Optimized ARROW-Based MMI Waveguides for High Fidelity Excitation Patterns for Optofluidic Multiplexing

Free-Space Excitation of Optofluidic Devices for Pattern-Based Single Particle Detection

Optofluidic sensors have enabled single molecule sensing using planar, waveguide dependent multi-spot fluorescence excitation. Here, we demonstrate a new approach to single-particle fluorescence sensing using free-space, top-down illumination of liquid-core antiresonant reflecting optical waveguide (ARROW) devices using two different multi-spot excitation techniques. First, the liquid core ARROW waveguide is excited with a focused beam through a slit pattern milled into an opaque aluminum film, showing comparable performance for single bead fluorescence detection as in-plane, multi-mode interference waveguide based excitation. The second top-down illumination technique images the spot pattern from a Y-splitter SiO₂ waveguide chip directly onto the detection device for efficient power utilization and circumventing the need for an opaque cover, producing a further 2.7x improvement in signal-to-noise ratio. The two top-down approaches open up new possibilities for chip-based optical particle sensing with relaxed alignment tolerances.

Performance Comparison of Flow-Through Optofluidic Biosensor Designs

Optofluidic flow-through biosensors are being developed for single particle detection, particularly as a tool for pathogen diagnosis. The sensitivity of the biosensor chip depends on design parameters, illumination format (side vs. top), and flow configuration (parabolic, two- and three-dimensional hydrodynamic focused (2DHF and 3DHF)). We study the signal differences between various combinations of these design aspects. Our model is validated against a sample of physical devices. We find that side-illumination with 3DHF produces the strongest and consistent signal, but parabolic flow devices process a sample volume more quickly. Practical matters of optical alignment are also discussed, which may affect design choice.

Optofluidic Flow-Through Biosensor Sensitivity - Model and Experiment

We present a model and simulation for predicting the detected signal of a fluorescence-based optical biosensor built from optofluidic waveguides. Typical applications include flow experiments to determine pathogen concentrations in a biological sample after tagging relevant DNA or RNA sequences. An overview of the biosensor geometry and fabrication processes is presented. The basis for the predictive model is also outlined. The model is then compared to experimental results for three different biosensor designs. The model is shown to have similar signal statistics as physical tests, illustrating utility as a pre-fabrication design tool and as a predictor of detection sensitivity.

7X multiplexed, optofluidic detection of nucleic acids for antibiotic-resistance bacterial screening

Rapid and accurate diagnosis of bacterial infections resistant to multiple antibiotics requires development of new bio-sensors for differentiated detection of multiple targets. This work demonstrates 7x multiplexed detection for antibiotic-resistance bacterial screening on an optofluidic platform. We utilize spectrally multiplexed multi-spot excitation for simultaneous detection of nucleic acid strands corresponding to bacterial targets and resistance genes. This is enabled by multi-mode interference (MMI) waveguides integrated in an optofluidic device. We employ a combinatorial three-color labeling scheme for the nucleic acid assays to scale up their multiplexing capability to seven different nucleic acids, representing three species and four resistance genes.

A Low-Cost Time-Correlated Single Photon Counting Portable DNA Analyzer

Photon-counting analysis of nucleic acids plays a key role in many diagnostics applications for its accurate and non-invasive nature. However, conventional photon-counting instrumentations are bulky and expensive due to the use of conventional optics and a lack of optimization of electronics. In this paper, we present a portable, low-cost time-correlated single photon-counting (TCSPC) analysis system for DNA detection. Both optical and electronic subsystems are carefully designed to provide effective emission filtering and size reduction, delivering good DNA detection and fluorescence lifetime extraction performance. DNA detection has been verified by fluorescence lifetime measurements of a V-carbazole conjugated fluorophore lifetime bioassay. The time-to-digital module of the proposed TCSPC system achieves a full width at half maximum (FWHM) timing resolution from 121 to 145 ps and a differential non-linearity (DNL) between −8.5% and +9.7% of the least significant bit (LSB) within the 500 ns full-scale range (FSR). With a detection limit of 6.25 nM and a dynamic range of 6.8 ns, the proposed TCSPC system demonstrates the enabling technology for rapid, point-of-care DNA diagnostics.

Liquid-core waveguide TCSPC sensor for high-accuracy fluorescence lifetime analysis

Liquid-core waveguide (LCW) has many advantages such as the elimination of optical artifacts typically exhibited in systems employing lenses and filters. However, due to the effect of temporal dispersion, LCWs are typically employed in steady-state fluorescence detection microsystems rather than in fluorescence lifetime measurement (FLM) systems. In this paper, we present a compact liquid-core waveguide time-correlated single-photon counting (LCW-TCSPC) sensor for FLM. The propagation of excitation within the LCW is analyzed both analytically and in simulations, with results in agreement with experimental characterization. Results reveal an optimal region within the LCW for highly accurate FLM. The proposed prototype achieves excellent excitation rejection and low temporal dispersion as a result of optimization of the propagation length of the excitation within the LCW. The prototype achieves a detection limit of 5 nM for Coumarin 6 in dimethyl sulfoxide with < 3% lifetime error. The techniques proposed for analyzing the LCW for TCSPC based FLM and prototype demonstration pave the way for developing high-performance fluorescence lifetime measurement for microfluidics and point-of-care applications. Graphical abstract A compact liquid-core waveguide time-correlated single-photon counting (LCW-TCSPC) sensor for fluorescence lifetime measurement (FLM) is presented. Results reveal an optimal propagation length region within the LCW for highly accurate FLM. The prototype achieves a detection limit of 5 nM for Coumarin 6 in dimethyl sulfoxide with < 3% lifetime error.