FPGA Integrated Optofluidic Biosensor for Real-Time Single Biomarker Analysis.

Md Nafiz Amin,Aaron R. Hawkins,Mohammad Julker Neyen Sampad,Holger Schmidt

doi:10.1109/jphot.2021.3127484

Abstract

Integrated optofluidic biosensors can fill the need for sensitive, amplification-free, multiplex single molecule detection which is relevant for containing the spread of infectious diseases such as COVID-19. Here, we demonstrate a rapid sample-to-answer scheme that uses a field programmable gate array (FPGA) to enable live monitoring of single particle fluorescence analysis on an optofluidic chip. Fluorescent nanobeads flowing through a micro channel are detected with 99% accuracy and particle concentrations in clinically relevant ranges from 3.4×104 to 3.4 × 106/ml are determined within seconds to a few minutes without the need for post-experiment data extraction and analysis. In addition, other extract salient experimental parameters such as dynamic flow rate changes can be monitored in real time. The sensor is validated with real-time fluorescence detection of single bacterial plasmid DNA at attomolar concentrations, showing excellent promise for implementation as a point of care (POC) diagnostic tool.

Highlights

THE need for sensitive, quick and compact diagnostic platforms for instant screening of infectious diseases has been brought into sharp focus by the COVID-19 pandemic [1], [2]
field programmable gate array (FPGA) integrated camera based real-time imaging has been implemented for various applications [26], [27], as has been for single molecule detection with avalanche photo detectors (APD) [29]
For the real-time analysis scheme, the APD output pulse signal is connected to a field programmable gate array (FPGA) (Xilinx Artix-7 FPGA AC701 Evaluation Kit), which is programmed with a custom written verilog code for acquiring and analyzing the input electronic signal for detecting the salient features of the collected fluorescence signal (The detail algorithm is explained in the “Algorithm Design” section)

Summary

INTRODUCTION

THE need for sensitive, quick and compact diagnostic platforms for instant screening of infectious diseases has been brought into sharp focus by the COVID-19 pandemic [1], [2]. For enhanced performance and applications, recently optofluidic devices have been developed exploiting optical properties such as fluorescence [8], [9], Raman scattering [10], and refractive index change [11] combined with different imaging systems [12]–[14] One of these approaches to an optofluidic analysis platform is based on liquid- and solid-core anti-resonant reflecting optical waveguides (ARROW) and has shown all the advantages of combining microfluidics and optical sample analysis on a single chip [15]–[17]. Real-time implementation enabled by a custom written Verilog program processes signal photon counts hierarchically in three parallel blocks which removes the time constrains of a serial processing scheme This approach is demonstrated with the real-time analysis of fluorescent nanobeads and individual bacterial plasmid DNAs. A comparison with MATLAB based post-processing analysis shows reliable target detection with 99% accuracy. We demonstrate the determination of dynamic changes in the particle flow rate as a result of mechanical pressure changes, illustrating the ability to monitor and adapt experimental parameters on the fly

EXPERIMENTAL PLATFORM DESIGN

Background

ALGORITHM DESIGN

RESULTS AND DISCUSSION

CONCLUSION