On the effect of digitising flows in networked microfluidic systems for nucleic acid analysis

The integration of molecular diagnostics and microfluidics has the potential to revolutionise human health care. The continuous discovery of genetic markers that correspond to particular cancer types and subtypes offers a large potential for non-invasive patient screening. Early and accurate diagnosis has the potential to lead to tailored treatments and a better patient prognosis. The research undertaken here at the Stokes Institute aims to develop a diagnostic tool through current advancements in genomics and microfluidics, for the accurate and early diagnosis of paediatric leukaemia. Applying microfluidics to the current molecular diagnostic protocols offers a decrease in costs through a reduction in consumable reagents and an increase in speed and consistency through integration of all the functional steps of qPCR. The research presented in this thesis focuses on the hydrodynamics of biphasic flow. Encapsulating the genetic material and PCR reagents into a micro-reactor (microfluidic plug) allows for individual and contamination-free processing. The pressure drop of individual plugs under a range of operational conditions is measured and presented. An analysis of the effect of the concentration of surfactant that is employed has on the biphasic hydrodynamics is examined. The data is subsequently analysed and compared to a theoretical approximation that is present in the literature. The ratio of biphasic fluidic resistance to single phase fluidic resistance is presented as a means to measure empirically the effect a second immiscible phase has on the hydrodynamics. A train of immiscible plugs is shown to have a lower pressure drop than a single plug of similar total length when the inter-plug spacing is sufficiently large. Three microfluidic manifolds were tested as microfluidic circuit elements. Fluidic manifolds provide a controllable means of distributing a single flow across numerous microfluidic capillaries and circuit elements. Two prototype manifolds were designed and compared to a commercially available product. The sensitivity of a manifold to changes in fluidic resistance and air contamination is also presented. Liquid bridges were employed as circuit elements and pressure taps. This is, to the best knowledge of the author, the first use of liquid bridges as pressure taps. The liquid bridges isolated the aqueous plugs from the pressure port taps preventing sense line contamination. A pressure transient analysis was carried out to determine the effect of the liquid bridges on biphasic flow. The incorporation of the three microfluidic elements into a single circuit was analysed under biphasic flow conditions. Two analytical models of microfluidic circuits are presented for the queuing and mixing of aqueous plugs prior to processing. The pressure drop data was used to validate the employment of a modified single phase analytical model for the design of biphasic microfluidic circuits for low Capillary and Reynolds number flows.