWM), the Ionian Sea (ION), the South Adriatic Sea (ADS) and the Levantine Sea (LEV). The decreasing eastward gradient of the mean severity across the subdomains reflects the well known gradients of the mean surface chlorophyll. More than 70% of the macro-events of chlorophyll occurred in NWM and ADS are classified as events of high severity and high anomaly with respect to the medians of the distributions of the mean severity and anomaly on the whole domain. Overall, the most severe macro-events are in NWM. ADS is the subdomain with the most persistent macro-events, possibly ascribed to the spatial constraints of the topography and of the circulation structure. In ION and LEV more than the 50% of macro-events show low values of both indexes, even if hot spots of macro-events heavily affecting the ecosystem can be observed in the North Ionian Sea, close to the southern coasts of Sicily and in the Rhodes Gyre regions. Focusing on some representative examples of macro-events further investigated, we observed that the model is able to reproduce the main features of timing and location of the chlorophyll patterns observed by remote sensing and that the physical forcing anomalies with respect to climatology appear to play the major role as trigger of the macro-events. Finally, the selected macro-events are characterized by phytoplankton subgroups (BFM parametrization of picophytoplankton, flagellates, diatoms, large phytoplankton) that evolve in space and time in different ways in the subdomains.