Supporting the Model-Driven Development of Real-time Embedded Systems with Run-Time Monitoring and Animation via Highly Customizable Code Generation

This paper presents a vision that allows the combined use of model-driven engineering, run-time monitoring, and animation for the development and analysis of components in real-time embedded systems. Key building block in the tool environment supporting this vision is a highly-customizable code generation process. Customization is performed via a configuration specification which describes the ways in which input is provided to the component, the ways in which run-time execution information can be observed, and how these observations drive animation tools. The environment is envisioned to be suitable for different activities ranging from quality assurance to supporting certification, teaching, and outreach and will be built exclusively with open source tools to increase impact. A preliminary prototype implementation is described.

Refractometry Studies of the Optical Properties of Polymer Films and the Development of Polymer Coated Refractive Index Sensors

Sensors for real-time monitoring of environmental contaminants are essential for protecting ecosystems and human health. Refractive index sensing is a non-selective technique that can be used to measure almost any analyte. Miniaturized refractive index sensors, such as silicon-on-insulator (SOI) microring resonators are one possible platform, but require coatings selective to the analytes of interest. A homemade prism refractometer is reported and used to characterize the interactions between polymer films and liquid or vapour-phase analytes. A camera was used to capture both Fresnel reflection and total internal reflection within the prism. For thin-films (d = 10 μm - 100 μm), interference fringes were also observed. Fourier analysis of the interferogram allowed for simultaneous extraction of the average refractive index and film thickness with accuracies of ∆n = 1-7 ×10-4 and ∆d < 3-5%. The refractive indices of 29 common organic solvents as well as aqueous solutions of sodium chloride, sucrose, ethylene glycol, glycerol, and dimethylsulfoxide were measured at λ = 1550 nm. These measurements will be useful for future calibrations of near-infrared refractive index sensors. A mathematical model is presented, where the concentration of analyte adsorbed in a film can be calculated from the refractive index and thickness changes during uptake. This model can be used with Fickian diffusion models to measure the diffusion coefficients through the bulk film and at the film-substrate interface. The diffusion of water and other organic solvents into SU-8 epoxy was explored using refractometry and the diffusion coefficient of water into SU-8 is presented. Exposure of soft baked SU-8 films to acetone, acetonitrile and methanol resulted in rapid delamination. The diffusion of volatile organic compound (VOC) vapours into polydimethylsiloxane and polydimethyl-co-polydiphenylsiloxane polymers was also studied using refractometry. Diffusion and partition coefficients are reported for several analytes. As a model system, polydimethyl-co-diphenylsiloxane films were coated onto SOI microring resonators. After the development of data acquisition software, coated devices were exposed to VOCs and the refractive index response was assessed. More studies with other polymers are required to test the viability of this platform for environmental sensing applications.

The roles of EFN-1 and seam cell V2 in the transmission of a stop cue for the posterior lateral microtubule in Caenorhabditis elegans

A functional nervous system requires the precise arrangement of all nerve cells and their neurites. To achieve this correct assembly, a myriad of molecular guidance cues works together to direct the outgrowth of neurites to their correct positions. The small nematode C. elegans provides the ideal model system to study the complex mechanisms of neurite guidance due to its relatively simple nervous system, composed of 302 neurons. I used two mechanosensory neurons, called the posterior lateral microtubule (PLM), to investigate the role of the ephrin and Eph receptor protein family in neurite termination in C. elegans. Activation of the C. elegans Eph receptor VAB-1 on the PLM growth cone is sufficient to cause PLM termination, but the identity and location of the activating ligand has not been established. In my thesis I investigated the ability of the ephrin ligand EFN-1 to activate VAB-1 to cause PLM termination when expressed on the same cell (in cis) and on opposing cells (in trans) to the receptor. I showed that EFN-1 is able to activate VAB-1 in cis and in trans to cause PLM termination. I also assessed the hypodermal seam cells as the source of the ephrin stop cue using fluorescently labelled and seam cell mutant transgenic worms. I found that although the PLM shows consistent termination on the seam cell V2 in wild type worms independent of PLM length, this process is not significantly disrupted in seam cell mutants. With this information I have created a new hypothesis that the PLM neurite is able the provide a positional cue for the developing seam cells, and have created a new transgenic strain which can be used to assess the impact of PLM and ALM cell ablation on seam cell position. My research is the first to demonstrate the ability of an ephrin ligand to activate its ephrin receptor in cis, and further research can investigate if this finding has in vivo applications.