Denoising of Fluorescence Image on the Surface of Quantum Dot/Nanoporous Silicon Biosensors

In the process of biological detection of porous silicon photonic crystals based on quantum dots, the concentration of target organisms can be indirectly measured via the change in the gray value of the fluorescence emitted from the quantum dots in the porous silicon pores before and after the biological reaction on the surface of the device. However, due to the disordered nanostructures in porous silicon and the roughness of the surface, the fluorescence images on the surface contain noise. This paper analyzes the type of noise and its influence on the gray value of fluorescent images. The change in the gray value caused by noise greatly reduces the detection sensitivity. To reduce the influence of noise on the gray value of quantum dot fluorescence images, this paper proposes a denoising method based on gray compression and nonlocal anisotropic diffusion filtering. We used the proposed method to denoise the quantum dot fluorescence image after DNA hybridization in a Bragg structure porous silicon device. The experimental results show that the sensitivity of digital image detection improved significantly after denoising

Simultaneous Refractive Index Sensing Using an Array of Suspended Porous Silicon Membranes

[EN] We propose a fast and cost-effective method for obtaining a miniaturized array-formatted sensor suitable for multiplexed detection. Our solution is based on the fabrication of multiple mu m-sized suspended porous silicon (PSi) membranes working as independent transducers. Our process can potentially integrate an array of up to 1000 sensing spots per cm(2). We also propose a simple and user-friendly optical platform to simultaneously interrogate each element of the array in real-time. The feasibility of this idea was proved performing several sensing experiments where we were able to detect refractive index (RI) variations with different transducers at the same time. An average experimental sensitivity of 685 nm/RIU (Refractive Index Unit) was achieved, with a theoretical limit of detection (LoD) of 2.10(-4) RIU. The analyzed sensing spots displayed similar behavior both in time and in magnitude. We believe that the high capabilities of the sensor presented in this work, along with the sensing mechanism, can be very useful for multi-parametric analysis and multi-target detection of biological samples.This work was supported in part by the Ministry of Economy and Competitiveness and Spanish National Research Council under Project TEC2015-63838-C3-1-R-OPTONANOSENS and in part by the Generalitat Valencia under Project AVANTI/2019/123.Martín-Sánchez, D.; Ivanova-Angelova, T.; García-Rupérez, J. (2020). Simultaneous Refractive Index Sensing Using an Array of Suspended Porous Silicon Membranes. IEEE Sensors Journal. 20(15):8497-8504. https://doi.org/10.1109/JSEN.2020.2983218S84978504201

Aptamer-based optical biosensors

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Simultaneous Refractive Index Sensing Using an Array of Suspended Porous Silicon Membranes

We propose a fast and cost-effective method for obtaining a miniaturized array-formatted sensor suitable for multiplexed detection. Our solution is based on the fabrication of multiple µm-sized suspended porous silicon (PSi) membranes working as independent transducers. Our process can potentially integrate an array of up to 1000 sensing spots per cm2 . We also propose a simple and user-friendly optical platform to simultaneously interrogate each element of the array in real-time. The feasibility of this idea was proved performing several sensing experiments where we were able to detect refractive index (RI) variations with different transducers at the same time. An average experimental sensitivity of 685 nm/RIU (Refractive Index Unit) was achieved, with a theoretical limit of detection (LoD) of 10-5 RIU. The analyzed sensing spots displayed similar behavior both in time and in magnitude. We believe that the high capabilities of the sensor presented in this work, along with the sensing mechanism, can be very useful for multi-parametric analysis and multi-target detection of biological samples

Porous silicon-based aptasensors: The next generation of label-free devices for health monitoring

Aptamers are artificial nucleic acid ligands identified and obtained from combinatorial libraries of synthetic nucleic acids through the in vitro process SELEX (systematic evolution of ligands by exponential enrichment). Aptamers are able to bind an ample range of non-nucleic acid targets with great specificity and affinity. Devices based on aptamers as bio-recognition elements open up a new generation of biosensors called aptasensors. This review focuses on some recent achievements in the design of advanced label-free optical aptasensors using porous silicon (PSi) as a transducer surface for the detection of pathogenic microorganisms and diagnostic molecules with high sensitivity, reliability and low limit of detection (LoD)

Highly sensitive and label-free digital detection of whole cell E. coli with interferometric reflectance imaging

