Hybrid quantum-classical polarizability model for single molecule biosensing.

Optical whispering gallery mode biosensors are able to detect single molecules through effects of their polarizability. We address the factors that affect the polarizability of amino acids, which are the building blocks of life, via electronic structure theory. Amino acids are detected in aqueous environments, where their polarizability is different compared to the gasphase due to solvent effects. Solvent effects include structural changes, protonation and the local field enhancement through the solvent (water). We analyse the impact of these effects and find that all contribute to an increased effective polarizability in the solvent. We also address the excess polarizability relative to the displaced water cavity and develop a hybrid quantum-classical model that is in good agreement with self-consistent calculations. We apply our model to calculate the excess polarizability of 20 proteinogenic amino acids and determine the minimum resolution required to distinguish the different molecules and their ionised conformers based on their polarizability.

Whispering-Gallery Mode Optoplasmonic Microcavities: From Advanced Single-Molecule Sensors and Microlasers to Applications in Synthetic Biology.

Optical microcavities, specifically, whispering-gallery mode (WGM) microcavities, with their remarkable sensitivity to environmental changes, have been extensively employed as biosensors, enabling the detection of a wide range of biomolecules and nanoparticles. To push the limits of detection down to the most sensitive single-molecule level, plasmonic nanorods are strategically introduced to enhance the evanescent fields of WGM microcavities. This advancement of optoplasmonic WGM sensors allows for the detection of single molecules of a protein, conformational changes, and even atomic ions, marking significant contributions in single-molecule sensing. This Perspective discusses the exciting research prospects in optoplasmonic WGM sensing of single molecules, including the study of enzyme thermodynamics and kinetics, the emergence of thermo-optoplasmonic sensing, the ultrasensitive single-molecule sensing on WGM microlasers, and applications in synthetic biology.

Roadmap on optical sensors.

Optical sensors and sensing technologies are playing a more and more important role in our modern world. From micro-probes to large devices used in such diverse areas like medical diagnosis, defence, monitoring of industrial and environmental conditions, optics can be used in a variety of ways to achieve compact, low cost, stand-off sensing with extreme sensitivity and selectivity. Actually, the challenges to the design and functioning of an optical sensor for a particular application requires intimate knowledge of the optical, material, and environmental properties that can affect its performance. This roadmap on optical sensors addresses different technologies and application areas. It is constituted by twelve contributions authored by world-leading experts, providing insight into the current state-of-the-art and the challenges their respective fields face. Two articles address the area of optical fibre sensors, encompassing both conventional and specialty optical fibres. Several other articles are dedicated to laser-based sensors, micro- and nano-engineered sensors, whispering-gallery mode and plasmonic sensors. The use of optical sensors in chemical, biological and biomedical areas is discussed in some other papers. Different approaches required to satisfy applications at visible, infrared and THz spectral regions are also discussed.

Moderate Multidimensional Poverty Index: Paving the Way Out of Poverty.

Eradicating poverty in all its forms, everywhere, requires indicators that measure sustainable pathways out of poverty, and not only the absence of acute poverty. This paper introduces a trial Moderate Multidimensional Poverty Index (MMPI) that reflects moderate rather than acute levels of multidimensional poverty. The MMPI adjusts nine of the 10 indicators of the global Multidimensional Poverty Index (global MPI) to reflect moderate poverty and create a meaningful superset of the acutely poor population. Although data-constrained, the trial MMPI outlines a methodology and potential indicators for a measure that would: (i) be meaningful and comparable across populations at higher levels of development; (ii) align with higher standards defined in Agenda 2030; and (iii) provide insight into aspects of intrahousehold deprivation. The MMPI is illustrated empirically using nationally representative household surveys from Bangladesh, Guatemala, Iraq, Serbia, Tanzania and Thailand. The results confirm the added value of having three nested measures of destitution, acute, and moderate multidimensional poverty. The MMPI also complements monetary measures with informative differences in poverty levels observed. The results demonstrate that a Moderate MPI is a desirable global poverty index, which is likely to illuminate thus far hidden aspects in of multidimensional poverty, such as intrahousehold deprivations in education. Challenges remain regarding data availability, and further study across additional countries is required before the MMPI structure can be finalised.

Anomalous DNA hybridisation kinetics on gold nanorods revealed via a dual single-molecule imaging and optoplasmonic sensing platform.

