Guiding Light to Detect Life: Nanowires for Optical Biosensing

Semiconductor nanowires provide a versatile platform for fluorescence-based detection enabled by their high refractive index and waveguiding properties, which amplify excitation and emission from surface-bound fluorophores. Together with their large surface-to-volume ratio, these features enable enhanced and even single-molecule sensitivity.This thesis explores the use of gallium phosphide (GaP) and silicon (Si) nanowires through integrated experimental and computational studies, demonstrating their capabilities for sensitive and quantitative biosensing applications. Using single-emitter localization on well-spaced vertical nanowires combined with brightfield microscopy and systematic analysis, detection ranges can extend over five orders of magnitude, reaching femtomolar levels in streptavidin-biotin assays. Similarly, immobilizing fluorescent molecular beacons on nanowires improves signal-to-background contrast and allows direct oligonucleotide detection at sub-nanomolar concentrations. The nanowire geometry also facilitates extraction of off-plane molecular positions: by modeling point spread functions and training convolutional neural networks on simulated datasets, axial localization accuracies below 100 nm are achieved, enabling tracking of labeled DNA diffusing in supported lipid bilayers.Nanowires also function effectively in complex sample environments. When embedded in polymer matrices and imaged through transparent substrates, they overcome scattering and absorption in opaque media, allowing sub-nanomolar detection of fluorescently labeled proteins in whole blood, lipid emulsions, and powdered milk without sample processing. Overall, this thesis expands the application scope of semiconductor nanowires for optical biosensing, demonstrating single-molecule detection, extended dynamic range, direct oligonucleotide sensing, three-dimensional localization, and operation in opaque biological samples.