A Methodology to Design Pipelined Simulated Annealing Kernel Accelerators on Space-Borne Field-Programmable Gate Arrays

Increased levels of science objectives expected from spacecraft systems necessitate the ability to carry out fast on-board autonomous mission planning and scheduling. Heterogeneous radiation-hardened Field Programmable Gate Arrays (FPGAs) with embedded multiplier and memory modules are well suited to support the acceleration of scheduling algorithms. A methodology to design circuits specifically to accelerate Simulated Annealing Kernels (SAKs) in event scheduling algorithms is shown. The main contribution of this thesis is the low complexity scoring calculation used for the heuristic mapping algorithm used to balance resource allocation across a coarse-grained pipelined data-path. The methodology was exercised over various kernels with different cost functions and problem sizes. These test cases were benchedmarked for execution time, resource usage, power, and energy on a Xilinx Virtex 4 LX QR 200 FPGA and a BAE RAD 750 microprocessor

Fluigi: an end-to-end software workflow for microfluidic design

One goal of synthetic biology is to design and build genetic circuits in living cells for a range of applications with implications in health, materials, and sensing. Computational design methodologies allow for increased performance and reliability of these circuits. Major challenges that remain include increasing the scalability and robustness of engineered biological systems and streamlining and automating the synthetic biology workflow of “specify-design-build-test.” I summarize the advances in microfluidic technology, particularly microfluidic large scale integration, that can be used to address the challenges facing each step of the synthetic biology workflow for genetic circuits. Microfluidic technologies allow precise control over the flow of biological content within microscale devices, and thus may provide more reliable and scalable construction of synthetic biological systems. However, adoption of microfluidics for synthetic biology has been slow due to the expert knowledge and equipment needed to fabricate and control devices. I present an end-to-end workflow for a computer-aided-design (CAD) tool, Fluigi, for designing microfluidic devices and for integrating biological Boolean genetic circuits with microfluidics. The workflow starts with a ``netlist" input describing the connectivity of microfluidic device to be designed, and proceeds through placement, routing, and design rule checking in a process analogous to electronic computer aided design (CAD). The output is an image of the device for printing as a mask for photolithography or for computer numerical control (CNC) machining. I also introduced a second workflow to allocate biological circuits to microfluidic devices and to generate the valve control scheme to enable biological computation on the device. I used the CAD workflow to generate 15 designs including gradient generators, rotary pumps, and devices for housing biological circuits. I fabricated two designs, a gradient generator with CNC machining and a device for computing a biological XOR function with multilayer soft lithography, and verified their functions with dye. My efforts here show a first end-to-end demonstration of an extensible and foundational microfluidic CAD tool from design concept to fabricated device. This work provides a platform that when completed will automatically synthesize high level functional and performance specifications into fully realized microfluidic hardware, control software, and synthetic biological wetware

Evolvable Smartphone-Based Point-of-Care Systems For In-Vitro Diagnostics

Recent developments in the life-science -omics disciplines, together with advances in micro and nanoscale technologies offer unprecedented opportunities to tackle some of the major healthcare challenges of our time. Lab-on-Chip technologies coupled with smart-devices in particular, constitute key enablers for the decentralization of many in-vitro medical diagnostics applications to the point-of-care, supporting the advent of a preventive and personalized medicine. Although the technical feasibility and the potential of Lab-on-Chip/smart-device systems is repeatedly demonstrated, direct-to-consumer applications remain scarce. This thesis addresses this limitation. System evolvability is a key enabler to the adoption and long-lasting success of next generation point-of-care systems by favoring the integration of new technologies, streamlining the reengineering efforts for system upgrades and limiting the risk of premature system obsolescence. Among possible implementation strategies, platform-based design stands as a particularly suitable entry point. One necessary condition, is for change-absorbing and change-enabling mechanisms to be incorporated in the platform architecture at initial design-time. Important considerations arise as to where in Lab-on-Chip/smart-device platforms can these mechanisms be integrated, and how to implement them. Our investigation revolves around the silicon-nanowire biological field effect transistor, a promising biosensing technology for the detection of biological analytes at ultra low concentrations. We discuss extensively the sensitivity and instrumentation requirements set by the technology before we present the design and implementation of an evolvable smartphone-based platform capable of interfacing lab-on-chips embedding such sensors. We elaborate on the implementation of various architectural patterns throughout the platform and present how these facilitated the evolution of the system towards one accommodating for electrochemical sensing. Model-based development was undertaken throughout the engineering process. A formal SysML system model fed our evolvability assessment process. We introduce, in particular, a model-based methodology enabling the evaluation of modular scalability: the ability of a system to scale the current value of one of its specification by successively reengineering targeted system modules. The research work presented in this thesis provides a roadmap for the development of evolvable point-of-care systems, including those targeting direct-to-consumer applications. It extends from the early identification of anticipated change, to the assessment of the ability of a system to accommodate for these changes. Our research should thus interest industrials eager not only to disrupt, but also to last in a shifting socio-technical paradigm