Bacterial infectious diseases are a major threat to human health. Timely and sensitive pathogenic bacteria detection is crucial in identifying the bacterial contaminations and preventing the spread of infectious diseases. Due to limitations of conventional bacteria detection techniques there have been concerted research efforts towards development of new biosensors. Biosensors offering label free, whole bacteria detection are highly desirable over those relying on label based or pathogenic molecular components detection. The major advantage is eliminating the additional time and cost required for labeling or extracting the desired bacterial components. Here, we demonstrate rapid, sensitive and label free E. coli detection utilizing interferometric reflectance imaging enhancement allowing for visualizing individual pathogens captured on the surface. Enabled by our ability to count individual bacteria on a large sensor surface, we demonstrate a limit of detection of 2.2 CFU/ml from a buffer solution with no sample preparation. To the best of our knowledge, this high level of sensitivity for whole E. coli detection is unprecedented in label free biosensing. The specificity of our biosensor is validated by comparing the response to target bacteria E. coli and non target bacteria S. aureus, K. pneumonia and P. aeruginosa. The biosensor performance in tap water also proves that its detection capability is unaffected by the sample complexity. Furthermore, our sensor platform provides high optical magnification imaging and thus validation of recorded detection events as the target bacteria based on morphological characterization. Therefore, our sensitive and label free detection method offers new perspectives for direct bacterial detection in real matrices and clinical samples.First author draf

New perspectives in silicon micro and nanophotonics

In the last two decades, there has been growing interest in silicon-based photonic devices for many optical applications: telecommunications, interconnects and biosensors. In this work, an advance overview of our results in this field is presented. Proposed devices allow overcoming silicon intrinsic drawbacks limiting its application as a photonic substrate. Taking advantages of both non-linear and linear effects, size reduction at nanometric scale and new two-dimensional emerging materials, we have obtained a progressive increase in device performance along the last years. In this work we show that a suitable design of a thin photonic crystal slab realized in silicon nitride can exhibit a very strong field enhancement. This result is very promising for all photonic silicon devices based on nonlinear phenomena. Moreover we report on the fabrication and characterization of silicon photodetectors working at near-infrared wavelengths based on the internal photoemission absorption in a Schottky junction. We show as an increase in device performance can be obtained by coupling light into both micro-resonant cavity and waveguiding structures. In addition, replacing metal with graphene in a Schottky junction, a further improve in PD performance can be achieved. Finally, silicon-based microarray for biomedical applications, are reported. Microarray of porous silicon Bragg reflectors on a crystalline silicon substrate have been realized using a technological process based on standard photolithography and electrochemical anodization of the silicon. Our insights show that silicon is a promising platform for the integration of various optical functionalities on the same chip opening new frontiers in the field of low-cost silicon micro and nanophotonics

Development of nanophotonic biosensor platform towards on-chip liquid biopsy

Liquid biopsy has the potential to enable diagnosis, prognosis, and monitoring of some diseases at an early stage using body fluids from patients. This minimally invasive, label-free detection method is less likely to harm the cell’s viability through binding to the surface protein. Smart integration of liquid biopsy designs with microfluidics on a single chip will lead to a considerable reduction in the detection time (due to controlled diffusion length), and the volumes of sample, agent and reagent, and the limit of detection. Optical label-free biosensors are a powerful tool to analyze biomolecular interactions and have been widely studied in the field of biomedical and biological science and engineering. Label-free detection enables direct measurement of key characteristic properties of the chemical compound, DNA molecule, peptide, protein, virus, or cell, while eliminating experimental uncertainty induced by the effect of the label on molecular conformation, thus reducing the time and effort required for bioassay. Existing optical label-free biosensors suffer from three limitations, including low detection sensitivity, slow molecules mass transfer, and poor throughput. The goal of this dissertation is to overcome these limitations through the development of a novel and efficient modality towards liquid biopsy-based bioassay with increased detection sensitivity, speed, and throughput. To increase the detection sensitivity, we investigate the optical bound states in the continuum (BIC) of slotted high-contrast grating (sHCG) structures. We demonstrate that the sHCG support BICs and high-Q resonant modes, and the slot position can be utilized to tune and optimize the linewidth of the high-Q resonances. To overcome the mass-transfer limitation and reduce the assay time, we propose a lateral flow-through optical biosensor integrating high-contrast gratings and microfluidics on a silicon-on-insulator platform. The biosensor design allows reducing the diffusion length to a submicron scale and enhancing direct interactions between the analytes and sensing structures. Finally, we develop a high-throughput, label-free exosome vesicles (EVs) detection microarray formed on a photonic crystal (PC) biosensor surface. We design and implement a hyperspectral imaging approach to quantify the antibody and EV absorptions on the PC-based microarray consisting of a panel of seven antibodies specific to multiple membrane receptors of the target EVs. We validate that the EV microarray by adopting it to detect EVs released by macrophages for the analysis of immune responses