Observing the hybridisation kinetics of DNA probes immobilised on plasmonic nanoparticles is key in plasmon-enhanced fluorescence detection of weak emitting species, and refractive index based single-molecule detection on optoplasmonic sensors. The role of the local field in providing plasmonic signal enhancements for single-molecule detection has been studied in great detail. Nevertheless, few studies have compared the experimental results in both techniques for single-molecule studies. Here we developed the first optical setup that integrates optoplasmonic and DNA-PAINT based detection of oligonucleotides to compare these sub-platforms and provide complementary insights into single molecule processes. We record the fluorescence and optoplasmonic sensor signals for individual, transient hybridisation events. The hybridisation events are observed in the same sample cell and over a prolonged time (i.e. towards high binding site occupancies). A decrease in the association rate over the measurement duration is reported. Our dual optoplasmonic sensing and imaging platform offers insight into the observed phenomenon, revealing that irreversible hybridisation events accumulate over detected step signals in optoplasmonic sensing. Our results point to novel physicochemical mechanisms that result in the stabilisation of DNA hybridisation on optically-excited plasmonic nanoparticles.

Optical sensors, 2022: introduction to the feature issue.

This feature issue of Optics Express highlights contributions from authors who presented their latest research at the OPTICA Optical Sensors and Sensing Congress, held in Vancouver, British Columbia, Canada from 11-15 July 2022. The feature issue comprises 9 contributed papers, which expand upon their respective conference proceedings. The published papers introduced here cover a range of timely research topics in optics and photonics for chip-based sensing, open-path and remote sensing and fiber devices.

Time-dependent Mandel Q parameter analysis for a hexagonal boron nitride single photon source.

The time-dependent Mandel Q parameter, Q(T), provides a measure of photon number variance for a light source as a function of integration time. Here, we use Q(T) to characterise single photon emission from a quantum emitter in hexagonal boron nitride (hBN). Under pulsed excitation a negative Q parameter was measured, indicating photon antibunching at an integration time of 100 ns. For larger integration times Q is positive and the photon statistics become super-Poissonian, and we show by comparison with a Monte Carlo simulation for a three-level emitter that this is consistent with the effect of a metastable shelving state. Looking towards technological applications for hBN single photon sources, we propose that Q(T) provides valuable information on the intensity stability of single photon emission. This is useful in addition to the commonly used g(2)(τ) function for the complete characterisation of a hBN emitter.

"Grafting-To" Covalent Binding of Plasmonic Nanoparticles onto Silica WGM Microresonators: Mechanically Robust Single-Molecule Sensors and Determination of Activation Energies from Single-Particle Events.

We hereby present a novel "grafting-to"-like approach for the covalent attachment of plasmonic nanoparticles (PNPs) onto whispering gallery mode (WGM) silica microresonators. Mechanically stable optoplasmonic microresonators were employed for sensing single-particle and single-molecule interactions in real time, allowing for the differentiation between binding and non-binding events. An approximated value of the activation energy for the silanization reaction occurring during the "grafting-to" approach was obtained using the Arrhenius equation; the results agree with available values from both bulk experiments and ab initio calculations. The "grafting-to" method combined with the functionalization of the plasmonic nanoparticle with appropriate receptors, such as single-stranded DNA, provides a robust platform for probing specific single-molecule interactions under biologically relevant conditions.

Allosteric Regulation of Glycogen Phosphorylase by Order/Disorder Transition of the 250' and 280s Loops.

Allostery is a fundamental mechanism of protein activation, yet the precise dynamic changes that underlie functional regulation of allosteric enzymes, such as glycogen phosphorylase (GlyP), remain poorly understood. Despite being the first allosteric enzyme described, its structural regulation is still a challenging problem: the key regulatory loops of the GlyP active site (250' and 280s) are weakly stable and often missing density or have large b-factors in structural models. This led to the longstanding hypothesis that GlyP regulation is achieved through gating of the active site by (dis)order transitions, as first proposed by Barford and Johnson. However, testing this requires a quantitative measurement of weakly stable local structure which, to date, has been technically challenging in such a large protein. Hydrogen-deuterium-exchange mass spectrometry (HDX-MS) is a powerful tool for studying protein dynamics, and millisecond HDX-MS has the ability to measure site-localized stability differences in weakly stable structures, making it particularly valuable for investigating allosteric regulation in GlyP. Here, we used millisecond HDX-MS to measure the local structural perturbations of glycogen phosphorylase b (GlyPb), the phosphorylated active form (GlyPa), and the inhibited glucose-6 phosphate complex (GlyPb:G6P) at near-amino acid resolution. Our results support the Barford and Johnson hypothesis for GlyP regulation by providing insight into the dynamic changes of the key regulatory loops.

