MSc thesis at DTU named "Fault tolerant architecture design for flow-based biochips"

Description: With the introduction at the beginning of 1990s of microfluidic components such as microvalves and micropumps, it was possible to realize “micro total analysis systems”, also called “lab-on-a- chip” and “biochips”, for the automation, miniaturization and integration of complex biochemical protocols. Microfluidic biochips are used in many application areas, such as, in vitro diagnostics (point-of-care, self-testing), drug discovery (high-throughput screening, hit characterization), biotech (process monitoring, process development), ecology (agriculture, environment, homeland security).

Flow-based microfluidic biochips are based on the manipulation of continuous fluid through fabricated micro- channels, using external pressure sources or integrated mechanical micro-pumps see Fig. 5(a). In these biochips, the basic building block is a microvalve, 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. Flow- based biochips are manufactured using multilayer soft lithography.

A potential roadblock in the deployment of microfluidic biochips is the lack of test techniques to screen defective devices before they are used for biochemical analysis. Defective chips lead to repetition of experiments, which is undesirable due to high reagent cost and limited availability of samples. However, flow-based biochips are also affected by faults, and defects can escape after-fabrication inspection and can affect the operation. The typical faults are: broken control channel; broken flow channel; leaking control channels; leaking control channels. Recent work has addressed the fault-modeling and the automated testing of flow-based biochips.

Based on these fault models and error detection techniques, the objective of this thesis is to propose approaches for the fault-tolerant design of flow-based biochips, such that the biochips can tolerate several permanent faults, given a cost budget and a biochip area. During the physical design of the biochip layout, redundancy can be introduced for on-chip components such as valves, channels and microfluidic units, increasing thus the yield. For example, if several mixing operations have to be performed, the physical design tools can decide to introduce two redundant mixers, although one mixer may be enough. The redundant mixer can be used in case the original mixer becomes faulty. Also, if a channel is critical in delivering fluids to several fluidic units, but may be affected by “leaking” or may become “broken”, then the physical design algorithms can decide to introduce a redundant channel. This redundant channel could be used during the normal operation to increase the throughput, and can be used as a backup once the original channel experiences failure.

The thesis will propose an algorithmic approach which will be integrated with the existing physical synthesis tools at the DTU Compute department. The proposed approach will be evaluated using several case studies.