Phd in MATHEMATICAL MODELS FOR ENGINEERING, ELECTROMAGNETICS AND
NANOSCIENCES

Thesis title: Multiplexable biosensing via Bloch Surface Waves sustained by one-dimensional Photonic Crystal for antigen, antibody, and miRNA biomarkers’ detection

In the frame of sensing and biosensing, many efforts have been spent within the last decade to improve several parameters such as miniaturization and streamline. To this purpose, optical sensing represents one of the most promising tools. This can be ascribed mainly to the intrinsic speed of information extraction from a sample, theoretically limited only from the speed of light in a medium, and the unique non-disruptive and non-invasive nature of light-matter interaction. With the aim of participating to the answer to the global demand of strategies to contrast rising life-threatening conditions, here a disposable optical biosensor based on one-dimensional photonic crystals (1DPC) is presented as an appealing diagnostic tool for different type of molecular biomarkers (peptides and oligonucleotides). The main goal has been set on early detection of biomolecular compounds identified as a systemic signature of conditions such as breast cancer, stroke, and infective diseases to increase the survival probability and improve life perspective of patients. As far as cancer is concerned, according to World Cancer Research Fund data published in 2020, breast cancer represents the most occurring cancer in women worldwide as well as the most common cancer. On the other hand, stroke, which is defined as medical condition in which poor blood flow to the brain causes cell death, can occur in two different forms: ischemic (insufficient blood flow) and haemorrhagic (vascular bleeding). Finally, the mankind, but not only, has become tragically familiar with extremely high infective respiratory syndromes because of the SARS CoV 2 pandemic. This made evidence of how rapid detection of the virions biomarkers or the immune system signature of response to infection can critically increase survival probabilities as well as a prompt contagion confinement. In order to assess positivity for a specific biomarker, a 1DPC coated biochip and an optical readout system are used. The SiO2 , Ta2O5 and TiO2 based photonic crystal nanostructures are deposited onto a disposable, prism-shaped, organic and disposable substrate made of TOPAS , a cyclic olefine copolymer, to excite the Bloch Surface Waves (BSW) by means of a prism coupling system (Kretschmann-Raether configuration). The whole setup is able to combine label-free (LF) and Fluorescence (FLUO) detection modes. This synergism leads to a real-time monitoring of the bioassay localized onto the 1DPC surface (LF mode) by tracing the refractive index changes of the 1DPC interface with the external medium, while providing a lower limit of detection exploiting resonant amplification end strong directionality collection of fluorescence emission (FLUO mode). Furthermore, we report on the optimization of the main parameters of the 1DPC surface chemistry modification process to show how the maximization of the biosensor detection ability has been carried out. Being based on organo-silane and organic compounds, the surface chemistry used reveals to be versatile and able to implement detection of different type of biomarkers: a protein in the case of breast cancer, an anti-human antibody for SARS-CoV 2, and a short oligonucleotide fragment in the case of stroke. A further improvement of the detection strategy is implemented by multiplexing the type of information that can be extracted per single test. This is achieved exploiting a high precision printing system to pattern the biochip sensing area with different molecular probes. Such a feature leads to a direct assessment of information about the presence of one or multiple biomarkers or the affinity of the same biomarker towards different molecular probes. For the sake of completeness, a preliminary study on birefringence of the TOPAS biochips is included. This side-investigation has been performed to generally improve the quality of the recorded signal. The polymeric, prism shaped substrates onto which the photonic crystal is deposited show birefringence features. This affects the properties of the light and, as a consequence, the information that the light brings with itself.