The use of microfluidic technology to compartmentalize an initial sample into discrete and isolated volumes is an important step for many biological and chemical applications, that allows molecules, cells, particles, reagents, and analytes to be spatially constrained, providing unique benefits for their characterization, sorting, and manipulation with low reagent consumption. Discretization can also increase the overall throughput and enable multiplexing.

In this dissertation, two platforms are described to enable microfluidic sample discretization and manipulation. First, (2D) microwell arrays fabricated in thermoplastic cyclic olefin copolymer (COP) are explored as a new approach toward the development of high throughput, low-cost components in disposable diagnostics by utilizing a passive discretization technique. Performance of various 2D array designs is characterized numerically and experimentally to assess the impact of thermoplastic surface energy, fluid flow rate, and device geometry on sample filling and discretization. The design principles are used to successfully scale up the platform without affecting device performance. Loop-mediated isothermal amplification (LAMP) on chip is used to demonstrate the platform’s potential for discretized nucleic acid testing.

Next, pin spotting in nanoliter-scale 2D arrays is demonstrated as technique for high resolution reagent integration to enable multiplexed testing in diagnostics. The potential for nucleic-acid diagnostics is evaluated by performing rolling circle amplification (RCA) on chip with integrated reagents.

Finally, an innovative platform enabling complex discretization and manipulation of aqueous droplets is presented. The system uses simple membrane displacement trap elements as an active technique to perform multiple functions including droplet discretization, release, metering, capture, and merging. Multi-layer polydimethylsiloxane (PDMS) devices with membrane displacement trap (MDT) arrays are used to discretize sample into nanoliter scale droplet volumes, and reliably manipulate individual droplets within the arrays. Performance is characterized for varying capillary number flows, membrane actuation pressures, trap and membrane geometries, and trapped droplet volumes, with operational domains established for each platform function. The novel approach to sample digitization and droplet manipulation is demonstrated through discretization of a dilute bacteria sample, metering of individual traps to generate droplets containing single bacteria, and merging of the resulting droplets to pair the selected bacteria within a single droplet.