Living Photonics: Lab-on-a-chip technologies for light coupling into biological cells

Student thesis: Doctoral thesis


This dissertation encompasses our research on Lab-on-a-Chip (LoC) technologies enabling light coupling into biological cell layers like bacterial biofilms or monolayers of eukaryotes, with the aim of making the cells act as living photonic components in the dual role of optical transducer and reporter. The concept of living photonics suggests a host of possibilities in terms of contactless and minimal invasive monitoring of biological processes based on a self-referenced spectral response over time. The implementation of such living photonic elements however presented a very multifaceted challenge, ranging from biological aspects over numerical simulations and optical design, advancements in low-cost micro-fabrication and adaptation of novel materials for PhLoC fabrication and cell culture to optical interfacing and data processing. In particular, we focussed on monitoring bacterial biofilms and mammalian cell monolayers for their relevance in public health. Bacterial biofilms are a major risk due to their ubiquity, resistance to biocides and dynamism and therefore require an intensive control, for which miniaturised and affordable instrumentation would be ideal, very few though is available. Cell monolayers on the other hand are studied extensively in relation with chronic conditions like cardiovascular diseases or diabetes, Our contributions regarding optical interfacing focus on robust and standardised optical connections to and from a PhLoC using a low-cost fast prototyping approach based on CO2-laser processing. In particular, careful characterisation of poly-methylmetacrylate (PMMA) laser machining allowed reliable ‘plug’ connections to standard 푆��푀��퐴�� fiber-optics connectors, which were benchmarked against commercial counterparts and applied to light coupling in thin film polymeric waveguides in a high Signal-to-Noise ratio (SNR) PhLoC configuration. Here, optical simulations were mainly employed in the design. In addition, we developed a modular software interface for integral control of laboratory equipment based on the cross platform and open source programming language Python. Besides taking care of the rather extensive data processing implicit in long-term spectral monitoring via efficient number crunching modules like Numpy, interfacing with the Qt software development kit proved apt for real time graphical feedback with fast response times. Our contributions regarding miniaturised monitoring instrumentation of bacterial biofilms focus on integrating photonic components in thermoplastic substrates - in particular commercial grade PMMA - to provide a cheap platform for the study of biofilm colonisation in water distribution systems. By locally modifying the surface in the detection zone, we achieved preferential adhesion and early optical detection of bacteria in static conditions via fiber-optics segments embedded in the modified substrates. For the implementation of prototypes resembling the flux and pressure conditions in real water distribution systems, we also explored the integration of polymeric waveguides with fluidic channels, successfully implementing novel fabrication strategies for the encapsulation of photolithographically obtained SU-8 structures in PMMA PhLoCs . Using these devices, and exploiting our positive results in terms of optical interconnects and software interface, monitoring of a circulating bacterial population suggested that bacterial surface colonisation can in such circumstances indeed be associated with a distinct spectral response over time. Last, we investigated the adjustments to the PhLoC paradigm necessary regarding the implementation of the much thinner mammalian cell monolayers as living photonics. Concretely, we focussed our efforts on the numerical evaluation an optimisation of light confinement in thin irregular layers in low-refractive index environments and the development of suitable strategies to couple light to such structures, taking into account the biological constrains, which were much more pronounced here as compared to biofilms. To that end, different materials were studied in terms of compatibility with the established material parameters, available microfabrication techniques and bio-compatibility. Finally, based on the results regarding suitable materials, we applied two of the resulting PhLoC architectures to in vitro cell cultures in different stages of differentiation or inflammatory processes, respectively.
Date of Award9 Nov 2017
Original languageEnglish
SupervisorAndreu Llobera Adán (Director), Francesc Xavier Muñoz Berbel (Director) & Veronica Ahufinger Breto (Tutor)


  • Cell-lightguides
  • Photonic lab-on-a-chip
  • Chip-to-world int

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