Minhass, Wajid Hassan

Mikrofluidiske biochips integrerer forskellige funktionaliteter til biokemiske analyser på en chip og har adskillige fordele sammenlignet med konventionelle biokemiske laboratorier. I denne afhandling fokuserer vi på flow-baserede biochips. Den grundlæggende byggesten i sådan en chip er ventilen (størrelse: 6×6 μm2), der kan fremstilles med en densitet på 1 million ventiler pr cm2. Ved at kombinere disse ventiler kan man fremstille komplekse enheder som mixere, skiftere og multipleksere og teknologien bliver derfor kaldt mikrofluidisk Very Large Scale Integration (mVLSI).Fremstillingsteknologien for mVLSI biochips har udviklet sig hurtigere end Moore’s lov. Dog er designmetodologierne stadig manuelle og bottom-up. Designere bruger tegneværktøjer, fx. AutoCAD, til manuelt at designe chippen. For at køre eksperimenter bliver applikationen manuelt mapped på chippens ventiler (sammenligneligt med gate-level design i elektroniske ICs). Da mVLSI chips nemt kan have tusindvis af ventiler kan denne manuelle process være meget tidskrævende, tilbøjelig til fejl og resultere i ineffektive designs og mappings.Vi foreslår, for første gang så vidt vi ved, en top-down modellerings og syntese metodologi til mVLSI biochips. Vi foreslår et modellerings framework for komponenterne og biochiparkitekturen. Ved brug af disse modeller præsenterer vi en arkitektural syntesemetodologi (som dækker trinene fra det skematiske de-sign til den fysiske syntese), hvilket resulterer i en applikationsspecifik mVLSI biochip. Vi foreslår også et framework til at mappe den biokemiske applikation på mVLSI biochips, hvor vi binder og planlægger operationerne og router fluiderne. Et kontrolsynteseframework til at afgøre den præcise aktiveringssekvens af ventilerne for at afvikle applikationen bliver også foreslået. For at reducere macro-assembly omkring chippen og forbedre skalerbarheden foreslår vi en metode til at minimisere pin count. Vi har evalueret de foreslåede metoder i stor udstrækning ved brug af real-life case studies og syntetiske benchmarks. Det foreslåede framework forventes at lette programmerbarhed og automation.Microfluidic biochips integrate different biochemical analysis functionalities on-chip and offer several advantages over the conventional biochemical laboratories. In this thesis, we focus on the flow-based biochips. The basic building block of such a chip is a valve which can be fabricated at very high densities, e.g., 1 million valves per cm2. By combining these valves, more complex units such as mixers, switches, multiplexers can be built up and the technology is therefore referred to as microfluidic Very Large Scale Integration (mVLSI).The manufacturing technology for the mVLSI biochips has advanced faster than Moore’s law. However, the design methodologies are still manual and bottom-up. Designers use drawing tools, e.g., AutoCAD, to manually design the chip. In order to run the experiments, applications are manually mapped onto the valves of the chips (analogous to exposure of gate-level details in electronic integrated circuits). Since mVLSI chips can easily have thousands of valves, the manual process can be very time-consuming, error-prone and result in inefficient designs and mappings.We propose, for the first time to our knowledge, a top-down modeling and synthesis methodology for the mVLSI biochips. We propose a modeling frame-work for the components and the biochip architecture. Using these models, we present an architectural synthesis methodology (covering steps from the schematic design to the physical synthesis), generating an application-specific mVLSI biochip. We also propose a framework for mapping the biochemical applications onto the mVLSI biochips, binding and scheduling the operations and performing fluid routing. A control synthesis framework for determining the exact valve activation sequence required to execute the application is also proposed. In order to reduce the macro-assembly around the chip and enhance chip scalability, we propose an approach for the biochip pin count minimization. We also propose a throughput maximization scheme for the cell culture mVLSI biochips, saving time and reducing costs. We have extensively evaluated the proposed approaches using real-life case studies and synthetic benchmarks. The proposed framework is expected to facilitate programmability and automation, enabling the emergence of a large biochip market

Online Research Database In Technology

System-Level Modeling and Synthesis Techniques for Flow-Based Microfluidic Very Large Scale Integration Biochips

http://orbit.dtu.dk/ws/files/54817147/phd286_Minhass_WH.pdf

System-Level Modeling and Synthesis Techniques for Flow-Based Microfluidic Very Large Scale Integration Biochips

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Online Research Database In Technology