Proposal for a hybrid clock system consisting of passive and active optical clocks and a fully stabilized microcomb.

Optical atomic clocks produce highly stable frequency standards and frequency combs bridge clock frequencies with hundreds of terahertz difference. In this paper, we propose a hybrid clock scheme, where a light source pumps an active optical clock through a microresonator-based nonlinear third harmonic process, serves as a passive optical clock via indirectly locking its frequency to an atomic transition, and drives a chip-scale microcomb whose mode spacing is stabilized using the active optical clock. The operation of the whole hybrid system is investigated through simulation analysis. The numerical results show: (i) The short-term frequency stability of the passive optical clock follows an Allan deviation of σy(τ) = 9.3 × 10-14τ-1/2 with the averaging time τ, limited by the population fluctuations of interrogated atoms. (ii) The frequency stability of the active optical clock reaches σy(τ) = 6.2 × 10-15τ-1/2, which is close to the quantum noise limit. (iii) The mode spacing of the stabilized microcomb has a shot-noise-limited Allan deviation of σy(τ) = 1.9 × 10-11τ-1/2. Our hybrid scheme may be realized using recently developed technologies in (micro)photonics and atomic physics, paving the way towards on-chip optical frequency comparison, synthesis, and synchronization.

Single Virus Detection on Silicon Photonic Crystal Random Cavities.

On-chip silicon microcavity sensors are advantageous for the detection of virus and biomolecules due to their compactness and the enhanced light-matter interaction with the analyte. While their theoretical sensitivity is at the single-molecule level, the fabrication of high quality (Q) factor silicon cavities and their integration with optical couplers remain as major hurdles in applications such as single virus detection. Here, label-free single virus detection using silicon photonic crystal random cavities is proposed and demonstrated. The sensor chips consist of free-standing silicon photonic crystal waveguides and do not require pre-fabricated defect cavities or optical couplers. Residual fabrication disorder results in Anderson-localized cavity modes which are excited by a free space beam. The Q ≈105 is sufficient for observing discrete step-changes in resonance wavelength for the binding of single adenoviruses (≈50 nm radius). The authors' findings point to future applications of CMOS-compatible silicon sensor chips supporting Anderson-localized modes that have detection capabilities at the level of single nanoparticles and molecules.

SARS-CoV-2 Tests: Bridging the Gap between Laboratory Sensors and Clinical Applications.

This review covers emerging biosensors for SARS-CoV-2 detection together with a review of the biochemical and clinical assays that are in use in hospitals and clinical laboratories. We discuss the gap in bridging the current practice of testing laboratories with nucleic acid amplification methods, and the robustness of assays the laboratories seek, and what emerging SARS-CoV-2 sensors have currently addressed in the literature. Together with the established nucleic acid and biochemical tests, we review emerging technology and antibody tests to determine the effectiveness of vaccines on individuals.

Microscale whispering-gallery-mode light sources with lattice-confined atoms.

Microlasers, relying on the strong coupling between active particles and optical microcavity, exhibit fundamental differences from conventional lasers, such as multi-threshold/thresholdless behavior and nonclassical photon emission. As light sources, microlasers possess extensive applications in precision measurement, quantum information processing, and biochemical sensing. Here we propose a whispering-gallery-mode microlaser scheme, where ultracold alkaline-earth metal atoms, i.e., gain medium, are tightly confined in a two-color evanescent lattice that is in the ring shape and formed around a microsphere. To suppress the influence of the lattice-induced ac Stark shift on the moderately-narrow-linewidth laser transition, the red-detuned trapping beams operate at a magic wavelength while the wavelength of the blue-detuned trapping beam is set close to the other magic wavelength. The tiny mode volume and high quality factor of the microsphere ensure the strong atom-microcavity coupling in the bad-cavity regime. As a result, both saturation photon and critical atom numbers, which characterize the laser performance, are substantially reduced below unity. We explore the lasing action of the coupled system by using the Monte Carlo approach. Our scheme may be potentially generalized to the microlasers based on the forbidden clock transitions, holding the prospect for microscale active optical clocks in precision measurement and frequency metrology.

Sensing Enzyme Activation Heat Capacity at the Single-Molecule Level Using Gold-Nanorod-Based Optical Whispering Gallery Modes.

