Abstract

As we strive to engineer biological systems, we must first understand the fundamental parts. This requires
us to examine vast arrays of genetic variation, potentially ranging from hundreds to millions of subtle differences
for each system, highlighting a need for high-throughput automation. Such automation is essential,
not only for facilitating rapid development through continuous cycles of design, construction, and testing,
but ultimately to integrate with machine learning algorithms: a synergy that will bypass the sluggish tempo
of natural evolution and unleash a massive wave of synthetic biology.
In addressing automation needs, this thesis delves into the development and implementation of droplet
and digital microfluidics technologies. These innovations mark a significant breakthrough in automation
while also introduce added benefits of miniaturization. Additionally, the use of optogenetics to control gene
expression presents an opportunity to interface biology with the highly established field of digital control
systems.
The thesis is structured into distinct chapters, each contributing uniquely to the field. The foreword acts
as a guide for the thesis. The first chapter offers a thorough exploration of droplet microfluidics in synthetic
biology, highlighting its critical role and projecting its contribution to the forthcoming bio-revolution.
This is followed by three primary research studies. The first study details innovative techniques in digital
microfluidics for DNA assembly and transformation. The second study focuses on developing optogenetic
control of gene expression, using a model-based design strategy. The third study discusses the integration
of optogenetic systems within a droplet-in-channel microfluidic environment, showcasing the potential for
future applications in synthetic biology and beyond. The concluding chapter serves as a reflection and ties
these works to a greater synthetic biology vision.
Through these studies, this thesis not only addresses the immediate needs of automation in synthetic biology
but also establishes a foundation for future research, highlighting the need for microfluidic technologies.