A Modular Design Approach For Programmable Cyber-Fluidic Systems

Digital microuidic biochips have emerged as a technology for miniaturizing and automating the traditional biochemical laboratory processes. The technology allows for direct programmatic control of droplets without the need for pumps, valves, or dened channels, which makes the digital microuidic biochips highly programmable and recongurable devices. Although the technology has already been in the research spotlight for over two decades, the digital microuidic biochips face signicant diculties in achieving wide-adoption and living up to the expectations for extensive miniaturization and automation of biomedical applications. Among the most signicant challenges is that digital microuidics is an interdisciplinary eld where the research is often focused on technology and component level rather than on a complete future proof system. Taking the digital microuidics past the step of technology demonstrators required bridging the gap between digital biochips presented in the context of application-specic short term research goals and a programmable applicationagnostic digital microuidics system. Hence, inspired by the heavily standardized microelectronics industry and modern computer architectures, this dissertation embarked on the journey to eciently connect the uidic and control domains into a vision for a modular and recongurable cyber-uidic architecture. The proposed architecture is based on the analysis of an extensive survey of existing technologies and systems, which conrmed that achieving the envisioned cyber-uidic architecture requires the design, fabrication, and operational aspects to be considered in symbiosis. The proposed cyber-uidic architecture is split into three loosely coupled parts; uidic, instrumentation, and virtual, where each part is deliberately designed in the context of its intrinsic relationships with the rest of the system. The cyber-uidic architecture was developed into a modular platform-based design, which allowed addressing the spectrum of accompanying challenges on a conceptual and technological level. The engineering research of the uidic system led to the development of a digital biochip with a large array of individually addressable electrodes, a novel design of recongurable embedded heaters, and an innovative low-cost coating method. This dissertation also discusses the design and implementation of the modular instrumentation system that embraces recongurability to provide an evolvable and scalable model for digital biochip instrumentation. We also conceptualized a software stack for programmable microuidics, including a uidic instruction set architecture, text and graphicalbased programming methods, and an execution model. The capabilities of the proposed cyber-uidic architecture and the constructed platform are demonstrated with several real-life protocols, namely performing a gene amplication by a polymerase chain reaction and magnetic beads-based enzymatic immunoassays targeting the detection of MRSA and SARS-CoV-2 spiked protein.