Here, we report a label-free gold nanoparticle-based single-molecule optical platform to study the immobilization, activity, and thermodynamics of single enzymes. The sensor uses plasmonic gold nanoparticles coupled to optical whispering gallery modes (WGMs) to probe enzyme conformational dynamics during turnover at a microsecond time resolution. Using a glucosidase enzyme as the model system, we explore the temperature dependence of the enzyme turnover at the single-molecule (SM) level. A recent physical model for understanding enzyme temperature dependencies (macromolecular rate theory; MMRT) has emerged as a powerful tool to study the relationship between enzyme turnover and thermodynamics. Using WGMs, SM enzyme measurements enable us to accurately track turnover as a function of conformational changes and therefore to quantitatively probe the key feature of the MMRT model, the activation heat capacity, at the ultimate level of SM. Our data shows that WGMs are extraordinarily sensitive to protein conformational change and can discern both multiple steps with turnover as well as microscopic conformational substates within those steps. The temperature dependence studies show that the MMRT model can be applied to a range of steps within turnover at the SM scale that is associated with conformational change. Our study validates the notion that MMRT captures differences in dynamics between states. The WGM sensors provide a platform for the quantitative analysis of SM activation heat capacity, applying MMRT to the label-free sensing of microsecond substates of active enzymes.

Review of optical sensing and manipulation of chiral molecules and nanostructures with the focus on plasmonic enhancements [Invited].

Chiral molecules are ubiquitous in nature; many important synthetic chemicals and drugs are chiral. Detecting chiral molecules and separating the enantiomers is difficult because their physiochemical properties can be very similar. Here we review the optical approaches that are emerging for detecting and manipulating chiral molecules and chiral nanostructures. Our review focuses on the methods that have used plasmonics to enhance the chiroptical response. We also review the fabrication and assembly of (dynamic) chiral plasmonic nanosystems in this context.

Whispering-gallery microlasers for cell tagging and barcoding: the prospects for in vivo biosensing.

Researchers in the field of whispering-gallery-mode (WGM) microresonators have proposed biointegrated low-threshold WGM lasers, to enable large-scale parallel single-cell tracking and barcoding. Although the reported devices have so far been primarily investigated in model applications, most recent results represent important steps towards the development of in vivo tags and sensors that utilize the unique and narrow spectral features of miniature WGM lasers.

Review of biosensing with whispering-gallery mode lasers.

Lasers are the pillars of modern optics and sensing. Microlasers based on whispering-gallery modes (WGMs) are miniature in size and have excellent lasing characteristics suitable for biosensing. WGM lasers have been used for label-free detection of single virus particles, detection of molecular electrostatic changes at biointerfaces, and barcode-type live-cell tagging and tracking. The most recent advances in biosensing with WGM microlasers are described in this review. We cover the basic concepts of WGM resonators, the integration of gain media into various active WGM sensors and devices, and the cutting-edge advances in photonic devices for micro- and nanoprobing of biological samples that can be integrated with WGM lasers.

Nonlinear Sensing with Whispering-Gallery Mode Microcavities: From Label-Free Detection to Spectral Fingerprinting.

Optical microresonators have attracted intense interests in highly sensitive molecular detection and optical precision measurement in the past decades. In particular, the combination of a high quality factor with a small mode volume significantly enhances the nonlinear light-matter interaction in whispering-gallery mode (WGM) microresonators, which greatly boost nonlinear optical sensing applications. Nonlinear WGM microsensors not only allow for label-free detection of molecules with an ultrahigh sensitivity but also support new functionalities in sensing such as the specific spectral fingerprinting of molecules with frequency conversion involved. Here, we review the mechanisms, sensing modalities, and recent progresses of nonlinear optical sensors along with a brief outlook on the possible future research directions of this rapidly advancing field.

Biosensors and Diagnostics for Fungal Detection.

Early detection is critical to the successful treatment of life-threatening infections caused by fungal pathogens, as late diagnosis of systemic infection almost always equates with a poor prognosis. The field of fungal diagnostics has some tests that are relatively simple, rapid to perform and are potentially suitable at the point of care. However, there are also more complex high-technology methodologies that offer new opportunities regarding the scale and precision of fungal diagnosis, but may be more limited in their portability and affordability. Future developments in this field are increasingly incorporating new technologies provided by the use of new format biosensors. This overview provides a critical review of current fungal diagnostics and the development of new biophysical technologies that are being applied for selective new sensitive fungal biosensors to augment traditional diagnostic methodologies.