High-throughput manipulation of droplets in microfluidic systems [electronic resource]

Droplet microfluidics, in which nanoliter- to picoliter-sized drops are used to encapsulate and compartmentalize molecules or cells, has enabled a wide range of biochemical applications. Examples include digital PCR and directed evolution of enzymes. This technology has demonstrated 100--1000x increase in throughput and up to 1,000,000 times reduction in cost compared with state-of-the-art methods using robots and microtiter plates. Nevertheless, aspects of the technology are not yet fully optimized. Specifically, cross-talk of droplet content and droplet instability during their interrogation compromise assay accuracy and limit the scalability of the technology. The first part of my thesis will focus on the design and synthesis of amphiphilic silica nanoparticles for the stabilization of aqueous drops in fluorinated oils for applications in droplet microfluidics. The success of droplet microfluidics has thus far relied on one type of surfactant (PFPE−PEG, or "EA-surfactants"). However, these surfactants have a key limitation: they cause inter-drop transport of small, hydrophobic molecules. Such transport leads to the cross-talk of droplet contents, and presents a key obstacle to the accurate interrogation of biochemical assays which often employ small hydrophobic molecules as the fluorophore in fluorogenic substrates. We show that such cross-talk is eliminated when surfactants are replaced with nanoparticles as stabilizers. The second part of my thesis will describe our study on the throughput of the serial interrogation of drops. In many biochemical assays, fluorescence is used as a read-out for the reactions occurring inside the drops, and can indicate the presence of cells or molecules of interest. Ability to enumerate fluorescent drops in a high throughput manner is thus advantageous for the rapid detection of various diseases such as sepsis or cancer. The optical detection of fluorescence signal is commonly performed in a serial manner, where drops are injected into a funnel-shaped microchannel consisting of a narrow constriction which forces the drops to arrange in a single file, and to ensure that drops enter the detection region one at a time. We show that the throughput of the serial interrogation process is limited by the rate at which droplets become unstable and undergo undesirable break-up as they flow through the constriction. The third part of my thesis will describe a high-throughput optofluidic droplet interrogation device capable of counting fluorescent drops at a throughput of 254,000 drops per second. I describe a novel approach by integrating the microfluidic channel directly on an image sensor. The device consists of 16 parallel microfluidic channels bonded directly to a filter-coated two-dimensional Complementary Metal-Oxide-Semiconductor (CMOS) sensor array. Fluorescence signals emitted from the drops are collected by the sensor that forms the bottom of the channel. The proximity of the drops to the sensor facilitates efficient collection of fluorescence emission from the drops, and overcomes the trade-off between light collection efficiency and field of view in conventional microscopy. The interrogation rate of the device is currently limited by the acquisition speed of CMOS sensor, and is expected to increase further as high-speed sensors become increasingly available.

Keywords: Mechanical Engineering.
Advisor: Tang Sindy (Sindy K.Y.) primary advisor. Thesis advisor
Criddle Craig advisor. Thesis advisor
Zheng Xiaolin