Search

Biosensors that couple hybridisation chain reaction amplification and fluorogenic silver nanoclusters (HCR-AgNCs) have the potential to enable simple and cost-effective detection of target analytes. These biosensors feature non-enzymatic amplification at mild conditions with a strong label-free fluorescence response. Whilst the proof-of-concept of these sensors have been promising, the design and developmental stages of HCR-AgNCs biosensors remain a challenge due to the lack of studies within the field itself. The primary aim of this thesis was to design and develop new HCR-AgNCs biosensors for specific detection of short nucleic acid sequences (i.e., DNA and microRNA (miR)). To achieve this, three novel HCR-AgNCs biosensors were developed by designing DNA probes with assistance of computational software, then validated via lab-based experiments such as feasibility tests, condition optimisation, as well as performance analysis in both buffer and complex samples. A ratiometric fluorescence HCR-AgNCs biosensor was first developed for miR detection, where emission of AgNCs changed from red to yellow in the absence and presence of miR-155. The ratiometric analysis has reduced the possibility of false measurement and increased the sensitivity of the assay, with limit of detection (LOD) measured at 1.18 fM. In the next study, a HCR biosensor was integrated with an externalised AgNCs probes via an 'end-to-end cluster transfer' mechanism, for DNA detection. This strategy simplified the designing process of DNA hairpins, ensured HCR predictability, and formed specific AgNCs species. In addition, the HCR-AgNCs biosensor exhibited high sensitivity towards the DNA target, with qualitative LOD at 1 pM and quantitative LOD at 3.35 fM. In the final study, magnetic-assistance was integrated into a ratiometric fluorescence HCR-AgNCs biosensor for the detection of miR-144-3p. The addition of magnetic beads (MBs) into the HCR-AgNCs biosensor facilitated a quick extraction and direct analysis of miR-144-3p, with LOD measured at 4.88 fM and satisfactory detection in raw human serum sample. The overall findings from these works conclude that by carefully designing the DNA probes used to construct HCR-AgNCs, one can develop a functional and stable HCRAgNCs biosensor without overcomplicating the detection process. Besides that, the concept of proximity-dependent AgNCs, introduced in each of the proposed biosensors, addressed some of the practical limitations posed by conventional HCR-AgNCs biosensors. Moreover, the implementation of different sensing mechanism and modifications (i.e., externalisation of AgNCs and MBs addition) in these studies highlight the versatility of HCR-AgNCs assays for different applications. Ultimately, the design and development efforts of HCR-AgNCs biosensors in this work can inspire further insights and research into this class of biosensors and facilitate extensive biosensing applications in the field of clinical diagnostics and beyond.

Significant penetration of distributed generation (DG) and the increasing automation level available for distribution networks have opened an option of splitting a network into subsystems and operating each as an "autonomous island". This is particularly important when a major contingency occurs. However, there are issues and challenges that must be addressed before islanded operation becomes viable, among which, ensuring seamless switching of a distribution subsystem from grid-connected to islanded mode is critically important. Unless the subsystem is a predesigned microgrid, it is highly possible that the subsystem load demand will exceed the generation capacity of island DGs. Therefore, an appropriate load shedding scheme must be implemented to ensure the islanded subsystem is power balanced. In this thesis, a switching control strategy is designed to deliver seamless islanding switching. This strategy comprises a multiple-DG coordination method and a single-step load shedding scheme. Mathematical studies and time-domain simulations that investigate the transients observed during the islanding switching process are both conducted, and together, they are used to address the transient stability issues of an islanded subsystem. This thesis focuses on a distribution subsystem consisting of a mix of synchronous and inverter-based DGs and a combination of static and dynamic loads. DG modelling and control is first introduced, and based on that, various types of method to achieve multiple-DG coordination, including an innovative multiple-master strategy, are investigated. The widely accepted master-slave strategy is used to coordinate DGs when the subsystem is islanded. The strategy demands a single dispatchable and controllable DG, such as a synchronous generator, to be the master, whilst requires the others, such as intermittent renewable-based DGs, to be the slaves. Dynamic load modelling is another critical part of this thesis. The transient stability of dynamic loads after major disturbances is investigated and then used to design the stability-oriented load shedding priority. The single-step load shedding scheme calculates the load shedding amount based on the power flow at the point of common coupling (PCC) and the spinning reserve available in the island. This scheme is activated by the tripping event of the PCC circuit breaker between the grid and the island, and then priorities the load to be shed according to the priority predetermined from the stability perspective. Mathematical analysis is first conducted on a simple subsystem to investigate the impact of DG settings on the islanding transients. A full-scale subsystem is also simulated in PSCAD/EMTDC and used to verify the effectiveness of the switching control strategy. In time-domain simulations, the subsystem is islanded following either a routine switching event or a permanent grid fault. Various factors that may affect the transient performance are analysed, such as the severity of the fault, the DG penetration level, the fault clearance time and the switching control delay. This thesis concludes that based on the proposed switching control strategy, the concept of seamless switching from grid-connected to islanded operation is technically viable.

