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Development of sustainable practices is an important goal in agriculture. One possibility involves the development of perennial cereal crops, but the mechanisms of perenniality first need to be understood. While in annual cereals flowering structures die following seed production, in perennial grasses, perenniality is achieved by maintaining at least one shoot in a vegetative state. There are two views on perennating tiller origin in perennial grasses: some authors suggest that all over-wintering tillers flower in spring and summer, leaving spring-initiated tillers to perennate, while others indicate that spring-initiated tillers are too immature to survive summer conditions, thereby implying that flowering must be prevented in some over-wintering tillers. An understanding of perenniality will therefore require an understanding of flowering control in these species. Temperate perennial grasses have dual induction requirements for flowering, where plants become competent to perceive inductive signals following vernalisation, and flowering is initiated by inductive photoperiods. Two hypotheses were formulated to test these models. The ‘environmental control hypothesis’ stated that all adequately vernalised perennial ryegrass tillers would flower on sufficient exposure to inductive photoperiods. Alternatively, the ‘spatial control hypothesis’ stated that in addition to the environmental mechanisms, a spatial control mechanism acts to regulate flowering. Two experiments were conducted to test these hypotheses. Perennial ryegrass and Italian (annual) ryegrass were induced to flower and differences between the annual and perennial habits at flowering time were observed. However neither hypothesis was proven. In the second experiment, flowering was studied in detail in individual tillers of perennial ryegrass. The eldest tiller flowered in all flowering plants. The second eldest tiller did not flower in 72% of plants with more than one reproductive tiller, while the third eldest tiller flowered in 94% of these plants. These data favour the spatial control hypothesis which suggests that a spatial regulatory mechanism might act to repress flowering in some competent perennial ryegrass tillers. These results were supported by studies of meristem morphology and by a preliminary gene expression study. Maintenance of older, established tillers in a vegetative state might allow the perennial plant a greater chance of survival during summer.

The behaviour of a large nuclear reactor can be described with sufficient accuracy using a nodal model, like the spatial model of a 540 MWe large Pressurized Heavy Water Reactor (PHWR). This model divides the reactor into divisions or nodes to create a spatial model in order to control the xenon induced oscillations that occur in PHWRs. However, being such a large scale system, a 72nd-order model, it makes controller design challenging. Therefore, a reduced order model is much more manageable. A convenient method of model reduction while maintaining the important dynamics characteristics of the process can be done by decoupling. Also, due to the nature of the system, decentralized controllers could serve as a better option because it allows each controller to be localized. This way, any control input to a zone only affects the desired zone and the zones most coupled with, thus not causing a respective change in neutron flux in the other zones. In this thesis, three decentralized controllers were designed using the spatial model of a 540 MWe large PHWR. A decoupling algorithm was designed to divide the system into three partitions containing 20, 27, and 25 states each. Reduced order sub-systems were thus created to produce optimal decentralized controllers. An optimal centralized controller was created to compare both approaches. The decentralized versus centralized controllers’ system responses were analyzed after a reactivity disturbance. A fail-safe study was done to highlight one of the advantages of decentralized controllers. / UOIT

This thesis represents the work that has been done by the author in the area of vibration analysis and control of smart structures during his PhD candidature. The research was concentrated on flexible structures, using piezoelectric materials as actuators and sensors. The thesis consists of four major parts. The first part (Chapter 2) is the modelling of piezoelectric laminate structures using modal analysis and finite element methods. The second part (Chapter 4) involves the model correction of pointwise and spatial models of resonant systems. The model correction solution compensates for the errors associated with the truncation of high frequency modes. The third part (Chapter 5) is the optimal placement methodology for general actuators and sensors. In particular, optimal placement of piezoelectric actuators and sensors over a thin plate are considered and implemented in the laboratory. The last part (Chapters 6 to 8) deals with vibration control of smart structures. Several different approaches for vibration control are considered. Vibration control using resonant, spatial H-2 and H-infinity control is proposed and implemented on real systems experimentally. It is possible, for certain modes, to obtain the very satisfactory result of up to 30 dB vibration reduction. / PhD Doctorate

The development of shape in multicellular organisms has intrigued human minds for millenia. Empowered by modern genetic techniques, molecular biologists are now striving to not only dissect developmental processes, but to exploit their modularity for the design of custom living systems used in bioproduction, remediation, and regenerative medicine. Currently, our capacity to harness this potential is fundamentally limited by a lack of spatiotemporal control over gene expression in multicellular systems. While several synthetic genetic circuits for control of multicellular patterning have been reported, hierarchical induction of gene expression domains has received little attention from synthetic biologists, despite its fundamental role in biological self-organization. In this thesis, I introduce the first synthetic genetic system implementing population-based AND logic for programmed hierarchical patterning of bacterial populations of Escherichia coli, and address fundamental prerequisites for implementation of an analogous genetic circuit into the emergent multicellular plant model Marchantia polymorpha. In both model systems, I explore the use of bacteriophage T7 RNA polymerase as a gene expression engine to control synthetic patterning across populations of cells. In E. coli, I developed a ratiometric assay of bacteriophage T7 RNA polymerase activity, which I used to systematically characterize different intact and split enzyme variants. I utilized the best-performing variant to build a three-color patterning system responsive to two different homoserine lactones. I validated the AND gate-like behavior of this system both in cell suspension and in surface culture. Then, I used the synthetic circuit in a membrane-based spatial assay to demonstrate programmed hierarchical patterning of gene expression across bacterial populations. To prepare the adaption of bacteriophage T7 RNA polymerase-driven synthetic patterning from the prokaryote E. coli to the eukaryote M. polymorpha, I developed a toolbox of genetic elements for spatial gene expression control in the liverwort: I analyzed codon usage across the transcriptome of M. polymorpha, and used insights gained to design codon-optimized fluorescent reporters successfully expressed from its nuclear and chloroplast genomes. For targeting of bacteriophage T7 RNA polymerase to these cellular compartments, I functionally validated nuclear localization signals and chloroplast transit peptides. For spatiotemporal control of bacteriophage T7 RNA polymerase in M. polymorpha, I characterized spatially restricted and inducible promoters. For facilitated posttranscriptional processing of target transcripts, I functionally validated viral enhancer sequences in M. polymorpha. Taking advantage of this genetic toolbox, I introduced inducible nuclear-targeted bacteriophage T7 RNA polymerase into M. polymorpha. I showed implementation of the bacteriophage T7 RNA polymerase/PT7 expression system accompanied by hypermethylation of its target nuclear transgene. My observations suggest operation of efficient epigenetic gene silencing in M. polymorpha, and guide future efforts in chassis engineering of this multicellular plant model. Furthermore, my results encourage utilization of spatiotemporally controlled bacteriophage T7 RNA polymerase as a targeted silencing system for functional genomic studies and morphogenetic engineering in the liverwort. Taken together, the work presented enhances our capacity for spatiotemporal gene expression control in bacterial populations and plants, facilitating future efforts in synthetic morphogenesis for applications in synthetic biology and metabolic engineering.