Optimization of Trustworthy Biomolecular Quantitative Analysis Using Cyber-Physical Microfluidic Platforms

Abstract

Considerable effort has been devoted in recent years to the design and implementation of microfluidic platforms for biomolecular quantitative analysis. However, today's platforms suffer from two major limitations: (1) they were optimized for sample-limited analyses, thus they are inadequate for practical quantitative analysis and the processing of multiple samples through independent pathways; (2) the integrity of these platforms and their biochemical operations is still an open question, since no protection schemes were developed against adversarial contamination or result-manipulation risks. Design optimization techniques for microfluidics have been studied in recent years, but they overlook the myriad complexities of biomolecular protocols and are yet to make an impact in microbiology research. The realization of microfluidic platforms for real-life quantitative analysis requires: (1) a new optimization flow that is based on the realistic modeling of biomolecular protocols, and (2) a microfluidic security flow that provides a high-level of confidence in the integrity of miniaturized quantitative analysis. Motivated by the above needs, this dissertation is focused on optimized and trustworthy transfer of benchtop biomolecular analysis, particularly epigenetic studies, to programmable and cyber-physical microfluidic biochips. The dissertation first presents a set of optimization mechanisms that leverages cyber-physical integration to enable real-time execution of multi-sample biomolecular analysis. The proposed methods include a resource-allocation scheme that responds to decisions about the protocol flow, an interactive firmware that collects and analyzes sensor data, and a spatio-temporal reconfiguration technique that aims to enhance the reliability of the microfluidic system. An envisioned design for an Internet-of-Things (IoT)-based microfluidics-driven service is also presented to cope with the complexity of coordinated biomolecular research. Next, this dissertation advances single-cell protocols by presenting optimized microfluidic methods for high-throughput cell differentiation. The proposed methods target pin-constrained design of reconfigurable microfluidic systems and real-time synthesis of a pool of heterogeneous cells through the complete flow of single-cell analysis. A performance model related to single-cell screening is also presented based on computational fluid-dynamics simulations. With the increasing complexity of microbiology research, optimized protocol preparation and fault-tolerant execution have become critical requirements in today's biomolecular frameworks. This dissertation presents a design method for reagent preparation for parameter-space exploration. Trade-offs between reagent usage and protocol efficiency are investigated. Moreover, an integrated design for automated error recovery in cyber-physical biochips is demonstrated using a fabricated chip. In order to ensure high confidence in the outcome of biomolecular experiments, appropriate security…