Many cellular activities including cell survival, proliferation, migration and differentiation are controlled by growth factors and their corresponding tyrosine kinases receptor (RTKs). Growth factor receptor activation is strictly regulated by protein tyrosine phosphatases (PTPs). Here I investigated whether the receptor protein tyrosine phosphatase (RPTP) LAR, which is known to modify the activity of several RTKs, also regulates platelet derived growth factor (PDGF) receptor activity and signalling. Mouse embryonic fibroblasts (MEFs) expressing mutant LAR lacking its phosphatase domains (LARΔP) showed reduced phosphorylation of PDGFβ receptor (PDGFβR) compared with wild type (WT) cells. This was rescued by re-expression of WT LAR. The decreased phosphorylation of the PDGFβR was independent of ligand concentration and occurred on all tyrosine residues, suggesting that LAR is required for full PDGFβR kinase activation. The decreased kinase activity reduced the amplitude or duration of the different signalling pathways activated downstream of the PDGFβR, and resulted in reduced proliferation in response to PDGF-BB. These findings demonstrate, for the first time, that LAR activity is required for PDGF-induced fibroblast proliferation. The inhibition of PDGFβR kinase activity in LARΔP cells was exerted via increased basal activity of the tyrosine kinase c-Abl and its substrate protein kinase Cδ (PKCδ). Ligand-induced PDGFβR dimerization is defective in LARΔP cells, possibly due to the observed increase in the Nherf2 protein associating with the PDGFβR. In summary, I have identified LAR as a new regulator of PDGFβR activity, and propose a novel mechanism where PDGF-induced activation of c-Abl serves as a negative feedback loop to terminate the PDGFβR kinase activity. This may occur via PKCδ activation promoting the association of Nherf2 with PDGFβR, thereby reducing ligand-induced receptor dimerization and kinase activation. In this model, LAR promotes PDGFβR activity by inactivating c-Abl.

Aiming at aggregating numerous distributed resources to provide immense computing power, Grid computing has emerged as a promising paradigm to run complex composite applications such as workflows. However, the inherent uncertainties of grid systems as well as the structural complexity of workflow applications make it extremely challenging to schedule workflows in an efficient way, regardless of whether the objective is to minimize execution time or meet specific user and/or system Quality of Service (QoS) requirements. For both these cases, this thesis considers scheduling problems motivated by grid uncertainties and advances the state-of-the-art by developing new techniques to address these problems.First, based on existing scheduling heuristics, a Monte-Carlo approach is developed to minimize the average makespan (i.e., the overall execution time) in the presence of task estimates exhibiting limited uncertainty in the form of (controlled) random behaviour. Next, a scenario where performance prediction is difficult to obtain and resource availability may vary over time, is considered. A low-cost efficient just-in-time heuristic is proposed to cope with grid uncertainties.After addressing these performance-driven scheduling problems, a QoS-driven problem, which considers not only the aforementioned uncertainties but also the uncertainty caused by queue-based scheduling, is examined. In order to tackle all these uncertainties, an integrated scheduling model consisting of three supportive techniques is developed. Extensive evaluation using simulation shows that the proposed techniques can achieve substantial improvements towards the ultimate goal of providing a good solution for QoS-driven workflow scheduling on the Grid.

