Bridging Scales – Nanofabrication and Microfluidics for Sensing and Cell Culture Platforms

QC 20250411

Abstract

Biology and medicine have seen groundbreaking discoveries, from ion channels to induced pluripotent stem cells, resulting in a paradigm shift. The advancements in physical sciences and engineering have always been pivotal in unlocking mysteries of biology and highlighting that the new frontiers lie in deepening our understanding at the single-cell and single-molecule levels. Applying different physical and engineering principles sheds new light on our understanding of complex biological systems at the single-cell and single-molecule level, enabling the development of various technologies such as single-molecule detection, organ-on-chip platforms, and organoids. The development of these technologies offers valuable insights into disease progression and personalized therapeutic strategies. The advancements in micro and nanofabrication propel the development of sensing platforms and biological devices that pave the way for novel solutions, ensuring the best of both worlds. This thesis aims to contribute to advancing the fields of single-molecule sensing and cell therapy by integrating biological discoveries and engineering advancements to develop novel engineering toolboxes. 

The first part of this thesis introduces and describes two approaches for single-molecule sensing and detection, specifically tunneling nanogaps and solid-state nanopore-based sensing platforms. The first work reports the custom measurement setup built during the project, which facilitates automated probing and testing arrays with hundreds of tunnel junctions in liquid with integrated microfluidics, current in the pA range, and at sampling rates up to 200 kHz. This setup highlights key electrical and microfluidic components and design choices to achieve a scalable measurement method, providing a platform for further studies and development in this field and enabling the potential for dynamic sensing. The second work in this thesis investigates the fabrication and electrical behavior of tunnel junctions in various gaseous and liquid media by feedback-controlled electromigration of microfabricated gold nanoconstrictions. This work maps the conductance stability and characteristics of the resulting tunnel junctions, highlighting various considerations and challenges in working with on-chip integrated tunnel junctions to guide future efforts. 

In the third work, we shift our focus to solid-state nanopores and demonstrate that the nanopores fabricated by controlled dielectric breakdown could be localized at the site of femtosecond laser exposure on a pristine silicon nitride membrane. We analyze the sensing potential of these nanopores by the translocation of double-stranded DNA through the pores. The fourth work uses the solid-state nanopore platform to detect and study the binding of Estrogen Receptor Alpha to the Estrogen Receptor Elements on the DNA. The work on tunnel junction and solid-state nanopore-based sensing modalities holds potential for further development in the field of single-(bio)molecule sensing.

The second part of this thesis presents a microfluidic chip platform that enables simple and fast reprogramming of somatic cells, such as fibroblasts, into induced pluripotent stem cells (iPSCs). These iPSCs can then be differentiated further into functional ectodermal cell types towards neural lineage, resulting in neural stem cells on the chip. Furthermore, using bulk-RNA sequencing, we observed that the microfluidic platform boosted commitment toward generating neural stem cells while reducing biological variability compared to a conventional well plate. Our method provides a simple platform with considerably reduced reagent requirements, cellular input, and manual labor, leading to substantial cost savings and holding potential for the highly controlled generation of clinical-grade iPSCs and differentiated cells for cellular therapeutics.

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