Plasmonic Sensor Could Enable Label-Free DNA Sequencing

Deep learning-driven forward and inverse design of nanophotonic nanohole arrays: streamlining design for tailored optical functionalities and enhancing accessibility

In nanophotonics, nanohole arrays (NHAs) are periodic arrangements of nanoscale apertures in thin films that provide diverse optical functionalities essential for various applications. Fully studying NHAs' optical properties and optimizing performance demands understanding both materials and geometric parameters, which presents a computational challenge due to numerous potential combinations. Efficient computational modeling is critical for overcoming this challenge and optimizing NHA-based device performance. Traditional approaches rely on time-consuming numerical simulation processes for device design and optimization. However, using a deep learning approach offers an efficient solution for NHAs design. In this work, a deep neural network within the forward modeling framework accurately predicts the optical properties of NHAs by using device structure data such as periodicity and hole radius as model inputs. We also compare three deep learning-based inverse modeling approaches-fully connected neural network, convolutional neural network, and tandem neural network-to provide approximate solutions for NHA structures based on their optical responses. Once trained, the DNN accurately predicts the desired result in milliseconds, enabling repeated use without wasting computational resources. The models are trained using over 6000 samples from a dataset obtained by finite-difference time-domain (FDTD) simulations. The forward model accurately predicts transmission spectra, while the inverse model reliably infers material attributes, lattice geometries, and structural parameters from the spectra. The forward model accurately predicts transmission spectra, with an average Mean Squared Error (MSE) of 2.44 × 10-4. In most cases, the inverse design demonstrates high accuracy with deviations of less than 1.5 nm for critical geometrical parameters. For experimental verification, gold nanohole arrays are fabricated using deep UV lithography. Validation against experimental data demonstrates the models' robustness and precision. These findings show that the trained DNN models offer accurate predictions about the optical behavior of NHAs.

Genomic variant benchmark: if you cannot measure it, you cannot improve it

Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future challenges. However, they depend on sequencing technology, reference genome, and available benchmarking methods. Thus, creating a genomic benchmark dataset is laborious and highly challenging, often involving multiple sequencing technologies, different variant calling tools, and laborious manual curation. In this review, we discuss the available benchmark datasets and their utility. Additionally, we focus on the most recent benchmark of genes with medical relevance and challenging genomic complexity.

Nanoplasmonic biosensors for precision medicine

Nanoplasmonic biosensors have a huge boost for precision medicine, which allows doctors to better understand diseases at the molecular level and to improve the earlier diagnosis and develop treatment programs. Unlike traditional biosensors, nanoplasmonic biosensors meet the global health industry's need for low-cost, rapid and portable aspects, while offering multiplexing, high sensitivity and real-time detection. In this review, we describe the common detection schemes used based on localized plasmon resonance (LSPR) and highlight three sensing classes based on LSPR. Then, we present the recent applications of nanoplasmonic in other sensing methods such as isothermal amplification, CRISPR/Cas systems, lab on a chip and enzyme-linked immunosorbent assay. The advantages of nanoplasmonic-based integrated sensing for multiple methods are discussed. Finally, we review the current applications of nanoplasmonic biosensors in precision medicine, such as DNA mutation, vaccine evaluation and drug delivery. The obstacles faced by nanoplasmonic biosensors and the current countermeasures are discussed.

A Review of Optical Imaging Technologies for Microfluidics

Microfluidics can precisely control and manipulate micro-scale fluids, and are also known as lab-on-a-chip or micro total analysis systems. Microfluidics have huge application potential in biology, chemistry, and medicine, among other fields. Coupled with a suitable detection system, the detection and analysis of small-volume and low-concentration samples can be completed. This paper reviews an optical imaging system combined with microfluidics, including bright-field microscopy, chemiluminescence imaging, spectrum-based microscopy imaging, and fluorescence-based microscopy imaging. At the end of the article, we summarize the advantages and disadvantages of each imaging technology.

Amplification-Free Identification and Determination of Nucleic Acids by Surface Plasmon Resonance and Surface-Enhanced Raman Spectroscopy

This review discusses contemporary approaches to designing sensory systems for the identification and determination of nucleic acids (NAs) without amplifying target molecules. Here we summarize the data about methods based on surface plasmon resonance and surface-enhanced Raman spectroscopy, as well as their possibilities, limitations, and prospects for further development.

Handheld plasmonic biosensor for virus detection in field-settings

After World Health Organization (WHO) announced COVID-19 outbreak a pandemic, we all again realized the importance of developing rapid diagnostic kits. In this article, we introduced a lightweight and field-portable biosensor employing a plasmonic chip based on nanohole arrays integrated to a lensfree-imaging framework for label-free detection of viruses in field-settings. The platform utilizes a CMOS (complementary metal-oxide-semiconductor) camera with high quantum efficiency in the spectral window of interest to monitor diffraction field patterns of nanohole arrays under the uniform illumination of an LED (light-emitting diode) source which is spectrally tuned to the plasmonic mode supported by the nanohole arrays. As an example for the applicability of our biosensor for virus detection, we could successfully demonstrate the label-free detection of H1N1 viruses, e.g., swine flu, with medically relevant concentrations. We also developed a low-cost and easy-to-use sample preparation kit to prepare the surface of the plasmonic chip for analyte binding, e.g., virus-antibody binding. In order to reveal a complete biosensor technology, we also developed a user friendly Python™ - based graphical user interface (GUI) that allows direct access to biosensor hardware, taking and processing diffraction field images, and provides virus information to the end-user. Employing highly sensitive nanohole arrays and lensfree-imaging framework, our platform could yield an LOD as low as 10³ TCID₅₀/mL. Providing accurate and rapid sensing information in a handheld platform, weighing only 70 g and 12 cm tall, without the need for bulky and expensive instrumentation, our biosensor could be a very strong candidate for diagnostic applications in resource-poor settings. As our detection scheme is based on the use of antibodies, it could quickly adapt to the detection of different viral diseases, e.g., COVID-19 or influenza, by simply coating the plasmonic chip surface with an antibody possessing affinity to the virus type of interest. Possessing this ability, our biosensor could be swiftly deployed to the field in need for rapid diagnosis, which may be an important asset to prevent the spread of diseases before turning into a pandemic by isolating patients from the population.