This dissertation presents two inter-related studies. Chapter 2 focuses on a study of three-dimensional numerical simulations of hydraulic fractures. Hydraulic fracturing is widely used to extract shale gas from shale formations. Pressurized water is injected into horizontal wells in shale formations to create fracture networks. If a network contains many fractures, the shale gas is easier to transport to the surface via this network. To date, the shapes of hydraulic fracture networks in shale formations are still not precisely known. This research is to numerically investigate three-dimensional hydraulic fractures with molecular dynamics simulations, which integrates the physics of linear elasticity and fracture mechanics as well as the discrete channel and fluid variables to dynamically see the propagation of hydraulic fractures. This approach allows an arbitrary number of cracks and arbitrary crack paths, and I have further developed a simulator to simulate the complex networks of hydraulic fractures in response to various states of stress in the shale formation. I have also proposed an extra term to implement the Poisson effect, which connecting deformations in perpendicular directions, for a future study for more complicated three-dimensional fracture networks such as echelon cracks. Chapter 3 presents the research on static cracks in a natural rubber sheet, seeking a strain energy functional that can accurately describe it. The type of static crack is due to the strain-induced crystallization of natural rubber and has two unusual features: pointy crack tips and a sharp boundary between the two regions with distinct deformations. When a latex rubber sheet is stretched beyond a critical stretch ratio, a slit that is cut in the middle will not cause this sheet to break apart but forms a static crack due to the crystallization of rubber. The pointy crack tips cannot be explained by the existing theories in fracture mechanics, and the sharp change of deformation is also puzzling. I have built molecular dynamics simulations to verify proposed strain energy functionals and see whether the particular crack shape in rubber can be implemented. I have got simulation results with the two features based on a strain energy functional curve with its two energy minima corresponding to the two phases. In hyperelasticity, the strain energy functional that describes the strain-induced crystallization in an isotropic material has not been mathematically formulated. The discovery shows an insight into a new form of the strain energy functional for phase separation with spatial complexity in nonlinear elasticity.

This thesis presents a modified picosecond interferometry method to study the optical properties of bulk black phosphorus (BP). BP is an emerging two-dimensional material which exhibits great potential for use in future nano-photonic and nano-electronic devices. BP differentiates itself from other two-dimensional materials such as graphene in that it possesses anisotropy in in-plane direction. It has zigzag and armchair in-plane crystalline direction, which gives its unique optical and electrical properties along these two directions, and the interlayers are under Van der Waals interactions. BP has direct band gap which is tunable via controlling the number of layers, strain and the applied electric field, making it a versatile material for use in semi-conductor industry. Currently, BP has been used as few-layer materials for devices such as photodetector and field effect transistor. However, the studies on the bulk optical properties of BP are still lacking, partially due to its tendency to degrade when exposed to air. This work focused on presenting picosecond interferometry as a new method for indirectly measuring the optical properties of BP and discuss the extended application of picosecond interferometry for studying other two-dimensional materials. Picosecond interferometry is a modified pump-probe method. It observes Brillouin scattering in a crystalline system to measure the optical and acoustic properties of the crystalline system. In this study, I modified the pump-probe system in our laboratory into a polarization-sensitive picosecond interferometry setup. I studied BP’s birefringent optical properties at several different wavelengths using picosecond interferometry. The Brillouin scattering signals was modelled by exponential decaying function. The polarization-resolved optical properties of BP were extracted by fitting the exponential decaying function. The thermal backgrounds of the measurement is analyzed with computational simulation.