Factories of the Future

Engineering; Industrial engineering; Production engineerin

Modern Applications in Optics and Photonics: From Sensing and Analytics to Communication

Optics and photonics are among the key technologies of the 21st century, and offer potential for novel applications in areas such as sensing and spectroscopy, analytics, monitoring, biomedical imaging/diagnostics, and optical communication technology. The high degree of control over light fields, together with the capabilities of modern processing and integration technology, enables new optical measurement systems with enhanced functionality and sensitivity. They are attractive for a range of applications that were previously inaccessible. This Special Issue aims to provide an overview of some of the most advanced application areas in optics and photonics and indicate the broad potential for the future

Automated liquid handling systems for microfluidic applications

Advances in microfluidic research have improved the quality of assays performed in micro-scale environments. Improvement of liquid handling techniques has enabled efficient reagent and drug use while minimising waste. The requirements for the applied techniques vary with applications and a custom integrated liquid handling solution was developed to accomplish some of these applications with minimal changes to the system. It is desirable to employ this technology to neuroscience research that requires a fluidic system that can test theories of reinforcement learning in neuronal cultures. An integrated system is therefore required to implement transport and manipulation of media and drugs loaded in a microfluidic device. One requirement for such an integrated system for liquid handling is a transport mechanism to deliver reagents and nutrients to cultures. A liquid flow control system is required to allow precise and timely control of flow rates through a microfluidic device. This can be extended to enable more sophisticated drug delivery approaches like gradient generation, spatial drug distribution and high temporal resolution of the drugs delivered. Another requirement for an integrated system is a liquid loading system that is capable of inserting specified drugs into the flow line. Such a loading system would allow any number of drugs to be loaded during an experimental process to the microfluidic device containing cells as part of an assay. The integration of these systems will allow researchers take advantage of the combined systems. Software development process should also be undertaken to improve the modularity of the integrated system so that hardware changes have marginal effects on the system operation. The project scope was the development of these liquid handling systems as well as their integration in hardware and software to enable their spatio-temporal drug delivery to neuronal cultures in microfluidic devices. The approach was to optimise performance of custom liquid handling system which was developed to realise fast flow rate changes within 1 second interval. Macro- and micro-scale solutions have been investigated in order to realise effective off-chip liquid loading capabilities. Emphasis has been placed on ease of use, modularity, rapid prototyping and precision. A commercial autoloader was identified as a starting point for sequential drug delivery. This was characterised for suitability and the constraints with this setup was used to identify additional requirements for the development of a novel sequential liquid injection system. The design process of the novel liquid injection system was unable to realise a working system due to mechanical and operational challenges encountered. A modular on-chip liquid manipulation system has been investigated and proposed to realise the sequential injection requirements. Rapid prototyping techniques that can promote ubiquitous microfluidic applications have been identified and verified. An integrated liquid manipulation system has been developed using the commercial autosampler that enables sequential loading of agonists into the microfluidic device as well as reliable chemical signalling of the loaded drugs by switching flow rates of the inputs to the device. This system will be beneficial towards research of other cell types within other research fields requiring similar functionality

A full-custom digital-signal-processing unit for real-time cortical blood flow monitoring

Master'sMASTER OF ENGINEERIN

Micromachines for Dielectrophoresis

An outstanding compilation that reflects the state-of-the art on Dielectrophoresis (DEP) in 2020. Contributions include: - A novel mathematical framework to analyze particle dynamics inside a circular arc microchannel using computational modeling. - A fundamental study of the passive focusing of particles in ratchet microchannels using direct-current DEP. - A novel molecular version of the Clausius-Mossotti factor that bridges the gap between theory and experiments in DEP of proteins. - The use of titanium electrodes to rapidly enrich T. brucei parasites towards a diagnostic assay. - Leveraging induced-charge electrophoresis (ICEP) to control the direction and speed of Janus particles. - An integrated device for the isolation, retrieval, and off-chip recovery of single cells. - Feasibility of using well-established CMOS processes to fabricate DEP devices. - The use of an exponential function to drive electrowetting displays to reduce flicker and improve the static display performance. - A novel waveform to drive electrophoretic displays with improved display quality and reduced flicker intensity. - Review of how combining electrode structures, single or multiple field magnitudes and/or frequencies, as well as variations in the media suspending the particles can improve the sensitivity of DEP-based particle separations. - Improvement of dielectrophoretic particle chromatography (DPC) of latex particles by exploiting differences in both their DEP mobility and their crossover frequencies