Color Routing via Cross-Polarized Detuned Plasmonic Nanoantennas in Large-Area Metasurfaces

Bidirectional nanoantennas are of key relevance for advanced functionalities to be implemented at the nanoscale and, in particular, for color routing in an ultracompact flat-optics configuration. Here we demonstrate a novel approach avoiding complex collective geometries and/or restrictive morphological parameters based on cross-polarized detuned plasmonic nanoantennas in a uniaxial (quasi-1D) bimetallic configuration. The nanofabrication of such a flat-optics system is controlled over a large area (cm²) by a novel self-organized technique exploiting ion-induced nanoscale wrinkling instability on glass templates to engineer tilted bimetallic nanostrip dimers. These nanoantennas feature broadband color routing with superior light scattering directivity figures, which are well described by numerical simulations and turn out to be competitive with the response of lithographic nanoantennas. These results demonstrate that our large-area self-organized metasurfaces can be implemented in real-world applications of flat-optics color routing from telecom photonics to optical nanosensing.

Scalable Fabrication of Quasi-One-Dimensional Gold Nanoribbons for Plasmonic Sensing

Plasmonic nanostructures have a wide range of applications, including chemical and biological sensing. However, the development of techniques to fabricate submicrometer-sized plasmonic structures over large scales remains challenging. We demonstrate a high-throughput, cost-effective approach to fabricate Au nanoribbons via chemical lift-off lithography (CLL). Commercial HD-DVDs were used as large-area templates for CLL. Transparent glass slides were coated with Au/Ti films and functionalized with self-assembled alkanethiolate monolayers. Monolayers were patterned with lines via CLL. The lifted-off, exposed regions of underlying Au were selectively etched into large-area grating-like patterns (200 nm line width; 400 nm pitch; 60 nm height). After removal of the remaining monolayers, a thin In2O3 layer was deposited and the resulting gratings were used as plasmonic sensors. Distinct features in the extinction spectra varied in their responses to refractive index changes in the solution environment with a maximum bulk sensitivity of ∼510 nm/refractive index unit. Sensitivity to local refractive index changes in the near-field was also achieved, as evidenced by real-time tracking of lipid vesicle or protein adsorption. These findings show how CLL provides a simple and economical means to pattern large-area plasmonic nanostructures for applications in optoelectronics and sensing.

Enhanced extraordinary optical transmission and refractive-index sensing sensitivity in tapered plasmonic nanohole arrays

The phenomenon of extraordinary optical transmission (EOT) caused by light through metallic nanohole arrays has attracted significant attention due to its potential applications for monolithic color filters and ultrasensitive label-free biosensing. However, the EOT spectra of these nanohole arrays have multiple resonance peaks that are spectrally close to each other due to the multiple resonance modes generated by different media on the upper and lower surfaces of metal. In addition, owing to the absorption loss of metal and the scattering of holes, the EOT resonance peaks have low transmission coefficient for practical applications. In this work, utilizing a tapered nanohole arrays structure which is stacked by multiple cylindrical holes with the same depth but different radii, we show that tapered nanohole arrays can effectively suppress the excitation of multiple resonance peaks, and a single EOT peak emerges in the transmission spectrum and simultaneously exhibits significantly enhanced transmission (∼7 times) and narrow linewidth (∼15 nm). The enhanced EOT of tapered nanohole arrays can be also found in other wavelength regions and plasmonic materials. Benefiting from isolated transmission peak, high transmission efficiency and extremely narrow linewidth, a highly sensitive plasmonic nanosensor with sensitivity of 1580 nm/RIU and figure of merit of 105 can be attained. We believe that the tapered nanohole structure would enable applications for ultrasensitive sensors, switches and efficient filters.

Advances in Surface Plasmon Resonance Imaging and Microscopy and Their Biological Applications

Surface plasmon resonance microscopy and imaging are optical methods that enable observation and quantification of interactions of nano- and microscale objects near a metal surface in a temporally and spatially resolved manner. This review describes the principles of surface plasmon resonance microscopy and imaging and discusses recent advances in these methods, in particular, in optical platforms and functional coatings. In addition, the biological applications of these methods are reviewed. These include the detection of a broad variety of analytes (nucleic acids, proteins, bacteria), the investigation of biological systems (bacteria and cells), and biomolecular interactions (drug-receptor, protein-protein, protein-DNA, protein-cell).

Nanohole array plasmonic biosensors: Emerging point-of-care applications

Point-of-care (POC) applications have expanded hugely in recent years and is likely to continue, with an aim to deliver cheap, portable, and reliable devices to meet the demands of healthcare industry. POC devices are designed, prototyped, and assembled using numerous strategies but the key essential features that biosensing devices require are: (1) sensitivity, (2) selectivity, (3) specificity, (4) repeatability, and (5) good limit of detection. Overall the fabrication and commercialization of the nanohole array (NHA) setup to the outside world still remains a challenge. Here, we review the various methods of NHA fabrication, the design criteria, the geometrical features, the effects of surface plasmon resonance (SPR) on sensing as well as current state-of-the-art of existing NHA sensors. This review also provides easy-to-understand examples of NHA-based POC biosensing applications, its current status, challenges, and future prospects.