Abstract: Mass sensitive mechanical resonator based biosensors are a promising label free biological sensing platform due to the capability for high sensitivity, fast response, accurate and real time measurement, integration with traditional electronics and flexible readout techniques. With the advancement of top down nano fabrication techniques, the dimensions of mechanical resonators scale from the micrometer down to the nanometer scale. Silicon carbonitride (SiCN) nanomechanical string resonator biosensors are advantageous in terms of large array integration, extremely high sensitivity and potential for multiple targets detection. However, there are two bottle-neck issues that have limited this type of biosensors from moving out of research labs and using in clinical applications. First, the biological detection sensitivity is determined by the mass of the string itself. Traditional methods of reducing the size of the strings are limited by lithography. Second, the commonly used surface modification techniques are either chemically unstable on SiCN surfaces or biologically incompatible, which causes instability and unreliability of the biosensing system. In this work, two novel methods have been proposed and implemented to solve these two problems and enhance the performance of this type of biosensors. First, a novel type of porous nanostring has been fabricated to reduce the mass of the string while avoiding the limitations of electron beam lithography (EBL). A helium ion beam was used to perform post-fabrication modification of the nanomechanical resonators. More precisely, arrays of pores were milled by ion beam along the length of glassy nanostrings. This post-fabrication method has the advantage of flexible and precise control over the dimensions, locations and the numbers of the milled patterns while with a high yield. The porous nanostrings had reduced mass and increased surface adsorption area. This method provides an alternative technique to achieve small-mass string and opens a new route to enhance the detection sensitivity of mechanical resonator based biosensors. In order to solve the second problem, diazonium salt reduction induced aryl film grafting was used, for the first time, on the SiCN nanostrings for bio-functionalization. This chemistry provides strong chemical adhesion and long term stability. First, diazonium chemistry was used to modify the surface of bare SiCN chip. The strong interfacial chemical bonding between the aryl film and SiCN surfaces was verified by X-ray photoelectron spectroscopy. Rabbit immunoglobulin G (IgG) sandwich immunoassays, with FITC and AuNP labels respectively, were performed on the modified SiCN surfaces. Scanning electron microscopic and confocal microscopic inspection of the samples showed uniform and dense coverage of the detection target on the samples. After this initial verification, the diazonium chemistry was adopted to bio-functionalize SiCN nanostring arrays. Anti-rabbit IgG and rabbit IgG were respectively immobilized onto diazonium modified nanostrings as probe and target. Immobilization of the probe and target were individually successfully observed by the significant downshifts of mechanical resonant frequencies of the nanostrings. A high resolution helium ion microscope was used to inspect the functionalized nanostrings and further verify the grafting of the analyte molecules on the nanostrings. As a proof of concept, diaznonium chemistry was demonstrated to be an effective modification method to functionalize SiCN nanostring mechanical resonator for its use as biosensor. These strategies enhance the detection sensitivity and stability of nanomechanical biosensors and potentially pave the way for the clinical applications.

Forty-eight multiparous Holstein cows were used to compare the response of dairy cows to a direct-fed mixture of cellulase and xylanase enzymes (1.25 L of enzyme concentrate/tonne of forage dry matter) applied to the forage portion (60% corn silage and 40% alfalfa hay) of a total mixed diet starting either in theclose-up dry period, at calving, or at peak milk production. Cows were blocked by calving date and, within blocks, randomly assigned to one of four treatment diets. Treatments were: 1) an untreated control diet, 2) enzyme addition to the forage from wk 6 to 18 postpartum, 3) enzyme addition to the forage from calving to wk 18 postpartum, and 4) enzyme addition to the forage from wk 4 prepartum to wk 18 postpartum. Total mixed diets were 65% forage and 35% concentrate prepartum, and 50:50 forage: concentrate postpartum. Production of milk, solid-corrected milk, fat-corrected milk, and energy-corrected milk was higher for cows fed enzyme-treated diets than for cows fed control diet. Production was similar for cows in all enzyme-treated groups, although numerically highest for cows that started receiving enzyme-treated forages right after parturition and lowest when started prepartum. Concentrations of fat, protein, and lactose in milk were similar for all treatments, with yields of protein and fat higher for cows fed enzyme-treated forages. Dry matter intakes and body condition scores, both prepartum and postpartum, were similar for all diets. Eating rates, as determined in two 24-h studies, were similar for control and enzyme-treated diets. Digestibility of diets tended to be slightly higher when forages were treated with enzymes. In conclusion, the feeding of enzyme-treated forages increased milk production. While it did not matter, statistically, when the feeding of enzyme-treated forages started, we recommend starting soon after parturition for economic reasons.